A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene

Abstract

BackgroundDuikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood. Here we present the first multi-locus phylogeny of this threatened group of tropical artiodactyls and use a Bayesian uncorrelated molecular clock to estimate divergence times.ResultsA total of 4152 bp of sequence data was obtained from two mitochondrial genes and four nuclear introns. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analysis of concatenated mitochondrial, nuclear and combined datasets. A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group. Findings indicate strong support for four major lineages within the subfamily, all of which date to the late Miocene/early Pliocene. The first of these to diverge was the dwarf duiker genus Philantomba, followed by the giant, eastern and western red duiker lineages, all within the genus Cephalophus. While these results uphold the recognition of Philantomba, they do not support the monotypic savanna-specialist genus Sylvicapra, which as sister to the giant duikers leaves Cephalophus paraphyletic. BEAST analyses indicate that most sister species pairs originated during the Pleistocene, suggesting that repeated glacial cycling may have played an important role in the recent diversification of this group. Furthermore, several red duiker sister species pairs appear to be either paraphyletic (C.callipygus/C. ogilbyi and C. harveyi/C. natalensis) or exhibit evidence of mitochondrial admixture (C. nigrifrons and C. rufilatus), consistent with their recent divergence and/or possible hybridization with each other.ConclusionsMolecular phylogenetic analyses suggest that Pleistocene-era climatic oscillations have played an important role in the speciation of this largely forest-dwelling group. Our results also reveal the most well supported species phylogeny for the subfamily to date, but also highlight several areas of inconsistency between our current understanding of duiker taxonomy and the evolutionary relationships depicted here. These findings may therefore prove particularly relevant to future conservation efforts, given that many species are presently regulated under the Convention for Trade in Endangered Species.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

“…S1, Table S4, Supporting information), thus suggesting a recent diversification of African common pangolins in the rainforest zone. Their times of origin concur with major periods of aridity in tropical Africa 1.7 and 1.0 Ma when the increased amplitude of dry periods was accompanied by rainforest contraction and major changes in African faunal assemblages (deMenocal ), notably in forest‐dwelling mammals (Johnston & Anthony ). Our Bayesian analyses gave high support for a basal dichotomy between Gabon + central LGB and coastal LGB‐DG‐UGB in the Middle Pleistocene (0.79–1.36 Ma), showing (i) closer affinities between the coastal LGB and western Africa and (ii) the existence of two distinct lineages within coastal LGB.…”

Distinct and Diverse: Range-Wide Phylogeography Reveals Ancient Lineages and High Genetic Variation in the Endangered Okapi (Okapia johnstoni)

“…3, node 16); C. rufilatus (node 17); C. nigrifrons from C. harveyi (node 17); C. natalensis (node 17); and C. spadix from C. silvicultor (node 19). These duiker lineages (nodes 16, 17 and 19) have previously been estimated to have diverged between 1.74–3.54, 1.18–2.38 to 0.80–1.91 mya respectively [47]. The divergence of the okapi lineages also appears to pre-date the emergence of many of today's described bushbuck subspecies, for example T. sylvaticus sylvaticus from T. sylvaticus meneliki and T. sylvaticus powelli , and approximately twice as old as the emergence of both T. scriptus decula and T. sylvaticus ornatus .…”

Where is the game? Wild meat products authentication in South Africa: a case study

“…silvicultor and C . spadix ) when using a multilocus phylogenetic approach [54], thus making Cephalophus paraphyletic. Similar results were obtained with whole mitochondrial sequence information by Hassanin et al .…”

“…[27] detected COI genetic distances below 3% between some Cephalophus species for their recent speciation processes estimated at ≤ one million years ago [54]. The interspecific distances for the common duiker shows an earlier speciation event, estimated at approximately 5.6 million years ago [27] (Figure  1).…”