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. 2019 Jun 13;19(1):121.
doi: 10.1186/s12862-019-1444-x.

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

Ashleigh B Smythe  1 , Oleksandr Holovachov  2 , Kevin M Kocot  3
Affiliations

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

Ashleigh B Smythe et al. BMC Evol Biol. .

Abstract

Background: 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, 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.

Results: We 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.

Conclusions: Expanded 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.

Keywords: Free-living; Nematoda; Parasitism; Phylogenomic.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Phylogeny of Nematoda based on the IQ-TREE maximum likelihood analysis of the PhyloTreePruner dataset. “Classification” bar on the left side serves as a scale and represents the relative known taxonomic diversity of different taxa within Nematoda: the height of each colored bar is proportional to a number of known species (also given in the brackets after each taxon name), with the height of the entire multicolored background rectangle equal to 100% of known nematode diversity. IQ-TREE / RAxML bootstrap support values < 100% are shown. “Habitat” describes the lifestyle for each analysed species, such as animal parasitic (animal par.), plant parasitic (plant par.), entomopathogenic or entomoparasitic (entomop.), free-living freshwater (freshwater), terrestrial (terrestrial) and marine (marine). Newly generated transcriptomes are marked with an asterisk
Fig. 2
Fig. 2
Phylogeny of Nematoda based on the IQ-TREE maximum likelihood analysis of the SCaFoS dataset. IQ-TREE / RAxML bootstrap support values < 100% are shown. Newly generated transcriptomes are marked with an asterisk
Fig. 3
Fig. 3
Phylogeny of outgroup taxa based on the IQ-TREE maximum likelihood analysis of the PhyloTreePruner (a) and SCaFoS (b) datasets. IQ-TREE / RAxML bootstrap support values < 100% are shown. Newly generated transcriptomes are marked with an asterisk
Fig. 4
Fig. 4
Simplified nematode phylogeny based on Fig. 2 indicating marine versus freshwater/terrestrial distribution for each order, considering the distribution of the majority of species. Notes: * includes equal number of marine, freshwater and terrestrial taxa, with molecular phylogenies suggesting terrestrial clades to be earlier (deeper); ** based on distribution of hosts, marine taxa may be of secondary origin; *** based on distribution of hosts; **** based on distribution of hosts and free-living stages
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