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There is considerable interest in the genetics of wolves (Canis lupus) because of their close relationship to domestic dogs (C. familiaris) and the need for informed conservation and management. This includes wolf populations in Southeast Alaska for which we determined genotypes of 305 wolves at 173662 single nucleotide polymorphism (SNP) loci. After removal of invariant and linked SNP, 123801 SNP were used to quantify genetic differentiation of wolves in Southeast Alaska and wolves, coyotes (C. latrans), and dogs from other areas in North America. There is differentiation of SNP allele frequencies between the species (wolves, coyotes, and dogs), although differentiation is relatively low between some wolf and coyote populations. There are varying levels of differentiation among populations of wolves, including low differentiation of wolves in interior Alaska, British Columbia, and the northern US Rocky Mountains. There is considerable differentiation of SNP allele frequencies of wolves in Southeast Alaska from wolves in other areas. However, wolves in Southeast Alaska are not a genetically homogeneous group and there are comparable levels of genetic differentiation among areas within Southeast Alaska and between Southeast Alaska and other geographic areas. SNP variation and other genetic data are discussed regarding taxonomy and management., (© The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

The congenic HG.CAST-(D17Mit196-D17Mit190) (HQ17(hg/hg)) mouse strain showed a significant departure on the expected 50%/50% offspring sex ratio in more than 2400 progeny (55.7% females). The entire pedigree file included data from 13 nonoverlapping purebred generations and an F(2) cross with the C57BL/6J inbred strain. Offspring sex ratio data were analyzed on the basis of 40 purebred HQ17(hg)(/hg) sires and 29 F(1) HQ17(hg)(/hg) x B6 sires under a Bayesian Binomial segregation model accounting for 4 different autosomal inheritance models of gene action (i.e., additive, dominance, recessive, and overdominance) and X-linked and Y-linked loci. For each model, the segregation effect was evaluated as a single regression coefficient for all sires or assuming 2 independent regression coefficients accounting for offspring sex ratio departures in purebred and F(1) sires, respectively. The deviance information criterion clearly favored the autosomal dominance model with different regression coefficients for the 2 groups of sires. Under this model, the dominance effect increased the percentage of female offspring by 4.3% (HQ17(hg)(/hg) purebred sires) and 8.2% (F(1) sires) with the highest posterior density regions ranging from 0.5% to 10.6% and from 1.3% to 14.4%, respectively. This article provides significant evidence of genetic determinism for sex ratio distortion in the HQ17(hg)(/hg) strain and develops new analytical tools to perform segregation studies on dichotomous traits.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison–cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date. [ABSTRACT FROM AUTHOR]

The Mexican gray wolf (Canis lupus baileyi) was historically distributed throughout the southwestern United States and northern Mexico. Extensive predator removal campaigns during the early 20th century, however, resulted in its eventual extirpation by the mid 1980s. At this time, the Mexican wolf existed only in 3 separate captive lineages (McBride, Ghost Ranch, and Aragón) descended from 3, 2, and 2 founders, respectively. These lineages were merged in 1995 to increase the available genetic variation, and Mexican wolves were reintroduced into Arizona and New Mexico in 1998. Despite the ongoing management of the Mexican wolf population, it has been suggested that a proportion of the Mexican wolf ancestry may be recently derived from hybridization with domestic dogs. In this study, we genotyped 87 Mexican wolves, including individuals from all 3 captive lineages and cross-lineage wolves, for more than 172 000 single nucleotide polymorphisms. We identified levels of genetic variation consistent with the pedigree record and effects of genetic rescue. To identify the potential to detect hybridization with domestic dogs, we compared our Mexican wolf genotypes with those from studies of domestic dogs and other gray wolves. The proportion of Mexican wolf ancestry assigned to domestic dogs was only between 0.06% (SD 0.23%) and 7.8% (SD 1.0%) for global and local ancestry estimates, respectively; and was consistent with simulated levels of incomplete lineage sorting. Overall, our results suggested that Mexican wolves lack biologically significant ancestry with dogs and have useful implications for the conservation and management of this endangered wolf subspecies. [ABSTRACT FROM AUTHOR]

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Polar bears (Ursus maritimus) and brown bears (Ursus arctos) are closely related species for which extensive mitochondrial and nuclear phylogenetic comparisons have been made. We used previously published genotype data for 8 microsatellite DNA loci from 930 brown bears in 19 populations and 473 polar bears in 16 populations to compare the population genetic relationships of extant populations of the species. Genetic distances (Nei standard distance = 1.157), the proportion of private alleles (52% of alleles are not shared by the species), and Bayesian cluster analysis are consistent with morphological and life-history characteristics that distinguish polar bears and brown bears as different species with little or no gene flow among extant populations. [ABSTRACT FROM PUBLISHER]

Exercise improves many aspects of human health, yet many people remain inactive even when exercise is prescribed. We previously created a backcross (BC) between mice selectively bred for high levels of voluntary wheel running (VWR) and fixed for “mini muscle” (MM), a recessive mutation causing ∼50% reduction in triceps surae mass. We previously showed that BC mice having the MM trait ran faster and further than mice without MM and that MM maps to chromosome 11. Here, we genotyped the BC with genome-wide single nucleotide polymorphisms to identify quantitative trait loci (QTL) controlling voluntary exercise and tissue and body mass traits and to determine whether these QTL interact with the MM locus or with sex. We detected 3 VWR QTL, representing the first voluntary exercise QTL mapped using this high running selection line, and 5 tissue mass QTL. Several interactions between trait QTL and the MM locus as well as sex were also identified. These results begin to explain the genetic architecture of VWR and further support MM as a locus having major effects, including its main effects on the muscle phenotype, its pleiotropic effects on wheel running and tissue mass traits, and through its interactions with other QTL and with sex. [ABSTRACT FROM PUBLISHER]

The sigmodontine South American rodent genus OIigoryzomys was first described as a subgenus of the genus Oryzom'ys to group together species distinguished by morphological measurements. To describe the dispersion patterns of this genus in South America, in this study, a total of 100 sequences were analyzed and compared with sequences of 9 Oligoryzomys species from GenBank. The sequences comprised 90 mitochondrial cytochrome b genes and 10 nuclear interphotoreceptor retinoid- binding protein genes, from 75 individuals of 7 species from 27 localities. Topologies of different phylogenetic trees revealed OIigoryzomys as a monophyletic genus containing 2 main species groups, one designated as the "Amazon-Cerrado" assemblage and the second as the "Pampa-Andean" dade. The north-to-south geographic pattern observed supports the hypothesis that the genus started from, the northern Andes, occupied the Amazon and the Cerrado, and later inhabited the more southern regions of South America. [ABSTRACT FROM AUTHOR]

Prolonged selective breeding of Hsd:ICR mice for high levels of voluntary wheel running has favored an unusual phenotype (mini-muscle [MM]), apparently caused by a single Mendelian recessive allele, in which hindlimb muscle mass is reduced by almost 50%. We recently described the creation and phenotypic characterization of a population suitable for mapping the genomic location of the MM gene. Specifically, we crossed females from a high-runner line fixed for the MM allele with male C57BL/6J. El males were then backcrossed to the MM parent females. Backcross (BC) mice exhibited a 50:50 ratio of normal to MM phenotypes. Here, we report on linkage mapping of MM in this BC population to a 2.6335-Mb interval on MMU I I. This region harbors ~100 expressed or predicted genes, many of which have known roles in muscle development and/or function, Identification of the genetic variation that underlies MM could potentially be very important in understanding both normal muscle function and disregulation of muscle physiology leading to disease. [ABSTRACT FROM AUTHOR]

Despite increased interest in applying single nucleotide polymorphism (SNP) data to questions in natural systems, one unresolved issue is to what extent the ascertainment bias induced during the SNP discovery phase will impact available analysis methods. Although most studies addressing ascertainment bias have focused on human populations, it is not clear whether existing methods will work when applied to other species with more complex demographic histories and more significant levels of population structure. Here we present findings from an empirical approach to exploring the effect of population structure on issues of ascertainment bias in the Eastern Fence Lizard, Sceloporus undulatus. We find that frequency spectra and summary statistics were highly sensitive to SNP discovery strategy, necessitating careful selection of the initial ascertainment panel. Randomly selected ascertainment panels performed equally well as ascertainment panels chosen to jointly sample geographic, phenotypic, and genetic diversity. Geographically restricted panels resulted in larger biases. Additionally, we found existing ascertainment bias correction methods, which were not developed for geographically structured data sets, were largely effective at reducing the impact of ascertainment bias. Because bias correction methods performed well even when underlying assumptions were violated, our results suggest tools are currently available to analyze SNP data in structured populations. [ABSTRACT FROM AUTHOR]

Deer in the genera Mazama and Odocoileus generally have two copies of a 75-base-pair (bp) repeat in the left domain of the control region of the mitochondrial DNA (mtDNA). Phylogenetic analyses further suggest an ancient origin for the duplication supporting a previously stated contention that this event occurred before the separation of Mazama and Odocoileus. However, white-tailed deer (Odocoileus viginianus) had three or four copies of a 75-bp repeat in the control region of their mtDNA in 7.8% of the individuals analyzed, and all of these animals were from the coastal plain of the southeastern United States. When copy 3 is present, it is very similar in sequence to copy 2, but variation suggests that copy 3 probably evolved multiple times from copy 2. The pattern of phylogenetic clustering of the haplotypes from across the coastal plato also suggests that phenotypes with three or four copies of the repeat have originated multiple times. The 44 observed haplotypes showed strong spatial subdivision across the area with subpopulations frequently showing complete shifts in haplotype frequencies from others taken from nearby areas. Many of the subpopulations right along the coast or on adjacent barrier islands have a limited number of haplotypes as would occur in populations undergoing drift because of small numbers of breeding females and limited female dispersal. [ABSTRACT FROM AUTHOR]

Fecal analysis is a useful tool for the investigation of food habits and species identity in mammals. However, it is generally difficult to identify the species based on the morphological features and contents of feces deposited by mammals of similar body size. Therefore we developed noninvasive DNA analysis methods using fecal samples for identification of the species and sex of four small sympatric carnivores living on the Tsushima Islands of Japan: the leopard cat (Felis bengalensis), Japanese marten (Martes melampus), Siberian weasel (Mustela sibirica), and feral cat (Felis catus). Based on DNA sequence data from previous phylogenetic studies, we designed species-specific primers for polymerase chain reaction (PCR) amplification of the partial mitochondrial cytochrome b gene (112-347 bp) to identify the species and primers for the partial SRY gene (135 bp) to determine the sex. Due to the adjustment of PCR conditions, those specific DNA fragments were successfully amplified and then applied for species and sex identification. Nucleotide sequences obtained from the PCR products corresponded with cytochrome b sequences of the carnivore species expected. The protocol developed could be a valuable tool in the management and conservation of the four carnivore species occurring on the Tsushima Islands. [ABSTRACT FROM AUTHOR]

The Sox9 gene of Acipenser sturio, one of the most primitive vertebrates, was analyzed. No sex-specific differences were observed. Sturgeon Sox9 consists of three exons and two introns with completely conserved exon-intron boundaries showing high levels of homology to other vertebrate Sox9 sequences, especially in the N-terminus region containing the HMG box. We found strong evidence for negative (purifying) selection. In contrast to previous studies of other fishes, we observed no evidence for gene duplication in sturgeon. Phylogenetic analyses of Sox9 evolution revealed a basal position for sturgeon Sox9. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the article "Genetic Distinctiveness of Alexander Archipelago Wolves (Canis lupus ligoni)."

Presents a study in the search for quantitative trait loci (QTL) for live weight traits between Pere David's deer (elaphurus davidianus) and red deer (cervus elaphus). Details on the hybrids and genotyping; Description of the phenotypes and its analysis; Discussion.

Presents information on a study which investigated the utility of microsatellites for managing captive Tursiops truncatus. Examination of genetic diversity among the loci; Alleles found among morphotypes of dolphins; Suggestions for use of genetic markers in captive propagation programs.

Presents information on a study which described analysis of randomly amplified polymorphic DNA in the search for markers which cosegregate with joint laxity in the domestic dog. Information on canine hip dysplasia; Identification of genetic markers; Efforts to establish genetic maps of the canine genome; Results of the study.

Presents information on a study of the random amplified polymorphic DNA (RAPD) in plant and animal species genetic studies. Application of RAPD to genetic studies of dogs; Use of Labrador retriever pedigree in the study; Polymorphism observed; Results of the study.

Presents a study on the development and characterization of a panel of Bos taurus x B. gaurus interspecific hybrid backcross offspring. Methodology and materials used in the study; Preparation of backcross offspring DNA; Information on the chromosome preparation and analysis; Results of the study; Discussion surrounding the results of the study.

The giant anteater (Myrmecophaga tridactyla) is found from Belize and Guatemala to Paraguay and Argentina. Its conservation status is considered vulnerable by IUCN. Here we report the isolation and characterization of six microsatellite loci. Positive loci for (GT)n were isolated using a magnetic bead hybridization selection protocol. The number of alleles per locus as well as the heterozygosity and PCR conditions are described. These loci will be useful for studying population structure, genetic diversity, and paternity in M. tridactyla wild populations. [ABSTRACT FROM AUTHOR]

Presents information on a study of random amplified polymorphic DNA (RAPD) technique. Use of the technique in studies of dogs; Modification of the protocol for RAPD analysis; Identification of sequence variants in single DNA bands.

A letter to the editor is presented about the article "Mexican Wolves Are a Valid Subspecies and an Appropriate Conservation Target."