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.     

Distribution of an increasing roe deer population in a fragmented Mediterranean landscape

This paper describes roe deer Capreolus capreolus distribution in central Spain, where the species has spread from the mountains into peripheral agricultural areas In this region, it is more abundant in forest fragments near the mountains than in those further away, in pine and oak woodlands than in sclerophyllous forests, and in forests with open water than in those lacking this resource The paper also analyzes whether habitat quality and geographic location of forests with respect to roe deer source areas are the two basic causes of its distribution, as predicted by some models of the species distribution in fragmented landscapes The results corroborate this hypothesis revealing that roe deer abundance is linked negatively to sclerophyllous forest cover and distance from mountains We conclude that this type of farmland seems to be sub-optimal for roe deer in comparison with forested, moist mountains     

Effects of population density and female body mass on litter size in European roe deer at a continental scale

Roe deer (Capreolus capreolus) has a wide distributional range in Europe and inhabits a broad range of habitats and environmental conditions. Thus, populations of roe deer show substantial variation in demographic parameters. We aimed to determine whether body mass and population density—which influence the reproductive potential of roe deer at a local scale—affect their reproductive potential at a biogeographical scale as well. We reviewed the literature (covering years 1948–2015) on in utero litter size in roe deer from 59 locations in 14 countries in Europe. Across study sites, mean litter size varied from 1.0 to 2.4 embryo or corpora lutea per female, and population density ranged from 4.5 to 73.5 individuals/km². Mean body mass varied from 11.2 to 20.8 kg in subadult females and from 12.1 to 22.4 kg in adult females. Between 46° and 56° N, body mass of females did not show a significant trend of increase, whereas between 56° and 63° N, it increased with latitude (Bergmann’s rule). We used linear mixed-effects models (LMMs) to analyse the influence of body mass and population density (analysed separately) on litter size. Females with larger body mass produced larger litters, and this pattern was pronounced at both higher and lower latitudes. Higher population densities negatively affected litter size in a sample of all females. This macroecological analysis showed that factors influencing the reproductive potential of roe deer females at local scales produce similar effects at the biogeographical scale.     

宏生态尺度上景观破碎化对物种丰富度的影响

生物多样性的地理格局及其形成机制是宏生态学与生物地理学的研究热点。大量研究表明,景观尺度上的生境破碎化对物种多样性的分布格局具有重要作用,但目前尚不清楚这种作用是否足以在宏生态尺度上对生物多样性地理格局产生显著影响。利用中国大陆鸟类和哺乳动物的物种分布数据,在100 km×100 km网格的基础上生成了这两个类群生物的物种丰富度地理格局,进一步利用普通最小二乘法模型和空间自回归模型研究了物种丰富度与气候、生境异质性、景观破碎化的相关关系。结果表明,景观破碎化因子与鸟类和哺乳动物的物种丰富度都具有显著的关联关系,其方差贡献率可达约30%—50%(非空间模型)和60%—80%(空间模型),略低于或接近于气候和生境异质性因子。方差分解结果显示,景观破碎化因子与气候和生境异质性因子的方差贡献率的重叠部分达20%—40%。相对鸟类而言,景观破碎化对哺乳动物物种丰富度的地理格局具有更高的解释率。     

Negative density-dependent emigration of males in an increasing red deer population

In species with polygynous mating systems, females are regarded as food-limited, while males are limited by access to mates. When local density increases, forage availability declines, while mate access for males may increase due to an increasingly female-biased sex ratio. Density dependence in emigration rates may consequently differ between sexes. Here, we investigate emigration using mark-recovery data from 468 young red deer Cervus elaphus marked in Snillfjord, Norway over a 20-year period when the population size has increased sixfold. We demonstrate a strong negative density-dependent emigration rate in males, while female emigration rates were lower and independent of density. Emigrating males leaving the natal range settled in areas with lower density than expected by chance. Dispersing males moved 42 per cent longer at high density in 1997 (37 km) than at low density in 1977 (26 km), possibly caused by increasing saturation of deer in areas surrounding the marking sites. Our study highlights that pattern of density dependence in dispersal rates may differ markedly between sexes in highly polygynous species. Contrasting patterns reported in small-scale studies are suggestive that spatial scale of density variation may affect the pattern of temporal density dependence in emigration rates and distances.     

A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models

Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics primarily uses landscape resistance surfaces (RSs) and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of RSs is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a new landscape genetic approach: least-cost transect analysis (LCTA). Habitat-matrix RSs were used to create least-cost paths, which were subsequently buffered to form transects in which the abundance of several landscape elements was quantified. To maintain objectivity, this analysis was repeated so that each landscape element was in turn regarded as migration habitat. The relationship between explanatory variables and genetic distances was then assessed following a mixed modelling approach to account for the nonindependence of values in distance matrices. Subsequently, the best fitting model was selected using the statistic. We applied LCTA and the mixed modelling approach to an empirical genetic dataset on the endangered damselfly, Coenagrion mercuriale. We compared the results to those obtained from traditional least-cost, effective and resistance distance analysis. We showed that LCTA is an objective approach that identifies both the most probable migration habitat and landscape elements that either inhibit or facilitate gene flow. Although we believe the statistical approach to be an improvement for the analysis of distance matrices in landscape genetics, more stringent testing is needed.     

Spatial modelling for population replacement of mosquito vectors at continental scale

Malaria is one of the deadliest vector-borne diseases in the world. Researchers are developing new genetic and conventional vector control strategies to attempt to limit its burden. Novel control strategies require detailed safety assessment to ensure responsible and successful deployments. Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii, two closely related subspecies within the species complex Anopheles gambiae sensu lato (s.l.), are among the dominant malaria vectors in sub-Saharan Africa. These two subspecies readily hybridise and compete in the wild and are also known to have distinct niches, each with spatially and temporally varying carrying capacities driven by precipitation and land use factors.We model the spread and persistence of a population-modifying gene drive system in these subspecies across sub-Saharan Africa by simulating introductions of genetically modified mosquitoes across the African mainland and its offshore islands. We explore transmission of the gene drive between the two subspecies that arise from different hybridisation mechanisms, the effects of both local dispersal and potential wind-aided migration to the spread, and the development of resistance to the gene drive. Given the best current available knowledge on the subspecies’ life histories, we find that an introduced gene drive system with typical characteristics can plausibly spread from even distant offshore islands to the African mainland with the aid of wind-driven migration, with resistance beginning to take over within a decade. Our model accounts for regional to continental scale mechanisms, and demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. As a result, it is well-placed to answer future questions relating to mosquito gene drives as important life history parameters become better understood.     

Disentangling demographic effects of red deer on chamois population dynamics

Investigating the impact of ecological factors on sex‐ and age‐specific vital rates is essential to understand animal population dynamics and detect the potential for interactions between sympatric species. We used block count data and autoregressive linear models to investigate variation in birth rate, kid survival, female survival, and male survival in a population of Alpine chamois Rupicapra rupicapra rupicapra monitored over 27 years within the Stelvio National Park, Central Italian Alps, as function of climatic variables, density dependence, and interspecific competition with red deer Cervus elaphus. We also used path analysis to assess the indirect effect of deer abundance on chamois growth rate mediated by each demographic parameter. Based on previous findings, we predicted that birth rate at [t] would negatively relate to red deer abundance at year [t − 1]; survival rates between [t] and [t + 1] would negatively relate to red deer abundance at year [t − 1] and to the interactive effect of winter precipitation at [t + 1] and chamois density at [t]. Our results showed that birth rate was positively related to spring–summer precipitation in the previous year, but this effect was hampered by increasing red deer abundance. Kid and female survival rates were negatively related to the combined effect of chamois abundance and winter precipitation. Male and female survival rates were negatively related to lagged red deer abundance. The path analysis supported a negative indirect effect of red deer abundance on chamois growth rate mediated by birth rate and female survival. Our results suggest that chamois population dynamics was largely explained by the synergistic effect of density dependence and winter harshness, as well as by interspecific competition with red deer, whose effects were seemingly stronger on the kid–female segment of the population.     

Spatio‐temporal feeding selection of red deer in a mountainous landscape

Understanding the dietary consumption and selection of wild populations of generalist herbivores is hampered by the complex array of factors. Here, we determine the influence of habitat, season, and animal density, sex, and age on the diet consumption and selection of 426 red deer (Cervus elaphus scoticus) culled in Fiordland National Park, New Zealand. Our site differs from studies elsewhere both in habitat (evergreen angiosperm‐dominated forests) and the intensity of hunting pressures. We predicted that deer would not consume forage in proportion to its relative availability, and that dietary consumption would change among and within years in response to hunting pressures that would also limit opportunities for age and sex segregation. Using canonical correspondence analysis, we evaluated the relative importance of different drivers of variation in diet consumption assessed from gut content and related these to available forage in the environment. We found that altitude explained the largest proportion of variation in diet consumption, reflecting the ability of deer to alter their consumption and selection in relation to their foraging grounds. Grasses formed a high proportion of the diet consumption, even for deer culled several kilometres from the alpine grasslands. In the winter months, when the alpine grasslands were largely inaccessible, less grass was eaten and deer resorted to woody plants that were avoided in the summer months. Surprisingly, there were no significant dietary differences between adults and juveniles and only subtle differences between the sexes. Sex‐based differences in diet consumption are commonly observed in ungulate species and we suggest that they may have been reduced in our study area owing to decreased heterogeneity in available forage as the diversity of palatable species decreased under high deer browsing pressures, or by intense hunting pressure.     

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31 500 km² region of France, using a 16 × 16 km² sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43–85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.     

Density-dependent population dynamics in clonal organisms: a modelling approach

1. Density dependence may act at several stages in an organisms life-cycle (e.g. on mortality, fecundity, etc.), but not all density-dependent processes necessarily regulate population size. In this paper I use a density manipulation experiment to determine the effects of density on the transition rates between different size classes of the clonal zoanthid Palythoa caesia Dana 1846. I then formulate a density-dependent matrix model of population dynamics of Palythoa , and perform a series of sensitivity analyses on the model to determine at what stage in the life-cycle regulation acts.
2. Seven of the 16 transition probabilities decreased with density, most of them being shrinkage (due to loss of tissue or fission) and stasis (the self–self transition) of medium and large colonies. The only probability to increase was for the stasis of large colonies. Recruitment was quadratically dependent on density, peaking at intermediate densities.
3. Equilibrium cover in the model was 84% and was reached in ≈40 years. To determine which density-dependent transitions were involved in population regulation, the strength of density dependence was varied in each independently. This sensitivity analysis showed that only changes in the probabilities of large colonies remaining large and producing medium colonies, were regulating.
4. These results suggest that regulation is primarily acting on fission of large colonies to produce intermediate-sized colonies, in combination with size specific growth rates. Fission rates decrease greatly with density, resulting in a greater proportion of large colonies at high densities and large colonies grow more slowly than small. Overall, this behaviour is very similar to that of clonal plants which have a phalanx type life history.     

Impulsive culling of a structured population on two patches

We consider a model for a creature inhabiting two patches between which migration may occur. The creature is assumed to have a life cycle with two stages, namely juvenile and adult, giving rise to a delay differential system. The creature could represent an insect crop pest whilst the patches could represent neighbouring farms. Given that it is common to control crop pests by adult impulsive culling, we impose an adult impulsive culling regime on each patch. We find conditions on the regimes such that the pest will be eradicated on both patches simultaneously. The regime on one patch is assumed to be independent of the regime on the other patch to reflect the possibility that the patches represent farms with different owners where each owner has autonomy in their pest control decisions. In the special case where the birth functions on both patches are of an Allee type, we calculate explicit finite upper bounds for the number of culls needed on each patch to guarantee eradication. Simulations corroborate our theoretical results.     

Effects of management at weaning on behaviour and weight gain of farmed red deer calves

Two studies were performed to determine whether there were behavioural or productive differences arising from two contrasting weaning practices for red deer; proximate vs. distant separation of dams and calves. In Experiment 1, 80 calves across two replicates were used. For each replicate, calves were separated from their mothers, weighed and allocated to one of two treatments (n=20 calves), either confinement in an unfamiliar paddock 100 m from their mothers for 2 weeks following weaning (treatment N), or transportation 2 km to a different farm (treatment F). Groups were observed during the following 6 days and weighed 14 days after weaning. In Experiment 2, the same procedure was performed out on two commercial farms, but using 40 calves per treatment group, without replication or weight recording. In Experiment 1 running, fenceline pacing and vocalising declined following weaning, with steeper declines for F than N calves for running and vocalising (P<0.01). Similar trends, with an indication of less vocalising and movement overall, were seen in Experiment 2. In contrast, mean post-weaning weight gains for N calves were higher than for F calves (3.0 compared with 2.4 kg, SED 0.48 kg; P<0.05). Weather variables (cloud, temperature and wind) were associated with behaviour in both studies (P<0.05), with a trend for pacing, calling and running to increase as conditions deteriorated (cloud cover and wind speed increased, and temperature decreased). It was concluded that distant separation appeared beneficial to the calves but more research was required to determine optimal weaning management. The study supported previous evidence that weaning should be carried out in good weather.