Development of microarray‐based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase I vs. cytochrome b as genetic markers

Abstract

Molecular methods are widely used for species identification of mammals. In particular, the mitochondrial cytochrome b gene sequence has proven helpful for this purpose. Microarray technology can now open up new perspectives for biodiversity monitoring. With microarrays, many thousands of genetically based characteristics can be tested on one microscopic glass slide called a 'chip'. A 'Mammalia-Chip', for example, could include redundant diagnostic markers to unambiguously identify all European mammal species. Of broader use, and therefore economically more relevant, could be a 'Biodiversity-Chip', containing diagnostic features to distinguish key species in the taxa of bacteria, lichen, molluscs, insects, fungi, mammals, etc. An important prerequisite for any mixed-phyla chip is a standardization of methods. One of the most promising genes as a universal marker for all eukaryotes is cytochrome oxidase I. We show that cytochrome oxidase I is adequate for the discrimination of different species of voles and shrews with cluster analysis. Based on these results we present a diagnostic microarray-chip using cytochrome oxidase I sequences for the identification of three species of Sorex (Soricidae, Insectivora) and four species of Microtus (Arvicolinae, Rodentia). We conclude that cytochrome oxidase I can be used as an alternative marker to cytochrome b in a mixed-phyla chip, or both genes can be used in combination to enhance redundance and thus robustness of a specific chip including small mammals.

Fossorial morphotype does not make a species in water voles

“…Altogether, 50 new haplotypes were found in our material from Europe and Asia, generating a total dataset of 70 different water vole cytb haplotypes (Pfunder et al 2004, Centeno-Cuadros and Godoy 2010, Schlegel et al 2012a. Within the 1117-bp long sequences considered here, 106 polymorphic sites were found with a total of 140 mutations, 105 of which were parsimony informative.…”

“…Included in the study were individuals sequenced for cytb but also museum vouchers of unknown genetic makeup from the same site as the genotyped material. Swiss and German sequences were downloaded from GenBank and their morphotype was not reported (Pfunder et al 2004, Schlegel et al 2012b. Swiss samples were from the range of a subspecies scherman (Meylan and Saucy 1995) and were assigned on this ground to the fossorial morphotype.…”

Sperm competition differentially affects swimming velocity and size of spermatozoa from closely related muroid rodents: head first

“…Phylogenetic effects were controlled using a subset of a phylogenetic tree (Gó mez Montoto et al 2011) reconstructed based on several mitochondrial, nuclear and ribosomal genes (Martin et al 2000, Lundrigan et al 2002, Jaarola et al 2004, Pfunder et al 2004, Suzuki et al 2004, Robovsky et al 2008, Tougard et al 2008, Bannikova et al 2010.…”

Mitochondrial lineages and DNA barcoding of closely related species in the mayfly genus Ephemerella (Ephemeroptera:Ephemerellidae)

“…Hebert and Gregory (2005) concluded that though DNA barcoding does not assure complete taxonomic resolution using a single gene region, in many cases when it fails the results can still be resolved fully with additional genetic or other data. Other genes, such as 16S rDNA (Vences et al 2004;Steinke et al 2005;Kappner and Bieler 2006;Aliabadian et al 2009) and Cyt b (Bradley and Baker 2001;Pfunder et al 2004;DeSalle et al 2005;Hajibabaei et al 2007), have been also advocated as standard or as complementary DNA barcoding markers.…”