DOI: 10.5061/dryad.n8pk0p35v
title: Data from: Recent, intricate speciation in Amazonia uncovered by a multilayered genomic analysis of tree squirrels

description: Accurate estimates of species diversity are essential for all biodiversity
 research. Delimiting species and understanding the underlying processes of
 speciation are also central components of systematic biology that frame
 our comprehension of the evolutionary mechanisms generating biodiversity.
 The South American tree squirrels (genus Guerlinguetus) are keystone
 mammals, widely distributed, that are critical in tree-seed predation and
 dispersal in one of the most fragile and threated ecosystems of the world,
 the tropical rainforests of South America. We obtained genomic data
 (ultraconserved elements and single nucleotide polymorphisms) to explore
 alternative hypotheses on species limits of this genus and to clarify
 recent and rapid speciation on continental-scale and dynamically evolving
 landscapes. Using a multilayered genomic approach that integrates
 fine-scale population genetic analyses with quantitative molecular species
 delimitation methods, we observed that (i) the most likely number of
 species within Guerlinguetus is six, contrasting with both classic
 morphological revision and mitochondrial species delimitation; (ii)
 incongruencies in species relationships still persist, which might be a
 response to population migration and gene flow taking place in the
 lowlands of eastern Amazonia and/or to the extremely rapid successive
 speciation events; and (iii) effective migration surfaces detected
 important geographic barriers associated with the major Amazonian riverine
 systems and the mountain ranges of the Guiana Shield. In conclusion, we
 uncovered unexpected and higher species diversity on Guerlinguetus and
 corroborate recent findings suggesting that much of the extant
 species-level diversity in Amazonia is young, dating back to the
 Quaternary. We also reinforce long-established hypotheses on the role of
 rivers and climate-driven forest dynamics in triggering Amazonian
 speciation.
description: # Data from: Recent, intricate speciation in Amazonia uncovered by a
 multilayered genomic analysis of tree squirrels This submission includes
 two sets of files: a data set zip file and a file with all the
 supplementary material. See descriptions below. ## Data sets All data sets
 produced in this study are publicly available as follow: Data set 1: UCE
 loci data set including 3,642 loci (1,495,138 bp) from 67 individuals of
 Guerlinguetus in addition to five outgroups. Data set 2: 1,169 filtered,
 unlinked SNPs called from 64 samples of Guerlinguetus. Data set 3: Reduced
 UCE loci data set including a subset of 500 loci (corresponding to the
 loci with the highest sample representativeness) from 67 specimens of
 Guerlinguetus in addition to one outgroup. Data set 4: Reduced SNP data
 set including 1,155 biallelic, unlinked SNPs from 17 specimens of
 Guerlinguetus. Data set 5: Reduced UCE loci data set including a subset of
 1,000 loci (corresponding to the loci with the highest sample
 representativeness) from 67 specimens of Guerlinguetus in addition to one
 outgroup. ## Supplementary Material All Supplementary Material for this
 study, including supplementary tables, figures, and additional text, are
 available in a single PDF file. Each supplementary item is accompanied by
 its respective caption containing relevant information.