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SRX3768932: UCE target enrichment of Sapajus-robustus-4-CPRJ2110
1 ILLUMINA (Illumina HiSeq 2500) run: 2.3M spots, 469.5M bases, 180.6Mb downloads

Design: Total genomic DNA was extracted from muscle and blood samples using the Qiagen DNeasy Blood & Tissue Kit, according to the manufacturer s protocol. Library preparation, sequence capture, and sequencing of ultraconserved elements were performed by RAPiD Genomics (Gainesville, FL, USA).
Submitted by: Universidade Federal do Para
Study: A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation
show Abstracthide Abstract
Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, libidinosus, apella, macrocephalus, and flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were interspersed in a widespread clade with no evidence for monophyly for any of these three morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys
Sample:
SAMN08637938 • SRS3023450 • All experiments • All runs
Library:
Name: Sapajus-robustus-4-CPRJ2110
Instrument: Illumina HiSeq 2500
Strategy: WGS
Source: GENOMIC
Selection: Hybrid Selection
Layout: PAIRED
Runs: 1 run, 2.3M spots, 469.5M bases, 180.6Mb
Run# of Spots# of BasesSizePublished
SRR68118932,324,406469.5M180.6Mb2018-06-06

ID:
5196308

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