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At least 235 records · Page 13Linked to original sources
USGS2018

The complete mitochondrial genome of the stalk-forming diatom Didymosphenia geminata

The complete mitogenome of the stalk-forming diatom Didymosphenia geminata collected from Mineral County, WV, USA was sequenced on the Ion Torrent PGM and Proton sequencers. The D. geminata mitogenome is 37,765 bp and encodes 35 protein coding genes, 25 tRNAs, and both large and small subunit ribosomal RNA genes. The nad 11 gene is split into two domains as observed in Phaeodactylum tricornutum , and D. geminata also lacks the large repeat region found in the P. tricornutum mitogenome. Gene order and content within the D. geminata mitogenome is similar to the diatom Berkeleya fennica .

Mitochondrial DNA Part B↗
USGS2018

The complete mitochondrial genome of Hine’s emerald dragonfly (Somatochlora hineana Williamson) via NGS sequencing

Here, we report the complete mitochondrial genome of the endangered Hine’s emerald dragonfly (HED), Somatochlora hineana Williamson. Data were generated via next generation sequencing (NGS) and assembled using a mitochondrial baiting and iterative mapping approach. The full length circular genome is 15,705 bp with 26.6% GC content. It contains the typical metazoan set of 37 genes: 13 protein-coding genes, 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, and an A + T-rich control region. To our knowledge, this is the first report of the complete HED mitogenome.

Mitochondrial DNA Part B↗
USGS2018

The complete maternal mitochondrial genome sequences of two imperiled North American freshwater mussels: Alasmidonta heterodon and Alasmidonta varicosa (Bivalvia: Unionoida: Unionidae)

The freshwater mussels Alasmidonta heterodon and A. varicosa historically inhabited rivers along the North American Atlantic coast from the Carolinas, U.S.A., to New Brunswick, CA. However, many populations have been extirpated, and A. heterodon is now federally listed in the U.S.A. as endangered, and both A. heterodon and A. varicosa are listed as vulnerable on the IUCN Red List. To facilitate genetic study of these species, we sequenced the complete female mitochondrial genomes of A. heterodon (15,909 bp; GenBank accession no. MG905826), and A. varicosa (15,693 bp; GenBank accession no. MG938673). Both mitogenomes contained 14 protein coding genes, 2 rRNA genes, and 22 tRNAs with the same gene order as reported for other members of the subfamily Anodontinae. When these two genomes were put into a phylogenetic context with other members of the Unionidae, they clustered together with other species in the subfamily Anodontinae, Tribe Anodontini.

Mitochondrial DNA Part B↗
USGS2020

Mitogenome of northern long-eared bat

The complete mitogenome of the northern long-eared bat ( Myotis septentrionalis) was determined to be 17,362 bp and contained 22 tRNA genes, 2 rRNA genes and one control region. The whole genome base composition was 33.8% GC. Phylogenetic analysis suggests that M. septentrionalis be positioned next to M. auriculus in the Nearctic subclade of the Myotis genus. This complete mitochondrial genome provides essential molecular markers for resolving phylogeny and future conservation efforts.

Mitochondrial DNA Part B↗
USGS2025

The complete mitochondrial genomes of the freshwater mussel Ortmanniana ligamentina (Lamarck, 1819): male and female mitotypes

Freshwater mussels of the Unionida order are important to freshwater ecosystems but are highly imperiled worldwide. Improving our understanding of these species is crucial to their continued conservation. Some Unionid mussels exhibit double uniparental inheritance (DUI) in which individuals have two mitochondrial genomes. Of those species with DUI, sequences of the female mitotype are most prevalent in genetic databases. Here, we demonstrate the ability to recover both mitotypes of Ortmanniana ligamentina (Lamarck, 1819) from a non-lethal collection method coupled with high-throughput sequencing. Increased male mitotype sequence representation facilitates understanding Unionid genetic diversity and development of molecular tools for species detection.

Missouri, Pennsylvania↗
USGS2014

Distribution and population genetics of walleye and sauger

Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the “blue pike”.

BMC Evolutionary Biology↗
USGS2009

Mechanisms of population heterogeneity among molting common mergansers on Kodiak Island, Alaska: Implications for genetic assessments of migratory connectivity

Quantifying population genetic heterogeneity within nonbreeding aggregations can inform our understanding of patterns of site fidelity, migratory connectivity, and gene flow between breeding and nonbreeding areas. However, characterizing mechanisms that contribute to heterogeneity, such as migration and dispersal, is required before site fidelity and migratory connectivity can be assessed accurately. We studied nonbreeding groups of Common Mergansers ( Mergus merganser ) molting on Kodiak Island, Alaska, from 2005 to 2007, using banding data to assess rates of recapture, mitochondrial (mt) DNA to determine natal area, and nuclear microsatellite genotypes to assess dispersal. Using baseline information from differentiated mtDNA haplogroups across North America, we were able to assign individuals to natal regions and document population genetic heterogeneity within and among molting groups. Band-recovery and DNA data suggest that both migration from and dispersal among natal areas contribute to admixed groups of males molting on Kodiak Island. A lack of differentiation in the Common Merganser's nuclear, bi-parentally inherited DNA, observed across North America, implies that dispersal can mislead genetic assessments of migratory connectivity and assignments of nonbreeding individuals to breeding areas. Thus multiple and independent data types are required to account for such behaviors before accurate assessments of migratory connectivity can be made.

Alaska↗
USGS1999

Genetic and morphometric assessment of an unusual tortoise (Gopherus agassizii) population in the Black Mountains of Arizona

Under recent regulatory designation of the U.S. Fish and Wildlife Service, desert tortoises (Gopherus agassizii) occurring east and south of the Colorado River constitute the Sonoran population, whereas those to the west and north form the Mojave population. These management units, distinguished by significant genetic, morphometric, and ecological differences, represent deep phylogenetic subdivisions within G. agassizii and are of high conservation value. We provide genetic and morphological profiles for an unusual tortoise population inhabiting the Black Mountains of Arizona, some 40 km east of the Colorado River. Both mitochondrial (mt) DNA and morphometric analyses revealed predominately Mojavean features: ten of eleven Black Mountain tortoises possessed Mojave mtDNA markers, and 24 of 37 animals exhibited Mojave morphometric phenotypes. Our results indicate west-to-east movement of tortoises across the Colorado River, though how or when a Mojave lineage became established in the Black Mountains is difficult to ascertain. Active dispersal, river meander, and human transport (early or modern peoples) serve as plausible explanations. Future management of the Black Mountain tortoises should emphasize the population's Mojavean affinities.

Journal of Herpetology↗
USGS2017

Genomics of Arctic cod

The Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. To better understand the population genetic structure and the role of natural selection acting on the maternally-inherited mitochondrial genome (mitogenome), a molecule often associated with adaptations to temperature, we analyzed genetic data collected from 11 biparentally-inherited nuclear microsatellite DNA loci and nucleotide sequence data from from the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and, for a subset of individuals, the entire mitogenome. In addition, due to potential of species misidentification with morphologically similar Polar cod (Arctogadus glacialis), we used ddRAD-Seq data to determine the level of divergence between species and identify species-specific markers. Based on the findings presented here, Arctic cod across the Pacific Arctic (Bering, Chukchi, and Beaufort Seas) comprise a single panmictic population with high genetic diversity compared to other gadids. High genetic diversity was indicated across all 13 protein-coding genes in the mitogenome. In addition, we found moderate levels of genetic diversity in the nuclear microsatellite loci, with highest diversity found in the Chukchi Sea. Our analyses of markers from both marker classes (nuclear microsatellite fragment data and mtDNA cytb sequence data) failed to uncover a signal of microgeographic genetic structure within Arctic cod across the three regions, within the Alaskan Beaufort Sea, or between near-shore or offshore habitats. Further, data from a subset of mitogenomes revealed no genetic differentiation between Bering, Chukchi, and Beaufort seas populations for Arctic cod, Saffron cod (Eleginus gracilis), or Walleye pollock (Gadus chalcogrammus). However, we uncovered significant differences in the distribution of microsatellite alleles between the southern Chukchi and central and eastern Beaufort Sea samples of Arctic cod. Finally, using ddRAD-Seq data, we identified species-specific markers and in conjunction with mitogenome data, identified an Arctic cod x Polar cod hybrid in western Canadian Beaufort Sea. Overall, the lack of genetic structure among Arctic cod within the Bering, Chukchi and Beaufort seas of Alaska is concordant with the absence of geographic barriers to dispersal and typical among marine fishes. Arctic cod may exhibit a genetic pattern of isolation-by-distance, whereby populations in closer geographic proximity are more genetically similar than more distant populations. As this signal is only found between our two fartherest localities, data from populations elsewhere in the species’ global range are needed to determine if this is a general characteristic. Further, tests for selection suggested a limited role for natural selection acting on the mitochondrial genome of Arctic cod, but do not exclude the possibility of selection on genes involved in nuclear-mitogenome interactions. Unlike previous genetic assessment of Arctic cod sampled from the Chukchi Sea, the high levels of genetic diversity found in Arctic cod assayed in this study, across regions, suggests that the species in the Beaufort and Chukchi seas does not suffer from low levels of genetic variation, at least at neutral genetic markers. The large census size of Arctic cod may allow this species to retain high levels of genetic diversity. In addition, we discovered the presence of hybridization between Arctic and Polar cod (although low in frequency). Hybridization is expected to occur when environmental changes modify species distributions that result in contact between species that were previously separated. In such cases, hybridization may be an evolutionary mechanism that promotes an increase in genetic diversity that may provide species occupying changing environments with locally-adapted genotypes and, therefore, phenotypes. Natural selection can only act on the standing genetic variation present within a population. Therefore, given its higher levels of genetic diversity in combination with a large population size, Arctic cod may be resilient to current and future environmental change, as high genetic diversity is expected to increase opportunities for positive selection to act on genetic variants beneficial in different environments, regardless of the source of that genetic variation.

OCS Study↗
USGS2025

Quantitative PCR detection of endangered diamond darter Crystallaria Cincotta in environmental DNA: Employing locked nucleic acids and blocking probe for specificity

This study presents a quantitative PCR (qPCR) assay for the detection of the endangered diamond darter Crystallaria cincotta from environmental DNA (eDNA) in water samples. The assay design is based on an alignment of mitochondrial cytochrome b DNA sequences from 58 individuals representing 25 percid species. Leveraging genetic differences, a species-specific qPCR assay was designed, incorporating alocked nucleic acid (LNA)-enriched probe and a secondary blocking probe to enhance specificity. The assay targets a 93-base pair fragment that includes a diagnostic single nucleotide polymorphism in the probe region; combined with multiple primer mismatches, this provides specificity for distinguishing C. cincotta from other sympatric percid species. Specificity was validated by testing genomic DNA from 16 percid species and synthetic templates, confirming no cross-reactivity. Performance metrics, including the standard curve, qPCR efficiency, limit of detection, and limit of quantification, are reported. The qPCR assay exhibited sufficient sensitivity to detect C. cincotta eDNA in environmental water samples collected from occupied riverine habitats. This study illustrates the effectiveness of LNA-enriched and blocking probes in developing species-specific qPCR assays for eDNA applications, demonstrating their utility in accurately distinguishing closely related species within diverse fish communities.

Conservation Genetics Resources↗
USGS2018

A simplified field protocol for genetic sampling of birds using buccal swabs

DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for amplifying mitochondrial and nuclear markers; however, buccal swab protocols often include steps (e.g., extended air-drying and storage under frozen conditions) not easily adapted to field settings. Furthermore, commercial extraction kits and swabs for buccal sampling can be expensive for large population studies. We therefore developed an efficient, cost-effective, and field-friendly protocol for sampling wild birds after comparing DNA yield among 3 inexpensive buccal swab types (2 with foam tips and 1 with a cotton tip). Extraction and amplification success was high (100% and 97.2% respectively) using inexpensive generic swabs. We found foam-tipped swabs provided higher DNA yields than cotton-tipped swabs. We further determined that omitting a drying step and storing swabs in Longmire buffer increased efficiency in the field while still yielding sufficient amounts of DNA for detailed population genetic studies using mitochondrial and nuclear markers. This new field protocol allows time- and cost-effective DNA sampling of juveniles or small-bodied birds for which drawing blood may cause excessive stress to birds and technicians alike.

Wilson Journal of Ornithology↗
USGS2012

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Proceedings of the National Academy of Sciences↗
USGS2010

Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee

The Antillean subspecies of the West Indian manatee Trichechus manatus is found throughout Central and South America and the Caribbean. Because of severe hunting pressure during the 17th through 19th centuries, only small populations of the once widespread aquatic mammal remain. Fortunately, protections in Belize reduced hunting in the 1930s and allowed the country's manatee population to become the largest breeding population in the Wider Caribbean. However, increasing and emerging anthropogenic threats such as coastal development, pollution, watercraft collision and net entanglement represent challenges to this ecologically important population. To inform conservation and management decisions, a comprehensive molecular investigation of the genetic diversity, relatedness and population structure of the Belize manatee population was conducted using mitochondrial and microsatellite DNA. Compared with other mammal populations, a low degree of genetic diversity was detected ( H E =0.455; N A =3.4), corresponding to the small population size and long-term exploitation. Manatees from the Belize City Cayes and Southern Lagoon system were genetically different, with microsatellite and mitochondrial F ST values of 0.029 and 0.078, respectively ( P ≤0.05). This, along with the distinct habitats and threats, indicates that separate protection of these two groups would best preserve the region's diversity. The Belize population and Florida subspecies appear to be unrelated with microsatellite and mitochondrial F ST values of 0.141 and 0.63, respectively ( P ≤0.001), supporting the subspecies designations and suggesting low vagility throughout the northern Caribbean habitat. Further monitoring and protection may allow an increase in the Belize manatee genetic diversity and population size. A large and expanding Belize population could potentially assist in the recovery of other threatened or functionally extinct Central American Antillean manatee populations.

Animal Conservation↗
USGS2023

Confirmation of significant sea turtle nesting activity on a remote island chain in the Gulf of Mexico

Globally, six of the seven sea turtle species are threatened or endangered and as such, monitoring reproductive activity for these species is necessary for effective population recovery. Remote beaches provide a challenge to conducting these surveys, which often results in data gaps that can hamper management planning. Throughout the summer of 2022, aerial surveys were conducted over the Chandeleur Islands in the Gulf of Mexico. Turtle crawls were photographed for subsequent review by 10 expert observers. Whenever possible, ground surveys were conducted, and samples of unhatched eggs or dead hatchlings were collected. A summary of historic reports of sea turtle nesting activity at this site was also compiled. On 11 days between May 4, 2022, and July 30, 2022, photographs of 55 potential sea turtle crawls were taken. Observers identified 54 of those as being made by a sea turtle. There was high-to-moderate certainty that 16 of those crawls were nests, that 14 were made by loggerheads, and that two were made by Kemp's ridleys. Observers were least certain of species identification when surveys were conducted during rainy weather. Genetic analyses based on mitochondrial and nuclear DNA were conducted on samples from five nests and those analyses confirmed that three nests were laid by Kemp's ridleys and two were laid by loggerheads. Historic records from the Chandeleur Islands substantiate claims that the Chandeleurs have supported sea turtle nesting activity for decades; however, the consistency of this activity remains unknown. Our aerial surveys, particularly when coupled with imaging, were a useful tool for documenting nesting activity on these remote islands. Future monitoring programs at this site could benefit from a standardized aerial survey program with a seaplane so trends in nesting activity could be determined particularly as the beach undergoes restoration.

Louisiana↗
USGS2011

Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae)

Imperiled Okaloosa darters ( Etheostoma okaloosae ) are small, benthic fish limited to six streams that flow into three bayous of Choctawhatchee Bay in northwest Florida, USA. We analyzed the complete mitochondrial cytochrome b gene and 10 nuclear microsatellite loci for 255 and 273 Okaloosa darters, respectively. Bayesian clustering analyses and AMOVA reflect congruent population genetic structure in both mitochondrial and microsatellite DNA. This structure reveals historical isolation of Okaloosa darter streams nested within bayous. Most of the six streams appear to have exchanged migrants though they remain genetically distinct. The U.S. Fish and Wildlife Service recently reclassified Okaloosa darters from endangered to threatened status. Our genetic data support the reclassification of Okaloosa darter Evolutionary Significant Units (ESUs) in the larger Tom’s, Turkey, and Rocky creeks from endangered to threatened status. However, the three smaller drainages (Mill, Swift, and Turkey Bolton creeks) remain at risk due to their small population sizes and anthropogenic pressures on remaining habitat. Natural resource managers now have the evolutionary information to guide recovery actions within and among drainages throughout the range of the Okaloosa darter.

Florida↗
USGS2018

Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae)

Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura . Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura . We recommend that C. viridipennis , currently generally treated as specifically distinct from C. chapmani , be returned to its former status as C. chapmani viridipennis , and that C. andrei , now generally regarded as synonymous with C. vauxi aphanes , again be recognized as a valid species. Widespread Neotropical species C. spinicaudus is paraphyletic with respect to more range-restricted species C. fumosa , C. egregia , and C. martinica . Geographically structured genetic variation within some other species of Chaetura , especially notable in C. cinereiventris , suggests that future study may lead to recognition of additional species in this genus. Biogeographic analysis indicated that Chaetura originated in South America and identified several dispersal events to Middle and North America following the formation of the Isthmus of Panama.

Molecular Phylogenetics and Evolution↗
USGS2008

Middle to late cenozoic geology, hydrography, and fish evolution in the American Southwest

An evaluation of the poorly understood Cenozoic hydrologic history of the American Southwest using combined geological and biological data yields new insights with implications for tectonic evolution. The Mesozoic Cordilleran orogen next to the continental margin of southwestern North America probably formed the continental divide. Mountain building migrated eastward to cause uplift of the Rocky Mountains during the Late Cretaceous to early Tertiary Laramide orogeny. Closed drainage basins that developed between the two mountain belts trapped lake waters containing fish of Atlantic affinity. Oligocene-Miocene tectonic extension fragmented the western mountain belt and created abundant closed basins that gradually filled with sediments and became conduits for dispersal of fishes of both Pacific and Atlantic affinity. Abrupt arrival of the modern Colorado River to the Mojave-Sonora Desert region at ca. 5 Ma provided a new conduit for fish dispersal. Great dissimilarities in modern fish fauna, including differences in their mitochondrial deoxyribonucleic acid (DNA), indicate that late Miocene runoff from the Colorado Plateau did not flow down the Platte or Rio Grande, or through the Lake Bonneville Basin. Fossil fishes from the upper Miocene part of the Bidahochi Formation on the Colorado Plateau have characteristics that reflect a habitat of large, swift-moving waters, and they are closely related to fossil fishes associated with the Snake and Sacramento Rivers. This evidence suggests that influx of fishes from the ancestral Snake River involved a major drainage, not merely small headwater transfers. ?? 2008 The Geological Society of America.

Conference Paper↗
USGS2005

The severity of Whirling disease among wild trout corresponds to the differences in genetic composition of tubifex tubifex populations in Central Colorado

We analyzed the geographic distribution of Tubifex tubifex from various river drainages in central Colorado by genetic screening with specific mitochondrial 16S ribosomal DNA (mt 16S rDNA) markers. Four distinct mt 16S rDNA lineages are evident. The sites varied with respect to land- and water-use practices. All sites represented habitats presumed capable of supporting oligochaetes. At the locations where whirling disease has had the greatest impact on resident rainbow trout, T. tubifex, representing lineages I and III (genotypes known to be susceptible to Mxyobolus cerebralis), were most commonly found. In contrast, at sites less affected by whirling disease, T. tubifex of lineages V and VI that are more resistant to M. cerebralis infections were more abundant. The predominance of resistant T. tubifex worms (lineages V and VI) at low-impact sites supports the conclusion that when these genotypes are in greater abundance, the potential for more severe effects of whirling disease on wild rainbow trout populations may be diminished. ?? American Society of Parasitologists 2005.

Journal of Parasitology↗