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1. Exploring rain forest diversification using demographic model testing in the African foam‐nest treefrog Chiromantis rufescens

   https://doi.org/10.1111/jbi.13716  

   Leaché, Adam D. ; Portik, Daniel M. ; Rivera, Danielle ; Rödel, Mark‐Oliver ; Penner, Johannes ; Gvoždík, Václav ; Greenbaum, Eli ; Jongsma, Gregory F. M. ; Ofori‐Boateng, Caleb ; Burger, Marius ; et al ( October 2019 , Journal of Biogeography)

   Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrogChiromantis rufescens.

   Guinean and Congolian rain forests, West and Central Africa.

   Chiromantis rufescens.

   We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples ofC. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial.

   Population structure withinC. rufescensresembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene.

   Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history ofC. rufescenswas shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients.

    

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2. Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake

   https://doi.org/10.1111/jbi.14709  

   Jones, II, Leonard N. ; Leaché, Adam D. ; Burbrink, Frank T. ( August 2023 , Journal of Biogeography)

   Current distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences or spatiotemporal differences. In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA.

   North America.

   Common gartersnake,Thamnophis sirtalis.

   We evaluate the effects of major river basins and the forest‐grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure and demographic analyses of single nucleotide polymorphism data and address range expansion history with ecological niche modelling using locality and historic climate data.

   We identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex‐linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA.

   Our results provide strong evidence for a Pliocene origin forT. sirtalisin central‐southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate‐mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.

    

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3. Extrinsically reinforced hybrid speciation within Holarctic ermine ( Mustela spp.) produces an insular endemic

   https://doi.org/10.1111/ddi.13234  

   Colella, Jocelyn P. ; Frederick, Lindsey M. ; Talbot, Sandra L. ; Cook, Joseph A. ; Brito, ed., José ( February 2021 , Diversity and Distributions)

   Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine (Mustela erminea), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics.

   Holarctic.

   We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods (iBPP,bPTP) assessed congruence between morphometric and genetic data.

   Our results support the recognition of at least three species within theM. ermineacomplex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy.

   Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic speciesM. haidarumis consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics.

    

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4. The geographic mosaic of arms race coevolution is closely matched to prey population structure

   https://doi.org/10.1002/evl3.184  

   Hague, Michael T. J. ; Stokes, Amber N. ; Feldman, Chris R. ; Brodie, Jr., Edmund D. ; Brodie, III, Edmund D. ( August 2020 , Evolution Letters)

   Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of “trait remixing” in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.

    

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5. Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world’s largest bats (Mammalia: Chiroptera)

   https://doi.org/10.1111/jbi.13750  

   Tsang, Susan M. ; Wiantoro, Sigit ; Veluz, Maria Josefa ; Sugita, Norimasa ; Nguyen, Y‐Lan ; Simmons, Nancy B. ; Lohman, David J. ( November 2019 , Journal of Biogeography)

   Islands provide opportunities for isolation and speciation. Many landmasses in the Indo‐Australian Archipelago (IAA) are oceanic islands, and founder‐event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group.

   Australasia, Indo‐Australian Archipelago, Madagascar, Pacific Islands.

   Pteropus(Pteropodidae).

   To infer the biogeographic history ofPteropus, we sequenced up to 6,169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognizedPteropusspecies and subspecies with threeAcerodonoutgroups usingBEASTand subsequently estimated ancestral areas using models implemented inBioGeoBEARS.

   Species‐level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor withAcerodon; founder‐event speciation out of Wallacea was a common inference.Pteropusspecies in Micronesia and the western Indian Ocean were also inferred to result from founder‐event speciation.

   Dispersal between regions of the IAA and the islands found therein fostered diversification ofPteropusthroughout the IAA and beyond. Dispersal inPteropusis far higher than in most other volant taxa studied to date, highlighting the importance of inter‐island movement in the biogeographic history of this large clade of large bats.

    

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