The first phylogenetic reconstruction of Nippostrongylinae (Nematoda: Heligmonellidae) reveals 3 new genera, the polyphyletic nature of Carolinensis and Vexillata, and identifies 5 clades with varying associations with mammals
Data files
Jul 14, 2025 version files 375.08 KB
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CorrelationofScientificNames2OTU.csv
6.92 KB
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infileITSNippo.nex
96.23 KB
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QINSINippoITS_28S_COX1_13DECmb.nex
266.93 KB
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README.md
5.01 KB
Abstract
The Nippostrongylinae is a group of strongylid nematodes that includes species typically associated with coprophagous mammals. In the New World, the taxon is represented by 82 species within 11 genera. To evaluate the phylogenetic signal from these characteristics, we use genetic data to reconstruct the first phylogeny for the Nippostrongylinae using nuclear and mitochondrial genes and include representatives of the most common and diverse genera. The reconstructed phylogeny features five distinct clades and allows us to identify three non-monophyletic taxa including Carolinensis, Vexillata and Hassalstrongylus. From these, Carolinensis s. l. is divided into four genera including Carolinensis, Boreostrongylus, Neoboreostrongylus n. gen. and Tepalcuanema n. gen. Stunkardionema is resurrected to include Vexillata noviberiae and Hassalstrongylus is divided into two, establishing Lovostrongylus n. gen. to include species that are closely related to Guerrerostrongylus and Trichofreitasia. Our results reveal the existence of an additional unnamed genus and underscore the usefulness of framing morphological characters in a comparative framework.
Dataset DOI: 10.5061/dryad.p2ngf1w3f
Description of the data and file structure
This dataset contains original sequences generated through Sanger chemistry using specimens collected from across the world. The matrices are made available so researchers can replicate and build upon the phylogeny proposed for the Nippostrongylinae of the New World. This phylogeny is available in Jiménez et al. (in review). Parasitology. Data were collected from Argentina, Canada, Ecuador, French Guiana, Mexico, Paraguay, and the United States. Ancillary sequences were obtained from GenBank. The phylogeny is used to propose a redefinition of several genera that were defined based on homoplastic characters. Files are in NEXUS format, and there is a table to correlate the proposed taxon names, GenBank numbers, and OTUs used by authors.
Methodology
For ITS and 28S, the alignment was performed using MAFFT software for secondary structure alignment using default QINSI settings (Katoh & Standley, 2013).optimality criteria of Maximum Likelihood using RAXML with 1,000 bootstrap replicates. Branch posterior probability was estimated using MrBayes 3.2 (Minh* et al., 2020; Ronquist et al.*, 2012) running 4 chains for 10 million generations, with sampling every 1,000 generations and a burn-in of 25%.
References (in this ReadMe)
Katoh, K. and Standley, D. M. (2013). MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30, 772-780. doi: 10.1093/molbev/mst010.
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A. and Lanfear, R. (2020). IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37, 1530 – 1534. doi: 10.1093/molbev/msaa015.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M. A. and Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539 - 542. doi: Doi 10.1093/Sysbio/Sys029.
Files and variables
File: infileITSNippo.nex
Description: Nexus file that includes the alignment of a fragment of ITS (ITS1, 5.8S ribosomal subunit, and ITS2). This dataset uses information available in GenBank and was used to expand the dataset to further test reciprocal monophyletic groupings.
File: QINSINippoITS_28S_COX1_13DECmb.nex
Description: Nexus file that includes the alignment of nuclear (ITS and 28S) and mitochondrial (Cytochrome Oxidase Subunit 1) gene regions of nematode parasites of coprophagous mammals, including cricetid, geomyid, and heteromyid rodents, as well as leoporids
File: CorrelationofScientificNames2OTU.csv
Description: This file links the proposed scientific names, which include new nomenclatural acts and the GenBank numbers and Operational Taxonomic Unit codes used by the authors.
Variables
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Taxon: Heligmosomoides americanus
Heligmosomoides bibullosus
Heligmosomum mixtum
Citellinema kinsellai
Ornithostrongylus quadriradiatus
Austrostrongylus victoriensis
Nippostrongylus brasiliensis
Nippostrongylus magnus
Orientostrongylus ezoensis
Heligmonoides speciosus
Lagostrongylus leporis
Chisholmia bainae
Boreostrongylus minutus
Tepalcuanema perezponcedeleoni
Carolinensis neotomae
Carolinensis carolinensis
Neoboreostrongylus kinsellai
Neoboreostrongylus dalrymplei
Malvinema sp.
Lovostrongylus sp.
Trichofreitasia sp.
Hassalstrongylus sp.
Hassalstrongylus petteri
Lovostrongylus bocqueti
Lovostrongylus dollfusi
Guerrerostrongylus marginalis
Stilestrongylus sp.
Vexillata armandae
Carolinensis sp.
Vexillata dessetae
Vexillata convoluta
Lovostrongylus dollfusi
Stunkardionema noviberiae
Mazzanema sp.
UNNAMED Heligmonellidae
*Hassalstrongylus aduncus *
Hassalstrongylus geolayarum
Mikenema lamothei
Stilestrongylus azarai
Guerrerostrongylus zeta
Unidentified
- Taxa used for reconstruction based on mitochondrial and nuclear genes
- Taxa used for reconstruction using ITS
Code/software
Alignments can be visualized with SewView and Mesquite.
Analyses can be completed in Mr.Bayes
Access information
Other publicly accessible locations of the data:
- Raw sequences available at: https://www.ncbi.nlm.nih.gov/
Data was derived from the following sources:
Datamatrix to reconstruct the phylogenetic relationships of the Nippostrongylinae in the New World. The datamatrix includes fragments of mitochondrial and nuclear gene regions. Mitochondrial genes include partial sequences of Cox1. Nuclear regions includes a fragment of ITS1, 5.8S ribosomal, ITS2, and a fragment of 28S ribosomal.
Data were collected from Argentina, Canada, Ecuador, French Guiana, Mexico, Paraguay and the United States. Ancillary sequences were obtained from GenBank. The phylogeny is used to propose a redefinition of several genera that were defined based on homoplastic characters. Files are in nexus format, and there is a table to correlate the proposed taxon names, GenBank numbers and OTUs used by authors.
For ITS and 28S, the alignment was performed using MAFFT software for secondary structure alignment using default QINSI settings (Katoh & Standley, 2013).optimality criteria of Maximum Likelihood using RAXML with 1,000 bootstrap replicates. Branch posterior probability was estimated using MrBayes 3.2 (Minh* et al., 2020; Ronquist et al.*, 2012) running 4 chains for 10 million generations, with sampling every 1,000 generations and a burn-in of 25%
Sequences were generated using Sanger chemistry based on specimens collected across the New World. Alignment for 28S enforced secondary structure. Detailed methods are found in the original manuscript: Jiménez et al., The first phylogenetic reconstruction of Nippostrongylinae (Nematoda: Heligmonellidae) reveals 3 new genera, the polyphyletic nature of Carolinensis and Vexillata, and identifies 5 clades with varying associations with mammals. Parasitology