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

Abstract

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.

Keywords: Ancient introgression; Sciuridae; Species tree; Ultraconserved elements; Wallacea.

Fig. 1

Map of Sulawesi with biogeographic barriers shown, as well as the approximate distribution of each species plotted within the inlaid maps. Species distributions estimated from [27, 28]. Individual samples are placed in the same color, and on the representative map of each sampled species. Species not included are in grey text in the center inlaid map, and P. rosenbergii is distributed on the islands north of the northern peninsula (Sangihe Islands). Base maps modified from Wikimedia Commons

Fig. 2

Whole mitochondrial genome phylogenetic tree. Support values are provided for both Maximum Likelihood and Bayesian Inference (ML/BI). Colors correspond to range maps in Fig. 1. Species with multiple individuals are detailed in Table 1

Fig. 3

Divergence dated whole mitochondrial genome phylogeny. Bayesian inference support values are shown and dates are provided in millions of years. Blue bars indicate the 95 % HPD for each dated node. The split from Sundaland to Sulawesi taxa is the node dated to 11.03 MYA

Fig. 4

Comparative analysis of UCEs, with several trees provided based on various partitioning schemes. All trees were generated with Maximum Likelihood via PHyML except F. a the complete matrix of 28 loci, (b) a tree of the 28 ‘most informative’ loci, including loci with the highest number of informative sites per locus. c a tree of 34 loci where Prosciurillus murinus and P. abstrusus were always present, (d) the tree containing 362 loci, which included at least 9 of the 11 taxa, and at least three informative sites per locus. e A tree of 2410 loci containing at least 9 of 11 taxa and at least a single informative site per locus. f ASTRAL species tree estimation, generated from the 362 loci dataset. Additional details about partitioning are found in the Methods

Fig. 5

Divergence dated UCE dataset with two independent analyses (see methods) shaded (95 % CI) in different colors (although almost entirely overlapping). The inlaid maps are geological reconstructions from [8], reprinted with permission, highlighting the approximate conformation and extent of subaerial land at 10 and 5 MYA. The green indicates land, yellow indicates highland habitat, red triangles represent volcanoes, and the shades of blue represent shallow-deep sea (light–dark blue)