DOI: 10.5061/dryad.p2ngf1w3f
title: 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

description: 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. 
description: 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 <em>28S</em>, 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.<em>, 2020;
 Ronquist</em> 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 <em>Carolinensis</em> and
 <em>Vexillata</em>, and identifies 5 clades with varying
 associations with mammals. Parasitology
description: # 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 Dataset DOI:
 [10.5061/dryad.p2ngf1w3f](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 * 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/](https://www.ncbi.nlm.nih.gov/) Data
 was derived from the following sources: *
 [https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/)