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Method: Network-based hierarchical population structure analysis for large genomic data sets
- Gili Greenbaum,
- Amir Rubin,
- Alan R. Templeton,
- and Noah A. Rosenberg
Genome Res. December 2019 29: 2020-2033; Published in Advance November 6, 2019, doi:10.1101/gr.250092.119
...along the northeast coast. (F) Branch not belonging to the primary European branch in Figure 2A, corresponding to the Iberian Peninsula and Morocco. Population structure extends on a north–south axis from Africa to Europe over the Strait of Gibraltar. (G) Branch corresponding to Morocco, showing fine...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...recombination map for a rhesus macaque pedigree using crossovers among 241 microsatellite loci (Rogers et al. 2006) also suggested reduced recombination per megabase in rhesus relative to human. Demographic analysis of two rhesus macaque populations The estimated effective population sizes, based on the number...
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Research: Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs
- Brian P. McEvoy,
- Joseph E. Powell,
- Michael E. Goddard,
- and Peter M. Visscher
Genome Res. June 2011 21: 821-829; Published in Advance April 25, 2011, doi:10.1101/gr.119636.110
.... Abstract Genetic and fossil evidence supports a single, recent (&lt;200,000 yr) origin of modern Homo sapiens in Africa, followed by later population divergence and dispersal across the globe (the “Out of Africa” model). However, there is less agreement on the exact nature of this migration event...
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Method: Inferring ancestry with the hierarchical soft clustering approach tangleGen
- Klara Elisabeth Burger,
- Solveig Klepper,
- Ulrike von Luxburg,
- and Franz Baumdicker
Genome Res. December 2024 34: 2244-2255; Published in Advance October 21, 2024, doi:10.1101/gr.279399.124
...clustering, and the corresponding nodes give the number of populations identified at that stage. For visualization, see Figure 3. Additionally, tangleGen offers a pruning option that allows to exclude the external branches in the tangles tree, which are not supported by a sufficient number of cuts...
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Resource: An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa
- Rosaria Scozzari,
- Andrea Massaia,
- Beniamino Trombetta,
- Giovanna Bellusci,
- Natalie M. Myres,
- Andrea Novelletto,
- and Fulvio Cruciani
Genome Res. March 2014 24: 535-544; Published in Advance January 6, 2014, doi:10.1101/gr.160788.113
...branches, and how they relate to the population genetics of Africa over a time horizon that begins well before the exit from the continent. Results A high-depth resequencing (average 503) of ;1.5 Mb of the MSY was performed in 68 unrelated males representing major Y chromosome haplogroups (Supplemental...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...populations from Madagascar and South Africa diverged around 200 kya, the two S. dumicola populations in North and South Namibia diverged 20 kya, and the two S. sarasinorum populations from Himalaya and Sri Lanka diverged ∼110 kya.The pseudodiploid of social species collapsed two heavily inbred diploid...
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Method: Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data
- Anand Bhaskar,
- Y.X. Rachel Wang,
- and Yun S. Song
Genome Res. February 2015 25: 268-279; Published in Advance January 6, 2015, doi:10.1101/gr.178756.114
...expansion factor inferred by Nelson et al. (2012) in the CEU subpopulation. The ancestral population bottlenecks reflect the out-of-Africa bottleneck and the European-Asian population split, and these parameters were set to those estimated by Keinan et al. (2007). The population size functions...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...and recombination. J Hered 101: S21–S33. doi:10.1093/jhered/esq009 ↵Asher JH. 1970. Parthenogenesis and genetic variability. II. One-locus models for various diploid populations. Genetics 66: 369–391. doi:10.1093/genetics/66.2.369 ↵Blouin M, Parsons M, Lacaille V, Lotz S. 1996. Use of microsatellite loci...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
..., as restriction fragment length polymorphisms, microsatellites, and small-scale DNA sequencing (e.g., Kreitman 1983) broadened the range of questions open to empirical investigation. With the recent flood of -wide single nucleotide polymorphism (SNP) data, and now the advent of fully sequenced population samples...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
...location of the source population. Patterns of microsatellite and haplotype diversity in theHumanGenomeDiversity Project (HGDP) panel fit this expectation, with the strongest negative correlation being observed between diversity and distance from sub-Saharan Africa (Ramachandran et al. 2005; Li et al. 2008...

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