Applicability of mitochondrial DNA for the identification of Arvicolid species from faecal samples: a case study from the threatened Cabrera’s vole
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.
- SourceAvailable from: Paulo C Alves[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 10/2012; · 7.43 Impact Factor
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ABSTRACT: A cost-effective, reliable and efficient method of obtaining DNA samples is essential in large-scale genetic analyses. This study examines the possibility of using a threatened vole species, Microtus cabrerae, as a model for the collection and preservation of faecal samples for subsequent DNA extraction with a protocol based on the HotSHOT technique. Through the examination of the probability of multi-copies (mitochondrial) and single copy (microsatellite) loci amplification (including the genotype error) and of the DNA yield (estimated by real-time qPCR), the new protocol was compared with both the frequently employed methods that successfully use ethanol to preserve faecal samples and with commercial kit-based DNA extraction. The single-tube HotSHOT-based protocol is a user-friendly, non-polluting, time-saving and inexpensive method of faeces sample collection, preservation and PCR-quality gDNA preparation. This technique therefore provides researchers with a new approach that can be employed in high-throughput, noninvasive genetic analyses of wild animal populations.European Journal of Wildlife Research · 1.36 Impact Factor
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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; · 1.71 Impact Factor
MOLECULAR DIAGNOSTICS AND DNA TAXONOMY
Applicability of mitochondrial DNA for theidentification of
Arvicolid species fromfaecal samples: acase study from the
threatened Cabrera’s vole
SAMER ALASAAD,*,†, RAMO´N C. SORIGUER,* MICHAEL J. JOWERS,* JUAN A. MARCHAL,
† ISMAEL ROMERO† and ANTONIO SA´NCHEZ†
*Estacio ´n Biolo ´gica de Don ˜ana, Consejo Superior de Investigaciones Cientı ´ficas (CSIC), Avda. Ame ´rico Vespucio S⁄N 41092 Sevilla,
Spain, †Departamento de Biologı ´a Experimental, Universidad de Jae ´n, Campus Las Lagunillas, S⁄N, E-23071, Jae ´n, Spain
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 advan-
taged 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 threa-
tened 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 spe-
cies 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 Cabre-
ra’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.
Keywords: Arvicolinae, generic primers, Microtus cabrerae, Mitochondrial DNA, nested PCR, noninvasive samples, spe-
cies identification, specific primers, threatened species
Received 17 August 2010; revision received 7 October 2010; accepted 13 October 2010
Recent advances in molecular methods and newly avail-
able techniques are rapidly and increasingly changing
the way wild populations are studied. Moreover, the use
of genetic data from noninvasive samples has become
essential in surveys and in conservation management.
Mitochondrial DNA is widely genotyped from faecal
samples because it tends to be easier to amplify even
after very long periods of storage and degradation,
mostly because it is usually present in cells in a high
number of copies (e.g. Berry & Sarre 2007; O’Reilly et al.
2008), while other genetic markers, such as microsatel-
lites (STR) and single nucleotide polymorphisms (SNP),
allow individual identification and sex determination.
Thus, these nuclear markers are widely used to assess
species population structure but are less suitable in
species identification (Taberlet et al. 1999). Of the ?4500
extant mammalian species, 40% are rodents (Musser &
Carleton 1993). One of the most diverse rodent lineages is
the subfamily Arvicolinae (lemmings, muskrats and
voles). Microtus is one of the most taxonomically diverse
rodent genera, including over 60 extant species (Chaline
et al. 1999). Molecular studies have shown that the Arvi-
colinae have a fast rate of nucleotide substitution across
the entire mtDNA genome as well as at each protein-
coding gene implying that their mtDNA genomes evolve
more rapidly than any other mammalian lineage (Conroy
& Cook 2000; Triant & Dewoody 2006). These findings
contrast with the apparent little phenotypic plasticity
within the species subfamily. This suggests that genes
responsible for morphological variation do not seem to be
influenced by either the rapid rate of mtDNA nucleotide
substitution or chromosomal rearrangements (Maruyama
& Imai 1981; Fink et al. 2004; Jaarola & Searle 2004).
The contrasting evidence between the high genetic
diversity and the phenotypic homogeneity within this
subfamily leads us to prepare a nested PCR-based
assessment method to differentiate arvicolid species with
Correspondence: Samer Alasaad, Fax: +34 954621125;
? 2010 Blackwell Publishing Ltd
Molecular Ecology Resources (2011) 11, 409–414doi: 10.1111/j.1755-0998.2010.02939.x
a noninvasive method, using the threatened Cabrera’s
vole (Microtus cabrerae) as a model species.
The threatened Iberian vole Microtus cabrerae (Thomas
1906) is only found in Portugal and Spain (Blanco & Gon-
za ´lez 1992; Cabral et al. 2005) and is currently listed
under the European Community Habitats Directive
(92⁄43⁄EEC) and the Berne Convention (82⁄72⁄CEE).
This species’ habitat requirement is very specific, and it is
always found in small populations in habitat patches that
require habitat protection and management if the few
remaining fragile populations are to be conserved (Pri-
mack 1993). M. cabrerae is very difficult to monitor in the
wild and hence conventional approaches such as trap-
ping or photography are mostly inefficient. Studies of
this threatened species are still needed if effective conser-
vation efforts are to be implemented to identify the key
factors that are currently subjecting populations at risk
(Gilpen & Soule ´ 1986).
Within this context, the use of indirect noninvasive
approaches is potentially of great interest, and more spe-
cifically, DNA extraction from faeces represents a valu-
able and powerful tool to use in surveys, in species
inventories and in demographic studies (Taberlet & Luik-
art 1999). Faeces are one of the best noninvasive animal
samples available for analyses because they are easy to
find in the wild and provide more information (e.g. diet,
stress hormone status, parasite infection and animal
DNA) than other sample types (Goymann 2005; Luikart
et al. 2008; Schwartz & Monfort 2008; Pauli et al. 2010).
Nevertheless, on the basis of just morphological charac-
teristics and content, it is generally difficult to identify
the faeces deposited by M. cabrerae from those of other
sympatric arvicolid species of similar body size (Arvicola
sapidus, M. duodecimcostatus, M. agrestis and M. lusitani-
Arvicola sapidus faecal samples were collected from caged
animals at Jerez and Granada Zoos and from trapped
free-ranging animals from various locations in Andalucia
(Spain), between 2009 and 2010. All samples were kept at
ambient temperature in the field and were then stored at
)20 ?C (for more details, see Table 1). Sixty-six tissue
samples from six Arvicolinae rodents (M. cabrerae,
M. duodecimcostatus, M. agrestis, M. lusitanicus, A. sapidus
and A. terrestris) present in the Iberian Peninsula were
collected from different locations in Spain and Portugal,
between 2005 and 2010. To examine the specificity of the
proposed method, and its applicability to other arvicolid
species, we included nine specimens from five arvicolid
species from Greece (M. thomasi and M. thomasi atticus),
Italy (M. savii and M. brachycercus), and a M. guentheri
sample from an unknown origin. An additional 16
sequences belonging to ten Arvicolinae vole species from
ten different countries worldwide were downloaded
from GenBank (for more details, see Table 1), and
included in an alignment (Table 2).
For the DNA extraction, three faecal pellets were ran-
domly collected from each animal (Table 1) and their pel-
let surfaces were washed by incubation for 10 min in a
buffer solution (Qiagen). The DNA was extracted from
the buffer solution using a blood DNA extraction kit
(Qiagen) (Maudet et al. 2004; Luikart et al. 2008). The
DNA was extracted from tissue samples following the
standard phenol⁄chloroform procedures (Sambrook et al.
1989). The DNA extractions were carried out in a steril-
ized laboratory exclusively for low DNA concentration
samples. Two blanks (reagents only) were included in
each extraction to monitor for contamination (Handt et al.
Control region sequences of all collected arvicolid vole
tissue samples were amplified using primers pair Pro+
and Phe+, as described by Haring et al. (2000). All the
control region sequences together with the others from
the GenBank were aligned and used to design a nested
PCR with two new primer pairs (arvicolid-generic prim-
ers and Cabrera’s vole-specific primers). Primers were
designed in Primer3 (v. 0.4.0) (Rozen & Skaletsky 2000).
Two consecutive PCRs were performed:
PCR I (a control PCR using arvicolid-generic primers, for
the mitochondrial control region fraction amplification
of all the studied arvicolid species): the 30-lL PCR
mixture contained 2 lL of gDNA (from tissue or faecal
samples), 0.25 lM of each primer (Pro+, see Haring
each dNTP, 3 lL of 1· kit-supplied PCR buffer
(Bioline), 1.5 mM MgCl2, 0.4% bovine serum albumin
(BSA), 1.5 lL DMSO and 0.2 lL (0.2 U⁄reaction) Taq
polymerase (Bioline). Samples were subjected to the
following thermal profile for amplification in a 2720
Thermal Cycler PTC-0200 DNA Engine thermal cycler
(Bio-Rad): 4 min at 94 ?C (initial denaturation), fol-
lowed by 30 cycles of three steps of 1 min at 94 ?C
(denaturation), 1 min at 55 ?C (annealing) and 50 s at
72 ?C (extension), before a final elongation of 5 min at
72 ?C. PCR blanks (reagents only) were included with
each PCR run.
PCR II (nested PCR using Cabrera’s vole-specific primers
to amply a fragment of M. cabrerae’s control region):
reagents and concentrations and thermal profile were
similar to PCR I, with the exception that 2 lL of PCR
I-product was used as template, and sprimers Pro+
and MicoMico were substituted with two new nested
primers, MiKa1 (5¢-ATTACTCCTTTAAACCATGG-3¢)
and MiKa2 (5¢-CTAATAGACAAAATAGGGATGGG-
G-3¢) (Table 2). Both sets of primers were tested on all
tissue and faecal samples listed in Table 1.
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410 MOLECULAR DIAGNOSTICS AND DNA TAXONOMY
Following the PCRs , 2 lL of each PCR product were
cleaned to remove excess primers and dNTPs, using the
following enzymatic reaction: 0.2 lL of 10· Antartic
phosphatase buffer, 3 units of E. coli exonuclease I and
1 unit of Antartic phosphatase in a final volume of 7 lL
(New England Biolabs). Samples were subjected to the
following thermal profile: 37 ?C for 45 min followed by
80 ?C for 15 min. Sequencing reactions were obtained,
using Pro+ and MicoMico primers, from both directions
using the Big Dye?Terminator v1.1 cycle sequencing kit
according to the manufacturer’s instructions (Applied
Biosystems), and labelled fragments were resolved on
an automated DNA sequencer (Applied Biosystems
3130xl genetic analyzer). DNA sequences were aligned
and edited using the software BIOEDIT v.7.0.9 (Hall 1999).
The average number of base differences between the
studied arvicolid species with the designed primers was
7.5⁄18 bp for MiKa1 and 8.3⁄24 bp for MiKa2 (Table 2).
The first set of PCR primers (Pro+⁄MicoMico: generic
for the studied rodent species) was used for the first
PCR run (PCR test), to evaluate the efficiency of the pro-
tocol for faecal DNA extraction and to evaluate the qual-
ity of the extracted DNA, because some PCR inhibitors
could be presented in the DNA extracted from faeces
(Beja-Pereira et al. 2009). The amplifications from the
generic arvicolid rodent primers were ?300 bp (Fig. 1).
The rate of PCR amplification success was 100% for tis-
sue samples (N = 75; see Table 1) and 95% for faecal
samples (N = 57; see Table 1). After the first PCR (test
PCR), we ran the nested PCR with the novel M. cabrerae-
specific primers MiKa1⁄MiKa2. The resulting amplified
fragments were ?140 bp (Fig. 1), and the rate of success
of this set of species-specific primers designed to
amplify the control region fraction in Cabrera’s vole
was the same as for the first PCR (PCR test). The failed
reactions were likely to be related to the bad conserva-
tion of the faecal samples and⁄or because of the ineffi-
ciency of the used method for DNA extraction from
faecal samples. This new nested PCR-based technique
was successfully tested in 60 random collected Arvicolid
faecal samples form from the National Park of Sierra Se-
gura (Jae ´n, Spain), from which 23 samples were identi-
fied as M. cabrerae. Seven haplotypes were identified
from the 50 M. cabrerae D-loop sequences, and no indels
were included in the alignment. Therefore, this marker
has a utility to assess intra-population variability in
The success and therefore applicability of our new
molecular-based technique as a tool for a simple and effi-
cient identification and differentiation of invasive and
noninvasive M. cabrerae samples among other arvicolid
species lies in (i) the high rate of nucleotide substitution
present across the entire mtDNA genome in Arvicolinae,
(ii) the high number of copies of the mitochondrial
control region and (iii) the use of the nested PCR. The
present study shows that this noninvasive nested PCR-
based technique allows the direct differentiation and
identification of faecal samples of one vole species from
other arvicolid species without the need for multiple
post-PCR manipulations of samples in sequencing reac-
tions and restriction digests. These manipulations add
time and cost to processing of samples and increase the
possibility of human error and⁄or contamination.
In this study, we used Cabrera’s vole as a model spe-
cies, showing that this is a rapid and inexpensive tech-
nique likely to have a large applicability to other model
vole organisms or even other nongeneric taxa. Arvicoli-
nae species conservation⁄protection and monitoring
programmes may include these noninvasive molecular-
based tools with the combination with other molecular
markers to provide answers to elucidate new data on
long-standing ecological and evolutionary questions.
Table 1 Species, countries and localities,
number of tissue and faecal samples for
Species CountryGeographical localities
Spain (Jae ´n, Madrid,
Ca ´diz and Granada);
M. thomasi atticus
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MOLECULAR DIAGNOSTICS AND DNA TAXONOMY 411
Table 2 Nested PCR primers and their binding sites on the sequence alignment of the mitochondrial control region for the studied specimens. The primer combination
Pro+⁄MicoMico is generic for arvicolid species including M. cabrerae. Primer MiKa1⁄Mika2 are specific for M. cabrerae
Dots indicate identical nucleotides to the M. cabrerae sequence. Dashes indicate gaps.
? 2010 Blackwell Publishing Ltd
412 MOLECULAR DIAGNOSTICS AND DNA TAXONOMY
Ana Pı ´riz (EBD-CSIC, Seville, Spain) is thanked for help with
troubleshooting in the laboratory. We thank Giagia-Athanaso-
poulou EB and Rovatsos MT for providing samples of M. thom-
asi and M. thomasi atticus. Gornung E and Castiglia R for
providing samples of M. savii and M. brachycercus. We are also
grateful to the Jerez de la Frontera and Granada Zoos for provid-
ing samples from M. cabrerae. This work was supported by the
programme ‘Ayudas a grupos de investigacio ´n’ to CVI 220 and
RNM118 investigation groups.
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