Prisoners in their habitat? Generalist dispersal by habitat specialists: a case study in southern water vole (Arvicola sapidus)

Relatedness dynamics and sex-biased dispersal in a seasonal cycle of corn mice from intensively managed agroecosystems

The sex-biased dispersal and kinship dynamics are important factors shaping the spatial distribution of individuals and are key parameters affecting a variety of ecological and evolutionary processes. Here, we studied the spatial distribution of related individuals within a population of corn mice Calomys musculinus in a seasonal cycle to infer dispersal patterns. The sampling was carried out from spring 2005 to winter 2006 in field borders of intensively managed agroecosystems. Genotyping data from 346 individuals with 9 microsatellites showed spatial genetic structure was weak for males, but not for females. The results indicate a complex spatial kinship dynamic of related females across all seasons. Which, contrary to our expectations, dispersal distances decrease with the increase of the population abundance. Meanwhile, male dispersal distances were greater when population abundance increased and thus the availability of active females. Males disperse greater distances to mate and sire offspring with distant females as a possible inbreeding avoidance mechanism. This study shows that C. musculinus is capable of much greater scattering distances than previously reported and that dispersal occurs fluidly and without barriers across the agroecosystem. The indirect benefit of dispersal on individual fitness could be related to relaxing the competition in the natal area and increasing the mating rate. Our study highlights the value of combining genetic relatedness, fieldwork observations, and behavioral data to estimate dispersal at a fine geographical scale.

Genetic variability and conservation of the endangered Pannonian root vole in fragmented habitats of an agricultural landscape

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.

Do predictive environmentally relevant concentrations of ZnO nanoparticles induce antipredator behavioral response deficit in Swiss mice?

The toxicity of zinc oxide nanoparticles (ZnO NPs) has been addressed in several studies; however, their effect on the mammalian group, even at environmentally relevant concentrations, remains poorly understood. The aims of the present study are to expose female Swiss mice to ZnO NP concentrations commonly faced by mammals who enter aquatic systems to perform different ecological functions and to assess the possible effects of such particles on their behavior. The test animals were placed in water added with ZnO NPs for 3 min, 2 times/day, for 21 days. Two experimental groups were set, NP1x, composed of animals subjected to ZnO NP concentration of 760 μg/L; and NP50x (control), which encompassed animals subjected to 38,000 μg/L. Based on field test results (OF), the contact with NPs did not induce locomotor deficits or anxiogenic and anxiolytic effect on the animal models. However, models exposed to NPs were not able to recognize the predatory threat posed by the presence of Pantherophis guttatus and Arapaima gigas; on the other hand, animals in the control group, who were not exposed to ZnO NPs, did not present antipredator behavioral response deficit. Furthermore, mice exposed to NPs were unable to distinguish real predators from plastic copies, and it suggests antipredator behavioral response deficit. High Zn concentrations in blood, liver, brain and skin samples are associated with deficit caused by the exposure to ZnO NPs. To the best of our knowledge, the current study is in the first to evidence that ZnO NPs induce changes in antipredator behavioral responses, even under ephemeral conditions and at low concentrations. However, the exposure to ZnO NPs can be a risk to the health of the assessed individuals and to the dynamics of their populations if the present antipredator behavioral response test results are extrapolated to the ecological context.

Small fish, large river: Surprisingly minimal genetic structure in a dispersal-limited, habitat specialist fish

Genetic connectivity is expected to be lower in species with limited dispersal ability and a high degree of habitat specialization (intrinsic factors). Also, gene flow is predicted to be limited by habitat conditions such as physical barriers and geographic distance (extrinsic factors). We investigated the effects of distance, intervening pools, and rapids on gene flow in a species, the Tuxedo Darter (Etheostoma lemniscatum), a habitat specialist that is presumed to be dispersal-limited. We predicted that the interplay between these intrinsic and extrinsic factors would limit dispersal and lead to genetic structure even at the small spatial scale of the species range (a 38.6 km river reach). The simple linear distribution of E. lemniscatum allowed for an ideal test of how these factors acted on gene flow and allowed us to test expectations (e.g., isolation-by-distance) of linearly distributed species. Using 20 microsatellites from 163 individuals collected from 18 habitat patches, we observed low levels of genetic structure that were related to geographic distance and rapids, though these factors were not barriers to gene flow. Pools separating habitat patches did not contribute to any observed genetic structure. Overall, E. lemniscatum maintains gene flow across its range and is comprised of a single population. Due to the linear distribution of the species, a stepping-stone model of dispersal best explains the maintenance of gene flow across its small range. In general, our observation of higher-than-expected connectivity likely stems from an adaptation to disperse due to temporally unstable and patchy habitat.

Generalist dispersal and gene flow of an endangered keystone specialist (Dipodomys ingens)

Movement ecology and dispersal capabilities inherently drive genetic structure across landscapes. Through understanding dispersal and gene flow of giant kangaroo rats (Dipodomys ingens), conservation efforts can be focused, and we can further understand how genetic structure persists in this highly endemic small mammal. Here, we genetically identify parent–offspring and sibship relationships among 239 giant kangaroo rats using 15 microsatellites in the northern part of the species range and describe the individual genetic-spatial variation using a Moran eigenvector map (MEM). We further employ two landscape genetic analyses (isolation by resistance [IBR] and least cost paths [LCPs]) and two individual-based genetic metrics (Dps and a codominant marker distance from GenAlEx) to determine landscape factors (precipitation, slope, vegetation community, and roads) that influence gene flow. We found 19 pairs of related individuals, of which 18 were less than 250 m apart, but one sibling pair was 5.52 km apart, suggesting greater dispersal capabilities than previously noted. We found hierarchal spatial genetic structure using a MEM, with 3–4 genetically similar regions and two genetically similar subregions. Finally, we found low correlative strength between landscape features and gene flow. IBR consistently outperformed LCPs, and there was evidence that regions with 250–350 mm of precipitation and slope ≤ 5° promoted connectivity. We recommend that managers focus on habitat protection rather than corridor maintenance, with the caveat that anthropogenic factors were minimally considered in this study.

Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils

Our understanding of the diversity and community dynamics of soil fungi has increased greatly through the use of DNA-based identification. Community characterization of metabolically active communities via RNA sequencing has previously revealed differences between 'active' and 'total' fungal communities, which may be influenced by the persistence of DNA from nonactive components. However, it is not known how fungal traits influence their prevalence in these contrasting community profiles. In this study, we coextracted DNA and RNA from soil collected from three Antarctic islands to test for differences between total and active soil fungal communities. By matching these geographically isolated fungi against a global dataset of soil fungi, we show that widely dispersed taxa are often more abundant in the total community, whilst taxa restricted to Antarctica are more likely to have higher abundance in the active community. In addition, we find that active communities have lower richness, and show a reduction in the abundance of the most dominant fungi, whilst there are consistent differences in the abundances of certain taxonomic groups between the total and active communities. These results suggest that the views of soil fungal communities offered by DNA- and RNA-based characterization differ in predictable ways.

Historical connections among river basins and climatic changes explain the biogeographic history of a water rat

Background

The water ratNectomys squamipes(Cricetidae: Sigmodontinae) is a semiaquatic rodent from eastern South America that shows shallow genetic structure across space, according to some studies. We tested the influence of hydrography and climatic changes on the genetic and phylogeographic structure of this semiaquatic small mammal.

Methods

DNA sequences of two mitochondrial genetic markers (Cyt b and D-loop) and six microsatellite loci from water rats were collected at 50 localities in five river basins in the Atlantic Forest along the eastern coast of South America. We evaluated the genetic structure within and among river basins, and we estimated divergence dates. Species distribution models for the present and past were built to identify possible gene flow paths.

Results

Mitochondrial data and species distribution models showed coherent results. Microsatellite loci showed a more complex pattern of genetic differentiation. The diversification ofN. squamipeshaplotypes occurred during the Pleistocene and the river basin cannot explain most of the genetic structure. We found evidence of population expansion during the last glacial maximum, and gene flow paths indicate historical connections among rivers in the Atlantic Forest.

Discussion

Historical connections among rivers in the Atlantic Forest may have allowedN. squamipesto disperse farther across and within basins, leading to shallow genetic structure. Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, thus challenging the forest refuge hypothesis.

Habitat specialist birds disperse farther and are more migratory than habitat generalist birds

Some theories predict habitat specialists should be less dispersive and migratory than generalists, while other theories predict the opposite. We evaluated the cross-species relationship between the degree of habitat specialization and dispersal and migration status in 101 bird species breeding in North America and the United Kingdom, using empirical estimates of the degree of habitat specialization from breeding bird surveys and mean dispersal distance estimates from large-scale mark-recapture studies. We found that habitat specialists dispersed farther than habitat generalists, and full migrants had more specialized habitat than partial migrants or resident species. To our knowledge this is the first large-scale, multi-species study to demonstrate a positive relationship between the degree of habitat specialization and dispersal, and it is opposite to the pattern found for invertebrates. This finding is particularly interesting because it suggests that trade-offs between the degree of habitat specialization and dispersal ability are not conserved across taxonomic groups. This cautions against extrapolation of trait co-occurrence from one species group to another. In particular, it suggests that efforts aimed at conserving the most habitat-specialist temperate-breeding birds will not lead to conservation of the most dispersal-limited species.

Variability in primary productivity determines metapopulation dynamics

Temporal variability in primary productivity can change habitat quality for consumer species by affecting the energy levels available as food resources. However, it remains unclear how habitat-quality fluctuations may determine the dynamics of spatially structured populations, where the effects of habitat size, quality and isolation have been customarily assessed assuming static habitats. We present the first empirical evaluation on the effects of stochastic fluctuations in primary productivity—a major outcome of ecosystem functions—on the metapopulation dynamics of a primary consumer. A unique 13-year dataset from an herbivore rodent was used to test the hypothesis that inter-annual variations in primary productivity determine spatiotemporal habitat occupancy patterns and colonization and extinction processes. Inter-annual variability in productivity and in the growing season phenology significantly influenced habitat colonization patterns and occupancy dynamics. These effects lead to changes in connectivity to other potentially occupied habitat patches, which then feed back into occupancy dynamics. According to the results, the dynamics of primary productivity accounted for more than 50% of the variation in occupancy probability, depending on patch size and landscape configuration. Evidence connecting primary productivity dynamics and spatiotemporal population processes has broad implications for metapopulation persistence in fluctuating and changing environments.

Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations

Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites.

The effect of a major drainage divide on the gene flow of a semiaquatic carnivore, the Eurasian otter

Major drainage divides (separating the water flow draining to different seas) may significantly affect the dispersal, distribution, and genetic structure of semiaquatic animals. Assessing this effect is important for the proper management of both endangered and invasive riparian species. Here, I determined the fine-scale impact of the drainage divide between the Baltic Sea and the Black Sea drainage basins on the genetic structure and dispersal of the Eurasian otter (Lutra lutra) in the Bieszczady Mountains (Poland and Slovakia). I investigated the genetic structure of the otter population and assessed 3 alternative dispersal models using 6 landscape genetics methods. The analyses were based on 48 individual genotypes obtained from 622 fecal and gland secretion samples collected in 2008–2011. Results indicate that the major drainage divide is not a barrier to gene flow for this population. This was established by analyses of population genetic structure and confirmed by analysis of the spatial distribution of samples originating from closely related individuals. In line with these findings, the best-supported dispersal model assumed that otters migrate through mountain passes, away from streams, thus revealing that they are able to cross a drainage divide. The genetic structure of the population studied exhibits an isolation-by-distance pattern; however, the locations of several repeatedly recorded or closely related individuals revealed the occurrence of long-distance movements. Confirmation of the high mobility of otters and their ability to cross a major drainage divide ridge suggest that landscape obstacles and discontinuity of river network are unlikely to stop otter dispersal, gene flow, and recolonization of new areas.

Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem

Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.

Spatio-temporal genetic structure of the rodent Calomys venustus in linear, fragmented habitats

Studies about habitat fragmentation, in terms of how it affects gene flow and genetic variability, have traditionally been conducted on island-like systems in which the remaining habitats form patches embedded in a matrix. However, in agroecosystems, remaining habitats usually form linear strips along fence lines, roads, and water courses (“border” habitats). We used the rodent Calomys venustus , a species inhabiting borders in central Argentina agroecosystems, as a model to address how genetic variability is structured in linear habitats. A total of 359 rodents were captured seasonally from spring 2005 to winter 2006. Genetic variability at microsatellite loci was uniformly high, despite significant variation in population size during the sampling period. Genetic differentiation, spatial autocorrelation, and causal modeling analyses suggested that dispersion patterns in this species depend mainly on geographic distance, with unfavorable habitat like dirt roads and crop fields posing only weak (or no) resistance to dispersal. Small-scale spatial genetic structure was related to different space use patterns by females and males. Our results showed that, although greatly reduced in area, border habitats can support stable populations of species without loss of either variability or genetic connectivity.

Los efectos de la fragmentación del hábitat sobre el flujo génico y la variabilidad genética, se han estudiado tradicionalmente en sistemas tipo islas, en los cuales los hábitats remanentes forman parches embebidos en una matriz. Sin embargo, en los agroecosistemas, éstos suelen tener forma lineal a lo largo de alambrados, caminos y corrientes de agua (hábitats de “borde”). En este trabajo, utilizamos al roedor Calomys venustus , especie típica de ambientes de borde en los agroecosistemas del centro de Argentina, como modelo para estudiar cómo la variabilidad genética se estructura en hábitats lineales. Un total de 359 roedores se capturaron estacionalmente desde la primavera de 2005 hasta el invierno de 2006. La variabilidad genética encontrada en loci de microsatélites fue siempre alta, a pesar de una variación significativa del tamaño poblacional a lo largo del período de estudio. Los análisis de diferenciación genética, autocorrelación genética espacial y modelado causal sugieren que los patrones de dispersión en esta especie dependen principalmente de la distancia geográfica, y que los hábitats desfavorables como caminos de tierra y campos de cultivo representan una barrera débil (o nula) para la dispersión. La estructura genética a escala pequeña estuvo relacionada al diferente uso del espacio por parte de machos y hembras. Nuestros resultados mostraron que a pesar de tener un área reducida, los hábitat de bordes pueden mantener poblaciones estables sin pérdida de variabilidad genética o reducción del flujo génico.

Single nucleotide polymorphism-based dispersal estimates using noninvasive sampling

Quantifying dispersal within wild populations is an important but challenging task. Here we present a method to estimate contemporary, individual-based dispersal distance from noninvasively collected samples using a specialized panel of 96 SNPs (single nucleotide polymorphisms). One main issue in conducting dispersal studies is the requirement for a high sampling resolution at a geographic scale appropriate for capturing the majority of dispersal events. In this study, fecal samples of brown bear (Ursus arctos) were collected by volunteer citizens, resulting in a high sampling resolution spanning over 45,000 km² in Gävleborg and Dalarna counties in Sweden. SNP genotypes were obtained for unique individuals sampled (n = 433) and subsequently used to reconstruct pedigrees. A Mantel test for isolation by distance suggests that the sampling scale was appropriate for females but not for males, which are known to disperse long distances. Euclidean distance was estimated between mother and offspring pairs identified through the reconstructed pedigrees. The mean dispersal distance was 12.9 km (SE 3.2) and 33.8 km (SE 6.8) for females and males, respectively. These results were significantly different (Wilcoxon’s rank-sum test: P-value = 0.02) and are in agreement with the previously identified pattern of male-biased dispersal. Our results illustrate the potential of using a combination of noninvasively collected samples at high resolution and specialized SNPs for pedigree-based dispersal models.

Landscape genetics for the empirical assessment of resistance surfaces: the European pine marten (Martes martes) as a target-species of a regional ecological network

Coherent ecological networks (EN) composed of core areas linked by ecological corridors are being developed worldwide with the goal of promoting landscape connectivity and biodiversity conservation. However, empirical assessment of the performance of EN designs is critical to evaluate the utility of these networks to mitigate effects of habitat loss and fragmentation. Landscape genetics provides a particularly valuable framework to address the question of functional connectivity by providing a direct means to investigate the effects of landscape structure on gene flow. The goals of this study are (1) to evaluate the landscape features that drive gene flow of an EN target species (European pine marten), and (2) evaluate the optimality of a regional EN design in providing connectivity for this species within the Basque Country (North Spain). Using partial Mantel tests in a reciprocal causal modeling framework we competed 59 alternative models, including isolation by distance and the regional EN. Our analysis indicated that the regional EN was among the most supported resistance models for the pine marten, but was not the best supported model. Gene flow of pine marten in northern Spain is facilitated by natural vegetation, and is resisted by anthropogenic landcover types and roads. Our results suggest that the regional EN design being implemented in the Basque Country will effectively facilitate gene flow of forest dwelling species at regional scale.

Fine-scale genetic response to landscape change in a gliding mammal

Understanding how populations respond to habitat loss is central to conserving biodiversity. Population genetic approaches enable the identification of the symptoms of population disruption in advance of population collapse. However, the spatio-temporal scales at which population disruption occurs are still too poorly known to effectively conserve biodiversity in the face of human-induced landscape change. We employed microsatellite analysis to examine genetic structure and diversity over small spatial (mostly 1-50 km) and temporal scales (20-50 years) in the squirrel glider (Petaurus norfolcensis), a gliding mammal that is commonly subjected to a loss of habitat connectivity. We identified genetically differentiated local populations over distances as little as 3 km and within 30 years of landscape change. Genetically isolated local populations experienced the loss of genetic diversity, and significantly increased mean relatedness, which suggests increased inbreeding. Where tree cover remained, genetic differentiation was less evident. This pattern was repeated in two landscapes located 750 km apart. These results lend support to other recent studies that suggest the loss of habitat connectivity can produce fine-scale population genetic change in a range of taxa. This gives rise to the prediction that many other vertebrates will experience similar genetic changes. Our results suggest the future collapse of local populations of this gliding mammal is likely unless habitat connectivity is maintained or restored. Landscape management must occur on a fine-scale to avert the erosion of biodiversity.

Effects of structural connectivity on fine scale population genetic structure of muskrat, Ondatra zibethicus

In heterogeneous landscapes, physical barriers and loss of structural connectivity have been shown to reduce gene flow and therefore lead to population structuring. In this study, we assessed the influence of landscape features on population genetic structure and gene flow of a semiaquatic species, the muskrat. A total of 97 muskrats were sampled from three watersheds near Sudbury, Ontario, Canada. We estimated population genetic structure using 11 microsatellite loci and identified a single genetic cluster and no genetic differences were found among the watersheds as a result of high levels of gene flow. At finer scales, we assessed the correlation between individual pairwise genetic distances and Euclidean distance as well as different models of least cost path (LCP). We used a range of cost values for the landscape types in order to build our LCP models. We found a positive relationship between genetic distance and least cost distance when we considered roads as corridors for movements. Open landscapes and urban areas seemed to restrict but not prevent gene flow within the study area. Our study underlines the high-dispersal ability of generalist species in their use of landscape and highlights how landscape features often considered barriers to animal movements are corridors for other species.

Influence of land mosaic composition and structure on patchy populations: the case of the water vole (Arvicola sapidus) in Mediterranean farmland

The ability of patchy populations to persist in human-dominated landscapes is often assessed using focal patch approaches, in which the local occurrence or abundance of a species is related to the properties of individual patches and the surrounding landscape context. However, useful additional insights could probably be gained through broader, mosaic-level approaches, whereby whole land mosaics with contrasting patch-network and matrix characteristics are the units of investigation. In this study we addressed this issue, analysing how the southern water vole (Arvicola sapidus) responds to variables describing patch-network and matrix properties within replicated Mediterranean farmland mosaics, across a gradient of agricultural intensification. Patch-network characteristics had a dominant effect, with the total amount of habitat positively influencing both the occurrence of water voles and the proportion of area occupied in land mosaics. The proportions of patches and area occupied by the species were positively influenced by mean patch size, and negatively so by patch isolation. Matrix effects were weak, although there was a tendency for a higher proportion of occupied patches in more intensive, irrigated agricultural landscapes, particularly during the dry season. In terms of conservation, results suggest that water voles may be able to cope well with, or even be favoured by, the on-going expansion of irrigated agriculture in Mediterranean dry-lands, provided that a number of patches of wet herbaceous vegetation are maintained within the farmland mosaic. Overall, our study suggests that the mosaic-level approach may provide a useful framework to understand the responses of patchy populations to land use change.