Which molecular markers for assessing which taxonomic level? The case study of the mite family Phytoseiidae (Acari: Mesostigmata)

Abstract

The use of molecular markers for resolving systematics issues has improved our knowledge of life history. However, for the taxa studied herein—the predatory mite family Phytoseiidae—molecular phylogeny is impeded by a lack of suitable markers for deeper taxonomic levels. This study aims (i) to establish DNA amplification protocols for molecular markers known to resolve supraspecific nodes in other taxa, (ii) to determine their individual performance in assessing the clustering of species, genera, tribes and subfamilies, and (iii) to characterize the additional information provided when markers are concatenated. A new phylogenetic index is proposed based on ecological concepts, considering trees as a community of nodes. New and efficient protocols for DNA amplification of six molecular markers are provided. The concatenated tree globally provides more robust and reliable information, especially for deeper nodes. However, for assessing species identification and within‐genera phylogenies, the combined use of six markers does not seem necessary, underlining the need to resize experiments depending on their taxonomic objectives. Finally, this study lays the methodological foundations with which to test the present Phytoseiidae classification as the first phylogeny obtained shows incongruence with the present morphological classification.

Molecular characterization of phytoseiid mites in Turkey based on the internal transcribed spacer (ITS) region, with a new record for the country

“…The present study correctly assigned the specimens to the species they belong to in the phylogenetic tree. However, we confirm here that ITS sequence is not very variable in phytoseiid mites and intraand interspecific distances are sometimes very close if not overlapping to those of species of different genera (Navajas et al 1999;dos Santos and Tixier 2016). This clearly shows that a simple and universal decision rule based on distance overlap cannot be applied at family level.…”

“…Various molecular markers have been used in mite identification so far (e.g., Navajas and Fenton, 2000;Cruickshank 2002;Dabert 2006;Ros and Breeuwer 2007;dos Santos and Tixier 2016). The internal transcribed spacers (ITS1 and ITS2) of the non-coding region of ribosomal DNA (rDNA) have variable sequences and are among the earliest markers used in Acari (Navajas et al 1992).…”

“…They have been reported to usually allow the separation of species (Cruikshank 2002;Tixier et al 2006). In addition, the ITS region has been reported as a reliable marker to investigate Phytoseiidae phylogeny at species and genus level (Navajas et al 1999;dos Santos and Tixier 2016).…”

Reappraisal of the sub species hypothesis for Gangetic dolphins based on mitochondrial genomics

“…This suggests that both genes can be potentially be used for in molecular taxonomic studies of differentiation of the species (Fig. 2) [56][57]. However, these ndings also raised concern about the inferences made in previous studies about the river dolphin/marine dolphin relationships using genes like Cyt B that show higher evolutionary rates (>0.1) [58,[26][27][28][29] or other segments such as hyper variable D-loop regions or non-coding regions [58,27].…”

Acari of Canada

“…Since Lindquist et al (1979), many molecular markers (e.g., ITS, COI, 16S, 18S, 28S) have been used to help elucidate species boundaries in the Acari (Navajas and Fenton 2000, Cruickshank 2002, Navajas and Navia 2010, dos Santos and Tixier 2017, Lehmitz and Decker 2017). In particular, the 658 bp ‘barcode’ region of COI (cytochrome c oxidase subunit I) has been promoted as a reliable determinant of species boundaries in animals (Hebert et al 2003); however, compared to other arthropod groups (Virgilio et al 2010, Wilson et al 2017), the paucity of barcode data available for Acari worldwide is striking (e.g., Navajas and Navia 2010).…”