skip to main content

Explore Research Products in the NSF-PAR

  • NSF Public Access
  • Search Results
  • Phylogenomic species delimitation in the ants of the Temnothorax salvini group ( Hymenoptera: Formicidae ): an integrative approach
Title: Phylogenomic species delimitation in the ants of the Temnothorax salvini group ( Hymenoptera: Formicidae ): an integrative approach
ABSTRACT

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.

  more » « less
NSF-PAR ID:
10452144
Author(s) / Creator(s):
 
Publisher / Repository:
Wiley-Blackwell
Date Published:
Journal Name:
Systematic Entomology
Volume:
46
Issue:
2
ISSN:
0307-6970
Page Range / eLocation ID:
p. 307-326
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ( , Insect Systematics and Diversity)
    Abstract

    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.

     
    more » « less
  2. ; ; ( , PeerJ)
    null (Ed.)
    Background Madagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar. Methods The diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses. Results Five species can be inferred based on the integrated evaluation of multiple lines of evidence; of these, three are new to science: Aphaenogaster bressleri sp. n ., A. gonacantha (Emery, 1899), A. makay sp. n. , A. sahafina sp. n. , and A. swammerdami Forel, 1886. In addition, three new synonymies were found for A. swammerdami Forel, 1886 ( A. swammerdami clara Santschi, 1915 syn. n. , A. swammerdami curta Forel, 1891 syn. n. and A. swammerdami spinipes Santschi, 1911 syn. n. ). Descriptions and redefinitions for each taxon and an identification key for their worker castes using qualitative traits and morphometric data are given. Geographic maps depicting species distributions and biological information regarding nesting habits for the species are also provided. 
    more » « less
  3. ; ; ; ; ; ; ; ; ( , Zoologica Scripta)
    Abstract

    PhyllotisWaterhouse 1837 is one of the most studied genera of South American cricetid rodents. As currently understood, it includes 20 small to medium‐sized species of predominantly rocky habitats. Among them, populations of the yellow‐rumped leaf‐eared mouse, traditionally referred toP. xanthopygus(Waterhouse 1837), are the most widely distributed, extending from central Peru to southern Chile and Argentina. Based mostly on molecular evidence, previous studies suggested thatP. xanthopygusconstitutes a species complex, being characterized by geographically structured and genetically divergent clades. In this work, we compare the molecular phylogenetic hypothesis for populations distributed on the eastern slopes of the central Andes with morphometric evidence using univariate and multivariate analyses. Quantitative morphological and molecular evidence suggests that at least four nearly cryptic species of theP. xanthopyguscomplex occur from southern Bolivia to west‐central Argentina. Three of these taxa have available names; one of them,P. caprinus, is currently recognized to the species level; the other two, the clades ofP. x. posticalis‐P. x. rupestrisandP. vaccarum, are both recognized as subspecies ofP. xanthopygus. The remaining taxon represents a new species distributed in the west‐central Andes of Argentina. We discuss our morphological results in the light of other sources of evidence (e.g. qualitative and quantitative state characters, genetic and phylogenetic studies, and cytogenetic data) and name the new species asP. pehuenche, honouring the original native people that historically inhabited west‐central Andes of Argentina.

     
    more » « less
  4. ; ; ; ( , Systematic Entomology)
    Abstract

    Rapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29 000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short‐winged grasshopper species complex (Melanoplus scudderigroup), where Pleistocene diversification has been hypothesized to generate more than 20 putative species with distinct male genitalic shapes. We found that, based on a maximum likelihood molecular phylogeny, each morphological species indeed forms a monophyletic group, contrary to the result from a previous mitochondrial DNA sequence study. By dating the diversification events, the species complex is estimated to have diversified during the Late Pleistocene, supporting the recent radiation hypothesis. Furthermore, coalescent‐based species delimitation analyses provide quantitative support for independent genetic lineages, which corresponds to the morphologically defined species. Our results also showed that male genitalic shape may not be predicted by evolutionary distance among species, not only indicating that this trait is labile, but also implying that selection may play a role in character divergence. Additionally, our findings suggest that the rapid speciation events in this flightless grasshopper complex might be primarily associated with the fragmentation of their grassland habitats during the Late Pleistocene. Collectively, our study highlights the importance of integrating multiple sources of information to delineate species, especially for a species complex that diversified rapidly, and whose divergence may be linked to ecological processes that create geographic isolation (i.e. fragmented habitats), as well as selection acting on characters with direct consequences for reproductive isolation (i.e. genitalic divergence).

     
    more » « less
  5. ; ; ; ; ; ( , Journal of Mammalogy)
    Abstract

    Using sequences from 2,615 ultraconserved element (UCE) loci and multiple methodologies we inferred phylogenies for the largest genetic data set of New World bats in the genus Myotis to date. The resulting phylogenetic trees were populated with short branch lengths and widespread conflict, hallmarks consistent with rapid adaptive radiations. The degree of conflict observed in Myotis has likely contributed to difficulties disentangling deeper evolutionary relationships. Unlike earlier phylogenies based on 1 to 2 gene sequences, this UCE data set places M. brandtii outside the New World clades. Introgression testing of a small subset of our samples revealed evidence of historical but not contemporary gene flow, suggesting that hybridization occurs less frequently in the Neotropics than the Nearctic. We identified several instances of cryptic lineages within described species as well as several instances of potential taxonomic oversplitting. Evidence from Central and South American localities suggests that diversity in those regions is not fully characterized. In light of the accumulated evidence of the evolutionary complexity in Myotis and our survey of the taxonomic implications from our phylogenies, it is apparent that the definition of species and regime of species delimitation need to be reevaluated for Myotis. This will require substantial collaboration and sample sharing between geneticists and taxonomists to build a system that is both robust and applicable in a genus as diverse as Myotis.

     
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email