Journal Club
Every Friday morning
2020
Apr 22: Lin, Z., Chen, L., Chen, X., Zhong, Y., Yang, Y., Xia, W., ... & Yang, Y. (2019). Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus). Science, 364(6446), eaav6312.
Apr 8: Whiting, J. R., & Fraser, B. A. (2020). Contingent Convergence: The ability to detect convergent genomic evolution is dependent on population size and migration. G3: Genes, Genomes, Genetics, 10(2), 677-693. https://doi.org/10.1534/g3.119.400970
Mar 11: Sendell-Price, A. T., Ruegg, K. C., & Clegg, S. M. (2020). Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection. Heredity, 124(4), 535-549. https://doi.org/10.1038/s41437-020-0298-8
Feb 26: Simkin, A., Geissler, R., McIntyre, A. B., & Grimson, A. (2020). Evolutionary Dynamics of microRNA target sites across vertebrate evolution. PLoS Genetics, 16(2), e1008285. https://doi.org/10.1371/journal.pgen.1008285
Feb 12: Becher, H., Jackson, B. C., & Charlesworth, B. (2020). Patterns of genetic variability in genomic regions with low rates of recombination. Current Biology, 30(1), 94-100. https://doi.org/10.1016/j.cub.2019.10.047
2019
Nov 29: Sigeman, H., Ponnikas, S., Chauhan, P., Dierickx, E., Brooke, M. D. L., & Hansson, B. (2019). Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes. Proceedings of the Royal Society B, 286(1916), 20192051. https://doi.org/10.1098/rspb.2019.2051
Nov 22: Kutschera, V. E., Poelstra, J. W., Botero-Castro, F., Dussex, N., Gemmell, N. J., Hunt, G. R., ... & Wolf, J. B. (2020). Purifying selection in corvids is less efficient on islands. Molecular biology and evolution, 37(2), 469-474. https://doi.org/10.1093/molbev/msz233
Nov 9: Lu, M., & He, X. (2019). Centromere repositioning causes inversion of meiosis and generates a reproductive barrier. Proceedings of the National Academy of Sciences, 116(43), 21580-21591. https://doi.org/10.1073/pnas.1911745116
Oct 18: Darbellay, F., & Necsulea, A. (2020). Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs. Molecular biology and evolution, 37(1), 240-259. https://doi.org/10.1093/molbev/msz212
Oct 11: Yang, Y., Servedio, M.R. & Richards-Zawacki, C.L. Imprinting sets the stage for speciation. Nature 574, 99–102 (2019). https://doi.org/10.1038/s41586-019-1599-z
Oct 4: Parker, D. J., Bast, J., Jalvingh, K., Dumas, Z., Robinson-Rechavi, M., & Schwander, T. (2019). Repeated evolution of asexuality involves convergent gene expression changes. Molecular biology and evolution, 36(2), 350-364. https://doi.org/10.1093/molbev/msy217
Sep 20: Speidel, L., Forest, M., Shi, S. et al. A method for genome-wide genealogy estimation for thousands of samples. Nat Genet 51, 1321–1329 (2019). https://doi.org/10.1038/s41588-019-0484-x
Sep 13: Yin, Z., Zhu, F., Lin, F. et al. Revisiting avian ‘missing’ genes from de novo assembled transcripts. BMC Genomics 20, 4 (2019). https://doi.org/10.1186/s12864-018-5407-1
June 14: Dumont, B. L. (2019). Significant Strain Variation in the Mutation Spectra of Inbred Laboratory Mice. Molecular biology and evolution.
May 17: Uricchio, L. H., Petrov, D. A., & Enard, D. (2019). Exploiting selection at linked sites to infer the rate and strength of adaptation. Nature ecology & evolution, 1.
May 10: Kim, K. W., Jackson, B. C., Zhang, H., Toews, D. P., Taylor, S. A., Greig, E. I., ... & Zeng, K. (2019). Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird. Nature communications.
Apr 26: Sultana, T., van Essen, D., Siol, O., Bailly-Bechet, M., Philippe, C., El Aabidine, A. Z., ... & Gilbert, N. (2019). The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection. Molecular cell, 74(3), 555-570.
Apr 12: Sackton, T. B., Grayson, P., Cloutier, A., Hu, Z., Liu, J. S., Wheeler, N. E., ... & Edwards, S. V. (2019). Convergent regulatory evolution and loss of flight in paleognathous birds. Science, 364(6435), 74-78.
Apr 5: Marques, D. A., Meier, J. I., & Seehausen, O. (2019). A combinatorial view on speciation and adaptive radiation. Trends in ecology & evolution.
Mar 22: Barrett et al (2019) Linking a mutation to survival in wild mice. Science 363: 499-504
Feb 15: Xie et al (2019) DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science 363: 81-84
Feb 8: Halldorsson et al (2019) Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science DOI: 10.1126/science.aau1043
Feb 1: Chen et al (2019) A quantitative framework for characterizing the evolutionary history of mammalian gene expression. Genome Res 29: 53-63
2018
Dec 14: Franchini et al (2018) Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nature Communications 9: 5136
Dec 7: Lawson et al (2018) A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots Nature Communications 9: 3258
Nov 30: Li & Ralph (2018) Local PCA Shows How the Effect of Population Structure Differs Along the Genome Genetics doi: 10.1534/genetics.118.301747
Nov 23: Kern & Hahn (2018) The Neutral Theory in Light of Natural Selection Mol. Biol. Evol. 35: 1366–1371
Nov 16: Damas et al (2018) Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes Genome Biology 19:155
Nov 2: Tavares et al (2018) Selection and gene flow shape genomic islands that control floral guides PNAS 115: 1006-11011
Oct 25: Mack et al (2018) Gene regulation underlies environmental adaptation in house mice Genome Research doi: 10.1101/gr.238998.118
Oct 19: Tang et al (2016) Specification and epigenetic programming of the human germ line Nature Reviews Genetics 17: 585–600
Sept 28: Siewert and Voight (2017) Detecting Long-Term Balancing Selection Using Allele Frequency Correlation. MBE 34: 2996-3005
Sept 21: Schrider and Kern (2018) Supervised machine learning for population genetics, A new paradigm. Cell doi: 10.1016/j.tig.2017.12.005
Sept 14: Brick et al (2018) Extensive sex differences at the initiation of genetic recombination Nature 561: 338–342
June 15: Nergadze et al (2018) Birth, evolution, and transmission of satellite-free mammalian centromeric domains Genome Research doi: 10.1101/gr.231159.117
June 7: O'Connor et al (2018) The evolution of immunity in relation to colonization and migration. Nature Ecology & Evolution 2: 841–849
May 25: Signor and Nuzhdin (2018) The Evolution of Gene Expression in cis and trans. Trends in Genetics. 34: 532-544
May 18: Kretschmer et al (2018) Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting. Genes. doi:10.3390/genes9040181
May 4: Choi et al (2018) Comparison of phasing strategies for whole human genomes. PLOS Genetics. doi:10.1371/journal.pgen.1007308
Apr 13: Smith et al (2018) Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans. PLOS Genetics. doi:10.1371/journal.pgen.1007254
Apr 6: Sinclair-Waters et al (2018) Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic. Mol Ecol 27:339-351
Mar 23: Underwood et al (2018) Epigenetic activation of meiotic recombination near Arabidopsis thalianacentromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Research doi:10.1101/gr.227116.117
Mar 16: Miles et al (2018) Macroevolutionary patterning of woodpecker drums reveals how sexual selection elaborates signals under constraint. Proceedings of the Royal Soceity B DOI: 10.1098/rspb.2017.2628
Mar 9: VanKuren & Long (2018) Gene duplicates resolving sexual conflict rapidly evolved essential gametogenesis functions. Nature Ecology & Evolution 2: 705–712
Mar 2: Mendoza et al (2018) Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature Ecology & Evolution. doi:10.1038/s41559-018-0476-8
Feb 23: Salmona J., Heller R., Lascoux M., Shafer A. (2017) Inferring Demographic History Using Genomic Data. In: . Population Genomics. Springer, Cham
Feb 16: Rodrigues et al (2018) Sex-Chromosome Recombination in Common Frogs Brings Water to the Fountain-of-Youth. Mol Biol Evol. doi.org/10.1093/molbev/mys008
Feb 9: Kasinathan & Henikoff (2018) Non-B-form DNA is enriched at centromeres. Mol Biol Evol. doi.org/10.1093/molbev/mys010
Feb 2: Dapper & Payseur (2018) Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium. Mol Biol Evol. 35:335-353.
Jan 26: Long et al (2018) Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology & Evolution. 2: 237–240.
Jan 19: Bay et al (2018) Genomic signals of selection predict climate-driven population declines in a migratory bird. Science. 359: 83-86.
2017
Dec 14: Schmitz et al (2017) Intron retention enhances gene regulatory complexity in vertebrates. Genome Biology. 18:216
Dec 7: Wu et al (2017) Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. Genome Biology. 18:217
Nov 30: Comeron (2017) Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies. Phil. Trans. R. Soc. B. doi.org/10.1098/rstb.2016.0471.
Nov 23: Murray et al (2017) Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science. 17:951-954
Nov 16: Branco et al (2017) Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism. PNAS. 114: 7067–7072
Nov 9: Tataru et al (2017) Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data. Genetics. 207:1103-1119
Oct 26: Bosse et al (2017) Recent natural selection causes adaptive evolution of an avian polygenic trait. Science. 358: 365-368
Oct 19: Blackmon et al (2017) Long-Term Fragility of Y Chromosomes Is Dominated by Short-Term Resolution of Sexual Antagonism. Genetics. doi.org/10.1534/genetics.117.300382
Oct 12: Wang et al (2017) Allele-Specific Expression Analysis Does Not Support Sex Chromosome Inactivation on the Chicken Z Chromosome. GBE. 9: 619–626
Oct 5: Yi (2017) Insights into Epigenome Evolution from Animal and Plant Methylomes. GBE. doi.org/10.1093/gbe/evx203
Sept 28: Guerrero & Hahn (2017) Speciation as a sieve for ancestral polymorphism. Molecular Ecology. DOI: 10.1111/mec.14290
Sept 22: Narasimhan et al (2017) Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes. Nature Communications. DOI: 10.1038/s41467-017-00323-y
Sept 15: Osada et al (2017) Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster. Genetics, 206: 2139–2148
Sept 8: Hooper & Price (2017) Chromosomal inversion differences correlate with range overlap in passerine birds. Nature Ecology & Evolution 1: 1526–1534
June 16: Ritz et al (2017) Variation in Recombination Rate: Adaptive or Not? Trends in Genetics https://doi.org/10.1016/j.tig.2017.03.003
May 29: Drury et al (2017) CRISPR/Cas9 gene drives in genetically variable and nonrandomly mating wild populations Science DOI: 10.1126/sciadv.1601910
May 19: Lefebure et al (2017) Less effective selection leads to larger genomes Genome Research 27: 1-13
May 12: Han et al (2017) Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin’s finches Genome Research 27: 1-12
May 5: Croze et al (2017) A genome-wide scan for genes under balancing selection in Drosophila melanogaster BMC Evolutionary Biology (2017) 17:15
April 28: Chiang et al (2017) The impact of structural variation on human gene expression Nature Genetics 49: 692–699
April 7: Chen et al (2017) Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species Mol Biol Evol 34:1417-1428
Mar 31: Dudchenko et al (2017) De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds Science DOI: 10.1126/science.aal3327
Mar 24: Kozak et al (2017) A combination of sexual and ecological divergence contributes to rearrangement spread during initial stages Mol Ecol DOI: 10.1111/mec.14036
Mar 17: Terekhanova et al (2017) Evolution of Local Mutation Rate and Its Determinants Mol Biol Evol DOI:10.1093/molbev/msx060
Mar 10: Limborg et al (2015) Recombination patterns reveal information about centromere location on linkage maps Molecular Ecology Resources 16: 655–661
Mar 3: Steige et al (2017) Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora PNAS 114: 1087-1092.
Feb 24: Seki et al (2017) Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features Nature Communications 8, DOI:10.1038/ncomms14229
Feb 17: Wright et al (2017) Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation Nature Communications 8, DOI:10.1038/ncomms14251
Feb 10: Van Doren et al (2017) Correlated patterns of genetic diversity and differentiation across an avian family bioRxiv Preprint doi: http://dx.doi.org/10.1101/097733
Feb 3: Warren et al (2017) A New Chicken Genome Assembly Provides Insight into Avian Genome Structure G3 7:109-117
2016
Dec 16: Pennell & Morrow (2013) Two sexes, one genome: the evolutionary dynamics of intralocus sexual conflict. Ecology and Evolution 3: 1819 – 1834
Dec 9: Juric et al (2016) The Strength of Selection against Neanderthal Introgression. PLOS Genetics DOI:10.1371/journal.pgen.1006340
Dec 2: Kovach et al (2016) Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones. Proceedings Of The Royal Society B. DOI: 10.1098/rspb.2016.1380
Nov 25: Rousselle et al (2016) Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 8: 3108-3119
Nov 18: Natarajan et al (2016) Predictable convergence in hemoglobin function has unpredictable molecular underpinnings. Science 6310: 336-339
Nov 11: Davey et al (2016) Recombination Suppression is Unlikely to Contribute to Speciation in Sympatric Heliconius Butterflies. bioRxiv
Nov 4: Chen et al (2016) Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay. Current Biology 26: 1-6
Oct 28: Session et al (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538: 336–343
Oct 21: Gawad et al (2016) Single-cell genome sequencing: current state of the science. Nature Reviews Genetics 17: 175-188
Oct 14: Knief et al (2016) Fitness consequences of polymorphic inversions in the zebra finch genome. Genome Biology 17:199 DOI: 10.1186/s13059-016-1056-3
Oct 7: Yeaman et al (2016) Convergent local adaptation to climate in distantly related conifers. Science 353:1431-1433
Sep 30: Wang et al (2016) Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia. PLOS Biology DOI:10.1371/journal.pbio.100250
Sep 23: Phung et al (2016) Determining the Effect of Natural Selection on Linked Neutral Divergence across Species. PLOS Genetics DOI:10.1371/journal.pgen.1006199
Sep 16: Elyashiv et al (2016) A Genomic Map of the Effects of Linked Selection in Drosophila. PLOS Genetics DOI:10.1371/journal.pgen.100613
June 10: Van't Hof et al (2016) The industrial melanism mutation in British peppered moths is a transposable element. Nature 534:102–105
June 3: Palazzo & Lee (2015) Non-coding RNA: what is functional and what is junk? Front. Genet. doi: 10.3389/fgene.2015.00002
May 27: Flood et al (2016) Whole-Genome Hitchhiking on an Organelle Mutation. Current Biology 26:1306–1311
May 20: Johnston et al (2016) Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries). Genetics 203: 583-598
May 13: Lamichhaney et al (2016) A beak size locus in Darwin’s finches facilitated character displacement during a drought. Science 352: 470-474
Apr 29: Charruau et al (2016) Pervasive Effects of Aging on Gene Expression in Wild Wolves. Molecular Biology and Evolution. doi: 10.1093/molbev/msw072
Apr 22: Farlow et al (2015) The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe. Genetics 201: 737-744
Apr 15: Gordon et al (2016) Long-read sequence assembly of the gorilla genome. Science. doi: 10.1126/science.aae0344
Apr 8: McDonald et al (2016) Sex speeds adaptation by altering the dynamics of molecular evolution. Nature doi:10.1038/nature17143
Apr 1: Coop (2016) Does linked selection explain the narrow range of genetic diversity across species. bioRxiv
Mar 18: Hernando-Herraez et al (2015) DNA Methylation: Insights into Human Evolution. PLOS Genetics doi: 10.1371/journal.pgen.1005661
Mar 11: Irwin et al (2016) Recurrent selection explains genomic regions of high relative but low absolute differentiation in the greenish warbler ring species. bioRxiv.
Mar 4: Lindholm et al (2016) The Ecology and Evolutionary Dynamics of Meiotic Drive. Trends in Ecology and Evolution http://dx.doi.org/10.1016/j.tree.2016.02.001
Feb 26: Galtier (2016) Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis. PLOS Genetics doi: 10.1371/journal.pgen.1005774
Feb 19: Amster & Sella (2016) Life history effects on the molecular clock of autosomes and sex chromosomes. PNAS 113:1588-1593
Feb 12: Singhal et al (2015) Stable recombination hotspots in birds. Science 350: 928-932
Feb 5: Ortiz-Barrientos et al (2016) Recombination Rate Evolution and the Origin of Species. Trends in Ecology and Evolution http://dx.doi.org/10.1016/j.tree.2015.12.016
Jan 29: Tuttle et al (2016) Divergence and functional degradation of a sex chromosome-like supergene. Current Biology http://dx.doi.org/10.1016/j.cub.2015.11.069
2015
Dec 18: Pipoly et al (2015) The genetic sex-determination system predicts adult sex ratios in tetrapods. Nature 527: 91–94
Dec 11: PAPER (1) Kuper et al (2015) A supergene determines highly divergent male reproductive morphs in the ruff. Nature Genetics doi:10.1038/ng.3443
PAPER (2) Lamichhaney et al (2015) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics doi:10.1038/ng.3430
Dec 4: Holleley et al (2015) Sex reversal triggers the rapid transition from genetic to temperature-dependent sex. Nature 523: 79–82
Nov 27: Ma et al (2015) Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis. PLOS Genetics doi: 10.1371/journal.pgen.1005387
Nov 20: Rogers (2015) Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans. Mol Biol Evol. doi:10.1093/molbev/msv204
Nov 13: Barson et al (2015) Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature. doi:10.1038/nature16062
Nov 6: Stephan (2015) Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation. Molecular Ecology. doi: 10.1111/mec.1328
Oct 23: Chaisson et al (2015) Genetic variation and the de novo assembly of human genomes. Nature Reviews Genetics 16:627–640.
Oct 16: Brusatte et al (2015) The Origin and Diversification of Birds. Current Biology 25:R888-898. doi: 10.1016/j.cub.2015.08.003
Oct 9: Deinum et al (2015) Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size. Molecular Biology and Evolution 32:2547–2558.
Oct 2: Laland et al (2015) The extended evolutionary synthesis: its structure, assumptions and predictions. Proc. R. Soc. B. DOI: 10.1098/rspb.2015.1019
Sep 25: Whitlock & Lotterhos (2015) Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST . American Naturalist. DOI: 10.1086/682949
Sep 18: Kemppainen et al (2015) Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. Molecular Ecology Resources. 15: 1031-1045
Sep 11: Huber et al (2015) Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular Ecology. DOI: 10.1111/mec.13351
June 12: Francioli et al (2015) Genome-wide patterns and properties of de novo mutations in humans. Nature 47: 822–826
June 5: Wallberg et al (2015) Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera. PLoS Genetics. doi: 10.1371/journal.pgen.1005189
May 22: Rice et al (2015) The Evolutionarily Stable Distribution of Fitness Effects. Genetics 200: 321-329
May 8: Martin et al (2015) Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution 69(6):1406-1422
Apr 17: Corbett-Detig et al (2015) Natural Selection Constrains Neutral Diversity across A Wide Range of Species. PLoS Biology doi:10.1371/journal.pbio.1002112
Apr 10: Charlesworth et al (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303
Mar 27: Munch et al (2014) Unraveling recombination rate evolution using ancestral recombination maps. BioEssays 36: 892-900
Mar 20: Wong et al (2015) Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Research doi:10.1101/gr.177840.114
Mar 13: Feulner et al (2015) Genomics of Divergence along a Continuum of Parapatric Population Differentiation. PLoS Genetics doi:10.1371/journal.pgen.1004966
Mar 6: Zhang et al (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346: 1311-1320
Feb 27: Nadeau et al (2014) Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Research 24: 1316–1333
Feb 20: Lamichhaney et al (2015) Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature 518: 371–375
Feb 13: Hollister et al (2014) Recurrent Loss of Sex Is Associated with Accumulation of Deleterious Mutations in Oenothera. Molecular Biology and Evolution 32: 896-905
Feb 6: Bank et al (2014) Thinking too positive? Revisiting current methods of population genetic selection inference. Trends in Genetics doi:10.1016/j.tig.2014.09.010
Jan 30: Gilbert et al (2015) Genome-Wide DNA Methylation Patterns in Wild Samples of Two Morphotypes
of Threespine Stickleback (Gasterosteus aculeatus). Molecular Biology and Evolution 32: 888-895
Jan 23: Natarajan et al (2015) Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin. Molecular Biology and Evolution 32: 978-997..
2014
Dec 19: Nuzzo (2014) Statistical errors. Nature 506: 150-152
Dec 11: Lesecque et al (2014) The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes. PLoS Genetics 10: e004790
Dec 5: Alcala and Vuilleumier (2014) Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations. Proceedings of the Royal Society B: doi: 10.1098/rspb.2014.1369
Nov 28: Cheng et al (2014). Principles of regulatory information conservation between mouse and human Nature 515: 371–375
Nov 21: Pratto et al (2014) Recombination initiation maps of individual human genomes. Science 346:
Nov 14: Amini et al (2014) Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nature Genetics 46: 1343–1349
Nov 7: Tiffin & Ross-Ibarra (2014). Advances and limits of using population genetics to understand local adaptation. Trends in Ecology and Evolution 29: 673–680
Oct 31: Purcell et al (2014). Convergent Genetic Architecture Underlies Social Organization in Ants. Current Biology 24: 2728–2732
Oct 24: Santos et al (2014). The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. Nature Communications 5: 5149
Oct 10: Bachtrog et al (2014). Sex determination: why so many ways of doing it?. PLoS Biology 12: e1001899
Sep 5: Romiguier et al (2014). Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature 515: 261–263
June 12: Cruickshank & Hahn (2014). Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology doi: 10.1111/mec.12796
May 16: Cortez et al (2014). Origins and functional evolution of Y chromosomes across mammals. Nature 508: 488-93
May 9: Benson et al (2014). Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage. PLoS Biology 12: e1001853
Apr 25: Lawrie & Petrov (2014). Comparative population genomics: power and principles for the inference of functionality. Trends in Genetics. doi: http://dx.doi.org/10.1016/j.tig.2014.02.002
Apr 11: Chung et al (2014). A single gene affects both ecological divergence and mate choice in Drosophila. Science 343: 1148-51
Apr 4: Hellenthal et al (2014). A Genetic Atlas of Human Admixture History. Science 343: 747-751
Mar 21: Enard et al (2014). Genome-wide signals of positive selection in human evolution. Genome Research 24: 885-895
Mar 14: Nam et al (2014). Strong selective sweeps associated with ampliconic regions in great ape X chromosomes. arXiv:1402.5790
Mar 7: Chen et al (2014). Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nature Genetics 46: 253–260
Feb 28: Horton et al (2014). Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes. PNAS 111: 1443–1448
Feb 21: Gompert et al (2014). Experimental evidence for ecological selection on genome variation in the wild. Ecology Letters 17: 369–379
Feb 14: Sankararaman et al (2014). The genomic landscape of Neanderthal ancestry in present-day humans. Nature doi:10.1038/nature12961
Feb 7: Campos et al (2014). The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Mol Biol Evol doi: 10.1093/molbev/msu056
Jan 24: Trier et al (2014). Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species. PLoS Genetics 10: e1004075
2013
Dec 13: Gregg et al (2013). The Human Mutation Rate Is Increasing, Even As It Slows. Mol Biol Evol 31: 253-257.
Dec 6: Corbett-Detig et al (2013). Genetic incompatibilities are widespread within species. Nature 504: 135–137
Nov 13: Vicoso et al (2013). Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biol 11:e1001643.
Nov 8: Lanfear et al. (2013). Population size and the rate of evolution. Trends in Ecology & Evolution doi: 10.1016/j.tree.2013.09.009
Nov 1: Eyre-Walker & Stoletzki (2013). The assessment of science: the relative merits of post-publication review, the impact factor, and the number of citations. PLoS Biol 11:e1001675.
Oct 25: Parker et al (2013). Genome-wide signatures of convergent evolution in echolocating mammals. Nature 502: 228–231
Oct 11: Stern (2013). The genetic causes of convergent evolution. Nature Reviews Genetics 14: 751–764
Oct 4: Messer & Petrov (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology & Evolution 28: 659-669
Sep 27: Martin et al (2013). Genome-wide evidence for speciation with gene flow in Heliconius butterflies. Genome Research doi:10.1101/gr.159426.113
Sep 20: De Maio et al (2013). Linking Great Apes Genome Evolution across Time Scales using Polymorphism-aware Phylogenetic Models. Mol Biol Evo, 30:2249–2262.
Sep 13: Hedrick (2013). Adaptive introgression in animals - examples and comparison to new mutation and standing variation as sources of adaptive variation. Mol Ecol 22: 4606-18
May 24: Sousa & Hey (2013). Understanding the origin of species with genome-scale data: modelling gene flow. Nature Reviews Genetics 14: 404–414
May 17: Filteau et al (2013). Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish (2013). Mol Biol Evol 30: 1384-96
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