Search

Variation in rate of infection and susceptibility of Pinus spp. to the fungus Cronartium harknessii (syn. Endocronartium harknessii), the causative agent of western gall rust, has been well documented. To test the hypothesis that there is a coevolutionary relationship between C. harknessii and its hosts, we examined genetic structure and virulence of C. harknessii associated with lodgepole pine (P. contorta var. latifolia), jack pine (P. banksiana), and their hybrids. A secondary objective was to improve assessment and diagnosis of infection in hosts. Using 18 microsatellites, we assessed genetic structure of C. harknessii from 90 sites within the ranges of lodgepole pine and jack pine. We identified two lineages (East and West, FST = 0.677) associated with host genetic structure (r = 0.81, P = 0.001), with East comprising three sublineages. In parallel, we conducted a factorial experiment in which lodgepole pine, jack pine, and hybrid seedlings were inoculated with spores from the two primary genetic lineages. With this experiment, we refined the phenotypic categories associated with infection and demonstrated that stem width can be used as a quantitative measure of host response to infection. Overall, each host responded differentially to the fungal lineages, with jack pine exhibiting more resiliency to infection than lodgepole pine and hybrids exhibiting intermediate resiliency. Taken together, the shared genetic structure between fungus and host species, and the differential interaction of the fungal species with the hosts, supports a coevolutionary relationship between host and pathogen. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The sister species, lodgepole pine (Pinus contorta var. latifolia Engelm.) and jack pine (Pinus banksiana Lamb), face pressures from a multitude of biotic agents, including mountain pine beetle (Dendroctonus ponderosae Hopkins, 1902) and their pathogenic fungal associates (e.g., Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & M.J. Wingf.), mistletoe (Arceuthobium americanum Nutt. ex A.Gray), and the pathogen causing western gall rust (Cronartium harknessii E. Meinecke). Here, we report new stem tissue transcriptome resources developed for lodgepole and jack pines subjected to these biotic stresses. The annotated transcriptomes were compared to determine species-specific responses to the necrotrophic G. clavigera and the biotrophic Cronartium harknessii. We focused on chitinases, a family that includes members with well-documented roles in defense. Putative chitinase family members were identified via annotation, sequence similarity to reference chitinase genes, phylogenetic analyses, and in silico motif characterization. RNA-Seq revealed marked differences in the responses of lodgepole and jack pine chitinases to G. clavigera and Cronartium harknessii. The potential for adaptive variation in chitinases was investigated by assessing the level of genetic differentiation between and within lodgepole and jack pines using single nucleotide polymorphisms within chitinases. These analyses illustrate the potential of combining transcriptomic and genotyping resources to investigate genotype–phenotype correlations for non-model species.

Hybridization of mule deer (Odocoileus hemionus) and white‐tailed deer (O. virginianus) appears to be a semi‐regular occurrence in western North America. Previous studies confirmed the presence of hybrids in a variety of sympatric habitats, but their developing molecular resources limited identification to the earliest, most admixed generations. For this reason, estimates of hybrid production in wild populations often rely on anecdotal reports. As well, white‐tailed deer populations’ continued encroachment into historically mule deer‐occupied habitats due to changes in land use, habitat homogenization, and a warming climate may increase opportunities for interspecific encounters. We sought to quantify the prevalence and extent of hybrid deer in the prairies of western Canada using a SNP assay with enhanced discriminating power. By updating the available molecular resources, we sought to identify and characterize previously cryptic introgression. We also investigated the influence of various parameters on hybridity by way of logistic regression. We observed overall hybridization rates of ~1.0%, slightly lower than that reported by previous studies, and found white‐tailed‐like hybrids to be more common than their mule deer‐like counterparts. Here, we build upon past studies of hybridization in North American deer by increasing hybrid detection power, expanding sample sizes, demonstrating a new molecular resource applicable to future research and observing asymmetrical directionality of introgression.

Polymorphisms within the prion protein gene (Prnp) are an intrinsic factor that can modulate chronic wasting disease (CWD) pathogenesis in cervids. Although wild European reindeer (Rangifer tarandus tarandus) were infected with CWD, as yet there have been no reports of the disease in North American caribou (R. tarandus spp.). Previous Prnp genotyping studies on approximately 200 caribou revealed single nucleotide polymorphisms (SNPs) at codons 2 (V/M), 129 (G/S), 138 (S/N), 146 (N/n) and 169 (V/M). The impact of these polymorphisms on CWD transmission is mostly unknown, except for codon 138. Reindeer carrying at least one allele encoding for asparagine (138NN or 138SN) are less susceptible to clinical CWD upon infection by natural routes, with the majority of prions limited to extraneural tissues. We sequenced the Prnp coding region of two caribou subspecies (n = 986) from British Columbia, Saskatchewan, Yukon, Nunavut and the Northwest Territories, to identify SNPs and their frequencies. Genotype frequencies at codon 138 differed significantly between barren‐ground (R. t. groenlandicus) and woodland (R. t. caribou) caribou when we excluded the Chinchaga herd (p

Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack‐associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.

Wildlife disease incidence is increasing, resulting in negative impacts on the economy, biodiversity, and potentially human health. Chronic wasting disease (CWD) is a fatal, transmissible spongiform encephalopathy of cervids (wild and captive) which continues to spread geographically resulting in exposure to potential new host species. The disease agent (PrPCWD) is a misfolded conformer of the cellular prion protein (PrPC). In Canada, the disease is endemic in Alberta and Saskatchewan, affecting mule and white-tail deer, with lesser impact on elk and moose. As the disease continues to expand, additional wild ungulate species including bison, bighorn sheep, mountain goat, and pronghorn antelope may be exposed. To better understand the species-barrier, we reviewed the current literature on taxa naturally or experimentally exposed to CWD to identify susceptible and resistant species. We created a phylogeny of these taxa using cytochrome B and found that CWD susceptibility followed the species phylogeny. Using this phylogeny we estimated the probability of CWD susceptibility for wild ungulate species. We then compared PrPC amino acid polymorphisms among these species to identify which sites segregated between susceptible and resistant species. We identified sites that were significantly associated with susceptibility, but they were not fully discriminating. Finally, we sequenced Prnp from 578 wild ungulates to further evaluate their potential susceptibility. Together, these data suggest the host-range for CWD will potentially include pronghorn, mountain goat and bighorn sheep, but bison are likely to be more resistant. These findings highlight the need for monitoring potentially susceptible species as CWD continues to expand.

Environmental change is altering forest insect dynamics worldwide. As these systems change, they pose significant ecological, social, and economic risk through, for example, the loss of valuable habitat, green space, and timber. Our understanding of such systems is often limited by the complexity of multiple interacting taxa. As a consequence, studies assessing the ecology, physiology, and genomics of each key organism in such systems are increasingly important for developing appropriate management strategies. Here we summarize the genetic and genomic contributions made by the TRIA project — a long-term study of the mountain pine beetle (Dendroctonus ponderosae Hopkins) system encompassing beetle, fungi, and pine. Contributions include genetic and genomic resources for species identification, sex determination, detection of selection, functional genetic analysis, mating system confirmation, hybrid stability tests, and integrated genetic studies of multiple taxa. These resources and subsequent findings have accelerated our understanding of the mountain pine beetle system, facilitating improved management strategies (e.g., enhancements to stand susceptibility indices and predictive models) and highlighting mechanisms for promoting resilient forests. Further, work from the TRIA project serves as a model for the increasing number and severity of invasive and native forest insect outbreaks globally (e.g., Dutch elm disease and thousand cankers disease).

In north-central Alberta, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb.) form a mosaic hybrid zone, the spatial extent of which remains poorly defined. We sought to refine the genetic and geographic distribution of this hybrid zone in western North America to provide information important in predicting future risk of mountain pine beetle (Dendroctonus ponderosae Hopkins) outbreaks. We used 29 single nucleotide polymorphism (SNP) markers to discriminate lodgepole pine, jack pine, and their hybrids. We compared and contrasted spatial patterns of hybridization in northern and southern forest zones based on the colonization history of the two species. We found that patterns of introgression were more similar between the zones than expected by chance, but there were significant differences between these regions at specific loci. Using logistic regression, we created a robust predictive model to distinguish among lodgepole pine, jack pine, and their hybrids using a combination of geographic and environmental predictors. Using model selection based on Akaike information criterion, we found that location, elevation, and moisture are important predictors for species class. Quantification of the genetic differences between these two regions, combined with an accurate model for predicting the spatial distribution of lodgepole pine, jack pine, and their hybrids, provides essential information for continued effective management of forest resources.

The genetic consequences of reintroductions are rarely considered after releases cease, but long-term viability depends on linked demography and genetic health. Reintroductions of swift foxes Vulpes velox began after 45 years of extirpation from Canada; these have resulted in national down-listing to ‘threatened’ status, and the re-establishment of a small contiguous population in Montana, US. Demographic growth has been associated with stable levels of genetic diversity and growing effective population size, but evidence of two genetic clusters, and a recent decline in abundance could be cause for conservation concern depending on underlying mechanisms. We analysed individuals from two time points at 18 microsatellite loci to investigate whether the genetic structure is a consequence of having used two separate release sites and non-equilibrium population dynamics, but our results suggest that the population is likely at mutation- and migration-drift equilibrium. We examined habitat effects on relative gene flow and found limited evidence for cropland to be a dispersal barrier, but effects of terrain roughness suggest that more rugged landscapes may reduce dispersal capacity. Using parentage analysis we determined maximum dispersal distances of up to 50 km for females and 100 km for males including movements in either direction across the international border, but no mixing of genetic clusters was seen in either country. Greater genetic connectivity among than within respective countries necessitates careful co-management between Canada, where the species has the highest levels of legislative protection, and contiguous areas of the United States where limited trapping for fur is now permitted. We encourage similar analyses of conservation populations across international borders to determine how optimal genetic management can best mesh with different policies and conservation approaches among countries.

Butterflies have played a pivotal role in our understanding of animal movement, but little is known about landscape-scale movement in highly vagile species with large ranges and open population structure. We investigate the effect of environment and landscape on both inter- and intraspecific genetic differentiation and population structure in the Papilio machaon group of swallowtail butterflies in Alberta, Canada. These butterflies exhibit strong hilltopping behaviour, where individuals congregate on topographical prominences to mate, and thus we expect topography to influence population connectivity. We use redundancy analysis to explore the relationship between two genetic datasets (mitochondrial DNA and microsatellites) and topographic, climatic and habitat-related environmental variables at multiple spatial scales. Shared variation across these environmental variables explained a large portion of both mitochondrial (≤ 75%) and microsatellite genetic variation (≤ 40%). Individual variables, such as elevation, terrain profile, solar radiation and precipitation, had moderate explanatory power; however, the water component of land cover had the greatest explanatory power of the individual variables and acted as a surrogate variable for the larval habitat of P. machaon. Despite high levels of retained ancestral polymorphism in the mitochondrial dataset, we found similar relationships between environmental characteristics and genetic variation. Finally, the spatial scale of our analyses greatly influenced our results, and without exploring the effect of scale we would have missed or discounted the effects of several environmental characteristics. This point emphasizes the importance of exploratory analysis in systems where there is little prior knowledge of movement dynamics and the influence of the environment.

Mule deer (Odocoileus hemionus) are endemic to a wide variety of habitats in western North America, many of which are shared in sympatry with their closely related sister-species white-tailed deer (Odocoileus virginianus), whom they hybridize with in wild populations. Although mule deer meet many ideal conditions for a molecular ecological research species, such as high abundance, ecological importance, and broad dispersal and gene flow, conservation genetic studies have been limited by a relative lack of existing genomic resources and inherent difficulties caused by introgression with white-tailed deer. Many molecular tools currently available for the study of cervids were designed using reference assemblies of divergent model species, specifically cattle (Bos taurus). Bovidae and Cervidae diverged approximately 28 million years ago, therefore, we sought to ameliorate the available resources by contributing the first mule deer whole genome sequence draft assembly with an average genome-wide read depth of 25X, using the white-tailed genome assembly (Ovir.te_1.0) as a reference. Comparing the two assemblies, we identified ∼33 million single nucleotide polymorphisms (SNPs) and insertion/deletion variants. We then verified fixed SNP differences between the two species and developed a 40-loci SNP assay capable of identifying pure mule deer, white-tailed deer, and interspecific hybrids. Assignment capacity of the panel, which was tested on simulated datasets, is reliable up to and including the third backcross hybrid generation. Identification of post-F1 hybrids will be necessary for hybrid zone population studies going forward, and the new mule deer assembly will be a valuable resource for genetic and comparative genomics studies.

Individual variation in quantitative traits clearly influence many ecological and evolutionary processes. Moderate to high heritability estimates of personality and life-history traits suggest some level of genetic control over these traits. Yet, we know very little of the underlying genetic architecture of phenotypic variation in the wild. In this study, we used a candidate gene approach to investigate the association of genetic variants with repeated measures of boldness and maternal performance traits (weaning mass and lactation duration) collected over an 11- and 28-year period, respectively, in a free-ranging population of grey seals on Sable Island National Park Reserve, Canada. We isolated and re-sequenced five genes: dopamine receptor D4 (DRD4), serotonin transporter (SERT), oxytocin receptor (OXTR), and melanocortin receptors 1 (MC1R) and 5 (MC5R). We discovered single nucleotide polymorphisms (SNPs) in each gene; and, after accounting for loci in linkage disequilibrium and filtering due to missing data, we were able to test for genotype-phenotype relationships at seven loci in three genes (DRD4, SERT, and MC1R). We tested for association between these loci and traits of 180 females having extreme shy-bold phenotypes using mixed-effects models. One locus within SERT was significantly associated with boldness (effect size = 0.189) and a second locus within DRD4 with weaning mass (effect size = 0.232). Altogether, genotypes explained 6.52-13.66% of total trait variation. Our study substantiates SERT and DRD4 as important determinants of behaviour, and provides unique insight into the molecular mechanisms underlying maternal performance variation in a marine predator.

Assessments of population genetic structure have become an increasing focus as they can provide valuable insight into patterns of migration and gene flow. structure, the most highly cited of several clustering-based methods, was developed to provide robust estimates without the need for populations to be determined a priori. structure introduces the problem of selecting the optimal number of clusters, and as a result, the ΔK method was proposed to assist in the identification of the "true" number of clusters. In our review of 1,264 studies using structure to explore population subdivision, studies that used ΔK were more likely to identify K = 2 (54%, 443/822) than studies that did not use ΔK (21%, 82/386). A troubling finding was that very few studies performed the hierarchical analysis recommended by the authors of both ΔK and structure to fully explore population subdivision. Furthermore, extensions of earlier simulations indicate that, with a representative number of markers, ΔK frequently identifies K = 2 as the top level of hierarchical structure, even when more subpopulations are present. This review suggests that many studies may have been over- or underestimating population genetic structure; both scenarios have serious consequences, particularly with respect to conservation and management. We recommend publication standards for population structure results so that readers can assess the implications of the results given their own understanding of the species biology.

This is the peer reviewed version of the following article: Cullingham, C.I., Miller, J.M., Peery, R.M., Dupuis, J.R., Malenfant, R.M., Gorrell, J.C., & Janes, J.K. (2020). Confidently identifying the correct K value using the ΔK method: When does K=2? Molecular Ecology, 29(5), 862-869, which has been published in final form at http://doi.org/10.1111/mec.15374. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions., Populations delineated based on genetic data are commonly used for wildlife conservation and management. Many studies use the program structure combined with the ΔK method to identify the most probable number of populations (K). We recently found K = 2 was identified more often when studies used ΔK compared to studies that did not. We suggested two reasons for this: hierarchical population structure leads to underestimation, or the ΔK method does not evaluate K = 1 causing an overestimation. The present contribution aims to develop a better understanding of the limits of the method using one, two and three population simulations across migration scenarios. From these simulations we identified the “best K” using model likelihood and ΔK. Our findings show that mean probability plots and ΔK are unable to resolve the correct number of populations once migration rate exceeds 0.005. We also found a strong bias towards selecting K = 2 using the ΔK method. We used these data to identify the range of values where the ΔK statistic identifies a value of K that is not well supported. Finally, using the simulations and a review of empirical data, we found that the magnitude of ΔK corresponds to the level of divergence between populations. Based on our findings, we suggest researchers should use the ΔK method cautiously; they need to report all relevant data, including the magnitude of ΔK, and an estimate of connectivity for the research community to assess whether meaningful genetic structure exists within the context of management and conservation.

Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying FST. However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.

Chronic wasting disease (CWD) is a contagious prion disease of cervids. The infectious agent is shed from animals at the preclinical and clinical stages of disease where it persists in the environment as a reservoir of CWD infectivity. In this study, we demonstrate that long-term incubation of CWD prions (generated from tg-mice infected with deer or elk prions) with illite, montmorillonite (Mte) and whole soils results in decreased recovery of PrPCWD, suggesting that binding becomes more avid and irreversible with time. This continual decline of immunoblot PrPCWD detection did not correlate with prion infectivity levels. Bioassay showed no significant differences in incubation periods between mice inoculated with 1% CWD brain homogenate (BH) and with the CWD-BH pre-incubated with quartz or Luvisolic Ae horizon for 1 or 30 weeks. After 55 weeks incubation with Chernozem and Luvisol, bound PrPCWD was not detectable by immunoblotting but remained infectious. This study shows that although recovery of PrPCWD bound to soil minerals and whole soils with time become more difficult, prion infectivity is not significantly altered. Detection of prions in soil is, therefore, not only affected by soil type but also by length of time of the prion&ndash, soil interaction.

Chronic wasting disease (CWD), an environmentally transmissible, fatal prion disease is endemic in North America, present in South Korea and has recently been confirmed in northern Europe. The expanding geographic range of this contagious disease of free-ranging deer, moose, elk and reindeer has resulted in increasing levels of prion infectivity in the environment. Soils are involved in CWD horizontal transmission, acting as an environmental reservoir, and soil mineral and organic compounds have the ability to bind prions. Upper horizons of soils are usually enriched with soil organic matter (SOM), however, the role of SOM in prion conservation and mobility remains unclear. In this study, we show that incubation of PrPCWD with humic acids (HA), a major SOM compound, affects both the molecular weight and recovery of PrPCWD. Detection of PrPCWD is reduced as HA concentration increases. Native HA extracted from pristine soils also reduces or entirely eliminates PrPCWD signal. Incubation of CWD prions with HA significantly increased incubation periods in tgElk mice demonstrating that HA can reduce CWD infectivity., Author summary Chronic wasting disease (CWD) is a contagious prion disease affecting several species of captive and wild cervids. Environmental prion contamination plays a major role in increasing incidence of CWD, with CWD infectivity being released into the environment by decaying carcasses, or shedding of biological fluids including urine, feces, and saliva. Horizontal transmission of CWD involves soils as an environmental reservoir of infectivity. Here, we tested the role of a soil organic matter compound, humic acid, for its ability to bind CWD prions and impact infectivity. A wide range of humic acid concentrations were examined representing the extensive spectrum of humic acid levels present in native soils. We found that incubation of CWD prions with high concentrations of humic acids (>2.5 g L-1) decreases the both CWD-prion signal and infectivity, whereas lower levels of humic acids did not significantly impact protein stability or infectivity. Our study provides new insights into soil-prion interactions, prions persistence in soil, and their bioavailability to grazing animals.

In the Canadian Rocky Mountains, the gray wolf ( Canis lupus ) has experienced range contractions and expansions, which can greatly affect pack stability as well as population structure. In addition, this area has a highly heterogeneous landscape that may form barriers to dispersal. To understand factors affecting pack structure and large-scale gene flow across the Rocky Mountains, we examined wolf genetic structure using 1,981 noninvasive and invasively collected samples. We sampled over 44 packs in Alberta and British Columbia and, from these, identified 540 individuals based on 12 microsatellites. Relatedness of individuals within packs was greater than between packs, and female relatedness was greater than males suggesting strong pack structure and female philopatry. Relatedness within packs was greater near major roads suggesting decreased dispersal from natal packs with proximity to roads. Across the study area, 2 significantly differentiated genetic clusters were identified, corresponding to a north/south split. Landcover distance was a significant correlate for 2 of 4 genetic distance measures, where packs in the north were in areas of dense coniferous forest, while packs in the south were primarily in open coniferous forest. These landcover differences suggest natal associations or could relate to prey distribution. Fine-scale investigation of pack dynamics across this continuous distribution, together with large-scale estimators of population structure, highlights different drivers of gene flow at the pack and population level.

Animal social behaviour can have important effects on the long-term dynamics of diseases. In particular, preferential spatial relationships between individuals can lead to differences in the rates of disease spread within a population. We examined the concurrent influence of genetic relatedness, sex, age, home range overlap, time of year, and prion disease status on proximal associations of adult Rocky Mountain mule deer (Odocoileus hemionus hemionus) in a chronic wasting disease endemic area. We also quantified the temporal stability of these associations across different sex, age, and disease status classes. We used three years of high frequency telemetry data from 74 individuals to record encounters within 25 m of each other, and to calculate seasonal home range overlap measured by volume of intersection (VI). The strength of pairwise spatial association between adult mule deer was independent of genetic relatedness, age and disease status. Seasonal variation in association strength was not consistent across years, perhaps due to annual changes in weather conditions. The influence of home range overlap on association strength varied seasonally, whereby associations were stronger in pre-rut and fawning than in the rest of the seasons. The sexes of individuals also interacted with both VI and season. At increasing levels of VI, associations were stronger between females than between males and between females and males. The strongest associations in pre-rut were between males, while the strongest in rut were between females and males. The temporal stability of associations was markedly dependant on the sex and the diagnosis of the associating pair. Our findings highlight the importance of considering concurrent effects of biological and environmental factors when seeking to understand the role of social preference in behavioural ecology and disease spread. Applying this knowledge in epidemiological modelling will shed light on the dynamics of disease transmission among mule deer.

In an attempt to slow or reverse the loss of biodiversity, conservation translocations have been implemented to restore wild populations of dwindling or extirpated species and have increased concurrently with multiplying threats to biodiversity. Here, we reviewed 554 translocation case studies from around the world in an effort to assess how frequently studies monitor populations post-translocation, and if performed, for what length of time monitoring was done. Our secondary objectives included investigating shifts in reintroduction research trends, including whether species of certain conservation statuses (global and local) were more likely to be subjects of translocation efforts, the factors cited as reasons for initial species declines, and the causes of failed translocation attempts. We found that the majority of studies conducted post-release monitoring for a period of 1–4 years, and the highest proportion of failures occurred within the first four years. Overall, the most important factor contributing to failure was the causes of initial decline of the species, and there was no evidence that success rates have increased over the past decade despite increasing knowledge in the field. Many translocations were focused on locally extirpated species that had low risk of global extinction, especially in North America, Europe, and Oceania. The driving forces of failed translocations varied with predation, management issues, and habitat factors as common challenges. Future programs should focus on addressing the initial cause of decline and ensure that resources are in place to support a minimum of four years of post-release monitoring to help ensure a successful outcome.

Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Analisis Temporal de la Estructura Genetica para Evaluar la Dinamica Poblacional de Zorros (Vulpes velox) Reintroducidos Resumen Las reintroducciones cada vez se usan mas para restablecer especies, pero la escasez de monitoreos post-liberacion a largo plazo ha limitado el entendimiento de cuando y si las poblaciones viables persisten subsecuentemente. Realizamos analisis geneticos temporales de poblaciones reintroducidas de zorros (Vulpes velox) en Canada (Alberta y Saskatchewan) y en los Estados Unidos (Montana). Usamos muestras colectadas con 4 anos de diferencia, a 17 anos del inicio de la reintroduccion, y 3 anos despues de la conclusion de las liberaciones. Para evaluar el exito del programa, obtuvimos el genotipo de 340 muestras de pelo, tomadas del rango conocido en el 2000 y 2001, y el 2005 y 2006 en 7 loci microsatelites. Comparamos la diversidad, el tamano efectivo de la poblacion y la conectividad genetica a traves del tiempo en cada poblacion. La diversidad se mantuvo estable a traves de tiempo y hubo evidencia del incremento en tamano de la poblacion efectiva. Determinamos la estructura de la poblacion en ambos periodos despues de corregir diferencias en los tamanos de muestra. La distribucion geografica de estas poblaciones correspondio aproximadamente con los lugares originales de liberacion, lo que sugiere que estos sitios tienen efectos residuales sobre la estructura de la poblacion. Sin embargo, dado que ambos sitios de reintroduccion tenian poblaciones originarias similares, la fragmentacion de habitat debida a cultivos, puede asociarse con la estructura poblacional que hallamos. Aunque nuestros resultados senalan la existencia de poblaciones crecientes y estables, analisis futuros de conectividad garantizan asegurar que ambas poblaciones no esten sujetas a efectos negativos de poblaciones pequenas. Nuestros resultados demuestran la importancia de anos de muestreo multiple para capturar en su totalidad las dinamicas de poblacion de poblaciones reintroducidas.

Accurate stock identification is important for forest management, yet this can be a challenge for tree species that hybridize naturally. Species discriminating molecular markers provide a means to identify stock with high accuracy. In Canada, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb) form a large hybrid zone in Alberta and Northwest Territories; within this hybrid zone, the identification of parentals and hybrids is difficult due to an overlap in morphological characteristics. Pure and hybrid ancestry can be resolved using microsatellite markers, but these are difficult and costly to type. We have developed a panel of SNP markers using 454 transcriptome sequence data that are more cost-effective, easier to score, and have greater discriminating power for differentiating species than microsatellites. Our SNP panel provides accurate and cost-efficient forest seed stock identification and will thereby facilitate reforestation and our pipeline can be applied to other hybrid systems globally.

[Aim] Understanding colonization dynamics is crucial for management of invasive species. We compare the genetic structure of historical (Central Europe) and recent (Spain) invasive populations with native and captive populations of the North American raccoon (Procyon lotor). Our aim was to analyse the effects of colonization age on genetic population structure, understand the role of captive individuals as potential founders and test the role of rivers for the dispersal of the species., [Location] North America, Spain, Central Europe., [Methods] We genotyped wild‐caught raccoons from Spain and Central Europe (N = 596), zoos (N = 57) and the native range (N = 153) at 16 microsatellite loci and sequenced a mitochondrial DNA fragment (Control Region). We analysed population genetic structuring with Bayesian assignment methods and a FCA. In a landscape genetic analysis, we tested the effect of waterways in the dispersal of the species., [Results] We detected 16 genetic clusters (in baps), supporting the hypothesis of multiple introductions and ongoing releases in the invasive range. The native population showed nearly no genetic structure, the Central European clusters showed signals of admixture, whereas the Spanish clusters were clearly separated. Admixture of the Central European clusters was probably caused by recent contact of populations with different origin. The landscape genetic analysis showed that rivers represent neither barriers nor corridors in Central Europe., [Main conclusions] As the Spanish populations are genetically more diverse than the Central European, we expect increased within‐population diversity when the still isolated populations merge after range expansion. As our results provide evidence for gene flow between zoos and free‐ranging populations, better control of pet trade is essential in the management efforts concerning this invasive species. Our study shows that genetic analyses can help to reconstruct invasion processes, which is important for better understanding and effective management of invasive species., The work was funded by the German Science Foundation (DFG, GRK 1319) as part of the interdisciplinary graduate school ‘Cooperation of Science and Jurisprudence in Improving Development and Use of Standards for Environmental Protection – Strategies for Risk Assessment and Management’.

Understanding the physical and genetic structure of hybrid zones can illuminate factors affecting their formation and stability. In north‐central Alberta, lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) and jack pine (Pinus banksiana Lamb) form a complex and poorly defined hybrid zone. Better knowledge of this zone is relevant, given the recent host expansion of mountain pine beetle into jack pine. We characterized the zone by genotyping 1998 lodgepole, jack pine, and hybrids from British Columbia, Alberta, Saskatchewan, Ontario, and Minnesota at 11 microsatellites. Using Bayesian algorithms, we calculated genetic ancestry and used this to model the relationship between species occurrence and environment. In addition, we analyzed the ancestry of hybrids to calculate the genetic contribution of lodgepole and jack pine. Finally, we measured the amount of gene flow between the pure species. We found the distribution of the pine classes is explained by environmental variables, and these distributions differ from classic distribution maps. Hybrid ancestry was biased toward lodgepole pine; however, gene flow between the two species was equal. The results of this study suggest that the hybrid zone is complex and influenced by environmental constraints. As a result of this analysis, range limits should be redefined.

Irruptive forest insect pests cause considerable ecological and economic damage, and their outbreaks have been increasing in frequency and severity. We use a phylogeographic approach to understand the location and progression of an outbreak by the MPB (Dendroctonus ponderosae Hopkins), an irruptive bark beetle that has caused unprecedented damage to lodgepole pine forests in western North America and is poised to expand its range across the boreal forest. We sampled MPB populations across British Columbia and Alberta and used phylogeographic methods to describe lineage diversification, characterize population structure, investigate expansion dynamics, and identify source populations of the outbreak. Using 1181 bp of mitochondrial DNA sequence from 267 individuals, we found high haplotype diversity, low nucleotide diversity, and limited lineage diversification. The overall pattern was consistent with isolation by distance at a continental scale, and with reduced diversity and population structure in the northerly, outbreak regions. Post-Pleistocene expansion was detected, however more recent expansion signals were not detected, potentially due to the size and rapid rate of range expansion. Based on the limited genetic structure, there were likely multiple source populations in southern British Columbia, although the magnitude of the demographic expansion and rate of spread have obscured the signature of these source populations. Our data highlight the need for caution in interpreting phylogeographic results for species with similar demographics.

The current epidemic of the mountain pine beetle (MPB), an indigenous pest of western North American pine, has resulted in significant losses of lodgepole pine. The leading edge has reached Alberta where forest composition shifts from lodgepole to jack pine through a hybrid zone. The susceptibility of jack pine to MPB is a major concern, but there has been no evidence of host-range expansion, in part due to the difficulty in distinguishing the parentals and their hybrids. We tested the utility of a panel of microsatellite loci optimized for both species to classify lodgepole pine, jack pine and their hybrids using simulated data. We were able to accurately classify simulated individuals, and hence applied these markers to identify the ancestry of attacked trees. Here we show for the first time successful MPB attack in natural jack pine stands at the leading edge of the epidemic. This once unsuitable habitat is now a novel environment for MPB to exploit, a potential risk which could be exacerbated by further climate change. The consequences of host-range expansion for the vast boreal ecosystem could be significant.

To successfully manage wildlife diseases, it is necessary to understand factors that influence spread. One approach is to analyze host movement and social structure, as these behaviors can be associated with the probability of transmission. Some populations of mule deer ( Odocoileus hemionus hemionus (Rafinesque, 1817)) in western Canada are infected with chronic wasting disease (CWD), a transmissible and fatal neurodegenerative disease. We used population analysis of spatial genetic structure of mule deer at broad and local scales to understand factors that influence spread. We genotyped 2535 mule deer sampled from Alberta, Saskatchewan, and portions of British Columbia using 16 microsatellite loci. We found weak genetic structure at broad spatial scales (overall FST = 0.008) that was well defined by geographic distance, indicating the risk of CWD spread from the focus of infection will decline gradually with increasing distance, but there are no barriers to the spread over time. At the local scale of approximately 2 km, elevated relatedness among CWD-infected individuals suggests transmission rates within social groups. Sex-biased spatial autocorrelation in genetic relatedness also indicates that female philopatry underlies the social structure, and therefore transmission among relatives is potentially driving local disease persistence.

Chronic wasting disease is a transmissible spongiform encephalopathy of cervids, similar to sheep scrapie that has only recently been detected in wild populations of white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus hemionus) in western Canada. Relatively little is known about local transmission dynamics of the disease or the potential for long-distance spread. We analysed the population genetic structure of over 2000 white-tailed deer sampled from Alberta, British Columbia, and Saskatchewan using microsatellite profiles and mtDNA sequencing to assess the relative risk of disease spread. There was very little differentiation among subpopulations and a weak trend of increasing differentiation with geographic distance. This suggests that the potential for long-distance disease spread through the dispersal of infected individuals is possible, yet the risk of spread should gradually diminish with distance from infection foci. Within subpopulations, females were more related than expected by chance (R > 0) within a radius of approximately 500 m. Sex-biased philopatry and social interactions among related females may facilitate local disease transmission within social groups. Local herd reduction may therefore be an effective tool for reducing the disease prevalence when implemented at the appropriate spatial scale.

Genetic profiling using fecal samples collected noninvasively in the wild can provide managers with an alternative to live-trapping. However, before embarking on a large-scale survey, feasibility of this methodology should be assessed for the focal species. Costs associated with fecal genotyping can be high because of the need for multiple amplifications to prevent and detect errors. Assessing the relative amount of target DNA before genotyping means samples can be eliminated where error rates will be high or amplification success will be low, thereby reducing costs. We collected fecal samples from an endangered population of swift fox (Vulpes velox) and employed target-DNA quantification and a screening protocol to assess sample quality before genetic profiling. Quantification was critical in identifying samples of low quality (68%

A landscape genetic simulation modelling approach is used to understand factors affecting raccoon rabies disease spread in southern Ontario, Canada. Using the Ontario Rabies Model, we test the hypothesis that landscape configuration (shape of available habitat) affects dispersal, as indicated by genetic structuring. We simulated range expansions of raccoons from New York into vacant landscapes in Ontario, in two areas that differed by the presence or absence of a landscape constriction. Our results provide theoretical evidence that landscape constriction acts as a vicariant bottleneck. We discuss implications for raccoon rabies spread.

Epidemiological models are useful tools for management to predict and control wildlife disease outbreaks. Dispersal behaviours of the vector are critical in determining patterns of disease spread, and key variables in epidemiological models, yet they are difficult to measure. Raccoon rabies is enzootic over the eastern seaboard of North America and management actions to control its spread are costly. Understanding dispersal behaviours of raccoons can contribute to refining management protocols to reduce economic impacts. Here, estimates of dispersal were obtained through parentage and spatial genetic analyses of raccoons in two areas at the front of the raccoon rabies epizootic in Ontario; Niagara (N = 296) and St Lawrence (N = 593). Parentage analysis indicated the dispersal distance distribution is highly positively skewed with 85% of raccoons, both male and female, moving < 3 km. The tail of this distribution indicated a small proportion (< 4%) moves more than 20 km. Analysis of spatial genetic structure provided a similar assessment as the spatial genetic correlation coefficient dropped sharply after 1 km. Directionality of dispersal would have important implications for control actions; however, evidence of directional bias was not found. Separating the data into age and sex classes the spatial genetic analyses detected female philopatry. Dispersal distances differed significantly between juveniles and adults, while juveniles in the Niagara region were significantly more related to each other than adults were to each other. Factors that may contribute to these differences include kin association, and spring dispersal. Changes to the timing and area covered by rabies control operations in Ontario are indicated based on these dispersal data.

Recently, an extensive study of 2,748 polar bears (Ursus maritimus) from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago—an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study’s main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1) highly unbalanced sample sizes and large amounts of systematically missing data; (2) incorrect calculation of FST and of significance levels; (3) misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and—importantly—we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada’s expected last sea-ice refugium. Although polar bears’ abundance, distribution, and population structure will certainly be negatively affected by ongoing—and increasingly rapid—loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

Primers have been developed for nine polymorphic tetranucleotide microsatellite loci isolated from the swift fox (Vulpes velox). These can be amplified in three multiplex reactions and all loci can be scored easily and without ambiguity. The number of alleles per locus ranged from three to 14 and the overall heterozygosities ranged from 0.54 to 1.00. All loci were in Hardy-Weinberg equilibrium, but two loci were in linkage disequilibrium. These loci will be used to monitor endangered swift fox populations on the Canadian prairies.

We have isolated and characterized 12 polymorphic tetranucleotide microsatellite loci in the raccoon (Procyon lotor). Three multiplex panels comprising the 12 loci were developed and 80 individuals from southeastern and western Ontario were genotyped; allele sizes were assigned without difficulty. One locus isolated was identified as an X-linked marker. The number of alleles per locus ranged from six to 25 with the average heterozygosity ranging from 0.674 to 0.925. These loci will be used to characterize raccoon population structure across North America, and the data used to further understand the spread of raccoon rabies.

Lodgepole pine (Pinus contorta var. latifolia) and jack pine (Pinus banksiana) hybridize in western Canada, an area of recent mountain pine beetle range expansion. Given the heterogeneity of the environment, and indications of local adaptation, there are many unknowns regarding the response of these forests to future outbreaks. To better understand this we aim to identify genetic regions that have adaptive potential. We used data collected on 472 single nucleotide polymorphism (SNP) loci from 576 tree samples collected across 13 lodgepole pine-dominated sites and four jack pine-dominated sites. We looked at the relationship of genetic diversity with the environment, and we identified candidate loci using both frequency-based (arlequin and bayescan) and correlation-based (matsam and bayenv) methods. We found contrasting relationships between environmental variation and genetic diversity for the species. While we identified a number of candidate outliers (34 in lodgepole pine, 25 in jack pine, and 43 interspecific loci), we did not find any loci in common between lodgepole and jack pine. Many of the outlier loci identified were correlated with environmental variation. Using rigorous criteria we have been able to identify potential outlier SNPs. We have also found evidence of contrasting environmental adaptations between lodgepole and jack pine which could have implications for beetle spread risk.

Forest trees exhibit a remarkable range of adaptations to their environment, but as a result of frequent and long-distance gene flow, populations are often only weakly differentiated. Lodgepole and jack pine hybridize in western Canada, which adds the opportunity for introgression through hybridization to contribute to population structure and (or) adaptive variation. Access to large sample size, high density SNP datasets for these species would improve our ability to resolve population structure, parameterize introgression, and separate the influence of demography from adaptation. To accomplish this, 454 transcriptome reads for lodgepole and jack pine were assembled using Newbler and MIRA, the assemblies mined for SNPs, and 1536 SNPs were selected for typing on lodgepole pine, jack pine, and their hybrids (N = 536). We identified population structure using both Bayesian clustering and discriminate analysis of principle components. Introgressed SNP loci were identified and their influence on observed population structure was assessed. We found that introgressed loci resulted in increased differentiation both within lodgepole and jack pine populations. These findings are timely given the recent mountain pine beetle population expansion in the hybrid zone, and will facilitate future studies of adaptive traits in these ecologically important species.

Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host-parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever-changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in the light of temporal population exposure to RRV (0-60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures.

Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos.

Irruptive forest insect pests cause considerable ecological and economic damage, and their outbreaks have been increasing in frequency and severity. We use a phylogeographic approach to understand the location and progression of an outbreak by the MPB (Dendroctonus ponderosae Hopkins), an irruptive bark beetle that has caused unprecedented damage to lodgepole pine forests in western North America and is poised to expand its range across the boreal forest. We sampled MPB populations across British Columbia and Alberta and used phylogeographic methods to describe lineage diversification, characterize population structure, investigate expansion dynamics, and identify source populations of the outbreak. Using 1181 bp of mitochondrial DNA sequence from 267 individuals, we found high haplotype diversity, low nucleotide diversity, and limited lineage diversification. The overall pattern was consistent with isolation by distance at a continental scale, and with reduced diversity and population structure in the northerly, outbreak regions. Post-Pleistocene expansion was detected, however more recent expansion signals were not detected, potentially due to the size and rapid rate of range expansion. Based on the limited genetic structure, there were likely multiple source populations in southern British Columbia, although the magnitude of the demographic expansion and rate of spread have obscured the signature of these source populations. Our data highlight the need for caution in interpreting phylogeographic results for species with similar demographics.

The current epidemic of the mountain pine beetle (MPB), an indigenous pest of western North American pine, has resulted in significant losses of lodgepole pine. The leading edge has reached Alberta where forest composition shifts from lodgepole to jack pine through a hybrid zone. The susceptibility of jack pine to MPB is a major concern, but there has been no evidence of host-range expansion, in part due to the difficulty in distinguishing the parentals and their hybrids. We tested the utility of a panel of microsatellite loci optimized for both species to classify lodgepole pine, jack pine and their hybrids using simulated data. We were able to accurately classify simulated individuals, and hence applied these markers to identify the ancestry of attacked trees. Here we show for the first time successful MPB attack in natural jack pine stands at the leading edge of the epidemic. This once unsuitable habitat is now a novel environment for MPB to exploit, a potential risk which could be exacerbated by further climate change. The consequences of host-range expansion for the vast boreal ecosystem could be significant.

Glacial cycles have played a dominant role in shaping the genetic structure and distribution of biota in northwestern North America. The two major ice age refugia of Beringia and the Pacific Northwest were connected by major mountain chains and bordered by the Pacific Ocean. As a result, numerous refugial options were available for the regions taxa during glacial advances. We reviewed the importance of glaciations and refugia in shaping northwestern North America’s phylogeographic history. We also tested whether ecological variables were associated with refugial history. The recurrent phylogeographic patterns that emerged were the following: (i) additional complexity, i.e. refugia within refugia, in both Beringia and the Pacific Northwest; and (ii) strong evidence for cryptic refugia in the Alexander Archipelago and Haida Gwaii, the Canadian Arctic and within the ice-sheets. Species with contemporary ranges that covered multiple refugia, or those with high dispersal ability, were significantly more likely to have resided in multiple refugia. Most of the shared phylogeographic patterns can be attributed to multiple refugial locales during the last glacial maximum or major physiographic barriers like rivers and glaciers. However, some of the observed patterns are much older and appear connected to the orogeny of the Cascade-Sierra chain or allopatric differentiation during historic glacial advances. The emergent patterns from this review suggest we should refine the classic Beringian-southern refugial paradigm for northwestern North American biota and highlight the ecological and evolutionary consequences of colonization from multiple refugia.

The correlation of landscape features with genetic discontinuities reveals barriers to dispersal that can contribute to understanding present and future spread of wildlife diseases. This knowledge can then be used for targeting control efforts. The impact of natural barriers on raccoon dispersal was assessed through genetic analysis of samples from two regions, Niagara (N = 666) and St. Lawrence (N = 802). These areas are transected by major rivers and are at the northern front of a raccoon rabies epizootic. Genetic clusters were identified in each region using Bayesian clustering algorithms. In the Niagara region, two clusters were identified corresponding to either side of the Niagara River. For the St. Lawrence region, spatially congruent clusters were not identified, despite the presence of the intervening St. Lawrence River. These genetic data are consistent with raccoon rabies incidence data where rabies has been detected across the St. Lawrence River in Ontario while no cases have been detected in Ontario across the Niagara River. This is despite expectations of rabies incidence in Niagara before the St. Lawrence based on the progression of rabies from New York. The results from the two regions suggest different permeabilities to raccoons between New York and Ontario that may be attributed to the rivers. However, other factors have also been explored that could contribute to this difference between these study sites including the shape of the landscape and resource distribution.

Landscape barriers influence movement patterns of animals, which in turn, affect spatio-temporal spread of infectious wildlife disease. We compare genetic data from computer simulations to those acquired from field samples to measure the effect of a landscape barrier on raccoon (Procyon lotor) movement, enabling risk assessment of raccoon rabies disease spread across the Niagara River from New York State into Ontario, an area currently uninfected by rabies. An individual-based spatially explicit model is used to simulate the expansion of a raccoon population to cross the Niagara River, for different permeabilities of the river to raccoon crossings. Since the model records individual raccoon genetics, the genetic population structure of neutral mitochondrial DNA haplotypes are characterised in the expanding population, every 25 years, using a genetic distance measure, phi ST, Mantel tests and a gene diversity measure. The river barrier effect is assessed by comparing genetic measures computed from model outputs to those calculated from 166 raccoons recently sampled from the same landscape. The "best fit" between modelled scenarios and field data indicate the river prevents 50% of attempts to cross the river. Founder effects dominated the colonizing genetic population structure, and, as the river barrier effect increased, its genetic diversity decreased. Using gene flow to calibrate the effect of the river as a barrier to movement provides an estimate of the effect of a river in reducing the likelihood of cross-river infection. Including individual genetic markers in simulation modelling benefits investigations of disease spread and control.

Background Lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia) is found in western North America, extending from the Yukon into British Columbia and Washington, and along the Rocky Mountains and eastern slopes to Colorado [1]. Jack pine (Pinus banksiana Lamb.) is a closely related species found east of the Rockies, mainly in Canada’s boreal forest from the Northwest Territories to Quebec [1]. Lodgepole and jack pine ranges overlap in northern Alberta and the Northwest Territories, where these species hybridize (Fig. 1). In the absence of reliable molecular markers, morphological characteristics are commonly used to distinguish lodgepole pine, jack pine and hybrids. However, hybrids and pure species can be difficult to visually distinguish, particularly at the presumed periphery of the hybrid zone, which is poorly described. Mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins) is indigenous to western North America. In the current MPB outbreak, more than 14 million hectares of mainly lodgepole pine forests have sustained MPB-caused mortality in British Columbia alone [2]. Following MPB long range dispersal into northwestern Alberta in 2006, MPB has continued its apparently unprecedented eastward spread into the lodgepole x jack pine hybrid zone of Alberta (Fig. 1). To better define this hybrid zone, we developed microsatellite and SNP markers that distinguish the pure species from hybrids. We then used the microsatellite markers to test the hypothesis that the MPB epidemic has spread into jack pine.