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

Informing Wildlife Corridor Creation through Population Genetics of an Arboreal Marsupial in a Fragmented Landscape

Habitat loss and fragmentation contribute significantly to the decline of arboreal mammal populations. As populations become fragmented and isolated, a reduction in gene flow can result in a loss of genetic diversity and have an overall impact upon long-term persistence. Creating wildlife corridors can mitigate such effects by increasing the movement and dispersal of animals, thus acting to reduce population isolation. To evaluate the success of a corridor, a before-after experimental research framework can be used. Here, we report the genetic diversity and structure of sugar glider (Petaurus breviceps) sampling locations within a fragmented landscape prior to the implementation of a wildlife corridor. This study used 5999 genome-wide SNPs from 94 sugar gliders caught from 8 locations in a fragmented landscape in south-eastern New South Wales, Australia. Overall genetic structure was limited, and gene flow was detected across the landscape. Our findings indicate that the study area contains one large population. A major highway dissecting the landscape did not act as a significant barrier to dispersal, though this may be because of its relatively new presence in the landscape (completed in 2018). Future studies may yet indicate its long-term impact as a barrier to gene flow. Future work should aim to repeat the methods of this study to examine the medium-to-long-term impacts of the wildlife corridor on sugar gliders, as well as examine the genetic structure of other native, specialist species in the landscape.

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.

Genetic Diversity, Population Structure, and Migration Scenarios of the Marsupial "Monito del Monte" in South-Central Chile

In this study, we quantified the 3 pivotal genetic processes (i.e., genetic diversity, spatial genetic structuring, and migration) necessary for a better biological understanding and management of the singular "living-fossil" and near-threatened mouse opossum marsupial Dromiciops gliroides, the "Monito del Monte," in south-central Chile. We used 11 microsatellite loci to genotype 47 individuals distributed on the mainland and northern Chiloé Island. Allelic richness, observed and expected heterozygosity, inbreeding coefficient, and levels of genetic differentiation were estimated. The genetic structure was assessed based on Bayesian clustering methods. In addition, potential migration scenarios were evaluated based on a coalescent theory framework and Bayesian approach to parameter estimations. Microsatellites revealed moderate to high levels of genetic diversity across sampled localities. Moreover, such molecular markers suggested that at least 2 consistent genetic clusters could be identified along the D. gliroides distribution ("Northern" and "Southern" cluster). However, general levels of genetic differentiation observed among localities and between the 2 genetic clusters were relatively low. Migration analyses showed that the most likely routes of migration of D. gliroides occurred 1) from the Southern cluster to the Northern cluster and 2) from the Mainland to Chiloé Island. Our results could represent critical information for future conservation programs and for a recent proposal about the taxonomic status of this unique mouse opossum marsupial.

Genetic analysis suggests dispersal among chimpanzees in a fragmented forest landscape in Uganda

Habitat fragmentation is a leading threat to global biodiversity. Dispersal plays a key role in gene flow and population viability, but the impact of fragmentation on dispersal patterns remains poorly understood. Among chimpanzees, males typically remain in their natal communities while females often disperse. However, habitat loss and fragmentation may cause severe ecological disruptions, potentially resulting in decreased fitness benefits of male philopatry and limited female dispersal ability. To investigate this issue, we genotyped nearly 900 non-invasively collected chimpanzee fecal samples across a fragmented forest habitat that may function as a corridor between two large continuous forests in Uganda, and used the spatial associations among co-sampled genotypes to attribute a total of 229 individuals to 10 distinct communities, including 9 communities in the corridor habitat and 1 in continuous forest. We then used parentage analyses to infer instances of between-community dispersal. Of the 115 parent-offspring dyads detected with confidence, members of 39% (N = 26) of mother-daughter dyads were found in different communities, while members of 10% (N = 5) of father-son dyads were found in different communities. We also found direct evidence for one dispersal event that occurred during the study period, as a female's sample found first in one community was found multiple times in another community 19 months later. These findings suggest that even in fragmented habitats, chimpanzee males remain in their natal communities while females tend to disperse. Corridor enhancement in unprotected forest fragments could help maintain gene flow in chimpanzees and other species amid anthropogenic pressures.

Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands

Background

Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia.

Results

We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines.

Conclusions

The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Background

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations.

Results

We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten.

Conclusions

Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Electronic supplementary material

The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.

Comparative Population Genetic Structure of the Endangered Southern Brown Bandicoot, Isoodon obesulus, in Fragmented Landscapes of Southern Australia

Genetic connectivity is a key factor for maintaining the persistence of populations in fragmented landscapes. In highly modified landscapes such us peri-urban areas, organisms’ dispersal among fragmented habitat patches can be reduced due to the surrounding matrix, leading to subsequent decreased gene flow and increased potential extinction risk in isolated sub-populations. However, few studies have compared within species how dispersal/gene flow varies between regions and among different forms of matrix that might be encountered. In the current study, we investigated gene flow and dispersal in an endangered marsupial, the southern brown bandicoot (Isoodon obesulus) in a heavily modified peri-urban landscape in South Australia, Australia. We used 14 microsatellite markers to genotype 254 individuals which were sampled from 15 sites. Analyses revealed significant genetic structure. Our analyses also indicated that dispersal was mostly limited to neighbouring sites. Comparisons of these results with analyses of a different population of the same species revealed that gene flow/dispersal was more limited in this peri-urban landscape than in a pine plantation landscape approximately 400 km to the south-east. These findings increase our understanding of how the nature of fragmentation can lead to profound differences in levels of genetic connectivity among populations of the same species.

It takes two to tango: Phagocyte and lymphocyte numbers in a small mammalian hibernator

Immunity is energetically costly and competes for resources with other physiological body functions, which may result in trade-offs that impair fitness during demanding situations. Endocrine mediators, particularly stress hormones, play a central role in these relationships and directly impact leukocyte differentials. To determine the effects of external stressors, energetic restraints and competing physiological functions on immune parameters and their relevance for fitness, we investigated leukocyte profiles during the active season of a small obligate hibernator, the edible dormouse (Glis glis), in five different study sites in south-western Germany. The highly synchronized yearly cycle of this species and the close adaptation of its life history to the irregular abundance of food resources provide a natural experiment to elucidate mechanisms underlying variations in fitness parameters. In contrast to previous studies on hibernators, that showed an immediate recovery of all leukocyte subtypes upon emergence, our study revealed that hibernation results in depleted phagocyte (neutrophils and monocytes) stores that recovered only slowly. As the phenomenon of low phagocyte counts was even more pronounced at the beginning of a low food year and primarily immature neutrophils were present in the blood upon emergence, preparatory mechanisms seem to determine the regeneration of phagocytes before hibernation is terminated. Surprisingly, the recovery of phagocytes thereafter took several weeks, presumably due to energetic restrictions. This impaired first line of defense coincides with lowest survival probabilities during the annual cycle of our study species. Reduced survival could furthermore be linked to drastic increases in the P/L ratio (phagocytes/lymphocytes), an indicator of physiological stress, during reproduction. On the other hand, moderate augmentations in the P/L ratio occurred during periods of low food availability and were associated with increased survival, but reproductive failure. In this case, the stress response probably represents an adaptive reaction that contributes to survival by activating energy resources. In contrast to our expectation, we could not detect an amplification of stress through high population densities. Summarized, results of our study clearly reveal that the leukocyte picture of active edible dormice responds sensitively to physiological conditions associated with hibernation, reproductive activity and food availability and can be linked to fitness parameters such as survival. Thus edible dormice represent an excellent model organism to investigate regulatory mechanisms of the immune system under natural conditions.

The vector tick Ixodes ricinus feeding on an arboreal rodent-the edible dormouse Glis glis

The reservoir competence and long life expectancy of edible dormice, Glis glis, suggest that they serve as efficient reservoir hosts for Lyme disease (LD) spirochetes. Their arboreality, however, may reduce the probability to encounter sufficient questing Ixodes ricinus ticks to acquire and perpetuate LD spirochetes. To define the potential role of this small arboreal hibernator in the transmission cycle of LD spirochetes, we examined their rate and density of infestation with subadult ticks throughout the season of activity. Of the 1081 edible dormice that we captured at five study sites in Southern Germany and inspected for ticks at 2946 capture occasions, 26 % were infested with at least one and as many as 26 subadult ticks on their ear pinnae. The distribution of ticks feeding on edible dormice was highly aggregated. Although only few individuals harbored nymphal ticks soon after their emergence from hibernation, the rate of nymphal infestation increased steadily throughout the season and reached about 35 % in September. Dormice inhabiting a site with few conspecifics seemed more likely to be infested by numerous ticks, particularly nymphs, than those individuals living in densely populated sites. Male dormice were more likely to be parasitized by numerous nymphs than were females, independent of their age and body mass. Our observation that season, population density, and sex affect the rates of ticks feeding on edible dormice suggests that the contribution of edible dormice to the transmission cycle of LD spirochetes depends mainly on their ranging behavior and level of activity.

Seasonal prevalence of Lyme disease spirochetes in a heterothermic mammal, the edible dormouse (Glis glis)

In Europe, dormice serve as competent reservoir hosts for particular genospecies of the tick-borne agent of Lyme disease (LD) and seem to support them more efficiently than do mice or voles. The longevity of edible dormice (Glis glis) and their attractiveness for ticks may result in a predominance of LD spirochetes in ticks questing in dormouse habitats. To investigate the role of edible dormice in the transmission cycle of LD spirochetes, we sampled skin tissue from the ear pinnae of dormice inhabiting five different study sites in south western Germany. Of 501 edible dormice, 12.6% harbored DNA of LD spirochetes. Edible dormice were infected most frequently with the pathogenic LD spirochete Borrelia afzelii. The DNA of B. garinii and B. bavariensis was detected in ca. 0.5% of the examined individuals. No spirochetal DNA was detectable in the skin of edible dormice until July, 6 weeks after they generally start to emerge from their obligate hibernation. Thereafter, the prevalence of spirochetal DNA in edible dormice increased during the remaining period of their 4 to 5 months of activity, reaching nearly 40% in September. Males were more than four times more likely to harbor LD spirochetes than females, and yearlings were almost twice more likely to be infected than adults. The seasonality of the prevalence of LD spirochetes in edible dormice was pronounced and may affect their role as a reservoir host in respect to other hosts.