Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation
Author(s)
Peng, Zuogang
Elango, Navin
Wildman, Derek E.
Yi, Soojin V.
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Abstract
Background: Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring
evolutionary histories because they escape the constraints of natural selection. For the majority of
taxa however, obtaining such markers is challenging. Advances in genomics have the potential to
alleviate the shortage of neutral markers. Here we present a method to develop numerous markers
from putatively neutral regions of primate genomes.
Results: We began with the available whole genome sequences of human, chimpanzee and
macaque. Using computational methods, we identified a total of 280 potential amplicons from
putatively neutral, non-coding, non-repetitive regions of these genomes. Subsequently we amplified,
using experimental methods, many of these amplicons from diverse primate taxa, including a ringtailed
lemur, which is distantly related to the genomic resources. Using a subset of 10 markers, we
demonstrate the utility of the developed markers in phylogenetic and evolutionary rate analyses.
Particularly, we uncovered substantial evolutionary rate variation among lineages, some of which
are previously not reported.
Conclusion: We successfully developed numerous markers from putatively neutral regions of
primate genomes using a strategy combining computational and experimental methods. Applying
these markers to phylogenetic and evolutionary rate variation analyses exemplifies the utility of
these markers. Diverse ecological and evolutionary analyses will benefit from these markers.
Importantly, methods similar to those presented here can be applied to other taxa in the near future.
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Date
2009-05-26
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