Genetic evidence for complex speciation of humans and chimpanzees

@article{Patterson2006GeneticEF,
  title={Genetic evidence for complex speciation of humans and chimpanzees},
  author={Nick J. Patterson and Daniel J. Richter and Sante Gnerre and Eric S. Lander and David Reich},
  journal={Nature},
  year={2006},
  volume={441},
  pages={1103-1108}
}
The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our… 
Complex speciation of humans and chimpanzees Arising from :
TLDR
The claim of hybridization is unwarranted because Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and—even if the null model could be rejected—they do not consider other explanations of a short divergence time on the X chromosome.
An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees.
TLDR
The simplest speciation model with instantaneous split adequately describes the human-chimpanzee speciation event, and there is no strong reason to involve complicated factors in explaining the autosomal data.
Insights into hominid evolution from the gorilla genome sequence
TLDR
A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing.
AnAutosomal Analysis Gives No Genetic Evidence for Complex Speciation of Humans and Chimpanzees
TLDR
The simplest speciation model with instantaneous split adequately describes the human–chimpanzee speciation event, and there is no strong reason to involve complicated factors in explaining the autosomal data.
Strong selection in the human-chimpanzee ancestor links the X chromosome to speciation
TLDR
Complete lineage sorting patterns between humans, chimpanzees and gorillas are studied to show that this low divergence is entirely due to megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced.
Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors
TLDR
Comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, the authors' evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior.
Analysis of Chimpanzee History Based on Genome Sequence Alignments
TLDR
Tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque provide a more precise understanding of demographic history.
Inferring the Process of Human–Chimpanzee Speciation
Although the fossil record around the times of the key speciation events that splits humans from orangutans, gorillas and chimpanzees is sparse, genetic comparisons of the extant apes enable us to
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
TLDR
The human–chimpanzee split is dated to at least 7–8 million years and the population split between Neanderthals and modern humans to 400,000–800,000 y ago, which suggests that molecular divergence dates may not be in conflict with the attribution of 6- to 7-million-y-old fossils to the human lineage and 400,,000-Y-old bones to the Neanderthal lineage.
...
...

References

SHOWING 1-10 OF 64 REFERENCES
Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences.
  • N. Takahata, Y. Satta
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1997
TLDR
It is argued that the human ancestral lineage branched off from the NWM and OWM earlier than once thought and that significant demographic changes might have occurred at different evolutionary stages, particularly at the hominid stage.
Complex speciation of humans and chimpanzees
TLDR
The claim of hybridization is unwarranted because Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and—even if the null model could be rejected—they do not consider other explanations of a short divergence time on the X chromosome.
Inferring the Mode of Speciation From Genomic Data
TLDR
Using 345 coding and 143 intergenic sequences from the African great apes, this work was able to reject the null hypothesis that the divergence time in the coding sequences (CDSs) andIntergenic sequences (IGSs) is the same between human and chimpanzee.
Initial sequence of the chimpanzee genome and comparison with the human genome
TLDR
It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates.
TLDR
Possible reasons for this high level of homoplasy in the O, M, and T lineages are discussed, and a computer simulation has been carried out to produce a model explaining the observed data.
A genome-wide comparison of recent chimpanzee and human segmental duplications
TLDR
It is determined that 33% of human duplications are not duplicated in chimpanzee, including some human disease-causing duplications, and that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications.
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees.
TLDR
The human lineage apparently had experienced a large reduction in effective population size after its separation from the chimpanzee lineage, suggesting that the gorilla lineage branched off 1.6 to 2.2 million years earlier than did the human-chimpanzee divergence.
Estimation of divergence times for major lineages of primate species.
TLDR
It is advisable to concatenate many gene sequences and use a multigene gamma distance for estimating divergence times rather than using the individual gene approach, and nuclear proteins are generally more suitable than mitochondrial proteins for time estimation.
Strong male-driven evolution of DNA sequences in humans and apes
TLDR
This study reinstates a high α in hominoids and supports the view that DNA replication errors are the primary source of germline mutation and suggests that closely related species are not suitable for estimating α.
...
...