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1. 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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2. Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests

   https://doi.org/10.1002/ece3.7951  

   Silva, Sofia Marques ; Ribas, Camila C. ; Aleixo, Alexandre ( July 2021 , Ecology and Evolution)

   We assessed population structure and the spatio‐temporal pattern of diversification in the Glossy AntshrikeSakesphorus luctuosus(Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens ofS.luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming thatS.luctuosusconsists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l.araguayae) and gathered circumstantial evidence indicating that the taxonS.hagmannimay represent a highly introgressed population between three distinct phylogroups ofS.luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspeciesS. l.luctuosus, but not for theS. l.araguayaepopulation. Our results support thatS.luctuosushas had a complex population history, resulting from a high dependence on southeastern “clear water” seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western “white water” flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences betweenvárzeas(“white water” floodplains, mostly in southwestern Amazonia) andigapós(“clear water” floodplains, especially located in the east) should be further explored as drivers of micro‐evolution for terrestrial species.

    

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3. Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

   https://doi.org/10.1111/jbi.13748  

   Marques-Souza, Sergio ; Machado Pellegrino, Katia C. ; Oliveira Brunes, Tuliana ; Carnaval, Ana Carolina ; Pacheco Damasceno, Roberta ; Lima de Oliveira Borges, Manoela ; Candia Gallardo, Carlos ; Rodrigues, Miguel Trefaut ( December 2019 , Journal of Biogeography)

   To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.

   Central Amazonia, Brazil.

   Squamata; Gymnophthalmidae;Loxopholis osvaldoi.

   We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).

   We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.

   Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

    

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4. 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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5. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation

   https://doi.org/10.1093/sysbio/syad020  

   Mcguire, Jimmy A. ; Huang, Xiaoting ; Reilly, Sean B. ; Iskandar, Djoko T. ; Wang-Claypool, Cynthia Y. ; Werning, Sarah ; Chong, Rebecca A. ; Lawalata, Shobi Z. S. ; Stubbs, Alexander L. ; Frederick, Jeffrey H. ; et al ( April 2023 , Systematic Biology)

   The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island’s long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species—9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.]

    

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