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Inference of human population history from individual whole-genome sequences

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Cited by:

  1. Wilton, Peter R. & Baduel, Pierre & Landon, Matthieu M. & Wakeley, John, 2017. "Population structure and coalescence in pedigrees: Comparisons to the structured coalescent and a framework for inference," Theoretical Population Biology, Elsevier, vol. 115(C), pages 1-12.
  2. Aoki, Kenichi & Wakano, Joe Yuichiro, 2022. "Hominin forager technology, food sharing, and diet breadth," Theoretical Population Biology, Elsevier, vol. 144(C), pages 37-48.
  3. Gideon S Bradburd & Peter L Ralph & Graham M Coop, 2016. "A Spatial Framework for Understanding Population Structure and Admixture," PLOS Genetics, Public Library of Science, vol. 12(1), pages 1-38, January.
  4. Hobolth, Asger & Jensen, Jens Ledet, 2014. "Markovian approximation to the finite loci coalescent with recombination along multiple sequences," Theoretical Population Biology, Elsevier, vol. 98(C), pages 48-58.
  5. Kevin J Liu & Jingxuan Dai & Kathy Truong & Ying Song & Michael H Kohn & Luay Nakhleh, 2014. "An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes," PLOS Computational Biology, Public Library of Science, vol. 10(6), pages 1-13, June.
  6. 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.
  7. Kimmel, Marek & Wojdyła, Tomasz, 2016. "Genetic demographic networks: Mathematical model and applications," Theoretical Population Biology, Elsevier, vol. 111(C), pages 75-86.
  8. Jewett, Ethan M. & Rosenberg, Noah A., 2014. "Theory and applications of a deterministic approximation to the coalescent model," Theoretical Population Biology, Elsevier, vol. 93(C), pages 14-29.
  9. Juraj Bergman & Rasmus Ø. Pedersen & Erick J. Lundgren & Rhys T. Lemoine & Sophie Monsarrat & Elena A. Pearce & Mikkel H. Schierup & Jens-Christian Svenning, 2023. "Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  10. Thomas Mailund & Anders E Halager & Michael Westergaard & Julien Y Dutheil & Kasper Munch & Lars N Andersen & Gerton Lunter & Kay Prüfer & Aylwyn Scally & Asger Hobolth & Mikkel H Schierup, 2012. "A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species," PLOS Genetics, Public Library of Science, vol. 8(12), pages 1-19, December.
  11. Barton, N.H. & Etheridge, A.M. & Kelleher, J. & Véber, A., 2013. "Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks," Theoretical Population Biology, Elsevier, vol. 87(C), pages 105-119.
  12. Per Unneberg & Mårten Larsson & Anna Olsson & Ola Wallerman & Anna Petri & Ignas Bunikis & Olga Vinnere Pettersson & Chiara Papetti & Astthor Gislason & Henrik Glenner & Joan E. Cartes & Leocadio Blan, 2024. "Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins," Nature Communications, Nature, vol. 15(1), pages 1-29, December.
  13. 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.
  14. Rong Wang & Chao-Nan Liu & Simon T. Segar & Yu-Ting Jiang & Kai-Jian Zhang & Kai Jiang & Gang Wang & Jing Cai & Lu-Fan Chen & Shan Chen & Jing Cheng & Stephen G. Compton & Jun-Yin Deng & Yuan-Yuan Din, 2024. "Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  15. Jason Flannick & Joshua M Korn & Pierre Fontanillas & George B Grant & Eric Banks & Mark A Depristo & David Altshuler, 2012. "Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-13, July.
  16. Yuan Yin & Huizhong Fan & Botong Zhou & Yibo Hu & Guangyi Fan & Jinhuan Wang & Fan Zhou & Wenhui Nie & Chenzhou Zhang & Lin Liu & Zhenyu Zhong & Wenbo Zhu & Guichun Liu & Zeshan Lin & Chang Liu & Jion, 2021. "Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
  17. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
  18. Alberto A. Campos & Cameron D. Bullen & Edward J. Gregr & Iain McKechnie & Kai M. A. Chan, 2022. "Steller’s sea cow uncertain history illustrates importance of ecological context when interpreting demographic histories from genomes," Nature Communications, Nature, vol. 13(1), pages 1-3, December.
  19. Ait Kaci Azzou, S. & Larribe, F. & Froda, S., 2016. "Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes," Theoretical Population Biology, Elsevier, vol. 111(C), pages 16-27.
  20. Kerdoncuff, Elise & Lambert, Amaury & Achaz, Guillaume, 2020. "Testing for population decline using maximal linkage disequilibrium blocks," Theoretical Population Biology, Elsevier, vol. 134(C), pages 171-181.
  21. Yupeng Sang & Zhiqin Long & Xuming Dan & Jiajun Feng & Tingting Shi & Changfu Jia & Xinxin Zhang & Qiang Lai & Guanglei Yang & Hongying Zhang & Xiaoting Xu & Huanhuan Liu & Yuanzhong Jiang & Pär K. In, 2022. "Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  22. Kim, Junhyong & Mossel, Elchanan & Rácz, Miklós Z. & Ross, Nathan, 2015. "Can one hear the shape of a population history?," Theoretical Population Biology, Elsevier, vol. 100(C), pages 26-38.
  23. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
  24. Johndrow, James E. & Palacios, Julia A., 2019. "Exact limits of inference in coalescent models," Theoretical Population Biology, Elsevier, vol. 125(C), pages 75-93.
  25. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  26. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  27. Yee Wen Low & Sitaram Rajaraman & Crystal M. Tomlin & Joffre Ali Ahmad & Wisnu H. Ardi & Kate Armstrong & Parusuraman Athen & Ahmad Berhaman & Ruth E. Bone & Martin Cheek & Nicholas R. W. Cho & Le Min, 2022. "Genomic insights into rapid speciation within the world’s largest tree genus Syzygium," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  28. Guangping Huang & Lingyun Song & Xin Du & Xin Huang & Fuwen Wei, 2023. "Evolutionary genomics of camouflage innovation in the orchid mantis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  29. 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.
  30. Xiaodong Liu & Long Lin & Mikkel-Holger S. Sinding & Laura D. Bertola & Kristian Hanghøj & Liam Quinn & Genís Garcia-Erill & Malthe Sebro Rasmussen & Mikkel Schubert & Patrícia Pečnerová & Renzo F. Ba, 2024. "Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  31. 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.
  32. Deng, Yun & Song, Yun S. & Nielsen, Rasmus, 2021. "The distribution of waiting distances in ancestral recombination graphs," Theoretical Population Biology, Elsevier, vol. 141(C), pages 34-43.
  33. Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
  34. 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.
  35. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  36. Mazet, Olivier & Rodríguez, Willy & Chikhi, Lounès, 2015. "Demographic inference using genetic data from a single individual: Separating population size variation from population structure," Theoretical Population Biology, Elsevier, vol. 104(C), pages 46-58.
  37. Yu-Ping Poh & Vera S Domingues & Hopi E Hoekstra & Jeffrey D Jensen, 2014. "On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-9, November.
  38. Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.
  39. Jörn Bethune & April Kleppe & Søren Besenbacher, 2022. "A method to build extended sequence context models of point mutations and indels," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
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