Corresponding author: Elena Buzan ( elena.buzan@upr.si ) Academic editor: Szabolcs Lengyel
© 2021 Krisztina A. Kelemen, Felicita Urzi, Elena Buzan, Győző F. Horváth, Filip Tulis, Ivan Baláž.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Kelemen KA, Urzi F, Buzan E, Horváth GF, Tulis F, Baláž I (2021) Genetic variability and conservation of the endangered Pannonian root vole in fragmented habitats of an agricultural landscape. Nature Conservation 43: 167-191. https://doi.org/10.3897/natureconservation.43.58798
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The distribution of the endangered glacial relict subspecies, the Pannonian root vole Alexandromys oeconomus mehelyi Éhik, 1928, is restricted to scattered localities in south-western Slovakia, which belong to the north-eastern zone of its range. Human-induced changes and fragmentation of the landscape have led to the gradual loss of suitable habitats and threaten its long-term survival. The study area in the Danubian Lowland is characterised by small habitat fragments and temporal fluctuations of the habitat area. Root voles were sampled at nine sites to study the level of genetic variability and structure of local subpopulations by scoring 13 microsatellite loci in 69 individuals. Genetic differentiation varied amongst local populations and we did not find a significant isolation-by-distance pattern. Bayesian clustering analysis suggested that dispersal effectively prevents marked genetic subdivision between studied habitat fragments. Significant pairwise differentiation between some subpopulations, however, may be the result of putatively suppressed gene flow. Low genetic diversity in the recent populations probably reflects the isolated location of the study area in the agricultural landscape, suggesting that long-term survival may not be assured. In order to maintain genetic diversity, it is essential to preserve (or even restore) habitats and ensure the possibility of gene flow; habitat protection is, therefore, recommended. Continuous assessment is necessary for effective conservation management and to predict the long-term survival chances of the Pannonian root vole in the study area.
Alexandromys oeconomus mehelyi, Danubian Lowland, landscape change, microsatellite analysis
The root vole Alexandromys (Microtus) oeconomus (Pallas, 1776) is the only extant Holarctic species of the Microtini tribe with twenty-five known subspecies distributed in the Northern Hemisphere (
As a result of glacial and postglacial changes in its distribution range, the root vole is currently represented by three subspecies in Western and Central Europe (
The distribution of Pannonian root vole in the territory of Slovakia is determined by the change of the landscape and its natural conditions in the postglacial era. Over the past 130 years, the Danubian Lowland in southern Slovakia has experienced significant landscape modifications, such as extensive flood protection interventions and construction of a channel network in agricultural lands. As a consequence, habitats preferred by the root vole are currently fragmented and isolated by agricultural lands in southern Slovakia (
Habitat loss and fragmentation caused by landscape modification affect wildlife populations worldwide (
The response of small mammalian populations to habitat fragmentation has been widely studied (e.g.
To ensure the viability of root vole populations or subpopulations, it is reasonable to study genetic variability and genetic structure as factors affecting the adaptive traits and future persistence of populations. Wetland habitats experienced fragmentation and significant shrinkage in south-western Slovakia and only a few habitat fragments are left for root voles. In the present survey, we used microsatellite analyses to study the genetic diversity and structure of Pannonian root vole subpopulations inhabiting remnant habitat fragments in the Danubian Lowland, where the greatest threat to their long-term survival is habitat loss, fragmentation and degradation (
Located in the south-western part of Slovakia, the study area lies in the Danubian Plain (Podunajská rovina), part of the Danubian Lowland, belonging to the Pannonian biogeographical region. The landscape was formed by the tributaries of the Danube (Little Danube and others) and by the southern Váh, Nitra and Žitava Rivers. Soil properties and climatic conditions make this region ideal for agriculture. In the area, wheat, sugar beets, sweet corn, vegetables, fruits and tobacco are grown. In the late 19th century, the study area was located in the centre of wet meadows interlaced by meanders of Žitava River, as shown by the
The distribution of the sampled localities of root vole subpopulations in the Danubian Lowland. The sampling sites found in the habitat fragments are indicated by letter and number codes. The insert shows the location of the study area in Slovakia.
The research was carried out in different types of habitat fragments like waterlogged areas overgrown by Carex spp. and Phragmites spp. at the edges of channels, oxbow lakes and remnants of former tributaries intersecting large areas of agricultural lands. Animals were captured with live traps baited with apple and cereals. One line transect of 25 traps with 10 m intervals was established for five consecutive nights in each trapping site. Trapping was conducted three times a year (spring, summer, autumn), from 2014 to 2017. Traps were inspected once a day. Upon capture, each vole was investigated for body weight, age and reproductive status before release. At the first capture, the tail tip of each vole was clipped for genetic analyses. The clipped tail tips were put immediately in 96% ethanol and preserved at -85 °C in the laboratory until DNA extraction. Trapping and sampling methods were realised in agreement with the rules of State Nature Protection of Slovak Republic “Species and habitats monitoring of European importance within the Habitats Directive and the Birds Directive” project. Due to the rarity and endangered status of the Pannonian root vole, sample sizes were low in some trapping transects and, therefore, a total of 69 tissue samples from nine sites were used in molecular analyses.
Five characteristics related to wetland habitat fragments were measured or calculated in six time periods between 2004 and 2019 (January 2004, March 2011, April 2014, March 2017, August 2017 and March 2019): 1) number of all habitat fragments presumably suitable for the Pannonian root vole; 2) number of temporarily suitable habitat fragments appearing occasionally, depending on water levels; 3) total area of all habitat fragments measured in hectares; 4) average size of habitat fragments (ha); and 5) overall connectivity of our region of interest. Suitable habitat fragments were delimited based on the subspecies’ known habitat preference for humid, densely vegetated areas (see Introduction), which markedly differed from the vegetation of agricultural parcels in the study area. The size of particular habitat fragments (ha) was calculated in QGIS software 3.4.12-Madeira (
Due to different trapping efforts at each study location, the size of each subpopulation was evaluated as the relative abundance (rA) of individuals captured at the location per 100 trap-nights (C/100TN), based on data without recaptures. The number of captured specimens (N) was recalculated into the transformed rA index assuming a random (Poisson) distribution (rA = (–ln (1-N/100) 100) of small mammals to remove the saturation effect caused by single traps (
We tested the correlation between average rA of Pannonian root vole and average habitat fragment size using Pearson correlation analysis, where both data were log-transformed due to non-normal distribution.
DNA extractions were performed using commercial Isolate II Genomic DNA Kit (Bioline) according to the manufacturer’s protocol with the following modifications: during pre-lysis, samples were incubated overnight at room temperature; after adding preheated Elution Buffer G (70 °C), the elution step covered the incubation of samples at room temperature for 30 minutes and after that at 70 °C for 5 minutes before elution.
The thirteen microsatellite loci included in the analyses were developed for Microtus arvalis: Mar003, Mar016, Mar049, Mar063, Mar076 (
Multiplex PCR reactions were performed in 12 μl volumes containing 2 μl (~80 ng) of DNA and a volume of 10 μl of the following mixture: 3.9 μl of KAPA2G Fast Multiplex Mix (KAPA Biosystems), 0.8 μl of BSA, 0.5 μl (concentration of 10 pm/ng) of each primer and RNase-free water to fill the volume to 10 μl. Amplification of DNA was carried out using peqSTAR 96X Universal thermal cycler (Peqlab).
To amplify microsatellites in Set 1A, Set 1B and Set 2 the PCR reaction consisted of the initial step at 94 °C for 7 minutes, 30 cycles including: denaturation at 94 °C for 1 minute, annealing at 55 °C in case of Set 2 and 60 °C in case of Set 1A and Set 1B for 2 minutes and extension at 72 °C for 90 seconds, followed by a final step at 72 °C for 10 minutes. Microsatellites in Set 3 were amplified in a PCR reaction including the following steps: 7 minutes at 95 °C, 35 cycles of 30 seconds at 94 °C, 1 minute at 57 °C and 90 seconds at 72 °C and after the cycles a final step of 10 minutes at 72 °C. To prepare the genotyping procedure 1 μl PCR product of each sample was mixed with 12 μl formamide and 0.3 μl GeneScan 500-LIZ size standard (Applied Biosystems). After a denaturation step of 5 minutes at 95 °C, a cooling step was implemented. Genotyping was carried out using ABI PRISM 310 Genetic Analyser (Applied Biosystems) and microsatellite genotypes were examined using GeneMapper software v.4.0 (Life Technologies).
We successfully genotyped 69 individual samples and the amplification success varied amongst markers (94.2–100%). The presence of null alleles may cause significant heterozygote deficit and deviation from the HWE. We therefore estimated the proportion of null alleles (NA) at each locus in each subpopulation using the programme FREENA (
Bayesian clustering of microsatellite genotypes was performed using STRUCTURE v.2.3.2 (
The mean number of alleles (A), observed (HO) and expected (HE) heterozygosity (
The programme FREENA was used to estimate global FST, by performing 10,000 permutations. In addition, a Monte Carlo test of likelihood ratio G-statistic (
Between 2004 and 2019, we identified 26 permanent habitat fragments as suitable habitats for root voles, in 14 of which their presence were confirmed. We have also identified several temporarily suitable fragments, the number of which varied seasonally and annually. All measured characteristics of potential habitats (number of fragments and temporary fragments, total area of all habitat fragments, mean fragment size and connectivity of the whole area) changed over the six time periods of study (see Table
Changes in patch characteristics during the six time periods between 2004 and 2019.
Time period | Area of all patches (ha) | Mean size of patches (ha) | No. of all patches | No. of temporary patches | Connectivity* |
---|---|---|---|---|---|
2004 March | 179.26 | 3.51 | 51 | 25 | 840705.8 |
2011 March | 210.19 | 3.28 | 64 | 38 | 975203.3 |
2014 April | 144.49 | 3.80 | 38 | 12 | 669245.9 |
2017 March | 149.73 | 3.56 | 42 | 16 | 679802.1 |
2017 August | 140.92 | 4.14 | 34 | 8 | 627252.9 |
2019 March | 143.26 | 4.21 | 34 | 8 | 642355.8 |
Change in the number of suitable habitat fragments for the Pannonian root vole in the north-western part of the study area over time. The green box in the insert shows the boundaries of the larger maps.
The average occupancy of fragmented habitats by the Pannonian root vole varied spatially (Fig.
Genetic structuring inferred from STRUCTURE analysis is presented in Fig.
Genetic structure of the sampled root vole subpopulations in the Danubian Lowland. The graph is based on STRUCTURE runs when K was fixed at 2–5. Each individual is represented by a line proportionally divided into colour segments corresponding to its membership in certain clusters. Black lines separate the individuals from different habitat fragments.
Clustering analysis did not give a strong evidence of structuring; therefore, measures of genetic diversity were calculated for all subpopulations separately and for all samples pooled together. Genetic diversity and HWE were not calculated for locations SK3, SK4 and SK7 due to their small sample size (N = 3).
The number of alleles per locus in subpopulations ranged from 2 (locus Moe4) to 16 (locus Moe7), and the mean number of alleles per locus (A) ranged from 4.31 to 5.62 (Table
Genetic diversity in root vole subpopulations and in the total population based on 13 microsatellite loci.
Location | A | AR | HE | HO | HWE | FIS | |
---|---|---|---|---|---|---|---|
P | ±SE | ||||||
SK1 | 5.62 | 5.46 | 0.657 | 0.586 | < 0.001* | 0.0000 | 0.161* |
SK2 | 5.08 | 5.00 | 0.654 | 0.574 | < 0.001* | 0.0002 | 0.176* |
SK5 | 4.62 | 4.49 | 0.631 | 0.562 | < 0.001* | 0.0003 | 0.161* |
SK6 | 5.15 | 5.02 | 0.651 | 0.619 | 0.006 | 0.0010 | 0.103* |
SK8 | 4.31 | 4.22 | 0.624 | 0.665 | 0.161 | 0.0059 | -0.013 |
SK9 | 4.62 | 4.50 | 0.655 | 0.669 | 0.228 | 0.0115 | 0.030 |
Total | 7.23 | 7.23 | 0.694 | 0.614 | < 0.001* | 0.0000 | 0.122* |
Subpopulations SK3, SK4 and SK7 were not included in FST analyses because of their small sample size (N = 3). The global FST for six subpopulation samples was 0.025 (95% CI: 0.01–0.041). The overall G-test was significant (P < 0.001), indicating genetic structuring amongst locations. Pairwise FST values were relatively low, although variable. The highest FST values were observed for SK8 and SK9. Pairwise genetic differentiation was not significant in most of the comparisons, except in cases where one subpopulation of the pair was always SK6, SK8 or SK9 (Table
Tests for genetic differentiation between nine root vole subpopulations in the Danubian Lowland. Below diagonal: pairwise FST values. Above diagonal: P values of G-tests implemented in FSTAT.
Location | SK1 | SK2 | SK5 | SK6 | SK8 | SK9 |
---|---|---|---|---|---|---|
SK1 | 0.234 | 0.307 | 0.185 | < 0.001** | 0.010 | |
SK2 | 0.015 | 0.344 | 0.099 | 0.064 | 0.020 | |
SK5 | 0.013 | 0.004 | 0.479 | 0.137 | 0.012 | |
SK6 | 0.010 | 0.009 | -0.002 | 0.001* | < 0.001** | |
SK8 | 0.071 | 0.021 | 0.016 | 0.045 | < 0.001*** | |
SK9 | 0.033 | 0.013 | 0.014 | 0.052 | 0.048 |
The FCA plot, based on individual genotypes, clearly separated SK1 along the first factorial axis (explaining 20.1% of variation) from all other subpopulations. The second axis (explaining 17.9% of variation) mainly separated the individuals from SK1 and SK9, while individuals from SK6 showed only a weak segregation (Fig.
Two-dimensional plots of FCA performed for nine subpopulations showing the 1st and 2nd (A) and the 1st and 3rd (B) axes. The proportion of explained variance is written in parentheses on each axis.
In the Analysis of Molecular Variance, significant genetic variation was attributed to the differences between subpopulations (4.4%, P < 0.001) and most of the variability occured within subpopulations (95.6%).
Our results show that genetic variation and differentiation in subpopulations of the Pannonian root vole is in good agreement with connectivity between habitat fragments, with temporary fragments playing an important role in vole migration between flood events.
The number, size and shape of habitat fragments in the studied region varies in time as the result of exogenous factors (precipitation, surface water levels, agricultural activities). These dynamic changes have an effect on fragment connectivity, suggesting that connectivity was positively influenced by the number of habitat fragments. As we have also noted, permanent habitat fragments, relatively distant from each other at one time, can change size and shape and become neighbouring habitats at another time. In addition, the temporary fragments can play the role of stepping stones during vole movements. Thus, despite the constant presence of habitat fragments and channel-side vegetation, fragment connectivity can vary seasonally and yearly, as can change the possibility of individuals’ replacement between the studied subpopulations. In Norway, root voles increased dispersal distance as a response to fragmentation, but it was less affected by connectivity (
Levels of genetic differentiation between the habitat fragments varied, but were mostly non-significant and we found no support for isolation by distance between subpopulations. Bayesian clustering in STRUCTURE did not reveal pronounced genetic structuring, indicated by approximately equal assignment probabilities to different clusters in all cases of K from 2 to 5. This result suggested that dispersal effectively prevents marked genetic subdivision between studied habitat fragments, which can be additionally confirmed by the lack of isolation by distance between fragments. Given the small geographical scale and landscape pattern of the study area, we would expect gene flow between localities to maintain very low or no differentiation between subpopulations. In a study conducted in the Netherlands,
Consistent with the changing possibility of individuals’ replacement between the studied fragments, AMOVA results also showed a low, but significant, percentage of variability between subpopulations. In addition, signs of genetic differentiation were detected between subpopulations SK8, SK9 and SK6, based on significant pairwise FST values and the FCA analysis confirmed the separation of these samples. Results may therefore indicate that dispersal is not unhindered between all subpopulations and root vole individuals in the network of studied habitat fragments may not be viewed as a panmictic population.
In a detailed study,
Subpopulations SK8 and SK9 tend to have lower levels of allelic richness, which is consistent with the possibly lower probability of dispersal through the agricultural land matrix compared to other sites. However, we did not find significant deviation from the Hardy-Weinberg equilibrium in these subpopulations. We observed deviations from the Hardy-Weinberg equilibrium in SK1, SK2 and SK5 and significant positive FIS coefficients in the same subpopulations, together with SK6, which may result from the social structure of root voles. Matriline-based groups in root vole populations (
Regarding individuals 3, 6, 7 and 8 (sampled in 2014 and 2015) in SK1, highlighted by clustering analyses, their high assignment probability to a separate cluster may reflect their distinct origin. Habitat fragment SK1 is the closest to the Danube River amongst the studied fragments and the floods in 2010 or 2013 potentially facilitated dispersal from further areas and the aforementioned individuals might be immigrants or their descendants. Other individuals that had relatively high assignment probabilities to the same cluster were captured in SK5 (individual 26 from 2015) and SK9 (individual 57 and 60). These can be found at a few kilometres distance from SK1, but given the small spatial scale, it is not unlikely that these specimens may be the offspring of dispersing individuals. Alternatively, it is also possible that genetic drift over time changed the genetic composition of subpopulations in the fragmented landscape; hence, some (but not all) samples collected in 2014 and 2015 were highlighted by STRUCTURE clustering. However, we are not able to declare which possibility is more plausible without genotyping individuals from other areas and without temporal analysis of samples.
The genetic diversity of the local subpopulations in the study area is relatively low; although the studied subpopulations probably have connections with each other due to the effect of extensive floods and the network of fragments and channels in the agricultural landscape, their reduced genetic variability is detectable compared to the pooled genetic variability of other populations of Pannonian root vole occurring closer to the more uninterrupted marshlands in Szigetköz, Hanság and Neusiedlersee Regions (
Landscape changes and habitat destruction resulted in the fragmented distribution of root vole habitats in the study area and fluctuating surface water levels induce considerable changes in habitat size, quality and connectivity to this day. Only one fragment (SK2) in our study area is protected as a Special Protection Area. However, for the long-term persistence of root vole populations, it would be critical to ensure legal protection of habitats. The importance of protected core areas has been demonstrated for water vole metapopulations (
It is expected that the overall genetic diversity of the subpopulations will decrease as a result of their small size and isolated location in the agricultural matrix. This implies that the restoration of habitats and corridors is indispensable for the long-term preservation of diversity, as has been stressed earlier (
The research was conducted by virtue of Dr. Michal Ambros’ appointment as mapping coordinator for important European small mammal species. This work was supported by the i) VEGA (grant No. 1/0277/19); ii) Slovenian Research Agency (programme group P1-0386); iii) the STARBIOS2 European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 709517 orientated to promote responsible research and innovation in biosciences; (iv) the RESBIOS European Union’s Horizon 2020 Research and Innovation Programme (No. 872146); and v) COST Action G-Bike (CA18134), supported by COST (European Cooperation in Science and Technology). We express our sincere thanks to Imrich Jakab, Jakub Kamenišťák, Peter Klimant, Anita Morvai, Balázs Somogyi, Michal Ševčík, Martina Zigová and to all who assisted in small mammal trapping. Language assistance was kindly provided by Balázs Trócsányi. We are grateful to the anonymous reviewers for their valuable comments on the earlier version of this paper.