Applicability of mitochondrial DNA for the identification of Arvicolid species from faecal samples: a case study from the threatened Cabrera’s vole

Molecular Ecology Resources (Impact Factor: 5.63). 02/2011; 11(2):409 - 414. DOI: 10.1111/j.1755-0998.2010.02939.x

ABSTRACT Arvicolid mitochondrial genomes evolve faster than in any other mammalian lineage. The genetic diversity exhibited by these rodents contrasts sharply with their phenotypic homogeneity. Furthermore, faecal droppings from Arvicolid rodents of similar body size are almost undistinguishable on the basis of pellet morphology and content. In this study, we advantaged from their high genetic diversity vs. phenotypic homogeneity to document the applicability of mtDNA extraction from vole droppings for latter identification of such via a rapid and efficient nested PCR-based technique using the threatened Microtus cabrerae as a model species. We sequenced the mitochondrial control region from 75 individuals belonging to 11 species of Arvicolinae from Spain, Portugal, Greece and Italy, and an additional 19 sequences from ten Microtus species from other countries were downloaded from Genbank. Based on these control region sequences, we successfully designed and applied a nested PCR for M. cabrerae-specific and arvicolid-generic mtDNA markers to differentiate Cabrera’s vole faecal samples among other species of the Arvicolinae subfamily. Although this study used Cabrera’s vole as a model species, similar techniques based on mtDNA sequences may find a broader applicability for noninvasive genetic conservation of vole species and their populations.

Download full-text


Available from: Ramón C. Soriguer, Jun 20, 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Capturing wild animals can be time consuming and difficult or even impractical. Noninvasive sampling is potentially a cost-effective and efficient means to monitor wild animals, thereby avoiding the need of capture and disturb species in the wild. On the basis of the morphological and genetic analyses of owl pellet contents, a so far undetected European snow vole (Chionomys nivalis) population was discovered in the Sierra Segura mountain range (Southern Spain). The mtDNA sequence from the newly discovered haplotype was compared with sequences from vole populations of the Sierra Nevada and Sierra Peñalara mountain ranges (Spain) and from Churwalden (Switzerland). The nine recovered haplotypes clustered in four distinct lineages according to their geographical origin. The vole sequence from the Sierra Segura owl pellet belonged to a new haplotype, constituting a new lineage. The evolutionary divergence between sequences from the Sierra Segura and other Spanish populations was higher than that among other Spanish haplotypes. The new snow vole haplotype from this new locality duplicates the number of occurrence sites of this critically endangered species in Southern Spain, which is of great interest for further conservation and management plans of the European snow vole in the most southwestern area of its entire distribution range.
    Mitochondrial DNA 03/2013; DOI:10.3109/19401736.2013.772148 · 1.70 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Many rodent species are currently under conservation threat. However, population monitoring and status assessment are extremely challenging because of small body size, low abundance and elusive behavior of rodents. Furthermore, invasive methods of capture and tissue collection commonly used to address such studies can induce an unacceptable amount of stress to sensitive species. As a result, noninvasive techniques have become more widely used, but relatively few studies have applied noninvasive techniques to rodents. Here we present two noninvasive alternatives for the collection of DNA from Franklin’s ground squirrels (Poliocitellus franklinii). We compared the quantity, purity and degradation of DNA extracted from plucked hair and fecal pellets to tail snip tissues. We recovered more DNA from tail snips than either plucked hair or fecal pellets. Both hair and fecal pellets recovered DNA with purity ratios similar to tail snips. As expected, DNA recovered from fecal pellets exhibited a high degree of degradation compared to hair and tail tissues. Careful planning of field and laboratory protocols is therefore necessary to compensate for challenges associated with noninvasive tissue types. While there is no tissue that can universally be applied to all research projects, both hair and feces are viable alternatives to traditional invasive procedures and can be applied to threatened and endangered rodent species.
    Natural Science 01/2013; 5(5A). DOI:10.4236/ns.2013.55A003
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free‐living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near‐species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt‐b)] and one nuclear gene [interphotoreceptor retinoid‐binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt‐b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt‐b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl‐pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.
    Molecular Ecology Resources 01/2013; 13(1). · 5.63 Impact Factor