Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

Ashleigh B Smythe,Kevin M Kocot,Oleksandr Holovachov

doi:10.1186/s12862-019-1444-x

Ashleigh B Smythe, Kevin M Kocot + Show 1 more

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https://doi.org/10.1186/s12862-019-1444-x

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Abstract

BackgroundNematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum.ResultsWe supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with a high proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA.ConclusionsExpanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment.

Highlights

Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms
Publicly available nematode and outgroup genomes and transcriptomes were supplemented with new transcriptomes from nine free-living nematodes, one nematomorph, and one kinorhynch for a total of 131 taxa sampled (Table 1, Additional file 2: Tables S1-S2)
Molecular phylogenetic studies have generally supported the existence of three major lineages and the monophyly of Chromadoria, but resolution of the deepest splits within Nematoda - relationships among Enoplia, Dorylaimia, and Chromadoria - has been recalcitrant

Summary

Introduction

Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum. Nematodes are ubiquitous and diverse metazoans that are found free-living in nearly every terrestrial and aquatic habitat and parasitizing most animals and plants. Neglected are the free-living marine nematodes, with only around 6900 species described [3] and no genomes published to date [4]. Nematode evolutionary history is interesting because of the diversity of niches they occupy – ranging from the blood and tissues of vertebrate and invertebrate animals, unicellular eukaryotes, all parts of plants, virtually every terrestrial habitat, and all aquatic environments including deep-sea hydrothermal vent communities – is unrivaled in Smythe et al BMC Evolutionary Biology (2019) 19:121

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