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1. Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

   https://doi.org/10.1111/mec.15574  

   McLaughlin, Jessica F. ; Faircloth, Brant C. ; Glenn, Travis C. ; Winker, Kevin ( September 2020 , Molecular Ecology)

   Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split‐migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (F_ST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

    

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2. Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): Implications for the evolution of Amazonian landscapes during the Quaternary

   https://doi.org/10.1111/jbi.13169  

   Ribas, Camila C. ; Aleixo, Alexandre ; Gubili, Chrysoula ; d'Horta, Fernando M. ; Brumfield, Robb T. ; Cracraft, Joel ( January 2018 , Journal of Biogeography)

   To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genusRhegmatorhinaat multiple taxonomic and temporal scales.

   Amazonia.

   Antbirds (Thamnophilidae).

   We sequenced four mtDNAand nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow.

   Dense sampling throughout the distribution ofRhegmatorhinarevealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNAlineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity.

   Based on broad‐scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first, mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long‐standing question of identifying the main drivers of Amazonian diversification.

    

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3. A topoclimate model for Quaternary insular speciation

   https://doi.org/10.1111/jbi.13689  

   García‐Olivares, Víctor ; Patiño, Jairo ; Overcast, Isaac ; Salces‐Castellano, Antonia ; López de Heredia, Unai ; Mora‐Márquez, Fernando ; Machado, Antonio ; Hickerson, Michael J. ; Emerson, Brent C. ( October 2019 , Journal of Biogeography)

   Understanding the drivers of speciation within islands is key to explain the high levels of invertebrate diversification and endemism often observed within islands. Here, we propose an insular topoclimate model for Quaternary diversification (ITQD), and test the general prediction that, within a radially eroded conical island, glacial climate conditions facilitate the divergence of populations within species across valleys.

   Gran Canaria, Canary Islands.

   TheLaparocerus tessellatusbeetle species complex (Coleoptera, Curculionidae).

   We characterize individual‐level genomic relationships using single nucleotide polymorphisms produced by double‐digest restriction site associated DNA sequencing (ddRAD‐seq). A range of parameter values were explored in order to filter our data. We assess individual relatedness, species boundaries, demographic history and spatial patterns of connectivity.

   The total number of ddRAD‐seq loci per sample ranges from 4,576 to 512, with 11.12% and 4.84% of missing data respectively, depending on the filtering parameter combination. We consistently infer four genetically distinct ancestral populations and two presumed cases of admixture, one of which is largely restricted to high altitudes. Bayes factor delimitation support the hypothesis of four species, which is consistent with the four inferred ancestral gene pools. Landscape resistance analyses identified genomic relatedness among individuals in two out of the four inferred species to be best explained by annual precipitation during the last glacial maximum rather than geographic distance.

   Our data reveal a complex speciation history involving population isolation and admixture, with broad support for the ITQD model here proposed. We suggest that further studies are needed to test the generality of our model, and enrich our understanding of the evolutionary process in island invertebrates. Our results demonstrate the power of ddRAD‐seq data to provide a detailed understanding of the temporal and spatial dynamics of insular biodiversity.

    

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4. 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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5. Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma)

   https://doi.org/10.1016/j.ympev.2022.107645  

   MacGuigan, Daniel J. ; Orr, Oliver D. ; Near, Thomas J. ( January 2023 , Molecular Phylogenetics and Evolution)

   The history of riverine fish diversification is largely a product of geographic isolation. Physical barriers that reduce or eliminate gene flow between populations facilitate divergence via genetic drift and natural selection, eventually leading to speciation. For freshwater organisms, diversification is often the product of drainage basin rearrangements. In young clades where the history of isolation is the most recent, evolutionary relationships can resemble a tangled web. One especially recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma nigrum) species complex, where traditional taxonomy and molecular phylogenetics indicate a history of gene flow and conflicting inferences of species diversity. Here we assemble a genomic dataset using double digest restriction site associated DNA (ddRAD) sequencing and use phylogenomic and population genetic approaches to investigate the evolutionary history of the complex of species that includes E. nigrum, E. olmstedi, E. perlongum, and E. susanae. We reveal and validate several evolutionary lineages that we delimit as species, highlighting the need for additional work to formally describe the diversity of the Etheostoma nigrum complex. Our analyses also identify gene flow among recently diverged lineages, including one instance involving E. susanae, a localized and endangered species. Phylogeographic structure within the Etheostoma nigrum species complex coincides with major geologic events, such as parallel divergence in river basins during Pliocene inundation of the Atlantic coastal plain and multiple northward post-glacial colonization routes tracking river basin rearrangements. Our study serves as a nuanced example of how low dispersal rates coupled with geographic isolation among disconnected river systems in eastern North America has produced one of the world’s freshwater biodiversity hotspots. 

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