Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes

Abstract

BackgroundThe cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique.ResultsWe conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4–7.8%) while that of nuclear genes was low (0.06–0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.ConclusionsOur research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-3242-5) contains supplementary material, which is available to authorized users.

Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia)

“…Similar to the study of Dabert et al [87], we equally observed that cox 1 or 28S alone are incapable of fully resolving phylogenetic relationships. This phenomenon can probably be caused by mito-nuclear discordance, which has already been recorded for mites and other taxa [100, 101] and was reviewed intensively [102]. Besides this assumption postulating diverging nuclear and mitochondrial phylogenies, the different taxonomic resolution of the two marker regions is likely caused by the loss of phylogenetic information.…”

Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding

“…In a lone study, a cysteine protease from H. longicornis when silenced by RNAi, showed to be involved with digestion of a blood meal and increased the number of Babesia parasites [94]. Recently, a cathepsin L from the tick, R. microplus (BmCL1), was shown to interact with thrombin at pH 7.5 and impair thrombin-induced fibrinogen clotting via a fibrinogenolytic activity [95]. In helminths, cysteine proteases are the most abundant category of proteins identified into excretion/secretion products [96] and have been shown to be involved with host immune evasion [97] and extracellular matrix degradation [98].…”

Persistence of single species of symbionts across multiple closely-related host species

“…In particular, we found that Trouessartia populations were more structured than those of Proctophyllodes , as was previously found in two different species of the same genera, e.g., 50% vs 19% of the variation explained by the among-infrapopulation genetic structure component in Trouessartia bifurcata (Trouessart) vs Proctophyllodes sylviae 32 . Nonetheless, contrasting effective population sizes 46 or processes such as hybridisation 19 may distort genetic estimates from a single-locus such as the COI used in this study, and therefore, studies using multilocus population genomic approaches (e.g., SNPs 15 ) are encouraged.…”