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1. Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin ( Lepidothrix coronata )

   https://doi.org/10.1093/evolut/qpad187  

   Moncrieff, Andre E; Faircloth, Brant C; Remsen, Rosalind C; Hiller, Anna E; Felix, Cristhian; Capparella, Angelo P; Aleixo, Alexandre; Valqui, Thomas; Brumfield, Robb T (October 2023, Evolution)

   Whitlock, Michael; Connallon, Tim (Ed.)

   Abstract Rivers frequently delimit the geographic ranges of species in the Amazon Basin. These rivers also define the boundaries between genetic clusters within many species, yet river boundaries have been documented to break down in headwater regions where rivers are narrower. To explore the evolutionary implications of headwater contact zones in Amazonia, we examined genetic variation in the Blue-capped Manakin (Lepidothrix coronata), a species previously shown to contain several genetically and phenotypically distinct populations across the western Amazon Basin. We collected restriction site-associated DNA sequence data (RADcap) for 706 individuals and found that spatial patterns of genetic structure indicate several rivers, particularly the Amazon and Ucayali, are dispersal barriers for L. coronata. We also found evidence that genetic connectivity is elevated across several headwater regions, highlighting the importance of headwater gene flow for models of Amazonian diversification. The headwater region of the Ucayali River provided a notable exception to findings of headwater gene flow by harboring non-admixed populations of L. coronata on opposite sides of a < 1-km-wide river channel with a known dynamic history, suggesting that additional prezygotic barriers may be limiting gene flow in this region. 

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2. Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard ( Elgaria coerulea )

   https://doi.org/10.1093/jhered/esad073  

   Leaché, Adam D; Davis, Hayden R; Feldman, Chris R; Fujita, Matthew K; Singhal, Sonal (November 2023, Journal of Heredity)

   Blair, Christopher (Ed.)

   Abstract Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single-nucleotide polymorphism data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least 10 distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species. 

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3. Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae)

   https://doi.org/10.1038/s41437-024-00682-5  

   Fonseca, Emanuel M; Pope, Nathaniel S; Peterman, William E; Werneck, Fernanda P; Colli, Guarino R; Carstens, Bryan C (June 2024, Heredity)

   Abstract One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard speciesNorops brasiliensis(Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation inN. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets. 

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4. Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel ( Sciurus carolinensis )

   https://doi.org/10.1111/mec.17230  

   Fusco, Nicole A.; Cosentino, Bradley J.; Gibbs, James P.; Allen, Maximilian L.; Blumenfeld, Alexander J.; Boettner, George H.; Carlen, Elizabeth J.; Collins, Merri; Dennison, Catherine; DiGiacopo, Devin; et al (December 2023, Molecular Ecology)

   Abstract Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest‐dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation‐by‐distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas. 

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5. Genomic Analyses Implicate the Amazon–Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab

   https://doi.org/10.3390/genes13122263  

   Peres, Pedro A; Bracken-Grissom, Heather; Timm, Laura E; Mantelatto, Fernando L (December 2022, Genes)

   The Amazon–Orinoco plume (AOP) is the world’s largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP’s formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species. 

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