Department of Ecology and Genetics

Publications

Table of contents:

2016

Beekman, M., Nieuwenhuis, B., Ortiz-Barrientos, D., Evans, J. (2016) Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi. Philosophical Transactions of the Royal Society of London. Biological Sciences 371: 20150541.

Bischof, R, Gregersen, E.R., Brøseth, H., Ellegren, H. & Flagstad, Ø. (2016) Non-invasive sampling reveals intra-sex territoriality in wolverines. Ecology and Evolution 6:1527-1536.

Bolivar, P., Mugal, C.F. Nater, A. & Ellegren, H. (2016) Recombination rate variation modulates gene sequence evolution mainly via GC-biased gene conversion, not Hill-Robertson interference, in an avian system. Molecular Biology and Evolution 33:216-227.

Eiler, A., Mondav, R., Sinclair, L., Fernandez-Vidal, L., Scofield, D.G., Schwientek, P., Martinez-Garcia, M., Torrents, D., McMahon, K.D., Andersson, S.G.E., Stepanauskas, R., Woyke, T. & Bertilsson, S. (2016) Turning fresh: radiation through rewiring of central metabolism in streamlined bacteria. The ISME Journal 10:1902-1914.

Ekblom, R. (2016) A bird’s eye view of a deleterious recessive allele. Journal of Animal Ecology 85:855-856.

Ellegren, H. & Galtier, N. (2016) Determinants of genetic diversity. Nature Reviews Genetics 17:422-433.

Figuet, E., Nabholz, B., Bonneau, M., Mas Carrio, E., Nadachowska-Brzyska, K., Ellegren, H. & Galiter, N. (2016) Life history traits, protein evolution and the nearly-neutral theory in amniotes. Molecular Biology and Evolution 33:1517-1527.

Foote, A.D., Vijay, N., Ávila-Arcos, M.C., Baird, R.W., Durban, J.W., Fumagalli, M., Gibbs, R.A., Hanson, M.B., Korneliussen, T.S., Martin, M.D., Robertson, K.M., Sousa, V.C., Vieira, F.G., Vinař, T., Wade, P., Worley, K.C., Excoffier, L., Morin, P.A., Gilbert, M.T.P. & Wolf, J.B.W. (2016) Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nature Communications 7:11693.

Fountain, T., Ravinet, M., Naylor, R., Reinhardt, K. & Butlin, R.K. (2016) A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius. G3: Genes| Genomes| Genetics 6:4059-4066.

Francis, R.M. (2016) Pophelper: an R package and web app to analyse and visualize population structure. Molecular Ecology Resources 17:27-32.

Gattepaille, L., Günther T. & Jakobsson, M. (2016) Inferring past effective population size from distributions of coalescent times. Genetics 204:1191-1206.

Günter, T. & Jakobsson, M. (2016) Genes mirror migrations and cultures in prehistoric Europe-a population genomic perspective. Current Opinion in Genetics and Development 41:115-123.

Hervella, M., Svensson, E.M., Alberdi, A., Günther, T., Izagirre, N., Munters, A.R., Alonso, S., Ioana, M., Ridiche, F., Soficaru, A., Jakobsson, M., Netea, M.G. & de-la-Rua, C. (2016) The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Scientific Reports 6: 25501

Humble, E., Martinez-Barrio, A., Forcada, J., Trathan, P.N., Thorne, M. a. S., Hoffmann, M., Wolf, J.B.W. & Hoffman, J.I. (2016) A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them. Molecular Ecology Resources 16: 909-921.

Jeong, C., Ozga, A.T., Witonsky, D.B., Malmström, H., Edlund, H., Hofman, C.A., Hagan, R.W., Jakobsson, M., Lewis, C.M., Aldenderfer, M.S., Di Rienzo, A. & Warinner, C. (2016) Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. Proceedings of the National Academy of Sciences USA 113:7485-7490.

Jolly, C., Rousseau, K., Prezeau, L., Vol, C., Tomkiewicz, J., Dufour, S., & Pasqualini, C. (2016) Functional characterisation of eel dopamine D2 receptors and involvement in the direct inhibition of pituitary gonadotrophins. Journal of Neuroendocrinology 28:DOI: 10.1111/jne.12411.

Kaj, I. & Mugal, C.F. (2016) The non-equilibrium allele frequency spectrum in a Poisson random field framework. Theoretical Population Biology 111:51-64.

Kalchhauser I., Kutschera V.E. & Burkhardt-Holm P. (2016) The complete mitochondrial genome of the invasive Ponto-Caspian goby Ponticola kessleri obtained from high-throughput sequencing using the Ion Torrent Personal Genome Machine. Mitochondrial DNA Part A 27:1887-1889.

Kardos, M., Husby, A., McFarlane, S.E., Qvarnström, A. & Ellegren, H. (2016) Whole genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Molecular Ecology Resources 16:216-227.

Kardos, M., Taylor, H.R., Ellegren, H., Luikart, G. & Allendorf, F.W. (2016) Genomics advances the study of inbreeding depression in the wild. Evolutionary Applications 9:1205-1218.

Kilinc, G.M., Omrak A., Özer, F., Günther, T., Büyükkarakaya, A.M., Bıcakcı, E., Baird, D., Dönertas, H.M., Ghalichi, A., Yaka, R., Koptekin, D., Acan, S.C., Parvizi, P., Krzewinska, M., Daskalaki, E.A., Yüncü E., Dagtaş, N.D., Fairbairn, A., Pearson, J., Mustafaoglu, G., Erdal, Y.S., Cakan, Y.G., Togan, I., Somel, M., Storå, J., Jakobsson, M. & Götherström, A. (2016) The demographic development of the first farmers in Anatolia. Current Biology 26:2659-2666.

Kutschera V.E., Frosch C., Janke A., Skírnisson K., Bidon T., Lecomte N., Fain S.R., Eiken H.-G., Hagen S.B., Arnason U., Laidre K. L., Nowak C. & Hailer F. (2016) High genetic variability of vagrant polar bears illustrates importance of population connectivity in fragmented sea ice habitats. Animal Conservation 19:337-349.
 

Maklakov, A.A. & Immler, S. (2016) The expensive germline and the evolution of ageing. Current Biology 26:R577–R586.

Monroe, M.J., Amundsen, T., Utne-Palm, A.C. & Mobley, K. (2016) Seasonal variation in male alternative reproductive tactics. Journal of Evolutionary Biology 29: 2362-2372.

Nadachowska-Brzyska, K., Burri, R., Smeds, L. & Ellegren, H. (2016) PSMC-analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Molecular Ecology 25:1058-1072.

Nieuwenhuis, B. & Immler, S. (2016) The evolution of mating-type switching for reproduction assurance. BioEssays 38:1141-1149.

Nieuwenhuis, B., James, T. (2016) The frequency of sex in fungiPhilosophical Transactions of the Royal Society of London. Biological Sciences 371: 20150540.

Omrak, A., Günther, T., Valdiosera, C., Svensson, E.M., Malmström, H., Kiesewetter, H., Aylward, W., Storå, J., Jakobsson, M. & Götherström, A. (2016) Genomic evidence establishes Anatolia as the source of the European Neolithic gene pool. Current Biology 25:270-275.

Rönnegård, L., McFarlane, E.S., Husby, A., Kawakami, T., Ellegren, H. & Qvarnström, A. (2016) Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation. Methods in Ecology and Evolution 7:792-799.

Schlebusch, C.M., Prins, F., Lombard, M., Jakobsson, M & Soodyall, H. (2016) The disappearing San of southeastern Africa and their genetic affinities. Human Genetics 135:1365.1373.

Shafer, A.B.A., Northrup, J.M., Wikelski, M., Wittemyer, G. & Wolf, J.B.W. (2016) Forecasting ecological genomics: High-tech animal instrumentation meets high-throughput sequencing. PLoS Biology 14: e1002350.

Shafer, A.B.A., Wolf, J.B.W., Alves, P.C., Bergström, L., Colling, G., Dalén, L., Meester, L.D., Ekblom, R., Fior, S., Hajibabaei, M., Hoezel, A.R., Hoglund, J., Jensen, E.L., Krützen, M., Norman, A.J., Österling, E.M., Ouborg, N.J., Piccolo, J., Primmer, C.R., Reed, F.A., Roumet, M., Salmona, J., Schwartz, M.K., Segelbacher, G., Thaulow, J., Valtonen, M., Vergeer, P., Weissensteiner, M., Wheat, C.W., Vilà, C. & Zieliński, P. (2016) Reply to Garner et al. Trends in Ecology & Evolution 31: 83–84.

Smeds, L., Mugal, C.F., Qvarnström, A. & Ellegren, H. (2016) High-resolution mapping of crossover and non-crossover recombination events by whole-genome re-sequencing of an avian pedigree. PLoS Genetics 12:e1006044.

Smeds, L., Qvarnström, A. & Ellegren, H. (2016) Direct estimate of the rate of germline mutation in a bird. Genome Research 26:1211-128.

Suh, A. (2016) The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves. Zoologica Scripta 45:50-62.

Suh, A., Witt, C.C., Menger, J., Sadanandan, K.R., Podsiadlowski, L., Gerth, M., Weigert, A., McGuire, J.A., Mudge, J., Edwards, S.V., Rheindt, F.E. (2016) Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nature Communications 7:11396.

Trillmich, F., Meise, K., Kalberer, S., Mueller, B., Piedrahita, P., Pörschmann, U., Wolf, J.B.W. & Krüger, O. (2016) On the challenge of interpreting census data: insights from a study of an endangered pinniped. PLoS One 11: e0154588.

Uebbing, S., Künstner, A., Mäkinen, H., Backström, N., Bolivar, P., Burri, R., Dutoit, L., Mugal, C.F., Nater, A., Aken, B., Flicek, P., Martin, F.J., Searle, S.M.J. & Ellegren, H. (2016) Divergence in gene expression within and between two closely related flycatcher species. Molecular Ecology 25:2015-2028.

Urbina, H., Scofield, D.G., Cafaro,M. & Rosling, A.(2016) DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico. Mycoscience 57:217-227.

Vijay, N., Bossu, C.M., Poelstra, J.W., Weissensteiner, M.H., Suh, A., Kryukov, A.P. & Wolf, J.B.W. (2016) Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex. Nature Communications 7: 13195.

von Rönn, J.A.C., Shafer, A.B.A. &Wolf, J.B.W. (2016) Disruptive selection without genome-wide evolution across a migratory divide. Molecular Ecology 25: 2529–2541.

Wang, J., Street, N.R., Scofield, D.G & Ingvarsson; P.K. (2016) Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species. Genetics 202:1185-1200.

Wang, J., Street, N.R., Scofield, D.G & Ingvarsson; P.K. (2016) Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens. Molecular Biology and Evolution 33:1754-1767.

Zieliński, P., Nadachowska‐Brzyska, K., Dudek, K., Babik, W. (2016) Divergence history of the Carpathian and smooth newts modeled in space and time. Molecular Ecology 25:3912–3928.

2015

Bossu, C.M. & Near, T.J. (2015) Ecological constraint and the evolution of sexual dichromatism in darters. Evolution: 69, 1219–1231.

Burri, R., Nater, A., Kawakami, T., Mugal, C.F., Olason, P.I., Smeds, L., Suh, A., Dutoit, L., Bureš, S., Garamszegi, L.Z., Hogner, S., Moreno, J., Qvarnström, A., Ružić, M., Sæther, S.A., Sætre, G.P., Török, J. & Ellegren, H. (2015) Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Research 25:1656-1665.

Cai, H., Shafer, A.B.A., Laguardia, A., Lin, Z., Liu, S. & Hu, D. (2015) Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii ). Scientific Reports  5: 17285

Camus, M.F., Wolf, J.B.W., Morrow, E.H., & Dowling, D.K. (2015) Single Nucleotides in the mtDNA Sequence Modify Mitochondrial Molecular Function and Are Associated with Sex-Specific Effects on Fertility and Aging. Current Biology: 25, 2717–2722.

Clarholm M., Skyllberg U., Rosling A. (2015) Organic acid induced release of nutrients from metal-stabilized soil organic matter – The unbutton model. Soil Biology and Biochemistry 84: 168-176.

Dedukh, D., Litvinchuk, S., Rosanov, J., Mazepa, G., Saifitdinova, A., Shabanov, D. & Krasikova, A. (2015) Optional endoreplication and selective elimination of parental genomes during oogenesis in diploid and triploid hybrid European water frogs. PLoS One 10: e0123304.

Douglas, G.M., Gos, G., Steige, K.A., Salcedo, A., Holm, K., Josephs, E.B., Arunkumar, R., Ågren, J.A., Hazzouri, K.M., Wang, W., Platts, A.E., Williamson, R.J., Neuffer, B., Lascoux, M., Slotte, T. & Wright, S.I. (2015) Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proceedings of the National Academy of Sciences USA 112: 2806-2811.

Duforet-Frebourg, N., Gattepaille, L.M., Blum, M.G.B., & Jakobsson, M. (2015) HaploPOP: a software that improves population assignment by combining markers into haplotypes. BMC Bioinformatics 16: 242. 

Foote, A.D., Liu, Y., Thomas, G.W.C., Vinař, T., Alföldi, J., Deng, J., Dugan, S., van Elk, C.E., Hunter, M.E., Joshi, V., Khan, Z., Kovar, C., Lee, S.L., Lindblad-Toh, K., Mancia, A., Nielsen, R., Qin, X., … Gibbs, R.A. (2015) Convergent evolution of the genomes of marine mammals. Nature Genetics: 47, 272–275.

Fonseca, R.R., Smith, B., Wales, N., Cappellini, E., Skoglund, P., Fumagalli, M., Samaniego, J.A., Carøe, C., Avila-Arcos, M., Korneliussen, T.S., Vieira, F.G., Jakobsson, M., Arriaza, B., Willerslev, E., Nielsen, R., Hufford, M., Albrechtsen, A., Ross-Ibarra, J. & Gilbert, M.T.P. (2015) The origin and evolution of maize in the American Southwest. Nature Plants: 14003

Gervasi, V., Brøseth, H., Nilse, E.B., Ellegren, H., Flagstad, Ø. & Linnell, J.D.C. (2015) Compensatory immigration counteracts contrasting conservation strategies of wolverines (Gulo gulo) within Scandinavia. Biological Conservation 191:632-639.

Griffin, R.M., Le Gall, D., Schielzeth, H. & Friberg, U. (2015) Within-population Y-linked genetic variation for lifespan in Drosophila melanogaster. Journal of Evolutionary Biology 28: 1940-1947.

Günther, T., Valdiosera, C., Malmström, H., Urena, I., Rodriguez-Varela, R., Sverrisdottir, O., Daskalaki, E.A., Skoglund, P., Naidoo, T., Svensson, E.M., Bermdez de Castro, J.M., Carbonell, E., Dunn, M., Storå, J., Iriartek, E., Arsuaga, J.L., Carretero, J.M., Götherström, A. & Jakobsson, M. (2015) Ancient Genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proceedings of the National Academy of Sciences USA, 112: 11917-11922.

Hossain, ASMM.,  Blackburne, BP., Shah, A. & Whelan, S. (2015) Evidence of statistical inconsistency of phylogenetic methods in the presence of multiple sequence alignment uncertainty. Genome Biology and Evolution. 7: 2102-2116.

Husby, A., Kawakami, T., Rönnegård, L., Smeds, L., Ellegren, H. & Qvarnström, A. (2015) Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait. Proceedings of the Royal Society of London, Series B 282:20150156.

Immler, S. & Otto, SP. (2015) The evolution of sex chromosomes in organisms with separate haploid sexes. Evolution 69: 694-708.

Jarvis, E.D., Mirarab, S., Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., da Fonseca, R.R., Alfaro-Núñez, A., Narula, N., Liu, L., Burt, D., Ellegren, H., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T. & Zhang G; Avian Phylogenomics Consortium. (2015) Phylogenomic analyses data of the avian phylogenomics project. Gigascience 4:4.

Jeglinski, J.W.E., Wolf, J.B.W., Werner, C., Costa, D.P., & Trillmich, F. (2015) Differences in foraging ecology align with genetically divergent ecotypes of a highly mobile marine top predator. Oecologia: 179, 1041–1052.

Kardos M.D., Luikart G., Bunch R., Dewey S., Edwards H., McWilliam S., Stephenson J., Allendorf F.W., Hogg J.T. & Kijas J. (2015) Whole genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep. Molecular Ecology 24: 5616-5632

Kardos M.D., Luikart G. & Allendorf F.W. (2015) Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees. Heredity 115: 63-72

Knief, U., Schielzeth, H., Ellegren, H., Kempenaers, B. & Forstmeier, W. (2015) A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata. Molecular Ecology 24:3846-3859.

Kopelman, N.M., Mayzel, J., Jakobsson, M., Rosenberg, N.A., & Mayrose, I. (2015) CLUMPAK: a program for clustering, assessment, and analysis of population structure results. Molecular Ecology Notes, 15: 1179-1191.

Kotrschal, A., Corral‐Lopez, A., Zajitschek, S., Immler, S., Maklakov, A.A. & Kolm, N. (2015) Positive genetic correlation between brain size and sexual traits in male guppies artificially selected for brain size. Journal of Evolutionary Biology, 28: 841-850.

Kuehnelt, D., Engstrom, K., Skroder, H., Kokarnig, S., Schlebusch, C., Kippler, M., Alhamdow, A., Nermell, B., Francesconi, K., Broberg, K., and Vahter, M. (2015) Selenium metabolism to the trimethylselenonium ion (TMSe) varies markedly because of polymorphisms in the indolethylamine N-methyltransferase gene. Am J Clin Nutr 102:1406-15.

Lopes, F., Hoffman, J.I., Valiati, V.H., Bonatto, S.L., Wolf, J.B.W., Trillmich, F., & Oliveira, L.R. (2015) Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management. Conservation Genetics: 16, 1099–1113.

Lundén K., Danielsson M., Brandström Durling M., Irrmark K., Nemesio Gorrie M., Stenlid J., O. Asiegbu F., Elfstrand M. (2015) Transcriptional Responses Associated with Virulence and Defence in the Interaction between Heterobasidion annosum s.s. and Norway Spruce. PLOS One 10.1371/journal.pone.0131182

Morin, P.A., Parsons, K.M., Archer, F.I., Ávila-Arcos, M.C., Barrett-Lennard, L.G., Dalla Rosa, L., Duchêne, S., Durban, J.W., Ellis, G.M., Ferguson, S.H., Ford, J.K., Ford, M.J., Garilao, C., Gilbert, M.T.P., Kaschner, K., Matkin, C.O., Petersen, S.D., … Foote, A.D. (2015) Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Molecular Ecology: 24, 3964–3979.

Poelstra, J.W., Vijay, N., Hoeppner, M.P., & Wolf, J.B.W. (2015) Transcriptomics of colour patterning and coloration shifts in crows. Molecular Ecology: 24, 4617–4628.

Malmström, H., Linderholm, A., Skoglund, P., Storå, J., Sjödin, P., Gilbert, T., Holmlund, G., Willerslev, E., Jakobsson, M., Liden, K. & Götherström, A. (2015 Ancient mitochondrial DNA from the Northern fringe of the Neolithic farming expansion sheds light on the dispersion process. Philosophical Transactions of the Royal Society B, 370: 20130373

Money, D. & Whelan, S. (2015) GeLL: A Generalised Likelihood Library for Phylogenetic Models. Bioinformatics 31: 2391-2393.

Monroe, M.J., South, S.H. & Alonzo, S.H. (2015) The evolution of fecundity is associated with female body size but not female-biased sexual size dimorphism among frogs. Journal of Evolutionary Biology 28: 1793-1803

Morin, P.A., Parsons, K.M., Archer, F.I., Ávila-Arcos, M.C., Barrett-Lennard, L.G., Dalla Rosa, L., Duchêne, S., Durban, J.W., Ellis, G.M., Ferguson, S.H., Ford, J.K., Ford, M.J., Garilao, C., Gilbert, M.T., Kaschner, K., Matkin, C.O., Petersen, S.D., Robertson, K.M., Visser, I.N., Wade, P.R., Ho, S.Y. & Foote, A.D. (2015) Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Molecular Ecology 24:3964-3979.

Mugal, C.D., Arndt, P.F, Holm, L. & Ellegren, H. (2015) Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes. G3 5:441-447.

Mugal, C.F., Weber, C.C. & Ellegren, H. (2015) GC-biased gene conversion links the recombination landscape and demography to genomic base composition. BioEssays 37:1317-1326. 

Nadachowska-Brzyska, K., Li, C., Smeds, L., Zhang, G. & Ellegren, H. (2015) Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Current Biology 25:1375-1380.

Nater, A., Burri, R., Kawakami, T., Smeds, L. & Ellegren, H. (2015) Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Systematic Biology 64:1000-1017.

Nater, A., Greminger, M.P., Arora, N., van Schaik, C.P., Goossens, B., Singleton, I., Verschoor, E.J., Warren, K.S. & Krützen. M. (2015) Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation. Molecular Ecology 24: 310-327.

Otto, S.P., Scott, M. & Immler, S. (2015) Evolution of haploid selection in animals in predominantly diploid organisms. Proceedings of the National Academy of Sciences USA 112:15952-15957

Platt II, R.N., Zhang, Y., Witherspoon, D.J., Xing, J., Suh, A., Keith, M.S., Jorde, L. B., Stevens, R.D., Ray, D.A. (2015) Targeted capture of phylogenetically informative Ves SINE insertions in genus Myotis. Genome Biology and Evolution 7: 1664-1675.

Pucholt, P., Sjödin, P., Weih, M., Rönnberg-Wästljung, A.C. & Berlin, S. (2015) Genome-wide transcriptional and physiological responses to drought stress in leavers and roots of two willow genotypes. BMC Plant Biology 15: 244.

Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Avila-Arcos, M.C., Malaspinas, A.-S., Eriksson, A., Moltke, I., Metspalu, M., Homburger, J.R., Wall, J., Cornejo, O.E., Moreno-Mayar, J.V., Korneliussen, T.S., Pierre, T., Rasmussen, M., Campos, P.F., de Barros Damgaard, P., Allentoft, M.E., Lindo, J., Metspalu, E., Rodrguez-Varela, R., Mansilla, J., Henrickson, C., Seguin-Orlando, A., Malmström, H., Stafford Jr., T., Shringarpure, S.S., Moreno-Estrada, A., Karmin, M., Tambets, K., Bergström, A., Xue, Y., Warmuth, V., Friend, A.D., Singarayer, J., Valdes, P., Balloux, F., Leboreiro, I., Vera, J.L., Rangel-Villalobos, H., Pettener, D., Luiselli, D., Davis, L.G., Heyer, H., Zollikofer, C.P.E., Ponce de Len, M.S., Smith, C.I., Grimes, V., Pike, K.-A., Deal, M., Fuller, B.T., Arriaza, B., Standen, V., Luz, M.F., Ricaut, F., Guidon, N., Osipova, L., Voevoda, M.I., Posukh, O.L., Balanovsky, O., Lavryashina, M., Bogunov, Y., Khusnutdinova, E., Gubina, M., Balanovska, E., Fedorova, S., Litvinov, S., Malyarchuk, B., Derenko, M., Mosher, M.J., Archer, D., Cybulski, J., Petzelt, B., Mitchell, J., Worl, R., Norman, P.J., Parham, P., Kemp, B.M., Kivisild, T., Tyler-Smith, C., Sandhu, M.S., Crawford, M., Villems, R., Smith, D.G., Waters, M.R., Goebel, T., Johnson, J.R., Malhi, R.S., Jakobsson, M., Meltzer, D.J., Manica, A., Durbin, R., Bustamante, C.D., Song, Y.S., Nielsen, R & Willerslev, E. (2015) Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884.

Rosling A., Midgley M.G., Cheeke T., Urbina H., Fransson P., Phillips R.P. (2015) Phosphorus cycling in deciduous forest soil differs between strands dominated by echo- and arbuscular mycorrhizal trees. New Phytologist 209: 1184-1195.

Samarra, F.I.P. & Foote, A.D. (2015) Seasonal movements of killer whales between Iceland and Scotland. Aquatic Biology: 24, 75–79.

Schadt C.W., Rosling A. (2015) Comment on “Global diversity and geography of soil fungi”. Science 348: 1438.

Schlebusch, C.M., Gattepaille, L.M., Engström, K., Vahter, M., Jakobsson, M., & Broberg, K. (2015) Human adaptation to arsenic rich environments. Molecular Biology and Evolution, 32: 1544-1555.

Schmid, M., Smith, J., Burt, D.W., Aken, B.L., Antin, P.B., Archibald, A.L., Ashwell, C., Blackshear, P.J., Boschiero, C., Brown, C.T., Burgess, S.C., Cheng, H.H., Chow, W., Coble, D.J., Cooksey, A., Crooijmans, R.P.M.A., Damas, J., Davis, R.V.N., de Konig, D.-J., Delany, M.E., Derrien, T., Desta, T.T., Dunn, I.C., Dunn, M. Ellegren, H. et al. (79 additional co-authors). (2015) Third report on chicken genes and chromosomes. Cytogenetics and Genome Research 145:78-179.

Shafer, A.B.A., Gattepaille, L.M., Stewart, R.E.A., & Wolf, J.B.W. (2015) Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Molecular Ecology: 24, 328–345.

Shafer, A.B.A., Wolf, J.B.W., Alves, P.C., Bergström, L., Bruford, M.W., Brännström, I., Colling, G., Dalén, L., De Meester, L., Ekblom, R., Fawcett, K.D., Fior, S., Hajibabaei, M., Hill, J.A., Hoezel, A.R., Höglund, J., Jensen, E.L., … Zieliński, P. (2015) Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution: 30, 78–87.

Smeds, L., Warmuth, V., Bolivar, P., Uebbing, S., Burri, R., Suh, A., Nater, A., Bureš, S., Garamszegi, L.Z., Hogner, S., Moreno, J., Qvarnström, A., Ružić, M., Sæther, S.A., Sætre, G.P., Török, J. & Ellegren H. (2015) Evolutionary analysis of the female-specific avian W chromosome. Nature Communications 6:7330.

Sork, V.L., Smouse, P.E., Grivet, D. & Scofield, D.G. (2015) Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Née). Evolutionary Ecology 29:927-945.

Steige, K.A., Reimegård, J., Koenig, D., Scofield, D.G. & Slotte, T. (2015) Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Molecular Biology and Evolution 32:2501–2514.

Suh, A. (2015) The specific requirements for CR1 retrotransposition explain the scarcity of retrogenes in birds. Journal of Molecular Evolution 81: 18-20.

Suh, A., Churakov, G., Ramakodi, M.P., Platt II, R.N., Jurka, J., Kojima, K.K., Caballero, J., Smit, A., Vliet, K., Hoffmann, F.G., Brosius, J., Green, R.E., Braun, E.L., Ray, D.A., Schmitz, J. (2015) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution 7: 205-217.

Suh, A., Smeds, L. & Ellegren, H. (2015) The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biology 13:e1002224.

Sun, Y., Whittle, C.A., Corcoran, P. & Johannesson H. (2015) Intron evolution in Neurospora: the role of mutational bias and selection. Genome Research 25:100-110.

Talavera, D., Lovell, S. & Whelan, S. (2015) Covariation is a poor measure of molecular coevolution. Molecular Biology and Evolution. 32: 2456-2468.

Taylor H.R., Kardos M.D., Rastad K.M. & Allendorf F.W. (2015) Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity. Conservation Genetics 16: 901-913

Uebbing, S., Konzer, A., Xu, L., Backström, N., Brunström, B., Bergquist, J. & Ellegren, H. (2015) Quantitative mass spectrometry reveals partial translational regulation for dosage compensation in chicken. Molecular Biology and Evolution 32:2716-2725.

von Rönn, J. A. C., Harrod, C., Bensch, S., & Wolf, J.B.W. (2015) Transcontinental migratory connectivity predicts parasite prevalence in breeding populations of the European barn swallow. Journal of Evolutionary Biology: 28, 535–546.

Weissensteiner, M.H., Poelstra, J.W., & Wolf, J.B.W. (2015) Low-budget ready-to-fly unmanned aerial vehicles: an effective tool for evaluating the nesting status of canopy-breeding bird species. Journal of Avian Biology: 46, 425–430.

Whelan, S., Allen, JE., Blackburne, B.P. & Talavera, D. (2015) ModelOMatic: fast and automated comparison between RY, nucleotide, amino acid, and codon substitution models. Systematic Biology 64: 42-55.

Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. (2015) Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349: aab3884.

Zuccolo, A., Scofield, D.G., De Paoli, E. & Morgante, M. (2015) The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution. Gene 568:89–99.


2014

Allen, J.E. & Whelan, S. (2014). Assessing the state of substitution models describing noncoding RNA evolution. Assessing the state of substitution models describing noncoding RNA evolution. Genome Biology and Evolution 6: 65-75.

Antoniazza, S., Kanitz, R., Neuenschwander, S., Burri, R., Gaigher, A., Roulin, A. & Goudet, J. (2014) Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl. Molecular Ecology 23: 5508-5523.

Backström, N. (2014) Adaptive evolution in passerine birds. Encyclopedia of Life Sciences July 2014.

Breton, G., Schlebusch, C.M., Lombard, M., Soodyall, H., Sjödin, P. & Jakobsson, M. (2014) Lactase Persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists. Current Biology 24: 852-858.

Burri, R., Promerová, M., Goebel, J. & Fumagalli, L. (2014) PCR-based isolation of multigene families: lessons from the avian MHC class IIB. Molecular Ecology Resources 14: 778-788.

Corcoran, P., Dettman, J. R., Sun, Y., Luque, E. M., Corrochano, L. M., Taylor, J. W., Lascoux, M. & Johannesson, H. (2014) A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system. Molecular Phylogenetics and Evolution 78: 136-147.

Ekblom, R. & Wolf, J.B.W. (2014). A field guide to whole-genome sequencing, assembly and annotation. Evolutionary Applications 7: 1026–1042.

Ekblom, R., Smeds, L. & Ellegren, H. (2014) Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. BMC Genomics 15: 467.

Ekblom, R., Wennekes, P., Horsburgh, G.J. & Burke, T. (2014) Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. Molecular Ecology Resources 14: 636–646.

Ellegren, H. (2014) Genome sequencing and population genomics in non-model organisms. Trends in Ecology and Evolution 29: 51-63.

Fransson, P. & Rosling, A. (2014). Fungal and bacterial community responses to Suillus variegatus extraradical mycelia and soil profile in Scots pine microcosms. Plant Soil 385: 255-272.

García-Pereira, M-J., Carvajal-Rodríguez, A., Whelan S., Caballero, A. & Quesada, H. (2014) Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers. Molecular Phylogenetics and Evolution 76: 102-109.

Green, R. E., Braun, E.L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M.W., St John, J.A., Capella-Gutiérrez, S., Castoe, T.A., Kern, C., Fujita, M.K., Opazo, J.C., Jurka, J., Kojima, K.K., Caballero, J., Hubley, R.M., Smit, A., Platt, R.N., Lavoie, C.A., Ramakodi, M.P., Finger Jr, J.W., Suh, A., Isberg, S.R., Miles, L., Chong, A.Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., Faircloth, B.C., McCormack, J., Burgess, S.C., Edwards, S.V., Lyons, E., Williams, C., Breen, M., Howard, J.T., Gresham, C.R., Peterson, D.G., Schmitz, J., Pollock, D.D., Haussler, D., Triplett, E.W., Zhang, G., Irie, N., Jarvis, E.D., Brochu, C.A., Schmidt, C.J., McCarthy, F.M., Hoffmann, F.G., Glenn, T.C., Gabaldón, T., Paten, B., Ray, D.A. (2014) Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346: 1335.

Immler, S., Hotzy, C., Alavioon, G., Petersson, E. & Arnqvist, G. (2014) Sperm variation within a single ejaculate affects offspring development in Atlantic salmon. Biology Letters 10: 20131040.

Immler, S. & Otto, S.P. (2014) Driven apart: the evolution of ploidy differences between the sexes under antagonistic selection. American Naturalist 183: 96-107.

Jarvis, E.D. et al. (Avian Phylogenomics Consortiuum) (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331.

Kardos, M., Allendorf, F.W. & Luikart, G. (2014) Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium? Molecular Ecology Resources 14: 519-530.

Kawakami, T., Backström, N., Burri, R., Husby, A., Olason, P., Rice, A.M., Ålund, M., Qvarnström, A. & Ellegren, H. (2014) Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k SNP array. Molecular Ecology Resources 14: 1248-1260.

Kawakami, T., Smeds, L., Backström, N., Husby, A., Qvarnström, A., Mugal, C.F., Olason, P. & Ellegren, H. (2014) A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Molecular Ecology 23: 4035-4058.

Krüger, O., Wolf, J.B.W., Jonker, R.M., Hoffman, J.I., & Trillmich, F. (2014). Disentangling the contribution of sexual selection and ecology to the evolution of size dimorphism in Pinnipeds. Evolution 68: 1485–1496.

Li, S., Schlebusch, C.M. & Jakobsson, M. (2014) Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proceedings of the Royal Society of London, Series B: Biological Sciences 281: 20141448

Liu, G., Shafer. A.B.A., Wang. W., Zimmerman. W., Hu. D., Chu. H., Cao. J. & Zhao. C. (2014) Evaluating the reintroduction project of Przewalski’s horse in China using genetic and pedigree data. Biological Conservation 171: 288–298.

Menkis, A., Urbina, H., James, T.Y. & Rosling, A. (2014). Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species. Fungal Biology 118: 943-955.

Mugal, C.F., Wolf, J.B.W., & Kaj, I. (2014). Why time matters: Codon evolution and the temporal dynamics of dN/dS. Molecular Biology and Evolution 31: 212–231.

Nater, A., Greminger, M. P., Arora, N., van Schaik, C. P., Goossens, B., Singleton, I., Verschoor, E. J., Warren, K. S. & Krützen, M. (2014), Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation. Molecular Ecology 24: 310–327

Northrup J.M., Shafer A.B.A., Anderson Jr. C.D., Coltman D.W. & Wittemyer, G. (2014) Fine scale genetic correlates to condition and migration in a wild cervid. Evolutionary Applications 7: 937–948.

Poelstra, J. W., Vijay, N., Bossu, C., Lantz, H., Ryll, B., Müller, I., Baglione, V., Unneberg, P., Wikelski, M,, Grabherr, M.G. & Wolf, J.B.W. (2014). The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410–1414.

Raghavan, M., DeGiorgio, M., Albrechtsen, A., Moltke, I., Skoglund, P., Korneliussen, T.S., Gronnøw, B., Appelt, M., Gulløv, H.C., Friesen, M., Fitzhugh, W., Malmström, H., Rasmussen, S., Olsen, J., Melchior, L., Fuller, B.T., Fahrni, S.M., Stafford Jr. T., Grimes, V., Renouf, M.A.P., Cybulski, J., Lynnerup, N., Lahr, M.M., Britton, K., Knecht, R., Arneborg, J., Metspalu, M., Cornejo, O.E., Malaspinas, A.-S., Wang, Y., Rasmussen, M., Raghavan, V., Hansen, T.V.O., Khusnutdinova, E., Pierre, T., Dneprovski, K., Andreasen, C., Lange, H., Hayes, M.G., Coltrain, J., Spitsyn, V.A., Götherström, A., Orlando, L., Kivisild, T., Villems, R., Crawford, M., Nielsen, F.C., Dissing, J., Heinemeier, J., Meldgaard, M., Bustamante, C., O’Rourke, D.H., Jakobsson, M., Gilbert, M.T.P., Nielsen, R., & Willerslev, E. (2014) The Genetic Prehistory of the New World Arctic. Science, 345: 1255832.

Raghavan, M., Skoglund, P., Graf, K., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford, T., Orlando, L., Metspalu, E., Karmin, M., Tambets, K., Rootsi, S., Mägi, R., Campos, P., Balanovska, E., Balanovsky, O., Khusnutdinova, E., Litvinov, S., Osipova, L., Federova, S., Voevoda, M., DeGiorgio, M., Sicheritz-Ponten, T., Brunak, S., Demeshchenko, S., Kivisild, T., Villems, R., Nielsen, R., Jakobsson, M. & Willerslev, E. (2014) Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505: 87-91.

Rasmussen, M., Anzick, S.L., Waters, M.R., Skoglund, P., DeGiorgio, M., Stafford Jr, T.W., Rasmussen, S., Moltke, I., Albrechtsen, A., Doyle, S.M., Poznik, G.D., Gudmundsdottir, V., Yadav, R., Sapfo, A., White, S.S., Allentoft, M., Cornejo, O.E., Tambets, K., Eriksson, A., Heintzman, P., Meiri, M., Karmin, M., Korneliussen, T.S., Pierre, T.L., Stenderup, J., Saag, L., Warmuth, V., Lopes, M.C., Brunak, S., Sicheritz-Ponten, T., Barnes, I., Collins, M., Orlando, L., Balloux, F., Manica, A., Gupta, R., Metspalu, M., Bustamante, C.D., Jakobsson, M., Nielsen, R. & Willerslev, E. (2014) The genome of a late Pleistocene human from a Clovis burial site in western Montana. Nature 506: 225-229.

Rieux, A., Eriksson, A., Li, M., Sobkowiak, B., Weinert, L. A., Warmuth, V., Ruiz-Linares, A., Manica, A. & Balloux, (2014) Improved calibration of the human mitochondrial clock using ancient genomes. Molecular Biology and Evolution 31: 2780-2792.

Romanov, M. N., Farre, M., Lithgow, P. E., Fowler, K. E., Skinner, B. M., O'Connor, R., Fonseka, G., Backström, N., Matsuda, Y., Nishida, C., Houde, P., Jarvis, E. D., Ellegren, H., Burt, D. W., Larkin, D. M. & Griffin, D. K. (2014) Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15: 1060.

Samils, N., Oliva, J., & Johannesson, H. (2014) Nuclear interactions in a heterokaryon: insight from the model Neurospora tetrasperma. Proceedings of the Royal Society of London Series B: Biological Sciences 281: 20140084.

Scofleld, D.G. 2014.  A definitive demonstration of fitness effects due to somatic mutation in a plant. Heredity 112: 361-362.

Seehausen, O., Butlin, R.K., Keller, I., Wagner, C.E., Boughman, J.W., Hohenlohe, P.A., Peichel, C.L., Saetre, G.P., Bank, C., Brännström, A., Brelsford, A., Clarkson, C.S., Eroukhmanoff, F., Feder, J.L., Fischer, M.C., Foote, A.D., Franchini, P., Jiggins, C.D., Jones, F.C., Lindholm, A.K., Lucek, K., Maan, M.E., Marques, D.A., Martin, S.H., Matthews, B., Meier, J.I., Möst, M., Nachman, M.W., Nonaka, E., Rennison, D.J., Schwarzer, J., Watson, E.T., Westram, A.M. & Widmer A. (2014) Genomics and the origin of species. Nature Reviews Genetics 15: 176-192.

Shafer A.B.A., Nielsen S.E., Northrup J.M. & Stenhouse G.B. (2014) Linking genotype, ecotype, and phenotype in an intensively managed large carnivore. Evolutionary Applications 7: 301–312.

Sjödin, P., Skoglund, P. & Jakobsson, M. (2014) Assessing the maximum contribution from ancient populations. Molecular Biology and Evolution 31: 1248-1260.

Sjöstrand, A., Sjödin, P. & Jakobsson, M. (2014) Private haplotypes can reveal local adaptation. BMC Genetics 15: 61.

Skoglund, P., Malmström, H., Omrak, A., Raghavan, M., Valdiosera, C., Günther, T., Hall, P., Tambets, K., Parik, J., Sjögren, K.-G., Apel, J., Willerslev, E., Storå, J., Götherström, A. & Jakobsson, M. (2014) Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 344: 747-750.

Skoglund, P., Northoff, B.H., Shunkov, M.V., Derevianko, A.P., Pääbo, S., Krause, J., & Jakobsson, M. (2014) Separating endogenous ancient DNA from modern-day contamination: application to a Siberian Neandertal. Proceedings of the National Academy of Sciences USA 111: 2229-2234.

Skoglund, P., Sjödin, P., Skoglund, T., Lascoux, M. & Jakobsson, M. (2014) Investigating population history using temporal genetic differentiation. Molecular Biology and Evolution 31: 2516-2527.

Slotte, T. (2014) The impact in linked selection on plant genomic variation. Briefings in Functional Genomics 13: 268-275.

Smeds, L., Kawakami, T., Burri, R., Bolivar, P., Husby, A., Qvarnström, A., Uebbing, S. & Ellegren, H. (2014) Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes. Nature Communications 5: 5448.

Suh, A., Churakov, G., Ramakodi, M.P., Platt II, R.N., Jurka, J., Kojima, K.K., Caballero, J., Smit, A., Hoffmann, F.G., Brosius, J., Green, R.E., Braun, E.L., Ray, D.A. & Schmitz, J. (2014) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution 11: 2015-217.

Suh, A., Weber, C.C., Kehlmaier, C., Braun, E.L., Green, R.E., Fritz, U., Ray, D.A. & Ellegren, H. (2014) Crocodilian and turtle paleoviruses suggest Early Mesozoic coexistence of amniotes and Hepadnaviridae. PLoS Genetics 10: e1004559.

Thompson, P.G., Smouse, P.E., Scofield, D.G. & Sork V.L.  (2014)  What seeds tell us about birds: a multi-year analysis of acorn woodpecker foraging movements.  Movement Ecology 2: 12.

Wang, B., Ekblom, R., Bunikis, I., Siitari, H. & Höglund, J. (2014) Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics 15: 180.

Weber, C.C., Boussau, B., Romiguier, J., Jarvis, E.D. & Ellegren, H. (2014) Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biology 15: 549.

Weber, C.C., Nabholz, B., Romiguier, J. & Ellegren, H. (2014) Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biology 15: 542.

Whelan, S., Allen, J.E., Blackburne, B.J. & Talavera, D. (2015) ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models. Systematic Biology 64: 42-55.

Whittle, C. A., Sun, Y., & Johannesson, H. (2014) Dynamics of transcriptome evolution in the model eukaryote Neurospora. Journal of Evolutionary Biology 27: 1125-1135.

Yazdi, H.P. & Ellegren, H. (2014) Old but not (so) degenerated: slow evolution of largely homomorphic sex chromosomes in ratites. Molecular Biology and Evolution 31: 1444-1453.

Zajitschek, S., Hotzy, C., Zajitschek, F. & Immler, S. (2014) Short term variation in sperm competition causes sperm mediated epigenetic effects on early offspring performance in the zebrafish. Proceedings of the Royal Society London Series B 281: 20140422.

Zhang, L., An, B., Backström, N., Ruan, L. & Liu, N. (2014) Phylogeography based delimitation of subspecies boundaries in the common pheasant (Phasianus colchicus). Biochemical Genetics 52: 38-51.

Zhang, Q. & Backström, N. (2014) Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence. Chromosoma 123: 165-168.

Zhang, Q., Hill, G. E., Edwards, S. V. & Backström, N. (2014) A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines. BMC Genomics 15: 305.


2013

Abbott, R., lbach. D., Ansell, S., Arntzen, J.W., Baird, S.J., Bierne, N., Boughman, J., Brelsford, A., Buerkle, C.A., Buggs, R., Butlin, R.K., Dieckmann, U., Eroukhmanoff, F., Grill, A., Cahan, S.H., Hermansen, J.S., Hewitt, G., Hudson, A.G., Jiggins, C., Jones, J., Keller, B., Marczewski, T., Mallet, J., Martinez-Rodriguez, P., Möst, M., Mullen, S., Nichols, R., Nolte, A.W., Parisod, C., Pfennig, K., Rice, A.M., Ritchie, M.G., Seifert, B., Smadja, C.M., Stelkens, R., Szymura, J.M., Väinölä, R., Wolf, J.B. & Zinner, D. (2013) Hybridization and speciation. Journal of Evolutionary Biology 26: 229–246.

Adolfsson, S. & Ellegren, H. (2013) Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches. Molecular Biology and Evolution 30: 806-810.

Backström, N., Shipilina, D., Blom, M.P. & Edwards, S.V. (2013). Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecology and Evolution 3: 655-666.

Backström, N., Sætre G.-P., & Ellegren, H. (2013) Inferring the demographic history of European Ficedula flycatcher populations. BMC Evolutionary Biology 13: 2.

Backström, N., Zhang, Q., and Edwards, S. V. 2013. Evidence from a house finch (Haemorhous mexicanus) spleen transcriptome for adaptive evolution and biased gene conversion in passerine birds. Molecular Biology and Evolution 30: 1046-1050.

Bourgoin, L., Friberg, U. & Maklakov, A.A. (2013). Intersexual correlation for same-sex behaviour in an insect. Animal Behaviour 85: 759-762.

Brandariz-Fonte, C., Leonard, J. A., Vega-Pla, J. L., Backström, N., Lindgren, G., Lippold, S., and Rico, C. 2013. Y-chromosome analysis in Retuertas horses. PLoS One 8: e64985.

Brandvain, Y., Slotte, T., Hazzouri, K., Wright, S.I. & Coop, G. (2013) Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genetics 9: e1003754.

Corl, A. & Ellegren, H. (2013) Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal. Molecular Phylogenetics and Evolution 67: 358-366.

Ellegren, H. (2013) The evolutionary genomics of birds. Annual Reviews of Ecology, Evolution and Systematics 44: 239-259.

Gattepaille, L.M., Jakobsson, M., & Blum, M.G.B. (2013) Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity 110: 409-419.

Griffin, R., Dean, R., Grace, J.L. & Friberg, U. (2013). The shared genome is a pervasive constraint on the evolution of sex-biased gene expression. Molecular Biology and Evolution 30: 2168-2176.

Hough, J., Immler, S., Barrett, S.C.H. & Otto, S.P. (2013) Evolutionarily stable sex ratios and mutation load. Evolution 67: 1915-1925.

Jakobsson, M., Edge, M.D. & Rosenberg, N. A. (2013)The relationship between FST and the frequency of the most frequent allele. Genetics 193: 515-528.

Jay, F., Sjödin, P., Jakobsson, M., & Blum, M.G.B. (2013) Anisotropic isolation by distance: the main orientations of human genetic differentiation. Molecular Biology and Evolution 30: 513-525.

Kotrschal, A., Rogell, B., Bundsen, A., Svensson, B., Zajitschek, S., Brännström, I., Immler, S., Maklakov, A. & Kolm, N. (2013) The benefit of evolving a larger brain: big-brained guppies perform better in a cognitive task. Animal Behaviour 86: e4-e6.

Kotrschal, A., Rogell, B., Bundsen, A., Svensson, B., Zajitschek, S., Brännström, I., Immler, S., Maklakov, A.A. & Kolm, N. (2013) Artificial selection on relative brain size in the guppy reveals costs and benefits of evolving a larger brain. Current Biology 23: 168-171.

Lehtovaara, A., Schielzeth, H., Flis, I. & Friberg, U. (2013). Heritability of lifespan is largely sex-limited in fruit flies. American Naturalist 182: 653-665.

Lenz TL, Mueller B, Trillmich F, Wolf JBW (2013) Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating. Proceedings of the Royal Society of London Series B: Biological Sciences 280: 20130714.

Lombard M., Schlebusch C.M. & Soodyall H. (2013) Bridging disciplines to better elucidate the evolution of early Homo sapiens in southern Africa. South African Journal of Science 109: 1-8.

Maklakov, A.A, Immler, S., Loveli, H., Flis, I. & Friberg, U. (2013). The effect of sexual harassment on lethal mutation rate in female Drosophila melanogaster. Proceedings of the Royal Society of London Series B: Biological Sciences 280: 20121874.

Mugal, C.F., Arndt, P.F. & Ellegren, H. (2013) Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype. Molecular Biology and Evolution 30: 1700-1712.

Mugal, C.F., Nabholz, B. & Ellegren, H. (2013) Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. BMC Genomics 14: 86.

Nabholz, B., Ellegren, H. & Wolf, J.B.W. (2013) High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes. Molecular Biology and Evolution 30: 272–284.

Nadachowska-Brzyska, K., Burri, R., Olason, P.I., Kawakami, T., Smeds, L. & Ellegren, H. (2013) Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data. PLoS Genetics 9: e1003942.

Parsch, J. & Ellegren, H. (2013) The evolutionary causes and consequences of sex-biased gene expression. Nature Reviews Genetics 14: 83-87.

Poelstra, J.W., Ellegren, H. & Wolf, J.B.W. (2013) An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone. Heredity 111: 467–473.

Rice, W.R., Friberg, U. & Gavrilets, S. (2013). Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model. BioEssays 35: 764-770.

Schlebusch C.M., Lombard, M. & Soodyall, H. (2013) MtDNA control region variation affirms diversity and deep sub-structure in populations from Southern Africa. BMC Evolutionary Biology 13: 56.

Schlebusch, C.M., Sjödin, P., Skoglund, P. & Jakobsson, M. (2013) Stronger signal of recent selection for lactase persistence in Maasai than in Europeans. European Journal of Human Genetics. 21: 550-553.

Schlebusch, C.M., Lewis (Jr), C.M., Vahter, M., Engström, K., Tito, R.Y., Obregón-Tito, A.J., Huerta, D., Polo, S.I., Medina, A.C., Brutsaert, T.D., Concha, G., Jakobsson, M., & Broberg, K. (2013). Possible positive selection for an arsenic-protective haplotype in humans, Environmental Health Perspectives 121: 53-58.

Shafer, A.B.A. & Wolf, J.B.W. (2013) Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology. Ecology Letters. 16: 940–950.

Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. (2013) Accurate sex identification of ancient human remains using DNA shotgun sequencing, Journal of Archaeological Science 40: 4477-4482.

Slotte, T., Hazzouri, K.M., Ågren, J.A., Koenig, D., Maumus, F., Guo, Y., Steige, K., Platts, A.E., Escobar, J.S., Newman, L.K., Wang, W., Mandakova, T., Vello, E., Smith, S.M., Steffen, J., Takuno, S., Brandvain, Y., Coop, G., Andolfatto, P., Hu, T.T., Blanchette, M., Clark, R.M., Queseville, H., Nordborg, M., Gaut, B.S., Lysak, M.A., Jenkins, J., Grimwood, J., Prochnick, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D. & Wright, S.I. (2013). The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics 45: 831-835.

Suh, A., Brosius, J., Schmitz, J. & Kriegs, J. O. (2013) The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses. Nature Communications 4: 1791.

Uebbing, S., Künstner, A., Mäkinen, H., Ellegren, H. Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biology and Evolution 5: 1555-1566.

Vijay, N., Poelstra, J.W., Künstner, A. & Wolf, J.B.W. (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology 22: 620–634.

Wolf, J.B.W. (2013) Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Molecular Ecology Resources 13: 559–572.

Wright, S.I., Kalisz, S. & Slotte, T. (2013) Evolutionary consequences of self-fertilization in plants. Proceedings of the Royal Society of London Series B: Biological Sciences 280: 20130133.

Zajitschek, F., Zajitschek, S.R.K., Friberg, U. & Maklakov. A.A. (2013). Interactive effects of sex, social environment, dietary restriction and methionine on survival and reproduction in fruit flies. AGE 35: 1193-1204.

Ålund, M., Immler, S., Rice, A.M. & Qvarnström, A. (2013) Low fertility of wild hybrid male flycatchers despite recent divergence. Biology Letters 9: 20130160.


2012

Chen, J., Uebbing, S., Gyllenstrand, N., Lagercrantz, U., Lascoux, M. & Källman, T. (2012) Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms. BMC Genomics 13:589.

Corcoran, P., Jacobson, D.J., Bidartondo, M.I., Hickey, P.C., Kerekes, J., Taylor J.W., Johannesson, H. (2012). Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetrasperma. Fungal Biology 116: 962-975

Corl, A. & Ellegren, H. (2012) The genomic signature of sexual selection in the genetic diversity of the sex chromosomes and autosomes. Evolution 66:2138-2149

Dean R, Perry JC, Pizzari T, Mank JE, & Wigby S (2012) Experimental Evolution of a Novel Sexually Antagonistic Allele. PLoS Genet 8(8):e1002917.

Ekblom R, Farrell LL, Lank DB & Burke T (2012) Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff. Ecology and Evolution 2(10): 2485–2500

Ekblom R, Slate J, Horsburgh GJ, Birkhead T & BurkeT (2012) Comparison between normalised and un-normalised 454-sequencing libraries for small-scale RNA-seq studies. Comparative and Functional Genomics Article ID 281693: 1-8.

Ellegren, H., Smeds, L., Burri, R., Olason, P.I., Backström, N., Kawakami, T., Künstner, A., Mäkinen, H., Nadachowska-Brzysja, K., Qvarnström, A., Uebbing, S. & Wolf, J.B.W. (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature 491:756-760.

Forstmeier, W., Schielzeth, H., Mueller, J.C., Ellegren, H. & Kempenaers, B. (2012) Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation. Molecular Ecology 21:3237-3249

Friberg, U., Stewart, A.D., & Rice, W.R. (2012) X and Y chromosome linked paternal effects on a life history trait. Biology Letters 8: 71-73.

Gattepaille, L.M. & Jakobsson, M. (2012) Combining markers into haplotypes can improve population structure inference. Genetics, 190: 159-174.

Gioti, A., Mushegian, A., Strandberg, R., Stajich, J.E.,Johannesson, H. (2012). Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements. Molecular Biology and Evolution 29(10):3215-3226

Gioti A., Wigby S.,  Wertheim B.,  Schuster E., Martinez, P.,  Pennington C. J., Partridge  L. &  Chapman T. (2012). Sex peptide of Drosophila melanogaster males is a global regulator of reproductive processes in females. Proc. R. Soc. B 279 (1746):4423-4432.

Gos G, Slotte T, Wright SI. 2012. Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella. BMC Evolutionary Biology. 12:152

Grace, J.L. & Shaw, K.L. (2012) Incipient sexual isolation inLaupala cerasina: females discriminate population-level divergence in acoustic characters. Current Zoology 58:416-425.

Immler, S, Gonzalez-Voyer, A & Bikkhead, TR. 2012. Distinct evolutionary patterns of morphometric sperm traits in passerine birds. Proc R Soc Lond Ser B: 4174-4182.

Immler, S, Griffith, SC, Zann, R & Birkhead, TR. 2012.  Intra-specific variance in sperm morphometry: a comparison between wild and domesticated zebra finches. Ibis 154:480-487.

Immler, S, Arnqvist, G & Otto SP. 2012. Ploidally antagonistic selection maintains stable genetic polymorphism. Evolution 66: 55-65.

Jackson B, Kawakami T, Cooper S, Galindo J, Butlin R (2012) A Genome Scan and Linkage Disequilibrium Analysis among Chromosomal Races of the Australian Grasshopper Vandiemenella viatica. PLoS ONE 7: e47549.

Kajtoch, L., Nadachowska-Brzyska, K., Babik, W. (2012) Development and characterization of microsatellite loci in the Centricnemus leucogrammus weevil. Molecular Biology Reports 39: 11131-11136.

Kawakami, Takeshi; and Butlin, Roger K (January 2012) Hybrid Zones. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0001752.pub2

Knief, U., Schielzeth, H., Kempenaers, B., Ellegren, H. & Forstmeier, W. (2012) QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in the zebra finch. Molecular Ecology 21:3704-3717.

Koblmüller, S,  Wayne, R.K., &  Leonard, J.A. (2012). Impact of Quaternary climatic changes and interspecific competition on the demographic history of a highly mobile generalist carnivore, the coyote.  Biology Letters, 8:644-647.

Legrand, D., Guillaume, O., Baguette, M., Cote, J., Trochet, A., Calvez, O., Zajitschek, S.R.K, Zajitschek, F.,Lecomte, J., Benard, Q, Le Galliard, J.-F. & Clobert, J.(2012). The Metatron: an experimental system to study dispersal and metaecosystem dynamics for terrestrial organisms. Nature Methods. 9:828-833.

Li, S. & Jakobsson, M. (2012) Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation. BMC Genetics, 13: 22

Li, J., Li, H., Jakobsson, M., Li, S., Sjödin, P. & Lascoux, M. (2012) Joint analysis of demography and selection in population genetics: Where do we stand and where could we go? Molecular Ecology, 21: 28-44.

Lippold, S.,  Knapp, M., Kuznetsova, T.,  Leonard, J.A., Benecke, N.,  Ludwig, A., Rasmussen, M., Weinstock, J., Willerslev, E., Shapiro, B., & Hofreiter, M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications 2: 450.

Lorenzen, E.D., D. Nogués-Bravo, L. Orlando, J. Weinstock, J. Binladen, K. A. Marske, A. Ugan, M. K. Borregaard, M. T. P. Gilbert, R. Nielsen, S. Y. W. Ho, T. Goebel, K. E. Graf, D. Byers, J. T. Stenderup, M. Rasmussen, P. F. Campos, J. A. Leonard, K.-P. Koepfli, D. Froese, G. Zazula, T. W. Stafford, K. Aaris-Sørensen, P. Batra, A. M. Haywood, J. S. Singarayer, P. J. Valdes, G. Boeskorov, J. A. Burns, S. P. Davydov, J. Haile, D. L. Jenkins, P. Kosintsev, T. Kuznetsova, X. Lai, L. D. Martin, H. G. McDonald, D. Mol, M. Meldgaard, K. Munch, E. Stephan, M. Sablin, R. S. Sommer, T. Sipko, E. Scott, M. A. Suchard, A. Tikhonov, R. Willerslev, R. K. Wayne, A. Cooper, M. Hofreiter, A. Sher, B. Shapiro, C. Rahbek, & E. Willerslev. (2011). Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479: 359–364.

Malmström, Vretemark M, Tillmar, A M Brandström-Durling, P Skoglund, MTP Gilbert, E Willerslev, G Holmlund & A Götherström (2012) Finding the founder of Stockholm – a kinship study based on Y-chromosomal, autosomal and mitochondrial DNA. Annals of Anatomy, 194:138–145

Menkis, A., Burokiene, D., Gaitnieks, T., Uotila, T., Johannesson, H., Rosling, A., Finlay, R., Stenlid, J. & Vasaitis, R. (2012).  Occurrence and impact of the root-rot biocontrol agent Phlebiopsis gigantea on soil fungal communities in Picea abies forests of northern Europe. FEMS Microbiology Ecology, 81 (2): 438-445. 

Nadachowska-Brzyska, K., Zielinski, P., Radwan, J. & Babik, W. (2012) Interspecific hybridization increases MHC class II diversity in two sister species of newts. Molecular Ecology 21:887-906.

Nam, K. & Ellegren, H. (2012). Recombination drives vertebrate genome contraction. PLoS Genetics 8: e1002680.

Noguera, J., Dean, R., Isaksson, C., Velando, A. & Pizzari, T. (2012) Age-specific oxidative status and the expression of pre- and post-copulatory sexually selected traits in male red junglefowl. Ecology and Evolution 2: 2155–2167

Nyström, V., Humphrey, J., Skoglund, P., McKeown, N.J., Vartanyan, S., Shaw, P.W., Liden, K., Jakobsson, M., Barnes, I., Angerbjörn, A., Lister, A. & Dalen, L. (2012) Microsatellite genotyping reveals end-Pleistocene shift in mammoth autosomal genetic variation. Molecular Ecology, 21: 3391-3402

Nygren, K., Wallberg, A., Samils, N., Stajich, J. E., Townsend, J. P., Karlsson, M., Johannesson, H. (2012) Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Evolutionary Biology 12: 229

Nygren, K., Strandberg, R., Gioti, R., Karlsson, M., Johannesson, H. (2012). Deciphering the relationship between mating system and the molecular evolution of the pheromone and receptor genes in Neurospora. Molecular Biology and Evolution 29(12): 3827-3842

Rice, W.R. Friberg, U. and Gavrilets, S. 2012. Homosexuality as a consequence of epigenetically canalized sexual development.The Quarterly Review of Biology 87:343-368

Schielzeth, H., Forstmeier, W., Kempenaers, B. & Ellegren, H. (2012) QTL linkage mapping of wing length in zebra finch using genome-wide SNP markers. Molecular Ecology 21: 329-339.

Schielzeth, H., Kempenaers, B., Ellegren, H. & Forstmeier, W. (2012) QTL linkage mapping of zebra finch beak colour shows an oligogenic control of a sexually selected trait. Evolution 66: 18-30

Schlebusch*, C. M, Skoglund*, P., Sjödin, P., Gattepaille, L. M., Hernandez, D., Jay, F., Li, S., De Jongh, M., Singleton, A., Blum, M. G. B., Soodyall, H. & Jakobsson, M. (2012) Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science, 338: 374-379

Schlebusch, C.M., Soodyall, H. & Jakobsson, M. (2012) Genetic variation of 15 autosomal STR loci in various populations from southern Africa. Forensic Science International: Genetics, 6: e20-e21.

Schlebusch CM, Soodyall H (2012) Extensive population structure in San, Khoe and Mixed Ancestry populations from southern Africa revealed by 44 short 5-SNP haplotypes. Human Biology. 84:695-724

Slotte T, Hazzouri KM, Stern DL, Andolfatto P, Wright SI. 2012. Genetic architecture and adaptive significance of the selfing syndrome in Capsella. Evolution 66:1360-1374

Sjödin, P., Sjöstrand, A., Jakobsson, M., & Blum, M.G.B. (2012) No evidence for a human bottleneck during the penultimate glacial period. Molecular Biology and Evolution, 29: 1850-1861

Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P., Willerslev, E., M. Thomas P. Gilbert, M. P. T., Götherström, A., & Jakobsson, M. (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science, 366: 466-469

St. Onge KR, Foxe JP, Li J, Li H, Holm K, Corcoran P, Slotte T, Lascoux M, Wright SI. 2012. Coalescent-based analysis distinguishes between allo- and autopolyploid origin in Shepherd's Purse (Capsella bursa-pastoris). Molecular Biology and Evolution. 29:1721-1733

Sun, Y., Corcoran, P., Menkis, A., Whittle, C.A., Andersson, S.G.E. & Johannesson, H. (2012). Large-scale introgression shapes the evolution of the mating-type chromosomes of the filamentous ascomycete Neurospora tetrasperma. PLoS Genetics 8(7): e1002820.

Wang, Z., Kin, K., Lopez-Giraldez, F., Johannesson, H. & Townsend, J.P. (2012). Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics and Biology 48(7): 533-543.

Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, & Höglund J (2012) Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biology 2: 120054.

Wang B, Ekblom R, Strand T, Portela-Bens S & Höglund J (2012) Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC. BMC Genomics 13 (1): 553

Whittle, C. A., Johannesson, H. (2012). Neurospora as a model to empirically test central hypotheses in eukaryotic genome evolution: Why this fungal genus offers promising opportunities. Bioessays 34:934-937

Whittle, C. A., Sun, Y. & Johannesson, H. (2012).  Genome-wide selection on codon usage at the population level in the fungal model organism Neurospora crassa. Molecular Biology and evolution 29: 1975-1986.

Yannic, G., Burri, R., Malikov, V.G., Vogel, P. (2012) Systematics of snow voles (Chionomys, Arvicolinae) revisited. Molecular Phylogenetics and Evolution 62: 806-815.

Zajitschek, F., Zajitschek, S.R.K., Friberg, U. & Maklakov. A.A. (2012) Interactive effects of sex, social environment, dietary restriction and methionine on survival and reproduction in fruit flies.  AGE 35: 1193-1204.

Zajitschek, S.R.K., Zajitschek, F., Miles, D., Clobert, J. (2012). The effect of coloration and temperature on sprint performance in male and female wall lizards.Biological Journal of the Linnean Society 107: 573-582.

Zajitschek, S.R.K., Zajitschek, F., Clobert, J. (2012). The importance of habitat resistance for movement decisions in the common lizard, Lacerta vivipara. BMC Ecology 12:13.


2011

Babiker, H.M.A., Schlebusch, C.M., Hassan, H.Y. & Jakobsson, M. (2011) Genetic variation and population structure among Sudanese populations as indicated by the 15 Identifiler STR loci. Investigative Genetics, 2: 12.

Backström N, Väli U. (2011) Sex- and species-biased gene flow in a spotted eagle hybrid zone. BMC Evol Biol. Apr 14;11:100.

Bailey, R.I., Innocenti, P., Morrow, E.H., Friberg, U. & Qvarnström, A. (2011) Female Drosophila melanogaster gene expression and mate choice: the X chromosome harbours candidate genes underlying sexual isolation. PLoS ONE 6: e17358.

Blum, M.G.B. & Jakobsson, M. (2011) Deep divergences of human gene trees and models of human origins. Molecular Biology and Evolution 28: 889-898.

Castroviejo-Fisher, S., Skoglund, P., Valadez, R., Vila, C. & Leonard, J.A. (2011) Vanishing native American dog lineages. BMC Evolutionary Biology 11: 73.

Chahal, H.S., Stals, K., Unterlander, M., Balding, D.J., Thomas, M.G., Kumar, A.V., Besser, G.M., Atkinson, A.B., Morrison, P.J., Howlett, T.A., Levy, M.J., Orme, S,M,, Akker, S.A., Abel, R.L., Grossman, A.B., Burger, J., Ellard, S. & Korbonits, M. (2011) AIP mutation in pituitary adenomas in the 18th century and today. New England Journal of Medicine 364: 43-50.

Daskalaki, E., Anderung, C., Humphrey, L. & Götherström, A., (2011) Further developments in molecular sex assignment: A blind test of 18th and 19th century human skeletons. Journal of Archaeological Science 38: 1326-1330.

Edwards, C., Ginja, C., Kantanen, J., Pérez-Pardal, L., Tresset, A., Stock, F., European Cattle Genetic Diversity Consortium (including Götherström, A.), Gama, L.T., Penedo, C., Bradley, D., Lenstra, J., Nijman, I., (2011) Dual origins of dairy cattle farming – evidence from a comprehensive survey of European Y-chromosomal variation. PLoS ONE 6: e15922.

Ellegren, H. (2011) The singing genome. Heredity 106: 533-534.

Ellegren, H. (2011) Sex chromosome evolution: recent progress and the influence of male and female heterogamety. Nature Reviews Genetics 12: 157-166.

Ellegren, H. (2011) Emergence of male-biased genes on the chicken Z-chromosome: Contrasts between male and female heterogametic systems. Genome Research 21:2082-2086.

Forstmeier, W. & Schielzeth, H. (2011). Cryptic multiple hypotheses testing in linear models: overestimated effect sizes and the winner's curse. Behavioural ecology and sociobiology 65 (1): 47-55.

Friberg, U., Stewart, A.D. & Rice, W.R. (2011) X and Y chromosome linked paternal effects on a life history trait. Biology Letters, 8: 71-73.

Friberg, U., Stewart, A.D. & Rice, W.R. (2011) Empirical evidence for son-killing X chromosomes and the operation of SA-zygotic drive PLoS ONE6: e23508.

Friberg, U., Miller, P.M., Stewart, A.D. & Rice, W.R. (2011) Mechanisms promoting the long-term persistence of a Wolbachia infection in a laboratory-adapted population of Drosophila melanogaster. PLoS ONE 6: e16448.

Gerbault, P., Liebert, A., Itan, Y., Powell, A., Currat, M., Burger, J., Swallow, D,M. & Thomas, M.G. (2011) Evolution of lactase persistance: an example of human niche construction. Philosophical Transactions of the Royal Society of London B 366: 863-878.

Horsfall, L.J., Zeitlyn, D., Tarekegn, A., Bekele, E., Thomas, M.G., Bradman, N. & Swallow, D.M. (2011) Prevalance of clinically relevant UGT1A alleles and haplotypes in African populations. Annals of Human Genetics 75: 236-246.

Huang*, L., Jakobsson*, M., Pemberton, T.J., Pritchard, J.K., Tishkoff, S.A. & Rosenberg, N.A. (2011) Haplotype variation and genotype imputation in African populations. Genetic Epidemiology, 35: 766-780.
*shared first authorship

Immler, S., Hamilton, M.B., Poslusny, N.J., Birkhead, T.R. & Epifanio, J.M. (2011) Postmating reproductive barriers in two unidirectionally hybridising sunfish (Centrarchidae: Lepomis). Journal of Evolutionary Biology 24: 111-120.

Immler, S., Pitnick, S., Parker, G.A., Durrant, K., Lüpold, S., Calhim, S. & Birkhead, T.R. (2011) Resolving variation in the reproductive trade-off between sperm size and number. Proceedings of the National Academy of Sciences USA 108: 5325-5330.

Künstner, A. Nabholz, B. & Ellegren, H. (2011). Evolutionary constraint in flanking regions of avian genes. Molecular Biology and Evolution, Molecular Biology and Evolution 28:2481-2489.

Künstner, A., Nabholz, B. & Ellegren, H. (2011) Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positively selected genes. Genome Biology and Evolution 3: 1381-1389.

Lindner, D.L., Vasaitis, R., Kubartová, A., Allmér, J., Johannesson, H., Banik, M & Stenlid, J. (2011) Initial fungal colonizer affects mass loss and fungal community development in Picea abies logs 6 yr after inoculation. Fungal Ecology 4: 449-460

Maklakov, AA*, Immler, S*, Gonzalez-Voyer, A, Rönn, J & Kolm, N. 2011. Brains and the city: big-brained passerine birds succeed in urban environments. Biol Lett 7: 730-732.
*shared first authorship

Mugal, C,F. & Ellegren, H. (2011) Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biology, Genome Biology 12:R58.

Müller, B., Pörschmann, U., Wolf, J. B. W. & Trillmich, F. (2011) Growth under uncertainty: The influence of marine variability on early development of Galapagos sea lions. Marine Mammal Science, 27 (2):350-365

Nabholz, B., Künstner, A., Wang, R., Jarvis, E.D. & Ellegren, H. (2011) Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Molecular Biology and Evolution, Molecular Biology and Evolution 28:2197-2210.

Nygren, K., Strandberg, R., Wallberg, A., Nabholz, B., Gustafsson, T., García, D., Cano, J., Guarro, J. & Johannesson, H. (2011). A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi. Molecular Phylogenetics and Evolution, 59 (3): 649-663.

Qiu S, Zeng K, Slotte T, Wright SI, Charlesworth D. 2011. Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species.Genome Biology and Evolution 3:868-880

Rice, A.M., Rudh, A., Ellegren, H. & Qvarnström, A. (2011) A guide to the genomics of ecological speciation in natural animal populations. Ecology Letters 14: 9-18.

Schielzeth, H., Bolund, E., Kempenaers, B. & Forstmeier, W. (2011) Quantitative genetics and fitness consequences of neophilia in zebra finches. Behavioural ecology 22 (1): 126-134

Sjödin P., François O. (2011) Wave-of-Advance Models of the Diffusion of the Y Chromosome Haplogroup R1b1b2 in Europe. PLoS One, 6: e21592

Skoglund, P., Götherström, A. & Jakobsson, M. (2011) Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves. Molecular Biology and Evolution 28: 1505-1517.

Skoglund, P. & Jakobsson, M. Archaic human ancestry in East Asia. (2011) Proceedings of the National Academy of Sciences USA, 108: 18301-18306.

Slotte T, Bataillon T, Hansen TT, St. Onge KR, Wright SI, Schierup MH. 2011. Genomic determinants of protein evolution and polymorphism in Arabidopsis.Genome Biology and Evolution 3:1210-1219

Smeds L, Künstner A (2011) ConDeTri - A Content Dependent Read Trimmer for Illumina Data. PLoS ONE 6(10): e26314. doi:10.1371/journal.pone.0026314

St. Onge KR, Källman T, Slotte T, Lascoux M, Palmé AE. 2011. Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. Molecular Ecology 20(16):3306-3320

Whittle, C.–A, Nygren, K. & Johannesson, H. (2011). Consequences of reproductive mode on genome evolution in fungi. Fungal Genetics and Biology, 48 (7): 661-667

Whittle, C.–A. & Johannesson, H. (2011). Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma . Heredity 107 (4): 305-314.

Whittle, C.–A., Sun, Y. and Johannesson, H. (2011).  Degeneration in codon usage within the region of suppressed recombination in the mating-type chromosomes of Neurospora tetrasperma. Eukaryotic Cell 10(4): 594-603

Whittle, C. A. and Johannesson, H. 2011. Evolution of mating-type loci and mating-type chromosomes in model species of filamentous ascomycetes In "THE MYCOTA XIV, Evolution of fungi and fungal-like organisms" J. Wöstemeyer and S.Pöeggeler (eds.), vol. XIV. Springer Verlag, Heidelberg.

Whittle CA, Sun Y, Johannesson H. 2011. Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta. Genome Biology and Evolution 3: 332-343

Wolf, J.B.W. & Bryk, J. (2011) General lack of global dosage compensation in ZZ/ZW systems ? Broadening the perspective with RNA-seq. BMC Genomics 12:91

Wolf, J.B.W., Traulsen, A. & James, R. (2011) Exploring the link between genetic relatedness r and social contact structure k in animal social networks. American Naturalist 177: 135:142.


2010

Akkoc, N., Sari, I., Akar, S., Binicier, O. & Thomas, M.G. (2010) Increased prevalence of M694V in patients with ankylosing spondylitis: additional evidence for a link with familial mediterranean fever. Arthitis Reumatics 62: 3059-3063.

Axelsson, E., Albrechtsen, A., As P. van, Li, L., Megens, H.J., Vereijken, A.L.J., Crooijmans, R.P.M.A., Groenen, M.A.M., Ellegren, H., Willerslev, E. & Nielsen, R. (2010) Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds. Heredity 105: 290-298.

Backström, N., Forstmeier, W., Schielzeth, H., Mellenius, H., Nam, K., Bolund, E., Webster, M.T., Öst, T., Schneider, M., Kempenaers, B. & Ellegren, H. (2010) The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Research 20: 485-495.

Backström, N., Lindell, J., Zhang, Y., Palkopoulou, E., Qvarnström, A., Saetre, G.P. & Ellegren, H. (2010) A high-density scan of the Z-chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection. Evolution 64: 3461-3475.

Backström, N., Palkopoulou, E., Qvarnström, A. & Ellegren, H. (2010) No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps. Molecular Ecology 19: 3394-3405.

Balding, D., Weale, M., Richards, M. & Thomas, M.G. (2010) Genetic and isotopic analysis and the UK border agency. Significance 7: 58-61.

Barnes, I., Duda, A., Pybus, O.G. & Thomas, M.G. (2010) Ancient urbanization predicts genetic resistance to tuberculosis. Evolution 65: 842-848.

Browning, S.L., Tarekegn, A,, Bekele, E., Bradman, N. & Thomas, M.G. (2010) CYP1A2 is more variable than previously thought: a genomic biography of the gene behind the human drug-metabolizing enzyme. Pharmacogenetical Genomics 20: 647-664.

Bryan, H.M., Sim, K.A., Darimont, C.T., Paquet, P.C., Wagner, B., Munoz-Fuentes, V., Smits, J.E. & Chilton, N.B. (2010) Identification of Paelaphostronglus odocoilei (Nematoda: Protostrongylidae) first-stage larvae in the feces of gray wolves (Canis lupus) by molecular methods. Journal of Wildlife Diseases 46: 297-302.

Brøseth, H., Flagstad, Ø., Wärdig, C., Johansson, M. & Ellegren, H. (2010) Large-scale noninvasive genetic monitoring of wolverines using scats reveals density dependent adult survival. Biological Conservation 143: 113-120.

Campos, P.F., Kristensen, T., Orlando, L., Sher, A., Kholodova, M.V., Götherström, A., Hofreiter, M., Drucker, D.G., Kosintsev, P., Tikhonov, A., Baryshnikov, G.F., Willerslev, E. & Gilbert, M.T. (2010) Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene. Molecular Ecology 19: 4863-4875.

Corl, A. Davis, A.R., Kuchta, S.R. & Sinervo, B. (2010) Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation. Proceedings of the National Academy of Sciences USA 107: 4254-4259.

Den Tex, R., Maldonado, J.E., Thorington, R., & Leonard, J.A. (2010) Nuclear copies of mitochondrial genes: another problem for ancient DNA Genetica 138: 979-984.

Den Tex, R., Thorington, R., Maldonado, J.E., & Leonard, J.A. (2010) Speciation dynamics in the SE Asian tropics: putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. Molecular Phylogenetics and Evolution 55: 711-720.

Eklund, J.A. & Thomas, M.G. (2010) Assessing the effects of conservation treatments on short sequences of DNA in vitro. Journal of Archaeological Science 37: 2831-2841.

Eklund, D.M., Svensson, E. & Kost, B. (2010) Physcomitrella patens: a model to investigate the role of RAC/ROP GTPase signalling in tip growth. Journal of Experimental Botany 61: 1917-1937.

Ellegren, H. (2010) Evolutionary stasis – the stable chromosomes of birds. Trends in Ecology and Evolution 25: 283-291.

Forstmeier, W. & Ellegren, H. (2010) Trisomy and triploidy are sources of embryo mortality in the zebra finch. Proceedings of the Royal Society of London, Series B 277: 2655-2660.

Goicoechea, N., De La Riva, I. & Padial, J.M. (2010) Recovering phylogenetic signal from frog mating calls. Zoologica Scripta 39: 141-154.

Hansson, B., Ljungqvist, M., Dawson, D.A., Mueller, J.C., Olano-Marin, J., Ellegren, H. & Nilsson, J.Å. (2010) Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus). Heredity 104: 67-78.

Immler, S., Pryke, S.R., Birkhead, T.R. & Griffith, S.C. (2010) Pronounced within-individual plasticity in sperm morphometry across social environments. Evolution 64: 1634-1643.

Itan, Y., Bryson, K. & Thomas, M.G. (2010) Detecting gene duplications in the human lineage. Annals of Human Genetics 74: 555-565.

Itan, Y., Jones, B.L., Ingram, C.J., Swallow, D.M.. & Thomas, M.G. (2010) A worldwide correlation of lactase persistence phenotype and genotypes. BMC Evolutionary Biology 10: 36.

Kohler, J., Koscinski, D., Padial, J.M., Chaparro, J.C., Handford, P., Lougheed, S.C. & De la Riva, I. (2010) Systematics of Andean gladiator frogs of the Hypsiboas pulchellus species group (Anura, Hylidae). Zoologica Scripta 39: 572-590.

Künstner, A., Wolf, J.B.W., Backstrom, N., Whitney, O., Balakrishnan, C. N., Day, L., Edwards, S. V., Janes, D. E., Schlinger, B. A., Wilson, R. K., Jarvis, E., Warren, W. C. & Ellegren, H. (2010) Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Molecular Ecology 19: 266-276.

Lavilla, E.O., Langone, J.A., Padial, J.M. & De Sa, R.O. (2010) The identity of the crackling, luminescent frog of Suriname (Rana typhonia Linnaeus, 1758) (Amphibia, Anura). Zootaxa 2671: 17-30.

Lira, J., Linderholm, A., Olaria, C., Brandström Durling, M., Gilbert, T.P., Ellegren, H., Willerslev, E., Lidén, K., Arsuaga, J.L. & Götherström, A. (2010) Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Molecular Ecology 19: 64-78.

Malmström, H., Linderholm, A., Lidén, K., Storå, J., Molnar, P., Holmlund, G., Jakobsson, M. & Götherström, A. (2010) High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe. BMC Evolutionary Biology. 10: 89.

Mank, J.E., Nam, K. & Ellegren, H. (2010) Faster-Z evolution is predominantly due to genetic drift. Molecular Biology and Evolution 27: 661-670.

Mank, J.E., Nam, K., Brunström, B. & Ellegren, H. (2010) Ontogenetic complexity of sexual dimorphism and sex-specific selection. Molecular Biology and Evolution 27: 1570-1578.

Menkis, A., Whittle, C.–A. & Johannesson, H. (2010) Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma. BMC Evolutionary Biology 10: 234.

Mugal, C.F., Wolf, J.B.W., von Grünberg H.H. & Ellegren, H. (2010) Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes. Genome Biology and Evolution 2010: 19-28.

Muñoz-Fuentes, V., Darimont, C.T., Paquet, P., & Leonard, J.A. (2010) The genetic legacy of extirpation and re-colonization in Vancouver Island wolves. Conservation Genetics 11: 547-556.

Nabholz, B., Jarvis, E.D. & Ellegren, H. (2010) Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study of the basal Passerida (Aves: Passeriformes) phylogeny. Molecular Phylogenetics and Evolution 57:466-470.

Nakagawa, S. & Schielzeth, H. (2010) Repeatability for Gaussian and non-Gaussian data: a practical guide for biologists. Biological Reviews 85: 935-956.

Nam, K., Mugal, C., Nabholz, B., Schielzeth, H., Wolf, J.B.W., Backström, N., Künstner, A., Balakrishnan, C.N., Heger, A., Ponting, C.P., Clayton, D.F. & Ellegren, H. (2010) Molecular evolution of genes in avian genomes. Genome Biology 11: R68.

Padial, J.M. & De La Riva, I. (2010) A response to recent proposals for integrative taxonomy. Biological Journal of the Linnean Society 101: 747-756.

Padial, J.M., Miralles, A., De la Riva, I. & Vences, M. (2010) The integrative future of taxonomy. Frontiers in Zoology 7: 16.

Schielzeth, H. & Bolund, E. (2010) Patterns of conspecific brood parasitism in zebra finches. Animal Behaviour 79: 1329-1337.

Parker, G.A., Immler, S., Pitnick, S. & Birkhead, T.R. (2010) Sperm competition games: sperm size (mass) and number in a sperm displacement model. Journal of Theoretical Biology 264: 1003-1023.
Poelstra, J. (2010) Speciation in shades of grey: the great grey shrike complex. Dutch Birding 32: 258-264.
Pörschmann, U., Trillmich, F., Müller, B. & Wolf, J. B. W. (2010) Male reproductive success and its behavioural correlates in a polygynous mammal, the Galápagos sea lion (Zalophus wollebaeki). Molecular Ecology 19, 2574-2586.
Qvarnström, A., Rice, A.M. & Ellegren, H. (2010) Speciation in Ficedula flycatchers. Philosophical Transactions of the Royal Society of London B: Biological Sciences 365: 1841-1852.

Reichart, L.M., Anderholm, S. Munoz-Fuentes, V. & Webster, M.S. (2010) Molecular identification of brood-parasitic females reveals an opportunistic reproductive tactic in ruddy ducks. Molecular Ecology 19: 401-413.
Rice, W.R., Gavrilets, S. & Friberg, U. (2010) The evolution of sex-specific grandparental harm. Proceedings of the Royal Society of London, Series B 277: 2727-2735.

Schielzeth, H. (2010) Mating preferences of zebra finches. Vogelwarte 48: 283-284.

Schlebusch CM (2010). Issues raised by use of ethnic-group names in genome study. Nature 464: 487.

Seddon, J.M., Berggren, K.T. & Fleeman, L.M. (2010) Evolutionary history of DLA class II haplotypes in canine diabetes mellitus through single nucleotide polymorphism genotyping. Tissue Antigens 75: 218-226.

Skoglund, P. & Höglund, J. (2010) Sequence polymorphism in candidate genes for differences in winter plumage between Scottish and Scandinavian willow grouse (Lagopus lagopus). PLoS One 5: e10334.

Slotte, T., Foxe, J.P., Hazzouri, K.M. & Wright S.I. (2010) Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Molecular Biology and Evolution 27: 1813-1821.

Staubach, F., Teschke, M., Voolstra, C.R., Wolf, J.B.W., Tautz, D. (2010) A test of the neutral model of expression change in natural populations of house mouse subspecies. Evolution 64: 549-560.

Strandberg, R., Nygren, K., Menkis, A., James, T. Y., Wik, L., Stajich, J. E. & Johannesson, H. (2010). Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genetics and Biology 47: 869-878.

Tautz, D., Ellegren, H. & Weigel, D. (2010) Next generation molecular ecology. Molecular Ecology Suppl 1: 266-276.

Vali, U., Dombrovski, V., Treinys, R., Bergmanis, U., Daroczi, S.J., Dravecky, M., Ivanovski, V., Lontkowski, J., Maciorowski, G., Meyburg, B.U., Mizera, T., Zeitz, R. & Ellegren, H. (2010) Widespread hybridization between the Greater Spotted Eagle Aquila clanga and the Lesser Spotted Eagle Aquila pomarina (Aves: Accipitriformes) in Europe. Biological Journal of the Linnean Society 100: 725-736.

Vali, U., Saag, P., Dombrovski, V., Meyburg, B.U., Maciorowski, G., Mizera, T., Treinys, R. & Fagerberg, S. (2010) Microsatellites and single nucleotide polymorphisms in avian hybrid identification: a comparative case study. Journal of Avian Biology 41: 34-49.

Veeramah, K.R., Connell, B.A., Pour, N.A., Powell, A., Plaster, C.A., Zeitlyn, D., Mendell, N.R., Weale, M.E., Bradman, N. & Thomas, M.G. (2010) Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria. BMC Evolutionary Biology 10: 9.

Völker, M., Backström, N., Skinner, B.M., Langley, E.J., Bunzey, S.K., Ellegren, H. & Griffin, D.K. (2010) Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Research 20: 503-511.

Wang, C., Szpiech, Z.A., Degnan, J.H., Jakobsson, M., Pemberton, T.J., Hardy, J.A., Singleton, A.B. & Rosenberg, N.A. (2010) Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology 9: 13.

Wang, Z.F., Shen, X., Liu, B., Su, J.P., Yonezawa, T., Yu, Y., Guo, S.C., Ho, S.Y.W., Vilá, C., Hasegawa, M. & Liu, J.Q. (2010) Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. Journal of Biogeography 37: 2332-2344.

Warren, W.C., Clayton, D.F., Ellegren, H., Arnold, A.P., Hillier, L.W., Künstner, A., Searle, S., White, S., Vilella, A.J., Fairley, S., Heger, A., Kong, L., Ponting, C.P., Jarvis, E.D., Mello, C.V., Minx, P., Lovell, P., Velho, T.A., Ferris, M., Balakrishnan, C.N., Sinha, S., Blatti, C., London, S.E., Li, Y., Lin, Y.C., George, J., Sweedler, J., Southey, B., Gunaratne, P., Watson, M., Nam, K., Backström, N., Smeds, L., Nabholz, B., Itoh, Y., Whitney, O., Pfenning, A.R., Howard, J., Völker, M., Skinner, B.M., Griffin, D.K., Ye, L., McLaren, W.M., Flicek, P., Quesada, V., Velasco, G., Lopez-Otin, C., Puente, X.S., Olender, T., Lancet, D., Smit, A.F., Hubley, R., Konkel, M.K., Walker, J.A., Batzer, M.A., Gu, W., Pollock, D.D., Chen, L., Cheng, Z., Eichler, E.E., Stapley, J., Slate, J., Ekblom, R., Birkhead, T., Burke, T., Burt, D., Scharff, C., Adam, I., Richard, H., Sultan, M., Soldatov, A., Lehrach, H., Edwards, S.V., Yang, S.P., Li, X., Graves, T., Fulton, L., Nelson, J., Chinwalla, A., Hou, S., Mardis, E.R. & Wilson, R.K. (2010) The genome of a songbird. Nature 464: 757-762.

Wolf, J.B.W., Bayer, T., Haubold, B., Schilhabel, M., Rosenstiel, P. & Tautz, D. (2010) Nucleotide divergence versus gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology 19: 162-175.

Wolf, J. B. W., Lindell, J. & Backstrom, N. (2010) Speciation genetics: current status and evolving approaches. Philosophical Transactions of the Royal Society B-Biological Sciences 365: 1717-1733.


2009

Anderson, T.M., vonHoldt, B.M., Candille, S.I., Musiani, M., Greco, C., Stahler, D.R., Smith, D.W., Padhukasahasram, B., Randi, E., Leonard, J.A., Bustamante, C.D., Ostrander, E.A., Tang, H., Wayne, R.K. & Barsh, G.S. (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323: 1339-1343.

Axelsson, E. & Ellegren, H. (2009) Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection. Molecular Biology and Evolution 26: 1073-1079.

Barsch, G.S., Anderson, T.M., Vonholdt, B.M., Candille, S.I., Musiani, M., Stahler, D.R., Leonard, J.A., Padhukasahasram, B., Randi, E., Bustamante, C.D., Ostrander, E.A., Tang, H. & Wayne, R.K. (2009) How the gray wolf got its color. Science 325: 34.

Bryan, H.M., Sim, K.A., Darimont, C.T., Paquet, P.C., Wagner, B., Muñoz-Fuentes, V., Smits, J.E. & Chilton, N.B. (2009) Identification of Parelaphostrongylus odocoilei (Nematoda: Protostrongylidae) first-stage larvae in the feces of gray wolves (Canis lupus) by molecular methods. Journal of Wildlife Diseases 46: 297-302.

Castroviejo-Fisher, S., *Guayasamin, J.M., Trueb, L., Rada, M. & Vilà, C. (2009) Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and their sister taxon Allophryne ruthveni. Zootaxa 2100: 1–97.

Castroviejo-Fisher, S,. Padial, J.M., Chaparro, J.C., Aguayo, R. & De la Riva, I. (2009) A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area. Zootaxa 2143, 24-44.

DeGiorgio, M., Jakobsson, M. & Rosenberg, N.A. (2009) Explaining worldwide patterns of human genetic variation through a coalescent-based serial founder model of migration outward from Africa. Proceedings of the National Academy of Sciences USA 106: 16057-16062.

Dowling, D., Maklakov, A.A., Friberg, U. & Hailer, F. (2009) Applying the genetic theories of ageing to the cytoplasm: cytoplasmic genetic covariation for fitness and lifespan. Journal of Evolutionary Biology 22: 818-827.

Eccard J., Wolf J.B.W. (2009) Effects of brood size on mixed paternity rates: a case for offspring-based estimators and confidence intervals. Animal Behaviour 78, 563-571.

Ellegren, H. (2009) A selection model of molecular evolution incorporating the effective population size. Evolution 63: 301-305.

Ellegren, H. (2009) Genomic evidence for a large-Z effect. Proceedings of the Royal Society of London, Series B 276: 361-366.

Ellegren, H. (2009) Is genetic diversity really higher in large populations? Journal of Biology 8: 41.

Ellegren, H. (2009) The different levels of genetic diversity in sex chromosomes and autosomes. Trends in Genetics 25: 278-284.

Gilbert, T., Jenkins, D., Higham, T., Rasmussen, M., Malmström, H., Svensson, E., Sanchez, J., Cummings, L., Yohe, R., Hofreiter, M., Götherström, A. & Willerslev, E. (2009) Response to comment on "DNA from pre-Clovis human coprolites in Oregon, North America". Science 325: 148.

Hagenblad, J., Olsson, M., Parker, H.G., Ostrander, E.A. & Ellegren, H. (2009) Population genomics of the inbred Scandinavian wolf. Molecular Ecology 18: 1341-1351.

Jakobsson, M. (2009) COMPASS: A program for generating serial samples under an infinite sites model. Bioinformatics, 25: 2845-2847.

James, T.Y., Johansson, S. & Johannesson, H. (2009) Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum. Mycological Research 113: 583-590.

Johnson, J.A., Tingay, R.E., Culver, M., Hailer, F., Clarke, M.L. & Mindell, D.P. (2009) Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle. Molecular Ecology 18: 54-63.

Koblmüller, S., Nord, M., Wayne, R.K. & Leonard, J.A. (2009) More is Better. Molecular Ecology 18: 4994-4996.

Koblmüller, S., Nord, M., Wayne, R.K. & Leonard, J.A. (2009) Origin and status of the Great Lakes wolf. Molecular Ecology 18: 2313-2316.

Leden, I., Götherström, A., Drenzel, L. & Svensson, B. (2009) HLA-B27 sequences identified in a mediaeval skeleton with ankylosing spondylitis. Annals of the Rheumatic Diseases 68: 757-758.

Malmström, H., Gilbert, M.T., Thomas, M.G., Brandström, M., Storå, J., Molnar, P., Andersen, P.K., Bendixen, C., Holmlund, G., Götherström, A. & Willerslev, E. (2009) Ancient DNA reveals lack of continuity between Neolithic Hunter-Gatherers and contemporary Scandinavians. Current Biology 19: 1758-1762.

Mank, J.E. & Ellegren, H. (2009) All dosage compensation is local: Gene-by-gene regulation of sex-biased gene expression on the chicken Z chromosome. Heredity 102: 312-320.

Mank, J.E. & Ellegren, H. (2009) Are sex-biased genes more dispensable? Biology Letters 23: 409-412.

Mank, J.E. & Ellegren, H. (2009) Sex-linkage of sexually antagonistic genes is predicted by female, but not male, effects in birds. Evolution 63: 1464-1472.

Mank, J.E. & Ellegren, H. (2009) Sex-bias in gene expression is not the same as dosage compensation. Heredity 103: 434.

Menkis, A., Bastiaans, E., Jacobson, D.J. & Johannesson, H. (2009) Phylogenetic and biological species diversity within the Neurospora tetrasperma species complex. Journal of Evolutionary Biology 22: 1923-1936.

Miller, W., Drautz, D.I., Janecka, J.E., Lesk, A.M., Ratan, A., Tomsho, L.P., Packard, M., Zhang, Y., McClellan, L.R., Qi, J., Zhao, F., Gilbert, M.T., Dalén, L., Arsuaga, J.L, Ericson, P.G., Huson, D.H., Helgen, K.M., Murphy, W.J., Götherström, A. & Schuster, S.C. (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research 19: 213-220.

Mugal, C.F., von Grünberg, H.H. & Peifer, M. (2009) Transcription-induced mutational strand bias and its effect on substitution rates in human genes, Molecular Biology and Evolution 26: 131-142.

Muñoz-Fuentes, V., Darimont, C.T., Wayne, R.K., Paquet, P. & Leonard, J.A. (2009) Ecological factors drive differentiation in wolves from British Columbia. Journal of Biogeography 36: 1516-1531.

Padial, J.M. & Tellería, J.L. (2009) Observations of the Felou gundi (Felovia vae Lataste, 1886) in central Mauritania (Rodentia: Ctenodactylidae). Mammalia 73: 153–154.

Padial, J.M., Chaparro, J.C., Köhler, J. & De la Riva, I. (2009) Rediscovery, resurrection and re-description of Rhinella leptoscelis (Boulenger, 1912) (Anura: Bufonidae). Zootaxa 2115: 56-64.

Padial, J.M., Castroviejo-Fisher, S. & De la Riva, I. (2009) The phylogenetic relationships of Yunganastes revisited (Anura: Terrarana). Molecular Phylogenetics and Evolution 52: 911–915.

Padial, J.M., Castroviejo-Fisher, S., Köhler, J., Vilà, C., Chaparro, J.C. & De la Riva, I. (2009) Deciphering the products of evolution at the species level: the need for an integrative taxonomy. Zoologica Scripta 38: 431–447.

Pemberton, T.J., Sandefur, C.I., Jakobsson, M. & Rosenberg, N.A. (2009) Sequence determinants of human microsatellite variability. BMC Genomics, 10: 612.

Schroeder, K.B., Jakobsson, M., Crawford, M.H., Schurr, T.G., Boca, S.M., Conrad, D.F., Tito, R.Y., Osipova, L.P., Tarskaia, L.A., Zhadanov, S.I., Wall, J.D., Pritchard, J.K., Malhi, R.S., Smith, D.G. & Rosenberg, N.A. (2009) Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution 26: 995-1016.

Wolf, J.B.W., Künstner, A., Nam, K., Jakobsson, M. & Ellegren, H. (2009) Non-linear dynamics of non-synonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biology and Evolution 1: 308-319.


2008

Anderung, C., Persson, P., Bouwman, A., Elburg, R. & Götherström, A. (2008) Fishing for ancient DNA. Forensic Science International: Genetics 2: 104-107

Axelsson., E., Hultin-Rosenberg, L., Brandström, M., Zwahlén, M., Clayton, D.F. & Ellegren, H. (2008) Natural selection in avian protein-coding genes expressed in brain. Molecular Ecology 17: 3008-3017.

Backström, N., Fagerberg, S. & Ellegren, H. (2008) Genomics of wild bird populations: a gene-based set of references markers spread across the avian genome. Molecular Ecology 17: 964-980.

Barrio-Amorós, C.L., & Castroviejo-Fisher, S. (2008) The taxonomic status of Rhaebo anderssoni (Melin, 1941) (Anura: Bufonidae). Salamandra 44: 59–67.

Barrio-Amorós, C.L., & Castroviejo-Fisher, S. (2008) Comments on the distribution, taxonomy and advertisement call of the Guyanan glass frog Hyalinobatrachium ignioculus (Anura: Centrolenidae). Salamandra 44: 235–240.

Berlin, S., Quintela, M. & Höglund, J. (2008) A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus). BMC Genetics 9: 89.

Björnerfeldt S, Hailer F, Nord M, Vila C (2008) Assortative mating and fragmentation within dog breeds. BMC Evolutionary Biology 8:28.

Backström, N., Karaiskou, N., Leder, E.H., Gustafsson, L. Primmer, C.R., Qvarnström, A. & Ellegren, H. (2008) A gene-based genetic linkage map of the collared flycatcher (Ficedula albicollis) reveals extensive synteny and gene order conservation during 100 million years of avian evolution. Genetics 179: 1479-1495.

Brandström, M. & Ellegren, H. (2008) Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Research 18: 881-887.

Buckley, M., Anderung, C., Gotherstrom, A., Penkman, K., Thomas-Oates, J., Collins, M. (2008) Red light for osteocalcin as a species-specific biomarker in archaeology; a comparison to DNA amplification success in four European sites. Journal of Archaeological Science 35: 1756-1764.

Castroviejo-Fisher, S., Señaris, J. C., Ayarzagüena, J. & Vilà, C. (2008) Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae). Herpetologica 64: 472-484.

Cruz, F., Vilà, C. & Webster, M.T. (2008) The legacy of domestication: Accumulation of deleterious mutations in the dog genome. Molecular Biology and Evolution 25: 2331-2336.

Dearborn DC, Hailer F, Fleischer RC (2008) Microsatellite Primers for Relatedness and Population Structure in Great Frigatebirds (Pelecaniformes: Fregatidae). Molecular Ecology Resources 8: 1399-1401.

Dowling, D.K., Friberg, U. & Lindell, J. (2008) Evolutionary implications of non-neutral mitochondrial genetic variation. Trends in Ecology and Evolution 23: 546-554.

Ellegren, H. & Sheldon, B.C. (2008) Genetic basis for fitness differences in natural populations. Nature 452: 169-175.

Ellegren, H. (2008) Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology 17: 1629-1631.

Ellegren, H. (2008) Platypus genome suggests a recent origin for the human X. Current Biology 18: 557-559.

Fox-Dobbs, K., Leonard. J.A. & Koch, P. L. (2008) Pleistocene megafauna from eastern Beringia: paleoecological and paleoenvironmental interpretations of stable carbon and nitrogen isotope and radiocarbon records. Palaeogeography, Palaeoclimatology, Palaeoecology 261: 30-46.

Francois, O., Blum, M. G. B., Jakobsson, M., & Rosenberg N. A. (2008) Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics, 4: e1000075.

Gilbert, T., Willerslev, E. Götherström, A.,, Naveran, N., Binladen J., Sanchez, J., Hofreiter, M., Jenkins, D. & Higham, T. (2008) Ancient DNA from coprolites reveal pre-Clovis human presence in North America. Science 320: 786-789.

Gilbert, T. et al. (22 co-authors including Götherström, A.) (2008) Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 320: 1787-1789.

Gilbert , T. et al. (22 co-authors including Götherström, A.) (2008) Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences USA 105: 8327-8332.

Guayasamin, J.M., Castroviejo-Fisher, S., Ayarzagüena, J., Trueb, L. & Vilà, C. (2008) Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 48: 574-595.

Guayasamin, J.M., Cisneros-Heredia, D.F. & Castroviejo-Fisher, S. (2008) Taxonomic identity of Cochranella petersi Goin, 1961 and Centrolenella ametarsia Flores, 1987. Zootaxa 1815: 25–34.

Hailer F, Leonard JA (2008) Hybridization among Three Native North American Canis Species in a Region of Natural Sympatry. PLoS ONE 3: e3333.

James, T. Y., Olson, Å., Stenlid, J. and Johannesson, H. 2008. Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum. Evolution 62: 2279-2296.

Karlsson, M., Nygren, K., Johannesson, H. (2008) The evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic Neurospora. Molecular Biology and Evolution 25: 168-178.

Kok, P.J.R. & Castroviejo-Fisher, S. (2008) Glassfrogs (Anura : Centrolenidae) of Kaieteur National Park, Guyana, with notes on the distribution and taxonomy of some species of the family in the Guiana Shield. Zootaxa 1680: 25–53.

Leonard, J.A. & Wayne, R.K. (2008) Native Great Lakes wolves were not restored. Biology Letters 4: 95-98.

Leonard, J.A. (2008) Ancient DNA applications for wildlife conservation. Molecular Ecology 17: 4186-4196.

Lindell, J. & Murphy, R.W. (2008) Simple identification of mitochondrial lineages in contact zones based on lineage-selective primers. Molecular Ecology Resources 8: 66-73.

Lindell, J., Mendez-De La Cruz, F.R. & Murphy, R.W. (2008) Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard (Urosaurus nigricaudus) of Baja California. Biological Journal of the Linnean Society 94: 89-104.

Linderholm, A., Malmström, H., Lidén, K., Holmlund, G. & Götherström, A. (2008) Cryptic contamination and making phylogenetic nonsense. PLoS ONE 3: e2316.

Malmstrom, H., Vila, C., Gilbert, M.T.P., Stora, J., Willerslev, E., Holmlund, G. & Gotherstrom, A. (2008) Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evolutionary Biology 8: 71.

Mank, J. E., Hultin-Rosenberg, L., Zwahlén, M. & Ellegren, H. (2008) Pleiotropic constraint hampers the resolution of sexual antagonism in vertebrate gene expression. American Naturalist 171: 35-43.

Mank, J.E., Hultin-Rosenberg, L., Webster, M.T. & Ellegren, H. (2008) The unique genomic properties of sex-biased genes: insights from avian microarray data. BMC Genomics 9: 148.

Menkis, A., Jacobson, D.J., Gustafsson, T., Johannesson, H. (2008) The mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma represents a model for early evolution of sex chromosomes. PLoS Genetics 4: e1000030.

Pemberton, T. J., Jakobsson, M., Conrad, D. F., Coop, G., Wall, J. D., Pritchard, J. K., Patel, P. I., & Rosenberg, N. A. (2008) Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Annals of Human Genetics 72: 535-546.

Reinius, B, Saetre, P., Leonard, J.A., Blekhman, R., Gilad, Y. & Jazin. E. (2008) An evolutionarily conserved sexual signature in the primate brain. PLoS Genetics 4: e1000100.

Roed, K.H., Flagstad, O., Nieminen, M., Holand, O., Dwyer, M.J., Rov, N. & Vila, C. (2008) Genetic analyses reveal independent domestication origins of Eurasian reindeer. Proceedings of the Royal Society of London Series B 275: 1849-1855.

Rosenberg, N. A. & Jakobsson, M. (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics 179: 2027-2036.

Schroeder, K.B., Jakobsson, M., Crawford, M.H., Schurr, T.G., Boca, S.M., Conrad, D.F., Tito, R.Y., Osipova, L.P.,Tarskaia, L.A., Zhadanov, S.I., Wall, J.D., Pritchard, J.K., Malhi, R.S., Smith, D.G. & Rosenberg, N.A. (2008) Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution 26: 995-1016.

Sundqvist, A.K., Ellegren, H. & Vilà, C. (2008) Wolf or dog? Genetic identification of predator from saliva collected around bite wounds on prey. Conservation Genetics 9: 1275-1279.

Svensson, E. & Götherström, A. (2008) Temporal fluctations of Y-chromosomal variation in Bos taurus. Biology Letters 4: 752-754.

Svensson, E.M., Götherström, A. & Vretemark M. (2008) A DNA test for sex identification in cattle confirms osteometric results. Journal of Archaeological Sciences 35: 942-946.

Szpiech, Z.A., Jakobsson, M. & Rosenberg, N.A. (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24: 2498-2504.

Temperley, N.D., Berlin, S., Paton, I.R., Griffin, D.K. & Burt, D.W. (2008) Evolution of the chicken Toll-like receptor gene family: A story of gene gain and gene loss. BMC Genomics 9: 62.

Valdiosera, C., Luis García-Garitagoitia, J, Garcia, N, Doadrio, I, Thomas, M., Hänni, C., Arsuaga, J.L., Barnes, I., Hofreiter, M., Orlando, L., Götherström, A., Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proceedings of the National Academy of Sciences USA 105:5123-5128.

Väli, U., Brandström, M., Johansson, M. & Ellegren, H. (2008) Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genetics 9: 8.

Väli, Ü., Einarsson, A., Waits, L., Ellegren, H. (2008). To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations? Molecular Ecology 17: 3808-3817.

Wik, L., Karlsson, M. & Johannesson, H. (2008) The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa. BMC Evolutionary Biology 8: 109.

Åberg, K., Axelsson, E., Saetre, P., Jiang, L., Wetterberg, L., Pettersson, U., Lindholm, E. & Jazin, E. (2008) Support for Schizophrenia Susceptibility Locus on Chromosome 2q Detected in a Swedish Isolate Using a Dense Map of Microsatellites and SNPs. American Journal of Medical Genetics B 147B: 1238-1244.


2007

Anderung, C., Hellborg, L., Seddon, J., Hanotte, O., Götherström, A. (2007) New X- and Y-specific SNPs and indels distinguishing between taurine (Bos Taurus) and indicine (Bos indicus) cattle: origin, introgression and admixture in African cattle. Animal Genetics 38: 595-600.

Anderung, C., Persson P, Bouwman A, Elburg R, Götherström, A. (2007) Fishing for ancient DNA. Forensic Science International: Genetics 2:104-107.

Arrendal, J., Vilà, C. and Björklund, M. (2007) Reliability of noninvasive genetic census of otters compared to field censuses. Conservation Genetics, 8: 1097-1107.

Bergfur, J., Johnson, R.K., Sandin, L., Goedkoop, W. and Nygren, K. (2007) Effects of nutrient enrichment on boreal streams: invertebrates, fungi and leaf-litter breakdown. Freshwater Biology 52: 1618-1633.

Björnerfeldt, S. & Vilà, C.. Evaluation of methods for single hair DNA amplification. Conservation Genetics 8: 977-981.

Brandström, M. & Ellegren, H. (2007) The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: a high frequency of deletions in tandem duplicates. Genetics 176: 1691-1701.

Castroviejo-Fisher, S., De la Riva, I. & Vilà, C. (2007) Transparent frogs show potential of natural world. Nature 449: 972.

Castroviejo-Fisher, S., Ayarzaguena, J. & Vila, C. (2007) A new species of Hyalinobatrachium (Centrolenidae: Anura) from Serrania de Perija, Venezuela. Zootaxa 1441: 51-62.

Ceresini, P.C., Shew, H.D., James, T.Y., Vilgalys, R.J. and Cubeta, M.A. (2007) Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci. BMC Evolutionary Biology 7: 163.

Dalén, L., Nyström, V., Valdiosera, C., Germonpré, M., Sablin, M., Turner, E., Angerbjörn, A., Arsuaga, J.L. & Götherström, A. (2007) Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proceedings of the National Academy of Sciences USA 104: 6726-6729.

Ellegren, H. (2007) A dinosaur’s view on genome size evolution. Current Biology 17: R470-472.

Ellegren, H. (2007) Avian molecular evolutionary genomics. Cytogenetics and Genome Research 117: 120-130.

Ellegren, H. (2007) Characteristics, causes and evolutionary consequences of male-biased mutation. Proceedings of the Royal Society London, Series B 274: 1-10.

Ellegren, H. & Parsch, J. (2007) The evolution of sex-biased genes and sex-biased gene expression. Nature Reviews Genetics 8: 689-698.

Ellegren, H., Hultin-Rosenberg, L., Brunström, B., Dencker, L., Kultima, K. & Scholtz, B. (2007) Faced with inequality: chicken does not have a general dosage compensation of sex-linked genes. BMC Biology 5: 40.

Engen, S., Ringsby, T.H., Lande, R., Jensen, H., Sæther, B.E., Lillegard, M. & Ellegren, H. (2007) Effective size of fluctuating populations with overlapping generations: extension of Wright’s formula for two sexes. Evolution 61: 1873-1885.

Geffen, E., Waidyaratne, S., Dalén, L., Angerbjörn, A., Vilà, C., Hersteinsson, P. Fuglei, E., White, P.A. Goltsman, M. & Wayne, R.K. (2007) Sea ice occurrence predicts genetic isolation in the Arctic fox. Molecular Ecology 16: 4241–4255.

Gilbert, M.T., Tomsho, LP, Rendulic, S, Packard, M, Drautz, DI, Sher, A, Tikhonov, A, Dalén, L, Kuznetsova, T, Kosintsev, P, Campos, PF, Higham, T, Collins, MJ, Wilson, AS, Shidlovskiy, F, Buigues, B, Ericson, PG, Germonpré, M, Götherström, A, Iacumin, P, Nikolaev, V, Nowak-Kemp, M, Willerslev, E, Knight, JR, Irzyk, GP, Perbost, CS, Fredrikson, KM, Harkins, TT, Sheridan, S, Miller, W. & Schuster, S.C. (2007) Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 317:1927-1930.

Hailer F, Helander B, Folkestad AO, Ganusevich SA, Garstad S, Hauff P, Koren C, Masterov VB, Nygård T, Rudnick JA, Saiko S, Skarphedinsson K, Volke V, Wille F, Vilà C. (2007) Phylogeography of the white-tailed eagle, a generalist with large dispersal capacity. Journal of Biogeography 34: 1193–1206.

Hedmark, E. & Ellegren, H. (2007) DNA-based monitoring of two newly founded Scandinavian wolverine populations. Conservation Genetics 8: 843-852.

Hedmark, E., Persson, J. & Ellegren, H. (2007) Paternity and mating system in wolverines. Wildlife Biology 13: 13-30.

Helander B, Hailer F & Vilà C (2007) Morphological and genetic sex identification of white-tailed eagle Haliaeetus albicilla nestlings. Journal of Ornithology 148: 435-442.

Hibbett, D. S., M. Binder, J. F. Bischoff, M. Blackwell, P. F. Cannon, O. E. Eriksson, S. Huhndorf, T. James, P. M. Kirk, R. Lucking, H. T. Lumbsch, F. Lutzoni, P. B. Matheny, D. J. McLaughlin, M. J. Powell, S. Redhead, C. L. Schoch, J. W. Spatafora, J. A. Stalpers, R. Vilgalys, M. C. Aime, A. Aptroot, R. Bauer, D. Begerow, G. L. Benny, L. A. Castlebury, P. W. Crous, Y.-C. Dai, W. Gams, D. M. Geiser, G. W. Griffith, C. Gueidan, D. L. Hawksworth, G. Hestmark, K. Hosaka, R. A. Humber, K. D. Hyde, J. E. Ironside, U. Koljalg, C. P. Kurtzman, K.-H. Larsson, R. Lichtwardt, J. Longcore, J. Miadlikowska, A. Miller, J.-M. Moncalvo, S. Mozley-Standridge, F. Oberwinkler, E. Parmasto, V. Reeb, J. D. Rogers, C. Roux, L. Ryvarden, J. P. Sampaio, A. Schüßler, J. Sugiyama, R. G. Thorn, L. Tibell, W. A. Untereiner, C. Walker, Z. Wang, A. Weir, M. Weiss, M. M. White, K. Winka, Y.-J. Yao and N. Zhang. (2007) A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547.

Kaiser, V.B., van Tuinen, M. & Ellegren, H. (2007) The phylogenetic position of the chicken revisited: insertion events of CR1 retrotransposable elements elucidate the order of speciation events in galliform species (Aves). Molecular Biology and Evolution, 24: 338-347.

Karlsson, M., Stenlid, J. & Olson, Å. (2007) Two hydrophobin genes from the conifer pathogen Heterobasidion annosum are expressed in aerial hyphae. Mycologia 99: 227-231.

Leonard, J.A., Shanks, O., Hofreiter, M., Kreuz, E., Hodges, L., Ream, W., Wayne, R.K. & Fleischer, R.C. (2007) Animal DNA in PCR reagents plagues ancient DNA research. Journal of Archaeological Science 34: 1361-1366.

Leonard, J.A., Vilà, C., Fox-Dobbs, K., Koch, P.L., Wayne, R.K. & Van Valkenburgh, B. (2007) Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Current Biology 17: 1146-1150.

Lindberg, J., Björnerfeldt, S., Bakken, M., Vilà, C., Jazin, E. & Saetre, P. (2007) Selection for tameness modulates the expression of heme related genes in silver foxes. Behaviour Brain Function 3: 18.

Linderholm, A., Lidén, K., Götherström, A. (2007) Pushing it back. Dating the CCR5 32bp deletion to the Mesolithic in Sweden and its implications for the Meso/Neo transition. Documenta Praehistorica 33: 29-37.

Malmström, H., Svensson, E.M., Gilbert, M.T., Willerslev, E., Gotherstrom, A. & Holmlund, G. (2007) More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA. Molecular Biology and Evolution 24: 998-1004.

Malmström, H., Vilà, C., Gilbert, M.T.P., Storå, J., Willerslev, E., Holmlund, G. & Götherström, A. (2007) Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evolutionary Biology 8: 71.

Mank, J.E. (2007) The evolution of sexually selected traits and antagonistic androgen expression in actinopterygiian fishes. American Naturalist 169: 142-149.

Mank, J.E. (2007) Mating preferences, sexual selection, and patterns of cladogenesis in ray-finned fishes. Journal of Evolutionary Biology 20: 597-602.

Mank, J.E., Axelsson, E. & Ellegren, H. (2007) Fast-X on Z: rapid evolution of sex-linked genes in birds. Genome Research 17: 618-624.

Mank, J.E. & Ellegren, H. (2007) Parallel divergence and degradation of the avian W sex chromosome. Trends in Ecology and Evolution 22: 389-391.

Mank, J.E., Hultin-Rosenberg, L., Axelsson, E. & Ellegren, H. (2007) Rapid evolution of female-biased, but not male-biased genes expressed in avian brain. Molecular Biology and Evolution 24: 2698-2706.

Menkis, A., Vasiliauskas, R., Taylor, A.F.S., Stenlid, J. And Finlay, R. (2007) Afforestation of abandoned farmland with conifer seedlings inoculated with three ectomycorrhizal fungi - impact on plant performance and ectomycorrhizal community. Mycorrhiza 17: 337-348.

Muñoz-Fuentes, V., Vilà, C., Green, A.J., Negro, J.J. & Sorenson, M.D. (2007) Hybridization between white-headed ducks and introduced ruddy ducks in Spain. Molecular Ecology 16: 629-638.

Musiani, M., Leonard, J.A., Cluff, H.D., Gates, C.C., Mariani, S., Paquet, P.C., Vilà, C. & Wayne, R.K. (2007) Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou. Molecular Ecology 16: 4149-4170.

Svensson, E.M., Anderung, C., Baubliene, J., Persson, P., Malmstrom, H., Smith, C., Vretemark, M., Daugnora, L. & Gotherstrom, A. (2007) Tracing genetic change over time using nuclear SNPs in ancient and modern cattle. Anim Genet. 38: 378-383.

Tingay R.E., Dawson D.A., Pandhal J., Clarke M.L., David V.A., Hailer F. & Culver M (2007) Isolation of 22 new Haliaeetus microsatellite loci and their characterization in the critically endangered Madagascar fish-eagle (Haliaeetus vociferoides) and three other Haliaeetus eagle species. Molecular Ecology Notes 7: 711-715.

Valdiosera, C., García, N., Anderung, C., Dalén, L., Crégut-Bonnoure, E., Kahlke, R., Stiller, M., Brandström M., Thomas, M., Arsuaga, JL., Götherström, A., Barnes, I. (2007) Staying out in the Cold: Glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Molecular Ecology 16: 5140-5148.

Vasiliauskas, R., Menkis, A., Finlay, R. and Stenlid, J. (2007) Wood-decay fungi in fine living roots of conifer seedlings. New Phytologist 174: 441-446.

Webster, M.T. & Hagberg, J. (2007) Is there evidence for convergent evolution around human microsatellites? Molecular Biology and Evolution 24: 1097-1100. 


2006

Anderung, C., Baubliene, J., Daugnora, L. & Götherström, A. (2006) Medieval remains from Lithuania indicate loss of a mitochondrial haplotypes in Bison bonasus. Molecular Ecology 15: 3083.

Aspi, J., Roininen, E., Ruokonen, M., Kojola, I. & Vilà, C. (2006) Genetic diversity, population structure, effective population size, and demographic history of the Finnish wolf population. Molecular Ecology 15: 1561­1576.

Backström, N., Brandström, M., Gustafsson, L., Qvarnström, A., Cheng, H. & Ellegren, H. (2006) Genetic mapping in a wild bird population. Genetics 174: 377-386.

Backström, N., Qvarnström, A., Gustafsson, L. & Ellegren, H. (2006) Levels of linkage disequilibrium (LD) in a wild bird population. Biology Letters 2: 435-438.

Berlin, S. & Ellegren, H. (2006) Accumulation of deleterious mutations on the female-specific W chromosome in birds. Journal of Molecular Evolution 62: 66-72.

Berlin, S., Brandström, M., Backström, N., Axelsson, E., Smith, N.G.C. & Ellegren, H. (2006) Substitution rate heterogeneity and the male mutation bias. Journal of Molecular Evolution 62: 226-233.

Bermejo, M., Rodríguez-Teijeiro, J.D., Illera, G., Barroso, A., Vilà, C. & Walsh, P.D. (2006) Ebola outbreak kills 5000 gorillas. Science 314: 1564.

Björnerfeldt, S., Webster, M.T. & Vilà, C. 2006. Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Research 16: 990-994.

Emilsson, L., Saetre, P. & Jazin, E. (2006) Low mRNA levels of RGS4 splice variants in Alzheimer's disease; Association between a rare haplotype and decreased mRNA expression. Synapse 59: 173-176.

Emilsson, L., Saetre, P. & Jazin, E. (2006) Alzheimer's disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signaling. Neurobiological Disease 21: 618-625.

Hailer F., Helander B., Folkestad AO., Ganusevich SA., Garstad S., Hauff P., Koren C., Nygård T., Volke V., Vilà C., Ellegren H. (2006) Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline. Biology Letters 2 316-319.

Hedmark, E. & Ellegren, H. (2006) A test of the multiplex pre-amplification approach in microsatellite genotyping of wolverine faecal DNA. Conservation Genetics 7: 289-293.

Kaiser, V.B. & Ellegren, H. (2006) Non-random distribution of genes with sex-biased expression in the chicken genome. Evolution 60: 1945-1951.

Karlsson, A.O., Wallerström, T., Götherström, A. & Holmlund, G. (2006) Y-chromosome diversity in Sweden – A long-time perspective. European Journal of Human Genetics 14: 963-970.

Leonard, J.A., Vilà, C. & Wayne, R.K. (2006) From wild wolf to domestic dog. Pp. 95-117 in: Ostrander, E.A., Giger, U. & Lindblad-Toh, K. (eds.), The Dog and Its Genome. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Maldonado, J.E., Leonard, J.A., Ortega, J., Miranda, G.A., Wayne, R.K. & Aguilera, R.J. (2006) Ten polymorphic microsatellite loci for the endangered Buena Vista Lake shrew (Sorex ornatus relictus). Molecular Ecology Notes 6: 349-352.

Muñoz-Fuentes, V., Green, A.J., Sorenson, M.D., Negro, J.J. & Vilà, C. (2006) The ruddy duck Oxyura jamaicensis in Europe: natural colonisation or human introduction? Molecular Ecology 15: 1441-1453.

Ramírez, O., Altet, L., Enseñat, C., Vilà, C., Sánchez, A. & Ruiz, A. (2006) Genetic assessment of the Iberian wolf Canis lupus signatus captive breeding program. Conservation Genetics 7: 861-878.

Saetre P., Strandberg E., Sundgren P-E., Petterson U., Jazin E. & Bergström T. (2006) The genetic contribution of canine personality traits. Genes Brain and Behavior 5: 240-248.

Seddon, J.M., Sundqvist, A.K., Björnerfeldt, S. & Ellegren, H. (2006) Genetic identification of immigrants in the Scandinavian wolf population. Conservation Genetics 7: 225-230.

Sundberg, R., Castensson, A. & Jazin, E. (2006) Statistical modelling in case-control real-time RT-PCR assays, for identification of differentially expressed genes in schizophrenia. Biostatistics 7: 130-144.

Sundqvist A-K., Björnerfeldt S., Leonard J., Hailer F., Hedhammar Å., Ellegren H. and Vilà C. (2006) Unequal contribution of sexes in the origin of dog breeds. Genetics 172: 1121-1128.

Thulin, C-G., Stone, J., Tegelström, H. & Walker, C.W. (2006) Species assignment and hybrid identification among Scandinavian hares Lepus europaeus and L. timidus. Wildlife Biology 12: 29-38.

Vilà, C., Leonard, J.A. & Beja-Pereira, A. (2006) Genetic documentation of horse and donkey domestication. Pp. 342-353 in: Zeder, M.A., Bradley, D.G., Emshwiller, E. & Smith, B.D. (eds.), Documenting Domestication: New Genetic and Archaeological Paradigms. University of California Press, Berkeley, CA.

Wayne, R.K., Leonard, J.A. & Vilà, C. (2006) Genetic analysis of dog domestication. Pp. 279-293 in: Zeder, M.A., Bradley, D.G., Emshwiller, E. & Smith, B.D. (eds.), Documenting Domestication: New Genetic and Archaeological Paradigms. University of California Press, Berkeley, CA.

Webster, M.T., Axelsson, E. & Ellegren, H. (2006) Strong regional biases in nucleotide substitution in the chicken genome. Molecular Biology and Evolution 23: 1203-1216.

Åberg, K., Saetre, P., Lindholm, E., Ekholm, B., Pettersson, U., Adolfsson, R. & Jazin, E. (2006) Human QKI, a new candidate gene for schizophrenia involved in myelination. American Journal of Medical Genetics B Neuropsychiatrial Genetics 5: 84-90.

Qvarnström, A., Haavie, J., Saether, S.A., Eriksson, D. & Pärt, T. (2006) Song similarity predicts hybridization in flycatchers. Journal of Evolutionary Biology 19: 1202-1209.


2005

Anderung, C., Bouwman, A., Persson, P., Carretero, J. M., Ortega, A. I., Arasuaga, J. L. Elburg, R., Smith, C. Ellegren, H. & Götherström, A. (2005) Genetics of Iberian Bronze Age cattle remains indicate prehistoric contacts over the Straits of Gibraltar. Proceedings of the National Academy of Sciences USA, 102: 8431-8435.

Axelsson, E., Webster, M.T., Smith, N.G., Burt, D.W. & Ellegren, H. (2005) Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Research 15: 120-125.

Backström, N., Ceplitis, H. & Ellegren, H. Gene conversion drives the evolution of HINTW, a multi-copy gene family on the avian W chromosome. Molecular Biology and Evolution 22: 1992-1999.

Barnett, R., Barnes, I., Phillips, M.J., Martin, L.D., Harington, C.R., Leonard, J.A. & Cooper, A. (2005) Evolution of the extinct sabretooths (Smilodon and Homotherium) and American cheetahlike cat (Miracinonyx). Current Biology 15: 589-590.

Belle, E.M., Webster, M.T. & Eyre-Walker, A. (2005) Why are young and old repetitive elements distributed differently in the human genome? Journal of Molecular Evolution 60: 290-296.

Berggren, K.T., Ellegren, H., Hewitt, G.M. & Seddon, J.M. (2005) Demographic effects have been more important than selection in shaping patterns of variation at MHC genes in European hedgehogs, Erinaceus europaeus and E. concolor. Heredity 95: 84-90.

Berggren, K.T. & Seddon, J.M. (2005) MHC promoter polymorphism in grey wolves and domestic dogs. Immunogenetics 57: 267-272.

Berlin, S, & Smith, N.G. (2005) Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test. BMC Evolutionary Biology 10:6.

Borge T, Lindroos K, Nadvornik P, Syvanen AC, Saetre GP. Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post-zygotic barriers to gene exchange. Journal of Evolutionary 18: 1416-1424.

Borge, T., Webster, M.T., Andersson, G. & Saetre, G.P. (2005) Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species. Genetics 171: 1861-1873.

Castensson, A., Aberg, K., McCarthy, S., Saetre, P., Andersson, B. & Jazin, E. Serotonin receptor 2C (HTR2C) and schizophrenia: examination of possible medication and genetic influences on expression levels. American Journal of Medical Genetics B Neuropsychiatrical Genetics 134: 84-89.

Ellegren, H. (2005) The avian genome uncovered. Trends in Ecology and Evolution 20: 180-186.

Ellegren, H. (2005) Evolution: natural selection in the evolution of humans and chimps. Current Biology 22: R919-922.

Ellegren, H. (2005) The dog has its day. Nature 438: 745-746.

Gautschi, B. & Koller, B. (2005) Polymorphic microsatellite markers for the goosander (Mergus merganser). Molecular Ecology Notes 5: 133-134.

Götherström, A., Anderung, C., Hellborg, L. Elburg, R., Smith, C. & Ellegren, H. (2005) Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe. Proceedings of the Royal Society London, Series B 272:2337-2344.

Hailer, F., Gautschi, B. & Helander, B. (2005) Development and multiplex PCR amplification of novel microsatellite markers in the white-tailed sea eagle, Haliaeetus albicilla (Aves: Falconiformes, Accipitridae). Molecular Ecology Notes 5: 938-940.

Hedmark, E. & Ellegren, H. (2005) Microsatellite genotyping of DNA isolated from claws left on tanned carnivore hides. International Journal of Legal Medicine 119:370-373.

Hellborg, L., Gunduz, I. & Jaarola, M. (2005) Analysis of sex-linked sequences supports a new mammal species in Europé. Molecular Ecology 14: 2025-2031.

Johannesson, H., Townsend, J.P., Hung, C.-H., Cole, G.T. & Taylor, J.W. (2005) Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii. Genetics 171: 109-117.

Leonard, J.A., Rohland, N., Glaberman, S., Fleischer, R.C., Caccone, A. & Hofreiter, M. (2005) A rapid loss of stripes: the evolutionary history of the extinct quagga. Proceedings of the Royal Society of London, Biology Letters 1: 291-295.

Leonard, J.A., Vilà, C. & Wayne, R.K. (2005) Legacy lost: genetic variability and population size of extirpated US gray wolves (Canis lupus). Molecular Ecology 14: 9-17.

Lindberg, J., Bjornerfeldt, S., Saetre, P., Svartberg, K., Seehuus, B., Bakken, M., Vila, C. & Jazin, E. (2005) Selection for tameness has changed brain gene expression in silver foxes. Current Biology15: R915-916.

Lislevand, T., Byrkjedal, I., Borge, T. & Saetre, G.P. (2005) Egg size in relation to sex of embryo, brood sex ratios and laying sequence in northern lapwings (Vanellus vanellus) Journal of Zoology 267: 81-87.

Malmström, H., Storå, J., Dalén, L., Holmlund, G. & Götherström, A. (2005) Extensive human DNA contamination in extracts from ancient dog bones and teeth. Molecular Biology and Evolution 22: 2040-2047

Muñoz-Fuentes, V., Gyllenstrand, N., Negro, J.J., Green, A.J. & Vilà, C. (2005) Microsatellite markers for the two Holarctic stifftails, the white-headed duck, Oxyura leucocephala, and the ruddy duck O. jamaicensis. Molecular Ecology Notes 5: 263-265.

Naslund, K., Saetre, P., von Salome, J., Bergstrom, T.F., Jareborg, N. & Jazin, E. (2005) Genome-wide prediction of human VNTRs. Genomics 85: 24-35.

Saetre P., Stark J.M. 2005. Microbial dynamics and carbon and nitrogen cycling following rewetting of two dry semiarid soils. Oecologia 142: 247-260.

Seddon, J.M. (2005) Canid-specific primers for molecular sexing using tissue or non-invasive samples.Conservation Genetics 6: 147-149.

Seddon, J. M., Parker, H.G., Ostrander, E.A. & Ellegren, H. (2005) SNPs in ecological and onservation studies: a test in the Scandinavian wolf population. Molecular Ecology 14: 503-511.

Strandberg E., Jacobsson J. & Saetre P. 2005. Direct and maternal genetic effects on behaviour in German Shepherd dogs in Sweden. Livestock Production Science 93: 33-42.

Vilà, C., Seddon, J.M. & Ellegren, H. (2005) Genes of domestic mammals augmented by backcrossing with wild ancestors. Trends in Genetics 21: 214-218.

Webster, M.T., Smith, N.G.C., Hultin-Rosenberg, L., Arndt, P.F. & Ellegren, H. Male-driven biased gene conversion governs the evolution of base composition in human Alu repeats. Molecular Biology and Evolution 22: 1468-1474.


2004

Arrendal, J.S.E., Walker, C.W., Sundqvist, A.-K., Hellborg, L.C., Vilà, C. (2004) Genetic assessment of a demographically successful translocation program. Conservation Genetics 5:79-88.

Axelsson, E., Smith, N.G.C., Sundström, H., Berlin, S., Ellegren, H. (2004) Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey. Molecular Biology and Evolution 21:1538-1547.

Berlin, S., Ellegren, H. (2004) Chicken W: A genetically uniform chromosome in a highly variable genome. Proceedings of the National Academy of Sciences USA 101:15967-15969.

Berlin, S., Smith, N.G., Ellegren, H. (2004) Do avian mitochondria recombine? Journal of Molecular Evolution 58:163-167.

Brohede, J., Arnheim, N., Ellegren, H. (2004) Single molecule analysis of the hypermutable tetranucleotide rpeat locus D21S1245 through sperm genotyping: A heterogeneous pattern of mutation but no clear male age effect. Molecular Biology and Evolution 21:58-64.

Burger, J., Rosendahl, W., Loriell, O., Hemmer, H., Eriksson, T., Götherström, A., Hiller, J., Coillins, M., Wess, T., Alt, K.W. (2004) Molecular phylogeny of the extinct cave lion Panthera leo spelaea. Molecular Phylogenetics and Evolution 30:841-849.

Ceplitis, H., Ellegren, H. (2004) Adaptive molecula evolution in HINTW, a female-specific gene in birds. Molecular Biology and Evolution 21:249-254.

Dalén, L., Götherström, A., Angerbjörn, A. (2004) Identifying species from pieces of faeces. Conservation Genetics 5:105-111.

Denk, A.G., Gautschi, B., Carter, K., Kempenaers, B. (2004) Seven polymorphic microsatellite loci for paternity assessment in the mallard (Anas platyrhynchos) Molecular Ecology Notes 4:506-508.

Durka, A.G., Bossdorf, O., Gautschi, B. (2004) Isolation and characterization of microsatellite loci in the invasive Alliaria petiolata (Brassicaceae). Molecular Ecology Notes 4:173-715.

Ekblom, R., Saether, S.A., Grahn, M., Fiske, P., Kålås, J.A., Höglund, J. (2004) MHC variation and mate choice in a lekking bird, the Great Snipe (Gallinago media). Molecular Ecology 13:3821-3828.

Ellegren, H. (2004) Vad är en människa? Forsking och framsteg 4:16.

Ellegren, H. (2004) DNA löser brott med djur. Kriminalteknik 3:10-11.

Ellegren, H. (2004) Genetisk forskning visar på den framgångsrike hingsten. Miljöforskning: (FORMAS) 2:22-24.

Ellegren, H. (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics 5:435-445.

Flagstad, Ö., Hedmark, E., Landa, A., Bröseth, H., Persson, J., Andersen, R., Segerström, P., Ellegren, H. (2004) Colonization history and non-invasive monitoring of a re-established wolverine (Gulo gulo) population. Conservation Biology 18:676-688.

Hedmark, E., Flagstad, Ö., Segerström, P., Persson, J., Landa, A., Ellegren, H. (2004) DNA-based individual and sex identification from wolverine (Gulo gulo) faeces and urine. Conservation Genetics 5:405-410.

Hellborg, L., Ellegren, H. (2004) Low levels of nucleotide diversity in mammalian Y chromosomes. Molecular Biology and Evolution 21:158-163.

International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.

International Chicken Polymorphism Map Consortium (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432:717-22.

Jensen, H., Saether, B.E., Ringsby, T.H., Tufto, J., Griffith, S.C., Ellegren, H. (2004) Lifetime reproductive success in relation to morphology in house sparrow (Passer domesticus). Journal of Animal Ecology 73:599-611.

Lindgren, G., Backström, N., Swenburne, J., Hellborg, L., Einarsson, A., Sandberg, K., Cothran, G., Vila, C., Binns, M., Ellegren, H. (2004) Limited number of patrilines in horse domestication. Nature Genetics 36:335-336.

Lindholm, E., Åberg, K., Ekholm, B., Pettersson, U., Adolfsson, R., Jazin, E. (2004) Reconstruction of ancestral haplotypes in a 12-generation schizophrenia pedigree. Psychiatrical Genetics 14:1-8.

Maldonado, J.E., Hertel, F., Vila, C. (2004) Discordant patterns of morphological variation in genetically divergent populations of ornate shrews (Sorex ornatus). Journal of Mammalogy 85:886-896.

Preece, P., Virley, D.J., Costandi, M., Coombes, R., Moss, S.J., Mudge, A.W., Jazin, E., Cairns, N.J. (2004) Amyloid precursor protein mRNA levels in Alzheimer's disease brain. Brain Research Molecular Brain Research 122:1-9.

Qvarnström, A., Torok, J., Saetre, G.P. (2004) Flycatcher song in allopatry and sympatry: convergence, divergence and reinforcement. Journal of Evolutionary Biology 17:227-237.

Saetre, P., Lindberg, J., Leonard, J., Olsson, K., Pettersson, U., Ellegren, H., Bergström, T., Vilà, C., Jazin, E. (2004) From wild wolf to domestic dog: Gene expression changes in the brain. Brain Research: Molecular Brain Research 126:198-206.

Seddon, J.M., Ellegren, H. (2004) A temporal analysis shows MHC loci in the Scandivavian wolf population are consistent with neutral evolution. Proceedings of the Royal Society London: Series B 271:2283-2291.

Smith, N.G., Brandström, M., Ellegren H. (2004) Evidence for turnover of functional noncoding DNA in mammalian genome evolution. Genomics 84:806-813.

Sundström, H., Webster, M.T., Ellegren, H. (2004) Reduced variation on the chicken Z chromosome. Genetics 167:377-385.

Webster, M.T., Smith, N.G.C. (2004) Fixation biases affecting human SNPs? Trends in Genetics 20:122-126.

Webster, M.T., Smith, N.G.C., Lercher, M.J., Ellegren, H. (2004) Gene expression, synteny, and local similarity in human noncoding mutation rates. Molecular Biology and Evolution 21:1820-1830.

Vilà, C., Leonard, J.A., Iriarte, A., O'Brien, S.J., Johnson, W.E., Wayne, R.K. (2004) Detecting the vanishing populations of the highly endangered Darwin's fox, Pseudalopex fulvipes. Animal Conservation 7:147-153.


2003

Bartosch-Härlid, A, Berlin, S, Smith, NGC, Møller, AP & Ellegren, H (2003) Life history and the male mutation bias. Evolution 57: 2398-2406.

Castensson, A., Emilsson, L., Sundberg, R. & Jazin E. (2003) Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis. Biological Psychiatry 54: 1212-1221.

Ellegren, H (2003) Levels of polymorphism on the sex-limited chromosome - a clue to Y from W? BioEssays 25: 163-167.

Ellegren, H, Smith, NGC & Webster, MT (2003) Mutation rate variation in the mammalian genome. Current Opinion in Genetics and Development 13:562-568.

Ellegren, H & Fridolfsson, AK (2003) Sex-specific mutation rates in salmonid fish. Journal of Molecular Evolution 56: 458-463.

Flagstad, Ø., Walker, C.W., Vilà, C., Sundqvist, A.-K., Fernholm, B., Hufthammer, A.K., Wiig, Ø., Koyola, I. & Ellegren, H. (2003). Two centuries of the Scandinavian wolf population: patterns of genetic variability and migration during an era of dramatic decline. Molecular Ecolology 12:869-880.

Flagstad, O. & Roed, K.H. (2003) Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences. Evolution 57: 658-670.

Guerin G, Bailey E, Bernoco D, Anderson I, Antczak DF, Bell K, Biros I, Bjornstad G, Bowling AT, Brandon R, Caetano AR, Cholewinski G, Colling D, Eggleston M, Ellis N, Flynn J, Gralak B, Hasegawa T, Ketchum M, Lindgren G, Lyons LA, Millon LV, Mariat D, Murray J, Neau A, Roed K, Sandberg K, Skow LC, Tammen I, Tozaki T, Van Dyk E, Weiss B, Young A, Ziegle J. (2003) The second generation of the International Equine Gene Mapping Workshop half-sibling linkage map. Animal Genetics 34:161-168

Hellborg, L. & Ellegren, H. (2003) Y chromosome conserved anchored tagged sites (YCATS) for the analysis of mammalian male-specific sequences. Molecular Ecology 12: 283-291.

Jensen H, Saether B.E., Ringsby, T.H., Tufto, J., Griffith, S.C. & Ellegren, H. (2003) Sexual variation in heritability and genetic correlations of morphological traits in house sparrow (Passer domesticus). Journal of Evolutionary Biology 16: 1296-307.

Lewis, C.M. et al (including Jazin, E.) (2003) Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia. American Journal of Human Genetics 73: 34-48.

Preece, P., Virley, D.J., Costandi, M,. Coombes, R., Moss, S.J., Mudge, A.W., Jazin, E. & Cairns, N.J. (2003) Beta-secretase (BACE) and GSK-3 mRNA levels in Alzheimer's disease. Brain Research Molecular Brain Research 116: 155-158.

Preece, P., Virley, D.J., Costandi, M., Coombes, R., Moss, S.J., Mudge, A.W., Jazin, E. & Cairns, N.J. (2003) An optimistic view for quantifying mRNA in post-mortem human brain. Brain Research Molecular Brain Research 116: 7-16.

Rueness, E.K., Jorde, P.E., Hellborg, L., Stenseth, N.C., Ellegren, H. & Jacobsen, K.S. (2003) Cryptic population structure in a large, mobile mammalian predator: the Scandinavian lynx. Molecular Ecology 12: 2623-2633.

Rueness, E.K., Stenseth, N.C., O’Donoghue, M., Boutin, S., Ellegren, H. & Jakobsen, K.S. (2003) The phylogeography of the Canadian lynx: coinciding genetic and ecological spatial structuring. Nature 425: 69-72.

Sætre, G.P., Borge, T., Lindroos, K., Haavie, J., Sheldon, B.C., Primmer, C. & Syvanen, A.C. (2003) Sex chromosome evolution and speciation in Ficedula flycatchers. Proceedings of the Royal Society of London Series B 270: 53-59.

Servedio, M.R. & Sætre, G.P. (2003) Speciation as a positive feedback loop between postzygotic and prezygotic barriers to gene flow. Proceedings of the Royal Society of London Series B 270: 1473-1479.

Smith NGC, Webster, MT & Ellegren, H (2003) A low rate of simultaneous double nucleotide mutations in primates. Molecular Biology and Evolution 20:47-53.

Smith, N.G. (2003) Are radical and conservative substitution rates useful statistics in molecular evolution? Journal of Molecular Evolution 57: 467-478.

Smith, N.G. & Eyre-Walker, A. (2003) Human disease genes: patterns and predictions. Gene 318:169-175.

Stenseth, N.C. & Sætre, G.P. (2003) Sexual selection forms the structure and dynamics of ecological communities. Proceedings of the National Academy of Sciences USA 100: 5576-5577.

Sundström, H., Webster, M.T. & Ellegren, H. (2003) Is the rate of insertion and deletion mutation male-biased? - Molecular evolutionary analysis of avian and primate sex chromosome sequences. Genetics 164: 259-268.

Valadez, R, Leonard, JA & Vilà, C (2003) A molecular view on the origin of the American dogs. AMMVEPE 14: 73-82 [in Spanish]

Vilà, C, Sundqvist, A-K, Flagstad, Ø, Seddon, J, Björnerfeldt, S, Kojola, I, Casulli, A, Sand, H, Wabakken, P & Ellegren, H (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proceedings of the Royal Society London, Series B 270: 91-97.

Vilà, C., Walker, C.W., Sundqvist, A-K., Flagstad, Ø., Andersone, Z., Casulli, A., Kojola, I., Valdmann, H., Halverson, J. & Ellegren, H. (2003) Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf-dog hybrids. Heredity 90:17-24.

Wayne, R.K. & Vilà, C. (2003) Molecular Genetic Studies of Wolves. Pp. 218-238 in: L.D. Mech and L. Boitani (eds.) Wolves: Behavior, Ecology, and Conservation. Chicago University Press.

Webster M.T., Smith, N.G.C. & Ellegren, H. (2003) Compositional evolution of the human and chimpanzee genomes. Molecular Biology and Evolution 20:278-286.

Webster, M.T., Clegg, J.B. & Harding, R.M. (2003) Common 5' beta-globin RFLP haplotypes harbour a surprising level of ancestral sequence mosaicism. Human Genetics 113: 123-139.


2002

Alfonso, J., Pollevick, G. D., Castensson, A., Jazin, E. & Frasch, A. C. (2002) Analysis of gene expression in the rat hippocampus using Real Time PCR reveals high inter-individual variation in mRNA expression levels. Journal of Neuroscience Research 67: 225-234.

Andersson-Ceplitis, H. & Bengtsson, B. O. (2002) Transmission rates and phenotypic effects of mitochondrial plasmids and cytotypes in Silene vulgaris. Evolution 56: 1586-1591.

Ayuso, A. & Vilá, C. (2002). Development of non-invasive techniques for the genetic study of Scandinavian wolves (Canis lupus). Acta Granatense 1: 77-90.

Balciuniene, J., Emilsson, L., Oreland, L., Pettersson, U. & Jazin, E. (2002) Investigation of the functional effect of monoamine oxidase polymorphisms in human brain. Human Genetics 110: 1-7.

Belle, E.M.S., Smith, N.G.C. & Eyre-Walker, A. (2002) Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. Journal of Molecular Evolution 55: 356-363.

Bond, B. C., Virley, D. J., Cairns, N. J., Hunter, A. J., Moore, G. B., Moss, S. J., Mudge, A. W., Walsh, F. S., Jazin, E. & Preece, P. (2002) The quantification of gene expression in an animal model of brain ischaemia using TaqMan real-time RT-PCR. Brain Research. Molecular Brain Research 106: 101.

Brohede, J., Primmer, C. R., Møller, A. P. & Ellegren, H. (2002) The rate and pattern of germline mutation differ between individual microsatellite loci. Nucleic Acids Research 30: 1997-2003.

Bures, S., Nadvornik, P. & Saetre, G.P. (2002) Hybridization and apparent hybridization between meadow pipit (Anthus pratensis) and water pipit (A-spinoletta). Hereditas 136: 254-256.

Dalén, L., Götherström, A., Tannerfeldt, M. & Angerbjörn, A. (2002) Is the endangered Arctic fox (Alopex lagopus) genetically isolated? Biological Conservation 105: 171-178.

Ellegren, H (2002) Dosage compensation: do birds do it as well? Trends in Genetics 18: 25-28.

Ellegren, H. (2002) Microsatellite evolution: a battle between replication slippage and point mutations. Trends in Genetics 18: 70.

Ellegren, H. (2002) Human mutation - blame (mostly) men. Nature Genetics 31: 9-10.

Ellegren, H. (2002) It took many mares to form the domestic horse. Trends in Genetics 18:500-501.

Ellegren, H. (2002) Mismatch repair and mutation biases in microsatellite DNA. Trends in Genetics 18: 552.

Emilsson, L., Saetre, P., Balciuniene, J., Castensson, A., Cairns, N. & Jazin, E. (2002) Increased monoamine oxidase messenger RNA expression levels in frontal cortex of Alzheimer's disease patients. Neuroscience Letters 326: 56-60.

Eyre-Walker, A., Keightley, P.D., Smith, N.G.C. & Gaffney, D. (2002) Quantifying the slightly deleterious mutation model of molecular evolution. Molecular Biology and Evolution 19: 2142-2149.

Galeuchet, D. J., Husi, R., Perret, C., Fischer, M. & Gautschi, B. (2002) Characterization of microsatellite loci in Lychnis flos-cuculi (Caryophyllaceae). Molecular Ecology Notes 2: 491-492.

Gautschi, B., Arter, M. K., Husi, R.E., Wettstein, W. & Schmid, B. (2002) Isolation and characterization of microsatellite loci in the globally endangered Corncrake, Crex crex Linne. Conservation Genetics 3: 451-453.

Gautschi, B., Widmer, A., Joshi, J. & Koella, J. C. (2002) Increased frequency of scale anomalies and loss of genetic variation in serially bottlenecked populations of the dice snake, Natrix tessellata. Conservation Genetics 3: 235-245.

Griffith, S. C., Owens, I. P. F. & Thuman, K. A. (2002) Extra pair paternity in birds: a review of interspecific variation and adaptive function. Molecular Ecology 11: 2195-2212.

Grundberg, L., Hårding, B. & Götherström, A. (2002) Björned - benanalyser ofh kulturhistoriska tolkningar. Undersökningar kring en nordsvenskt begravningsplats från tidig medeltid. Hikuin 27: 219-232.

Götherström, A., Stenbäck, N. & Storå, J. (2002) Jettböle Middle Neolithic Site of the Åland Islands - Human Remains, Ancient DNA and Pottery. European Journal of Archaeology 5: 42-69.

Götherström, A., Angerbjörn, A., Collins, M. & Lidén, K. (2002) Bone preservation and DNA amplification. Archaeometry 44: 395-404.

Götherström, A. (2002) The Values of Stallions and Mares Medieval Upper Class Svealand. JONAS 13: 75-78.

Hellborg, L, Walker, CW, Rueness, EK, Stacy, JE, Kojola, I, Valdmann, H, Vilá, C, Zimmermann, B, Jakobsen, KS & Ellegren, H (2002) Differentiation and levels of genetic variation in northern European lynx (Lynx lynx) populations revealed by microsatellites and mitochondrial DNA analysis. Conservation Genetics 3: 97-111.

Hipkiss, T., Hornfeldt, B., Eklund, U. & Berlin, S. (2002) Year-dependent sex-biased mortality in supplementary-fed Tengmalm's owl nestlings. Journal of Animal Ecology 71: 693-699.

Hipkiss, T., Hörnfeldt, B., Lundmark, A., Norbäck, M. & Ellegren, H. (2002) Sex ratio and age structure of nomadic Tengmalm’s owls: a molecular approach. Journal of Avian Biology 33: 107-110.

Hurst, L. D. & Ellegren, H. (2002) Mystery of the mutagenic male. Nature 420: 365-366.

Lawson, L. J. & Hewitt, G. M. (2002) Comparison of substitution rates in ZFX and ZFY introns of sheep and goat related species supports the hypothesis of male-biased mutation rates. Journal of Molecular Evolution 54: 54-61.

Leden ,I., Svensson, B., Harding, B., Nuorala, E., Liden K. & Gotherstrom, A. (2002) Paleopathology can be beneficial for current rheumatologic research. Läkartidningen 99: 1060.

Leonard, J.A., Wayne, R.K., Wheeler, J., Valadez, R., Guillen, S. & Vilá, C. (2002). Ancient DNA evidence for Old World origin of New World dogs. Science 298: 1613-1616.

Lercher, M.J., Smith, N.G.C., Eyre-Walker, A. & Hurst, L.D. (2002) The evolution of isochores: evidence from SNP frequency distributions. Genetics 162: 1805-1810.

Massat, I. et al (30 co-authors including Jazin, E.) (2002) Positive association of dopamine D2 receptor polymorphism with bipolar affective disorder in a European multicenter association study of affective disorders. American Journal of Medical Genetics 114: 177-185.

Primmer, C. R., Borge, T., Lindell, J. & Saetre, G. P. (2002) Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Molecular Ecology 11: 603-612.

Saether, S. A. (2002) Kin selection, female preferences and the evolution of leks: direct benefits may explain kin structuring. Animal Behaviour 63: 1017-1019.

Saether, S. A. (2002) Female calls in lek-mating birds: indirect mate choice, female competition for mates, or direct mate choice? Behavioural Ecology 13: 344-352.

Seddon, J. M. & Ellegren, H. (2002) MHC class II genes in European wolves: a comparison with dogs. Immunogenetics 54: 590-600.

Seddon, J. M., Santucci, F., Reeve, N. & Hewitt, G. M. (2002) Caucasus Mountains divide postulated postglacial colonization routes in the white-breasted hedgehog, Erinaceus concolor. Journal of Evolutionary Biology 15: 463-467.

Smith, N.G.C. & Eyre-Walker, A. (2002) Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.

Smith, N.G.C. & Eyre-Walker, A. (2002) The compositional evolution of the murid genome. Journal of Molecular Evolution 55:197-201.

Smith, N.G.C. & Lercher, M.J. (2002) Regional similarities in polymorphism in the human genome extend over many megabases. Trends in Genetics 18:281-283.

Smith, N. G. C., Webster, M. T. & Ellegren, H. (2002) Deterministic mutation rate variation in the human genome. Genome Research 12:1350-1356.

Spong, G. & Hellborg, L. (2002) A near-extinction event in lynx: Do microsatellite data tell the tale? Conservation Ecology 6: 15.

Webster, M. T., Smith, N. G. C. & Ellegren, H. (2002) Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proceedings of the National Academy of Sciences U S A 99:8748-5873.

Webster, M. T., Wells, R. S. & Clegg, J. B. (2002) Analysis of variation in the human beta-globin gene cluster using a novel DHPLC technique. Mutataion Research 501:99-103.


2001

Arnold, K.E., Griffith, S.C. & Goldizen, A.W. (2001) Sex-biased hatching sequences in the cooperatively breeding Noisy Miner. Journal of Avian Biology 32: 219-223.

Berlin, S. & Ellegren, H. (2001) Clonal inheritance of avian mitochondrial DNA. Nature 413: 37-38.

Ellegren, H. & Carmichael, A. (2001) Multiple and independent cessation of recombination between avian sex chromosomes. Genetics 158: 325-331.

Ellegren, H. (2001) Hens, cocks and avian sex determination. A quest for genes on Z or W? EMBO Reports 2: 192-196.

Flagstad, Ø., Syvertsen, P.O., Stenseth, N.C. & Jakobsen, K.S. (2001) Environmental change and rates of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation. Proceedings of the Royal Society of London, Series B 268: 667-677.

Girman, D.J., Vilá, C., Geffen, E., Creel, S., Mills, M.G.L., McNutt, J.W., Ginsberg, J., Kat, P.W., Mamiya, K.H. & Wayne, R.K. (2001) Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus). Molecular Ecology 10: 1703-1723.

Griffith, S.C. & Sheldon, B.C. (2001) Phenotypic plasticity in the expression of sexually selected traits: neglected components of variation. Animal Behaviour 61: 987-993.

Hedrick, P., Fredrickson, R. & Ellegren, H. (2001) Evaluation of d2, a microsatellite measure of inbreeding and outbreeding, in wolves with a known pedigree. Evolution 55: 1256-1260.

Holen, O.H., Saetre, G-P., Slagsvold, T. & Stenseth, N.C. (2001) Parasites and supernormal manipulation. Proceedings of the Royal Society of London, Series B 168: 2551-2558.

Leech, D.I., Hartley, I.R., Stewart, I.R.K., Griffith, S.C. & Burke, T. (2001) No effect of parental quality or extrapair paternity on brood sex ratio in the blue tit (Parus caeruleus). Behavioural Ecology 12: 674-680.

Lindgren, G., Breen, M., Godard, S., Bowling, A., Murray, J., Scavone, M., Skow, L., Sandberg, K., Guerin, G., Binns, M. & Ellegren, H. (2001) Mapping of 13 horse genes by fluorescence in-situ hybridization (FISH) and somatic cell hybrid analysis. Chromosome Research. 9: 53-59.

Lindgren, G., Swinburne, J.E., Breen, M., Mariat, D., Sandberg, K., Guerin, G. Ellegren, H., & Binns, M.M. (2001) Physical anchorage and orientation of equine linkage groups by FISH mapping BAC clones containing microsatellite markers. Animal Genetics 32: 37-39.

Maldonado, J.E., Vilá, C. & Wayne, R.K. (2001) Tripartite geneticsubdivisions in the ornate shrew (Sorex ornatus) Molecular Ecology 10: 127-147.

Montell, H., Fridolfsson, A.K. & Ellegren, H. (2001) Contrasting levels of nucleotide diversity on the avian Z and W sex chromosomes. Molecular Biology and Evolution 18:2010-2016.

Saetre, G.P., Borge, T., Lindell, J., Moum, T., Primmer, C.R., Sheldon, B.C., Haavie, J., Johnsen, A. & Ellegren. H. (2001) Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers. Molecular Ecology 10: 737-749.

Saetre, G-P., Borge, T. & Moum, T. (2001) A new bird species? The taxonomic status of “the Atlas Flycatcher” assessed from DNA sequence analysis. Ibis 143: 494-497.

Saetre, G-P:, Borge, T., Lindell, J., Moum, T., Primmer, C.R., Sheldon, B.C., Johnsen, A. & Ellegren, H. (2001) Speciation, introgressive hybridization and non-linear rate of molecular evolution in flycatchers. Molecular Ecology 10: 737-749

Sandel, J.K., Benatar, G.R., Burke, K.M., Walker, C.W., Lacher, T.E. & Honeycutt, R.L. (2001) Use and selection of winter hibernacula by the eastern pipistrelle (Pipistrellus subflavus) in Texas. Journal of Mammology 82: 173-178.

Seddon, J.M., Santucci, F., Reeve, N.J. & Hewitt, G.M. (2001) DNA footprints of European hedgehogs, Erinaceus europaeus and E. concolor: Pleistocene refugia, postglacial expansion and colonization routes. Molecular Ecology 10: 2187-2198.

Spong, G., Hellborg, L. & Cree,l S. (2001) Sex ratio of leopards taken in trophy hunting: genetic data from Tanzania. Conservation Genetics 1:169-171.

Sundqvist, A.K., Ellegren, H., Olivier, M. & Vilá, C. (2001) Y chromosome haplotyping in Scandinavian wolves (Canis lupus) based on microsatellite markers. Molecular Ecology 10: 1959-1966.

Walker, C.W., Vila, C., Landa, A., Linden, M. & Ellegren, H. (2001) Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations. Molecular Ecology 10: 53-63.

Wayne, R.K. & Vilá, C. (2001) Phylogeny and origin of the domestic dog. In: The Genetics of the Dog (Ruvinsky, A. & Sampson, J. eds.) CABI international, Oxon. Pp. 1-13.

Veen, T., Borge, T., Griffith, S.C., Saetre, G-P., Gustafsson, L., Bures, S. & Sheldon, B.C. (2001) Hybridization and adaptive mate choice in flycatchers. Nature 411:45-50.

Vilá, C., Ellegren, H., Gotherstrom, A., Leonard, J.A. & Wayne, R.K. (2001) Tales from the DNA of domestic horses - Reply. Science 292: 218-219.

Vila, C., Leonard, J.A., Gotherstrom, A., Marklund, S., Sandberg, K., Liden, K., Wayne, R.K. & Ellegren, H. (2001) Widespread origins of domestic horse lineages. Science 291:474-477.

Weeks P. & Griffith, S.C. (2001) Sex ratios of Red-billed Oxpecker groups. Ostrich 72: 212-214.


2000

Bensch S & Härlid A (2000) Mitochondrial genomic rearrangements in songbirds. Molecular Biology and Evolution 17: 107-113.

Berlin S, Merila J & Ellegren H (2000) Isolation and characterization of polymorphic microsatellite loci in the common frog, Rana temporaria. Molecular Ecology 9: 1938-1939.

Carmichael AN, Fridolfsson AK, Halverson J & Ellegren H (2000) Male-biased mutation rates revealed from Z and W chromosome-linked ATP synthase alpha-subunit (ATP5A1) sequences in birds. Journal of Molecular Evolution 50: 443-447.

Cordero PJ, Griffith SC, Aparicio JM & Parkin DT (2000) Sexual dimorphism in house sparrow eggs. Behavioural Ecology and Sociobiology 48: 353-357.

Ellegren H (2000) Evolution of the avian sex chromosomes and their role in sex determination. Trends in Ecology and Evolution 15: 188-192.

Ellegren H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nature Genetics 24: 400-402.

Ellegren H (2000) Microsatellite mutations in the germline: implications for evolutionary inference. Trends in Genetics 16: 551-558.

Flagstad O, Syvertsen PO, Stenseth NC, Stacy JE, Olsaker I, Roed KH, Jakobsen KS (2000) Genetic variability in Swayne's hartebeest, an endangered antelope of Ethiopia. Conservation Biology 14: 254-264.

Fridolfsson AK & Ellegren H (2000) Molecular evolution of the avian CHD1 genes on the Z and W sex chromosomes. Genetics 155: 1903-1912.

Griffith SC (2000) A trade-off between reproduction and a condition-dependent sexually selected ornament in the house sparrow, Passer domesticus. Proceedings of the Royal Society, London, Series B 267: 1115-1120.

Griffith SC (2000) High fidelity on islands: a comparative study of extra-pair paternity in passerine birds. Behavioral Ecology 11: 265-273.

Haavie J, Sætre GP & Moum T (2000) Discrepancies in population differentiation at microsatellites, mitochondrial DNA and plumage colour in the pied flycatcher - inferring evolutionary processes. Molecular Ecology 9: 1137-1148.

Hornfeldt B, Hipkiss T, Fridolfsson AK, Eklund U & Ellegren H (2000) Sex ratio and fledging success of supplementary-fed Tengmalm's owl broods. Molecular Ecology 9: 187-192.

Lindgren G (2000) Ten equine dinucleotide microsatellite repeats HTG18-19, HTG22-24, HTG26-27, HGT29-30 and HTG32. Animal Genetics 31: 145-146.

Qvarnström A, Griffith SC & Gustafsson L (2000) Male-male competition and parental care in collared flycatchers: an experiment controlling for differences in territory quality. Proceedings of the Royal Society, London, Series B 267: 2547-2552.

Sætre GP & Moum T (2000) A simple molecular method for species identification of pied and collared flycatchers. Hereditas 132: 171-172.

Sætre GP (2000) Sexual signals and speciation. In: Espmark, Y., Amundsen, T. & Rosenqvist, G. (Eds.), Animal Signals. Signalling and Signal Design in Animal Communication. Pp: 237-257. Tapir Academic Press, Trondheim, Norway.

Seddon JM & Baverstock PR (2000) Evolutionary lineages of RT1.Ba in the Australian Rattus. Molecular Biology and Evolution 17: 768-772.

Swinburne J, Gerstenberg C, Breen M, Aldridge V, Lockhart L, Marti E, Antczak D, Eggleston-Stott M, Bailey E, Mickelson J, Roed K, Lindgren G, von Haeringen W, Guerin G, Bjarnason J, Allen T & Binns M (2000) First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families. Genomics 66: 123-134.

Walker CW, Harveson LA, Pittman MT, Tewes ME & Honeycutt RL (2000) Microsatellite variation in two populations of mountain lions (Puma concolor) in Texas. Southwestern Naturalist 45: 196-203.


1999

Alonso P, Barrientos LM, Fernández A, Llaneza L, Rico M, de la Torre JA and Vilà C (1999) Current status of the wolf in Spain. Quercus 157: 24-25.

Berg C, Halldin K, Fridolfsson AK, Brandt I and Brunstrom B (1999) The avian egg as a test system for endocrine disrupters: effects of diethylstilbestrol and ethynylestradiol on sex organ development. Science of the Total Environment 233: 57-66.

Brohede J and Ellegren H (1999) Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences. Proceedings of the Royal Society of London, Series B 266: 825-833.

Dale S, Slagsvold T, Lampe, H. and Sætre GP (1999) Population divergence in sexual ornaments: the white forehead patch of Norwegian pied flycatchers is small and unsexy. Evolution 53: 1235-1246.

Ellegren H (1999) Inbreeding and relatedness in Scandinavian grey wolves Canis lupus. Hereditas 130: 239-244.

Ellegren H, Carlson A and Stenberg I (1999) Genetic structure and variability of white-backed woodpecker (Dendrocopos leucotos) populations in northern Europe. Hereditas 130: 291-299.

Flagstad O, Olsaker I and Roed KH (1999) The use of heterologous primers for analysing microsatellite variation in hartebeest Alcelaphus buselaphus. Hereditas 130: 337-340.

Fridolfsson AK and Ellegren H (1999) A simple and universal method for molecular sexing of non-ratite birds. Journal of Avian Biology 30: 116-121.

Griffith SC, Owens IPF and Burke T (1999) Environmental determination of a sexually selected trait. Nature 400: 358-360.

Griffith SC, Owens IPF and Burke T (1999) Female choice and annual reproductive success favour less-ornamented male house sparrows. Proceedings of the Royal Society of London, Series B 266: 765-770.

Griffith SC, Stewart, IRK, Owens IPF, Dawson DA and Burke T (1999) Contrasting levels of extra-pair paternity in mainland and island populations of the house sparrow (Passer domesticus): is there an 'island effect'? Biological Journal of the Linnean Society 68: 303-316.

Guerin G, Bailey E, Bernoco D, Anderson I, Antczak DF, Bell K, Binns MM, Bowling AT, Brandon R, Cholewinski G, Cothran EG, Ellegren H, Forster M, Godard S, Horin P, Ketchum M, Lindgren G, McPartlan H, Meriaux JC, Mickelson JR, Millon LV, Murray J, Neau A, Roed K and Ziegle J (1999) Report of the International Equine Gene Mapping Workshop: male linkage map. Animal Genetics 30: 341-354.

Harlid A and Arnason U (1999) Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters. Proceedings of the Royal Society of London, Series B 266: 305-309.

Hartley IR, Griffith SC, Wilson K, Shepherd M and Burke T (1999) Nestling sex ratios in the polygynously breeding corn bunting, Miliaria calandra. Journal of Avian Biology 30: 7-14.

Hessman O, Lindberg D, Einarsson A, Lillhager P, Carling T, Grimelius L, Eriksson B, Akerstrom G, Westin G and Skogseid B (1999) Genetic alterations on 3p, 11q13, and 18q in nonfamilial and MEN 1-associated pancreatic endocrine tumors. Genes Chromosomes and Cancer 26: 258-264.

Lindgren G, Persson H and Ellegren H (1999) Five equine dinucleotide microsatellite loci HTG17, HTG20, HTG21, HTG28 and HTG31. Animal Genetics 30: 70-71.

Lyrholm T, Leimar O, Johanneson B and Gyllensten U (1999) Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations. Proceedings of the Royal Society of London, Series B 266: 347-354.

Sætre GP, Král M, Bures S and Ims R (1999) Dynamics of a clinal hybrid zone and a comparison with island hybrid zones of flycatchers. Journal of Zoology, London 247: 53-64.

Sætre GP, Post E and Král M (1999) Can environmental fluctuation prevent competitive exclusion in sympatric flycatchers? Proceedings of the Royal Society of London, Series B 266: 1247-1251.

Saino N, Ellegren H and Moller AP (1999) No evidence for adjustment of sex allocation in relation to paternal ornamentation and paternity in barn swallows. Molecular Ecology 8: 399-406.

Saino N, Primmer CR, Ellegren and Møller AP (1999) Breeding synchrony and paternity in the barn swallow (Hirundo rustica). Behavioural Ecology and Sociobiology 45: 211-218.

Sheldon BC and Ellegren H (1999) Sexual selection resulting from extrapair paternity in collared flycatchers. Animal Behaviour 57: 285-298.

Sheldon BC, Andersson S, Griffith SC, Örnborg J and Sendecka J (1999) Ultraviolet colour variation influences blue tit sex ratios. Nature 402: 874-877.

Sheldon BC, Davidson P and Lindgren G (1999) Mate replacement in experimentally widowed collared flycatchers (Ficedula albicollis): determinants and outcomes. Behavioural Ecology and Sociobiology 46: 141-148.

Vilà C (1999) Dog domestication. Relationship between dog and wolf. Scientific American (spanish ed) March: 45-47.

Vilà C and Wayne RK (1999) Hybridization between dogs and wolves. Conservation Biology 13: 195-198.

Vilà C, Amorim IR, Leonard JA, Posadas D, Castroviejo J, Petrucci-Fonseca F, Crandall KA, Ellegren H and Wayne RK (1999) Mitochondrial DNA phylogeography and population history of the gray wolf Canis lupus. Molecular Ecology 8: 2089-2103.

Vilà C., Maldonado J and Wayne RK (1999) Phylogenetic relationships, evolution and genetic diversity of the domestic dog. Journal of Heredity 90: 71-77.