Assessing the permeability of landscape features to animal movement: using genetic structure to infer functional connectivity

A Bocage Landscape Restricts the Gene Flow of Pest Vole Populations

The population dynamics of most animal species inhabiting agro-ecosystems may be determined by landscape characteristics, with agricultural intensification and the reduction of natural habitats influencing dispersal and hence limiting gene flow. Increasing landscape complexity would thus benefit many endangered species by providing different ecological niches, but it could also lead to undesired effects in species that can act as crop pests and disease reservoirs. We tested the hypothesis that a highly variegated landscape influences patterns of genetic structure in agricultural pest voles. Ten populations of fossorial water vole, Arvicola scherman, located in a bocage landscape in Atlantic NW Spain were studied using DNA microsatellite markers and a graph-based model. The results showed a strong isolation-by-distance pattern with a significant genetic correlation at smaller geographic scales, while genetic differentiation at larger geographic scales indicated a hierarchical pattern of up to eight genetic clusters. A metapopulation-type structure was observed, immersed in a landscape with a low proportion of suitable habitats. Matrix scale rather than matrix heterogeneity per se may have an important effect upon gene flow, acting as a demographic sink. The identification of sub-populations, considered to be independent management units, allows the establishment of feasible population control efforts in this area. These insights support the use of agro-ecological tools aimed at recreating enclosed field systems when planning integrated managements for controlling patch-dependent species such as grassland voles.

Population connectivity in voles (Microtus sp.) as a gauge for tall grass prairie restoration in midwestern North America

Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ’success.’ One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise F_ST, then potential demographic effects explored by computing migration rates, effective population size (N_e), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of N_e and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives.

Tracing Real-Time Transnational Hydrologic Sensitivity and Crop Irrigation in the Upper Rhine Area over the Exceptional Drought Episode 2018–2020 Using Open Source Sentinel-2 Data

Climate and regional land-use and landcover change (LUCC) impact the ecosystem of the Upper Rhine Area (URA) and transform large parts of the landscape into strongly irrigated agricultural cropland. The increase of long-term drought periods and the trend towards low summer precipitation totals trigger an increase in groundwater scarcity and amplify the negative effects of extensive irrigation purposes and freshwater consumption in a hydrologically sensitive region in Central Europe. This article presents qualitative transnational open source remote sensing temporal series of vegetation indices (NDVI) and groundwater level development to tracing near real-time vegetation change and socio-ecological feedbacks during periods of climate extremes in the Upper Rhine Area (2018–2020). Increased freshwater consumption caused a dramatic drop in groundwater availability, which eventually led to a strong degradation of the vegetation canopy and caused governmental regulations in July 2020. Assessing vegetation growth behavior and linking groundwater reactions in the URA through open source satellite data contributes to a rapidly accessible understanding of the ecosystem’s feedbacks on the local to the transnational scale and further enables risk management and eco-political regulations in current and future decision-making processes.

First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison's prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.

Differing, multiscale landscape effects on genetic diversity and differentiation in eastern chipmunks

Understanding how habitat loss and fragmentation impact genetic variation is a major goal in landscape genetics, but to date, most studies have focused solely on the correlation between intervening matrix and genetic differentiation at a single spatial scale. Several caveats exist in these study designs, among them is the inability to include measures of genetic diversity in addition to differentiation. Both genetic metrics help predict population persistence, but are expected to function at differing spatial scales, which requires a multiscale investigation. In this study, we sampled two distinct spatial scales in 31 independent landscapes along a gradient of landscape context (i.e., forest amount, configuration, and types of intervening matrix) to investigate how landscape heterogeneity influences genetic diversity and differentiation in the forest-associated eastern chipmunk (Tamias striatus). Overall, quality of intervening matrix was correlated with genetic differentiation at multiple spatial scales, whereas only configuration was associated with regional scale genetic diversity. Habitat amount, in contrast, did not influence genetic differentiation or diversity at either spatial scale. Based on our findings, landscape effects on genetic variation appears to differ based on spatial scale, the type of genetic response variable, and random variation among landscapes, making extrapolation of results from single scale, unreplicated studies difficult. We encourage landscape geneticists to utilize multiscale, replicated landscapes with both genetic diversity, and differentiation to gain a more comprehensive understanding of how habitat loss and fragmentation influence genetic variation.

Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird

Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population‐level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for having high dispersal abilities. We used a landscape genetic approach to test hypotheses of landscape effects on dispersal behavior of the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered subspecies endemic to the Hawaiian Islands. We created a suite of alternative resistance surfaces representing biologically plausible a priori hypotheses of how gallinules might navigate the landscape matrix and ranked these surfaces by their ability to explain observed patterns in genetic distance among 12 populations on the island of O`ahu. We modeled effective distance among wetland locations on all surfaces using both cumulative least‐cost‐path and resistance‐distance approaches and evaluated relative model performance using Mantel tests, a causal modeling approach, and the mixed‐model maximum‐likelihood population‐effects framework. Across all genetic markers, simulation methods, and model comparison metrics, surfaces that treated linear water features like streams, ditches, and canals as corridors for gallinule movement outperformed all other models. This is the first landscape genetic study on the movement behavior of any waterbird species to our knowledge. Our results indicate that lotic water features, including drainage infrastructure previously thought to be of minimal habitat value, contribute to habitat connectivity in this listed subspecies.

High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure

Habitat associations are a function of habitat preferences and dispersal capabilities, both of which can influence how species responded to Quaternary climatic changes and contemporary habitat heterogeneity. Predicting resultant genetic structure is not always straightforward, especially in species where high dispersal potential and habitat preferences yield opposing predictions. The American badger has high dispersal capabilities that predict widespread panmixia, but avoids closed-canopy forests and clay soils, which could restrict gene flow and create ecologically based population genetic structure. We used mitochondrial sequence and microsatellite data sets to characterize how these opposing forces contribute to genetic structure in badgers at a continent-wide scale. Our data revealed an overall lack of ecologically based population genetic structure, suggesting that high dispersal capabilities were sufficiently realized to overcome most habitat-based genetic structure. At a broadscale, badger gene flow is limited only by geographic distance (isolation by distance) and large water barriers (Lake Michigan and the Mississippi River). The absence of genetic structure in a species with strong avoidance of unsuitable habitats advances our understanding of when and how genetic structure emerges in widespread, highly mobile species.

Evaluating the influence of life-history characteristics on genetic structure: a comparison of small mammals inhabiting complex agricultural landscapes

Conversion of formerly continuous native habitats into highly fragmented landscapes can lead to numerous negative demographic and genetic impacts on native taxa that ultimately reduce population viability. In response to concerns over biodiversity loss, numerous investigators have proposed that traits such as body size and ecological specialization influence the sensitivity of species to habitat fragmentation. In this study, we examined how differences in body size and ecological specialization of two rodents (eastern chipmunk; Tamias striatus and white‐footed mouse; Peromyscus leucopus) impact their genetic connectivity within the highly fragmented landscape of the Upper Wabash River Basin (UWB), Indiana, and evaluated whether landscape configuration and complexity influenced patterns of genetic structure similarly between these two species. The more specialized chipmunk exhibited dramatically more genetic structure across the UWB than white‐footed mice, with genetic differentiation being correlated with geographic distance, configuration of intervening habitats, and complexity of forested habitats within sampling sites. In contrast, the generalist white‐footed mouse resembled a panmictic population across the UWB, and no landscape factors were found to influence gene flow. Despite the extensive previous work in abundance and occupancy within the UWB, no landscape factor that influenced occupancy or abundance was correlated with genetic differentiation in either species. The difference in predictors of occupancy, abundance, and gene flow suggests that species‐specific responses to fragmentation are scale dependent.