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Abstract
Environments are heterogeneous in space and time, and the permeability of landscape and climatic barriers to gene flow may change over time. When barriers are present, they may start populations down the path toward speciation, but if they become permeable before the process of speciation is complete, populations may once more merge. In Southern Africa, aridland biomes play a central role in structuring the organization of biodiversity. These biomes were subject to substantial restructuring during Plio‐Pleistocene climatic fluctuations, and the imprint of this changing environment should leave genetic signatures on the species living there. Here, we investigate the role of adjacent aridland biome boundaries in structuring the genetic diversity within a widespread generalist bird, the Cape Robin‐chat (Cossypha caffra). We find evidence supporting a central role for aridland biomes in structuring populations across Southern Africa. Our findings support a scenario wherein populations were isolated in different biome refugia, due to separation by the exceptionally arid Nama Karoo biome. This biome barrier may have arisen through a combination of habitat instability and environmental unsuitability, and was highly unstable throughout the Plio‐Pleistocene. However, we also recovered a pattern of extensive contemporary gene flow and admixture across the Nama Karoo, potentially driven by the establishment of homesteads over the past 200 years. Thus, the barrier has become permeable, and populations are currently merging. This represents an instance where initial formation of a barrier to gene flow enabled population differentiation, with subsequent gene flow and the merging of populations after the barrier became permeable.
Highlights
It is well documented that spatial heterogeneity plays a role in how organisms disperse across habitats and landscapes, which in turn shapes patterns of gene flow (Manel, Schwartz, Luikart, & Taberlet, 2003)
Since biomes are not static over time, we hypothesize that demographic and population genetic signatures within C. caffra will reflect spatial patterns of dynamic biome change if the historical landscape has been important in structuring genetic diversity
We identified regions of habitat stability by classifying presence or absence of habitat types in each gridcell for each time period and used the classified biome layers to partition the landscape into stable and unstable areas to capture the spatial extent of habitat refugia (e.g., Carnaval et al, 2009; Graham et al, 2006)
Summary
It is well documented that spatial heterogeneity plays a role in how organisms disperse across habitats and landscapes, which in turn shapes patterns of gene flow (Manel, Schwartz, Luikart, & Taberlet, 2003). Recent GIS-based analyses for Southern African birds suggest that aridland refugia may have played an important role in shaping macroecological diversity patterns in and among regional biomes (Huntley et al, 2016; Huntley, Midgley, Barnard, & Valdes, 2014). Despite this biome-genetic diversification relationship, few empirical studies have evaluated the role of temporal habitat stability (i.e., habitat persistence through time) in structuring genetic diversity. Since biomes are not static over time, we hypothesize that demographic and population genetic signatures within C. caffra will reflect spatial patterns of dynamic biome change if the historical landscape has been important in structuring genetic diversity. We further expect that the signatures of ephemeral barriers will be detectable by using a combination of analytical approaches and markers
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