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

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. 

Methods
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