Multilocus phylogenetics in a widespread African anuran lineage (Brevicipitidae: Breviceps) reveals patterns of diversity reflecting geoclimatic change

Abstract

Aim To investigate models assessing the influence of geomorphology and climatic shifts on species diversification in sub‐Saharan Africa by reconstructing the pattern and timing of phylogenetic relationships of rain frogs (Brevicipitidae: Breviceps). Location Sub‐Saharan Africa, south of the Congo Basin. Methods Multilocus sequence data were generated for near complete species‐level sampling of the genus Breviceps. Phylogenetic relationships were inferred via Bayesian inference and maximum likelihood analyses on both concatenated and single‐gene datasets. Network analyses identified locus‐specific reticulate relationships among taxa. Bayesian methods were used to infer dates of divergence among Breviceps lineages, and niche modelling was used to identify possible adaptive divergence. Results Breviceps is monophyletic and comprised of two major, largely allopatric subclades. Diversity within each subclade is concentrated in two areas with contrasting geologic and climatic histories: the arid/semiarid winter rainfall zone in the south‐western (SW) Cape, and the semitropical East Coast that receives predominantly summer rainfall. Recognized species diversity in the SW Cape based on phenotypic variation is consistent with observed genetic patterns whereas the East Coast is shown to harbour unexpectedly high genetic diversity and up to seven putative, cryptic species. Niche models show significant overlap between closely related species. Main conclusions Dating analyses indicate that diversification of Breviceps occurred rapidly within the Miocene, with only a moderate decline over the Plio‐Pleistocene, suggesting that this process might be slowed but ongoing. Our findings suggest that a combination of two models, a landscape barrier model and climate fluctuation model, can explain patterns of diversification in Breviceps. This demonstrates that Miocene epeirogenic events and climatic shifts may have had a considerable influence on contemporary patterns of biodiversity. Topographic complexity and relative geoclimatic stability in the East have promoted cryptic diversification in allopatry, and this area clearly harbours numerous undescribed taxa and is in need of detailed biotic investigation.

Exceptional Enlargement of the Mitochondrial Genome Results from Distinct Causes in Different Rain Frogs (Anura: Brevicipitidae: Breviceps)

“…They used a total of 24 Breviceps taxa and applied some young calibration points within afrobatrachian lineages in their dating analyses. These differences in the data analysis could account for the differences in estimated divergence ages between our study and that of Nielsen et al [54].…”

“…The resultant phylogenies of afrobatrachian taxa completely match those of recent studies [16,23,54] (Figure 3), excluding the Afrobatrachia+Microhylidae clade not supported in Feng et al [19]. Specifically, (1) Afrobatrachia is monophyletic, (2) Microhylidae becomes the sister taxon of Afrobatrachia, (3) Brevicipitidae forms a clade with Hemisotidae (this clade is called Xenosyneunitanura [16,23].…”

“…The detailed phylogenetic lineage and evolutionary period of these large genomic modifications have not been clarified. This study shows that the mt genomes of B. poweri and B. mossambicus are not markedly rearranged from the typical neobatrachian type, although B. adspersus branches between these species' lineages ( Figure 1 and see [54]). Therefore, it can be concluded that the unique mt genome of B. adspersus evolved only in the lineage leading to this species.…”

“…Specifically, (1) Afrobatrachia is monophyletic, (2) Microhylidae becomes the sister taxon of Afrobatrachia, (3) Brevicipitidae forms a clade with Hemisotidae (this clade is called Xenosyneunitanura [16,23]. However, for the Breviceps divergences, younger ages have been esti-mated by Nielsen et al [54] (20 and 18 Ma for the divergences of 4 and 5, respectively). They used a total of 24 Breviceps taxa and applied some young calibration points within afrobatrachian lineages in their dating analyses.…”

“…The gene rearrangements in animal mt genomes are considered to reflect animal evolution (e.g., [23,[58][59][60]), and the rearranged gene orders found in this study can be regarded as novel phylogenetic markers for brevicipitid taxa. Specifically, the O L -trnsNW can be considered characteristic of some members of the B. mossambicus group [54], while the cytb-trnsHS-CR can be regarded as a synapomorphy of Breviceps.…”