Rapid ecological specialization despite constant population sizes

Background. The bushbuck, Tragelaphus scriptus, is the most widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes, occurring in approximately 73% of the total land area of sub-Saharan Africa. This species was found to consist of two genetically divergent lineages based on the mitochondrial (mt)DNA control region. One lineage inhabited the north-western half of the African continent (T. scriptus) while the other lineage (T. sylvaticus) was found in the south-eastern half. The complex was also found to comprise an unprecedented example of 23 phylogenetically distinct groups (‘ecotypes’), with montane and desert phenotypes potentially resulting from convergent evolution. The current study aim to test hypotheses regarding historical demography and adaptation of bushbuck using a higher-resolution framework, with faster evolving nuclear markers(MGF, PRKCI, SPTBN, and THY) as well as three further mitochondrial markers (cytochrome b, 12S rRNA, and 16S rRNA). Methods. Genealogies were reconstructed for the nuclear and mitochondrial data sets and for each gene independently to test the non-monphyly of the bushbuck complexe in a multi loci framework. In addition, we reconstruct the phylogeographic history of the bushbuck complex by a Bayesian discrete phylogeographic approach of our nucDNA data set to investigate its geographic diffusion and ancestral sequence location. Results. We uncovered two evolutionarily divergent lineages and geographically restricted lineages (Sylvaticus and Scriptus) of bushbuck using phylogenetics. Molecular dating indicates that these lineages last shared a common ancestor ∼2.54 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms do not have any support for expanding population. Both BSPs and EBSPs indicate that the Scriptus and Sylvaticus lineages have remained relatively stable during the last 225-450Kya. Discussion. Both nucDNA and mtDNA support previously findings of two genetically divergent Sylvaticus and Scriptus lineages, despite them coming into secondary contact in several geographic regions. The three mtDNA loci confirmed 15 of the previously defined ecotypes, 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 ecotype meneliki of the Ethiopian highlands, which formed a monophyletic group at three of the four nucDNA loci. The independent evolution of this group relative to phenotypically similar montane ecotypes in Africa confirm previously suggestions of convergence within the bushbuck complex.