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Lyme disease is the most prevalent vector-borne disease in north temperate areas worldwide, with the majority of cases reported in the northeastern United States. The transmission cycle involves ticks, deer, small mammalian hosts such as mice, and numerous other species. Levi et al. (2012) suggested that Canis latrans (Coyote) abundance and Vulpes vulpes (Red Fox) scarcity are strong predictors of Lyme disease cases in eastern North America, with Odocoileus virginianus (White-tailed Deer) abundance being less important. This suggestion was based on correlations of disease dynamics with human harvests of canids, as it has been suggested that Red Foxes occur at a lower abundance because of Coyote predation. Because Red Foxes are more effective predators of small mammals, the authors of that work contend that the lower Red Fox abundance results in an increase in the incidence of Lyme disease. This paper re-examines the evidence used by Levi at al. (2012) to reach their conclusions. We address the following points: 1) Levi et al. did not provide data on rodent populations or Lyme disease incidence; 2) Coyotes eat rodents, so a Coyote-induced reduction of Red Fox populations might not result in increased rodent populations; 3) Coyote harvests are poor indicators of Coyote abundance; 4) both Red Fox numbers and rodent numbers fluctuate dramatically due to factors such as disease and weather; 5) some of the data used by Levi et al. (2012) were from regions with western Coyotes, while other data were from areas with hybrid eastern Coyotes, thus confounding the situation; and 6) Levi et al. did not consider important alternative hypotheses, such as habitat fragmentation and climate change. Additionally, the historical dynamics of the Lyme disease system are unknown given that Canis lupus lycaon (= Canis lycaon) (Eastern Wolf) and Urocyon cinereoargenteus (Gray Foxes) originally lived in most of the northeast, while Red Foxes and Coyotes were historically absent from most of the area. We suggest proceeding with caution before concluding that the presence of Coyotes (or the reduction of Red Foxes) is the primary cause of increased incidence of Lyme disease cases in the eastern United States. [ABSTRACT FROM AUTHOR]

Peripheral populations of widespread species are often considered unworthy of conservation efforts; however, they may be adapted to the conditions found at the range edge and are therefore important to the future evolutionary potential of the species. Blanchard’s Cricket Frog (Acris blanchardi Harper, 1947) is widespread and abundant throughout the central United States, but is declining at the northern edge of its range. To assess the distinctiveness and conservation value of the northern populations, we investigated the spatial genetic structure and phylogeography of this anuran using mitochondrial control region sequences. Analysis of 479 individuals identified 101 haplotypes, with relatively low nucleotide diversity. Two moderately divergent clades were found. One was restricted to the southwest, which was probably a refugium during the Pleistocene, whereas the other occurred primarily across the north and is likely the result of postglacial colonization. The genetic distinctiveness of northern populations indicates the potential for adaptive differences of individuals in this region relative to those in the south. We therefore conclude that conservation efforts are justified for the declining northern populations of Blanchard’s Cricket Frog, and we use the spatial genetic structure described here to develop specific recommendations for this anuran. On considère souvent que les populations périphériques d’espèces à large répartition ne valent pas les efforts de conservation; elles peuvent, cependant, être adaptées aux conditions qui prévalent à la périphérie de l’aire de répartition et ainsi être importantes pour le potentiel évolutif futur de l’espèce. La rainette grillon de Blanchard (Acris blanchardi Harper, 1947) est une espèce largement répandue et abondante dans tout le centre des États-Unis, mais elle est en déclin à la marge nord de son aire de répartition. Afin d’évaluer la particularité et la valeur de conservation des populations nordiques, nous avons étudié la structure génétique et la phylogéographie de cet anoure à l’examen des séquences de la région de contrôle mitochondriale. Une analyse de 479 individus a révélé l’existence de 101 haplotypes, avec une diversité relativement basse des nucléotides. Il existe deux clades à divergence moyenne. L’un est restreint à la région sud-ouest, qui a probablement servi de refuge au pléistocène, alors que l’autre est surtout répandu dans tout le nord et résulte vraisemblablement de la colonisation postglaciaire. La différenciation génétique des populations nordiques laisse croire à un potentiel de différences adaptives chez les animaux de cette région par rapport aux animaux du sud. Nous concluons qu’il est justifié de déployer des efforts de conservation pour les populations nordiques déclinantes de la rainette grillon de Blanchard; nous utilisons la structure génétique spatiale décrite ici pour mettre de l’avant des recommandations spécifiques au sujet de cet anoure. [ABSTRACT FROM AUTHOR]

Mitochondrial heteroplasmy has been identified in a variety of species and can result from either paternal leakage, whereby sperm mitochondria enter the ova during fertilization, or more commonly by the “survival” and proliferation of mutant variants within an organism. From an evolutionary perspective, this process represents the generation of new mitochondrial diversity within a species. Although this has been documented in some mammalian species, it has been reported from relatively few wild mammalian populations and in no wild nonhuman population has the transfer and segregation of mitochondrial heteroplasmy been tracked through multiple generations. We report on the first case of the identification and tracking of mitochondrial control region heteroplasmy through 3 generations in the North Atlantic right whale, Eubalaena glacialis. We also identify the full segregation to the mutant variant within a single generation and thus the development of a new haplotype (haplotype G) in a maternal lineage of this endangered species. Witnessed here is the generation of mitochondrial diversity in a genetically depauperate species. [ABSTRACT FROM PUBLISHER]

Background: A clear association of amino acid variation in the prion protein gene (PRNP) with susceptibility and resistance to classical scrapie exists in sheep, but not in goats. In this study we examined DNA sequence variation in the PRNP of 149 animals from two scrapie-infected herds of Saanen dairy goats, and identified 6 nonsynonymous variants in the coding region. Results: In the larger herd, all of the 54 scrapie-affected goats tested had at least one allele with the arginine (R) codon at position 211, with 52 being homozygous for that variant. No animal homozygous for the glutamine (Q) codon at 211 were affected and only two heterozygotes (R/Q) were affected. A weak association was found at position 146 and no significant associations were found with amino acid variation at the remaining four variant positions (142, 143, 222 and 240), however, the allelic variation was low. Similar patterns were observed in the second scrapie-affected herd. Conclusion: We also evaluated previous studies on goat herds affected with scrapie and this relationship of R susceptibility and Q resistance at 211 was present independent of the genotypes at the other positions including 222. The fact that glutamine at 211 provides a significant protective property to scrapie irrespective of the other positions could be important for breeding strategies aimed at improving herd resistance to scrapie, while maintaining important productivity traits. [ABSTRACT FROM AUTHOR]

North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugf-DRB1 and 5 alleles were assigned to the locus Eug/-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with > 4 alleles) and at least 3 class I loci (with > 6 alleles). Class II sequences were significandy different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species. [ABSTRACT FROM AUTHOR]

North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species. [ABSTRACT FROM PUBLISHER]

In the absence of obvious barriers to dispersal microsatellite studies of vagile mammalian carnivores frequently find panmictic-like genetic structure over wide scales, whereas high levels of differentiation at much finer scales are detected with mitochondrial DNA (mtDNA). Given the maternal inheritance of mtDNA, these differences are often attributed to male-biased dispersal, remnants of postglacial range expansion, or both. Based on such contrasting results, it is not always clear how to delineate contemporary populations. We investigated the genetic structure of American black bears (Ursus americanus) over a wide geographic area (>1,700 km) that has no obvious physiogeographic barriers to gene flow. We analyzed a 315-base pair fragment of the mtDNA control region from 660 individual bears from 23 regions of Ontario, Canada. Relative to black bear studies based on nuclear data, mitochondrial analyses revealed much stronger patterns of genetic structure among regions (0.09 < FST < 0.44), even at small-scale intervals (<150 km), which likely reflects strong female philopatry combined with male-biased dispersal. The patterns of genetic differentiation among regions were consistent with previously described historical patterns in black bears, specifically the division of the species into 2 phylogeographic clades (coastal and continental). We confirmed that further subdivision of the continental clade occurs in a region where obvious physiogeographic barriers do not exist. We postulate that this small-scale differentiation can be explained by residual patterns from postglacial recolonization routes on either side of the Great Lakes. We suggest that it was maintained through extreme female philopatry due to habitat saturation following the postglacial geographic expansion. Based on our results, we propose that a combination of several molecular markers can be more useful in defining population units for conservation and management decisions than biparentally inherited microsatellites. [ABSTRACT FROM AUTHOR]

Interpretation of the genetic composition and taxonomic history of wolves in the western Great Lakes region (WGLR) of the United States has long been debated and has become more important to their conservation given the recent changes in their status under the Endangered Species Act. Currently, the two competing hypotheses on WGLR wolves are that they resulted from hybridization between (i) grey wolves ( Canis lupus) and western coyotes ( C. latrans) or (ii) between grey wolves and eastern wolves ( C. lycaon). We performed a genetic analysis of sympatric wolves and coyotes from the region to assess the degree of reproductive isolation between them and to clarify the taxonomic status of WGLR wolves. Based on data from maternal, paternal and bi-parental genetic markers, we demonstrate a clear genetic distinction between sympatric wolves and coyotes and conclude that they are reproductively isolated and that wolf-coyote hybridization in the WGLR is uncommon. The data reject the hypothesis that wolves in the WGLR derive from hybridization between grey wolves and western coyotes, and we conclude that the extant WGLR wolf population is derived from hybridization between grey wolves and eastern wolves. Grey-eastern wolf hybrids ( C. lupus × lycaon) comprise a substantial population that extends across Michigan, Wisconsin, Minnesota and western Ontario. These findings have important implications for the conservation and management of wolves in North America, specifically concerning the overestimation of grey wolf numbers in the United States and the need to address policies for hybrids. [ABSTRACT FROM AUTHOR]

Background: Phylogenetic studies of wild Canis species have relied heavily on the mitochondrial DNA control region (mtDNA CR) to infer species relationships and evolutionary lineages. Previous analyses of the CR provided evidence for a North American evolved eastern wolf (C. lycaon), that is more closely related to red wolves (C. rufus) and coyotes (C. latrans) than grey wolves (C. lupus). Eastern wolf origins, however, continue to be questioned. Therefore, we analyzed mtDNA from 89 wolves and coyotes across North America and Eurasia at 347 base pairs (bp) of the CR and 1067 bp that included the ATPase6 and ATPase8 genes. Phylogenies and divergence estimates were used to clarify the evolutionary history of eastern wolves, and regional comparisons of nonsynonomous to synonomous substitutions (dN/dS) at the ATPase6 and ATPase8 genes were used to elucidate the potential role of selection in shaping mtDNA geographic distribution. Results: We found high concordance across analyses between the mtDNA regions studied. Both had a high percentage of variable sites (CR = 14.6%; ATP = 9.7%) and both phylogenies clustered eastern wolf haplotypes monophyletically within a North American evolved lineage apart from coyotes. Divergence estimates suggest the putative red wolf sequence is more closely related to coyotes (DxyCR = 0.01982 ± 0.00494 SD; DxyATP = 0.00332 ± 0.00097 SD) than the eastern wolf sequences (DxyCR = 0.03047 ± 0.00664 SD; DxyATP = 0.00931 ± 0.00205 SD). Neutrality tests on both genes were indicative of the population expansion of coyotes across eastern North America, and dN/dS ratios suggest a possible role for purifying selection in the evolution of North American lineages. dN/dS ratios were higher in European evolved lineages from northern climates compared to North American evolved lineages from temperate regions, but these differences were not statistically significant. Conclusions: These results demonstrate high concordance between coding and non-coding regions of mtDNA, and provide further evidence that the eastern wolf possessed distinct mtDNA lineages prior to recent coyote introgression. Purifying selection may have influenced North American evolved Canis lineages, but detection of adaptive selection in response to climate is limited by the power of current statistical tests. Increased sampling and development of alternative analytical tools will be necessary to disentangle demographic history from processes of natural selection. [ABSTRACT FROM AUTHOR]

Abstract: The entire genome of a mid-Atlantic raccoon strain rabies virus (RRV) isolated in Canada was sequenced; this is the second North American wildlife rabies virus isolate to be fully characterized. The overall organization and length of the genome was similar to that of other lyssaviruses. The nucleotide sequence identity of the raccoon strain ranged between 32.7% and 85.0% when compared to other lyssaviruses, while the deduced amino acid sequence identity ranged between 22.9% and 94.2% with the nucleoprotein and polymerase being the most conserved. Notable features of RRV include the phosphoprotein''s four amino acid extension compared to most other rabies viruses, and a nucleotide substitution immediately prior to the normal start codon that results in an additional methionine at the beginning of the L protein. This is the first report of the RRV L gene sequence and its 2128 amino acid product. Rates of non-synonymous and synonymous nucleotide changes within the lyssavirus L gene identified the conserved blocks II, III and IV as being most constrained. Analysis of L gene codon substitution patterns favoured models that supported positive selection, but only one site, corresponding to Leu62 of the RRV L protein, was identified as being under weak positive selection. [Copyright &y& Elsevier]

We have isolated and characterized 17 tetranucleotide microsatellite loci for Blanchard's cricket frog ( Acris crepitans blanchardi), an anuran common in the central USA. Sixteen loci were organized into four multiplex amplification reactions. These loci were highly polymorphic when screened in 55 individuals from two distant populations, with 11–48 alleles per locus (average = 24.8). Observed and expected heterozygosities ranged from 0.18 to 0.97 and from 0.17 to 0.96, respectively. Nine loci were also polymorphic in Acris crepitans crepitans, with seven polymorphic in Acris gryllus. Five loci amplified in all three taxa. These loci will be useful for population- and species-level investigations of this widespread group. [ABSTRACT FROM AUTHOR]

The comment by Romero and Kannada is presented as a critique of our previous work and suggests that our conclusions are in direct conflict with the historic whaling information reviewed in their paper. However, the critique is based on a misinterpretation of the geographical, temporal, and taxonomic focus of our previous work. The source of the putative conflict appears to stem from the misinterpretation that our results, focused solely on the impact of Basque whaling in the 16th and 17th centuries on the western North Atlantic right whale, were intended to be representative of all whaling of both right and bowhead whales throughout the North Atlantic. To demonstrate this, we briefly review our original results and conclusions and show that the information reviewed by Romero and Kannada does not challenge any aspect of our original work. As such, their comment is not a critique of our paper, but rather a brief review of the history of whaling in the North Atlantic. [ABSTRACT FROM AUTHOR]

Deals with a study which developed a polymerase chain reaction-based method for gender determination in a wide variety of marine and terrestrial mammals. Materials and methods; Results; Discussion.

AbstractIn order to assess levels of major histocompatibility complex (Mhc) variation within the St Lawrence beluga (Delphinapterus leucas) the variation at the beluga Mhc DRB1 class II locus was assessed by single-strand conformation polymorphism (SSCP) analysis of the peptide-binding region for 313 whales collected from 13 sampling locations across North America. In addition, samples from west Greenland and the St Lawrence were also typed at the DQB locus, allowing comparison to a previous study and assessment of linkage disequilibrium of alleles at the two loci. Comparisons of DRB1 and DQB allele frequencies among all sampling locations indicated genetic structure (α < 0.005). Most of this structure resulted from differences between the different wintering groups. Significant genetic structure (α = 0.05) exists among each pair of the following groups at both the DRB1 and DQB loci; St Lawrence, Hudson Strait, Bering Sea, Cunningham Inlet, and Davis Strait (minus Cunningham Inlet), except the St Lawrence and Hudson Strait for the DQB locus. In the St Lawrence population, six of the eight DRB1 alleles are present representing all five known allelic lineages. Evidence of linkage disequilibrium between the DRB1 and DQB is present in two sampling locations, the St Lawrence and Nuussuaq (α = 0.05). Analysis of probable DRB1–DQB haplotypes among groups of beluga suggests a haplotype reduction in the St Lawrence. [ABSTRACT FROM AUTHOR]

Range expansion is a widespread biological process, with well‐described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome‐wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction‐associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well‐publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts. Here, we evaluate two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front. Furthermore, we identified 12 SNPs, located either within genes or regulatory regions, that were consistently associated with range expansion, some of which have functions putatively associated with dispersal behavior. [ABSTRACT FROM AUTHOR]

The processes leading to genetic isolation influence a population’s local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus) are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP). To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i) a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii) under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been irreversibly modified by humans, and form strong barriers to movement. [ABSTRACT FROM AUTHOR]

Aim Understanding carnivore distribution is important for management decisions that aim to restore naturally regulated ecosystems and preserve biodiversity. Eastern Wolves, a species at risk in Canada, are centralized in Algonquin Provincial Park and their ability to disperse and establish themselves elsewhere is limited by human-caused mortality associated with hunting, trapping and vehicle collisions. Here, we refine our understanding of Eastern Wolf distribution and provide the first estimates of their effective population size. Location Southern Ontario and Gatineau Quebec. Methods We used non-invasive samples, as well as blood samples archived from other research projects, collected between 2010 and 2014 to generate autosomal microsatellite genotypes at 12 loci for 98 Canis individuals. We utilized Bayesian and multivariate clustering analyses to identify Eastern Wolves in regions that were previously unsampled. Both linkage disequilibrium and temporal approaches were used to estimate effective population size of Eastern Wolves. Results Assignment tests identified 34 individuals as Eastern Wolves, primarily in or near two provincial parks: Killarney and Queen Elizabeth II Wildlands. Eastern Coyotes were identified in Bon Echo Provincial Park, Frontenac Provincial Park and Gatineau Park, whereas many of the samples were admixed among the different Canis types. Effective population size ( Ne) estimates ranged from 24.3 to 122.1 with a harmonic mean of 45.6. Main conclusions The identification of Eastern Wolves in the regions of Killarney and Queen Elizabeth II Wildlands Provincial Parks extends the range of Eastern Wolves north of the French River and southward into previously unidentified regions. The effective population size is low and raises concerns for long-term persistence of this threatened carnivore; estimates are dangerously close to critical values recommended for short-term persistence. These results provide important information for upcoming Eastern Wolf recovery plans associated with federal and provincial endangered species legislation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: The use of genome-wide single nucleotide polymorphisms (SNPs) in wildlife conservation is growing rapidly and promises to revolutionize the field of population genetics. However, genomic data should not be interpreted in isolation of other biological and complementary genetic data. Here, we used recently published genome-wide SNP data from Canis species in combination with data from more traditional genetic markers and evidence from non-genetic fields to show how a broader frame of reference is important for interpretation of genomic data. We conducted a principal components analysis (PCA) and phylogenetic analysis of 48K SNP data to show that a three-species model of Canis evolution in North America is not rejected by the data and deserves further investigation with more representative samples from Algonquin Park. We also demonstrate how a holistic perspective provides a more complete picture of evolutionary processes underlying diversification and speciation events in the genus Canis. Overall, we highlight the importance of careful examination and synthesis of all lines of evidence for the implementation of effective conservation policies for endangered species. [Copyright &y& Elsevier]

Abstract: The first report of the raccoon variant of rabies virus was in Ontario, Canada in 1999. As part of the control of this outbreak a Point Infection Control (PIC) strategy of trapping and euthanizing vector species was implemented. To evaluate whether this strategy was indeed removing diseased animals, rabies diagnosis was performed on these specimens. During a PIC program conducted in 2003, 721 animals (raccoons, striped skunks and red foxes) were collected and euthanized and brain material from each specimen was divided into two halves; one half was submitted for rabies diagnosis by a direct fluorescent antibody (DFA) test while the other was tested using a sensitive real-time reverse-transcriptase polymerase chain reaction (RT-qPCR), to detect raccoon rabies virus (RRV) RNA. This latter assay can detect less than ten viral copies in 200ng of total cellular RNA. All 721 PIC brain samples were negative by the DFA test but ten of them (5 raccoons, 5 skunks) tested positive for raccoon rabies virus by the RT-qPCR assay albeit at low levels. Three of these samples were confirmed by sequencing of the PCR products. Little correlation was observed between clinical rabies DFA positive scoring categories and viral copy number as determined by RT-qPCR. [Copyright &y& Elsevier]

This study examined the genetic nature and relatedness of Canis latrans (Coyotes) in eastern Massachusetts (i.e., eastern Coyotes). We characterized 67 animals at the mitochondrial DNA control region, and 55 of those at 8 microsatellite loci. Structure analysis and factorial correspondence analysis of the microsatellite genotypes indicated that the eastern Coyotes in Massachusetts clustered with other northeastern Canis populations and away from western Coyotes, C. lycaon (Eastern Wolves), and C. lupus (Gray Wolves). They contained mitochondrial haplotypes from both western Coyotes and Eastern Wolves, consistent with their hybrid origin from these two species. There was no evidence of either C. lupus familiaris (Domestic Dog) or Gray Wolf mitochondrial DNA in the animals. These results indicate that the eastern Coyote should more appropriately be termed "Coywolf" to reflect their hybrid (C. latrans x lycaon) origin. Genetic data were also used to assess parental and kinship relationships, and confirmed that family units typically contain an unrelated breeding pair and their offspring. Lastly, a synthesis of knowledge of the eastern Coyote as well as implications for Wolf recovery in the northeast US is provided. [ABSTRACT FROM AUTHOR]

Baleen whales have among the lowest reproductive rates in the animal kingdom, coupled with high energetic demands on lactating mothers to support the rapid growth of their offspring. Because each offspring represents a large portion of a female's reproductive effort, strong selection pressure should be in place to minimize the potential for misplaced parental effort. However, we describe a case in which two North Atlantic right whale (Eubalaena glacialis) offspring were switched between mothers and remained with their "adopted" mothers throughout their first year of life (until they were weaned). The most reasonable explanation is that this swap was an accident caused by the females calving in close spatial and temporal proximity. The calves likely associated with the wrong mothers before any mother-offspring recognition system had developed, and an association then formed between these non-biological mother-offspring pairs. These data raise intriguing questions regarding how often this may occur in other wildlife populations, what mechanisms are used for mother-offspring recognition in whales, and how long it takes for this recognition to develop. [ABSTRACT FROM AUTHOR]

Abstract: Legal and illegal killing of animals near park borders can significantly increase the threat of extirpation for populations living within ecological reserves, especially for wide-ranging large carnivores that regularly travel into unprotected areas. While the consequences of human-caused mortality near protected areas generally focus on numerical responses, little attention has been given to impacts on social dynamics. For wolves, pack structure typically constitutes an unrelated breeding pair, their offspring, and close relatives, but intense harvest may increase adoption of unrelated individuals into packs. Concerns that high human-caused mortality outside Algonquin Park, Canada threatened the persistence of eastern wolves, led to implementation of a harvest ban in surrounding townships. We combined ecological and genetic data to show that reducing anthropogenic causes of mortality can restore the natural social structure of kin-based groups despite the absence of a marked change in density. Since implementation of the harvest ban, human-caused mortality has decreased (P =0.000006) but been largely offset by natural mortality, such that wolf density has remained relatively constant at approximately three wolves/100km2. However, the number of wolf packs with unrelated adopted animals has decreased from 80% to 6% (P =0.00003). Despite the high kinship within packs, incestuous matings were rare. Our results indicate that even in a relatively large protected area, human harvesting outside park boundaries can affect evolutionarily important social patterns within protected areas. This research demonstrates the need for conservation policy to consider effects of harvesting beyond influences on population size. [Copyright &y& Elsevier]

Sampling of feces for genetic studies of wild populations can be problematic because of the low quality and quantity of template DNA obtained. We used cotton swabs in the field to isolate the mucous layer on the surface of fresh wolf (Canis lupus, C. lycaon, and their hybrids) scats followed by immediate preservation, and compared microsatellite genotyping of DNA from these fresh field swabs (FS) to that of previously frozen laboratory swabs (LS). In single polymerase chain reactions (PCRs) of 2 multiplexes, amplification at 8 loci was higher in the FS samples (FS = 50%, LS = 15%; P 5 0.02) because proportion, quantity, and quality of large fragment wolf nuclear DNA from these samples was greater (2.5-25%, 6.25-62.5 ng/swab, 35% amplified at 1,000 base pairs [bp]) than from the LS samples (1.9%-10%, 4.7-25 ng/ swab, 10% amplified at 1,000 bp). Paired blood and fresh field-swabbed samples had identical genotypes. In 84 multiplex PCRs we found no evidence of allelic dropout associated with low template quality or quantity. We conclude that field swabbing of fresh wolf scat facilitates field storage and reduces the need for multiple amplifications at single microsatellite loci, thereby reducing the genotyping costs for wildlife projects that use noninvasive samples. [ABSTRACT FROM AUTHOR]

Many long-term studies of wildlife populations rely on individual identification based on natural markings or genetic profiling, or both. However, only rarely are these 2 independent data sets systematically compared with each other to estimate the error rates inherent in these studies. Here, >25 years of photo-identification data on the endangered North Atlantic right whale (Eubalaena glacialis) were compared with high-resolution genetic profiles, available for >75% of the individuals in the photo-identification catalog, in order to identify sources and rates of errors associated with both methods of individual identification. The resulting estimates were 0.0308 errors/identification for the photo-identification data, and 0.00121 errors/locus and 0.0327 errors/multilocus profile for the genetic data. These are among the lowest error rates yet reported, and indicate that the approaches used provide reliable means of individual identification for this species. However, despite these low error rates, the large size of the data sets results in a nonnegligible estimated number of errors, indicating that the potential for these errors needs to be incorporated into other analyses that are based on these data. A similar situation likely exists in other long-term studies where, although error rates are assumed to be low, the size of the data set results in a large number of errors that will influence subsequent analyses. Regularly conducting and reporting extensive database comparisons such as this is invaluable for maintaining the integrity of long-term data sets by identifying where sources of error are occurring and how protocols can be improved to lower error rates in the future. [ABSTRACT FROM AUTHOR]

Four "races" of wolves have been described in Ontario as follows: 1) Canis lupus hudsonicus inhabiting the subarctic tundra, 2) A race (Ontario type) of the eastern timber wolf (Canis lupus lycaon) that inhabits the boreal forests, 3) A second race (Algonquin type) of C. l. lycaon that inhabit the deciduous forests of the upper Great Lakes, and 4) A small wolf (Tweed type) in central Ontario that has been proposed to be a hybrid between the Algonquin type wolf and expanding coyotes, Canis latrans. Using mitochondrial DNA (mtDNA) control region sequences and 8 microsatellite loci, we developed DNA profiles for 269 wolves from across Ontario. The distribution of mtDNA was predominantly coyote and the eastern wolf, Canis lycaon, in Algonquin Park and the southern Frontenac Axis with a combination of these mtDNA and gray wolf mtDNA in northern Ontario. Bayesian clustering grouped northern Ontario wolves independent of mtDNA with a second grouping of eastern and Tweed wolves from Algonquin. Individual clustering identified 3 groups represented by 1) northern Ontario wolves, 2) eastern wolves, and 3) Tweed wolves from the Frontenac Axis. Genomic representation analyses indicate that the Tweed wolves are hybrids between the coyote and the eastern wolf and represent the Ontario distribution of the eastern coyote, whereas the wolves in the upper Great Lakes region represent products of historic and/or continuing hybridization between C. lycaon and C. lupus. There was low structuring among wolves in these regions, and Algonquin suggesting a larger northern connected metapopulation with gene flow between the Ontario and Algonquin types. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: 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, ϕ 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. [Copyright &y& Elsevier]

The North Atlantic right whale, Eubalaena glacialis (Müller, 1776), is one of the world's most endangered large cetaceans. It is widely believed that Basque whalers caused the most dramatic decline of this species in the western North Atlantic during the early-16th and 17th centuries. Previous osteological analysis of 17 historic bones suggested that 50% of the Basque harvest consisted of right whales and 50% of bowhead whales, Balaena mysticetus L., 1758. This 50:50 ratio has been used to estimate pre-exploitation population size, which has subsequently formed the basis of recovery goals and plans for the North Atlantic right whale. Genetic analysis of 21 bones, 13 identified as right whales and 8 as bowhead whales through osteological examination, indicates that in fact only 1 bone was a right whale and 20 were bowhead whales. Additionally, preliminary microsatellite analyses of this specimen are not consistent with the hypothesis that whaling resulted in the low genetic variation found in this species today. These results differ from what would be expected based on any previous view of Basque whaling, and raise questions regarding the impact of Basque whaling on this species. [ABSTRACT FROM AUTHOR]

Recent genetic data indicate that the eastern wolf is not a subspecies of the gray wolf (Canis lupus), but is a North American wolf more similar to the red wolf (C. rufus) and closely related to the coyote (C. latrans). The eastern wolf has been proposed as a separate species, C. lycaon. The largest protected area containing this wolf is Algonquin Provincial Park in Ontario, Canada, which is bounded to the south by areas containing the Tweed wolf or eastern coyote, a hybrid of the western coyote and eastern wolf. We assessed the relationships of animals in the park by using DNA profiles that comprised the genotype from 17 autosomal and 4 Y-linked microsatellite loci and the mitochondrial DNA control region. These profiles were used to establish maternity, paternity, and kin relationships for 102 wolves that were studied from 24 packs over a 12-year period. Genetic data do not support the hypothesis that a pack comprises an unrelated breeding pair and their offspring. There is evidence of frequent pack splitting, pack fusion, and adoption. Some unrelated individuals in the packs were identified as immigrants into the park. We found high levels of genetic structuring between the Tweed wolves to the southeast and the Algonquin Park wolves (RST = 0.114). Lower levels of genetic differentiation with animals to the north and west (RST = 0.057 and RST = 0.036) and high genetic diversity suggest that park animals are not an island population but the southern part of a larger metapopulation of C. lycaon. [ABSTRACT FROM AUTHOR]

The Magadi tilapia (Alcolapia grahami, formerly Oreochromis alcalicus grahami) is a remarkable example of teleost life in an extreme environment. Typical conditions include water pH = 10, titration alkalinity> 300 mM, osmolality = 525 mOsm, temperatures ranging from 23° to 42°C, and O2 levels fluctuating diurnally between extreme hyperoxia and anoxia. A number of relatively small tilapia populations are present in various thermal spring lagoons around the margin of the lake separated by kilometers of solid trona crust (floating Na2CO3) underlain by anoxic water. Despite the apparent isolation of different populations, annual floods may provide opportunities for exchange of fish across the surface of the trona and subsequent gene flow. To assess the question of isolation among Lake Magadi populations, we analyzed the variable control region of the mitochondrial DNA (mtDNA) from six lagoons. A total of seven mtDNA haplotypes, including three common haplotypes, were observed in all six populations. Several of the Lake Magadi populations showed haplotype frequencies indicative of differentiation, while others showed very little. How- ever, differentiation among lagoon populations was discordant with their geographical distribution along the shoreline. All populations exhibited the unusual trait of 100% ureotelism but specialized morphological and physiological characteristics were observed among several of the lagoon systems. in addition, distinct differences were observed in the osmolality among the lagoons with levels as high as 1,400-1,700 mOsm kg-1, with corresponding differences in the natural levels of whole-body urea. These levels of osmotic pressure proved fatal to fish from less alkaline systems but remarkably were also fatal to the fish that inhabited lagoons with this water chemistry. Upon more detailed inspection, specific adaptations to differential conditions in the lagoon habitat were identified that allowed survival of these cichlids. Additional evidence against potential for gene flow among lagoons despite the sharing of common mtDNA haplotypes was that the osmolality of floodwaters following a heavy rain showed lethal levels exceeding 1,700 mOsm kg in isolation, different mtDNA hap lotypes would be predicted to go to fixation in different populations due to rapid generation times and the small effective population sizes in a number of lagoons. We propose a model of balancing selection to maintain common mtDNA sequences through a common selection pressure among lagoons that is based on microhabitats utilized by the tilapia. [ABSTRACT FROM AUTHOR]

Genetic variation was examined for moose (Alces alces) from Riding Mountain, Isle Royale, and Pukaskwa national parks; northwestern, Nipigon, northeastern, and central Ontario; New Brunswick; and Newfoundland. The national parks were identified as maintaining potentially different local selection pressures due to the absence of hunting and the presence or absence of the parasite Parelaphostrongylus tenuis. Genetic variation was estimated using neutral DNA markers, assessed by multilocus DNA fingerprinting and five microsatellite loci, and the functional antigen binding region (ARS) (exon 2) of the major histocompatibility complex (MHC) gene DRB. There was discordance in the allelic diversity observed at the neutral loci compared with the MHC DRB locus in a number of populations. Ontario populations demonstrated higher levels of variability at the neutral loci and relatively low levels at the DRB locus. Conversely, the Isle Royale population has the lowest genetic variability, consistent with a historic small founding event, at the neutral DNA markers and relatively high variability at the MHC gene. Relatively high levels of genetic variation at the DRB locus were observed in protected park populations concomitant with the absence of white-tailed deer (Odocoileus virginianus) or the parasite P tenuis and an absence of hunting. Gene flow was observed among the neighboring geographic regions within Ontario, including Pukaskwa National Park, with evidence of isolation-bydistance among more distant regions within Ontario. The discordant patterns between DNA markers suggest that neutral DNA markers may not accurately reflect adaptive variation present at functional loci. [ABSTRACT FROM AUTHOR]

Abstract: We examined six historical specimens of the endangered North Atlantic right whale (Eubalaena glacialis) using DNA isolated from documented baleen plates from the late nineteenth and early twentieth centuries. Sequences from the mitochondrial DNA (mtDNA) control region from these samples were compared with those from a near-exhaustive survey (269 of approximately 320 individuals) of the remaining right whales in the western North Atlantic Ocean. Our results suggest that there has been only relatively modest change in maternal lineage diversity over the past century in the North Atlantic right whale population. Any significant reduction in genetic variation in the species most likely occurred prior to the late nineteenth century. One historical specimen was from the last documented female capable of propagating one of the maternal lineages in the population today; no females in the existing population have been found to carry this mtDNA haplotype. Analysis of the only specimens from the eastern North Atlantic right whale population ever to be examined revealed that eastern and western North Atlantic right whales may not have been genetically differentiated populations. Loss of gene diversity experienced by North Atlantic right whales over the last century has been modest, and the six decades of protection have been successful in maintaining much of the maternal lineage diversity that was present in the late nineteenth century. [ABSTRACT FROM AUTHOR]

Most individuals with cat eye syndrome (CES) have a supernumerary bisatellited chromosome which, on the basis of cytogenetic evidence, has been reported to originate from either chromosome 13 or 22. To resolve this question, a single-copy DNA probe, D22S9, was isolated and localized to 22ql1 by in situ hybridization to metaphase chromosomes. The number of copies of this sequence was determined in CES patients by means of Southern blots and densitometry analysis of autoradiographs. In patients with the supernumerary chromosome, four copies were found, whereas in one patient with a duplication of part of chromosome 22, there were three copies. Therefore, the syndrome results from the presence of either three or four copies of DNA sequences from 22q11; there is no evidence that sequences from other chromosomes are involved. This work demonstrates how DNA sequence dosage analysis can be used to study genetic disorders that are not readily amenable to standard cytogenetic analysis. [ABSTRACT FROM AUTHOR]

The cover image, by Linda Rutledge et al., is based on the Biodiversity Research Patchy distribution and low effective population size raise concern for an at‐risk top predator, DOI: 10.1111/ddi.12496. Photo Credit: Michael Runtz. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the article “Molecular and Evolutionary History of Melanism in North American Gray Wolves,” by T. M. Anderson and colleagues in the March 6, 2009 issue.