Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

Genetic and demographic consequences of range contraction patterns during biological annihilation

Species range contractions both contribute to, and result from, biological annihilation, yet do not receive the same attention as extinctions. Range contractions can lead to marked impacts on populations but are usually characterized only by reduction in extent of range. For effective conservation, it is critical to recognize that not all range contractions are the same. We propose three distinct patterns of range contraction: shrinkage, amputation, and fragmentation. We tested the impact of these patterns on populations of a generalist species using forward-time simulations. All three patterns caused 86-88% reduction in population abundance and significantly increased average relatedness, with differing patterns in declines of nucleotide diversity relative to the contraction pattern. The fragmentation pattern resulted in the strongest effects on post-contraction genetic diversity and structure. Defining and quantifying range contraction patterns and their consequences for Earth's biodiversity would provide useful and necessary information to combat biological annihilation.

The smell of success: Reproductive success related to rub behavior in brown bears

Several species of bears are known to rub deliberately against trees and other objects, but little is known about why bears rub. Patterns in rubbing behavior of male and female brown bears (Ursus arctos) suggest that scent marking via rubbing functions to communicate among potential mates or competitors. Using DNA from bear hairs collected from rub objects in southwestern Alberta from 2011–2014 and existing DNA datasets from Montana and southeastern British Columbia, we determined sex and individual identity of each bear detected. Using these data, we completed a parentage analysis. From the parentage analysis and detection data, we determined the number of offspring, mates, unique rub objects where an individual was detected, and sampling occasions during which an individual was detected for each brown bear identified through our sampling methods. Using a Poisson regression, we found a positive relationship between bear rubbing behavior and reproductive success; both male and female bears with a greater number of mates and a greater number of offspring were detected at more rub objects and during more occasions. Our results suggest a fitness component to bear rubbing, indicate that rubbing is adaptive, and provide insight into a poorly understood behaviour.

Using bear rub data and spatial capture-recapture models to estimate trend in a brown bear population

Trends in population abundance can be challenging to quantify during range expansion and contraction, when there is spatial variation in trend, or the conservation area is large. We used genetic detection data from natural bear rubbing sites and spatial capture-recapture (SCR) modeling to estimate local density and population growth rates in a grizzly bear population in northwestern Montana, USA. We visited bear rubs to collect hair in 2004, 2009-2012 (3,579-4,802 rubs) and detected 249-355 individual bears each year. We estimated the finite annual population rate of change 2004-2012 was 1.043 (95% CI = 1.017-1.069). Population density shifted from being concentrated in the north in 2004 to a more even distribution across the ecosystem by 2012. Our genetic detection sampling approach coupled with SCR modeling allowed us to estimate spatially variable growth rates of an expanding grizzly bear population and provided insight into how those patterns developed. The ability of SCR to utilize unstructured data and produce spatially explicit maps that indicate where population change is occurring promises to facilitate the monitoring of difficult-to-study species across large spatial areas.

Den site selection by male brown bears at the population's expansion front

Brown bears (Ursus arctos) spend about half of the year in winter dens. In order to preserve energy, bears may select denning locations that minimize temperature loss and human disturbance. In expanding animal populations, demographic structure and individual behavior at the expansion front can differ from core areas. We conducted a non-invasive study of male brown bear den sites at the male-biased, low-density western expansion front of the Scandinavian brown bear population, comparing den locations to the available habitat. Compared to the higher-density population core in which intraspecific avoidance may affect den site selection of subordinate bears, we expected resource competition in the periphery to be low, and all bears to be able to select optimal den sites. In addition, bears in the periphery had access to free-ranging domestic sheep during summer. We found that males in the periphery denned on high-elevation slopes, probably providing good drainage, longer periods of consistent, insulating snow cover and fewer melting-freezing events. Forests were the principal denning habitat and no dens were found in alpine areas. The Scandinavian brown bears have a history of intense harvest, including culling at the den. This may have exerted a selection pressure to avoid denning in open alpine habitat which compared to forests provide little cover. The bears denned away from main roads and in steep, rugged terrain, probably limiting human access. The odds for finding a bear den decreased with increasing distance to the population core where females could be found. Previous studies have documented directed movement of male brown bears from the male-biased population periphery toward the core areas during the mating season. In this way, denning males may be trading off between low resource competition and access to sheep in the low-density periphery, and mating opportunities in the higher-density population core.

Relationship between effective and demographic population size in continuously distributed populations

Genetic monitoring of wild populations can offer insights into demographic and genetic information simultaneously. However, widespread application of genetic monitoring is hindered by large uncertainty in the estimation and interpretation of target metrics such as contemporary effective population size, Ne . We used four long-term genetic and demographic studies (≥9 years) to evaluate the temporal stability of the relationship between Ne and demographic population size (Nc ). These case studies focused on mammals that are continuously distributed, yet dispersal-limited within the spatial scale of the study. We estimated local, contemporary Ne with single-sample methods (LDNE, Heterozygosity Excess, and Molecular Ancestry) and demographic abundance with either mark-recapture estimates or catch-per-unit effort indices. Estimates of Ne varied widely within each case study suggesting interpretation of estimates is challenging. We found inconsistent correlations and trends both among estimates of Ne and between Ne and Nc suggesting the value of Ne as an indicator of Nc is limited in some cases. In the two case studies with consistent trends between Ne and Nc , FIS was more stable over time and lower, suggesting FIS may be a good indicator that the population was sampled at a spatial scale at which genetic structure is not biasing estimates of Ne . These results suggest that more empirical work on the estimation of Ne in continuous populations is needed to understand the appropriate context to use LDNe as a useful metric in a monitoring programme to detect temporal trends in either Ne or Nc .

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.

Nature vs. Nurture: Evidence for Social Learning of Conflict Behaviour in Grizzly Bears

The propensity for a grizzly bear to develop conflict behaviours might be a result of social learning between mothers and cubs, genetic inheritance, or both learning and inheritance. Using non-invasive genetic sampling, we collected grizzly bear hair samples during 2011-2014 across southwestern Alberta, Canada. We targeted private agricultural lands for hair samples at grizzly bear incident sites, defining an incident as an occurrence in which the grizzly bear caused property damage, obtained anthropogenic food, or killed or attempted to kill livestock or pets. We genotyped 213 unique grizzly bears (118 M, 95 F) at 24 microsatellite loci, plus the amelogenin marker for sex. We used the program COLONY to assign parentage. We evaluated 76 mother-offspring relationships and 119 father-offspring relationships. We compared the frequency of problem and non-problem offspring from problem and non-problem parents, excluding dependent offspring from our analysis. Our results support the social learning hypothesis, but not the genetic inheritance hypothesis. Offspring of problem mothers are more likely to be involved in conflict behaviours, while offspring from non-problem mothers are not likely to be involved in incidents or human-bear conflicts themselves (Barnard's test, p = 0.05, 62.5% of offspring from problem mothers were problem bears). There was no evidence that offspring are more likely to be involved in conflict behaviour if their fathers had been problem bears (Barnard's test, p = 0.92, 29.6% of offspring from problem fathers were problem bears). For the mother-offspring relationships evaluated, 30.3% of offspring were identified as problem bears independent of their mother's conflict status. Similarly, 28.6% of offspring were identified as problem bears independent of their father's conflict status. Proactive mitigation to prevent female bears from becoming problem individuals likely will help prevent the perpetuation of conflicts through social learning.