The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances

The negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species.

Genotyping-by-sequencing based SNP discovery in a non-model rodent, the endangered hazel dormouse

The hazel dormouse Muscardinus avellanarius presents an exemplary non-model species that is both locally threatened and whose genetic status is not fully understood owing to insufficient resolution of the currently available molecular tools. We performed normalized Genotyping-by-Sequencing (nGBS) on 48 hazel dormouse samples collected across the species European distribution, aiming at discovering useful single nucleotide polymorphism (SNP) markers for the assessment of population structure and genomic diversity. The analyses of > 24,000 SNPs showed a high divergence between the Eastern and Western lineage of the species with high rates of SNP allele fixation, consistent with previous studies suggesting the divergence of lineages occurred over 2 mya. These results indicate that investigating inter-lineage as well as within-lineage genetic composition will be a conclusive approach for identifying conservation strategies in the future. Results presented here indicate the highest genetic divergence in the Italian and Lithuanian populations. We document how nGBS allows the discovery of SNPs that can characterize patterns of genetic variation at multiple spatial scales in a non-model organism. We document how nGBS allows the discovery of SNPs that can characterize patterns of genetic variation at multiple spatial scales in a non-model organism, potentially informing monitoring and conservation strategies.

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.

What we (don't) know about the effects of habitat loss and fragmentation on felids

Felid species have intrinsic ecological traits that make them particularly susceptible to the threats of habitat loss and fragmentation. We collate current knowledge of the effects of habitat loss and fragmentation on felids, describing trends, investigating the allocation of research effort and identifying knowledge gaps. We searched the scientific literature and categorized articles according to conceptual and methodological approaches. We reviewed 162 articles and observed that scientific knowledge is unevenly distributed among topics and species. Habitat suitability and patch–landscape configuration are the most studied topics. The allocation of research effort is unrelated to variables that describe conservation priorities, such as threat status and habitat availability within a species’ range, but it is related to body size, suggesting that charismatic attributes influence the choice of target species. Countries with less research effort are also those with less economic development, and thus North America and Europe are the centres of knowledge generation of reviewed studies. The responses of sixteen felid species to habitat loss and fragmentation remain unknown. Of these the Andean mountain cat Leopardus jacobita, the Bornean bay cat Pardofelis badia, the flat-headed cat Prionailurus planiceps and the fishing cat Prionailurus viverrinus most urgently require research because they are threatened with extinction. We recommend the use of theoretical approaches, through modelling exercises, as a first step to address the lack of information about the effects of habitat loss and fragmentation on felids, especially for those species for which there are large knowledge gaps.

Genetic consequences of forest fragmentation for a highly specialized arboreal mammal--the edible dormouse

Habitat loss and fragmentation represent the most serious extinction threats for many species and have been demonstrated to be especially detrimental for mammals. Particularly, highly specialized species with low dispersal abilities will encounter a high risk of extinction in fragmented landscapes. Here we studied the edible dormouse (Glis glis), a small arboreal mammal that is distributed throughout Central Europe, where forests are mostly fragmented at different spatial scales. The aim of this study was to investigate the effect of habitat fragmentation on genetic population structures using the example of edible dormouse populations inhabiting forest fragments in south western Germany. We genotyped 380 adult individuals captured between 2001 and 2009 in four different forest fragments and one large continuous forest using 14 species-specific microsatellites. We hypothesised, that populations in small forest patches have a lower genetic diversity and are more isolated compared to populations living in continuous forests. In accordance with our expectations we found that dormice inhabiting forest fragments were isolated from each other. Furthermore, their genetic population structure was more unstable over the study period than in the large continuous forest. Even though we could not detect lower genetic variability within individuals inhabiting forest fragments, strong genetic isolation and an overall high risk to mate with close relatives might be precursors to a reduced genetic variability and the onset of inbreeding depression. Results of this study highlight that connectivity among habitat fragments can already be strongly hampered before genetic erosion within small and isolated populations becomes evident.

Impact of human pressure and forest fragmentation on the Endangered Barbary macaque Macaca sylvanus in the Middle Atlas of Morocco

Overexploitation of forests by humans can lead to highly fragmented populations of forest-dependent species that have poor dispersal abilities. We tested the influence of habitat quality, landscape structure and human pressure on densities of the Barbary macaque Macaca sylvanus in the largest wild population, in the Middle Atlas of Morocco. We surveyed 14 forest fragments of 5–142 km2 that are separated from each other by an inhospitable matrix. We estimated the habitat quality of these forest patches by analysing the vegetation structure and the intensity of human pressure. We studied the distribution of forest patches and estimated macaque densities by combining line-transect sampling and complete group counts. We estimated mean density of individuals to be 9 km−2 (range 0.2–23 km−2). Differentiation of forest patches by a principal component analysis did not show any significant relationship between vegetation type and macaque density. A linear regression model showed that human pressure had a negative impact on density and that density responded positively to patch size. Patch shape, connectivity and altitude did not explain variation in population density. The size of this population is estimated to be c. 5,000 individuals. The survival of several small subpopulations is seriously threatened. As the Middle Atlas is the stronghold of this Endangered species, we recommend modifying forestry practices, reducing overgrazing by livestock within forests, and halting clear-cutting of holm oaks.

Distribution of wild mammal assemblages along an urban-rural-forest landscape gradient in warm-temperate East Asia

Urbanization may alter mammal assemblages via habitat loss, food subsidies, and other factors related to human activities. The general distribution patterns of wild mammal assemblages along urban-rural-forest landscape gradients have not been studied, although many studies have focused on a single species or taxon, such as rodents. We quantitatively evaluated the effects of the urban-rural-forest gradient and spatial scale on the distributions of large and mid-sized mammals in the world's largest metropolitan area in warm-temperate Asia using nonspecific camera-trapping along two linear transects spanning from the urban zone in the Tokyo metropolitan area to surrounding rural and forest landscapes. Many large and mid-sized species generally decreased from forest landscapes to urban cores, although some species preferred anthropogenic landscapes. Sika deer (Cervus nippon), Reeves' muntjac (Muntiacus reevesi), Japanese macaque (Macaca fuscata), Japanese squirrel (Sciurus lis), Japanese marten (Martes melampus), Japanese badger (Meles anakuma), and wild boar (Sus scrofa) generally dominated the mammal assemblage of the forest landscape. Raccoon (Procyon lotor), raccoon dog (Nyctereutes procyonoides), and Japanese hare (Lepus brachyurus) dominated the mammal assemblage in the intermediate zone (i.e., rural and suburban landscape). Cats (feral and free-roaming housecats; Felis catus) were common in the urban assemblage. The key spatial scales for forest species were more than 4000-m radius, indicating that conservation and management plans for these mammal assemblages should be considered on large spatial scales. However, small green spaces will also be important for mammal conservation in the urban landscape, because an indigenous omnivore (raccoon dog) had a smaller key spatial scale (500-m radius) than those of forest mammals. Urbanization was generally the most important factor in the distributions of mammals, and it is necessary to consider the spatial scale of management according to the degree of urbanization.