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1. Global domination by crazy ants: phylogenomics reveals biogeographical history and invasive species relationships in the genus Nylanderia (Hymenoptera: Formicidae)

   https://doi.org/10.1111/syen.12423  

   Williams, Jason L. ; Zhang, Yuanmeng Miles ; Lloyd, Michael W. ; LaPolla, John S. ; Schultz, Ted R. ; Lucky, Andrea ( January 2020 , Systematic Entomology)

   Nylanderia(Emery) is one of the world's most diverse ant genera, with 123 described species worldwide and hundreds more undescribed. Fifteen globetrotting or invasive species have widespread distributions and are often encountered outside their native ranges. A molecular approach to understanding the evolutionary history and to revision ofNylanderiataxonomy is needed because historical efforts based on morphology have proven insufficient to define major lineages and delimit species boundaries, especially where adventive species are concerned. To address these problems, we generated the first genus‐wide genomic dataset ofNylanderiausing ultraconserved elements (UCEs) to resolve the phylogeny of major lineages, determine the age and origin of the genus, and describe global biogeographical patterns. Sampling from seven biogeographical regions revealed a Southeast Asian origin ofNylanderiain the mid‐Eocene and four distinct biogeographical clades in the Nearctic, the Neotropics, the Afrotropics/Malagasy region, and Australasia. The Nearctic and Neotropical clades are distantly related, indicating two separate dispersal events to the Americas between the late Oligocene and early Miocene. We also addressed the problem of misidentification that has characterized species‐level taxonomy inNylanderiaas a result of limited morphological variation in the worker caste by evaluating the integrity of species boundaries in six of the most widespreadNylanderiaspecies. We sampled across ranges of species in theN. bourbonicacomplex (N. bourbonica(Forel) + N. vaga(Forel)), theN. fulvacomplex (N. fulva(Mayr) + N. pubens(Forel)), and theN. guatemalensiscomplex (N. guatemalensis(Forel) + N. steinheili(Forel)) to clarify their phylogenetic placement. Deep splits within these complexes suggest that some species names – specificallyN. bourbonicaandN. guatemalensis– each are applied to multiple cryptic species. In exhaustively samplingNylanderiadiversity in the West Indies, a ‘hot spot’ for invasive taxa, we found five adventive species among 22 in the region; many remain morphologically indistinguishable from one another, despite being distantly related. We stress that overcoming the taxonomic impediment through the use of molecular phylogeny and revisionary study is essential for conservation and invasive species management.

    

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2. Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae)

   https://doi.org/10.1002/ece3.10025  

   Newton, Lacie G. ; Starrett, James ; Jochim, Emma E. ; Bond, Jason E. ( April 2023 , Ecology and Evolution)

   Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population‐level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genusAptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, theAptostichus icenogleicomplex, which comprises the three sibling species,A. barackobamai,A. isabella, andA. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species‐based approach. We used genomic‐scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries withinA. icenoglei.

    

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3. Phylogenomic species delimitation in the ants of the Temnothorax salvini group ( Hymenoptera: Formicidae ): an integrative approach

   https://doi.org/10.1111/syen.12463  

   Prebus, Matthew M. ( December 2020 , Systematic Entomology)

   The members of theTemnothorax salvini(Forel) species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two‐speciessalvinigroup concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model‐based approaches to species delimitation based on target‐enriched genomic data. With molecular data from thousands of ultraconserved elements (UCEs), mitochondrial genome sequences and morphometric data, I use an integrated approach to species delimitation within thesalvinigroup. Morphometric data were analysed using cluster analysis of principal component analysis (PCA) output. I use several popular methods of molecular species delimitation, including bPTP, BPP and STACEY, using a novel approach to filtering UCE data based on posterior predictive checks of nucleotide substitution model adequacy. In addition, I use iBPP to integrate morphometric PCA data and filtered UCE data in a ‘total evidence’ analysis. I use geographical range data for an independent contrast to discriminate among competing species delimitation hypotheses. Furthermore, I investigate the evolutionary timescale and biogeographical history of the group and find that it arose roughly 13 Ma ago in habitats associated with present day mid‐to‐high elevations of the mountain complex spanning southern Mexico to northern Nicaragua. In addition, dispersal of thesalvinigroup into the Southern Sierra Madre in Mexico, lowland habitats and the southern Central American cordilleras in Costa Rica and Panama subsequent to mountain building in southern Central America 5–8 Ma ago appears to follow a taxon‐cycle dynamic, with the lowland‐adaptedT. aztecusrepresenting the most recent expansion phase. I find that thesalvinigroup, which previously contained two named species, is composed of nine, all of which are morphologically diagnosablea posteriori.

    

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4. Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

   https://doi.org/10.1093/isd/ixab001  

   Longino, John T ; Branstetter, Michael G ( March 2021 , Insect Systematics and Diversity)

   Hines, Heather (Ed.)

   Abstract The ant genus Syscia  Roger, 1861 is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work, the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites, but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size. 

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5. Species Paraphyly and Social Parasitism: Phylogenomics, Morphology, and Geography Clarify the Evolution of the Pseudomyrmex elongatulus Group (Hymenoptera: Formicidae), a Mesoamerican Ant Clade

   https://doi.org/10.1093/isd/ixab025  

   Ward, Philip S. ; Branstetter, Michael G. ; Sosa-Calvo, ed., Jeffrey ( January 2022 , Insect Systematics and Diversity)

   Using genetic, morphological, and geographical evidence, we investigate the species-level taxonomy and evolutionary history of the Pseudomyrmex elongatulus group, a clade of ants distributed from southwestern United States to Costa Rica. Through targeted enrichment of 2,524 UCE (ultraconserved element) loci we generate a phylogenomic data set and clarify the phylogenetic relationships and biogeographic history of these ants. The crown group is estimated to have originated ~8 Ma, in Mexico and/or northern Central America, and subsequently expanded into southern Central America and the southwestern Nearctic. The P. elongatulus group contains a mix of low- and high-elevation species, and there were apparently multiple transitions between these habitat types. We uncover three examples of one species—of restricted or marginal geographical distribution—being embedded phylogenetically in another species, rendering the latter paraphyletic. One of these cases involves an apparent workerless social parasite that occurs sympatrically with its parent species, with the latter serving as host. This suggests a sympatric origin of the parasite species within the distribution range of its host. Species boundaries are tested using three molecular delimitation approaches (SODA, bPTP, BPP) but these methods generate inflated species estimates (26–46 species), evidently because of a failure to distinguish population structure from species differences. In a formal taxonomic revision of the P. elongatulus group, based on almost 3,000 specimens from ~625 localities, we allow for geographic variation within species and we employ distinctness-in-sympatry criteria for testing hypotheses about species limits. Under these guidelines we recognize 13 species, of which nine are new: P. arcanus, sp. nov. (western Mexico); P. capillatus, sp. nov. (western Mexico); P. cognatus, sp. nov. (Chiapas, Mexico to Nicaragua); P. comitator, sp. nov. (Chiapas, Mexico); P. ereptor, sp. nov. (Veracruz, Mexico); P. exoratus, sp. nov. (southeastern Mexico, Honduras); P. fasciatus, sp. nov. (Chiapas, Mexico to Costa Rica); P. nimbus, sp. nov. (Costa Rica); and P. veracruzensis, sp. nov. (Veracruz, Mexico). Our study highlights the value of combining phylogenomic, phenotypic, and geographical data to resolve taxonomic and evolutionary questions.

    

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