Selected interesting publications from other labs that have been or will be discussed in the lab.
Veller, C., et al. 2023. Recombination and selection against introgressed DNA. Evolution 77:1131–1144.
Dutheil, J. Y. 2023. On the estimation of genome-average recombination rates. BioRxiv 2023.
Waldvogel, A-M., and Pfenninger, M. 2021. Temperature dependence of spontaneous
mutation rates. Genome Res. 31:1582–1589.
Berner, D. et al. 2023. Chromosome-Level Assemblies of the Pieris mannii Butterfly Genome Suggest Z-Origin and Rapid Evolution of the W Chromosome. Genome Biol. Evol. 15:6.
Cotto, C & Day, T. 2023. A null model for the distribution of fitness effects of mutations. PNAS 120:e2218200120.
Rivas-González, I. et al. 2023. Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science 380:925.
Wright, C. J. et al. 2023. Chromosome evolution in Lepidoptera. BioRxiv 2023. doi: https://doi.org/10.1101/2023.05.12.540473
Evans, C. et al. 2018. Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions. Briefings in Bioinformatics 19:776-792.
Yoshido, A. & Marec, F. 2023. Deviations in the Z:A ratio disrupt sexual development in the eri silkmoth, Samia cynthia ricini. Genetics 224:iyad023.
Barroso, G. V. & Dutheil, J. Y. 2023. The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation. Peer Community Journal 3:e40.
Steward, R. A. et al. 2022. Alternative splicing in seasonal plasticity and the potential for adaptation to environmental change. Nature Communications 13:755.
Cancelled due to field work.
Cancelled due to field work.
Wellband, K. et al. 2018. Chromosomal fusion and life history‐associated genomic variation contribute to within‐river local adaptation of Atlantic salmon. Molecular Ecology 28:1439-1459.
Huber, L. A. et al. 2018. Gene expression drives the evolution of dominance. Nature Communications. 9:2750.
Bergeron, L. A. et al. 2023. Evolution of the germline mutation rate across vertebrates. Nature. 615:285-291.
Yan, S. M. et al. 2021. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife. 10:e67615.
Riesch, R. et al. 2017. Transitions between phases of genomic differentiation during stick-insect speciation. Nature Ecol. Evol. 2017:1-13.
Duntsch, L. et al. 2023. Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine. Molecular Ecology. 0:1-15.
Sokolovskis, K. et al. 2023. Migration direction in a songbird explained by two loci. Nat. Comm. 14:165.
Hooper, D. M. & Price, T. D. 2017. Chromosomal inversion differences correlate with range overlap in passerine birds. Nature Ecol. Evol. 1:1526-1534.
Hemstrom, W. B. 2022. Population genetics of a recent range expansion and subsequent loss of migration in monarch butterflies. Molecular Ecology 31:4544-4557.
Samuk, K. et al. 2020. Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura. Current Biology 30:1517-1528.
Anderson, S. A. S., & Weir, J. T. 2022. The role of divergent ecological adaptation during allopatric speciation in vertebrates. Science 378:1214-1218.
Näsvall, K. 2022. Rates and patterns of genome evolution in Lepidoptera. Thesis Kappa 2022.
Lynch, M. et al. 2022. The Linkage-Disequilibrium and Recombinational Landscape in Daphnia pulex. Genome Biol. Evol. 14:11.
Xiong, T. et al. 2022. Admixture of evolutionary rates across a butterfly hybrid zone. eLife 2022:78135.
Mackintosh, A. et al. 2022. Chromosome fissions and fusions act as barriers to gene flow between Brenthis fritillary butterflies. BioRxiv 2022.
Iiam, S. E. et al. 2019. Photoperiodic and clock regulation of the vitamin A pathway in the brain mediates seasonal responsiveness in the monarch butterfly. PNAS. 116:25214-25221.
Kozak, G. M. et al. 2017. A combination of sexual and ecological divergence contributes to rearrangement spread during initial stages of speciation. Mol. Ecol. 26:2331-2347.
Hejase, H. A. et al. 2020. Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. PNAS 117:30554-30565.
Yan, Z. et al. 2020. Evolution of a supergene that regulates a trans-species social polymorphism. Nature Ecology & Evolution 4:240–249.
Doyle, T. et al. 2022. Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration. Mol. Ecol. 2022:1-19.
Arnqvist, G. & Sayadi, A. 2022. A possible genomic footprint of polygenic adaptation on population divergence in seed beetles? BioRxiv 2022.
Wiklund, C. & Friberg, M. 2022. Testing the migration syndrome: Comparative fecundity of migratory and non-migratory nymphaline butterflies. Ecol. Entomol. 2022:1-7.
Hofstatter, P. G. et al. 2022. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 185:3153–3168.
Natola, L. et al. 2022. Population genomics of an emergent tri-species hybrid zone. Mol. Ecol. 2022:00-12.
Lucek, K. 2018. Evolutionary mechanisms of varying chromosome numbers in the radiation of Erebia butterflies. Genes 9:166.
Chase, M. & Mugal, C. 2022. The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome. BioRxiv 2022.
Pazhenkova, E. A. & Lukhtanov, V. A. 2022. Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera. BioRxiv 2022.
Hernández-Roldán, J. L., et al. 2016. Integrative analyses unveil speciation linked to host plant shift in Spialia butterflies. Mol. Ecol. 25:4267-4284.
Nadachowska-Brzyska, K., et al. 2022. Navigating the temporal continuum of effective population size. Meth. Ecol. Evol. 13:22-41.
Bertorelle, G., et al. 2022. Genetic load: genomic estimates and applications in non-model animals. Nat. Rev. Genet. 2022.
Haldane, J. B. S. 1957. The cost of natural selection. J. Genet. 33:511-524.
Bertorelle, G., et al. 2022. Genetic load: genomic estimates and applications in non-model animals. Nat. Rev. Genet. 2022.
Lukyanchikova, V., et al. 2022. Anopheles mosquitoes reveal new principles of 3D
genome organization in insects. Nat. Comm. 13:1960.
Hu, C. K., et al. 2022. Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior. Cell Rep. 38:110360.
Lewis, J. J., et al. 2022. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol. Evol. 13:evab128.
Liu, Z., et al. 2022. Chromosomal Fusions Facilitate Adaptation to Divergent
Environments in Threespine Stickleback. Mol. Biol. Evol. 39:msab358.
Messer, P. W., and Petrov, D. A. 2013. Frequent adaptation and the McDonald–Kreitman test. PNAS. 110:8615–8620.
Lange, J. D., et al. 2022. A Population Genomic Assessment of Three Decades of
Evolution in a Natural Drosophila Population. Mol. Biol. Evol. 39:msab368.
Cao, J., et al. 2022. Population genomic signatures of the oriental fruit moth related to the Pleistocene climates. Communic. Biol. 5:142.
Chen, J., et al. 2022. Hunting for beneficial mutations: conditioning on SIFT scores when estimating the distribution of fitness effect of new mutations. Genome Biol. Evol. 14:evab151.
Singhal, S., et al. 2022. No link between population isolation and speciation rate in squamate reptiles. PNAS 119:e2113388119.
Pan, Z. et al. 2022. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat. Comm. 12:5848.
Monroe, J.G. et al. 2021. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 2022.
Von Seth, J. et al. 2021. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat. Comm. 12:2393.
Sigeman, H. et al. 2021. Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration. Mol. Biol. Evol. 38:5275–5291.
Le Roy, C. et al. 2021. Adaptive evolution of flight in Morpho butterflies. Science 374:1158–1162.
Rosser, N. et al. 2021. Complex basis of hybrid female sterility and Haldane's rule in Heliconius butterflies: Z-linkage and epistasis. Mol. Ecol. 00:1–19.
Lefébure, T. et al. 2017. Less effective selection leads to larger genomes. Genome Res. 27:1016–1028.
Lukhtanov, V. A. et al. 2020. Karyotype evolution and flexible (conventional versus inverted) meiosis in insects with holocentric chromosomes: a case study based on Polyommatus butterflies. Biol. J. Linn. Soc. 130:683–699.
Pertoldi, C. et al. 2021. Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia). Ecol. Evol. 11:12790–12800.
Johri, P. et al. 2021. Statistical inference in population genomics. BioRxiv 2021.
Isildak, U., Stella, A. and Fumagalli, M. 2021. Distinguishing between recent balancing selection and incomplete sweep using deep neural networks. Mol. Ecol. Res. https://doi.org/10.1111/1755-0998.13379
Vernaz, G. et al. 2021. Mapping epigenetic divergence in the massive radiation of lake Malawi cichlid fishes. Nat. Comm. 12:5870.
Gompert, Z. et al. 2021. Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species. Molecular Ecology [Early View].
Näsvall, K., Shipilina, D. et al. 2021. Genome assembly, annotation and linkage mapping of the painted lady (Vanessa cardui). Manuscript.
Zhang, Y. et al. 2021. A widely diverged locus involved in locomotor adaptation in Heliconius butterflies. Sci. Adv. 7:eabh2340.
Mongue, A. J. et al. 2021. Support for faster and more adaptive Z chromosome evolution in two divergent lepidopteran lineages. Evolution [Early Online].
Kardos, M. et al. 2021. The crucial role of genome-wide genetic variation in conservation. BioRxiv 2021.
Seixas, F. A. et al. 2021. Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. Genome Biol. Evol. evab069.
Podsiadlowski, L. et al. 2021. The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology. Genome Biol. Evol. evab122.
Chakraborty, M. et al. 2021. Evolution of genome structure in the Drosophila simulans species complex. Gen. Res. 31:380-396.
Kelleher, J. et al. 2019. Inferring whole-genome histories in large population datasets. Nat. Genet. 51:1330–1338.
Lund-Hansen, K. K. et al. 2021. Sexually antagonistic coevolution between the sex chromosomes of Drosophila melanogaster. PNAS 118:e2003359118.
Merlin, C. et al. 2020. Monarch butterfly migration moving into the genetic era. Trends Genet. 36:689-701.
Jay, P. et al. 2021. Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nature Genetics 53:288-293.
Palahí, A. 2021. Large-scale population resequencing and linkage disequilibrium analysis reveal causes and consequences of fine-scale recombination rate variation in wood whites (Leptidea sinapis). Master Sci. Report 2021.
Rifkin, J. L. et al. 2020. Widespread recombination suppression facilitates plant sex chromosome evolution. Mol. Biol. Evol. 38:1018-1030.
Kawakami, T. et al. 2017. Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds. Mol. Ecol. 26:4158-4172.
Zhang, W. et al. 2021. Testing Implications of the Omnigenic Model for the Genetic Analysis of Loci Identified through Genome- wide Association. Curr. Biol. 31:1092-1098.
Lewis, J. J. et al. 2016. ChIP-Seq-Annotated Heliconius erato genome highlights patterns of cis-regulatory evolution in Lepidoptera. Cell Reports. 16:2855-2863.
Mayrose, I. & Lysak, M. A. 2020. The evolution of chromosome numbers: mechanistic models and experimental approaches. GBE. 13:[Advanced access].
Buffalo, V. & Coop, G. 2020. Estimating the genome-wide contribution of selection to temporal allele frequency change. PNAS. 117:20672-20680.
Polychronopoulos, D. et al. 2017. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucl. Acids Res. 45:12611-12624.
Phung, T. N. et al. 2016. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species. PLoS Genet. 12:e1006199.
Tigano, A. et al. 2021. Chromosome size affects sequence divergence between species through the interplay of recombination and selection. BioRxiv.
Kahilainen, A. et al. 2021. Alternative developmental and transcriptomic responses to host plant water limitation in a butterfly metapopulation. BioRxiv.
Jiao, W-B. & Schneeberger, K. 2020. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat. Comm. 11:989.
Cheng, X. & DeGiorgio, M. 2020. Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection. Mol. Biol. Evol. 37:3267–3291.
Massonnet, M. et al. 2020. The genetic basis of sex determination in grapes. Nat. Comm. 11:2902.
Booker, T. R. et al. 2020. Global adaptation complicates the interpretation of genome scans for local adaptation. Evol. Lett. [Online early].
Todesco, M. et al. 2020. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584:602-607.
Josephs, E. et al. 2019. Detecting adaptive differentiation in structured populations with genomic data and common gardens. Genetics 211:989-1004.
Nosil, P. et al. 2020. Ecology shapes epistasis in a genotype– phenotype–fitness map for stick insect colour. Nat. Ecol. Evol. 4:1673–1684.
Lowry, D. B. et al. 2019. QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient. PNAS. 116:12933–12941.
Feng, S. et al. 2020. Dense sampling of bird diversity increases power of comparative genomics. Nature. 587:252-257.
Van Boheemen, L. A. & Hodgins, K. A. 2020. Rapid repeatable phenotypic and genomic adaptation following multiple introductions. Molecular Ecology. 29:4102–4117.
Liu, X. et al. 2019. Trans Effects on Gene Expression Can Drive Omnigenic Inheritance. Cell. 177:1022–1034.
Booker, T. R. et al. 2020. Variation in recombination rate affects detection of outliers in genome scans under neutrality. Molecular Ecology. [Online early].
Ebdon, S. et al. 2020. The Pleistocene species pump past its prime: evidence from European butterfly sister species. BioRxiv.
Höglund, A. et al. 2020. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat. Ecol. Evol. [Online early].
Näsvall, K. et al. 2020. Base composition, codon usage and patterns of gene sequence evolution in butterflies. Manuscript [In Prep.]
Fang, B. et al. 2020. On the causes of geographically heterogeneous parallel evolution in sticklebacks. Nat. Ecol. Evol. 4:1105-1115.
Boman, J. et al. 2020. The effects of gBGC on diversity within and between butterfly genomes. [Manuscript for submission].
Kirch et al. 2020. Pleistocene stickleback genomes reveal the constraints on parallel evolution. BioRxiv [Online Early].
Becher et al. 2020. Patterns of genetic variability in genomic regions with low rates of recombination. Current Biology 30:94-100.
Neopane & Xu. 2020. Adaptive divergence of meiotic recombination rate in ecological speciation. BioRxiv [Online Early].
Orteu & Jiggins. 2020. The genomics of coloration provides insights into adaptive evolution. Nat. Rev. Genet. [Online Early].
Flagel et al. 2018. The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference. MBE 36:220-238.
Meisel et al. 2019. The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence. BMC Biol. 17:100.
Bohutínská et al. 2020. Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives. BioRxiv 2020-03-25.
Hill & Robertson. 1966. The effect of linkage on limits to artificial selection. Genetic. Res. 8:269-294.
Pearse et al. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout. Nat. Ecol. Evol. 3:1731-1742.
Xirocostas et al. 2020. The sex with the reduced sex chromosome dies earlier: a comparison across the tree of life. Biol. Lett. 16:20190867.
Martin et al. 2020. Whole-chromosome hitchhiking driven by a male-killing endosymbiont. PLoS Biol. 18:e3000610.
Thomas et al. 2020. Gene content evolution in the arthropods. Genome Biol. 21:15.
Berg, P. R., Star, B., Pampoulie, C., Sodeland, M., Barth, J. M. I., Knutsen, H., Jakobsen, K. S., and Jentoft, S. 2016. Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod. Scientific Reports 6: 23246.
Cong, Q., Shen, J., Warren, A. D., Borek, D., Otwinowski, Z., and Grishin, N. V. 2016. Speciation in cloudless sulphurs gleaned from complete genomes. Genome Biology and Evolution [Early Online].
Martin, S. H., Möst, M., Palmer, W. J., Salazar, C., McMillan W. O., Jiggins, F. M., and Jiggins, C. D. 2016. Natural selection and genetic diversity in the butterfly Heliconius melpomene. BioRxiv [Not peer-reviewed].
Biscotti, M. A., Olmo, E., and Heslop-Harrison, J. S. 2015. Repetitive DNA in eukaryotic genomes. Chromosome Research 23: 415-420.
Payseur, B., and Rieseberg, L. 2016. A genomic perspective on hybridization and speciation. Molecular Ecology [In Press]
Ganapathy, G., Howard, J. T., Ward, J. M., et al. (24 authors with Jarvis, E. D. last author). 2014. High-coverage sequencing and annotated assemblies of the budgerigar. GigaScience 3: 11e
Dion-Cote, A-M., Symonova, R., Rab, P., and Bernatchez, L. Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring. Proceedings B 282: 20142862.
Zhang, G., Li, C., Li, Q., et al. (106 authors with Wang, J. last author). 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346: 1311-1320.
Ahola, V., Lehtonen, R., Somervuo, P., et al. (47 authors with Hanski, I. last author). 2014. The Glanville fritillary genome retains ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications 5: 4737.
Santos, M. E., Braasch, I., Boileau, N., Meyer, B. S., Sauteur, L., Böhne, A., Belting, H.-G., Affolter, M., and Salzburger, W.. 2014. The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. Nature Communications 5: 5149.
Ruegg, K., and Anderson, E. C., Boone, J., Poulös, J., and Smith, T. B. 2014. A role for migration-linked genes and genomic islands in divergence of a songbird. Molecular Ecology 23: 4757-4769.
Zhan, S., Zhang, W., Niitepold, K., Hsu, J., Haeger, J. F., Zalucki, M. P., Altizer, S., de Roode, J. C., Reppert, S. M., and Kronforst, M. R.. 2014. The genetics of monarch butterfly migration and warning colouration. Nature [Early View].
Bures, P., and Zedek, F. 2014. Holokinetic drive: centromere drive in chromosomes without centromeres. Evolution 68: 2412-2420.
Sherman, N. A., Victorine, A., Wang, R. J., and Moyle, L. C. 2014. Interspecific tests of allelism reveal the evolutionary timing and pattern of accumulation of reproductive isolation mutations. PLoS Genetics 10: e1004623.
Brawand, D., Wagner, C. E., Li, Y. I. et al. (75 authors with Di Palma, F. last author). 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature [Early View].
Carneiro, M., Albert, F. W., Afonso, S., Pereira, R. J., Burbano, H., Campos, R., Melo-Ferreira, J., Blanco-Aguiar, J. A., Villafuerte, R., Nachman, M. W., Good, J. M., and Ferrand, N. 2014. The genomic architecture of population divergence between subspecies of the European rabbit. PLoS Genetics 10: e1003519.
Gossmann, T. I., Santure, A. W., Sheldon, B. C., Slate, J., and Zeng, K. 2014. Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biology and Evolution 6: 2061-2075.
Lukhtanov, V. A., Kandul, N. P., Plotkin, J. B., Dantchenko, A. V., Haig, D., and Pierce, N. 2005. Reinforcement of pre-zygotic isolation and karyotype evolution in Agrodiaetus butterflies. Nature 436: 385-389.
Zhan, S., Merlin, C., Boore, J. L., and Reppert, S. M. 2011. The Monarch butterfly genome yields insights into long-distance migration. Cell 147: 1-15.
Ekblom, R., and Wolf, J. B. W. 2014. A field guide to whole-genome sequencing, assembly and annotation. Evolutionary Applications ISSN 1752-4571.
Cruickshank, T. E., and Hahn, M. W. 2014. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology 23: 3133–3157.
Dinca, V., Wiklund, C., Lukhtanov, V. A., Kodandaramaiah, U., Noren, K., Dapporto, L., Wahlberg, N, Vila, R., and Friberg, M. 2013. Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex. Journal of Evolutionary Biology 26: 2095-2106.
Alcaide, M., Scordato, E. S. C., Price, T., and Irwin, D. E. 2014. Genomic divergence in a ring species complex. Nature [In Press]
Rastas, P., Paulin, L., Hanski, I., Jehtonen, R., and Auvinen, P. 2013. Lep-MAP: fast and accurate linkage map construction for large SNP datasets. Bioinformatics 29: 3128-3134.
Trier, C. N., Hermansen, J. S., Saetre, G-P., and Bailey, R. I. 2014. Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid italian sparrow and its parent species. PLoS Genetics 10:e1004075.
Campos, J. L., Halligan, D. L., Haddrill, P. R., and Charlesworth, B. 2014. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Molecular Biology and Evolution [Advanced Access]
Chen, S., Zhang, G., Shao, C., 41 co-authors, and Wang, J. 2014. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nature Genetics [Advanced Access]
van Oers, K., Santure, A. W., De Cauwer, I., van Bers, N. E. M., Crooijmans, R. P. M. A., Sheldon, B. C., Visser, M. E., Slate, J., and Groenen, M. A. M. 2014. Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates. Heredity 112: 307-316.
Rheindt, F. E., Fujita, M. K., Wilton, P. R., and Edwards, S. V. 2014. Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology 63: 134-152.