10.5061/DRYAD.85JN3
Valencia, Lina Maria
The University of Texas at Austin
Martins, Amely
The University of Texas at Austin
Ortiz Valencia, Edgardo Manuel MartÃn
Di Fiore, Anthony
The University of Texas at Austin
Ortiz, Edgardo M.
The University of Texas at Austin
Data from: A RAD-sequencing approach to genome-wide marker discovery,
genotyping, and phylogenetic inference in a diverse radiation of primates
Dryad
dataset
2019
double-digest RAD sequencing
reduced representation sequencing
non-model taxa
New World primates
SNP markers
20-25 mya
Platyrrhini
restriction enzyme digests
National Science Foundation
https://ror.org/021nxhr62
1540270
2019-07-19T00:00:00Z
2019-07-19T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0201254
20214214131 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Until recently, most phylogenetic and population genetics studies of
nonhuman primates have relied on mitochondrial DNA and/or a small number
of nuclear DNA markers, which can limit our understanding of primate
evolutionary and population history. Here, we describe a cost-effective
reduced representation method (ddRAD-seq) for identifying and genotyping
large numbers of SNP loci for taxa from across the New World monkeys, a
diverse radiation of primates that shared a common ancestor ~20-26 mya. We
also estimate, for the first time, the phylogenetic relationships among 15
of the 22 currently-recognized genera of New World monkeys using ddRAD-seq
SNP data using both maximum likelihood and quartet-based coalescent
methods. Our phylogenetic analyses robustly reconstructed three
monophyletic clades corresponding to the three families of extant
platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as
basal within the radiation. At the genus level, our results conformed well
with previous phylogenetic studies and provide additional information
relevant to the problematic position of the owl monkey (Aotus) within the
family Cebidae, suggesting a need for further exploration of incomplete
lineage sorting and other explanations for phylogenetic discordance,
including introgression. Our study additionally provides one of the first
applications of next-generation sequencing methods to the inference of
phylogenetic history across an old, diverse radiation of mammals and
highlights the broad promise and utility of ddRAD-seq data for molecular
primatology.
Samples used in this studySamples used in the phylogenetic study. Each
sample has an associated code that corresponds to the name of the files of
the R1 and R2 raw reads.Samples_Study.xlsxData matrices of concatenated
SNPs - iPYRADData matrices for the concatenated SNPs (.phy) for each one
of the ipyrad assembly methods. .map files contains information about SNP
position in each locus. This information will be used by tetrad to sample
only one SNP per locus when analyzing each quartet sample in the
analysis.DataMatrices_iPYRAD.tar.gzatelidae.tar.gzRaw reads for the
samples belonging to the Atelidae familyOWM.tar.gzRaw reads for the
samples belonging to the Old World Monkeyscebidae.tar.gzRaw reads for the
samples belonging to the Cebidae familypitheciidae.tar.gzRaw reads for the
samples belonging to the Pitheciidae family
Neotropics