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

Citations

Cited by:

1. Gabriele Senczuk & Marika Di Civita & Luigina Rillo & Alessandra Macciocchi & Mariaconsiglia Occidente & Giorgio Saralli & Valentina D’Onofrio & Tiziana Galli & Christian Persichilli & Claudio Di Giov, 2023. "The genome-wide relationships of the critically endangered Quadricorna sheep in the Mediterranean region," PLOS ONE, Public Library of Science, vol. 18(10), pages 1-15, October.
2. 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.
3. 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.
4. 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.
5. Heng Du & Lei Zhou & Zhen Liu & Yue Zhuo & Meilin Zhang & Qianqian Huang & Shiyu Lu & Kai Xing & Li Jiang & Jian-Feng Liu, 2024. "The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. Patar Sinaga & Ewelina Klichowska & Arkadiusz Nowak & Marcin Nobis, 2024. "Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia," PLOS ONE, Public Library of Science, vol. 19(2), pages 1-25, February.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. Soraggi, Samuele & Wiuf, Carsten, 2019. "General theory for stochastic admixture graphs and F-statistics," Theoretical Population Biology, Elsevier, vol. 125(C), pages 56-66.
21. 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.
22. repec:plo:pgen00:1006971 is not listed on IDEAS
23. 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.
24. 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.
25. Svend V Nielsen & Andrew H Vaughn & Kalle Leppälä & Michael J Landis & Thomas Mailund & Rasmus Nielsen, 2023. "Bayesian inference of admixture graphs on Native American and Arctic populations," PLOS Genetics, Public Library of Science, vol. 19(2), pages 1-22, February.
26. 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.
27. 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.
28. 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.
29. Yawen Zhang & Bo Zhang & Ziwei Li & Fengxiang Hou & Yan Zhao & Junjie Jin & Bin Song & Wenjie Gu, 2025. "Whole-genome resequencing data reveal the genetic diversity of local chickens in southern Zhejiang and surrounding areas in China," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 70(3), pages 113-120.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.