Abstract
In recent decades, great strides have been made using various kinds of data including molecular sequences to clarify the phylogenetic relationships of nematodes. Although SSU rDNA sequences are among the most widely used markers in nematode phylogeny, there are areas within Nematoda that do not seem amenable to resolution by this single nuclear gene. The use of the complete mitochondrial genome (mitogenome) is an alternative and powerful molecular method for inferring phylogenies and is frequently used in nematodes. Here we present an overview of the contributions of mitogenome phylogenies in the phylum Nematoda. The nematode mitogenome has several practical strengths as a phylogenetic marker, and has yielded well-supported results for clades which were not well resolved using other approaches. We discuss places where nematode mitogenomes have sometimes produced alternative tree topologies compared to nuclear gene phylogenies, review to what extent mitochondrial gene order is useful in nematode phylogenetics, and make recommendations for promising future areas of research.
Highlights
Well-reconstructed phylogenies are essential to interpreting much of biological research
Members of clade III have major impacts on human and animal health, and understanding their phylogenetic relationships to non-parasitic nematodes can inform our understanding of the evolution of zooparasitism
In the revised nematode classification system based on SSU rDNA data (De Ley and Blaxter, 2002, 2004), the four groups within clade III were each treated as infraorders (Oxyuridomorpha, Spiruromorpha, Rhigonematomorpha, and Ascaridomorpha) and placed in the suborder Spirurina along with two additional groups, Gnathostomatomorpha and Dracunculoidea (Figure 1A)
Summary
Well-reconstructed phylogenies are essential to interpreting much of biological research. There are branches in the nematode phylogenetic tree that have not been well resolved using SSU rDNA (or other single gene sequences). Recent phylogenomic analyses of whole genomes or transcriptome information have produced results that are largely consistent with the relationships among major nematode clades supported by SSU phylogenies (Blaxter and Koutsovoulos, 2015; Smythe et al, 2019).
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