Recent, intricate speciation in Amazonia uncovered by a multilayered genomic analysis of tree squirrels

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 nu..., , , # 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 repr...