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Methods: A new approach to estimate parameters of speciation models with application to apes
- Celine Becquet and
- Molly Przeworski
Genome Res. October 2007 17: 1505-1519; Published in Advance August 21, 2007, doi:10.1101/gr.6409707
...that the two chimpanzee species became reproductively isolated in allopatry ∼850 Kya, while Western and Central chimpanzee populations split ∼440 Kya but continued to exchange migrants. Similarly, Eastern and Western gorillas and Sumatran and Bornean orangutans appear to have experienced gene flow since...
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Research: Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
- Asher D. Cutter and
- Jae Young Choi
Genome Res. August 2010 20: 1103-1111; Published in Advance May 27, 2010, doi:10.1101/gr.104331.109
...exploration of variation among species in the relative roles of positive and negative selection shaping genomic patterns of polymorphism. Finally, our contrasts between multiple reproductively isolated lineages demonstrate explicitly the confounding effect of ancestral polymorphism on an inference of RAM...
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Method: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
- Igor Rodrigues Costa,
- Francisco Prosdocimi,
- and W. Bryan Jennings
Genome Res. September 2016 26: 1257-1267; Published in Advance July 19, 2016, doi:10.1101/gr.203950.115
...ancestral effective population sizes (Na) for the human–chimpanzee ancestor (NHC), human–chimpanzee–gorilla ancestor (NHCG), and human– chimpanzee–gorilla–orangutan ancestor (NHCGO). (B) Inferred speciation time in millions of years ago (Mya) between: human and chimpanzee lineages (τH-C), divergence leading...
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Research: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
- Gang Li,
- Brian W. Davis,
- Eduardo Eizirik,
- and William J. Murphy
Genome Res. January 2016 26: 1-11; Published in Advance October 30, 2015, doi:10.1101/gr.186668.114
...maintain species-level distinctiveness (Roca et al. 2005; Good et al. 2008; Ellegren et al. 2012; Garrigan et al. 2012; Toews and Brelsford 2012; Cahill et al. 2013, 2014; Cui et al. 2013; Martin et al. 2013; Kutschera et al. 2014; Sullivan et al. 2014). However, incomplete lineage sorting (ILS) is assumed...
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Perspective: Phylogenomics of primates and their ancestral populations
- Adam Siepel
Genome Res. November 2009 19: 1929-1941; Published in Advance October 3, 2009, doi:10.1101/gr.084228.108
...for these populations with any certainty. Incomplete lineage sorting As discussed above, local genealogies discordant with the species phylogeny, due to incomplete lineage sorting (ILS), are expected to Figure 5. Aligned human (Hum), chimpanzee (Pan), gorilla (Gor), and orangutan (Pon) sequences, showing substitutions...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...and natural selectionThe time of divergence (i.e., branch lengths) between human, chimpanzee, gorilla, orangutan, macaque, marmoset, tarsier, galago (a.k.a. bush baby), and mouse lemur was obtained from 10kTrees, which uses Bayesian inference to estimate these (Arnold et al. 2010). Measures of natural...
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Method: Genome-scale coestimation of species and gene trees
- Bastien Boussau,
- Gergely J. Szöllősi,
- Laurent Duret,
- Manolo Gouy,
- Eric Tannier,
- and Vincent Daubin
Genome Res. February 2013 23: 323-330; Published in Advance November 6, 2012, doi:10.1101/gr.141978.112
.... Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res 21: 349–356. Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet...
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Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...the relationships among humans, chimpanzees, gorillas, and orangutans. He or she unwisely follows Witherspoon’s protocol exactly and targets Alu elements from the Yb8/9 family. As a result, they will find a plethora of insertions in the human but nothing of interest from any of the other taxa because these families...

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