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1. 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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2. The population genetics of speciation by cascade reinforcement

   https://doi.org/10.1002/ece3.9773  

   Anderson, Carlie B. ; Ospina, Oscar ; Beerli, Peter ; Lemmon, Alan R. ; Banker, Sarah E. ; Hassinger, Alyssa Bigelow ; Dye, Mysia ; Kortyna, Michelle L. ; Lemmon, Emily Moriarty ( February 2023 , Ecology and Evolution)

   Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isolation among populations of the same species. Here, we investigated the population genetic outcomes of cascade reinforcement in North American chorus frogs (Hylidae:Pseudacris). Specifically, we estimated the frequency of hybridization among three taxa, assessed genetic structure within the focal species,P.feriarum, and ascertained the directionality of gene flow withinP.feriarumacross replicated contact zones via coalescent modeling. Through field observations and preliminary experimental crosses, we assessed whether hybridization is possible under natural and laboratory conditions. We found that hybridization occurs amongP.feriarumand two conspecifics at a low rate in multiple contact zones, and that gene flow within the former species is unidirectional from allopatry into sympatry with these other species in three of four contact zones studied. We found evidence of substantial genetic structuring withinP.feriarumincluding a divergent western allopatric cluster, a behaviorally‐distinct sympatric South Carolina cluster, and several genetically‐overlapping clusters from the remainder of the distribution. Furthermore, we found sub‐structuring between reinforced and nonreinforced populations in the two most intensely‐sampled contact zones. Our literature review indicated thatP.feriarumhybridizes with at least five heterospecifics at the periphery of its range providing a mechanism for further intraspecific diversification. This work strengthens the evidence for cascade reinforcement in this clade, revealing the geographic and genetic landscape upon which this process can contribute to the proliferation of species.

    

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3. Rivers, not refugia, drove diversification in arboreal, sub‐Saharan African snakes

   https://doi.org/10.1002/ece3.7429  

   Allen, Kaitlin E. ; Greenbaum, Eli ; Hime, Paul M. ; Tapondjou N., Walter P. ; Sterkhova, Viktoria V. ; Kusamba, Chifundera ; Rödel, Mark‐Oliver ; Penner, Johannes ; Peterson, A. Townsend ; Brown, Rafe M. ( May 2021 , Ecology and Evolution)

   The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo‐species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river‐refuge hypotheses on diversification in the arboreal sub‐Saharan African snake genusToxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo‐distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within bothToxicodryasspecies, corresponding geographically to river barriers and divergence times from the mid‐Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river‐refuge hypotheses in favor of the river‐barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east‐central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.

    

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4. Genetic divergence and ephemeral barriers: Reconciling genetic and geological timescales within geogenomics

   Araya-Donoso, R ; Alonso-Alonso, P ; Maag, G ; Dorsey, R ; Bennett, S ; Wilder, B ; Kusumi, K ; Munguia-Vega, A ; Dolby G ( December 2021 , American Geophysical Union)

   Understanding the timescales on which different geologic processes influence genetic divergence is crucial to defining and testing geogenomic hypotheses and characterizing Earth- life evolution. To see if we can recover a genetic signal produced by a hypothetical physical barrier to gene flow, we used a geographically explicit simulation approach. We used the CDMetaPop software to simulate heritable genetic, nonadaptive, data for 20 geographically distinct populations distributed throughout the Baja California peninsula of Mexico, a landscape where a transpeninsular seaway barrier has been proposed to have isolated the southern peninsula and caused the observed latitudinal genetic divergence in over 80 terrestrial species. We simulated 10,000 generations of isolation by a barrier under two dispersal scenarios (1 km and 100 km of max. dispersal from population of origin per generation) and three DNA substitution rates (10-7, 10-8 and 10-9 nucleotide substitutions per site per generation). Our simulations indicate that a physical barrier can produce strong genetic divergence within 10,000 generations, comparable to the continuum of values observed in nature for different taxonomic groups and geological settings. We found that the generation time of the organism was by far the most important factor dictating the rate of divergence. Evaluating different generation times (0.02, 0.2, 2 and 20 years), showed that species with longer generation times require longer periods of isolation to accumulate genetic divergence over 10k generations (~1 My). Simulating 10,000 generations of gene flow following removal of the barrier showed that the divergence signal eroded quickly, in less than 1,000 generations in every scenario, a pattern supported by theory from population genetics. These results are particularly relevant to geogenomic studies because they show that ephemeral gene flow barriers produce different magnitudes of genetic signals depending on attributes of the organism, particularly generation time, and that if reproductive isolation is not achieved during isolation, then the evolutionary signal of an ephemeral barrier may not develop. This work helps guide the limits of detectability when integrating genomic data with geological and climatic processes. 

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5. Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA ‐seq analyses

   https://doi.org/10.1002/ece3.1865  

   Edwards, Taylor ; Tollis, Marc ; Hsieh, PingHsun ; Gutenkunst, Ryan N. ; Liu, Zhen ; Kusumi, Kenro ; Culver, Melanie ; Murphy, Robert W. ( January 2016 , Ecology and Evolution)

   Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genusGopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNAand four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree.RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ∂a∂i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ∂a∂i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).

    

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