Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Gutenkunst, Ryan N.; Hernandez, Ryan D.; Williamson, Scott H.; Bustamante, Carlos D.

doi:10.1371/journal.pgen.1000695

Title: Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Journal Article · Fri Oct 23 00:00:00 EDT 2009 · PLoS Genetics

DOI:https://doi.org/10.1371/journal.pgen.1000695· OSTI ID:1627278

Gutenkunst, Ryan N. ^[1]; Hernandez, Ryan D. ^[2]; Williamson, Scott H. ^[3]; Bustamante, Carlos D. ^[3]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Center for Nonlinear Studies. Theoretical Biology and Biophysics
Univ. of Chicago, IL (United States). Human Genetics
Cornell Univ., Ithaca, NY (United States). Biological Statistics and Computational Biology

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1627278

Journal Information:: PLoS Genetics, Vol. 5, Issue 10; ISSN 1553-7404

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (54)

Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis Hey, Jody; Nielsen, Rasmus Genetics, Vol. 167, Issue 2 https://doi.org/10.1534/genetics.103.024182	journal	June 2004
Ascertainment bias in studies of human genome-wide polymorphism Clark, A. G. Genome Research, Vol. 15, Issue 11 https://doi.org/10.1101/gr.4107905	journal	November 2005
A novel DNA sequence database for analyzing human demographic history Wall, J. D.; Cox, M. P.; Mendez, F. L. Genome Research, Vol. 18, Issue 8 https://doi.org/10.1101/gr.075630.107	journal	August 2008
The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations Marth, Gabor T.; Czabarka, Eva; Murvai, Janos Genetics, Vol. 166, Issue 1 https://doi.org/10.1534/genetics.166.1.351	journal	January 2004
The strong-migration limit in geographically structured populations Nagylaki, Thomas Journal of Mathematical Biology, Vol. 9, Issue 2 https://doi.org/10.1007/BF00275916	journal	April 1980
Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice Caicedo, Ana L.; Williamson, Scott H.; Hernandez, Ryan D. PLoS Genetics, Vol. 3, Issue 9 https://doi.org/10.1371/journal.pgen.0030163	journal	January 2007
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome Boyko, Adam R.; Williamson, Scott H.; Indap, Amit R. PLoS Genetics, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pgen.1000083	journal	May 2008
Can one learn history from the allelic spectrum? Myers, Simon; Fefferman, Charles; Patterson, Nick Theoretical Population Biology, Vol. 73, Issue 3 https://doi.org/10.1016/j.tpb.2008.01.001	journal	May 2008
Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques Hernandez, R. D.; Hubisz, M. J.; Wheeler, D. A. Science, Vol. 316, Issue 5822 https://doi.org/10.1126/science.1140462	journal	April 2007
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Inferring Human Population Sizes, Divergence Times and Rates of Gene Flow From Mitochondrial, X and Y Chromosome Resequencing Data Garrigan, Daniel; Kingan, Sarah B.; Pilkington, Maya M. Genetics, Vol. 177, Issue 4 https://doi.org/10.1534/genetics.107.077495	journal	December 2007
Python for Scientific Computing Oliphant, Travis E. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.58	journal	January 2007
Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow Cox, Murray P.; Woerner, August E.; Wall, Jeffrey D. BMC Genetics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2156-9-76	journal	January 2008
A Genomewide Admixture Map for Latino Populations Price, Alkes L.; Patterson, Nick; Yu, Fuli The American Journal of Human Genetics, Vol. 80, Issue 6 https://doi.org/10.1086/518313	journal	June 2007
On the number of segregating sites in genetical models without recombination Watterson, G. A. Theoretical Population Biology, Vol. 7, Issue 2 https://doi.org/10.1016/0040-5809(75)90020-9	journal	April 1975
Power of deep, all-exon resequencing for discovery of human trait genes Kryukov, G. V.; Shpunt, A.; Stamatoyannopoulos, J. A. Proceedings of the National Academy of Sciences, Vol. 106, Issue 10 https://doi.org/10.1073/pnas.0812824106	journal	February 2009
Updated Three-Stage Model for the Peopling of the Americas Mulligan, Connie J.; Kitchen, Andrew; Miyamoto, Michael M. PLoS ONE, Vol. 3, Issue 9 https://doi.org/10.1371/journal.pone.0003199	journal	September 2008
Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans Keinan, Alon; Mullikin, James C.; Patterson, Nick Nature Genetics, Vol. 39, Issue 10 https://doi.org/10.1038/ng2116	journal	September 2007
Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases Kondrashov, Alexey S. Human Mutation, Vol. 21, Issue 1 https://doi.org/10.1002/humu.10147	journal	December 2002
Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes Voight, B. F.; Adams, A. M.; Frisse, L. A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 51 https://doi.org/10.1073/pnas.0507325102	journal	December 2005
Maximum-Likelihood Estimation of Demographic Parameters Using the Frequency Spectrum of Unlinked Single-Nucleotide Polymorphisms Adams, Alison M.; Hudson, Richard R. Genetics, Vol. 168, Issue 3 https://doi.org/10.1534/genetics.104.030171	journal	November 2004
A Three-Stage Colonization Model for the Peopling of the Americas Kitchen, Andrew; Miyamoto, Michael M.; Mulligan, Connie J. PLoS ONE, Vol. 3, Issue 2 https://doi.org/10.1371/journal.pone.0001596	journal	February 2008
On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas Hey, Jody PLoS Biology, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pbio.0030193	journal	May 2005
Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation Li, J. Z.; Absher, D. M.; Tang, H. Science, Vol. 319, Issue 5866 https://doi.org/10.1126/science.1153717	journal	February 2008
Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes Akey, Joshua M.; Eberle, Michael A.; Rieder, Mark J. PLoS Biology, Vol. 2, Issue 10 https://doi.org/10.1371/journal.pbio.0020286	journal	September 2004
Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies Fenner, Jack N. American Journal of Physical Anthropology, Vol. 128, Issue 2 https://doi.org/10.1002/ajpa.20188	journal	October 2005
Diffusion models in population genetics Kimura, Motoo Journal of Applied Probability, Vol. 1, Issue 02 https://doi.org/10.1017/S0021900200108368	journal	December 1964
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution Hwang, D. G.; Green, P. Proceedings of the National Academy of Sciences, Vol. 101, Issue 39 https://doi.org/10.1073/pnas.0404142101	journal	August 2004
Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection Hernandez, R. D.; Williamson, S. H.; Bustamante, C. D. Molecular Biology and Evolution, Vol. 24, Issue 8 https://doi.org/10.1093/molbev/msm108	journal	April 2007
Pattern of Sequence Variation Across 213 Environmental Response Genes Livingston, R. J. Genome Research, Vol. 14, Issue 10a https://doi.org/10.1101/gr.2730004	journal	September 2004
Darwinian and demographic forces affecting human protein coding genes Nielsen, R.; Hubisz, M. J.; Hellmann, I. Genome Research, Vol. 19, Issue 5 https://doi.org/10.1101/gr.088336.108	journal	March 2009
Calibrating a coalescent simulation of human genome sequence variation Schaffner, S. F. Genome Research, Vol. 15, Issue 11 https://doi.org/10.1101/gr.3709305	journal	November 2005
Genotype, haplotype and copy-number variation in worldwide human populations Jakobsson, Mattias; Scholz, Sonja W.; Scheet, Paul Nature, Vol. 451, Issue 7181 https://doi.org/10.1038/nature06742	journal	February 2008
Going East: New Genetic and Archaeological Perspectives on the Modern Human Colonization of Eurasia Mellars, P. Science, Vol. 313, Issue 5788 https://doi.org/10.1126/science.1128402	journal	August 2006
A practical difference scheme for Fokker-Planck equations Chang, J. S.; Cooper, G. Journal of Computational Physics, Vol. 6, Issue 1 https://doi.org/10.1016/0021-9991(70)90001-X	journal	August 1970
Methods for High-Density Admixture Mapping of Disease Genes Patterson, Nick; Hattangadi, Neil; Lane, Barton The American Journal of Human Genetics, Vol. 74, Issue 5 https://doi.org/10.1086/420871	journal	May 2004
Recent and ongoing selection in the human genome Nielsen, Rasmus; Hellmann, Ines; Hubisz, Melissa Nature Reviews Genetics, Vol. 8, Issue 11 https://doi.org/10.1038/nrg2187	journal	November 2007
Simultaneous inference of selection and population growth from patterns of variation in the human genome Williamson, S. H.; Hernandez, R.; Fledel-Alon, A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 22 https://doi.org/10.1073/pnas.0502300102	journal	May 2005
Consistency of estimators of population scaled parameters using composite likelihood Wiuf, Carsten Journal of Mathematical Biology, Vol. 53, Issue 5 https://doi.org/10.1007/s00285-006-0031-0	journal	September 2006
Residuals in Generalized Linear Models Pierce, Donald A.; Schafer, Daniel W. Journal of the American Statistical Association, Vol. 81, Issue 396 https://doi.org/10.1080/01621459.1986.10478361	journal	December 1986
A Composite-Likelihood Approach for Detecting Directional Selection From DNA Sequence Data Zhu, Lan; Bustamante, Carlos D. Genetics, Vol. 170, Issue 3 https://doi.org/10.1534/genetics.104.035097	journal	May 2005
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences Drummond, A. J. Molecular Biology and Evolution, Vol. 22, Issue 5 https://doi.org/10.1093/molbev/msi103	journal	February 2005
Placing confidence limits on the molecular age of the human-chimpanzee divergence Kumar, S.; Filipski, A.; Swarna, V. Proceedings of the National Academy of Sciences, Vol. 102, Issue 52 https://doi.org/10.1073/pnas.0509585102	journal	December 2005
Y Chromosome Evidence for Anglo-Saxon Mass Migration Weale, Michael E.; Weiss, Deborah A.; Jager, Rolf F. Molecular Biology and Evolution, Vol. 19, Issue 7 https://doi.org/10.1093/oxfordjournals.molbev.a004160	journal	July 2002
The Late Pleistocene Dispersal of Modern Humans in the Americas Goebel, T.; Waters, M. R.; O'Rourke, D. H. Science, Vol. 319, Issue 5869 https://doi.org/10.1126/science.1153569	journal	March 2008
A new approach to estimate parameters of speciation models with application to apes Becquet, C.; Przeworski, M. Genome Research, Vol. 17, Issue 10 https://doi.org/10.1101/gr.6409707	journal	September 2007
New Estimates of Intergenerational Time Intervals for the Calculation of Age and Origins of Mutations Tremblay, Marc; Vézina, Hélène The American Journal of Human Genetics, Vol. 66, Issue 2 https://doi.org/10.1086/302770	journal	February 2000
Residuals in Generalized Linear Models Pierce, Donald A.; Schafer, Daniel W. Journal of the American Statistical Association, Vol. 81, Issue 396 https://doi.org/10.2307/2289071	journal	December 1986
Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data Nielsen, Rasmus; Hubisz, Melissa J.; Clark, Andrew G. Genetics, Vol. 168, Issue 4 https://doi.org/10.1534/genetics.104.031039	journal	September 2004
Generating samples under a Wright-Fisher neutral model of genetic variation Hudson, R. R. Bioinformatics, Vol. 18, Issue 2 https://doi.org/10.1093/bioinformatics/18.2.337	journal	February 2002
Population genetics of polymorphism and divergence. Sawyer, S. A.; Hartl, D. L. Genetics, Vol. 132, Issue 4 https://doi.org/10.1093/genetics/132.4.1161	journal	December 1992
Directional Selection and the Site-Frequency Spectrum Bustamante, Carlos D.; Wakeley, John; Sawyer, Stanley Genetics, Vol. 159, Issue 4 https://doi.org/10.1093/genetics/159.4.1779	journal	December 2001
Inference of Population Structure Using Multilocus Genotype Data Pritchard, Jonathan K.; Stephens, Matthew; Donnelly, Peter Genetics, Vol. 155, Issue 2 https://doi.org/10.1093/genetics/155.2.945	journal	June 2000
The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Braverman, J. M.; Hudson, R. R.; Kaplan, N. L. Genetics, Vol. 140, Issue 2 https://doi.org/10.1093/genetics/140.2.783	journal	June 1995

Cited By (385)

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it: Prospects & Overviews Lachance, Joseph; Tishkoff, Sarah A. BioEssays, Vol. 35, Issue 9 https://doi.org/10.1002/bies.201300014	journal	July 2013
Population Genetics and Objectivity in Species Diagnosis: Population Genetics and Species Diagnosis Hey, Jody; Pinho, Catarina Evolution, Vol. 66, Issue 5 https://doi.org/10.1111/j.1558-5646.2011.01542.x	journal	January 2012
The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin Mousavi-Derazmahalleh, Mahsa; Nevado, Bruno; Bayer, Philipp E. Theoretical and Applied Genetics, Vol. 131, Issue 12 https://doi.org/10.1007/s00122-018-3171-x	journal	September 2018
Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow Ravinet, M.; Faria, R.; Butlin, R. K. Journal of Evolutionary Biology, Vol. 30, Issue 8 https://doi.org/10.1111/jeb.13047	journal	August 2017
Pleistocene climatic changes drive diversification across a tropical savanna Potter, Sally; Xue, Alexander T.; Bragg, Jason G. Molecular Ecology, Vol. 27, Issue 2 https://doi.org/10.1111/mec.14441	journal	December 2017
Evolution of barrier loci at an intermediate stage of speciation with gene flow Liu, Xiaodong; Glémin, Sylvain; Karrenberg, Sophie National Institutes of Health https://doi.org/10.1101/703108	posted_content	January 2019
Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach Chan, Kin Onn; Brown, Rafe M. Zoological Journal of the Linnean Society, Vol. 190, Issue 1 https://doi.org/10.1093/zoolinnean/zlz151	journal	November 2019
Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent Imamura, Hideo; Downing, Tim; Van den Broeck, Frederik eLife, Vol. 5 https://doi.org/10.7554/elife.12613	journal	March 2016
A reference genome for common bean and genome-wide analysis of dual domestications Schmutz, Jeremy; McClean, Phillip E.; Mamidi, Sujan Nature Genetics, Vol. 46, Issue 7 https://doi.org/10.1038/ng.3008	journal	June 2014
Exploring population size changes using SNP frequency spectra Liu, Xiaoming; Fu, Yun-Xin Nature Genetics, Vol. 47, Issue 5 https://doi.org/10.1038/ng.3254	journal	April 2015
Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth Martin, Christopher H.; Crawford, Jacob E.; Turner, Bruce J. Proceedings of the Royal Society B: Biological Sciences, Vol. 283, Issue 1823 https://doi.org/10.1098/rspb.2015.2334	journal	January 2016
Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period Sjödin, Per; E. Sjöstrand, Agnès; Jakobsson, Mattias Molecular Biology and Evolution, Vol. 29, Issue 7 https://doi.org/10.1093/molbev/mss061	journal	February 2012
Genome-wide single nucleotide polymorphism scan suggests adaptation to urbanization in an important pollinator, the red-tailed bumblebee ( Bombus lapidarius L.) Theodorou, Panagiotis; Radzevičiūtė, Rita; Kahnt, Belinda Proceedings of the Royal Society B: Biological Sciences, Vol. 285, Issue 1877 https://doi.org/10.1098/rspb.2017.2806	journal	April 2018
Genomic resources and their influence on the detection of the signal of positive selection in genome scans Manel, S.; Perrier, C.; Pratlong, M. Molecular Ecology, Vol. 25, Issue 1 https://doi.org/10.1111/mec.13468	journal	December 2015
Variation of the adaptive substitution rate between species and within genomes Moutinho, Ana Filipa; Bataillon, Thomas; Dutheil, Julien Y. Evolutionary Ecology, Vol. 34, Issue 3 https://doi.org/10.1007/s10682-019-10026-z	journal	December 2019
Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island Choi, Jae Young; Purugganan, Michael; Stacy, Elizabeth A. Molecular Biology https://doi.org/10.1101/698225	posted_content	January 2019
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event Winker, Kevin; Glenn, Travis C.; Faircloth, Brant C. PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5735	journal	January 2018
Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies ( Zea mays parviglumis and Zea mays mexicana ) Aguirre‐Liguori, Jonás A.; Gaut, Brandon S.; Jaramillo‐Correa, Juan Pablo Molecular Ecology https://doi.org/10.1111/mec.15098	journal	June 2019
Demographic History of the Human Commensal Drosophila melanogaster Arguello, J. Roman; Laurent, Stefan; Clark, Andrew G. Genome Biology and Evolution, Vol. 11, Issue 3 https://doi.org/10.1093/gbe/evz022	journal	January 2019
Exploring Approximate Bayesian Computation for inferring recent demographic history with genomic markers in nonmodel species Elleouet, Joane S.; Aitken, Sally N. Molecular Ecology Resources, Vol. 18, Issue 3 https://doi.org/10.1111/1755-0998.12758	journal	February 2018
Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna Wong, Edgar L. Y.; Nevado, Bruno; Osborne, Owen G. Molecular Ecology, Vol. 29, Issue 2 https://doi.org/10.1111/mec.15319	journal	December 2019
A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig Bianco, Erica; Nevado, Bruno; Ramos-Onsins, Sebastián E. PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0118867	journal	March 2015
Demographic model selection using random forests and the site frequency spectrum Smith, Megan L.; Ruffley, Megan; Espíndola, Anahí Molecular Ecology, Vol. 26, Issue 17 https://doi.org/10.1111/mec.14223	journal	July 2017
The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps Mosca, E.; Eckert, A. J.; Di Pierro, E. A. Molecular Ecology, Vol. 21, Issue 22 https://doi.org/10.1111/mec.12043	journal	October 2012
Genetic isolation between two recently diverged populations of a symbiotic fungus Branco, Sara; Gladieux, Pierre; Ellison, Christopher E. Molecular Ecology, Vol. 24, Issue 11 https://doi.org/10.1111/mec.13132	journal	April 2015
Recent Progress in Polymorphism-Based Population Genetic Inference Crisci, Jessica L.; Poh, Yu-Ping; Bean, Angela Journal of Heredity, Vol. 103, Issue 2 https://doi.org/10.1093/jhered/esr128	journal	January 2012
Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe Mattingsdal, Morten; Jorde, Per Erik; Knutsen, Halvor Molecular Ecology, Vol. 29, Issue 1 https://doi.org/10.1111/mec.15310	journal	October 2019
Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia Fulgione, Andrea; Koornneef, Maarten; Roux, Fabrice Molecular Biology and Evolution, Vol. 35, Issue 3 https://doi.org/10.1093/molbev/msx300	journal	December 2017
Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting Tyrmi, Jaakko S.; Vuosku, Jaana; Acosta, Juan J. G3: Genes\|Genomes\|Genetics https://doi.org/10.1101/647412	posted_content	January 2019
How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data Fagundes, Nelson J. R.; Tagliani-Ribeiro, Alice; Rubicz, Rohina Genetics and Molecular Biology, Vol. 41, Issue 1 suppl 1 https://doi.org/10.1590/1678-4685-gmb-2017-0087	journal	January 2018
Recent population genomic insights into the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations Apata, Mario; Pfeifer, Susanne P. Heredity, Vol. 124, Issue 2 https://doi.org/10.1038/s41437-019-0285-0	journal	November 2019
Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia Parobek, Christian M.; Lin, Jessica T.; Saunders, David L. Proceedings of the National Academy of Sciences, Vol. 113, Issue 50 https://doi.org/10.1073/pnas.1608828113	journal	November 2016
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis Bryant, David; Bouckaert, Remco; Felsenstein, Joseph Molecular Biology and Evolution, Vol. 29, Issue 8 https://doi.org/10.1093/molbev/mss086	journal	March 2012
New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era Gao, Feng; Ming, Chen; Hu, Wangjie G3: Genes\|Genomes\|Genetics, Vol. 6, Issue 6 https://doi.org/10.1534/g3.116.028233	journal	March 2016
When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis Leroy, Thibault; Caffier, Valérie; Celton, Jean‐Marc New Phytologist, Vol. 210, Issue 4 https://doi.org/10.1111/nph.13873	journal	February 2016
Genomic Data Reveal a Complex Making of Humans Alves, Isabel; Šrámková Hanulová, Anna; Foll, Matthieu PLoS Genetics, Vol. 8, Issue 7 https://doi.org/10.1371/journal.pgen.1002837	journal	July 2012
WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data Foll, Matthieu; Shim, Hyunjin; Jensen, Jeffrey D. Molecular Ecology Resources https://doi.org/10.1101/009696	posted_content	September 2014
Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia Chen, Ningbo; Cai, Yudong; Chen, Qiuming Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04737-0	journal	June 2018
Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group Fouet, Caroline; Kamdem, Colince; Gamez, Stephanie Evolutionary Applications, Vol. 10, Issue 9 https://doi.org/10.1111/eva.12492	journal	June 2017
Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations Lorente-Galdos, Belen; Lao, Oscar; Serra-Vidal, Gerard Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1684-5	journal	April 2019
The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States Massatti, Rob; Knowles, L. Lacey Ecography, Vol. 43, Issue 5 https://doi.org/10.1111/ecog.04840	journal	January 2020
Divergence of tropical pitvipers promoted by independent colonization events of dry montane Andean habitats Salazar‐Valenzuela, David; Kuch, Ulrich; Torres‐Carvajal, Omar Journal of Biogeography, Vol. 46, Issue 8 https://doi.org/10.1111/jbi.13661	journal	April 2019
Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon Shapiro, M. D.; Kronenberg, Z.; Li, C. Science, Vol. 339, Issue 6123 https://doi.org/10.1126/science.1230422	journal	January 2013
The demographic history and mutational load of African hunter-gatherers and farmers Lopez, Marie; Kousathanas, Athanasios; Quach, Hélène Nature Ecology & Evolution https://doi.org/10.1101/131219	posted_content	May 2017
PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data Liu, Shenglin; Hansen, Michael M. Molecular Ecology Resources, Vol. 17, Issue 4 https://doi.org/10.1111/1755-0998.12606	journal	October 2016
Higher Levels of Neanderthal Ancestry in East Asians than in Europeans Wall, Jeffrey D.; Yang, Melinda A.; Jay, Flora Genetics, Vol. 194, Issue 1 https://doi.org/10.1534/genetics.112.148213	journal	May 2013
Modeling the Multiple Facets of Speciation-with-Gene-Flow Towards Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus Clupeaformis) Rougeux, Clement; Bernatchez, Louis; Gagnaire, Pierre-Alexandre Genome Biology and Evolution https://doi.org/10.1101/068932	posted_content	December 2016
Early split between African and European populations of Drosophila melanogaster Kapopoulou, Adamandia; Kapun, Martin; Pavlidis, Pavlos Research Gate https://doi.org/10.1101/340422	posted_content	January 2018
Inferring Demographic History Using Two-Locus Statistics Ragsdale, Aaron P.; Gutenkunst, Ryan N. Genetics, Vol. 206, Issue 2 https://doi.org/10.1534/genetics.117.201251	journal	June 2017
Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach Boitard, Simon; Rodríguez, Willy; Jay, Flora PLOS Genetics, Vol. 12, Issue 3 https://doi.org/10.1371/journal.pgen.1005877	journal	March 2016
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark Dierickx, Elisa G.; Sin, Simon Yung Wa; van Veelen, H. Pieter J. Proceedings of the Royal Society B: Biological Sciences, Vol. 287, Issue 1922 https://doi.org/10.1098/rspb.2019.2613	journal	March 2020
The origin and adaptive evolution of domesticated populations of yeast from Far East Asia Duan, Shou-Fu; Han, Pei-Jie; Wang, Qi-Ming Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05106-7	journal	July 2018
Model‐based demographic inference of introgression history in European whitefish species pairs' Rougeux, Clément; Gagnaire, Pierre‐Alexandre; Bernatchez, Louis Journal of Evolutionary Biology, Vol. 32, Issue 8 https://doi.org/10.1111/jeb.13482	journal	May 2019
Exploring rain forest diversification using demographic model testing in the African foam‐nest treefrog Chiromantis rufescens Leaché, Adam D.; Portik, Daniel M.; Rivera, Danielle Journal of Biogeography, Vol. 46, Issue 12 https://doi.org/10.1111/jbi.13716	journal	October 2019
No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt ( Lissotriton montandoni ) Zieliński, P.; Nadachowska-Brzyska, K.; Wielstra, B. Molecular Ecology, Vol. 22, Issue 7 https://doi.org/10.1111/mec.12225	journal	February 2013
Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau Li, Long; Abbott, Richard J.; Liu, Bingbing Molecular Ecology, Vol. 22, Issue 20 https://doi.org/10.1111/mec.12466	journal	October 2013
Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares Jones, Matthew R.; Mills, L. Scott; Alves, Paulo Célio Science, Vol. 360, Issue 6395 https://doi.org/10.1126/science.aar5273	journal	June 2018
On the relative ease of speciation with periodic gene flow Linck, Ethan; Battey, C. J. Semantic Scholar https://doi.org/10.1101/758664	posted_content	January 2019
ABLE: blockwise site frequency spectra for inferring complex population histories and recombination Beeravolu, Champak R.; Hickerson, Michael J.; Frantz, Laurent A. F. Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1517-y	journal	September 2018
Population transcriptomes reveal synergistic responses of DNA polymorphism and RNA expression to extreme environments on the Qinghai-Tibetan Plateau in a predatory bird Pan, Shengkai; Zhang, Tongzuo; Rong, Zhengqin Molecular Ecology, Vol. 26, Issue 11 https://doi.org/10.1111/mec.14090	journal	April 2017
The Power to Detect Quantitative Trait Loci Using Resequenced, Experimentally Evolved Populations of Diploid, Sexual Organisms Baldwin-Brown, James G.; Long, Anthony D.; Thornton, Kevin R. Molecular Biology and Evolution, Vol. 31, Issue 4 https://doi.org/10.1093/molbev/msu048	journal	January 2014
Efficiently inferring the demographic history of many populations with allele count data. Kamm, Jack; Terhorst, Jonathan; Durbin, Richard Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.41076	text	January 2020
Robust Demographic Inference from Genomic and SNP Data Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia PLoS Genetics, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pgen.1003905	journal	October 2013
Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is linked to behavioral differentiation Provost, Kaiya L.; Mauck, William M.; Smith, Brian Tilston Ecology and Evolution https://doi.org/10.1002/ece3.4596	journal	December 2018
The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus Herman, Adam; Brandvain, Yaniv; Weagley, James Molecular Ecology, Vol. 27, Issue 22 https://doi.org/10.1111/mec.14877	journal	October 2018
Computationally Efficient Composite Likelihood Statistics for Demographic Inference Coffman, Alec J.; Hsieh, Ping Hsun; Gravel, Simon Molecular Biology and Evolution, Vol. 33, Issue 2 https://doi.org/10.1093/molbev/msv255	journal	November 2015
Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes Rougemont, Quentin; Gagnaire, Pierre-Alexandre; Perrier, Charles Molecular Ecology, Vol. 26, Issue 1 https://doi.org/10.1111/mec.13664	journal	July 2016
WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data Foll, Matthieu; Shim, Hyunjin; Jensen, Jeffrey D. Molecular Ecology Resources, Vol. 15, Issue 1 https://doi.org/10.1111/1755-0998.12280	journal	June 2014
“Ghost Introgression” As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex Zhang, Dezhi; Tang, Linfang; Cheng, Yalin Molecular Biology and Evolution, Vol. 36, Issue 11 https://doi.org/10.1093/molbev/msz170	journal	July 2019
Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement Lu, Kun; Wei, Lijuan; Li, Xiaolong Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09134-9	journal	March 2019
Time Dependency of Molecular Evolutionary Rates? Yes and No Subramanian, Sankar; Lambert, David M. Genome Biology and Evolution, Vol. 3 https://doi.org/10.1093/gbe/evr108	journal	January 2011
Convergence in form and function overcomes non-parallel evolutionary histories in a Holarctic fish Jacobs, Arne; Carruthers, Madeleine; Yurchenko, Andrey PLOS Genetics https://doi.org/10.1101/265272	posted_content	January 2019
Bee conservation in the age of genomics Lozier, Jeffrey D.; Zayed, Amro Conservation Genetics, Vol. 18, Issue 3 https://doi.org/10.1007/s10592-016-0893-7	journal	October 2016
Phylogeography of a widespread eastern North American shrub, Viburnum lantanoides Park, Brian; Donoghue, Michael J. American Journal of Botany, Vol. 106, Issue 3 https://doi.org/10.1002/ajb2.1248	journal	March 2019
Archaeological and genetic insights into the origins of domesticated rice Gross, B. L.; Zhao, Z. Proceedings of the National Academy of Sciences, Vol. 111, Issue 17 https://doi.org/10.1073/pnas.1308942110	journal	April 2014
Mito-nuclear discordance across a recent contact zone for California voles Lin, Dana; Bi, Ke; Conroy, Christopher J. Ecology and Evolution, Vol. 8, Issue 12 https://doi.org/10.1002/ece3.4129	journal	May 2018
Genomic parallelism and lack thereof in contrasting systems of three-spined sticklebacks Liu, Shenglin; Ferchaud, Anne-Laure; Grønkjaer, Peter Molecular Ecology, Vol. 27, Issue 23 https://doi.org/10.1111/mec.14782	journal	July 2018
The global diversity of the major parasitic nematode Haemonchus contortus is shaped by human intervention and climate Sallé, G.; Doyle, S. R.; Cortet, J. https://doi.org/10.1101/450692	posted_content	April 2019
Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen Kelly, Amy C.; Ward, Todd J. PLOS ONE, Vol. 13, Issue 3 https://doi.org/10.1371/journal.pone.0194616	journal	March 2018
On the origins and domestication of the olive: a review and perspectives Besnard, Guillaume; Terral, Jean-Frédéric; Cornille, Amandine Annals of Botany, Vol. 121, Issue 3 https://doi.org/10.1093/aob/mcx145	journal	January 2017
EVIDENCE OF ADAPTATION FROM ANCESTRAL VARIATION IN YOUNG POPULATIONS OF BEACH MICE: EVOLUTION OF A BENEFICIAL ALLELE IN PEROMYSCUS Domingues, Vera S.; Poh, Yu-Ping; Peterson, Brant K. Evolution, Vol. 66, Issue 10 https://doi.org/10.1111/j.1558-5646.2012.01669.x	journal	May 2012
Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps Jacobs, Guy S.; Sluckin, Timothy J.; Kivisild, Toomas Genetics, Vol. 203, Issue 4 https://doi.org/10.1534/genetics.115.185900	journal	August 2016
Joint estimation of contamination, error and demography for nuclear DNA from ancient humans Racimo, Fernando; Renaud, Gabriel; Slatkin, Montgomery PLOS Genetics https://doi.org/10.1101/022285	posted_content	January 2016
The population genomics of plant adaptation Siol, Mathieu; Wright, Stephen I.; Barrett, Spencer C. H. New Phytologist, Vol. 188, Issue 2 https://doi.org/10.1111/j.1469-8137.2010.03401.x	journal	August 2010
Impact of demography on linked selection in two outcrossing Brassicaceae species Mattila, Tiina M.; Laenen, Benjamin; Horvath, Robert Ecology and Evolution, Vol. 9, Issue 17 https://doi.org/10.1002/ece3.5463	journal	August 2019
Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa Kavembe, Geraldine D.; Kautt, Andreas F.; Machado-Schiaffino, Gonzalo Molecular Ecology, Vol. 25, Issue 7 https://doi.org/10.1111/mec.13461	journal	January 2016
Classic Selective Sweeps Were Rare in Recent Human Evolution Hernandez, R. D.; Kelley, J. L.; Elyashiv, E. Science, Vol. 331, Issue 6019 https://doi.org/10.1126/science.1198878	journal	February 2011
The genomics of selection in dogs and the parallel evolution between dogs and humans Wang, Guo-dong; Zhai, Weiwei; Yang, He-chuan Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms2814	journal	May 2013
Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations Kamm, John A.; Terhorst, Jonathan; Song, Yun S. Journal of Computational and Graphical Statistics, Vol. 26, Issue 1 https://doi.org/10.1080/10618600.2016.1159212	journal	January 2017
Gene flow in the anemone Anthopleura elegantissima limits signatures of local adaptation across an extensive geographic range Cornwell, Brendan H. Molecular Ecology, Vol. 29, Issue 14 https://doi.org/10.1111/mec.15506	journal	July 2020
Searching for Sympatric Speciation in the Genomic Era Richards, Emilie J.; Servedio, Maria R.; Martin, Christopher H. BioEssays, Vol. 41, Issue 7 https://doi.org/10.1002/bies.201900047	journal	June 2019
Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers Sikora, Martin; Seguin-Orlando, Andaine; Sousa, Vitor C. Science, Vol. 358, Issue 6363 https://doi.org/10.1126/science.aao1807	journal	October 2017
Genetic Evidence of Paleolithic Colonization and Neolithic Expansion of Modern Humans on the Tibetan Plateau Qi, Xuebin; Cui, Chaoying; Peng, Yi Molecular Biology and Evolution, Vol. 30, Issue 8 https://doi.org/10.1093/molbev/mst093	journal	May 2013
Understanding the origin of species with genome-scale data: modelling gene flow Sousa, Vitor; Hey, Jody Nature Reviews Genetics, Vol. 14, Issue 6 https://doi.org/10.1038/nrg3446	journal	May 2013
Receding ice drove parallel expansions in Southern Ocean penguins Cole, Theresa L.; Dutoit, Ludovic; Dussex, Nicolas Proceedings of the National Academy of Sciences, Vol. 116, Issue 52 https://doi.org/10.1073/pnas.1904048116	journal	December 2019
Speciation with gene flow: Evidence from a complex of alpine butterflies ( Coenonympha , Satyridae) Capblancq, Thibaut; Mavárez, Jesús; Rioux, Delphine Ecology and Evolution, Vol. 9, Issue 11 https://doi.org/10.1002/ece3.5220	journal	May 2019
Efficiently Inferring the Demographic History of Many Populations With Allele Count Data Kamm, Jack; Terhorst, Jonathan; Durbin, Richard Journal of the American Statistical Association, Vol. 115, Issue 531 https://doi.org/10.1080/01621459.2019.1635482	journal	July 2019
The aggregate site frequency spectrum for comparative population genomic inference Xue, Alexander T.; Hickerson, Michael J. Molecular Ecology, Vol. 24, Issue 24 https://doi.org/10.1111/mec.13447	journal	December 2015
Genomic approaches for studying crop evolution Schreiber, Mona; Stein, Nils; Mascher, Martin Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1528-8	journal	September 2018
A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation Moyle, Robert G.; Manthey, Joseph D.; Hosner, Peter A. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3335	journal	January 2017
Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review Cayuela, Hugo; Rougemont, Quentin; Prunier, Jérôme G. Molecular Ecology, Vol. 27, Issue 20 https://doi.org/10.1111/mec.14848	journal	September 2018
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards Brandley, Matthew C.; Bragg, Jason G.; Singhal, Sonal BMC Evolutionary Biology, Vol. 15, Issue 1 https://doi.org/10.1186/s12862-015-0318-0	journal	April 2015
Inference of population splits and mixtures from genome-wide allele frequency data Pickrell, Joseph; Pritchard, Jonathan Nature Precedings https://doi.org/10.1038/npre.2012.6956.1	journal	March 2012
Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins Raposo do Amaral, Fabio; Maldonado-Coelho, Marcos; Aleixo, Alexandre Molecular Ecology, Vol. 27, Issue 20 https://doi.org/10.1111/mec.14843	journal	September 2018
Rapid niche expansion by selection on functional genomic variation after ecosystem recovery Jacobs, Arne; Carruthers, Madeleine; Eckmann, Reiner Nature Ecology & Evolution, Vol. 3, Issue 1 https://doi.org/10.1038/s41559-018-0742-9	journal	December 2018
Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference van Dorp, Lucy; Balding, David; Myers, Simon PLOS Genetics, Vol. 11, Issue 8 https://doi.org/10.1371/journal.pgen.1005397	journal	August 2015
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection Lam, Hon-Ming; Xu, Xun; Liu, Xin Nature Genetics, Vol. 42, Issue 12 https://doi.org/10.1038/ng.715	journal	November 2010
Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference Quinto-Cortés, Consuelo D.; Woerner, August E.; Watkins, Joseph C. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28539-y	journal	July 2018
Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs Chan, Kin Onn; Alexander, Alana M.; Grismer, L. Lee Molecular Ecology, Vol. 26, Issue 20 https://doi.org/10.1111/mec.14296	journal	September 2017
Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations Alcala, Nicolas; Vuilleumier, Séverine Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1794 https://doi.org/10.1098/rspb.2014.1369	journal	November 2014
Climate change and human colonization triggered habitat loss and fragmentation in Madagascar Salmona, Jordi; Heller, Rasmus; Quéméré, Erwan Molecular Ecology, Vol. 26, Issue 19 https://doi.org/10.1111/mec.14173	journal	June 2017
A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data Mather, Niklas; Traves, Samuel M.; Ho, Simon Y. W. Ecology and Evolution, Vol. 10, Issue 1 https://doi.org/10.1002/ece3.5888	journal	December 2019
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia Rasmussen, M.; Guo, X.; Wang, Y. Science, Vol. 334, Issue 6052 https://doi.org/10.1126/science.1211177	journal	September 2011
Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species Nunziata, Schyler O.; Lance, Stacey L.; Scott, David E. Molecular Ecology, Vol. 26, Issue 4 https://doi.org/10.1111/mec.13988	journal	January 2017
Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation Jouganous, Julien; Long, Will; Ragsdale, Aaron P. Genetics, Vol. 206, Issue 3 https://doi.org/10.1534/genetics.117.200493	journal	May 2017
Understanding rare and common diseases in the context of human evolution Quintana-Murci, Lluis Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1093-y	journal	November 2016
How to fail at species delimitation Carstens, Bryan C.; Pelletier, Tara A.; Reid, Noah M. Molecular Ecology, Vol. 22, Issue 17 https://doi.org/10.1111/mec.12413	journal	July 2013
A genomic history of Aboriginal Australia. Malaspinas, Anna-Sapfo; Westaway, Michael C.; Muller, Craig Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.30300	text	January 2016
Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape Hotaling, Scott; Muhlfeld, Clint C.; Giersch, J. Joseph Journal of Biogeography, Vol. 45, Issue 2 https://doi.org/10.1111/jbi.13125	journal	November 2017
Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants Keinan, A.; Clark, A. G. Science, Vol. 336, Issue 6082 https://doi.org/10.1126/science.1217283	journal	May 2012
Sky, sea, and forest islands: Diversification in the African leaf‐folding frog Afrixalus paradorsalis (Anura: Hyperoliidae) of the Lower Guineo‐Congolian rain forest Charles, Kristin L.; Bell, Rayna C.; Blackburn, David C. Journal of Biogeography, Vol. 45, Issue 8 https://doi.org/10.1111/jbi.13365	journal	June 2018
Extensive recent secondary contacts between four European white oak species Leroy, Thibault; Roux, Camille; Villate, Laure New Phytologist, Vol. 214, Issue 2 https://doi.org/10.1111/nph.14413	journal	January 2017
Genomic variation associated with local adaptation of weedy rice during de-domestication Qiu, Jie; Zhou, Yongjun; Mao, Lingfeng Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15323	journal	May 2017
Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. ‘macula’ Takuno, Shohei; Miyagi, Ryutaro; Onami, Jun-ichi BMC Evolutionary Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s12862-019-1387-2	journal	March 2019
Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians Barratt, Christopher D.; Bwong, Beryl A.; Jehle, Robert Molecular Ecology, Vol. 27, Issue 21 https://doi.org/10.1111/mec.14862	journal	October 2018
Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species ( Coffea mauritiana ) in Reunion Island Garot, Edith; Joët, Thierry; Combes, Marie‐Christine New Phytologist, Vol. 224, Issue 2 https://doi.org/10.1111/nph.16052	journal	June 2019
Best available science still supports an ancient common origin of Devils Hole and Devils Hole pupfish Sağlam, İsmail K.; Baumsteiger, Jason; Smith, Matt J. Molecular Ecology, Vol. 27, Issue 4 https://doi.org/10.1111/mec.14502	journal	February 2018
Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution Van Belleghem, Steven M.; Vangestel, Carl; De Wolf, Katrien PLOS Genetics, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pgen.1007796	journal	November 2018
Genomic Identification of Founding Haplotypes Reveals the History of the Selfing Species Capsella rubella Brandvain, Yaniv; Slotte, Tanja; Hazzouri, Khaled M. PLoS Genetics, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pgen.1003754	journal	September 2013
The global diversity of Haemonchus contortus is shaped by human intervention and climate Sallé, G.; Doyle, S. R.; Cortet, J. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12695-4	journal	October 2019
Coupling Wright-Fisher and coalescent dynamics for realistic simulation of population-scale datasets Nelson, Dominic; Kelleher, Jerome; Ragsdale, Aaron P. PLOS Genetics https://doi.org/10.1101/674440	posted_content	June 2019
Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Li, Junrui; Li, Haipeng; Jakobsson, Mattias Molecular Ecology, Vol. 21, Issue 1 https://doi.org/10.1111/j.1365-294x.2011.05308.x	journal	October 2011
Bayesian inference of ancient human demography from individual genome sequences Gronau, Ilan; Hubisz, Melissa J.; Gulko, Brad Nature Genetics, Vol. 43, Issue 10 https://doi.org/10.1038/ng.937	journal	September 2011
Adaptive Landscape of Protein Variation in Human Exomes Patel, Ravi; Scheinfeldt, Laura B.; Sanderford, Maxwell D. Molecular Biology and Evolution, Vol. 35, Issue 8 https://doi.org/10.1093/molbev/msy107	journal	May 2018
Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters Sard, Nicholas; Robinson, John; Kanefsky, Jeannette Evolutionary Applications, Vol. 12, Issue 5 https://doi.org/10.1111/eva.12779	journal	January 2019
Estimating heritability of complex traits in admixed populations with summary statistics Luo, Yang; Li, Xinyi; Wang, Xin Human Molecular Genetics https://doi.org/10.1101/503144	posted_content	January 2018
Genomics advances the study of inbreeding depression in the wild Kardos, Marty; Taylor, Helen R.; Ellegren, Hans Evolutionary Applications, Vol. 9, Issue 10 https://doi.org/10.1111/eva.12414	journal	October 2016
Evolutionary perspectives on polygenic selection, missing heritability, and GWAS Uricchio, Lawrence H. Human Genetics, Vol. 139, Issue 1 https://doi.org/10.1007/s00439-019-02040-6	journal	June 2019
Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins Carmi, Shai; Hui, Ken Y.; Kochav, Ethan Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5835	journal	September 2014
Unbiased estimation of linkage disequilibrium from unphased data Ragsdale, Aaron P.; Gravel, Simon Molecular Biology and Evolution https://doi.org/10.1101/557488	posted_content	January 2019
Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation Gray, Levi N.; Barley, Anthony J.; Poe, Steven Molecular Ecology, Vol. 28, Issue 3 https://doi.org/10.1111/mec.14970	journal	February 2019
Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry Shriner, Daniel; Tekola-Ayele, Fasil; Adeyemo, Adebowale Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep06055	journal	August 2014
The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference Flagel, Lex; Brandvain, Yaniv; Schrider, Daniel R. Molecular Biology and Evolution, Vol. 36, Issue 2 https://doi.org/10.1093/molbev/msy224	journal	December 2018
Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow Christe, Camille; Stölting, Kai N.; Paris, Margot Molecular Ecology, Vol. 26, Issue 1 https://doi.org/10.1111/mec.13765	journal	August 2016
Disruptive selection without genome-wide evolution across a migratory divide von Rönn, Jan A. C.; Shafer, Aaron B. A.; Wolf, Jochen B. W. Molecular Ecology, Vol. 25, Issue 11 https://doi.org/10.1111/mec.13521	journal	March 2016
Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models Sousa, Vitor C.; Carneiro, Miguel; Ferrand, Nuno Genetics, Vol. 194, Issue 1 https://doi.org/10.1534/genetics.113.149211	journal	May 2013
Tropical specialist vs. climate generalist: Diversification and demographic history of sister species of Carlia skinks from northwestern Australia Afonso Silva, Ana C.; Bragg, Jason G.; Potter, Sally Molecular Ecology, Vol. 26, Issue 15 https://doi.org/10.1111/mec.14185	journal	June 2017
Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes Alza, Luis; Lavretsky, Philip; Peters, Jeffrey L. Ecology and Evolution, Vol. 9, Issue 17 https://doi.org/10.1002/ece3.5538	journal	August 2019
Recent advances in conservation and population genomics data analysis Hendricks, Sarah; Anderson, Eric C.; Antao, Tiago Evolutionary Applications, Vol. 11, Issue 8 https://doi.org/10.1111/eva.12659	journal	August 2018
A Genetic Atlas of Human Admixture History Hellenthal, G.; Busby, G. B. J.; Band, G. Science, Vol. 343, Issue 6172 https://doi.org/10.1126/science.1243518	journal	February 2014
Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass Wang, Le; Wan, Zi Yi; Lim, Huan Sein Molecular Ecology, Vol. 25, Issue 15 https://doi.org/10.1111/mec.13714	journal	July 2016
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals Vernot, B.; Tucci, S.; Kelso, J. Science, Vol. 352, Issue 6282 https://doi.org/10.1126/science.aad9416	journal	March 2016
Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions Weldenegodguad, Melak; Popov, Ruslan; Pokharel, Kisun Frontiers in Genetics https://doi.org/10.1101/390369	posted_content	January 2018
The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments Ferchaud, Anne-Laure; Hansen, Michael M. Molecular Ecology, Vol. 25, Issue 1 https://doi.org/10.1111/mec.13399	journal	November 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 Shafer, Aaron B. A.; Gattepaille, Lucie M.; Stewart, Robert E. A. Molecular Ecology, Vol. 24, Issue 2 https://doi.org/10.1111/mec.13034	journal	January 2015
The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression Jacobs, Arne; Hughes, Martin; Robinson, Paige Genes, Vol. 9, Issue 6 https://doi.org/10.3390/genes9060280	journal	May 2018
On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference? Mazet, O.; Rodríguez, W.; Grusea, S. Heredity, Vol. 116, Issue 4 https://doi.org/10.1038/hdy.2015.104	journal	December 2015
Genomic inferences of domestication events are corroborated by written records in Brassica rapa Qi, Xinshuai; An, Hong; Ragsdale, Aaron P. Molecular Ecology, Vol. 26, Issue 13 https://doi.org/10.1111/mec.14131	journal	May 2017
Analysis of genome-wide differentiation between native and introduced populations of the cupped oysters Crassostrea gigas and Crassostrea angulata Gagnaire, Pierre-Alexandre; Lamy, Jean-Baptiste; Cornette, Florence Genome Biology and Evolution https://doi.org/10.1101/292144	posted_content	March 2018
Global drivers of diversification in a marine species complex Silva, Catarina N. S.; Murphy, Nicholas P.; Bell, James J. https://doi.org/10.1101/2019.12.13.874883	posted_content	December 2019
The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation Martin, Christopher H.; Höhna, Sebastian; Crawford, Jacob E. Proceedings of the Royal Society B: Biological Sciences, Vol. 284, Issue 1860 https://doi.org/10.1098/rspb.2017.0537	journal	August 2017
Minimal-assumption inference from population-genomic data Weissman, Daniel B.; Hallatschek, Oskar eLife https://doi.org/10.1101/084459	posted_content	October 2016
Role of genetic introgression during the evolution of cultivated rice (Oryza sativa L.) Civáň, Peter; Brown, Terence A. BMC Evolutionary Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12862-018-1180-7	journal	April 2018
multi‐dice : r package for comparative population genomic inference under hierarchical co‐demographic models of independent single‐population size changes Xue, Alexander T.; Hickerson, Michael J. Molecular Ecology Resources, Vol. 17, Issue 6 https://doi.org/10.1111/1755-0998.12686	journal	May 2017
A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum Derbyshire, Mark Charles; Denton-Giles, Matthew; Hane, James K. PLOS ONE, Vol. 14, Issue 3 https://doi.org/10.1371/journal.pone.0214201	journal	March 2019
HTT haplotypes contribute to differences in Huntington disease prevalence between Europe and East Asia Warby, Simon C.; Visscher, Henk; Collins, Jennifer A. European Journal of Human Genetics, Vol. 19, Issue 5 https://doi.org/10.1038/ejhg.2010.229	journal	January 2011
Estimation of contemporary effective population size and population declines using RAD sequence data Nunziata, Schyler O.; Weisrock, David W. Heredity, Vol. 120, Issue 3 https://doi.org/10.1038/s41437-017-0037-y	journal	December 2017
Genomic legacy of the African cheetah, Acinonyx jubatus Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0837-4	journal	December 2015
Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed Zou, Jun; Mao, Lingfeng; Qiu, Jie Plant Biotechnology Journal, Vol. 17, Issue 10 https://doi.org/10.1111/pbi.13115	journal	April 2019
Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps Garud, Nandita R.; Messer, Philipp W.; Buzbas, Erkan O. PLOS Genetics, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pgen.1005004	journal	February 2015
Population genomics of natural and experimental populations of guppies ( Poecilia reticulata ) Fraser, Bonnie A.; Künstner, Axel; Reznick, David N. Molecular Ecology, Vol. 24, Issue 2 https://doi.org/10.1111/mec.13022	journal	January 2015
The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards Laurent, Stefan; Pfeifer, Susanne P.; Settles, Matthew L. Molecular Ecology, Vol. 25, Issue 1 https://doi.org/10.1111/mec.13385	journal	October 2015
Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing Zeng, Lin; Ming, Chen; Li, Yan Molecular Biology and Evolution, Vol. 35, Issue 1 https://doi.org/10.1093/molbev/msx276	journal	November 2017
Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic Jeffery, N. W.; DiBacco, C.; Wringe, B. F. Heredity, Vol. 119, Issue 3 https://doi.org/10.1038/hdy.2017.22	journal	April 2017
Genomic evidence for convergent evolution of a key trait underlying divergence in island birds Cooper, Elizabeth A.; Uy, J. Albert C. Molecular Ecology, Vol. 26, Issue 14 https://doi.org/10.1111/mec.14116	journal	April 2017
Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks Bunnefeld, Lynsey; Frantz, Laurent A. F.; Lohse, Konrad Genetics, Vol. 201, Issue 3 https://doi.org/10.1534/genetics.115.179861	journal	September 2015
Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest Cheng, Tingcai; Wu, Jiaqi; Wu, Yuqian Nature Ecology & Evolution, Vol. 1, Issue 11 https://doi.org/10.1038/s41559-017-0314-4	journal	September 2017
The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure Rodríguez, Willy; Mazet, Olivier; Grusea, Simona Heredity, Vol. 121, Issue 6 https://doi.org/10.1038/s41437-018-0148-0	journal	October 2018
Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism Fumagalli, Matteo; Camus, Stephane M.; Diekmann, Yoan eLife, Vol. 8 https://doi.org/10.7554/elife.41517	journal	June 2019
Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference Rosen, Zvi; Bhaskar, Anand; Roch, Sebastien Genetics, Vol. 210, Issue 2 https://doi.org/10.1534/genetics.118.300733	journal	July 2018
A legacy of geo‐climatic complexity and genetic divergence along the lower Colorado River: Insights from the geological record and 33 desert‐adapted animals Dolby, Greer A.; Dorsey, Rebecca J.; Graham, Matthew R. Journal of Biogeography, Vol. 46, Issue 11 https://doi.org/10.1111/jbi.13685	journal	August 2019
Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation Racimo, Fernando Genetics, Vol. 202, Issue 2 https://doi.org/10.1534/genetics.115.178095	journal	November 2015
Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism Novikova, Polina Yu; Hohmann, Nora; Nizhynska, Viktoria Nature Publishing Group https://doi.org/10.5167/uzh-125188	text	January 2016
Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism Novikova, Polina Yu; Hohmann, Nora; Nizhynska, Viktoria Nature Genetics, Vol. 48, Issue 9 https://doi.org/10.1038/ng.3617	journal	July 2016
Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates Badouin, H.; Gladieux, P.; Gouzy, J. Molecular Ecology, Vol. 26, Issue 7 https://doi.org/10.1111/mec.13976	journal	January 2017
Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data Blair, Christopher; Ané, Cécile Systematic Biology, Vol. 69, Issue 3 https://doi.org/10.1093/sysbio/syz056	journal	September 2019
Demographic history of speciation in a Senecio altitudinal hybrid zone on Mt. Etna Filatov, Dmitry A.; Osborne, Owen G.; Papadopulos, Alexander S. T. Molecular Ecology, Vol. 25, Issue 11 https://doi.org/10.1111/mec.13618	journal	April 2016
Climate explains recent population divergence, introgression and persistence in tropical mountains: phylogenomic evidence from Atlantic Forest warbling finches do Amaral, Fábio Raposo; Alvarado-Serrano, Diego F.; Maldonado-Coelho, Marcos https://doi.org/10.1101/439265	posted_content	October 2018
History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly ( Neodiprion lecontei ) Bagley, Robin K.; Sousa, Vitor C.; Niemiller, Matthew L. Molecular Ecology, Vol. 26, Issue 4 https://doi.org/10.1111/mec.13972	journal	January 2017
Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes ( Pantherophis guttatus complex) Myers, Edward A.; McKelvy, Alexander D.; Burbrink, Frank T. Molecular Ecology, Vol. 29, Issue 4 https://doi.org/10.1111/mec.15358	journal	February 2020
Inferring recent historic abundance from current genetic diversity Palsbøll, Per J.; Zachariah Peery, M.; Olsen, Morten T. Molecular Ecology, Vol. 22, Issue 1 https://doi.org/10.1111/mec.12094	journal	November 2012
A community-maintained standard library of population genetic models Adrion, Jeffrey R.; Cole, Christopher B.; Dukler, Noah eLife https://doi.org/10.1101/2019.12.20.885129	posted_content	January 2019
Robust and scalable inference of population history from hundreds of unphased whole genomes Terhorst, Jonathan; Kamm, John A.; Song, Yun S. Nature Genetics, Vol. 49, Issue 2 https://doi.org/10.1038/ng.3748	journal	December 2016
The deleterious mutation load is insensitive to recent population history Simons, Yuval B.; Turchin, Michael C.; Pritchard, Jonathan K. Nature Genetics, Vol. 46, Issue 3 https://doi.org/10.1038/ng.2896	journal	February 2014
Neo-sex chromosomes, genetic diversity and demographic history in the Critically Endangered Raso lark Dierickx, Elisa; Sin, Simon; Veelen, Pieter van Proceedings of the Royal Society B: Biological Sciences https://doi.org/10.1101/617563	posted_content	January 2019
Extensive X-linked adaptive evolution in central chimpanzees Hvilsom, C.; Qian, Y.; Bataillon, T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 6 https://doi.org/10.1073/pnas.1106877109	journal	January 2012
Eukaryote hybrid genomes. Runemark, Anna; Vallejo-Marin, Mario; Meier, Joana I. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.47431	text	January 2019
Host hybridization as a potential mechanism of lateral symbiont transfer in deep‐sea vesicomyid clams Breusing, Corinna; Johnson, Shannon B.; Vrijenhoek, Robert C. Molecular Ecology, Vol. 28, Issue 21 https://doi.org/10.1111/mec.15224	journal	September 2019
Assessing population structure in the face of isolation by distance: Are we neglecting the problem? Perez, Manolo F.; Franco, Fernando F.; Bombonato, Juliana R. Diversity and Distributions, Vol. 24, Issue 12 https://doi.org/10.1111/ddi.12816	journal	July 2018
Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations Spence, Jeffrey P.; Song, Yun S. Science Advances https://doi.org/10.1101/532168	posted_content	January 2019
Inferring responses to climate dynamics from historical demography in neotropical forest lizards Prates, Ivan; Xue, Alexander T.; Brown, Jason L. Proceedings of the National Academy of Sciences, Vol. 113, Issue 29 https://doi.org/10.1073/pnas.1601063113	journal	July 2016
The genetics of monarch butterfly migration and warning colouration Zhan, Shuai; Zhang, Wei; Niitepõld, Kristjan Nature, Vol. 514, Issue 7522 https://doi.org/10.1038/nature13812	journal	October 2014
Pleistocene climate changes, and not agricultural spread, accounts for range expansion and admixture in the dominant grassland species Lolium perenne L. Blanco‐Pastor, José Luis; Manel, Stéphanie; Barre, Philippe Journal of Biogeography https://doi.org/10.1111/jbi.13587	journal	May 2019
Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations Thompson, Elizabeth A. Genetics, Vol. 194, Issue 2 https://doi.org/10.1534/genetics.112.148825	journal	June 2013
The Landscape of Extreme Genomic Variation in the Highly Adaptable Atlantic Killifish Reid, Noah M.; Jackson, Craig E.; Gilbert, Don Genome Biology and Evolution, Vol. 9, Issue 3 https://doi.org/10.1093/gbe/evx023	journal	March 2017
The inference of sex-biased human demography from whole-genome data Musharoff, Shaila; Shringarpure, Suyash; Bustamante, Carlos D. PLOS Genetics, Vol. 15, Issue 9 https://doi.org/10.1371/journal.pgen.1008293	journal	September 2019
Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L. Bird, Kevin A.; An, Hong; Gazave, Elodie Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.00321	journal	March 2017
Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data Stuglik, Michał T.; Babik, Wiesław Ecology and Evolution, Vol. 6, Issue 13 https://doi.org/10.1002/ece3.2152	journal	June 2016
Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula DiBattista, Joseph D.; Saenz‐Agudelo, Pablo; Piatek, Marek J. Ecology and Evolution, Vol. 10, Issue 10 https://doi.org/10.1002/ece3.6199	journal	April 2020
Dispersal capacity and genetic relatedness in Acropora cervicornis on the Florida Reef Tract Drury, Crawford; Paris, Claire B.; Kourafalou, Vassiliki H. Coral Reefs, Vol. 37, Issue 2 https://doi.org/10.1007/s00338-018-1683-0	journal	April 2018
Out of southern East Asia: the natural history of domestic dogs across the world Wang, Guo-Dong; Zhai, Weiwei; Yang, He-Chuan Cell Research, Vol. 26, Issue 1 https://doi.org/10.1038/cr.2015.147	journal	December 2015
Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals Nagasaki, Masao; Yasuda, Jun; Katsuoka, Fumiki Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9018	journal	August 2015
Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.) Souissi, Ahmed; Bonhomme, François; Manchado, Manuel Heredity, Vol. 121, Issue 6 https://doi.org/10.1038/s41437-018-0079-9	journal	May 2018
An intercross population study reveals genes associated with body size and plumage color in ducks Zhou, Zhengkui; Li, Ming; Cheng, Hong Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04868-4	journal	July 2018
Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania Mondal, Mayukh; Bertranpetit, Jaume; Lao, Oscar Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-018-08089-7	journal	January 2019
Partial genomic survival of cave bears in living brown bears Barlow, Axel; Cahill, James A.; Hartmann, Stefanie Nature Ecology & Evolution, Vol. 2, Issue 10 https://doi.org/10.1038/s41559-018-0654-8	journal	August 2018
DNA analysis of an early modern human from Tianyuan Cave, China Fu, Q.; Meyer, M.; Gao, X. Proceedings of the National Academy of Sciences, Vol. 110, Issue 6 https://doi.org/10.1073/pnas.1221359110	journal	January 2013
Determining the factors driving selective effects of new nonsynonymous mutations Huber, Christian D.; Kim, Bernard Y.; Marsden, Clare D. Proceedings of the National Academy of Sciences, Vol. 114, Issue 17 https://doi.org/10.1073/pnas.1619508114	journal	April 2017
What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species Campbell, C. Ryan; Poelstra, J. W.; Yoder, Anne D. Biological Journal of the Linnean Society, Vol. 124, Issue 4 https://doi.org/10.1093/biolinnean/bly063	journal	June 2018
Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California Cridland, Julie M.; Ramirez, Santiago R.; Dean, Cheryl A. Genome Biology and Evolution, Vol. 10, Issue 2 https://doi.org/10.1093/gbe/evy007	journal	January 2018
Historical demography of the Caribbean spiny lobster Panulirus argus (Latreille, 1804) (Decapoda: Achelata: Palinuridae) in the Florida Keys, USA inferred using single nucleotide polymorphisms (SNPs) Baeza, J. Antonio; Umaña-Castro, Rodolfo; Mejia-Ortiz, Luis M. Journal of Crustacean Biology, Vol. 39, Issue 4 https://doi.org/10.1093/jcbiol/ruz019	journal	June 2019
Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans Cornejo, Omar E.; Lefébure, Tristan; Pavinski Bitar, Paulina D. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mss278	journal	December 2012
Evidence for Increased Levels of Positive and Negative Selection on the X Chromosome versus Autosomes in Humans Veeramah, Krishna R.; Gutenkunst, Ryan N.; Woerner, August E. Molecular Biology and Evolution, Vol. 31, Issue 9 https://doi.org/10.1093/molbev/msu166	journal	May 2014
The Role of Phylogenetically Conserved Elements in Shaping Patterns of Human Genomic Diversity Woerner, August E.; Veeramah, Krishna R.; Watkins, Joseph C. Molecular Biology and Evolution, Vol. 35, Issue 9 https://doi.org/10.1093/molbev/msy145	journal	August 2018
Robust Estimation of Recent Effective Population Size from Number of Independent Origins in Soft Sweeps Khatri, Bhavin S.; Burt, Austin Molecular Biology and Evolution, Vol. 36, Issue 9 https://doi.org/10.1093/molbev/msz081	journal	April 2019
Unbiased Estimation of Linkage Disequilibrium from Unphased Data Ragsdale, Aaron P.; Gravel, Simon Molecular Biology and Evolution, Vol. 37, Issue 3 https://doi.org/10.1093/molbev/msz265	journal	November 2019
Reproductive isolation between phylogeographic lineages scales with divergence Singhal, Sonal; Moritz, Craig Proceedings of the Royal Society B: Biological Sciences, Vol. 280, Issue 1772 https://doi.org/10.1098/rspb.2013.2246	journal	December 2013
King penguin demography since the last glaciation inferred from genome-wide data Trucchi, Emiliano; Gratton, Paolo; Whittington, Jason D. Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1787 https://doi.org/10.1098/rspb.2014.0528	journal	July 2014
Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus) Harris, Stephen E.; Munshi-South, Jason Molecular Ecology https://doi.org/10.1101/038141	posted_content	September 2017
Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group Fouet, Caroline; Kamdem, Colince; Gamez, Stephanie Evolutionary Applications https://doi.org/10.1101/068239	posted_content	April 2017
Sequence and structural diversity of mouse Y chromosomes Morgan, Andrew P.; de Villena, Fernando Pardo-Manuel Molecular Biology and Evolution https://doi.org/10.1101/096297	posted_content	January 2017
Human demographic history has amplified the effects of background selection across the genome Torres, Raul; Szpiech, Zachary A.; Hernandez, Ryan D. PLOS Genetics https://doi.org/10.1101/181859	posted_content	January 2018
Bayesian coalescent inference of in-host evolution using Next Generation Sequencing Leen, Gayle; Baguelin, Marc Research Gate https://doi.org/10.1101/407965	posted_content	January 2018
Dating genomic variants and shared ancestry in population-scale sequencing data Albers, Patrick K.; McVean, Gil PLOS Biology https://doi.org/10.1101/416610	posted_content	January 2019
Testing for population decline using maximal linkage disequilibrium blocks Kerdoncuff, Elise; Lambert, Amaury; Achaz, Guillaume Theoretical Population Biology https://doi.org/10.1101/703595	posted_content	January 2019
Haplotype-based inference of the distribution of fitness effects Vecchyo, Diego Ortega-Del; Lohmueller, Kirk E.; Novembre, John Oxford Academics https://doi.org/10.1101/770966	posted_content	January 2019
Evaluating species interactions as a driver of phytophagous insect divergence de Medeiros, Bruno A. S.; Farrell, Brian D. Communications Biology https://doi.org/10.1101/842153	posted_content	October 2020
Congruent demographic responses to Pleistocene geological processes in Sumatran parachuting frogs: a comparison of target-capture and ddRADseq for population genomic analyses O’Connell, Kyle A.; Oaks, Jamie R.; Hamidy, Amir Molecular Ecology https://doi.org/10.1101/843664	posted_content	January 2019
De novo transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set Singhal, Sonal Molecular Ecology Resources, Vol. 13, Issue 3 https://doi.org/10.1111/1755-0998.12077	journal	February 2013
Detecting Range Expansions from Genetic Data: Detecting Range Expansions from Genetic data Peter, Benjamin M.; Slatkin, Montgomery Evolution, Vol. 67, Issue 11 https://doi.org/10.1111/evo.12202	journal	August 2013
Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift Moura, Andre E.; Kenny, John G.; Chaudhuri, Roy Molecular Ecology, Vol. 23, Issue 21 https://doi.org/10.1111/mec.12929	journal	October 2014
A population genomics insight into the Mediterranean origins of wine yeast domestication Almeida, Pedro; Barbosa, Raquel; Zalar, Polona Molecular Ecology, Vol. 24, Issue 21 https://doi.org/10.1111/mec.13341	journal	September 2015
A genomic perspective on hybridization and speciation Payseur, Bret A.; Rieseberg, Loren H. Molecular Ecology, Vol. 25, Issue 11 https://doi.org/10.1111/mec.13557	journal	March 2016
Behavioural response to song and genetic divergence in two subspecies of white‐crowned sparrows ( Zonotrichia leucophrys ) Lipshutz, Sara E.; Overcast, Isaac A.; Hickerson, Michael J. Molecular Ecology, Vol. 26, Issue 11 https://doi.org/10.1111/mec.14002	journal	January 2017
Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex Phuong, Mark A.; Bi, Ke; Moritz, Craig Molecular Ecology, Vol. 26, Issue 18 https://doi.org/10.1111/mec.14238	journal	August 2017
Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection Portik, Daniel M.; Leaché, Adam D.; Rivera, Danielle Molecular Ecology, Vol. 26, Issue 19 https://doi.org/10.1111/mec.14266	journal	August 2017
Greenlandic Inuit show genetic signatures of diet and climate adaptation Fumagalli, Matteo; Moltke, Ida; Grarup, Niels Science, Vol. 349, Issue 6254 https://doi.org/10.1126/science.aab2319	journal	September 2015
Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species Li, Shengbin; Li, Bo; Cheng, Cheng Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0557-1	journal	December 2014
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx Abascal, Federico; Corvelo, André; Cruz, Fernando Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-1090-1	journal	December 2016
Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history Li, Yong; Cao, Ke; Zhu, Gengrui Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1648-9	journal	February 2019
A framework for incorporating evolutionary genomics into biodiversity conservation and management Hoffmann, Ary; Griffin, Philippa; Dillon, Shannon Climate Change Responses, Vol. 2, Issue 1 https://doi.org/10.1186/s40665-014-0009-x	journal	January 2015
Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I. PLoS Genetics, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pgen.1003942	journal	November 2013
The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies. Fraïsse, Christelle; Roux, Camille; Gagnaire, Pierre-Alexandre Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.31492	text	January 2018
Extracting population genetics information from a diploid genome sequence Osada, Naoki Frontiers in Ecology and Evolution, Vol. 2 https://doi.org/10.3389/fevo.2014.00007	journal	April 2014
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event Winkler, Kevin; Glenn, Travis C.; Faircloth, Brant C. https://doi.org/10.7287/peerj.preprints.27035v1	posted_content	July 2018
Evolutionary networks from RAD seq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea Blanco‐Pastor, José Luis; Bertrand, Yann J. K.; Liberal, Isabel María American Journal of Botany, Vol. 106, Issue 9 https://doi.org/10.1002/ajb2.1352	journal	September 2019
Genomic analyses provide insights into the history of tomato breeding Lin, Tao; Zhu, Guangtao; Zhang, Junhong Nature Genetics, Vol. 46, Issue 11 https://doi.org/10.1038/ng.3117	journal	October 2014
Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis) Rougeux, Clément; Bernatchez, Louis; Gagnaire, Pierre-Alexandre Genome Biology and Evolution, Vol. 9, Issue 8 https://doi.org/10.1093/gbe/evx150	journal	August 2017
Genomic Basis of Convergent Island Phenotypes in Boa Constrictors Card, Daren C.; Adams, Richard H.; Schield, Drew R. Genome Biology and Evolution, Vol. 11, Issue 11 https://doi.org/10.1093/gbe/evz226	journal	October 2019
GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data Noskova, Ekaterina; Ulyantsev, Vladimir; Koepfli, Klaus-Peter GigaScience, Vol. 9, Issue 3 https://doi.org/10.1093/gigascience/giaa005	journal	February 2020
Genomic Divergence during Speciation Driven by Adaptation to Altitude Chapman, Mark A.; Hiscock, Simon J.; Filatov, Dmitry A. Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst168	journal	September 2013
Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana Huber, Christian D.; Nordborg, Magnus; Hermisson, Joachim Molecular Biology and Evolution, Vol. 31, Issue 11 https://doi.org/10.1093/molbev/msu247	journal	August 2014
Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys Zhou, Xuming; Meng, Xuehong; Liu, Zhijin Molecular Biology and Evolution, Vol. 33, Issue 10 https://doi.org/10.1093/molbev/msw150	journal	August 2016
PoMo: An Allele Frequency-Based Approach for Species Tree Estimation De Maio, Nicola; Schrempf, Dominik; Kosiol, Carolin Systematic Biology, Vol. 64, Issue 6 https://doi.org/10.1093/sysbio/syv048	journal	July 2015
Genomic islands of divergence or opportunities for introgression? Bay, Rachael A.; Ruegg, Kristen Proceedings of the Royal Society B: Biological Sciences, Vol. 284, Issue 1850 https://doi.org/10.1098/rspb.2016.2414	journal	March 2017
The Time and Place of European Admixture in Ashkenazi Jewish History Xue, James; Lencz, Todd; Darvasi, Ariel PLOS Genetics https://doi.org/10.1101/063099	posted_content	January 2016
Robust estimation of recent effective population size from number of independent origins in soft sweeps Khatri, Bhavin S.; Burt, Austin Molecular Biology and Evolution https://doi.org/10.1101/472266	posted_content	January 2018
Assessing connectivity despite high diversity in island populations of a malaria mosquito Bergey, Christina M.; Lukindu, Martin; Wiltshire, Rachel M. Evolutionary Applications, Vol. 13, Issue 2 https://doi.org/10.1111/eva.12878	journal	September 2019
Population‐level inferences from environmental DNA—Current status and future perspectives Sigsgaard, Eva Egelyng; Jensen, Mads Reinholdt; Winkelmann, Inger Eleanor Evolutionary Applications, Vol. 13, Issue 2 https://doi.org/10.1111/eva.12882	journal	September 2019
On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes: genetic variation and adaptive potential in fishes Bernatchez, L. Journal of Fish Biology, Vol. 89, Issue 6 https://doi.org/10.1111/jfb.13145	journal	September 2016
Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing Lozier, J. D. Molecular Ecology, Vol. 23, Issue 4 https://doi.org/10.1111/mec.12636	journal	January 2014
Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus ) Rittmeyer, Eric N.; Austin, Christopher C. Molecular Ecology, Vol. 24, Issue 2 https://doi.org/10.1111/mec.13030	journal	January 2015
Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Bailey, Susan F.; Bataillon, Thomas Molecular Ecology, Vol. 25, Issue 1 https://doi.org/10.1111/mec.13378	journal	October 2015
Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum Le Gac, Mickael; Metegnier, Gabriel; Chomérat, Nicolas Molecular Ecology, Vol. 25, Issue 20 https://doi.org/10.1111/mec.13815	journal	September 2016
Incipient speciation driven by hypertrophied lips in Midas cichlid fishes? Machado-Schiaffino, Gonzalo; Kautt, Andreas F.; Torres-Dowdall, Julian Molecular Ecology, Vol. 26, Issue 8 https://doi.org/10.1111/mec.14029	journal	March 2017
Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations Fuentes-Pardo, Angela P.; Ruzzante, Daniel E. Molecular Ecology, Vol. 26, Issue 20 https://doi.org/10.1111/mec.14264	journal	September 2017
Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics Mastretta‐Yanes, Alicia; Xue, Alexander T.; Moreno‐Letelier, Alejandra Molecular Ecology, Vol. 27, Issue 2 https://doi.org/10.1111/mec.14461	journal	January 2018
The role of hybridization during ecological divergence of southwestern white pine ( Pinus strobiformis ) and limber pine ( P. flexilis ) Menon, Mitra; Bagley, Justin C.; Friedline, Christopher J. Molecular Ecology, Vol. 27, Issue 5 https://doi.org/10.1111/mec.14505	journal	March 2018
Genomic evidence for asymmetric introgression by sexual selection in the common wall lizard Yang, Weizhao; While, Geoffrey M.; Laakkonen, Hanna Molecular Ecology, Vol. 27, Issue 21 https://doi.org/10.1111/mec.14861	journal	October 2018
Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons Card, Daren C.; Perry, Blair W.; Adams, Richard H. Molecular Ecology, Vol. 27, Issue 23 https://doi.org/10.1111/mec.14885	journal	October 2018
Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes Nevado, Bruno; Contreras-Ortiz, Natalia; Hughes, Colin New Phytologist, Vol. 219, Issue 2 https://doi.org/10.1111/nph.15243	journal	June 2018
Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene Linnen, C. R.; Poh, Y. -P.; Peterson, B. K. Science, Vol. 339, Issue 6125 https://doi.org/10.1126/science.1233213	journal	March 2013
Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data Gravel, Simon; Zakharia, Fouad; Moreno-Estrada, Andres PLoS Genetics, Vol. 9, Issue 12 https://doi.org/10.1371/journal.pgen.1004023	journal	December 2013
An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression Akiyama, Tokiho; Katsumura, Takafumi; Nakagome, Shigeki PLOS ONE, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pone.0178373	journal	June 2017
Estimating Allele Age and Selection Coefficient from Time-Serial Data Malaspinas, Anna-Sapfo; Malaspinas, Orestis; Evans, Steven N. Genetics, Vol. 192, Issue 2 https://doi.org/10.1534/genetics.112.140939	journal	October 2012
Independent Molecular Basis of Convergent Highland Adaptation in Maize Takuno, Shohei; Ralph, Peter; Swarts, Kelly Genetics, Vol. 200, Issue 4 https://doi.org/10.1534/genetics.115.178327	journal	June 2015
The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit Pedersen, Casper-Emil T.; Lohmueller, Kirk E.; Grarup, Niels Genetics, Vol. 205, Issue 2 https://doi.org/10.1534/genetics.116.193821	journal	February 2017
Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent Imamura, Hideo; Downing, Tim; Van Den Broeck, Frederik Charité - Universitätsmedizin Berlin https://doi.org/10.17169/refubium-18558	text	January 2016
The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies Fraïsse, Christelle; Roux, Camille; Gagnaire, Pierre-Alexandre PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5198	journal	January 2018
Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA ‐seq analyses Edwards, Taylor; Tollis, Marc; Hsieh, PingHsun Ecology and Evolution, Vol. 6, Issue 2 https://doi.org/10.1002/ece3.1865	journal	January 2016
Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community? Slatyer, Rachel A.; Schoville, Sean D.; Nufio, César R. Ecology and Evolution, Vol. 10, Issue 2 https://doi.org/10.1002/ece3.5961	journal	December 2019
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants Fu, Wenqing; O’Connor, Timothy D.; Jun, Goo Nature, Vol. 493, Issue 7431 https://doi.org/10.1038/nature11690	journal	November 2012
Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions Qiu, Qiang; Wang, Lizhong; Wang, Kun Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms10283	journal	December 2015
Estimating the mutation load in human genomes Henn, Brenna M.; Botigué, Laura R.; Bustamante, Carlos D. Nature Reviews Genetics, Vol. 16, Issue 6 https://doi.org/10.1038/nrg3931	journal	May 2015
Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs Thomé, Maria Tereza C.; Carstens, Bryan C. Proceedings of the National Academy of Sciences, Vol. 113, Issue 29 https://doi.org/10.1073/pnas.1601064113	journal	July 2016
Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains Polato, Nicholas R.; Gill, Brian A.; Shah, Alisha A. Proceedings of the National Academy of Sciences, Vol. 115, Issue 49 https://doi.org/10.1073/pnas.1809326115	journal	November 2018
Using bioinformatics to predict the functional impact of SNVs Cline, M. S.; Karchin, R. Bioinformatics, Vol. 27, Issue 4 https://doi.org/10.1093/bioinformatics/btq695	journal	December 2010
Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago Sato, Takehiro; Nakagome, Shigeki; Watanabe, Chiaki Molecular Biology and Evolution, Vol. 31, Issue 11 https://doi.org/10.1093/molbev/msu230	journal	August 2014
Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua Molecular Biology and Evolution, Vol. 33, Issue 10 https://doi.org/10.1093/molbev/msw129	journal	July 2016
Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species Thom, Gregory; Amaral, Fabio Raposo Do; Hickerson, Michael J. Systematic Biology, Vol. 67, Issue 4 https://doi.org/10.1093/sysbio/syy004	journal	January 2018
Inferring the Demographic History of Inbred Species From Genome-Wide SNP Frequency Data Blischak, Paul D.; Barker, Michael S.; Gutenkunst, Ryan N. Molecular Biology and Evolution https://doi.org/10.1101/2019.12.20.881474	posted_content	December 2019
Geometry of the sample frequency spectrum and the perils of demographic inference Rosen, Zvi; Bhaskar, Anand; Roch, Sebastian Genetics https://doi.org/10.1101/233908	posted_content	December 2017
Genome-wide sampling suggests island divergence accompanied by cryptic epigenetic plasticity in Canada lynx Johnson, J. B.; Murray, D. L.; Shafer, A. B. A. BioRxiv https://doi.org/10.1101/316711	posted_content	January 2018
genomalicious : serving up a smorgasbord of R functions for population genomic analyses Thia, Joshua A.; Riginos, Cynthia Research Gate https://doi.org/10.1101/667337	posted_content	January 2019
The consequences of not accounting for background selection in demographic inference Ewing, Gregory B.; Jensen, Jeffrey D. Molecular Ecology, Vol. 25, Issue 1 https://doi.org/10.1111/mec.13390	journal	October 2015
Inferring the age of a fixed beneficial allele Ormond, Louise; Foll, Matthieu; Ewing, Gregory B. Molecular Ecology, Vol. 25, Issue 1 https://doi.org/10.1111/mec.13478	journal	December 2015
Detecting hybridization using ancient DNA Schaefer, Nathan K.; Shapiro, Beth; Green, Richard E. Molecular Ecology, Vol. 25, Issue 11 https://doi.org/10.1111/mec.13556	journal	March 2016
Genomic and phenomic analysis of island ant community assembly Darwell, Clive T.; Fischer, Georg; Sarnat, Eli M. Molecular Ecology, Vol. 29, Issue 9 https://doi.org/10.1111/mec.15326	journal	January 2020
Speciation history of European ( Anguilla anguilla ) and American eel ( A. rostrata ), analysed using genomic data Nikolic, Natacha; Liu, Shenglin; Jacobsen, Magnus W. Molecular Ecology, Vol. 29, Issue 3 https://doi.org/10.1111/mec.15342	journal	January 2020
Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection Wang, Mingcheng; Zhang, Lei; Zhang, Zhiyang New Phytologist, Vol. 225, Issue 3 https://doi.org/10.1111/nph.16215	journal	October 2019
Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes Hsieh, PingHsun; Vollger, Mitchell R.; Dang, Vy Science, Vol. 366, Issue 6463 https://doi.org/10.1126/science.aax2083	journal	October 2019
Genetic diversity in India and the inference of Eurasian population expansion Xing, Jinchuan; Watkins, W. Scott; Hu, Ya Genome Biology, Vol. 11, Issue 11 https://doi.org/10.1186/gb-2010-11-11-r113	journal	November 2010
The functional spectrum of low-frequency coding variation Marth, Gabor T.; Yu, Fuli; Indap, Amit R. Genome Biology, Vol. 12, Issue 9 https://doi.org/10.1186/gb-2011-12-9-r84	journal	January 2011
A genome-wide scan for signatures of directional selection in domesticated pigs Moon, Sunjin; Kim, Tae-Hun; Lee, Kyung-Tai BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1330-x	journal	February 2015
Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts Brandenburg, Jean-Tristan; Mary-Huard, Tristan; Rigaill, Guillem PLOS Genetics, Vol. 13, Issue 3 https://doi.org/10.1371/journal.pgen.1006666	journal	March 2017
Evolutionary history of Tibetans inferred from whole-genome sequencing Hu, Hao; Petousi, Nayia; Glusman, Gustavo PLOS Genetics, Vol. 13, Issue 4 https://doi.org/10.1371/journal.pgen.1006675	journal	April 2017
Human demographic history has amplified the effects of background selection across the genome Torres, Raul; Szpiech, Zachary A.; Hernandez, Ryan D. PLOS Genetics, Vol. 14, Issue 6 https://doi.org/10.1371/journal.pgen.1007387	journal	June 2018
Inference of Historical Population-Size Changes with Allele-Frequency Data Lynch, Michael; Haubold, Bernhard; Pfaffelhuber, Peter G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 1 https://doi.org/10.1534/g3.119.400854	journal	January 2020
Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth H., Simons, Lee; J., Turner, Bruce; H., Martin, Christopher The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/wfvq-2737	text	January 2016
Diverse demographic histories in a guild of hymenopteran parasitoids Walton, William; Stone, Graham; Lohse, Konrad Molecular Ecology https://doi.org/10.22541/au.162015867.78632536/v1	posted_content	May 2021
Fine-grained habitat-associated genetic connectivity in an admixed population of mussels in the small isolated Kerguelen Islands Fraïsse, Christelle; Haguenauer, Anne; Gérard, Karin Peer Community Journal, Vol. 1 https://doi.org/10.24072/pcjournal.18	journal	January 2021
Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella Brandvain, Yaniv; Slotte, Tanja; Hazzouri, Khaled arXiv https://doi.org/10.48550/arxiv.1307.4118	preprint	January 2013
WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data Foll, Matthieu; Shim, Hyunjin; Jensen, Jeffrey D. arXiv https://doi.org/10.48550/arxiv.1409.8529	text	January 2014
Open source libraries and frameworks for biological data visualisation: A guide for developers Wang, Rui; Perez‐Riverol, Yasset; Hermjakob, Henning PROTEOMICS, Vol. 15, Issue 8 https://doi.org/10.1002/pmic.201400377	journal	February 2015
Early Austronesians: Into and Out Of Taiwan Ko, Albert Min-Shan; Chen, Chung-Yu; Fu, Qiaomei The American Journal of Human Genetics, Vol. 94, Issue 3 https://doi.org/10.1016/j.ajhg.2014.02.003	journal	March 2014
Biased Gene Conversion Skews Allele Frequencies in Human Populations, Increasing the Disease Burden of Recessive Alleles Lachance, Joseph; Tishkoff, Sarah A. The American Journal of Human Genetics, Vol. 95, Issue 4 https://doi.org/10.1016/j.ajhg.2014.09.008	journal	October 2014
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity Gossmann, Toni I.; Shanmugasundram, Achchuthan; Börno, Stefan Current Biology, Vol. 29, Issue 10 https://doi.org/10.1016/j.cub.2019.04.020	journal	May 2019
The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives Simons, Yuval B.; Sella, Guy Current Opinion in Genetics & Development, Vol. 41 https://doi.org/10.1016/j.gde.2016.09.006	journal	December 2016
Population structure and coalescence in pedigrees: Comparisons to the structured coalescent and a framework for inference Wilton, Peter R.; Baduel, Pierre; Landon, Matthieu M. Theoretical Population Biology, Vol. 115 https://doi.org/10.1016/j.tpb.2017.01.004	journal	June 2017
Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection Chang, Hsiao-Han; Hartl, Daniel L. Parasitology, Vol. 142, Issue S1 https://doi.org/10.1017/s0031182014000067	journal	February 2014
Deep resequencing reveals excess rare recent variants consistent with explosive population growth Coventry, Alex; Bull-Otterson, Lara M.; Liu, Xiaoming Nature Communications, Vol. 1, Issue 1 https://doi.org/10.1038/ncomms1130	journal	November 2010
Fast diffusion of domesticated maize to temperate zones Li, Xiaolong; Jian, Yinqiao; Xie, Chuanxiao Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-02125-0	journal	May 2017
Inferring the Dynamics of Effective Population Size Using Autosomal Genomes Hou, Zheng; Luo, Yin; Wang, Zhisheng Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep20079	journal	February 2016
MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus Ewing, Gregory; Hermisson, Joachim Bioinformatics, Vol. 26, Issue 16 https://doi.org/10.1093/bioinformatics/btq322	journal	June 2010
On Characterizing Adaptive Events Unique to Modern Humans Crisci, Jessica L.; Wong, Alex; Good, Jeffrey M. Genome Biology and Evolution, Vol. 3 https://doi.org/10.1093/gbe/evr075	journal	January 2011
Ancient and Recent Selective Pressures Shaped Genetic Diversity at AIM2-Like Nucleic Acid Sensors Cagliani, Rachele; Forni, Diego; Biasin, Mara Genome Biology and Evolution, Vol. 6, Issue 4 https://doi.org/10.1093/gbe/evu066	journal	March 2014
Partner-Drug Resistance and Population Substructuring of Artemisinin-Resistant Plasmodium falciparum in Cambodia Parobek, Christian M.; Parr, Jonathan B.; Brazeau, Nicholas F. Genome Biology and Evolution, Vol. 9, Issue 6 https://doi.org/10.1093/gbe/evx126	journal	June 2017
Impacts of Recurrent Hitchhiking on Divergence and Demographic Inference in Drosophila Lange, Jeremy D.; Pool, John E. Genome Biology and Evolution, Vol. 10, Issue 8 https://doi.org/10.1093/gbe/evy142	journal	July 2018
Concordant changes in gene expression and nucleotides underlie independent adaptation to hydrogen-sulfide-rich environments Brown, Anthony P.; Arias-Rodriguez, Lenin; Yee, Muh-Ching Genome Biology and Evolution https://doi.org/10.1093/gbe/evy198	journal	September 2018
Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation Nakagome, S.; Mano, S.; Kozlowski, L. Molecular Biology and Evolution, Vol. 29, Issue 6 https://doi.org/10.1093/molbev/mss006	journal	January 2012
Genomic Analyses of Three Malaria Vectors Reveals Extensive Shared Polymorphism but Contrasting Population Histories O’Loughlin, Samantha M.; Magesa, Stephen; Mbogo, Charles Molecular Biology and Evolution, Vol. 31, Issue 4 https://doi.org/10.1093/molbev/msu040	journal	January 2014
Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America Razifard, Hamid; Ramos, Alexis; Della Valle, Audrey L. Molecular Biology and Evolution, Vol. 37, Issue 4 https://doi.org/10.1093/molbev/msz297	journal	January 2020
Thinking too positive? Revisiting current methods of population-genetic selection inference Bank, Claudia; Ewing, Gregory B.; Ferrer-Admettla, Anna Trends in Genetics https://doi.org/10.1101/009654	journal	September 2014
Inference of super-exponential human population growth via efficient computation of the site frequency spectrum for generalized models Gao, Feng; Keinan, Alon Genetics https://doi.org/10.1101/022574	journal	July 2015
Archaic adaptive introgression in TBX15/WARS2 Racimo, Fernando; Gokhman, David; Fumagalli, Matteo Molecular Biology and Evolution https://doi.org/10.1101/033928	journal	October 2016
Potential for rapid genetic adaptation to warming in a Great Barrier Reef coral Matz, Mikhail V.; Treml, Eric A.; Aglyamova, Galina V. PLOS Genetics https://doi.org/10.1101/114173	journal	June 2017
Genomic inferences of domestication events are corroborated by written records in Brassica rapa Qi, Xinshuai; An, Hong; Ragsdale, Aaron Molecular Ecology https://doi.org/10.1101/118372	journal	March 2017
Fantastic beasts and how to sequence them: genomic approaches for obscure model organisms Matz, Mikhail V. https://doi.org/10.1101/165928	journal	August 2017
Machine Learning for Population Genetics: A New Paradigm Schrider, Daniel R.; Kern, Andrew D. Trends in Genetics https://doi.org/10.1101/206482	journal	October 2017
The Wright-Fisher Site Frequency Spectrum as a Perturbation of the Coalescent’s Melfi, Andrew; Viswanath, Divakar Theoretical Population Biology https://doi.org/10.1101/332817	journal	May 2018
The demographic history of African Drosophila melanogaster Kapopoulou, Adamandia; Pfeifer, Susanne P.; Jensen, Jeffrey D. Genome Biology and Evolution https://doi.org/10.1101/340406	journal	June 2018
The Site Frequency Spectrum under Finite and Time-Varying Mutation Rates Melfi, Andrew; Viswanath, Divakar https://doi.org/10.1101/375907	journal	July 2018
Pleistocene climate changes explain large-scale genetic variation in a dominant grassland species, Lolium perenne L Blanco-Pastor, J. L.; Manel, S.; Barre, P. https://doi.org/10.1101/414227	journal	September 2018
Quantification of GC-biased gene conversion in the human genome Glémin, Sylvain; Arndt, Peter F.; Messer, Philipp W. Genome Research, Vol. 25, Issue 8 https://doi.org/10.1101/gr.185488.114	journal	May 2015
Population history provides foundational knowledge for utilizing and developing native plant restoration materials Massatti, Rob; Prendeville, Holly R.; Larson, Steve Evolutionary Applications, Vol. 11, Issue 10 https://doi.org/10.1111/eva.12704	journal	September 2018
Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes Gladieux, Pierre; Ropars, Jeanne; Badouin, Hélène Molecular Ecology, Vol. 23, Issue 4 https://doi.org/10.1111/mec.12631	journal	January 2014
Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations Spence, Jeffrey P.; Song, Yun S. Science Advances, Vol. 5, Issue 10 https://doi.org/10.1126/sciadv.aaw9206	journal	October 2019
Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing de Gruijter, Johanna Maria; Lao, Oscar; Vermeulen, Mark Investigative Genetics, Vol. 2, Issue 1 https://doi.org/10.1186/2041-2223-2-24	journal	December 2011
Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies Machado, Moara; Magalhães, Wagner CS; Sene, Allan Investigative Genetics, Vol. 2, Issue 1 https://doi.org/10.1186/2041-2223-2-3	journal	January 2011
A world in a grain of sand: human history from genetic data Colonna, Vincenza; Pagani, Luca; Xue, Yali Genome Biology, Vol. 12, Issue 11 https://doi.org/10.1186/gb-2011-12-11-234	journal	January 2011
Sampling strategies for frequency spectrum-based population genomic inference Robinson, John D.; Coffman, Alec J.; Hickerson, Michael J. BMC Evolutionary Biology, Vol. 14, Issue 1 https://doi.org/10.1186/s12862-014-0254-4	journal	December 2014
Evolutionary processes in non-model tree species and species complexes: inference from natural populations Heuertz, Myriam Unpublished https://doi.org/10.13140/rg.2.2.24008.24321	text	January 2019
An Evolutionary Framework for Association Testing in Resequencing Studies King, C. Ryan; Rathouz, Paul J.; Nicolae, Dan L. PLoS Genetics, Vol. 6, Issue 11 https://doi.org/10.1371/journal.pgen.1001202	journal	November 2010
A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans Stewart, Chip; Kural, Deniz; Strömberg, Michael P. PLoS Genetics, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pgen.1002236	journal	August 2011
Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome Lohmueller, Kirk E.; Albrechtsen, Anders; Li, Yingrui PLoS Genetics, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pgen.1002326	journal	October 2011
Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral Matz, Mikhail V.; Treml, Eric A.; Aglyamova, Galina V. PLOS Genetics, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pgen.1007220	journal	April 2018
Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia Schrider, Daniel R.; Ayroles, Julien; Matute, Daniel R. PLOS Genetics, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pgen.1007341	journal	April 2018
An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations Platt, Alexander; Pivirotto, Alyssa; Knoblauch, Jared PLOS Genetics, Vol. 15, Issue 8 https://doi.org/10.1371/journal.pgen.1008340	journal	August 2019
Eukaryote hybrid genomes Runemark, Anna; Vallejo-Marin, Mario; Meier, Joana I. PLOS Genetics, Vol. 15, Issue 11 https://doi.org/10.1371/journal.pgen.1008404	journal	November 2019
Both Positive and Negative Selection Pressures Contribute to the Polymorphism Pattern of the Duplicated Human CYP21A2 Gene Szabó, Julianna Anna; Szilágyi, Ágnes; Doleschall, Zoltán PLoS ONE, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pone.0081977	journal	November 2013
The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population López, Saioa; García, Óscar; Yurrebaso, Iñaki PLoS ONE, Vol. 9, Issue 8 https://doi.org/10.1371/journal.pone.0104367	journal	August 2014
Adaptive Human CDKAL1 Variants Underlie Hormonal Response Variations at the Enteroinsular Axis Chang, Chia Lin; Cai, James J.; Huang, Shang Yu PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0105410	journal	September 2014
On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations Poh, Yu-Ping; Domingues, Vera S.; Hoekstra, Hopi E. PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0110579	journal	November 2014
Bayesian inference of selection in the Wright-Fisher diffusion model Gory, Jeffrey J.; Herbei, Radu; Kubatko, Laura S. Statistical Applications in Genetics and Molecular Biology, Vol. 17, Issue 3 https://doi.org/10.1515/sagmb-2017-0046	journal	June 2018
Using Ancient Samples in Projection Analysis Yang, Melinda A.; Slatkin, Montgomery G3 Genes\|Genomes\|Genetics, Vol. 6, Issue 1 https://doi.org/10.1534/g3.115.023788	journal	January 2016
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies Chen, Jun; Källman, Thomas; Ma, Xiao-Fei G3 Genes\|Genomes\|Genetics, Vol. 6, Issue 7 https://doi.org/10.1534/g3.116.028753	journal	July 2016
A Temporal Perspective on the Interplay of Demography and Selection on Deleterious Variation in Humans Koch, Evan; Novembre, John G3 Genes\|Genomes\|Genetics, Vol. 7, Issue 3 https://doi.org/10.1534/g3.117.039651	journal	March 2017
General Triallelic Frequency Spectrum Under Demographic Models with Variable Population Size Jenkins, Paul A.; Mueller, Jonas W.; Song, Yun S. Genetics, Vol. 196, Issue 1 https://doi.org/10.1534/genetics.113.158584	journal	January 2014
On Detecting Selective Sweeps Using Single Genomes Sinha, Priyanka; Dincer, Aslihan; Virgil, Daniel Frontiers in Genetics, Vol. 2 https://doi.org/10.3389/fgene.2011.00085	journal	January 2011
Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data Crawford, Jacob E.; Lazzaro, Brian P. Frontiers in Genetics, Vol. 3 https://doi.org/10.3389/fgene.2012.00066	journal	January 2012
Genomic Signatures of Reinforcement Garner, Austin; Goulet, Benjamin; Farnitano, Matthew Genes, Vol. 9, Issue 4 https://doi.org/10.3390/genes9040191	journal	April 2018
Biallelic Mutation-Drift Diffusion in the Limit of Small Scaled Mutation Rates Vogl, Claus arXiv https://doi.org/10.48550/arxiv.1409.2299	preprint	January 2014
The expected neutral frequency spectrum of linked sites Ferretti, Luca; Klassmann, Alexander; Raineri, Emanuele arXiv https://doi.org/10.48550/arxiv.1604.06713	preprint	January 2016
Bayesian inference of species trees using diffusion models Stoltz, Marnus; Bauemer, Boris; Bouckaert, Remco arXiv https://doi.org/10.48550/arxiv.1909.07276	preprint	January 2019
Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences Pouyet, Fanny; Aeschbacher, Simon; Thiéry, Alexandre Benoit Xavier eLife Sciences Publications https://doi.org/10.7892/boris.120988	text	January 2018

Similar Records

Rare key functional domain missense substitutions in MRE11A, RAD50, and NBNcontribute to breast cancer susceptibility: results from a Breast Cancer Family Registry case-control mutation-screening study

Journal Article · Tue Jun 03 00:00:00 EDT 2014 · Breast Cancer Research · OSTI ID:1627278

Damiola, Francesca; Pertesi, Maroulio; Oliver, Javier; +17 more

Genome-Wide Association Study Reveals Complex Genetic Architecture of Cadmium and Mercury Accumulation and Tolerance Traits in Medicago truncatula

Journal Article · Fri Jan 28 00:00:00 EST 2022 · Frontiers in Plant Science · OSTI ID:1627278

Paape, Timothy; Heiniger, Benjamin; Domingo, Miguel Santo; +3 more

Genetic Variation in DNA of Coho Salmon from the Lower Columbia River : Final Report 1993.

Technical Report · Thu Apr 01 00:00:00 EST 1993 · OSTI ID:1627278

Fobes, Stephen; Knudsen, Kathy; Allendorf, Fred

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Genetics & Heredity

Title: Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Citation Formats

References (54)

Cited By (385)

Similar Records

Related Subjects