Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,959

Inference of Population Structure Using Multilocus Genotype Data

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000) · Genetics · doi:10.1093/genetics/155.2.945 · Cited by 33,871

ESTIMATION OF AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE FROM A SMALL NUMBER OF INDIVIDUALS

Nei, M. (1978) · Genetics · doi:10.1093/genetics/89.3.583 · Cited by 11,368

Application of Phylogenetic Networks in Evolutionary Studies

Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,895

Solving Least Squares Problems

Lawson, C. L., & Hanson, R. J. (1995) · doi:10.1137/1.9781611971217 · Cited by 7,103

Probabilistic Graphical Models: Principles and Techniques - Adaptive Computation and Machine Learning

Koller, D., & Friedman, N. (2009) · The MIT Press eBooks · Cited by 6,653

Untitled work

(2009) · Cited by 6,153

Population Structure and Eigenanalysis

Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280

A draft sequence of the Neandertal genome

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318

Mitochondrial DNA and human evolution

Cann, R. L., Stoneking, M., & Wilson, A. C. (1987) · Nature · doi:10.1038/325031a0 · Cited by 3,100

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

Brandenburg, J., Mary‐Huard, T., Rigaill, G. J., Hearne, S., Corti, H., Joets, J., Vitte, C., Charcosset, A., Nicolas, S., & Tenaillon, M. I. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006666 · Cited by 94

A latitudinal phylogeographic diversity gradient in birds

Smith, B. T., Seeholzer, G. F., Harvey, M. G., Cuervo, A. M., & Brumfield, R. T. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2001073 · Cited by 94

The Discovery of Wild Date Palms in Oman Reveals a Complex Domestication History Involving Centers in the Middle East and Africa

Gros‐Balthazard, M., Galimberti, M., Kousathanas, A., Newton, C., Ivorra, S., Paradis, L., Vigouroux, Y., Carter, R. A., Tengberg, M., Battesti, V., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.06.045 · Cited by 89

A genomic map of climate adaptation in Mediterranean cattle breeds

Flori, L., Moazami‐Goudarzi, K., Alary, V., Araba, A., Boujenane, I., Boushaba, N., Casabianca, F., Casu, S., Ciampolini, R., d’Acier, A. C., et al. (2018) · Molecular Ecology · doi:10.1111/mec.15004 · Cited by 95

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep

Chen, Z., Xu, Y., Xie, X.-L., Wang, D., Aguilar‐Gómez, D., Liu, G., Li, X., Esmailizadeh, A., Rezaei, V., Kantanen, J., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02817-4 · Cited by 93

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

Verdu, P., Pemberton, T. J., Laurent, R., Kemp, B. M., González‐Oliver, A., Gorodezky, C., Hughes, C. E., Shattuck, M. R., Petzelt, B., Mitchell, J., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004530 · Cited by 93

Diverse genetic mechanisms underlie worldwide convergent rice feralization

Qiu, J., Jia, L., Wu, D., Weng, X., Chen, L., Sun, J., Chen, M., Mao, L., Jiang, B., Ye, C., et al. (2020) · Genome biology · doi:10.1186/s13059-020-01980-x · Cited by 88

VolcanoFinder: Genomic scans for adaptive introgression

Setter, D., Mousset, S., Cheng, X., Nielsen, R., DeGiorgio, M., & Hermisson, J. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008867 · Cited by 97

Genetic evidence for the origin ofAedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean

Soghigian, J., Gloria‐Soria, A., Robert, V., Goff, G. L., Failloux, A., & Powell, J. R. (2020) · Molecular Ecology · doi:10.1111/mec.15590 · Cited by 95

Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Sikora, M., Carpenter, M. L., Moreno‐Estrada, A., Henn, B. M., Underhill, P. A., Sánchez‐Quinto, F., Zara, I., Pitzalis, M., Sidore, C., Busonero, F., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004353 · Cited by 90

Selection-driven trait loss in independently evolved cavefish populations

Moran, R. L., Richards, E. J., Ornelas‐García, C. P., Gross, J. B., Donny, A. E., Wiese, J., Keene, A. C., Kowalko, J. E., Rohner, N., & McGaugh, S. E. (2023) · Nature Communications · doi:10.1038/s41467-023-37909-8 · Cited by 87

Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken

Luo, W., Luo, C., Wang, M., Guo, L., Chen, X., Li, Z., Zheng, M., Folaniyi, B. S., Luo, W., Shu, D., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-71421-z · Cited by 87

A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan

Kanzawa‐Kiriyama, H., Kryukov, K. A., Jinam, T. A., Hosomichi, K., Saso, A., Suwa, G., Ueda, S., Yoneda, M., Tajima, A., Shinoda, K., et al. (2016) · Journal of Human Genetics · doi:10.1038/jhg.2016.110 · Cited by 87

The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data

Pugach, I., Duggan, A. T., Merriwether, D. A., Friedlaender, F. R., Friedlaender, J. S., & Stoneking, M. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx333 · Cited by 89

Population Genomics Provide Insights into the Evolution and Adaptation of the Eastern Honey Bee (Apis cerana)

Chen, C., Wang, H., Liu, Z., Chen, X., Tang, J., Meng, F., & Shi, W. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy130 · Cited by 85

Quaternary climate changes as speciation drivers in the Amazon floodplains

Thom, G., Xue, A. T., Sawakuchi, A. O., RIBAS, C. C., Hickerson, M. J., Aleixo, A. L. P., & Miyaki, C. Y. (2020) · Science Advances · doi:10.1126/sciadv.aax4718 · Cited by 85

Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data

Reid, N. M., Hird, S. M., Brown, J. M., Pelletier, T. A., McVay, J. D., Satler, J. D., & Carstens, B. C. (2013) · Systematic Biology · doi:10.1093/sysbio/syt057 · Cited by 86

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

Williams, J. L., Hall, S. J. G., Corvo, M. D., Ballingall, K. T., Colli, L., Ajmone‐Marsan, P., & Biscarini, F. (2015) · Animal Genetics · doi:10.1111/age.12376 · Cited by 88

Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes

Bigey, F., Segond, D., Friedrich, A., Guézenec, S., Bourgais, A., Huyghe, L., Agier, N., Nidelet, T., & Sicard, D. (2020) · Current Biology · doi:10.1016/j.cub.2020.11.016 · Cited by 93

Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Kim, D., Taylor, A. T., & Near, T. J. (2022) · Scientific Reports · doi:10.1038/s41598-022-11743-2 · Cited by 84

Genome analyses suggest the presence of polyploidy and recent human‐driven expansions in eight global populations of the honeybee pathogen N osema ceranae

Pelin, A., Selman, M., Aris‐Brosou, S., Farinelli, L., & Corradi, N. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12883 · Cited by 84

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation

Ludlow, C. L., Cromie, G. A., Garmendia‐Torres, C., Sirr, A., Hays, M., Field, C., Jeffery, E. W., Fay, J. C., & Dudley, A. M. (2016) · Current Biology · doi:10.1016/j.cub.2016.02.012 · Cited by 84

Impacts of the Human Gut Microbiome on Therapeutics

Vázquez‐Baeza, Y., Callewaert, C., Debelius, J. W., Hyde, E. R., Marotz, C. A., Morton, J. T., Swafford, A. D.-E., Vrbanac, A. F., Dorrestein, P. C., & Knight, R. D. (2017) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-042017-031849 · Cited by 87

Global Genetic Diversity, Introgression, and Evolutionary Adaptation of Indicine Cattle Revealed by Whole Genome Sequencing

Chen, N., Xia, X., Hanif, Q., Zhang, F., Dang, R., Huang, B., Lyu, Y., Luo, X., Zhang, H., Yan, H., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43626-z · Cited by 83

Fine scale mapping of genomic introgressions within the Drosophila yakuba clade

Turissini, D. A., & Matute, D. R. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006971 · Cited by 88

Powerful Inference with the D-Statistic on Low-Coverage Whole-Genome Data

Soraggi, S., Wiuf, C., & Albrechtsen, A. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.300192 · Cited by 86

A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits

Lu, Q., Huang, L., Liu, H., Garg, V., Gangurde, S. S., Li, H., Chitikineni, A., Guo, D., Pandey, M. K., Li, S., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01660-7 · Cited by 83

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds

Yurchenko, A. A., Yudin, N. S., Айтназаров, Р. Б., Plyusnina, A. V., Brukhin, V. B., Андреевич, С. В., Lhasaranov, B., Popov, R. G., Paronyan, I. A., Plemyashov, K. V., et al. (2017) · Heredity · doi:10.1038/s41437-017-0024-3 · Cited by 84

Adaptive introgression and maintenance of a trispecies hybrid complex in range‐edge populations of Populus

Chhatre, V. E., Evans, L. M., DiFazio, S. P., & Keller, S. R. (2018) · Molecular Ecology · doi:10.1111/mec.14820 · Cited by 83

Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe

Corre, V. L., Siol, M., Vigouroux, Y., Tenaillon, M. I., & Délye, C. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006633117 · Cited by 88

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Saenz‐Agudelo, P., DiBattista, J. D., Piatek, M. J., Gaither, M. R., Harrison, H. B., Nanninga, G. B., & Berumen, M. L. (2015) · Molecular Ecology · doi:10.1111/mec.13471 · Cited by 81

Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes–Amazonia Divide

Gnecchi‐Ruscone, G. A., Sarno, S., Fanti, S. D., Gianvincenzo, L., Giuliani, C., Boattini, A., Bortolini, E., Corcia, T. D., Mellado, C. S., Francia, T. J. D., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz066 · Cited by 82

A polyploid admixed origin of beer yeasts derived from European and Asian wine populations

Fay, J. C., Liu, P., Ong, G. T., Dunham, M. J., Cromie, G. A., Jeffery, E. W., Ludlow, C. L., & Dudley, A. M. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000147 · Cited by 81

Genomic insight into the origins and dispersal of the Brazilian coastal natives

Silva, M. A. C. E., Nunes, K., Lemes, R. B., Mas-Sandoval, À., Amorim, C. E. G., Krieger, J. E., Mill, J. G., Salzano, F. M., Bortolini, M. C., Pereira, A. D. C., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1909075117 · Cited by 82

Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Kutanan, W., Liu, D., Kampuansai, J., Srikummool, M., Srithawong, S., Shoocongdej, R., Sangkhano, S., Ruangchai, S., Pittayaporn, P., Arias, L., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab124 · Cited by 82

The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination

Lofgren, L. A., Ross, B. S., Cramer, R. A., & Stajich, J. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001890 · Cited by 85

Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species

Nazareno, A. G., Dick, C. W., & Lohmann, L. G. (2017) · Molecular Ecology · doi:10.1111/mec.14142 · Cited by 81

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization

Elworth, R. A. L., Ogilvie, H. A., Zhu, J., & Nakhleh, L. K. (2019) · Computational biology · doi:10.1007/978-3-030-10837-3_13 · Cited by 81

Differentiated demographic histories and local adaptations between Sherpas and Tibetans

Zhang, C., Lü, Y., Feng, Q., Wang, X., Lou, H., Liu, J., Ning, Z., Yuan, K., Wang, Y., Zhou, Y., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1242-y · Cited by 80

Applying f 4 ‐statistics and admixture graphs: Theory and examples

Lipson, M. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13230 · Cited by 82

An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons

Weedall, G. D., Riveron, J. M., Hearn, J., Irving, H., Kamdem, C., Fouet, C., White, B. J., & Wondji, C. S. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008822 · Cited by 82

Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple

Ma, Y., Liu, D., Wariss, H. M., Zhang, R., Tao, L., MILNE, R. I., & Sun, W. (2021) · Molecular Ecology · doi:10.1111/mec.16289 · Cited by 80

The genomic history and global expansion of domestic donkeys

Todd, E. T., Tonasso‐Calvière, L., Chauvey, L., Schiavinato, S., Fages, A., Seguin‐Orlando, A., Clavel, P., Khan, N., Pérez-Pardal, L., Rosa, L. P., et al. (2022) · Science · doi:10.1126/science.abo3503 · Cited by 85

Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes

Rose, N. H., Badolo, A., Sylla, M., Akorli, J., Otoo, S., Gloria‐Soria, A., Powell, J. R., White, B. J., Crawford, J. E., & McBride, C. S. (2023) · eLife · doi:10.7554/elife.83524 · Cited by 80

Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States

Niu, J., Ma, S., Zheng, S., Zhang, C., Lu, Y., Si, Y., Tian, S., Shi, X., Liu, X., Naeem, M. K., et al. (2023) · The Plant Cell · doi:10.1093/plcell/koad229 · Cited by 80

Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti

Gloria‐Soria, A., Soghigian, J., Kellner, D., & Powell, J. R. (2019) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0007930 · Cited by 86

Understanding divergent domestication traits from the whole-genome sequencing of swamp- and river-buffalo populations

Luo, X., Zhou, Y. J., Zhang, B., Zhang, Y., Wang, X., Feng, T., Li, Z., Cui, K., Wang, Z., Luo, C., et al. (2020) · National Science Review · doi:10.1093/nsr/nwaa024 · Cited by 81

Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.

Bird, K. A., An, H., Gazave, É., Gore, M. A., Pires, J. C., Robertson, L. D., & Labate, J. A. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00321 · Cited by 79

Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

Shinzato, C., Mungpakdee, S., Arakaki, N., & Satoh, N. (2015) · Scientific Reports · doi:10.1038/srep18211 · Cited by 80

Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

Wang, M., Wang, S., Li, Y., Jhala, Y. V., Thakur, M. K., Otecko, N. O., Si, J., Chen, H.-M., Shapiro, B., Nielsen, R., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa113 · Cited by 80

Gene reuse facilitates rapid radiation and independent adaptation to diverse habitats in the Asian honeybee

Ji, Y., Li, X., Ji, T., Tang, J., Qiu, L., Hu, J., Dong, J., Luo, S., Liu, S., Frandsen, P. B., et al. (2020) · Science Advances · doi:10.1126/sciadv.abd3590 · Cited by 78

Statistical Inference in the Wright–Fisher Model Using Allele Frequency Data

Tataru, P., Simonsen, M., Bataillon, T. M., & Hobolth, A. (2016) · Systematic Biology · doi:10.1093/sysbio/syw056 · Cited by 79

The genetic heritage of Alpine local cattle breeds using genomic SNP data

Senczuk, G., Mastrangelo, S., Ciani, E., Battaglini, L. M., Cendron, F., Ciampolini, R., Crepaldi, P., Mantovani, R., Bongioni, G., Pagnacco, G., et al. (2020) · Genetics Selection Evolution · doi:10.1186/s12711-020-00559-1 · Cited by 76

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Li, D., Sun, G., Zhang, M., Cao, Y., Zhang, C., Fu, Y., Li, F., Li, G., Jiang, R., Han, R., et al. (2020) · BMC Genomics · doi:10.1186/s12864-020-06900-8 · Cited by 78

Back to the Origins: Background and Perspectives of Grapevine Domestication

Grassi, F., & Lorenzis, G. D. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094518 · Cited by 76

Thrice out of Asia and the adaptive radiation of the western honey bee

Dogantzis, K. A., Tiwari, T., Conflitti, I. M., Dey, A., Patch, H. M., Muli, E., Garnery, L., Whitfield, C. W., Stolle, E., Alqarni, A. S., et al. (2021) · Science Advances · doi:10.1126/sciadv.abj2151 · Cited by 81

Maritime route of colonization of Europe

Paschou, P., Petros Drineas, B., Yannaki, E., Razou, A., Kanaki, K., Tsetsos, F., Padmanabhuni, S. S., Michalodimitrakis, M., Renda, M. C., Pavlović, S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320811111 · Cited by 84

Human ancestry correlates with language and reveals that race is not an objective genomic classifier

Baker, J. L., Rotimi, C. N., & Shriner, D. (2017) · Scientific Reports · doi:10.1038/s41598-017-01837-7 · Cited by 78

Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri

Wang, G., Zhang, B.-L., Zhou, W., Li, Y., Jin, J., Shao, Y., Yang, H., Yan-hu, L., Fang, Y., Chen, H.-M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1716257115 · Cited by 80

Phylogenetic Networks: A Review of Methods to Display Evolutionary History

Morrison, D. (2014) · Annual Research & Review in Biology · doi:10.9734/arrb/2014/8230 · Cited by 77

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

Martin, C. H., Crawford, J. E., Turner, B. J., & Simons, L. H. (2016) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2015.2334 · Cited by 75

Human population dynamics and Yersinia pestis in ancient northeast Asia

Kılınç, G. M., Kashuba, N., Koptekin, D., Bergfeldt, N., Dönertaş, H. M., Rodríguez-Varela, R., Shergin, D., Ivanov, G., Kichigin, D., Pestereva, K., et al. (2021) · Science Advances · doi:10.1126/sciadv.abc4587 · Cited by 75

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Xu, W. F., Wu, D., Yang, T., Sun, C., Wang, Z., Han, B., Wu, S., Yu, A., Chapman, M. A., Muraguri, S., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02333-y · Cited by 76

Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species

Thom, G., do Amaral, F. R., Hickerson, M. J., Aleixo, A. L. P., Araújo-Silva, L. E., RIBAS, C. C., Choueri, É. L., & Miyaki, C. Y. (2018) · Systematic Biology · doi:10.1093/sysbio/syy004 · Cited by 75

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

Pfeifer, S. P., Laurent, S., Sousa, V. C., Linnen, C. R., Foll, M., Excoffier, L., Hoekstra, H. E., & Jensen, J. D. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy004 · Cited by 75

Speciation Associated with Shifts in Migratory Behavior in an Avian Radiation

Gómez‐Bahamón, V., Márquez, R., Jahn, A. E., Miyaki, C. Y., Tuero, D. T., Laverde-R., O., Restrepo, S., & Cadena, C. D. (2020) · Current Biology · doi:10.1016/j.cub.2020.01.064 · Cited by 80

Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle

Jemaa, S. B., Mastrangelo, S., Lee, S. H., Lee, J. H., & Boussaha, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-76576-3 · Cited by 76

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

Segherloo, I. H., Freyhof, J., Berrebi, P., Ferchaud, A., Geiger, M. F., Laroche, J., Levin, B., Normandeau, É., & Bernatchez, L. (2021) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2021.107204 · Cited by 76

Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa

Kolář, F., Šrámková, G., Záveská, E., Nagano, A. J., Hyklová, L., Lučanová, M., Kudoh, H., & Marhold, K. (2016) · Molecular Ecology · doi:10.1111/mec.13721 · Cited by 74

Beyond broad strokes: sociocultural insights from the study of ancient genomes

Racimo, F., Sikora, M., Linden, M. V., Schroeder, H., & Lalueza‐Fox, C. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0218-z · Cited by 80

Detecting and Measuring Selection from Gene Frequency Data

Vitalis, R., Gautier, M., Dawson, K. J., & Beaumont, M. (2013) · Genetics · doi:10.1534/genetics.113.152991 · Cited by 80

Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

Shi, S., Shao, D., Yang, L., Liang, Q., Han, W., Xue, Q., Qu, L., Leng, L., Li, Y., Zhao, X., et al. (2022) · Journal of Advanced Research · doi:10.1016/j.jare.2022.07.005 · Cited by 76

Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes

Martin, C. H., & Feinstein, L. C. (2014) · Molecular Ecology · doi:10.1111/mec.12658 · Cited by 73

Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa

Forsman, Z. H., Knapp, I. S. S., Tisthammer, K. H., Eaton, D. A. R., Belcaid, M., & Toonen, R. J. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.03.023 · Cited by 78

The demographic history of Atlantic salmon ( Salmo salar ) across its distribution range reconstructed from approximate Bayesian computations*

Rougemont, Q., & Bernatchez, L. (2018) · Evolution · doi:10.1111/evo.13486 · Cited by 77

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

Kubota, S., Iwasaki, T., Hanada, K., Nagano, A. J., Fujiyama, A., Toyoda, A., Sugano, S., Suzuki, Y., Hikosaka, K., Itô, M., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005361 · Cited by 74

The advantages of going large: genome‐wide SNP s clarify the complex population history and systematics of the threatened western pond turtle

Spinks, P. Q., Thomson, R. C., & Shaffer, H. B. (2014) · Molecular Ecology · doi:10.1111/mec.12736 · Cited by 74

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

Wei, T., Kim, T., & Park, Y. (2016) · Rice · doi:10.1186/s12284-016-0129-y · Cited by 72

Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest

Bracewell, R., Bentz, B., Sullivan, B. T., & Good, J. M. (2017) · Nature Communications · doi:10.1038/s41467-017-01761-4 · Cited by 74

Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence

Page, A. M. L., Gibson, J., Meyer, R. S., & Chapman, M. A. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz062 · Cited by 72

Diversity of copy number variation in the worldwide goat population

Liu, M., Zhou, Y., Rosen, B. D., Tassell, C. P. V., Stella, A., Tosser‐Klopp, G., Rupp, R., Palhière, I., Colli, L., Sayre, B. L., et al. (2018) · Heredity · doi:10.1038/s41437-018-0150-6 · Cited by 72

Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul

Brucato, N., André, M., Tsang, R., Saag, L., Kariwiga, J., Sesuki, K., Beni, T., Pomat, W. S., Muke, J., Meyer, V., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab238 · Cited by 72

Population Histories and Genomic Diversity of South American Natives

Silva, M. A. C. E., Ferraz, T., Couto-Silva, C. M., Lemes, R. B., Nunes, K., Comas, D., & Hünemeier, T. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab339 · Cited by 75

River network rearrangements promote speciation in lowland Amazonian birds

Musher, L. J., Giakoumis, M., Albert, J. S., Del‐Rio, G., Rêgo, M. A., Thom, G., Aleixo, A. L. P., RIBAS, C. C., Brumfield, R. T., Smith, B. T., et al. (2022) · Science Advances · doi:10.1126/sciadv.abn1099 · Cited by 71

Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage

Belkadi, A., Pedergnana, V., Cobat, A., Itan, Y., Vincent, Q. B., Abhyankar, A., Shang, L., Baghdadi, J. E., Bousfiha, A. A., Alcaïs, A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1606460113 · Cited by 76

Deterministic Parallel Analysis: An Improved Method for Selecting Factors and Principal Components

Dobriban, E., & Owen, A. B. (2018) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/rssb.12301 · Cited by 71

Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce

Chen, J., Li, L., Milesi, P., Jansson, G., Berlin, M., Karlsson, B., Aleksic, J., Vendramin, G. G., & Lascoux, M. (2019) · Evolutionary Applications · doi:10.1111/eva.12801 · Cited by 71

Siberian genetic diversity reveals complex origins of the Samoyedic‐speaking populations

Karafet, T. M., Osipova, L. P., Savina, O. V., Hallmark, B., & Hammer, M. F. (2018) · American Journal of Human Biology · doi:10.1002/ajhb.23194 · Cited by 70

Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers

Kovačević, L., Tambets, K., IlumäE, A.-M., Kushniarevich, A., Yunusbayev, B., Solnik, A., Bego, T., Primorac, D., Škaro, V., Leskovac, A. R., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105090 · Cited by 73

On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

Pilot, M., Malewski, T., Moura, A. E., Grzybowski, T., Oleński, K., Ruść, A., Kamiński, S., Fadel, F. R., Mills, D. S., Alagaili, A. N., et al. (2015) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2015.2189 · Cited by 70

Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure ofCoccidioides

Teixeira, M. D. M., & Barker, B. M. (2016) · Emerging infectious diseases · doi:10.3201/eid2206.151565 · Cited by 70

Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism

Card, D. C., Schield, D. R., Adams, R. H. J., Corbin, A. B., Perry, B. W., Andrew, A. L., Pasquesi, G. I. M., Smith, E. N., Ježková, T., Boback, S. M., et al. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.05.034 · Cited by 70

Comparative genome analyses reveal the unique genetic composition and selection signals underlying the phenotypic characteristics of three Chinese domestic goat breeds

Guo, J., Zhong, J., Li, L., Zhong, T., Wang, L., Song, T., & Zhang, H. (2019) · Genetics Selection Evolution · doi:10.1186/s12711-019-0512-4 · Cited by 72

Inference of natural selection from ancient DNA

Dehasque, M., Ávila‐Arcos, M. C., Díez‐del‐Molino, D., Fumagalli, M., Guschanski, K., Lorenzen, E. D., Malaspinas, A., Marquès‐Bonet, T., Martin, M. D., Murray, G. G. R., et al. (2020) · Evolution Letters · doi:10.1002/evl3.165 · Cited by 78

An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages

Nespolo, R. F., Villarroel, C. A., Oporto, C. I., Tapia, S. M., Vega-Macaya, F., Urbina, K., Chiara, M. D., Mozzachiodi, S., Mikhalev, E., Thompson, D. A., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008777 · Cited by 70

Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals

Tournebize, R., Chu, G., & Moorjani, P. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010243 · Cited by 71

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression

Ivanov, V., Lee, K. M., & Mutanen, M. (2018) · Molecular Ecology · doi:10.1111/mec.14564 · Cited by 69

GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars

D’Agostino, N., Taranto, F., Camposeo, S., Mangini, G., Fanelli, V., Gadaleta, S., Miazzi, M. M., Pavan, S., di Rienzo, V., Sabetta, W., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-34207-y · Cited by 74

Population structure, genetic connectivity, and adaptation in the Olympia oyster ( Ostrea lurida ) along the west coast of North America

Silliman, K. (2019) · Evolutionary Applications · doi:10.1111/eva.12766 · Cited by 68

Distinct genetic variation and heterogeneity of the Iranian population

Mehrjoo, Z., Fattahi, Z., Beheshtian, M., Mohseni, M., Poustchi, H., Ardalani, F., Jalalvand, K., Arzhangi, S., Mohammadi, Z., Khoshbakht, S., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008385 · Cited by 70

Migration from trees to graphs

Bahcall, O. G. (2012) · Nature Genetics · doi:10.1038/ng.2514

Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies

Reyna-Blanco, C. S., Caduff, M., Galimberti, M., Leuenberger, C., & Wegmann, D. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae137 · Cited by 2

Inference of complex population histories using whole-genome sequences from multiple populations

Steinrücken, M., Kamm, J., Spence, J. P., & Song, Y. S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1905060116 · Cited by 81

Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow

Lipson, M., Loh, P., Levin, A., Reich, D., Patterson, N. J., & Berger, B. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst099 · Cited by 119

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data

Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906