Phylogenomics of primates and their ancestral populations Export

@article{citeulike:5887975, abstract = {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 \^{a}€œlifting the hood\^{a}€ 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.}, author = {Siepel, Adam}, citeulike-article-id = {5887975}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.084228.108}, citeulike-linkout-1 = {http://genome.cshlp.org/content/gr.084228.108v1/.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/gr.084228.108v1/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19801602}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19801602}, day = {3}, doi = {10.1101/gr.084228.108}, issn = {1549-5477}, journal = {Genome Research}, keywords = {evolution, phylogenetics, popgen, primates, review}, month = {November}, number = {11}, pages = {1929--1941}, posted-at = {2009-11-02 19:00:34}, priority = {2}, title = {Phylogenomics of primates and their ancestral populations}, url = {http://dx.doi.org/10.1101/gr.084228.108}, volume = {19}, year = {2009} }

TY - JOUR ID - citeulike:5887975 L3 - citeulike-article-id:5887975 N2 - 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. IS - 11 JF - Genome Research SN - 1549-5477 EP - 1941 TI - Phylogenomics of primates and their ancestral populations VL - 19 SP - 1929 KW - evolution KW - phylogenetics KW - popgen KW - primates KW - review AU - Siepel, Adam PY - 2009/11/03/ UR - http://dx.doi.org/10.1101/gr.084228.108 ER -