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

Abstract

BackgroundThe 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.ResultsOur 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0650-z) contains supplementary material, which is available to authorized users.

Whole mitochondrial genome capture from faecal samples and museum‐preserved specimens

“…These traits are shared with museum‐preserved specimens (Burrell, Disotell, & Bergey, ; Mulligan, ; Sawyer, Krause, Guschanski, Savolainen, & Pääbo, ; Taberlet et al., ), another sample source that reduces the need for invasive sampling of modern populations. Thanks to advances in molecular and analytical approaches, the use of natural history collections for genomic analyses has become increasingly popular in recent years (e.g., Bi et al., ; Good, Vanderpool, Keeble, & Bi, ; Guschanski et al., ; Hawkins, Hofman et al., ; Hawkins, Leonard et al., Lim & Braun, ; Mason, Li, Helgen, & Murphy, ; McCormack, Tsai, & Faircloth, ; Weiß et al., ). Historical collections offer the chance to study species and populations that are difficult to sample in the wild or are extinct, and provide a snapshot of the past, allowing the investigation of temporal population dynamics (Wandeler, Hoeck, & Keller, ; Xenikoudakis et al., ).…”

“…Typically, bait construction relies on the availability of prior sequence knowledge, considerable bioinformatics expertize for bait design and requires synthesis of expensive capture probes. Recently, alternative methods, in which a high‐quality DNA sample is used as template for bait construction, have been developed and successfully applied to nonmodel organisms (e.g., Bi et al., ; Carpenter et al., ; Gasc, Peyretaillade, & Peyret, ; Good et al., ; Hawkins, Hofman et al., ; Hawkins, Leonard et al., ; Lim & Braun, ; Mariac et al., ; McCormack et al., ; Peñalba et al., ; Snyder‐Mackler et al., ). In the widely used capture method described in Maricic, Whitten, and Pääbo (), baits are constructed by PCR‐amplifying genome regions of interest from a high‐quality sample.…”

“…The hybridization reaction allows target enrichment across large phylogenetic distances from degraded low‐quality samples (Guschanski et al., ; Peñalba et al., ), making it suitable for noninvasive samples. This simple and cost‐effective method has been applied to high‐quality modern (e.g., Li et al., ; Lippold et al., ), ancient (e.g., Dabney et al., ; Meyer et al., ; Thalmann et al., ) and museum‐preserved samples (e.g., Guschanski et al., ; Hawkins, Leonard et al., ; Hawkins, Hofman et al., ; Liedigk et al., ), but possible biases that can arise from target enrichment have not been systematically evaluated. These include preferential retention of specific fragment sizes, reduced capture efficiency of damaged molecules and capture performance in the face of closely related contaminating sequences.…”

Museomics of tree squirrels: A dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul

“…The use of historical samples in molecular studies has increased substantially in the last two decades (see review in [14,29]) and is helping to reveal hidden diversity, to unveil puzzling phylogenetic relationships, and to place rare and elusive mammal species/lineages in a phylogenetic context [16,[30][31][32], including in squirrels [33]. For Neotropical mammal groups, the study of historical museum samples using high-throughput sequencing to address phylogenetic and taxonomic questions is growing, becoming more feasible, and holding lots of promise [34,35].…”

“…Libraries were multiplexed in equimolar ratios for target capture and enrichment of Ultraconserved Elements (UCEs) using similar procedures as described in [33]. For historical samples we pooled up to four libraries and for modern samples up to eight libraries.…”