Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest-dwelling species--the European roe deer--in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 x 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the 'least cost distance' (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.     

Genetic effect of transportation infrastructure on roe deer populations (Capreolus capreolus)

Anthropogenic transportation infrastructure is a major factor of habitat fragmentation leading to genetic population fragmentation in wildlife. Assessing and understanding the impact of this deterministic factor on genetic diversity and divergence of populations is crucial to appraise the viability of wildlife populations in fragmented landscapes. In this study, the roe deer is used as an example species for the assessment of genetic differentiation of populations separated by an anthropogenic barrier. In order to detect genetic discontinuities, we screened 12 polymorphic microsatellites on 222 individuals out of 11 roe deer populations that were sampled on the east and the westside of a fenced motorway in Central Switzerland. The interaction between landscape structure and microevolutionary processes such as gene flow and drift were assessed and evaluated by different population genetic methods like F-statistics, Mantel test, spatial autocorrelation analyses, Monmonier algorithm, and principal component analysis in conjunction with geographic information system data (synthesis map). We revealed an influence of the transportation infrastructure on genetic divergence of the roe deer population examined, but no impact on genetic diversity was detected. Based on the achieved genetic findings, recommendations for management implementation were made.     

The structural and functional connectivity of the grassland plant Lychnis flos-cuculi

Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity.     

Genetic assessment of environmental features that influence deer dispersal: implications for prion-infected populations

The landscape can influence host dispersal and density, which in turn, affect infectious disease transmission, spread, and persistence. Understanding how the landscape influences wildlife dispersal and pathogen epidemiology can enhance the efficacy of disease management in natural populations. We applied landscape genetics to examine relationships among landscape variables, dispersal of white-tailed deer hosts and transmission/spread of chronic wasting disease (CWD), a fatal prion encephalopathy. Our focus was on quantifying movements and population structure of host deer in infected areas as a means of predicting the spread of this pathology and promoting its adaptive management. We analyzed microsatellite genotypes of CWD-infected and uninfected deer from two disease foci (Southern Wisconsin, Northern Illinois). We quantified gene flow and population structure using F _ST, assignment tests, and spatial autocorrelation analyses. Gene flow estimates were then contrasted against a suite of landscape variables that potentially mediate deer dispersal. Forest fragmentation and grassland connectivity promoted deer movements while rivers, agricultural fields and large urbanized areas impeded movement. Landscape variables, deer dispersal, and disease transmission covaried significantly and positively in our analyses. Habitats with elevated host gene flow supported the concept of dispersal-mediated CWD transmission by reflecting a concomitant, rapid CWD expansion. Large, interrelated social groups isolated by movement barriers overlapped disease foci, suggesting that philopatry exacerbated CWD transmission. Our results promote adaptive management of CWD by predicting patterns of its spread and identifying habitats at risk for invasion. Further, our landscape genetics approach underscores the significance of topography and host behavior in wildlife disease transmission.     

The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States

One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.     

Do landscape barriers affect functional connectivity of populations of an endangered damselfly?

1. Landscape genetic approaches were used to assess functional connectivity of populations of the endangered damselfly Coenagrion mercuriale in a fragmented agricultural landscape in Switzerland. Spatial genetic clustering methods combined with interpolation by kriging and landscape genetic corridor analysis were applied to identify landscape elements that enhance or hinder dispersal and gene flow. 2. Spatial genetic clustering analysis divided the sampled populations into a northern and a southern genetic group. The boundary between the two groups coincided with a hill ridge intersecting the study area. Landscape corridor analysis identified five landscape elements that significantly affected gene flow. Elevation change, Euclidian distance, patches of forest and flowing waterbodies acted as barriers, whereas open agricultural land enhanced gene flow between populations of C. mercuriale. 3. This study showed that movement of C. mercuriale was not restricted to its preferred habitat (i.e. streams). Populations linked via continuous open agricultural land were functionally well connected if they were not more than about 1.5–2 km apart. In contrast, substantial elevation change and larger forest patches separated populations. These findings may serve as a basis to define conservation units and should be considered when planning connectivity measures, such as determining the locations of stepping stones, or the restoration of streams.     

Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 × 87 km), significant population structure was found using F -statistics ( F _ST = 0.019) and the program structure , with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.     

Landscape genetics and the spatial distribution of chronic wasting disease

Predicting the spread of wildlife disease is critical for identifying populations at risk, targeting surveillance and designing proactive management programmes. We used a landscape genetics approach to identify landscape features that influenced gene flow and the distribution of chronic wasting disease (CWD) in Wisconsin white-tailed deer. CWD prevalence was negatively correlated with genetic differentiation of study area deer from deer in the area of disease origin (core-area). Genetic differentiation was greatest, and CWD prevalence lowest, in areas separated from the core-area by the Wisconsin River, indicating that this river reduced deer gene flow and probably disease spread. Features of the landscape that influence host dispersal and spatial patterns of disease can be identified based on host spatial genetic structure. Landscape genetics may be used to predict high-risk populations based on their genetic connection to infected populations and to target disease surveillance, control and preventative activities.     

Prediction of habitat suitability,connectivity, and corridors in the future to conserve roe deer (Capreolus capreolus) as a locally endangered species in northern Iran

Roe deer is a protected species in Iran as its population and distribution in the country have considerably declined. Roe deer are threatened by several factors such as habitat fragmentation and road mortality, so studying their distribution and movement through the increasing habitat destruction and fragmentation is necessary. This will become increasingly important because climate change will transform the species’ future habitat and connectivity patterns. We evaluated the roe deer’s potential distribution range in northern Iran and, for the first time, developed connectivity models and designed corridors for the present and future to make better conservation plans. We collected 91 points indicating the presence of roe deer in the study region. After developing ensemble models using six species distribution algorithms, we defined high-ranked habitat cores using the concept of landscape suitability prioritization. From these, we designed connectivity and corridors in two time-frames with the help of least-cost paths and circuit theories to predict the potential movement throughout the study area. We estimated that the overall core habitats for roe deer in the present and future periods are, respectively, around 1200 km² and 2600 km², corresponding to 2 and 4 percent of the whole area. This suggests that the habitat core will expand in the future as a result of climate change. Similarly, the connectivity among the cores will strengthen. We also conclude that the temperature-driven and anthropogenic variables significantly affect the distribution of roe deer in northern Iran. It is necessary that conservationists and managers consider the designed corridors in the present study while planning conservation strategies.     

Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City

In this study, I examine the influence of urban canopy cover on gene flow between 15 white-footed mouse (Peromyscus leucopus) populations in New York City parklands. Parks in the urban core are often highly fragmented, leading to rapid genetic differentiation of relatively nonvagile species. However, a diverse array of 'green' spaces may provide dispersal corridors through 'grey' urban infrastructure. I identify urban landscape features that promote genetic connectivity in an urban environment and compare the success of two different landscape connectivity approaches at explaining gene flow. Gene flow was associated with 'effective distances' between populations that were calculated based on per cent tree canopy cover using two different approaches: (i) isolation by effective distance (IED) that calculates the single best pathway to minimize passage through high-resistance (i.e. low canopy cover) areas, and (ii) isolation by resistance (IBR), an implementation of circuit theory that identifies all low-resistance paths through the landscape. IBR, but not IED, models were significantly associated with three measures of gene flow (Nm from F(ST) , BayesAss+ and Migrate-n) after factoring out the influence of isolation by distance using partial Mantel tests. Predicted corridors for gene flow between city parks were largely narrow, linear parklands or vegetated spaces that are not managed for wildlife, such as cemeteries and roadway medians. These results have implications for understanding the impacts of urbanization trends on native wildlife, as well as for urban reforestation efforts that aim to improve urban ecosystem processes.     

Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease

1. Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases.
2. We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white‐tailed deer (Odocoileus virginianus) in the Mid‐Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units.
3. Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle (F_ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however.
4. Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity.
5. These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.

     

Do roe deer react to wildlife warning reflectors? A test combining a controlled experiment with field observations

Millions of animals are killed by vehicle collisions each year. As mitigation measures, wildlife warning reflectors have become increasingly popular, although clear evidence for their effectiveness is lacking. A reason for inconclusive results in the literature may be that most previous studies on the effectiveness of wildlife warning reflectors compare animal-vehicle collision rates with and without reflectors, a setting characterised by low event rates and weak experimental control. Animal behaviour can be expected to provide a more direct evidence for a possible effect of reflectors. In this study, we analyse roe deer behaviour in the presence of a blue semicircle reflector, one of the most frequently applied wildlife warning reflectors in Germany and other parts of Europe. Behavioural response to these reflectors (classified as no reaction, vigilance, short-distance flight and long-distance flight) was recorded both under controlled experimental conditions with captive roe deer and for free-ranging roe deer at road sections with traffic occurrence. We used generalised linear mixed models (GLMMs) to test if reflector presence induced threat-related behaviour (vigilance, flight) and movement away from the reflectors. We found no significant evidence that the light stimulus emitted by reflectors was perceived as a threat or induced evasive movement. We conclude that our study provides no evidence that blue semicircle reflectors induce behaviour in roe deer that seems suitable to reduce roe deer-vehicle collisions.     

Making the connection: expanding the role of restoration genetics in restoring and evaluating connectivity

The success of restoration activities is affected by connectivity with the surrounding landscape. From a genetic perspective, landscape connectivity can influence gene flow, effective size, and genetic diversity of populations, which in turn have impacts on the fitness and adaptive potential of species in restored areas. Researchers and practitioners are increasingly using genetic data to incorporate elements of connectivity into restoration planning and evaluation. We show that genetic studies of connectivity can improve restoration planning in three main ways. First, by comparing genetic estimates of contemporary and historical gene flow and population size, practitioners can establish historical baselines that may provide targets for restoration of connectivity. Second, empirical estimates of dispersal, landscape resistance to movement, and adaptive genetic variance can be derived from genetic data and used to parameterize existing restoration planning tools. Finally, restoration actions can also be targeted to remove barriers to gene flow or mitigate pinch‐points in corridors. We also discuss appropriate methods for evaluating the restoration of gene flow over timescales required by practitioners. Collaboration between restoration geneticists, ecologists, and practitioners is needed to develop practical and innovative ways to further incorporate connectivity into restoration practice.     

Where movement happens: scale‐dependent landscape effects on genetic differentiation in the European tree frog

Functional connectivity among fragmented populations depends on the landscape matrix between occupied habitat patches and its effect on the frequency of animal movement and gene flow. The quantification of landscape effects on gene flow should therefore be scale‐dependent. Here, we explored the impact of different spatial scales in a landscape genetic analysis of the European tree frog Hyla arborea in a fragmented landscape in Switzerland. We examined the effects of landscape elements and geographic distance on genetic differentiation at three distance classes reflecting varying frequencies of tree frog movement. We calculated pairwise F_ST‐values and assembled 16 landscape elements within 1 km wide corridors between all pairs of tree frog breeding sites. Per distance class, we computed a multiple regression model with stepwise backward elimination and permutation testing. At distances of<2 km, only a larger river acted as a barrier to gene flow. At distances>2 km, geographic distance had a negative effect on gene flow as had landscape elements such as forests and roads. In general, hedgerows and various structure‐rich landscape elements positively affected gene flow. As we found distinct scale‐dependent landscape effects on gene flow, future landscape genetic studies should analyse the effects of landscape variables at different spatial dimensions relevant for the movement and dispersal of the study organisms. Corresponding studies should also carefully consider relevant correlations among the landscape elements tested and should preferentially replicate their analysis at the landscape‐level in order to avoid idiosyncratic results owing to the particular scale and landscape studied.     

Diet quality and immunocompetence influence parasite load of roe deer in a fragmented landscape

The influence of landscape structure and host diet on parasite load of wildlife is still largely unknown. We studied a roe deer (Capreolus capreolus) population in a fragmented agricultural landscape in southern France to explore the relationship of gastrointestinal nematode load with spleen mass (to index immunocompetence), faecal nitrogen (to index diet quality), landscape structure and age of 33 hunt-harvested roe deer. Gastrointestinal worm counts were negatively related to faecal nitrogen and spleen mass, explaining respectively 24.7% and 9.2% of the observed variability in parasite load. Landscape structure did not appear to have a direct influence on gastrointestinal worm counts, but since animals from more open areas have a diet that is richer in nitrogen, its influence may be indirect. In conclusion, in the study area, the colonisation of the agricultural landscape does not seem to have increased the risk of gastrointestinal nematode parasitism for roe deer, possibly because access to high-quality food enhances immunocompetence.

     

A comparison of regression methods for model selection in individual‐based landscape genetic analysis

Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate‐induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow and thereby inform such conservation actions. However, there are currently many methods available for model selection in landscape genetics, and considerable uncertainty as to which provide the greatest accuracy in identifying the true landscape model influencing gene flow among competing alternative hypotheses. In this study, we used population genetic simulations to evaluate the performance of seven regression‐based model selection methods on a broad array of landscapes that varied by the number and type of variables contributing to resistance, the magnitude and cohesion of resistance, as well as the functional relationship between variables and resistance. We also assessed the effect of transformations designed to linearize the relationship between genetic and landscape distances. We found that linear mixed effects models had the highest accuracy in every way we evaluated model performance; however, other methods also performed well in many circumstances, particularly when landscape resistance was high and the correlation among competing hypotheses was limited. Our results provide guidance for which regression‐based model selection methods provide the most accurate inferences in landscape genetic analysis and thereby best inform connectivity conservation actions.     

老爷岭南部狍冬季移动、卧息生境选择及其适宜性评价

在动物生境研究中,移动生境和卧息生境是生境研究的焦点。开展移动生境和卧息生境选择,并在此基础上进行生境评价,有利于深入了解动物对移动和卧息生境条件的需求,制定科学合理的栖息地保护计划。以东北虎（Panthera tigris altaica）的主要猎物物种之一-狍（Capreolus pygargus）为研究对象,于2017-2019年冬季积雪覆盖期在老爷岭南部通过随机布设28个大样方和84条用于足迹链跟踪的样线收集狍的移动点和卧息点信息,再结合近年来收集的东北虎出现点,利用广义可加模型（GAM）和最大熵模型（MaxEnt）进行狍移动、卧息生境选择及评价研究。移动生境选择研究表明,狍在移动的过程中偏好选择坡度小、距农田距离>500 m、远离道路、居民点和低海拔或较高海拔的区域;移动生境评价分析表明,移动适宜和次适宜生境面积之和为1318.16 km²,占研究区域面积的51.28%,当加入虎活动点影响因子后,狍移动适宜和次适宜生境面积之和为901.52 km²,适宜和次适宜生境面积之和减少了31.61%。狍卧息生境选择研究表明,水源、农田、道路和雪深是影响狍卧息的关键因素,其中雪深对狍卧息生境选择的贡献率达到70.13%;卧息生境评价表明,卧息适宜和次适宜生境面积之和为1243.77 km²,占研究区域面积的48.39%,当加入虎出现点因子后,适宜生境和次适宜生境面积之和减少了61.00%,仅为485.02 km²。研究认为,虎的出现对狍移动和卧息生境选择均产生影响,虎的活动及捕食行为可能会减少狍的活动范围和频次,狍远离虎活动区域卧息休息,压缩了狍适宜卧息的空间。     

Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual‐based sampling across an urban‐rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban‐rural landscape. We assessed functional connectivity by applying an individual‐based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector‐based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built‐up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man‐made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers.     

Population structure of spotted salamanders (Ambystoma maculatum) in a fragmented landscape

Understanding the impacts of landscape-level processes on the population biology of amphibians is critical, especially for species inhabiting anthropogenically modified landscapes. Many pond-breeding amphibians are presumed to exist as metapopulations, but few studies demonstrate the extent and consequences of this metapopulation structure. Gene flow measures may facilitate the construction of more realistic models of population structure than direct measures of migration. This is especially true for species that are cryptic, such as many amphibians. We used eight polymorphic microsatellite loci to determine the genetic population structure of spotted salamanders ( Ambystoma maculatum ) breeding at 17 ponds in northeastern Ohio, a landscape fragmented by roads, agriculture, urban areas and the Cuyahoga River. Using a variety of analyses (Bayesian clustering, F -statistics, AMOVA) we generated a model of salamander population genetic structure. Our data revealed patterns of genetic connectivity that were not predicted by geographical distances between ponds (no isolation by distance). We also tested for a relationship between population structure and several indices of landscape resistance, but found no effect of potential barriers to dispersal on genetic connectivity. Strong overall connectivity among ponds, despite the hostile habitat matrix, may be facilitated by a network of riparian corridors associated with the Cuyahoga River; however, high gene flow in this system may indicate a general ability to disperse and colonize beyond particular corridors.