DOI: 10.5061/dryad.djh9w0wc0
title: Data from: Phylogenomics of Amazonian squirrel monkeys (<em>Saimiri</em>: Primates, Cebidae)

description: Phylogenetic relationships among squirrel monkeys (genus Saimiri) are
 still poorly resolved. Here, we gathered the first phylogenomic dataset
 for Saimiri using double-digest restriction-site associated DNA sequencing
 (ddRadseq) to construct a phylogeny for squirrel monkeys in Amazonia. All
 the phylogenomic analyses strongly support the division of the genus into
 two main clades, corresponding to the Gothic and Roman arch groups based
 on morphology, and they provided strong support for five major lineages.
 Structure analyses showed evidence for population clusters based on
 geography within these lineages, but also gene flow/hybridization across
 clusters. Our time-calibrated tree confirmed that the diversification of
 Amazonian Saimiri occurred during the Pleistocene.
description: # Data from: Phylogenomics of Amazonian squirrel monkeys (*Saimiri*:
 Primates, Cebidae) Dataset DOI:
 [10.5061/dryad.djh9w0wc0](10.5061/dryad.djh9w0wc0) ### Files and variables
 #### File: Eastern.str **Description:** For all structure files, data was
 converted from .fasta into structure (.str) format, where the first column
 indicates the sample name, the second indicates population, and the rest
 of the columns give genotype using standard STRUCTURE notation. Thus, the
 number of columns - 2 gives the number of sites represented. Subset of
 data from the Main dataset, filtered to only include individuals
 identified morphologically as part of the Eastern clade (n = 25; 70,099
 sites). #### File: Roman.str **Description:** Subset of data from the Main
 dataset, filtered to only include individuals identified morphologically
 as part of the Roman clade (n = 5; 20,512 sites). #### File: macrodon.str
 **Description:** Subset of data from the Main dataset, filtered to only
 include individuals identified morphologically as part of the macrodon
 clade, N = 15; 113,220 sites. #### File: Main_RAXML.nex
 **Description:** Nexus alignment file of all SNPS for the 56 sequences
 analyzed for the main ML-based analysis (and the basis of figure 2). SNPs
 were pulled if at a site there was variation across samples at the site
 not caused from N or? (missing data). Ambiguous data (IUPAC ambiguity
 characters DO count as variation). Used for RAXML analysis. N = 56;
 518,558 sites. #### File: TimeTree.nex **Description:** Nexus alignment
 file of SNPs for select Saimiri samples, as well as a Sapajus sample as
 outgroup. This dataset was filtered to only include sites that had at
 least 85% of samples represented at a given site. Used for BEAST2
 analysis. N = 13 + Outgroup; 297,748 sites. #### File: ustus.str
 **Description:** Subset of data from the Main dataset, filtered to only
 include individuals identified morphologically as part of the ustus clade
 (n = 6; 32,138 sites). #### File: strMain_cleaned.str
 **Description:** strMain_cleaned.str is all snps from Main_RAXML but
 filtered to not include any ambiguous sites (IUPAC ambiguity symbols).
 #### File: U_SNP_75_Coverage_56Samps.nex **Description:** The U SNP file
 includes only the "best" (highest coverage) SNP per read, making
 it a more representative dataset for a given genome than all SNPs as in
 Main_RAXML.nex (which includes every SNP, even if more than one is on a
 read). This alignment file filtered a larger U SNP file to include only
 sites that had at least 75% coverage across samples per site. #### File:
 U_SNP_75_Coverage_50Samps.nex **Description:** This alignment filtered out
 6 samples that had poorer coverage from the previous dataset, and THEN
 filtered to include sites that had at least 75% coverage across samples
 per site. ## Code/software UGENE (ugene.net) is a free bioinformatics tool
 that one may use to view NEXUS files (ending in .nex), available for all
 major operating systems. For Structure files (ending in .str), one may
 view them using a standard table viewer (such as R using the
 "read.table" command. ## Access information Other publicly
 accessible locations of the data: * None Data was derived from the
 following sources: * This does not apply to our datasets.