skip to main content

Explore Research Products in the NSF-PAR

  • NSF Public Access
  • Search Results
  • Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering
Title: Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering

Background.Applying quantitative morphological approaches in systematics research is a promising way to discover cryptic biological diversity. Information obtained through twenty-first century science poses new challenges to taxonomy by offering the possibility of increased objectivity in independent and automated hypothesis formation. In recent years a number of promising new algorithmic approaches have been developed to recognize morphological diversity among insects based on multivariate morphometric analyses. These algorithms objectively delimit components in the data by automatically assigning objects into clusters.

Method.In this paper, hypotheses on the diversity of the MalagasyNesomyrmex angulatusgroup are formulated via a highly automated protocol involving a fusion of two algorithms, (1) Nest Centroid clustering (NC clustering) and (2) Partitioning Algorithm based on Recursive Thresholding (PART). Both algorithms assign samples into clusters, making the class assignment results of different algorithms readily inferable. The results were tested by confirmatory cross-validated Linear Discriminant Analysis (LOOCV-LDA).

Results.Here we reveal the diversity of a unique and largely unexplored fragment of the Malagasy ant fauna using NC-PART-clustering on continuous morphological data, an approach that brings increased objectivity to taxonomy. We describe eight morphologically distinct species, including seven new species:Nesomyrmex angulatus(Mayr, 1862),N. bidentatussp. n.,N. clypeatussp. n.,N. deviussp. n.,N. exiguussp. n.,N. fragilissp. n.,N. gracilissp. n., andN. hirtellussp. n.. An identification key for their worker castes using morphometric data is provided.

Conclusions.Combining the dimensionality reduction feature of NC clustering with the assignment of samples into clusters by PART advances the automatization of morphometry-based alpha taxonomy.

  more » « less
NSF-PAR ID:
10015325
Author(s) / Creator(s):
 ;  
Publisher / Repository:
PeerJ
Date Published:
Journal Name:
PeerJ
Volume:
4
ISSN:
2167-8359
Page Range / eLocation ID:
e1796
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ( , 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
  2. ; ; ( , Organisms Diversity & Evolution)
    Abstract The genus Ponera includes over 60 extant species worldwide. These tiny, endogeic predator ants are predominantly distributed in the Indomalaya and Australasia regions, with a few additional Holarctic species. Herein, we explore and describe the diversity of the Malagasy Ponera fauna through an integrative taxonomic approach. We obtained our morphological species hypotheses from multivariate analyses of ten continuous morphometric characters. Species boundaries and reliability of morphological clusters were tested via confirmatory Linear Discriminant Analysis (LDA), cross-validation (LOOCV), and analyses of a mitochondrial COI gene fragment. According to the combined application of the analyses, altogether, three species are inferred in the Malagasy region, Ponera petila Wilson (1957), P. swezeyi Wheeler (1933), and P. adumbrans Csősz & Fisher sp. n. Ponera petila and P. swezeyi belong to the Indo-Australian Ponera tenuis group; the third species, P. adumbrans sp. n., is morphologically similar to the Papua New Guinean P. clavicornis Emery (1900). Furthermore, Linear Discriminant Analysis classified the type specimens of P. bableti Perrault (1993), along with a P. petila cluster with posterior p  = 1. Therefore, we propose the new junior synonymy of P. bableti with P. petila . Madagascar’s extant biodiversity is predominantly explained by colonization events from the African continent across the Mozambique channel via rafting. However, since no native Ponera species are known from the Afrotropical continent, and the closest congeners have an almost exclusively Indo-Australian distribution, the likelihood of an Indo-Australian origin of the Malagasy Ponera fauna is implied. 
    more » « less
  3. ; ( , ZooKeys)
    The Camponotus subgenus Myrmosaga subgen. rev. from the Malagasy region is revised based on analysis of both qualitative morphological characters and morphometric traits. The multivariate analysis used the Nest Centroid (NC)-clustering method to generate species hypotheses based on 19 continuous morphological traits of minor workers. The proposed species hypotheses were confirmed by cumulative Linear Discriminant Analysis (LDA). Morphometric ratios for the subsets of minor and major workers were used in species descriptions and redefinitions. The present study places the subgenus Myrmopytia syn. nov. in synonymy to Myrmosaga . It recognizes 38 species, of which 19 are newly described: C. aina sp. nov. , C. aro sp. nov. , C. asara sp. nov. , C. atimo sp. nov. , C. bemaheva sp. nov. , C. bozaka sp. nov. , C. daraina sp. nov. , C. harenarum sp. nov. , C. joany sp. nov. , C. karsti sp. nov. , C. kelimaso sp. nov. , C. lokobe sp. nov. , C. mahafaly sp. nov. , C. niavo sp. nov. , C. rotrae sp. nov. , C. sambiranoensis sp. nov. , C. tapia sp. nov. , C. tendryi sp. nov. , C. vano sp. nov. Eleven species are redescribed: C. aurosus Roger, C. cervicalis Roger, C. dufouri Forel, C. gibber Forel, C. hagensii Forel, C. hova Forel, C. hovahovoides Forel, C. immaculatus Forel, C. quadrimaculatus Forel, C. roeseli Forel, C. strangulatus Santschi. The following are raised to species and redescribed: C. becki Santschi stat. nov. , C. boivini Forel stat. rev. , C. cemeryi Özdikmen stat. rev. , C. mixtellus Forel stat. nov. , C. radamae Forel stat. nov. Camponotus maculatus st. fairmairei Santschi syn. nov. , is synonymized under C. boivini . The following are synonymized under C. cervicalis : Camponotus cervicalis gaullei Santschi, syn. nov. ; Camponotus perroti Forel, syn. nov. ; Camponotus perroti aeschylus Forel, syn. nov. ; Camponotus gerberti Donisthorpe, syn. nov. Camponotus dufouri imerinensis Forel, syn. nov. is a synonym of C. dufouri , Camponotus hova var. obscuratus Emery, syn. nov. is a synonym of C. hova , Camponotus quadrimaculatus opacata Emery, syn. nov. is a synonym of C. immaculatus , Camponotus maculatus st. legionarium Santschi, syn. nov. is a synonym of C. roeseli , Camponotus hova maculatoides Emery, syn. nov. is a synonym of C. strangulatus . The following are synonymized under C. quadrimaculatus : Camponotus kelleri Forel, syn. nov. , Camponotus kelleri var. invalidus Forel, syn. nov. , Camponotus quadrimaculatus sellaris Emery, syn. nov. As C. imitator Forel, C. liandia Rakotonirina & Fisher, and C. lubbocki Forel have been recently described and redescribed, only diagnoses and taxonomic discussions are provided. This revision also includes an illustrated species identification key, taxonomic discussions, images, and distribution maps for each species superimposed on the ecoregions of Madagascar. 
    more » « less
  4. ; ; ; ; ; ( , Systematic Entomology)
    Abstract

    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.

     
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al ( , Methods in Ecology and Evolution)
    Abstract

    Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that is rapid, affordable and non‐invasive. The longstanding needs of the eDNA community are modular informatics tools, comprehensive and customizable reference databases, flexibility across high‐throughput sequencing platforms, fast multilocus metabarcode processing and accurate taxonomic assignment. Improvements in bioinformatics tools make addressing each of these demands within a single toolkit a reality.

    The new modular metabarcode sequence toolkitAnacapa(https://github.com/limey-bean/Anacapa/) addresses the above needs, allowing users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data. A novel aspect ofAnacapais its database building module, “Creating Reference libraries Using eXisting tools” (CRUX), which generates comprehensive reference databases for specific user‐defined metabarcoding loci. TheQuality Control and ASV Parsingmodule sorts and processes multiple metabarcoding loci and processes merged, unmerged and unpaired reads maximizing recovered diversity.DADA2then detects amplicon sequence variants (ASVs) and theAnacapa Classifiermodule aligns these ASVs toCRUX‐generated reference databases usingBowtie2. Lastly, taxonomy is assigned to ASVs with confidence scores using a Bayesian Lowest Common Ancestor (BLCA) method. TheAnacapa Toolkitalso includes anrpackage,ranacapa, for automated results exploration through standard biodiversity statistical analysis.

    Benchmarking tests verify that theAnacapa Toolkiteffectively and efficiently generates comprehensive reference databases that capture taxonomic diversity, and can assign taxonomy to both MiSeq and HiSeq‐length sequence data. We demonstrate the value of theAnacapa Toolkitin assigning taxonomy to seawater eDNA samples collected in southern California.

    TheAnacapa Toolkitimproves the functionality of eDNA and streamlines biodiversity assessment and management by generating metabarcode specific databases, processing multilocus data, retaining a larger proportion of sequencing reads and expanding non‐traditional eDNA targets. All the components of theAnacapa Toolkitare open and available in a virtual container to ease installation.

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