Data from: 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 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.