Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Abstract

Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.

How many species of whipworms do we share? Whipworms from man and other primates form two phylogenetic lineages

“…Blouin et al 1998, Peng et al 2007, Jex et al 2009), allowing high resolution in deep analyses of closely related lineages (Callejón et al 2012). However, when comparing rDNA and cox1 data alone, support of branches is higher in trees based on nuclear data.…”

Genetic relationships among species ofContracaecumRailliet & Henry, 1912 andPhocascarisHöst, 1932 (Nematoda: Anisakidae) from pinnipeds inferred from mitochondrialcox2sequences, and congruence with allozyme data

“…On the other hand, analyses of the substitution patterns for mtDNA genes of nematodes have suggested that they are very useful markers for identifying and differentiating cryptic species and for determining relationships of closely related species (Blouin et al,1998;Blouin, 2002;Hu et al, 2004 andreferences therein, Hu &Gasser, 2006). The same mtDNA region was demonstrated to be useful in distinguishing closely related anisakid taxa previously characterized by allozyme markers, belonging to the genus Anisakis (Valentini et al, 2006), and to the genus Contracaecum maturing in fish-eating birds .…”

Red vent syndrome in wild Atlantic salmon Salmo salar in Scotland is associated with Anisakis simplex sensu stricto (Nematoda: Anisakidae)

“…cox1 mtDNA was also sequenced from nematodes found in cavity and vent. The cox1 mtDNA is considered to evolve faster than rDNA (Blouin et al 1998), but again, no clear differences in the cox1 sequence were observed between the vent larvae and those from the body cavity, and between individuals with polymorphisms in their ITS rDNA. There is insufficient data to comment on whether the 2 conserved nucleotide/amino acid differences in the cox1 sequence between anisakid specimens infecting RVS salmon and those infecting herring populations around the British Isles (Cross et al 2007) is due to species or population differences.…”