Abstract
BackgroundThe bushbuck, Tragelaphus scriptus, is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage (T. s. scriptus) inhabits the north-western half of the African continent while Sylvaticus (T. s. sylvaticus) is found in the south-eastern half. Here we test hypotheses of historical demography and adaptation in bushbuck using a higher-resolution framework, with four nuclear (MGF, PRKCI, SPTBN, and THY) and three new mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA).MethodsGenealogies were reconstructed for the mitochondrial and nuclear data sets, with the latter dated using fossil calibration points. We also inferred the demographic history of Scriptus and Sylvaticus using coalescent-based methods. To obtain an overview of the origins and ancestral colonisation routes of ancestral bushbuck sequences across geographic space, we conducted discrete Bayesian phylogeographic and statistical dispersal-vicariance analyses on our nuclear DNA data set.ResultsBoth nuclear DNA and mtDNA support previous findings of two genetically divergent Sylvaticus and Scriptus lineages. The three mtDNA loci confirmed 15 of the previously defined haplogroups, including those with convergent phenotypes. However, the nuclear tree showed less phylogenetic resolution at the more derived parts of the genealogy, possibly due to incomplete lineage sorting of the slower evolving nuclear genome. The only exception to this was the montane Menelik’s bushbuck (Sylvaticus) of the Ethiopian highlands, which formed a monophyletic group at three of four nuclear DNA loci. We dated the coalescence of the two lineages to a common ancestor ∼2.54 million years ago. Both marker sets revealed similar demographic histories of constant population size over time. We show that the bushbuck likely originated in East Africa, with Scriptus dispersing to colonise suitable habitats west of the African Rift and Sylvaticus radiating from east of the Rift into southern Africa via a series of mainly vicariance events.DiscussionDespite lower levels of genetic structure at nuclear loci, we confirmed the independent evolution of the Menelik’s bushbuck relative to the phenotypically similar montane bushbuck in East Africa, adding further weight to previous suggestions of convergent evolution within the bushbuck complex. Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continent’s extant large mammalian diversity.
Highlights
The bushbuck (Tragelaphus scriptus) is a well-known, highly diverse species complex of spiral-horned antelopes
The two groups are separated in the west and south by the Lower Congo valley and the Congo basin respectively, but in eastern Africa Scriptus and Sylvaticus come into secondary contact from the northern end of the Albertine rift along the Imatong and Didinga Mountains of South Sudan following the rift into the Ethiopian Highlands
Structure and divergence Phylogenetic analyses of mitochondrial (Fig 2A) and nuclear (Fig. 2B) multilocus alignments yielded highly concordant maximum likelihood (ML) topologies. Both marker sets recovered two well supported Scriptus and Sylvaticus lineages, the level of phylogenetic resolution was much higher for mtDNA, which recovered all 23 clades originally identified using control region DNA (Moodley and Bruford 2007)
Summary
The bushbuck (Tragelaphus scriptus) is a well-known, highly diverse species complex of spiral-horned antelopes. The two groups are separated in the west and south by the Lower Congo valley and the Congo basin respectively, but in eastern Africa Scriptus and Sylvaticus come into secondary contact from the northern end of the Albertine rift along the Imatong and Didinga Mountains of South Sudan following the rift into the Ethiopian Highlands (white arrows, Fig. 1) Within this zone of contact, the phenotypic integrity of each form may be maintained through habitat preference; the Scriptus form inhabits the lowlands while the large, dark and heavy-coated Sylvaticus montane ecotype inhabits the high altitude forests, evidence of gene flow has been observed (Moodley and Bruford 2007). Perhaps the most surprising result of our analysis was that both Scriptus and Sylvaticus populations remained relatively constant throughout the Pleistocene, which is remarkable given that this was a period of major climatic and tectonic change in Africa, and responsible for driving the evolution of much of the continents extant large mammal diversity
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