Journal Club

Every Friday morning

2018

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. GBE9: 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

May 3: Browning & Browning (2011). Haplotype phasing: existing methods and new developments. Nature Reviews Genetics 12: 703-714

Apr 26: Vicoso et al (2013). Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution.

Apr 19: Leffler et al (2013). Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees. Science 339: 1578-1582

Apr 12: Graur et al (2013). On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE. Genome Biology and Evolution 5: 578-590

Mar 22: Cutter & Payseur (2013). Genomic signatures of selection at linked sites: unifying the disparity among species. Nature Reviews Genetics 14: 262–274

Mar 15: Cowley & Oakey (2013). Transposable Elements Re-Wire and Fine-Tune the Transcriptome. PLoS Genetics 9: e1003234. doi:10.1371/journal.pgen.1003234

Mar 8: Smith et al (2013). Sequencing of the sea lamprey (Petromyzon marinus)
genome provides insights into vertebrate evolution. Nature Genetics doi:10.1038/ng.2568

Mar 1: Barrett et al (2013). Telomere length and dynamics predict mortality in a wild longitudinal study. Molecular Ecology 22:249–59.

Feb 22: Schneider & Grosschedl (2007). Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes & Development 21:3027–43.

Feb 15: Farré et al (2013). Recombination Rates and Genomic Shuffling in Human and Chimpanzee - A New Twist in the Chromosomal Speciation Theory. Molecular Biology and Evolution. doi:10.1093/molbev/mss272

Feb 8: Wang et al (2013) A Y-like social chromosome causes alternative colony organization in fire ants. Nature 493: 664–668

Jan 25: Akashi et al . (2012). Weak selection and protein evolution. Genetics 192: 15–31

2012

Dec 14: Lartillot (2012). Phylogenetic patterns of GC-biased gene conversion in placental mammals, and the evolutionary dynamics of recombination landscapes. Molecular Biology and Evolution. doi:10.1093/molbev/mss239

Dec 7: Rubin et al (2012). Strong signatures of selection in the domestic pig genome. PNAS 109: 19529-36

Nov 23: The 1000 Genomes Project Consortium (2012). An integrated map of genetic variation from 1,092 human genomes. Nature 49: 56-65

Nov 16:  Lamichhaney et al. (2012). Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. PNAS doi:10.1073/pnas.1216128109

Nov 9: Huang et al (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490: 497-501

Nov 2: Comeron et al (2012) The Many Landscapes of Recombination in Drosophila melanogaster. PLoS Genetics 8: e1002905

Oct 26: Meisel et al (2012) Faster-X Evolution of Gene Expression in Drosophila. PLoS Genetics 8: e1003013

Oct 19: Miller et al (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. PNAS 109: E2382-E2390

Oct 12: Ruiz-Herrera et al (2012) Molecular cytogenetic and genomic insights into chromosomal evolution. Heredity 108: 28-36

Oct 5: The Heliconius Genome Consortium (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487: 94-98

Sep 28: The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74

Sep 21: Nilsen & Graveley (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457-463

Sep 14: Karl et al (2012) Common misconceptions in molecular ecology: echoes of the modern synthesis. Molecular Ecology 21: 4171-4189

Sep 7: Wang et al (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150: 402-412

Aug 31: Qu et al (2012) Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. Genome Research 22: 1419-1425

Aug 24: Koren et al (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology 30:693-700

May 25: Fungtammasan et al (2012) A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Genome Research doi:10.1101/gr.134395.111

May 11: Martincorena et al (2012) Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature 485: 95-98

May 4: Mackay et al (2012) The Drosophila melanogaster genetic reference panel. Nature 482: 173-178

April 27: Auton et al (2012) A fine-scale chimpanzee genetic map from population sequencing. Science 336: 193-198

April 20: Pessia et al (2012) Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proceedings of the National Academy of Sciences USA 109: 5346-5351

April 13: Jones et al (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55-61 and Hoekstra (2012) Stickleback is the catch of the day. Nature 484: 46-47

March 23: Capra & Pollard (2011) Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biology and Evolution 3: 516-527

March 9: Roesti et al (2012) Genome divergence during evolutionary diversification as revealed in replicate lake–stream stickleback population pairs. Molecular Ecology doi: 10.1111/j.1365-294X.2012.05509.x

Feb 24: Stringham et al (2012) Divergence, convergence, and the ancestry of feral populations in the domestic rock pigeon. Current Biology 22: 302–308

Feb 17: Gompert et al (2012) Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species. Evolution doi: 10.1111/j.1558-5646.2012.01587.x and Perry et al (2011) Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome research doi:10.1101/gr.130468.111

Feb 10: Branca et al (2011) Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proceedings of the National Academy of Sciences USA 108:E864-70

Feb 3: Hvilsom et al (2012) Extensive X-linked adaptive evolution in central chimpanzees. Proceedings of the National Academy of Sciences USA doi:10.1073/pnas.1106877109

Jan 27: Lorenzen et al (2011) Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479: 359-364

Jan 13: Webster & Hurst (2011) Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends in Genetics doi:10.1016/j.tig.2011.11.002

2011

Dec 19 (Mon): Fournier-Level et al (2011) A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89

Dec 9: Moreau et al (2011) Deep human genealogies reveal a selective advantage to be on an expanding wave front. Science 334: 1148-1150

Dec 2: Venditti et al (2011) Multiple routes to mammalian diversity. Nature 479: 393–396

Nov 11: Gertz et al (2011) Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genetics 7: e1002228

Oct 28: Brawand et al (2011) The evolution of gene expression levels in mammalian organs. Nature 478:343-8

Oct 21: Milot et al (2011) Evidence for evolution in response to natural selection in a contemporary human population. Proceedings of the National Academy of Sciences USA 108:17040-5

Oct 14: Kenney-Hunt & Cheverud (2009) Differential dominance of pleiotropic loci for mouse skeletal traits. Evolution 63: 1845–1851

Oct 7: Alföldi et al (2011) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477: 587–591

Sep 30: Jiang et al (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Research 21: 1543-1551

Sep 16: Abi-Rached et al (2011) The shaping of modern human immune systems by multiregional admixture with archaic humans. Science doi:10.1126/science.1209202

Sep 9: Weetman et al (2011) Gene flow–dependent genomic divergence between Anopheles gambiae M and S forms. Molecular Biology and Evolution doi:10.1093/molbev/msr199

Sep 2: Joron et al (2011) Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry. Nature doi:10.1038/nature10341

Aug 26: Lowe et al (2011) Three periods of regulatory innovation during vertebrate evolution. Science 333: 1019-1024

Aug 19: Rothberg et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352

June 17: Al-Dous et al (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology 29: 521-527

May 27: Nielsen et al (2011) Genotype and SNP calling from next-generation sequencing data. Nature Review Genetics 12: 443-51.

May 20: Cutter & Moses (2011) Polymorphism, divergence, and the role of recombination in Saccharomyces cerevisiae genome evolution. Molecular Biology and Evolution 28: 1745-1754

May 13: Walters & Hardcastle (2011) Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. Genome Biology and Evolution doi:10.1093/gbe/evr036     

May 6: Hopkins & Rausher (2011) Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii. Nature 469: 411–414 

April 29: Keightley et al (2011) Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics 187: 1153-1161

April 15: Markova-Raina & Petrov (2011) High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Research doi:10.1101/gr.115949.110

April 8: Lawniczak et al (2010) Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science 330: 512-514 and Neafsey et al (2010) SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes. Science 330: 514-517

April 1: McLean et al (2011) Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471: 216-219

March 25: Innocenti & Morrow (2010) The sexually antagonistic genes of Drosophila melanogaster. Plos Biology 8:e1000335

March 18: Connallon & Clark (2011) Association between sex-biased gene expression and mutations with sex-specific phenotypic consequences in Drosophila. Genome Biology and Evolution 3: 151-155

March 11: Manceau et al (2011) The developmental role of Agouti in color pattern evolution. Science 331: 1062-1065

March 4: Matute et al (2010) A test of the snowball theory for the rate of evolution of hybrid incompatibilities. Science 329:1518-1521 and Moyle & Nakazato (2010) Hybrid incompatibility “snowballs” between Solanum species. Science 329:1521-1523

Feb 25: Shimada et al (2011) A high incidence of selection on physiologically important genes in the three-spined stickleback, Gasterosteus aculeatus. Molecular Biology and Evolution 28:181-193

Feb 18: Zheng-Bradley et al (2010) Large scale comparison of global gene expression patterns in human and mouse. Genome Biology 11:R124

Feb 11: Hobolth et al (2011) Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Research doi:10.1101/gr.114751.110

Feb 4: Domazet-Loso & Tautz (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468:815-819

Jan 28: Keren et al (2010) Alternative splicing and evolution: diversification, exon definition and function. Nature Review Genetics 11:345-355

Jan 21: Eory et al (2010) Distributions of selectively constrained sites and deleterious mutation rates in the Hominid and Murid genomes. Molecular Biology and Evolution 27:177-192

Jan 14: Szulkin et al (2010) Heterozygosity-fitness correlations: a time for reappraisal. Evolution 64:1207-1217

2010

Dec 17: Roach et al (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328:636-639

Dec 10: Aslam et al (2010) A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes. BMC Genomics 11:647.

Dec 3: Xiong et al (2010) RNA sequencing shows no dosage compensation of the active X-chromosome. Nature Genetics 42:1043-1047.

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Oct 29: Hammer et al (2010) The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nature Genetics 42: 830-832.

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Oct 8: Richards et al (2010) What role does heritable epigenetic variation play in phenotypic evolution. BioScience 60:232-237

Sep 30: Rockman et al (2010) Selection at linked sites shapes heritable phenotypic variation in C. elegans. Science 330:372-375

Sep 13: Boyko et al (2010) A simple genetic architecture underlies morphological variation in dogs. PLoS Biology 8:e1000451.

June 4: Michel et al (2010) Widespread genomic divergence during sympatric speciation. Proceedings of the National Academy of Sciences USA 107:9724-9729.

May 7: Rice et al (2008) Sexually antagonistic “zygotic drive” of the sex chromosomes. PLoS Genetics 4:e1000313.

April 16: Laurent et al (2010) Dynamic changes in the human methylome during differentiation. Genome Research 20:320-331.

April 9: Zhao et al (2010) Somatic sex identity is cell autonomous in the chicken. Nature 464:237-242.

March 26: Rubin et al (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464:587-591.

March 12: Chen et al (2010) Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Research 20:447-457.

March 5: Hohenlohe et al (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RASD tags. PLoS Genetics 6:e1000862.

Feb 27: Presgraves (2010) The molecular evolutionary basis of species formation. Nature Reviews Genetics 11:175-180.

Feb 19: Fisher & Hoekstra (2010) Competition drives cooperation among closely related sperm of deer mice. Nature 463: 801-803.

Feb 12: Naurin et al (2010) Why does dosage compensation differ between XY and ZW taxa? Trends in Genetics 26:15-20.

Feb 5: Li et al (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311-317.

Jan 29: Andrés et al (2009) Targets of balancing selection in the human genome. Molecular Biology and Evolution 26:2755-2764.

Jan 22: Chan et al (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327:302-305.

Jan 15: Hodgkinson & Eyre-Walker (2010) Human triallelic sites: evidence for a new mutational mechanism? Genetics 184:233-241.