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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., Competing Interests: The authors declare no competing financial interests in relation to this work., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Mountains host greater avian diversity than lowlands at the same latitude due to their greater diversity of habitats stratified along an elevation gradient. Here we test whether this greater ecological heterogeneity promotes sympatric speciation. We selected accentors (Prunellidae), an avian family associated with mountains of the Palearctic, as a model system. Accentors differ in their habitat/elevation preferences and south-central Siberia and Himalayan regions each host 6 of the 13 species in the family. We used sequences of the mtDNA ND2 gene and the intron 9 of the Z chromosome specific ACO1 gene to reconstruct a complete species-level phylogeny of Prunellidae. The tree based on joint analysis of both loci was used to reconstruct the family's biogeographic history and to date the diversification events. We also analyzed the relationship between the node age and sympatry, to determine the geographic mode of speciation in Prunellidae. Our data suggest a Miocene origin of Prunellidae in the Himalayan region. The major division between alpine species (subgenus Laiscopus) and species associated with shrubs (subgenus Prunella) and initial diversification events within the latter happened within the Himalayan region in the Miocene and Pliocene. Accentors colonized other parts of the Palearctic during the Pliocene-Pleistocene transition. This spread across the Palearctic resulted in rapid diversification of accentors. With only a single exception dating to 0.91 Ma, lineages younger than 1.5 Ma are allopatric. In contrast, sympatry values for older nodes are >0. There was no relationship between node age and range symmetry. Allopatric speciation (not to include peripatric) is the predominant geographic mode of speciation in Prunellidae despite the favorable conditions for ecological diversification in the mountains and range overlaps among species.

The Riverine Barriers Hypothesis (RBH) posits that tropical rivers can be effective barriers to gene flow, based on observations that range boundaries often coincide with river barriers. Over the last 160 years, the RBH has received attention from various perspectives, with a particular focus on vertebrates in the Amazon Basin. To our knowledge, no molecular assessment of the RBH has been conducted on birds in the Afrotropics, despite its rich avifauna and many Afrotropical bird species being widely distributed across numerous watersheds and basins. Here, we provide the first genetic evidence that an Afrotropical river has served as a barrier for birds and for their lice, based on four understory bird species collected from sites north and south of the Congo River. Our results indicate near-contemporaneous, Pleistocene lineage diversification across the Congo River in these species. Our results further indicate differing levels of genetic variation in bird lice; the extent of this variation appears linked to the life-history of both the host and the louse. Extensive cryptic diversity likely is being harbored in Afrotropical forests, in both understory birds and their lice. Therefore, these forests may not be "museums" of old lineages. Rather, substantial evolutionary diversification may have occurred in Afrotropical forests throughout the Pleistocene, supporting the Pleistocene Forest Refuge Hypothesis. Strong genetic variation in birds and their lice within a small part of the Congo Basin forest indicates that we may have grossly underestimated diversity in the Afrotropics, making these forests home of substantial biodiversity in need of conservation.