DOI: 10.5061/dryad.7v5p3
title: Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

description: 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.
description: 157k_362Loci_align_9plusNexus file of 362 UCE loci from a minimum of nine individuals, with at least three informative sites. The total alignment is over 157,000 bp.ML tree of Mitogenomes plus UCE outgroupsMitochondrial tree, generated through Maximum Likelihood.Mitogene_Tree_DCSPriorMitogenome BEAST xml file from this publication.FcC_infoFasConCat data partitioning text file.FcC_supermatrixFasConCat supermatrix fasta file.28ConpleteGeneTreesSubset of 28 UCE loci from complete data matrix.NJst_362LociSpTreeSpecies tree from NJst.157kUCEsBEAST xml file for 362 UCE loci dataset.157k_38subsetsZipped folder containing each of the 38 data partitions selected from the k-means algorithm.