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. Electronic supplementary material The online version of this article (10.1186/s12862-019-1444-x) contains supplementary material, which is available to authorized users.

The structure and genetic diversity of a California Cucumber mosaic virus (CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3 nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.RNA viruses are intrinsically heterogeneous, partly because of the error-prone nature of RNA replication (14,20). In addition, genetic exchange (either by recombination or by reassortment) can be another major evolutionary force which is able to rapidly increase variation and is proposed to have evolved to offset fitness losses due to the accumulation of deleterious mutations through the effect known as Muller's ratchet (6). Other evolutionary factors such as selection, genetic drift, and bottleneck effects can serve to decrease diversity. However, in spite of the high potential for variability of RNA viruses, most RNA virus populations analyzed so far are genetically stable with relatively low diversity (17).Cucumber mosaic virus (CMV) is a tripartite, positive-sense plant RNA virus (Fig. 1). CMV occurs naturally worldwide and has perhaps the widest host range among all plant viruses, including some monocotyledonous and a great number of dicotyledonous plant hosts (26). RNA1 encodes the 1a protein, which together with the RNA2-encoded 2a protein forms the viral component of the replicase complex (19). RNA2 also encodes a second protein, 2b. The 2b coding region overlaps the coding region for the C-terminal portion of the 2a protein but is in a different reading frame register. The CMV 2b protein functions in host-specific long-distance movement (12, 13) and as a virulence determinant by suppressing posttranscriptional gene silencing (3). RNA3 encodes two proteins. The 3a protein is a cell-to-cell movement protein (MP), and the 3b protein is the capsid protein (CP), which is also involved in cell-to-cell movement and aphid-mediated CMV transmission from plant to plant (5, 27, 28). (16), and nucleotide sequence analysis (8,9,33,34,39). Most of these studies were phylogenetically oriented and allowed the subdivisio...

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The number of nuclear small subunit (SSU) ribosomal RNA (rRNA) sequences for Nematoda has increased dramatically in recent years, and although their use in constructing phylogenies has also increased, relatively little attention has been given to their alignment. Here we examined the sensitivity of the nematode SSU data set to different alignment parameters and to the removal of alignment ambiguous regions. Ten alignments were created with CLUSTAL W using different sets of alignment parameters (10 full alignments), and each alignment was examined by eye and alignment ambiguous regions were removed (creating 10 reduced alignments). These alignment ambiguous regions were analyzed as a third type of data set, culled alignments. Maximum parsimony, neighbor-joining, and parsimony bootstrap analyses were performed. The resulting phylogenies were compared to each other by the symmetric difference distance tree comparison metric (SymD). The correlation of the phylogenies with the alignment parameters was tested by comparing matrices from SymD with corresponding matrices of Manhattan distances representing the alignment parameters. Differences among individual parsimony trees from the full alignments were frequently correlated with the differences among alignment parameters (580/1000 tests), as were trees from the culled alignments (403/1000 tests). Differences among individual parsimony trees from the reduced alignments were less frequently correlated with the differences among alignment parameters (230/1000 tests). Differences among majority-rule consensus trees (50%) from the parsimony analysis of the full alignments were significantly correlated with the differences among alignment parameters, whereas consensus trees from the reduced and culled analyses were not correlated with the alignment parameters. These patterns of correlation confirm that choice of alignment parameters has the potential to bias the resultant phylogenies for the nematode SSU data set, and suggest that the removal of alignment ambiguous regions reduces this effect. Finally, we discuss the implications of conservative phylogenetic hypotheses for Nematoda produced by exploring alignment space and removing alignment ambiguous regions for SSU rDNA.