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At least 19 recordsLinked to original sources
USGS2006

Microsatellite DNA and mitochondrial DNA variation in polar bears ( Ursus maritimus ) from the Beaufort and Chukchi seas, Alaska

Radiotelemetry data have shown that polar bears (Ursus maritimus Phipps, 1774) occur in separate subpopulations in the Chukchi Sea and the southern Beaufort Sea. However, segregation is not absolute, and there is overlap of ranges of animals in each subpopulation. We used genetic variation at eight microsatellite DNA loci and mitochondrial DNA (mtDNA) to further assess the degree of spatial structure of polar bears from the Chukchi and southern Beaufort seas. Microsatellite allele frequencies and mtDNA haplotype frequencies of bears from the southern Beaufort and Chukchi seas did not differ significantly. Lack of differentiation at both maternally inherited mtDNA and bi-parentally inherited microsatellite loci suggests that gene flow between the two areas is mediated by both sexes. The genetic data indicate that polar bears in the southern Beaufort and Chukchi seas compose one interbreeding population. However, there is considerable fidelity to ranges in each area, particularly by adult females. The combined genetic and movement data suggest that polar bears could be managed as Beaufort Sea and Chukchi Sea subpopulations of a combined southern Beaufort Sea and Chukchi Sea population. ?? 2006 NRC.

Canadian Journal of Zoology↗
USGS2002

Microsatellite DNA and mitochondrial DNA variation in remnant and translocated sea otter ( Enhydra lutris ) populations

All existing sea otter ( Enhydra lutris ) populations have suffered at least 1, and in some cases 2, population bottlenecks. The 1st occurred during the 18th and 19th centuries as a result of commercial hunting that eliminated sea otters from much their native range and reduced surviving populations to small remnants. The 2nd bottleneck occurred when small numbers of otters were reintroduced, via translocation, to areas where the species had been eliminated. We examined genetic variation at 7 microsatellite loci and the mitochondrial DNA (mtDNA) control region in 3 remnant populations, Amchitka Island (Aleutian Islands, Alaska), central coastal California, and Prince William Sound (Alaska), and in 2 reintroduced populations, southeast Alaska and Washington, that were founded with transplants from Amchitka, and in the case of southeast Alaska, individuals from Prince William Sound as well. We found no evidence of reduced genetic diversity in translocated populations. Average expected microsatellite heterozygosities ( H E ) were similar in all populations (range, 0.40–0.47), and mtDNA haplotype diversities were higher in reintroduced populations (0.51 for both Washington and southeast Alaska) than in remnant populations ( X̄ = 0.35; range, 0.18–0.45). The levels of genetic diversity we observed within sea otter populations were relatively low when compared with other mammals and are thought to be the result of fur trade exploitation.

Alaska, California, Washington↗
USGS1992

A study of the genetic relationships within and among wolf packs using DNA fingerprinting and mitochondrial DNA

DNA fingerprinting and mitochondrial DNA analyses have not been used in combination to study relatedness in natural populations. We present an approach that involves defining the mean fingerprint similarities among individuals thought to be unrelated because they have different mtDNA genotypes. Two classes of related individuals are identified by their distance in standard errors above this mean value. The number of standard errors is determined by analysis of the association between fingerprint similarity and relatedness in a population with a known genealogy. We apply this approach to gray wolf packs from Minnesota, Alaska, and the Northwest Territories. Our results show that: (1) wolf packs consist primarily of individuals that are closely related genetically, but some packs contain unrelated, non-reproducing individuals; (2) dispersal among packs within the same area is common; and (3) short-range dispersal appears more common for female than male wolves. The first two of these genetically-based observations are consistent with behavioral data on pack structure and dispersal in wolves, while the apparent sex bias in dispersal was not expected.

Behavioral Ecology and Sociobiology↗
USGS1991

Mitochondrial-DNA phylogeny of deer (Cervidae)

Mitochondrial-DNA restriction-site maps were constructed for several cervid taxa in the subfamilies Cervinae and Odocoileinae. Parsimony analyses of restriction sites and pair-wise analyses of genetic distances resulted in dendrograms congruent with the subfamily designations. Relationships within the Odocoileinae determined from genetic distances generally were concordant with those for nuclear-encoded allozymes and morphology. However, mitochondrial-DNA relationships were incongruent with some generic designations and intraspecific divergence in Odocoileus hemionus was greater than that between some genera. Because mitochondrial DNA exhibits considerable intraspecific variation and is inherited as a single locus, relationships based on mitochondrial DNA may not be concordant with true species phylogenies.

Journal of Mammalogy↗
USGS1991

Inter- and intraspecific mitochondrial DNA variation in North American bears (Ursus)

We assessed mitochondrial DNA variation in North American black bears (Ursus americanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus). Divergent mitochondrial DNA haplotypes (0.05 base substitutions per nucleotide) were identified in populations of black bears from Montana and Oregon. In contrast, very similar haplotypes occur in black bears across North America. This discordance of haplotype phylogeny and geographic distribution indicates that there has been maintenance of polymorphism and considerable gene flow throughout the history of the species. Intraspecific mitochondrial DNA sequence divergence in brown bears and polar bears is lower than in black bears. The two morphological forms of U. arctos, grizzly and coastal brown bears, are not in distinct mtDNA lineages. Interspecific comparisons indicate that brown bears and polar bears share similar mitochondrial DNA (0.023 base substitutions per nucleotide) which is quite divergent (0.078 base substitutions per nucleotide) from that of black bears. High mitochondrial DNA divergence within black bears and paraphyletic relationships of brown and polar bear mitochondrial DNA indicate that intraspecific variation across species' ranges should be considered in phylogenetic analyses of mitochondrial DNA.

Canadian Journal of Zoology↗
USGS1991

Introgression of coyote mitochondrial DNA into sympatric North American gray wolf populations

Mitochondrial DNA (mtDNA) genotypes of gray wolves and coyotes from localities throughout North America were determined using restriction fragment length polymorphisms. Of the 13 genotypes found among the wolves, 7 are clearly of coyote origin, indicating that genetic transfer of coyote mtDNA into wolf populations has occurred through hybridization. The transfer of mtDNA appears unidirectional from coyotes into wolves because no coyotes sampled have a wolf-derived mtDNA genotype. Wolves possessing coyote-derived genotypes are confined to a contiguous geographic region in Minnesota, Ontario, and Quebec, and the frequency of coyote-type mtDNA in these wolf populations is high (>50%). The ecological history of the hybrid zone suggests that hybridization is taking place in regions where coyotes have only recently become abundant following conversion of forests to farmlands. Dispersing male wolves unable to find conspecific mates may be pairing with female coyotes in deforested areas bordering wolf territories. Our results demonstrate that closely related species of mobile terrestrial vertebrates have the potential for extensive genetic exchange when ecological conditions change suddenly.

Evolution↗
USGS1996

Mitochondrial-DNA variation among subspecies and populations of sea otters (Enhydra lutris)

We used restriction-enzyme analysis of polymerase-chain reaction-amplified, mitochondrial DNA (mtDNA) to assess genetic differentiation of subspecies and populations of sea otters, Enhydra lutris , throughout the range of the species. There were several haplotypes of mtDNA in each subspecies and geographically separate populations. MtDNA sequence divergence of haplotypes of sea otters was 0.0004–0.0041 base substitutions per nucleotide. E. L nereis appears to have monophyletic mitochondrial DNA, while E. I. lutris and E. I. kenyoni do not. Different frequencies of haplotypes of mtDNA among populations reflect current restriction of gene flow and the unique histories of different populations. There are two or three haplotypes of mtDNA and diversity of haplotypes is 0.1376–0.5854 in each population of otters. This is consistent with theoretical work, which suggests that population bottlenecks of sea otters probably did not result in major losses of genetic variation for individual populations, or the species as a whole.

Journal of Mammalogy↗
USGS2015

Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.

European Russia↗
USGS1992

Intraspecific mitochondrial DNA variation in North American cervids

Intraspecific variation in mitochondrial DNA of North American cervids was assessed with restriction enzymes to determine relationships among populations and subspecies. No variation was detected in moose ( Alces alces ) and little in elk ( Cervus elaphus ). Caribou ( Rangifer tarandus ), white-tailed deer ( Odocoileus virginianus ), and mule deer ( Odocoileus hemionus ) possessed considerable variation. Characteristic genotypes exist in caribou and white-tailed deer from different geographic areas although subspecies are not discernable as distinct mtDNA assemblages. Except for O. hemionus , intraspecific mtDNA sequence divergences are small (<2%). Subspecies of mule deer have divergent mtDNA (7%) and are the only subspecies of cervids with distinct genotypes.

Journal of Mammalogy↗
USGS2002

Comparison of mitochondrial DNA control region sequence and microsatellite DNA analyses in estimating population structure and gene flow rates in Atlantic sturgeon Acipenser oxyrinchus

Atlantic sturgeon Acipenser oxyrinchus is large, long-lived, and anadromous with subspecies distributed along the Atlantic (A. oxyrinchus oxyrinchus) and Gulf of Mexico (A. o. desotoi) coasts of North America. Although it is not certain if extirpation of some population units has occurred, because of anthropogenic influences abundances of all populations are low compared with historical levels. Informed management of A. oxyrinchus demands a detailed knowledge of its population structure, levels of genetic diversity, and likelihood to home to natal rivers. We compared the use of mitochondrial DNA (mtDNA) control region sequence and microsatellite nuclear DNA (nDNA) analyses in identifying the stock structure and homing fidelity of Atlantic and Gulf coast populations of A. oxyrinchus. The approaches were concordant in that they revealed moderate to high levels of genetic diversity and suggested that populations of Atlantic sturgeon are highly structured. At least six genetically distinct management units were detected using the two approaches among the rivers surveyed. Mitochondrial DNA sequences revealed a significant cline in haplotype diversity along the Atlantic coast with monomorphism observed in Canadian populations. High levels of nDNA diversity were also observed among populations along the Atlantic coast, including the two Canadian populations, probably resulting from the more rapid rate of mutational and evolutionary change at microsatellite loci. Estimates of gene flow among populations were similar between both approaches with the exception that because of mtDNA monomorphism in Canadian populations, gene flow estimates between them were unobtainable. Analyses of both genomes provided high resolution and confidence in characterizing the population structure of Atlantic sturgeon. Microsatellite analysis was particularly informative in delineating population structure in rivers that were recently glaciated and may prove diagnostic in rivers that are geographically proximal along the south Atlantic coast of the US.

Journal of Applied Ichthyology↗
USGS1994

Phylogeny and evolution of the auks (subfamily Alcinae) based on mitochondrial DNA sequences

The genetic divergence and phylogeny of the auks was assessed by mitochondrial DNA sequence comparisons in a study using 19 of the 22 auk species and two outgroup representatives. We compared more than 500 nucleotides from each of two mitochondrial genes encoding 12S rRNA and the NADH dehydrogenase subunit 6. Divergence times were estimated from transversional substitutions. The dovekie ( Alle alle ) is related to the razorbill ( Alca torda ) and the murres ( Uria spp). Furthermore, the Xantus's murrelet ( Synthliboramphus hypoleucus ) and the ancient ( Synthliboramphus antiquus ) and Japanese murrelets ( Synthliboramphus wumizusume ) are genetically distinct members of the same main lineage, whereas brachyramphine and synthliboramphine murrelets are not closely related. An early adaptive radiation of six main species groups of auks seems to trace back to Middle Miocene. Later speciation probably involved ecological differentiations and geographical isolations.

PNAS↗
USGS2000

Phylogeography of mitochondrial DNA variation in brown bears and polar bears

We analyzed 286 nucleotides of the middle portion of the mitochondrial cytochrome b gene of 61 brown bears from three locations in Alaska and 55 polar bears from Arctic Canada and Arctic Siberia to test our earlier observations of paraphyly between polar bears and brown bears as well as to test the extreme uniqueness of mitochondrial DNA types of brown bears on Admiralty, Baranof, and Chichagof (ABC) islands of southeastern Alaska. We also investigated the phylogeography of brown bears of Alaska's Kenai Peninsula in relation to other Alaskan brown bears because the former are being threatened by increased human development. We predicted that: (1) mtDNA paraphyly between brown bears and polar bears would be upheld, (2) the mtDNA uniqueness of brown bears of the ABC islands would be upheld, and (3) brown bears of the Kenai Peninsula would belong to either clade II or clade III of brown bears of our earlier studies of mtDNA. All of our predictions were upheld through the analysis of these additional samples.

Alaska↗
USGS1993

Mitochondrial DNA variation in chinook salmon and chum salmon detected by restriction enzyme analysis of polymerase chain reaction products

We analyze intraspecific mitochondrial DNA variation in chinook salmon from drainages in the Yukon River, the Kenai River, and Oregon and California rivers; and chum salmon from the Yukon River and vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified seperately using the polymerase chain reaction and then digested with at least 19 restrictions enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base subsitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (8) occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rviers and four occurred in the Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock seperation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2000

Mitochondrial DNA diversity North American and European Atlantic salmon with emphasis on the downeast rivers of Maine

The displacement loop and NADH-1 dehydrogenase regions of mitochondrial DNA (mtDNA) were amplified by the polymerase chain reaction in 954 Atlantic salmon and digested with 40 restriction endonucleases. Variation was detected with 10 enzymes, resulting in 21 composite haplotypes which were strongly patterned geographically with a major discontinuity observed between most North American (NA) and European salmon. Significant heterogeneity of haplotype frequencies was found within and among all classification levels (continent, country, and river). Haplotype frequencies were significantly different across continents, within European samples, within NA samples, within Canadian samples, within wild Maine samples, within captive Maine strains, and between captive and wild Maine strains. Nine haplotypes occurred only in NA, seven in Maine, three only in Maine, and 11 occurred only in Europe. Some Maine rivers had only a single haplotype, suggesting that effective population sizes may be low. The second most frequent European haplotype occurred in tributaries to one Newfoundland river. Gene trees based on parsimony and genetic distance suggest that the haplotypes are monophyletic within each continent, and that the haplotype found on both continents is intermediate between those of Europe and NA, suggesting common ancestry of all haplotypes.

Maine↗
USGS2002

Sequence analysis of the mitochondrial DNA control region of ciscoes (genus Coregonus ): Taxonomic implications for the Great Lakes species flock

Sequence variation in the control region (D-loop) of the mitochondrial DNA (mtDNA) was examined to assess the genetic distinctiveness of the shortjaw cisco ( Coregonus zenithicus ). Individuals from within the Great Lakes Basin as well as inland lakes outside the basin were sampled. DNA fragments containing the entire D-loop were amplified by PCR from specimens of C. zenithicus and the related species C. artedi , C. hoyi , C. kiyi , and C. clupeaformis . DNA sequence analysis revealed high similarity within and among species and shared polymorphism for length variants. Based on this analysis, the shortjaw cisco is not genetically distinct from other cisco species.

Molecular Ecology↗
USGS2008

Genetic characterization of Kenai brown bears (Ursus arctos): Microsatellite and mitochondrial DNA control region variation in brown bears of the Kenai Peninsula, south central Alaska

We collected data from 20 biparentally inherited microsatellite loci, and nucleotide sequence from the maternally inherited mitochondrial DNA (mtDNA) control region, to determine levels of genetic variation of the brown bears (Ursus arctos L., 1758) of the Kenai Peninsula, south central Alaska. Nuclear genetic variation was similar to that observed in other Alaskan peninsular populations. We detected no significant inbreeding and found no evidence of population substructuring on the Kenai Peninsula. We observed a genetic signature of a bottleneck under the infinite alleles model (IAM), but not under the stepwise mutation model (SMM) or the two-phase model (TPM) of microsatellite mutation. Kenai brown bears have lower levels of mtDNA haplotypic diversity relative to most other brown bear populations in Alaska. ?? 2008 NRC.

Canadian Journal of Zoology↗
USGS1991

Mitochondrial DNA in wildlife forensic science: Species identification of tissues

A common problem in wildlife law enforcement is identifying the species of origin of carcasses, meat, or blood when morphological characters such as hair or bones are not available. Immunological and protein electrophoretic (allozyme or general protein) procedures have been used in species identification with considerable success (Bunch et al. 1976, McClymont et al. 1982, Wolfe 1983, Mardini 1984, Pex and Wolfe 1985, Dratch 1986), However, immunological tests often are not sensitive enough to distinguish closely related species. Furthermore, electrophoretically detectable protein polymorphisms may be lacking in certain populations or species and may not be species-specific. Analysis of DNA in human and wildlife forensics has been shown to be a potentially powerful tool for identification of individuals (Jeffreys et al. 1985, Vassartet al. 1987, Thommasen et al. 1989). Differences in copy number and nucleotide sequence of repetitive sequences in the nuclear (chromosomal) DNA result in hypervariability and individual-specific patterns which have been termed DNA "fingerprints." However, these patterns may be too variable for species identification necessitating analyses of more conservative parts of the genome. Mitochondrial DNA (mtDNA) is haploid, maternally inherited, similar in nucleotide sequence among conspecifics from the same geographic region, and more suitable for species identification, in contrast to hypervariable DNA fingerprints. MtDNA has several characteristics which make it useful as a species-specific marker. In mammals, individuals have a single mtDNA genotype shared by all tissues. Because mtDNA is haploid and reflects only maternal ancestry, the mtDNA gene number in a population is 4 times less than the nuclear gene number (Birky et al. 1983). This can result in relatively rapid loss or fixation of mtDNA genotypes so that all individuals in a population may be descended from a single ancestral female in as few as 4N ( N = population size) generations (Avise et al., 1984). This suggests there is great potential for identification of species-specific or population-specific mtDNA genotypes, Within species, mtDNA genotypes are thought to be selectively neutral, i.e., there is little evidence that genotypes differ in fitness (Nigro and Prout 1990).

Wildlife Society Bulletin↗
USGS1996

Breeding populations of northern pintails have similar mitochondrial DNA

Northern pintails (Anas acuta) are highly nomadic, which may result in high levels of gene flow among nesting areas. To assess the extent of genetic differentiation among nesting areas, we analyzed mitochondrial DNA (mtDNA) variation in northern pintail females from three regions: Alaska, California, and midcontinent prairies and parklands. Abundant mtDNA variation was evident (20 genotypes among 289 birds), but there was no significant genetic differentiation of nesting areas within or among regions. Results indicate that pintails have had historically large breeding population sizes and a high rate of gene flow among North American nesting areas. Specific nesting areas are not independent units, but part of a larger continental population. High rates of gene flow suggest that over time, localized reductions in recruitment or survival may be compensated for by immigration.

Canadian Journal of Zoology↗