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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]

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]

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.

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]

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]

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]

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]

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.