Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
| Main Authors: | Valencia, Lina Maria, Martins, Amely, Ortiz Valencia, Edgardo Manuel MartÃn, Di Fiore, Anthony, Ortiz, Edgardo M. |
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| Format: | info dataset Journal |
| Terbitan: |
, 2019
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5089873 |
Daftar Isi:
- 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 familyFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1540270