Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Background: The Indonesian island of Sulawesi has a complex geological
history. It is composed of several landmasses that have arrived at a near
modern configuration only in the past few million years. It is the largest
island in the biodiversity hotspot of Wallacea—an area demarcated by the
biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal
fauna of Sulawesi is transitional between Asian and Australian faunas.
Sulawesi’s three genera of squirrels, all endemic (subfamily
Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian
origin and have evolved a variety of phenotypes that allow a range of
ecological niche specializations. Here we present a molecular phylogeny of
this radiation using data from museum specimens. High throughput
sequencing technology was used to generate whole mitochondrial genomes and
a panel of nuclear ultraconserved elements providing a large genome-wide
dataset for inferring phylogenetic relationships. Results: Our analysis
confirmed monophyly of the Sulawesi taxa with deep divergences between the
three endemic genera, which predate the amalgamation of the current island
of Sulawesi. This suggests lineages may have evolved in allopatry after
crossing Wallace’s line. Nuclear and mitochondrial analyses were largely
congruent and well supported, except for the placement of Prosciurillus
murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with
P. murinus between or outside of Hyosciurus and Rubrisciurus, separate
from other species of Prosciurillus. A deep but monophyletic history for
the four included species of Prosciurillus was recovered with the nuclear
data. Conclusions: The divergence of the Sulawesi squirrels from their
closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back
the age estimate of this ancient adaptive radiation prior to the formation
of the current conformation of Sulawesi. Generic level diversification
took place around 9.7 MYA, opening the possibility that the genera
represent allopatric lineages that evolved in isolation in an ancient
proto-Sulawesian archipelago. We propose that incongruence between
phylogenies based on nuclear and mitochondrial sequences may have resulted
from biogeographic discordance, when two allopatric lineages come into
secondary contact, with complete replacement of the mitochondria in one
species.