Search USGS⌕ Search

SEARCH · Search USGS

Results for “Mitochondrial DNA”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
USGS2000

Molecular analysis of population genetic structure and recolonization of rainbow trout following the Cantara spill

Mitochondrial DNA (mtDNA) sequence and allelic frequency data for 12 microsatellite loci were used to analyze population genetic structure and recolonization by rainbow trout, Oncorhynchus mykiss , following the 1991 Cantara spill on the upper Sacramento River, California. Genetic analyses were performed on 1,016 wild rainbow trout collected between 1993 and 1996 from the mainstem and in 8 tributaries. Wild trout genotypes were compared to genotypes for 79 Mount Shasta Hatchery rainbow trout. No genetic heterogeneity was found 2 years after the spill (1993) between tributary populations and geographically proximate mainstem fish, suggesting recolonization of the upper mainstem directly from adjacent tributaries. Trout collections made in 1996 showed significant year-class genetic variation for mtDNA and microsatellites when compared to fish from the same locations in 1993. Five years after the spill, mainstem populations appeared genetically mixed with no significant allelic frequency differences between mainstem populations and geographically proximate tributary trout. In our 1996 samples, we found no significant genetic differences due to season of capture (summer or fall) or sampling technique used to capture rainbow trout, with the exception of trout collected by electrofishing and hook and line near Prospect Avenue. Haplotype and allelic frequencies in wild rainbow trout populations captured in the upper Sacramento River and its tributaries were found to differ genetically from Mount Shasta Hatchery trout for both years, with the notable exception of trout collected in the lower mainstem river near Shasta Lake, where mtDNA and microsatellite data both suggested upstream colonization by hatchery fish from the reservoir. These data suggest that the chemical spill in the upper Sacramento River produced significant effects over time on the genetic population structure of rainbow trout throughout the entire upper river basin.

California↗
USGS2009

Genetic structure in the Anaxyrus boreas species group (anura, Bufonidae): an evaluation of the Southern Rocky Mountain population

The Anaxyrus boreas species group is comprised of four species endemic to the western United States: A. boreas, A. canorus, A. exsul, and A. nelsoni. Disjunct populations of the widespread western toad Anaxyrus boreas from Colorado and southern Wyoming, the southern rocky mountain population (SRMP), were previously candidates for listing under the United States Endangered Species Act (ESA) as a distinct population segment (DPS), but were removed due to a lack of significant genetic differentiation in preliminary studies. The purpose of this study was to conduct phylogeographic and population genetic analyses of A. boreas and three related species using mitochondrial DNA sequence data and nuclear microsatellite genotype data. The study is specifically focused on testing the evolutionary significance of the SRMP.

Final Report↗
USGS2015

Shoal basses: A clade of cryptic identity

Shoal basses are a cryptic clade composed of Micropterus spp. restricted to the Apalachicola River system and three southeastern Atlantic slope river drainages in the southeastern United States. This reciprocally monophyletic clade includes the Shoal Bass M. cataractae (endemic to the Apalachicola River system), the Chattahoochee Bass M. chattahoochae, and two undescribed forms from the Altamaha, Ogeechee, and Savannah River drainages. Members of the shoal bass clade can be distinguished from all other species of Micropterus basses using 20 diagnostic characters (characteristic attributes) found in mitochondrial DNA (NADH dehydrogenase subunit 2) gene sequences. Each member of the clade additionally possesses unique characteristic attributes, which along with morphological and meristic characters can be used to diagnose this cryptic biodiversity. Biologists and managers have previously regarded the shoal basses in the Chattahoochee, Savannah, Altamaha and Ogeechee River systems as belonging to a single taxon synonymous with the Redeye Bass M. coosae, which is endemic to the Mobile River drainage. With these and previous analyses (including description of the Shoal Bass), we now recognize that what was once considered a single taxon actually comprises seven species, each of which is endemic to a single southeastern drainage. Recognizing and documenting the actual diversity of Micropterus spp. provides important information for managers who may wish to avoid stocking or translocations that could compromise the genetic integrity of native bass populations. Introductions of nonnative basses, including Alabama Bass M. henshalli, Spotted Bass M. punctulatus, and Smallmouth Bass M. dolomieu currently threaten the integrity of native shoal bass species in streams of the Chattahoochee, Altamaha, Ogeechee, and Savannah River systems.

Conference Paper↗
USGS1997

Population genetic studies of the polar bear ( Ursus maritimus ): A summary of available data and interpretation of results

A summary of existing population genetics literature is presented for polar bears ( Ursus maritimus ) and interpreted in the context of the species' life-history characteristics and regional heterogeneity in environmental regimes and movement patterns. Several nongenetic data sets including morphology, contaminant levels, geographic variation in reproductive characteristics, and the location and distribution of open-water foraging habitat suggest some degree of spatial structuring. Eleven populations are recognized by the IUCN Polar Bear Specialist Group. Few genetics studies exist for polar bears. Interpretation and generalizations of regional variation in intra- and interpopulation levels of genetic variability are confounded by the paucity of data from many regions and by the fact that no single informative genetic marker has been employed in multiple regions. Early allozyme studies revealed comparatively low levels of genetic variability and no compelling evidence of spatial structuring. Studies employing mitochondrial DNA (mtDNA) also found low levels of genetic variation, a lack of phylogenetic structure, and no significant evidence for spatial variation in haplotype frequency. In contrast, microsatellite variable number of tandem repeat (VNTR) loci have revealed significant heterogeneity in allele frequency among populations in the Canadian Arctic. These regions are characterized by archipelgic patterns of sea-ice movements. Further studies using highly polymorphic loci are needed in regions characterized by greater polar bear dependency on pelagic sea-ice movements and in regions for which no data currently exist (i.e., Laptev and Novaya Zemlya/Franz Josef).

Book chapter↗
USGS1997

Population genetic studies of the sea otter ( Enhydra lutris ): A review and interpretation of available data

C urrent information about the utility of genetic markers for estimating population structuring in sea otters ( Enhydra lutris ) is reviewed. Analyses of spatial population structuring with biochemical and molecular genetic markers are discussed in the context of the species' ecology and history of exploitation. Studies that have used a diversity of genetic markers including allozymes, mitochondrial DNA (mtDNA), and multilocus minisatellites revealed that geographically spearated populations of sea otters are highly differentiated, though little evidence for phylogeographic structuring was suggested. Analyses of population relationships based on mtDNA haplotype frequency distribution suggested that populations can be separated into four major groups: (1) California; (2) Prince William Sound, Alaska; (3) Kodiak Island, Alaska, and islands of the Aleutian archipelago, including the Commander Islands; and (4) the Kuril Islands. Populations from locales separated by large geographic distances often shared haplotypes, suggesting recent common ancestry and some degree of historical gene flow. THe large differences among populations in nuclear and mtDNA gene frequency suggested strong constrains on contemporary gene flow and/or considerable drift in gene frequencies due to population bottlenecks. No evidence for microgeographic structuring was noted. Levels of genetic diversity within populations varied greatly across the species range but were not related to contemporary estimates of population size.

Conference Paper↗
USGS2003

A genetic study to aid in restoration of murres, guillemots and murrelets to the Gulf of Alaska

Genetic data are needed to aid in restoring several species of seabirds to the Gulf of Alaska. We analyzed sequence variation in mitochondrial DNA, microsatellite DNA and nuclear introns in samples of commom murres ( Uria aalge ), pigeon guillemots ( Cepphus columba ) and marbled murrelets ( Brachyramphus marmoratus ) from throughout the North Pacific. Data were analyzed using traditional approaches, nested clade analyses and assignment tests. No cryptic species were found, and there was no strong evidence for inbreeding, low genetic variation, or souce or sink regions in any them. Pacific common murres constitute a single genetic management unit (MU), but hybridization occurs between common and thick-billed murres ( U. lomvia ). In contrast, gene flow in pigeon guillemots is very restricted and population genetic structure is very strong; guillemots from the spill area are part of a MU that extends from the Alaska Peninsula to somewhere between Prince William Sound and Vancouver Island. Marbled murrelets in the spill area are part of a MU that extends from the Alaska Peninsula to at least British Columbia; tree- and ground-nesting murrelets are not genetically differentiated. Little if any hybridization occurs between marbled and Kittlitz's murrelets.

Alaska↗
USGS2003

Population genetic structure of Santa Ynez rainbow trout – 2001 based on microsatellite and mtDNA analyses

Microsatellite allelic and mitochondrial DNA (mtDNA) haplotype diversity are analyzed in eight rainbow trout ( Oncorhynchus mykiss ) collections: two from tributaries flowing into the upper Santa Ynez River watershed at Gibraltar Reservoir (Camuesa and Gidney creeks); three from tributaries between Gibraltar and Jameson reservoirs (Fox, Blue Canyon, and Alder creeks); one from a tributary above Jameson Reservoir (Juncal Creek); Jameson Reservoir; and one from the mainstem Santa Ynez River above the Jameson Reservoir. Both analyses reveal a high degree of population structure. Thirteen microsatellite loci are amplified from 376 fish. Population pairwise comparisons show significant differences in allelic frequency among all populations with the exception of Juncal Creek and Jameson Reservoir (p = 0.4). Pairwise F st values range from 0.001 (Juncal Creek and Jameson Reservoir) to 0.17 (Camuesa and Juncal creeks) with an overall value of 0.021. Regression analyses (Slatkin 1993) supports an isolation-bydistance model in the five populations below Jameson Reservoir (intercept = 1.187, slope = -0.41, r2 = 0.67). A neighbor-joining bootstrap value of 100% (based on 2000 replicate trees) separates the populations sampled above and below Juncal Dam. Composite haplotypes from 321 fish generated using mtDNA sequence data (Dloop) reveal four previously described haplotypes (MYS1, MYS3, MYS5 and MYS8; Nielsen et al. 1994a), and one (MYS5) was found in all populations. Mean haplotype diversity is 0.48. Pairwise F st values from mtDNA range from -0.019 to 0.530 (0.177 over all populations) and are larger than those for microsatellites in 26 of 28 pairwise comparisons. In addition, the mtDNA and microsatellites provide contrasting evidence of the relationship of Fox and Alder creeks to the other six populations. Discrepancies between the two markers are likely due to the unique properties of the two marker types and their value in revealing historic (mtDNA) versus contemporary (microsatellites) genetic relationships. The contrasting results may indicate how relationships among the upper Santa Ynez River populations have changed since the installation of Juncal Dam. Comparisons of mtDNA haplotype frequencies from fish collected for this study with samples analyzed previously in JLN’s laboratory (1993) reveal significant differences in mtDNA haplotypes for Fox and Alder creeks. In the 2001 samples from this study, there is a loss of three haplotypes despite larger sample sizes. AMOVA analysis of what we term “upper” (Alder, Fox, Blue Canyon, Camuesa, Gidney creeks and the upper Santa Ynez mainstem) and “lower” (Hilton, Salsipuedes and the lower mainstem Santa Ynez River) Santa Ynez River populations (1993-2001) reveal that 11% of the variance in haplotypes is found between the upper and lower drainage. A comparison of the mtDNA data from this study with those available for southern California coastal and California hatchery O. mykiss populations yields F st values of 0.15 and 0.47, respectively. Differentiation of mtDNA haplotypes for population pairs of Santa Ynez River and hatchery fish show no significant differentiation between wild and at least one hatchery strain in Cachuma Reservoir, Hilton Creek, and the Lower Santa Ynez River.

California↗
USGS2009

Genetic conservation and paddlefish propagation

The conservation of genetic diversity of our natural resources is overwhelmingly one of the central foci of 21st century management practices. Three recommendations related to the conservation of paddlefish Polyodon spathula genetic diversity are to (1) identify genetic diversity at both nuclear and mitochondrial DNA loci using a suggested list of 20 sampling locations, (2) use genetic diversity estimates to develop genetic management units, and (3) identify broodstock sources to minimize effects of supplemental stocking on the genetic integrity of native paddlefish populations. We review previous genetic work on paddlefish and described key principles and concepts associated with maintaining genetic diversity within and among paddlefish populations and also present a genetic case study of current paddlefish propagation at the U.S. Fish and Wildlife Service Gavins Point National Fish Hatchery. This study confirmed that three potential sources of broodfish were genetically indistinguishable at the loci examined, allowing the management agencies cooperating on this program flexibility in sampling gametes. This study also showed significant bias in the hatchery occurred in terms of male reproductive contribution, which resulted in a shift in the genetic diversity of progeny compared to the broodfish. This shift was shown to result from differential male contributions, partially attributed to the mode of egg fertilization. Genetic insights enable implementation of a paddlefish propagation program within an adaptive management strategy that conserves inherent genetic diversity while achieving demographic goals.

American Fisheries Society Symposium↗
USGS1989

Gopherus agassizii : Desert tortoise

The desert tortoise is one of four allopatric North American tortoises. It occurs in the Mojave and Sonoran deserts of the southwestern United States and Mexico. Auffenberg (1976) divided the genus Gopherus (consisting of four species, G. agassizi , G. berlandieri , G.flavomarginatus , and G. polyphemus ) in two osteological groups. Bramble (1982), using morphological and palaeontological data, divided the genus Gopherus into two separate complexes, each with two species. He established a new genus, Scaptochelys , for agassizi and berlandieri , retaining Gopherus for polyphemus and flavomarginatus . Bour and Dubois (1984) noted that Xerobates Agassiz had priority over Scaptochelys Bramble. Using mitochondrial DNA (mtDNA), Lamb et al. (1989) evaluated the evolutionary relationships of the North American tortoises, particularly the desert tortoise. They concluded that the mtDNA analysis provides strong support for generic recognition of the two distinct species groups described by Bramble (1982). Until a few decades ago, the desert tortoise was widespread at lower elevations throughout the Mojave and Sonoran deserts of the U.S.A. In the northern and western parts of the geographic range, large and relatively homogeneous populations with densities exceeding 1,000/sq km extended throughout parts of California, and probably into Nevada and Utah. In terms of biomass, the tortoise played an important role in the ecosystems. In most areas, numbers have declined dramatically and the extent of populations has been reduced. Most populations are now isolated and low in numbers. Conservation of the desert tortoise is a highly visible and political issue in the U.S.A., but not in Mexico.

Book chapter↗
USGS2008

Tracing the first steps of American sturgeon pioneers in Europe

Background. A Baltic population of Atlantic sturgeon was founded ???1,200 years ago by migrants from North America, but after centuries of persistence, the population was extirpated in the 1960s, mainly as a result of over-harvest and habitat alterations. As there are four genetically distinct groups of Atlantic sturgeon inhabiting North American rivers today, we investigated the genetic provenance of the historic Baltic population by ancient DNA analyses using mitochondrial and nuclear markers. Results. The phylogeographic signal obtained from multilocus microsatellite DNA genotypes and mitochondrial DNA control region haplotypes, when compared to existing baseline datasets from extant populations, allowed for the identification of the region-of-origin of the North American Atlantic sturgeon founders. Moreover, statistical and simulation analyses of the multilocus genotypes allowed for the calculation of the effective number of individuals that originally founded the European population of Atlantic sturgeon. Our findings suggest that the Baltic population of A. oxyrinchus descended from a relatively small number of founders originating from the northern extent of the species' range in North America. Conclusion. These results demonstrate that the most northerly distributed North American A. oxyrinchus colonized the Baltic Sea ???1,200 years ago, suggesting that Canadian specimens should be the primary source of broodstock used for restoration in Baltic rivers. This study illustrates the great potential of patterns obtained from ancient DNA to identify population-of-origin to investigate historic genotype structure of extinct populations. ?? 2008 Ludwig et al; licensee BioMed Central Ltd.

BMC Evolutionary Biology↗
USGS2013

Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

Mitochondrial DNA↗
USGS2008

Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization

Spatial genetic structure in populations of mosquitofish ( Gambusia ) sampled throughout the south-eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south-eastern Mississippi to north-eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrooki to the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species-specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.

Molecular Ecology↗
USGS2011

Comparative mitochondrial genetics of North American and Eurasian mergansers with an emphasis on the endangered scaly-sided merganser (Mergus squamatus)

The scaly-sided merganser, Mergus squamatus , is considered one of the most threatened sea duck species in the Palearctic with limited breeding and wintering distribution in China and Russia. To provide information for future conservation efforts, we sequenced a portion of the mitochondrial (mt) DNA control region in four species of mergansers and three additional sea duck taxa to characterize the evolutionary history of the scaly-sided merganser, infer population trends that may have led to its limited geographic distribution, and to compare indices of genetic diversity among species of mergansers. Scaly-sided mergansers exhibit substantially lower levels of mtDNA genetic diversity ( h = 0.292, π = 0.0007) than other closely related sea ducks and many other avian taxa. The four haplotypes observed differed by a single base pair suggesting that the species has not experienced a recent population decline but has instead been at a low population level for some time. A phylogenetic analysis placed the scaly-sided merganser basal to North American and European forms of the common merganser, M. merganser . Our inclusion of a small number of male samples doubled the number of mtDNA haplotypes observed, suggesting that additional genetic variation likely exists within the global population if there is immigration of males from unsampled breeding areas.

Conservation Genetics↗
USGS2019

Temporal variation in genetic structure within the threatened spectacled eider

We examined the genetic structure of the threatened spectacled eider 14–18 years after the initial assessment to evaluate the influence of population recovery on diversity. Concordant with the initial assessment, spectacled eiders were highly structured at mitochondrial (mt) DNA and lacked differentiation at microsatellite loci. The degree and spatial pattern of structure has changed at mtDNA; a 33.0–40.3% reduction in overall FST and ΦST, respectively, and a marked reduction in pairwise FST (-83.1 to -91.4%) among Alaska sites. Reduction in genetic structure is suggestive of increased female dispersal within Alaska. These findings highlight the importance of reevaluating genetic diversity as species recover from declines as microevolutionary and demographic processes are dynamic and continually shape associations among populations.

Alaska↗
USGS2021

Coalescent methods reconstruct contributions of natural colonization and stocking to origins of Michigan inland Cisco (Coregonus artedi)

Fish population structure in previously glaciated regions is often influenced by natural colonization processes and human-mediated dispersal, including fish stocking. Endemic populations are of conservation interest because they may contain rare and unique genetic variation. While coregonines are native to certain Michigan inland lakes, some were stocked with fish from Great Lakes sources, calling into question the origin of extant populations. While most stocking targeted lake whitefish ( Coregonus clupeaformis ), cisco ( C. artedi ) were also stocked from the Great Lakes to inland waterbodies. We used population genetic data (microsatellite genotypes and mitochondrial (mt)DNA sequences), coalescent modeling, and approximate Bayesian computation to investigate the origins of 12 inland Michigan cisco populations. The spatial distribution of mtDNA haplotypes suggests Michigan is an introgression zone for two ancestral cisco lineages associated with separate glacial refugia. Low levels of genetic diversity and high levels of genetic divergence were observed for populations located well inland of the Great Lakes relative to populations occupying waterbodies near the Great Lakes. Estimates of recent Great Lakes gene flow ranged from 27 to 48% for populations near the Great Lakes shoreline but were substantially lower (under 8%) for populations further inland. Inland lakes with elevated recent gene flow estimates may have been recipients of stocked coregonine fry, including cisco. Low levels of genetic diversity paired with a high likelihood of endemism as indicated by strong genetic divergence and low Great Lakes population inputs suggest the analyzed cisco populations occupying southern Michigan kettle lakes are of elevated conservation interest.

Michigan↗
USGS2003

Isolation and characterization of novel waterfowl microsatellite loci: Cross-species comparisons and research applications

Waterfowl constitute an ecologically diverse group which are the subject of extensive research (e.g. see reviews in Batt et al . 1992), and are intensively managed (Nichols et al .1995). Genetic studies utilizing allozyme electrophoresis and mitochondrial (mt)DNA have provided valuable information on waterfowl ecology and evolutionary history (Cooke & Buckley 1987). However, highly variable molecular genetic markers (e.g. multilocus minisatellites; Triggs et al. 1992) have not generally been identified for this group.

Molecular Ecology↗
USGS2010

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

PNAS↗
USGS2016

Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda)

The mitochondrial genomes of three North American stygobiont amphipods Stygobromus tenuis potomacus , S. foliatus and S. indentatus collected from Caroline County, VA, were sequenced using a shotgun sequencing approach on an Illumina NextSeq500 (Illumina Inc., San Diego, CA). All three mitogenomes displayed 13 protein-coding genes, 22 tRNAs and two rRNAs typical of metazoans. While S. tenuis and S. indentatus displayed identical gene orders similar to the pancrustacean ground pattern, S. foliatus displayed a transposition of the trnL2 - cox2 genes to after atp8-atp6 . In addition, a short atp8 gene, longer rrnL gene and large inverted repeat within the Control Region distinguished S. foliatus from S. tenuis potomacus and S. indentatus . Overall, it appears that gene order varies considerably among amphipods, and the addition of these Stygobromus mitogenomes to the existing sequenced amphipod mitogenomes will prove useful for characterizing evolutionary relationships among various amphipod taxa, as well as investigations of the evolutionary dynamics of the mitogenome in general.

Mitochondrial DNA Part B↗