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

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1. Thomas L. Schmidt & Nancy M. Endersby-Harshman & Anthony R. J. Rooyen & Michelle Katusele & Rebecca Vinit & Leanne J. Robinson & Moses Laman & Stephan Karl & Ary A. Hoffmann, 2024. "Global, asynchronous partial sweeps at multiple insecticide resistance genes in Aedes mosquitoes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
2. Alejandro Ochoa & John D Storey, 2021. "Estimating FST and kinship for arbitrary population structures," PLOS Genetics, Public Library of Science, vol. 17(1), pages 1-36, January.
3. Marina Muzzio & Josefina M B Motti & Paula B Paz Sepulveda & Muh-ching Yee & Thomas Cooke & María R Santos & Virginia Ramallo & Emma L Alfaro & Jose E Dipierri & Graciela Bailliet & Claudio M Bravi & , 2018. "Population structure in Argentina," PLOS ONE, Public Library of Science, vol. 13(5), pages 1-13, May.
4. Baharian, Soheil & Gravel, Simon, 2018. "On the decidability of population size histories from finite allele frequency spectra," Theoretical Population Biology, Elsevier, vol. 120(C), pages 42-51.
5. Jun Gojobori & Nami Arakawa & Xiayire Xiaokaiti & Yuki Matsumoto & Shuichi Matsumura & Hitomi Hongo & Naotaka Ishiguro & Yohey Terai, 2024. "Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
6. Hobolth, Asger & Siren, Jukka, 2016. "The multivariate Wright–Fisher process with mutation: Moment-based analysis and inference using a hierarchical Beta model," Theoretical Population Biology, Elsevier, vol. 108(C), pages 36-50.
7. Stephen R. Doyle & Martin Jensen Søe & Peter Nejsum & Martha Betson & Philip J. Cooper & Lifei Peng & Xing-Quan Zhu & Ana Sanchez & Gabriela Matamoros & Gustavo Adolfo Fontecha Sandoval & Cristina Cut, 2022. "Population genomics of ancient and modern Trichuris trichiura," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
8. Yvonne Willi & Kay Lucek & Olivier Bachmann & Nora Walden, 2022. "Recent speciation associated with range expansion and a shift to self-fertilization in North American Arabidopsis," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
9. Humberto García-Ortiz & Francisco Barajas-Olmos & Cecilia Contreras-Cubas & Miguel Ángel Cid-Soto & Emilio J. Córdova & Federico Centeno-Cruz & Elvia Mendoza-Caamal & Isabel Cicerón-Arellano & Marlen , 2021. "The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
10. Philippe Gambette & Leo van Iersel & Mark Jones & Manuel Lafond & Fabio Pardi & Celine Scornavacca, 2017. "Rearrangement moves on rooted phylogenetic networks," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-21, August.
11. Alexandros G. Sotiropoulos & Epifanía Arango-Isaza & Tomohiro Ban & Chiara Barbieri & Salim Bourras & Christina Cowger & Paweł C. Czembor & Roi Ben-David & Amos Dinoor & Simon R. Ellwood & Johannes Gr, 2022. "Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
12. Mateja Janeš & Minja Zorc & Maja Ferenčaković & Ino Curik & Peter Dovč & Vlatka Cubric-Curik, 2021. "Genomic Characterization of the Three Balkan Livestock Guardian Dogs," Sustainability, MDPI, vol. 13(4), pages 1-16, February.
13. Alice Feurtey & Cécile Lorrain & Megan C. McDonald & Andrew Milgate & Peter S. Solomon & Rachael Warren & Guido Puccetti & Gabriel Scalliet & Stefano F. F. Torriani & Lilian Gout & Thierry C. Marcel &, 2023. "A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
14. Buzbas, Erkan Ozge & Verdu, Paul, 2018. "Inference on admixture fractions in a mechanistic model of recurrent admixture," Theoretical Population Biology, Elsevier, vol. 122(C), pages 149-157.
15. Youjie Zhao & Chengyong Su & Bo He & Ruie Nie & Yunliang Wang & Junye Ma & Jingyu Song & Qun Yang & Jiasheng Hao, 2023. "Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
16. Renzo F. Balboa & Laura D. Bertola & Anna Brüniche-Olsen & Malthe Sebro Rasmussen & Xiaodong Liu & Guillaume Besnard & Jordi Salmona & Cindy G. Santander & Shixu He & Dietmar Zinner & Miguel Pedrono &, 2024. "African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
17. Ningbo Chen & Xiaoting Xia & Quratulain Hanif & Fengwei Zhang & Ruihua Dang & Bizhi Huang & Yang Lyu & Xiaoyu Luo & Hucai Zhang & Huixuan Yan & Shikang Wang & Fuwen Wang & Jialei Chen & Xiwen Guan & Y, 2023. "Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
18. He Yu & Alexandra Jamieson & Ardern Hulme-Beaman & Chris J. Conroy & Becky Knight & Camilla Speller & Hiba Al-Jarah & Heidi Eager & Alexandra Trinks & Gamini Adikari & Henriette Baron & Beate Böhlendo, 2022. "Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
19. Pei-Kuan Cong & Wei-Yang Bai & Jin-Chen Li & Meng-Yuan Yang & Saber Khederzadeh & Si-Rui Gai & Nan Li & Yu-Heng Liu & Shi-Hui Yu & Wei-Wei Zhao & Jun-Quan Liu & Yi Sun & Xiao-Wei Zhu & Pian-Pian Zhao , 2022. "Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
20. Rozaimi Mohamad Razali & Juan Rodriguez-Flores & Mohammadmersad Ghorbani & Haroon Naeem & Waleed Aamer & Elbay Aliyev & Ali Jubran & Andrew G. Clark & Khalid A. Fakhro & Younes Mokrab, 2021. "Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
21. Felix Riede & Christian Hoggard & Stephen Shennan, 2019. "Reconciling material cultures in archaeology with genetic data requires robust cultural evolutionary taxonomies," Palgrave Communications, Palgrave Macmillan, vol. 5(1), pages 1-9, December.
22. Rachel L. Moran & Emilie J. Richards & Claudia Patricia Ornelas-García & Joshua B. Gross & Alexandra Donny & Jonathan Wiese & Alex C. Keene & Johanna E. Kowalko & Nicolas Rohner & Suzanne E. McGaugh, 2023. "Selection-driven trait loss in independently evolved cavefish populations," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
23. David B. Stern & Nathan W. Anderson & Juanita A. Diaz & Carol Eunmi Lee, 2022. "Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
24. Ran Tian & Yaolei Zhang & Hui Kang & Fan Zhang & Zhihong Jin & Jiahao Wang & Peijun Zhang & Xuming Zhou & Janet M. Lanyon & Helen L. Sneath & Lucy Woolford & Guangyi Fan & Songhai Li & Inge Seim, 2024. "Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
25. Soraggi, Samuele & Wiuf, Carsten, 2019. "General theory for stochastic admixture graphs and F-statistics," Theoretical Population Biology, Elsevier, vol. 125(C), pages 56-66.
26. Elena Arciero & Sufyan A. Dogra & Daniel S. Malawsky & Massimo Mezzavilla & Theofanis Tsismentzoglou & Qin Qin Huang & Karen A. Hunt & Dan Mason & Saghira Malik Sharif & David A. Heel & Eamonn Sherida, 2021. "Fine-scale population structure and demographic history of British Pakistanis," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
27. Crystal M. Tomlin & Sitaram Rajaraman & Jeanne Theresa Sebesta & Anne-Cathrine Scheen & Mika Bendiksby & Yee Wen Low & Jarkko Salojärvi & Todd P. Michael & Victor A. Albert & Charlotte Lindqvist, 2024. "Allopolyploid origin and diversification of the Hawaiian endemic mints," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
28. Chris J. Brauer & Jonathan Sandoval-Castillo & Katie Gates & Michael P. Hammer & Peter J. Unmack & Louis Bernatchez & Luciano B. Beheregaray, 2023. "Natural hybridization reduces vulnerability to climate change," Nature Climate Change, Nature, vol. 13(3), pages 282-289, March.
29. Lejla Kovacevic & Kristiina Tambets & Anne-Mai Ilumäe & Alena Kushniarevich & Bayazit Yunusbayev & Anu Solnik & Tamer Bego & Dragan Primorac & Vedrana Skaro & Andreja Leskovac & Zlatko Jakovski & Katj, 2014. "Standing at the Gateway to Europe - The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-15, August.
30. Feng Liu & Jiantao Zhao & Honghe Sun & Cheng Xiong & Xuepeng Sun & Xin Wang & Zhongyi Wang & Robert Jarret & Jin Wang & Bingqian Tang & Hao Xu & Bowen Hu & Huan Suo & Bozhi Yang & Lijun Ou & Xuefeng L, 2023. "Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
31. S Elfekih & P Etter & W T Tay & M Fumagalli & K Gordon & E Johnson & P De Barro, 2018. "Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories," PLOS ONE, Public Library of Science, vol. 13(1), pages 1-17, January.