Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome‐wide sequence data for seven amphibians

Abstract

High-throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The "vanishing refuge" diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non-forest habitats. Complex arrangements of geographical barriers (hydrology and topography) and ecological gradients between forest and non-forest habitats may have further influenced the region's biodiversity, but elucidation of general diversification processes has been limited by lack of suitable data. Here, we explicitly test alternative diversification modes in the coastal forests using genome-wide single nucleotide polymorphisms, mtDNA, spatial and environmental data for three forest (Arthroleptis xenodactyloides, Leptopelis flavomaculatus and Afrixalus sylvaticus) and four generalist (Afrixalus fornasini, A. delicatus, Leptopelis concolor and Leptopelis argenteus) amphibians. Multiple analyses provide insight about divergence times, spatial population structure, dispersal barriers, environmental stability and demographic history. We reveal highly congruent intra-specific diversity and population structure across taxa, with most divergences occurring during the late Pliocene and Pleistocene. Although stability models support the existence of some forest refugia, dispersal barriers and demographic models point towards idiosyncratic diversification modes across taxa. We identify a consistent role for riverine barriers in the diversification of generalist taxa, but mechanisms of diversification are more complex for forest taxa and potentially include topographical barriers, forest refugia and ecological gradients. Our work demonstrates the complexity of diversification processes in this region, which vary between forest and generalist taxa, but also for ecologically similar species with shared population boundaries.

Genome‐scale sampling suggests cryptic epigenetic structuring and insular divergence in Canada lynx

“…Historical demography was assessed using the program ∂a∂i (Gutenkunst, Hernandez, Williamson, & Bustamante, 2009), which can be used to assess the fit between various demographic scenarios and the expected allele frequency spectrum according to diffusion equations; moreover it is suitable for our neutral SNP data (Shafer, Gattepaille, Stewart, & Wolf, 2015). For model selection, we used the demographic models outlined in Charles et al, 2018 ( Figure S5, Table S4), within the model selection framework described in Portik et al (2017) and compared to simulations generated using the process within Barratt et al, 2018. Further details on the methods involving our demographic inferences can be found in Supporting Information.…”

Biome stability predicts population structure of a southern African aridland bird species

“…For species endemic to a particular biome, it can be hypothesized that the history of the biome will be reflected in the demographic history of the species. This has been demonstrated for both glacial and habitat refugia, with glacial refugia having shaped the distribution of diversity in the Northern Hemisphere (Hewitt, 2004), and habitat refugia, in particular tropical forest refugia, having served as important harbors for species diversity and genetic diversity in the Australian Wet Tropics (Graham, Moritz, & Williams, 2006), the Brazilian Atlantic Forests (Carnaval, Hickerson, Haddad, Rodrigues, & Moritz, 2009), and the lowland and montane forests of Africa (e.g., Barratt et al, 2018; Fjeldså & Bowie, 2008; Huntley, Keith, Castellanos, Musher, & Voelker, 2019; Portik et al, 2017; Voelker, Outlaw, & Bowie, 2010). However, for widespread habitat‐generalist species, the role of habitats and habitat refugia in structuring diversity is less certain, since by definition, these species are not limited to a particular habitat type and possess traits that allow them to utilize a range of habitats and resources.…”

Recent global changes have decoupled species richness from specialization patterns in North American birds

“…These rich communities are found in areas which experienced high climate velocity in the past, but are also intensively used by humans and beneficiate from a mild climate, favouring high levels of productivity. These results tend to indicate that the potential specialization level of those communities could be limited, due to high climate velocity in the past (Barratt et al, 2018; Dalsgaard et al, 2011; Sandel et al, 2011) and that this potential has been largely eroded by the intensive use of lands by humans (Clavel et al, 2011; Devictor et al, 2008). The human activities were already strongly driving the pattern during the first decade of the study, suggesting that the pattern has been shaped and altered by human activities for decades and probably centuries.…”