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1. Genomic data support the taxonomic validity of Middle American livebearers Poeciliopsis gracilis and Poeciliopsis pleurospilus (Cyprinodontiformes: Poeciliidae)

   https://doi.org/10.1371/journal.pone.0262687  

   Ward, Sarah J.; McMahan, Caleb D.; Khakurel, Basanta; Wright, April M.; Piller, Kyle R. (January 2022, PLOS ONE)

   Aguirre, Windsor E. (Ed.)

   Poeciliopsis (Cyprinodontiformes: Poeciliidae) is a genus comprised of 25 species of freshwater fishes. Several well-known taxonomic uncertainties exist within the genus, especially in relation to the taxonomic status of Poeciliopsis pleurospilus and P . gracilis . However, to date, no studies have been conducted to specifically address the taxonomic status of these two species. The goal of this study was to examine the taxonomic validity of P . pleurospilus and P . gracilis using genomic data (ddRADseq) in phylogenetic, population genetic, and species delimitation frameworks. Multiple analyses support the recognition of both taxa as distinct species and also permits us to revise their respective distributions. A species delimitation analysis indicates that P . pleurospilus and P . gracilis are distinct species, each of which consists of two distinct lineages that are geographically structured. Phylogenetic and population genetic analyses provide clear evidence that individuals of P . gracilis are distributed north and west of the Isthmus of Tehuantepec in both Pacific and Atlantic river systems in Mexico, whereas individuals of P . pleurospilus are distributed in both Atlantic and Pacific river systems south and east of the Isthmus of Tehuantepec, from southern Mexico to Honduras. 

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2. A phylogenomic overview of the ant genus Tapinoma Foerster, 1850 (Formicidae: Dolichoderinae), with the phylogeographic history of the ghost ant Tapinoma melanocephalum

   https://doi.org/10.1093/isd/ixaf035  

   Pérez-Flores, Oscar; Branstetter, Michael G; Longino, John T; Matos-Maraví, Pável; Borovanska, Michaela; Janda, Milan (September 2025, Insect Systematics and Diversity)

   Abstract The ant genus Tapinoma Foerster, 1850 is a moderately diverse group (81 valid species) that occurs worldwide. It includes the tramp species T. melanocephalum, whose evolutionary history, biogeographic origin, and population limits remain unclear. Here, we present a time-calibrated phylogeny and a biogeographic history inference of the genus based on thousands of Ultraconserved Element (UCE) loci. Focusing on T. melanocephalum, we used single nucleotide polymorphisms from UCE loci and COI sequences to analyze species boundaries based on nuclear and mitochondrial DNA. We recovered a monophyletic Tapinoma with an estimated crown age corresponding to middle Eocene (49.4 to 34.4 Ma). Phylogenomic data differentiated T. melanocephalum from T. jandai, a recently established species based on morphology, and revealed that the 2 species diverged ∼12 Ma. Population genetic analyses identified considerable molecular divergence among sampled T. melanocephalum populations, and a heterogeneous genetic structure, showing a weak relationship between genetic differentiation and geographic distance. A phylogeographic comparison of habitat preferences of T. melanocephalum revealed an ecological shift from undisturbed to urban environments, a phenomenon which may have facilitated its ubiquitous and global distribution. Our study presents the first phylogenomic framework for this globally distributed ant genus and molecularly delineates a worldwide pest ant species. 

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3. Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.)

   https://doi.org/10.1002/ece3.10983  

   Starrett, James; Jochim, Emma_E; Quayle, Iris_L; Zahnle, Xavier_J; Bond, Jason_E (March 2024, Ecology and Evolution)

   Abstract The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider,Promyrmekiaphila korematsuisp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genusPromyrmekiaphilaand its constituent species, which also includesP. clathrataandP. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages withinP. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergentP. clathratalineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence inPromyrmekiaphilaat the population–species interface. 

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4. Differential patterns of connectivity in Western Pacific hydrothermal vent metapopulations: A comparison of biophysical and genetic models

   https://doi.org/10.1111/eva.13326  

   Breusing, Corinna; Johnson, Shannon B.; Mitarai, Satoshi; Beinart, Roxanne A.; Tunnicliffe, Verena (December 2021, Evolutionary Applications)

   Abstract Hydrothermal ecosystems face threats from planned deep‐seabed mining activities, despite the fact that patterns of realized connectivity among vent‐associated populations and communities are still poorly understood. Since populations of vent endemic species depend on larval dispersal to maintain connectivity and resilience to habitat changes, effective conservation strategies for hydrothermal ecosystems should include assessments of metapopulation dynamics. In this study, we combined population genetic methods with biophysical models to assess strength and direction of gene flow within four species of the genusAlviniconcha(A. boucheti,A. kojimai,A. strummeriandA. hessleri) that are ecologically dominant taxa at Western Pacific hydrothermal vents. In contrast to predictions from dispersal models, among‐basin migration inA. bouchetioccurred predominantly in an eastward direction, while populations within the North Fiji Basin were clearly structured despite the absence of oceanographic barriers. Dispersal models and genetic data were largely in agreement for the otherAlviniconchaspecies, suggesting limited between‐basin migration forA. kojimai, lack of genetic structure inA. strummeriwithin the Lau Basin and restricted gene flow between northern and southernA. hessleripopulations in the Mariana back‐arc as a result of oceanic current conditions. Our findings show that gene flow patterns in ecologically similar congeneric species can be remarkably different and surprisingly limited depending on environmental and evolutionary contexts. These results are relevant to regional conservation planning and to considerations of similar integrated analyses for any vent metapopulations under threat from seabed mining. 

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5. Genomic Analyses of Phenotypic Differences Between Native and Invasive Populations of Diffuse Knapweed (Centaurea diffusa)

   https://doi.org/10.3389/fevo.2020.577635  

   Turner, Kathryn G.; Ostevik, Kate L.; Grassa, Christopher J.; Rieseberg, Loren H. (January 2021, Frontiers in Ecology and Evolution)

   null (Ed.)

   Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed [ Centaurea diffusa Lam. (Asteraceae)]. To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7,058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation. 

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