Phylogenomics of primates and their ancestral populations

Siepel, A. (November 2009) Phylogenomics of primates and their ancestral populations. Genome Res, 19 (11). pp. 1929-41. ISSN 1088-9051

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DOI: 10.1101/gr.084228.108


Genome assemblies are now available for nine primate species, and large-scale sequencing projects are underway or approved for six others. An explicitly evolutionary and phylogenetic approach to comparative genomics, called phylogenomics, will be essential in unlocking the valuable information about evolutionary history and genomic function that is contained within these genomes. However, most phylogenomic analyses so far have ignored the effects of variation in ancestral populations on patterns of sequence divergence. These effects can be pronounced in the primates, owing to large ancestral effective population sizes relative to the intervals between speciation events. In particular, local genealogies can vary considerably across loci, which can produce biases and diminished power in many phylogenomic analyses of interest, including phylogeny reconstruction, the identification of functional elements, and the detection of natural selection. At the same time, this variation in genealogies can be exploited to gain insight into the nature of ancestral populations. In this Perspective, I explore this area of intersection between phylogenetics and population genetics, and its implications for primate phylogenomics. I begin by "lifting the hood" on the conventional tree-like representation of the phylogenetic relationships between species, to expose the population-genetic processes that operate along its branches. Next, I briefly review an emerging literature that makes use of the complex relationships among coalescence, recombination, and speciation to produce inferences about evolutionary histories, ancestral populations, and natural selection. Finally, I discuss remaining challenges and future prospects at this nexus of phylogenetics, population genetics, and genomics.

Item Type: Paper
Uncontrolled Keywords: Animals Evolution, Molecular Genetic Variation Genome/genetics Genomics/*methods Humans Models, Genetic *Phylogeny Polymorphism, Genetic Primates/classification/*genetics Sequence Analysis, DNA
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date: November 2009
Date Deposited: 13 Jan 2015 20:31
Last Modified: 13 Jan 2015 20:31
PMCID: PMC2775601
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