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Results for “Mitochondrial DNA Part A”

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At least 19 recordsLinked to original sources

USGS2018

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6 , three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Mitochondrial DNA Part A↗

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↗

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↗

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↗

USGS2006

Genetic variation among subspecies of Least Tern (Sterna antillarum): Implications for conservation

DNA sequence variation from two nuclear introns and part of the mitochondrial cytochrome-b gene were used to Evaluate population structure among three subspecies of Least Term that nest in the United States (California [Sterna antillarum browni], Interior [S. a. athalassos], Eastern [S. a. antillarum]). Sequence variation was highest for nuclear intron XI (Gadp) within the glyceraldehyde-3-phosphate dehydrogenase gene. The second nuclear intron was fixed for the same allele in all subspecies. Fixation indices, FST and MST, for Gadp indicated genetic divergence between California and Interior subspecies. Estimates of nuclear gene flow were <4 individuals/generation, except between the Interior and Eastern subspecies (4 individuals/generation). Genetic indices for mitochondrial DNA did not differ among subspecies, and gene flows (reflecting female dispersal) ranged from 10 to 83 individuals/generation. Reservations are expressed about the validity of the current subspecific divisions and further research is required, including their taxonomic relationship to the Little Tern (Sterna albifrons).

Waterbirds↗

USGS2013

Genetic structure, diversity and subspecies status of Gull-billed Terns (Gelochelidon nilotica) from the United States

Gull-billed Terns (Gelochelidon nilotica) are among the most widespread, yet scarce, Charadriiformes in the world. Two subspecies are recognized in the United States: G. n. aranea breeds along the U.S. Atlantic and Gulf coasts and G. n. vanrossemi breeds in the Salton Sea and San Diego Bay of California. Conservation concerns exist for the species due to its low abundance in the United States and apparent declines in some parts of its North American range. We used nuclear microsatellite markers and mitochondrial DNA sequences to assess genetic diversity and differentiation patterns among Gull-billed Tern populations from Virginia, Texas, and California. We also tested for evidence of population bottlenecks, and evaluated the support our data provide for the North American subspecies. Genetic diversity was highest in Texas and underscored the importance of habitat in that large population. Significant population differentiation existed, but could not be consistently identified using various analytical approaches and suggested that the magnitude of differentiation was low. No evidence for bottlenecks was identified. Our data could not distinguish individuals from different subspecies and therefore do not support the current intraspecific taxonomy. Tenable explanations for many findings are related to the low site tenacity demonstrated by the species.

Waterbirds↗

USGS2013

Genetic relationships among some subspecies of the Peregrine Falcon ( Falco peregrinus L.), inferred from mitochondrial DNA control-region sequences

The ability to successfully colonize and persist in diverse environments likely requires broad morphological and behavioral plasticity and adaptability, and this may partly explain why the Peregrine Falcon ( Falco peregrinus ) exhibits a large range of morphological characteristics across their global distribution. Regional and local differences within Peregrine Falcons were sufficiently variable that ∼75 subspecies have been described; many were subsumed, and currently 19 are generally recognized. We used sequence information from the control region of the mitochondrial genome to test for concordance between genetic structure and representatives of 12 current subspecies and from two areas where subspecies distributions overlap. Haplotypes were broadly shared among subspecies, and all geographic locales shared a widely distributed common haplotype (FalconCR2). Haplotypes were distributed in a star-like phylogeny, consistent with rapid expansion of a recently derived species, with observed genetic patterns congruent with incomplete lineage sorting and/or differential rates of evolution on morphology and neutral genetic characters. Hierarchical analyses of molecular variance did not uncover genetic partitioning at the continental level, despite strong population-level structure ( F ST = 0.228). Similar analyses found weak partitioning, albeit significant, among subspecies ( F CT = 0.138). All reconstructions placed the hierofalcons' (Gyrfalcon [ F. rusticolus ] and Saker Falcon [ F. cherrug ]) haplotypes in a well-supported clade either basal or unresolved with respect to the Peregrine Falcon. In addition, haplotypes representing Taita Falcon ( F. fasciinucha ) were placed within the Peregrine Falcon clade.

The Auk↗

USGS2020

Conservation genetics of imperiled striped whipsnake in Washington

Conservation of wide-ranging species is aided by population genetic information that provides insights into adaptive potential, population size, interpopulation connectivity, and even extinction risk in portions of a species range. The Striped Whipsnake (Masticophis taeniatus) occurs across 11 western U.S. states and into Mexico but has experienced population declines in parts of its range, particularly in the state of Washington. We analyzed nuclear and mitochondrial DNA extracted from 192 shed skins, 63 muscle tissue samples, and one mouth swab to assess local genetic diversity and differentiation within and between the last known whipsnake populations in Washington. We then placed that information in a regional context to better understand levels of differentiation and diversity among whipsnake populations in the northwestern portion of the range of the species. Microsatellite data analyses indicated that there was comparable genetic diversity between the two extant Washington populations, but gene flow may be somewhat limited. We found moderate to high levels of genetic differentiation among states across all markers, including five microsatellites, two nuclear genes, and two mitochondrial genes. Pairwise state-level comparisons and dendrograms suggested that Washington whipsnakes are most closely related to those in Oregon, and distinct from Idaho, Nevada, and Utah, approximately following an isolation by distance model. We conclude that Washington populations of whipsnakes have experienced recent isolating events, but they have yet to lose genetic diversity. The longevity and high vagility of the species may provide opportunity for conservation of whipsnakes in the state as long as shrubland habitat is available

Washington↗

USGS2024

Analysis of mitochondrial DNA sequence data demonstrates that monophyly of myotis occultus is complicated by greater sampling of myotis lucifugus

The validity of Myotis occultus as a species unique from Myotis lucifugus has been a source of debate. Most recently, many authorities treat M. occultus as a distinct species, at least in part because a previous study showed that M. occultus and M. l. carissima (the subspecies that occurs in closest geographic proximity to M. occultus ) form separate monophyletic clades based on sequences of two mitochondrial genes (cytochrome- b [cytb] and cytochrome oxidase subunit II [COII]). We re-evaluated the phylogenetic relationship between M. occultus and M. lucifugus based on mitochondrial sequences using an expanded dataset of cytb and COII sequences that originated from more genetically diverse specimens of M. lucifugus collected across a broader geographic area. Based on a phylogenetic analysis, we found that M. occultus sublineages embedded within a well-supported clade that included some specimens of M. lucifugus . These results indicate that the previous genetic analysis demonstrating that M. occultus and M. lucifugus form distinct monophyletic groups is unsupported by our larger dataset. Future research will likely need to focus on genetic work involving whole-genome sequencing of nuclear DNA to better resolve the true taxonomic relationship between M. occultus and M. lucifugus . La valides de Myotis occultus como una especie distinta a Myotis lucifugus ha sido fuente de debate. Recientemente, muchas autoridades han considerado M. occultus como una especie diferente, en parte porque un estudio anterior mostró que M. occultus y M. l. carissima (la subespecie con la mayor proximidad geográfica a M. occultus) forman clados monofiléticos separados basados en secuencias de dos genes mitocondriales (el citocromo-b [cytb] y la subunidad II de citocromo oxidasa [COII]). Nosotros hemos reevaluado la relación filogenética entre M. occultus y M. lucifugus usando una ampliada colección de datos que contiene secuencias de los genes mitocondriales cytb y COII de especímenes de M. lucifugus genéticamente más diversos que fueron muestreados en un área geográfica más extensa. Nuestro análisis filogenético muestra que los sublinajes de M. occultus están incrustados dentro de un clado bien respaldado que incluye algunos especímenes de M. lucifugus. Estos resultados indican que el análisis genético anterior que demostró que M. occultus y M. lucifugus forman grupos monofiléticos distintos no está respaldado por nuestra más amplia colección de datos. Es probable que para resolver mejor la verdadera relación taxonómica entre M. occultus y M. lucifugus sea necesario el uso de secuenciación del genoma completo del ADN nuclear.

Southwestern Naturalist↗

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↗

USGS2025

Bovine SNP array-based genetic assessment of American plains bison at American Prairie

American plains bison ( Bison bison bison , bison hereafter) experienced an extreme demographic bottleneck in the late 1800s. The species has since rebounded but is primarily managed as small and isolated herds due to habitat and sociopolitical limitations. Thus, reintroducing bison and allowing herds to achieve as much of their natural dynamics as possible is a major conservation goal. Concerns about genetic diversity loss in small, isolated herds and the persistence of cattle-origin variants from historical crossbreeding efforts have made genetic analysis an important part of bison conservation. The limitations of the current conservation genetic tools which are based on traditional markers such as microsatellites and mitochondrial DNA sequences, may be overcome with genome-wide genotyping panels commonly developed for agricultural species. Bison reintroduction in the grasslands at American Prairie began in 2005. Genetic analysis on these herds has yet to be conducted. We used the Illumina 777K Bovine genotyping panel to obtain data from 197 bison and 179 domestic cows to understand the current population genetic state of bison at American Prairie and gain insight on cattle ( Bos taurus ) introgression. Overall, bison at American Prairie currently have relatively high genetic diversity, low inbreeding, and no obvious signs of cattle introgression. A more comprehensive evaluation of introgression, likely including whole-genome sequence data, would clarify this finding. These results can serve as a baseline for future comparison as part of a genetic monitoring framework.

Journal of Heredity↗

USGS2010

Polyphyly of Campylorhamphus , and description of a new genus for C. pucherani (Dendrocolaptinae)

We investigated the phylogenetic relationships of Campylorhamphus pucherani using DNA sequences from three mitochondrial genes and a nuclear intron, as well as 84 morphological characters from the skeleton, the integument, and the musculature. The molecular phylogeny indicated that C. pucherani is not part of Campylorhamphus ; instead, it is the sister species to Drymornis bridgesii , in a clade that also contains Lepidocolaptes . The morphological phylogeny also placed C. pucherani in a clade that contains Drymornis and Lepidocolaptes . Using a morphometric analysis of size and shape diversity, we demonstrated that the inclusion of C. pucherani in Drymornis would create an excessively heterogeneous genus compared with other dendrocolaptine genera. Because no generic name is available for C. pucherani , we describe the new genus Drymotoxeres for this species.

The Auk↗

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↗

USGS2003

Conservation genetics of North American freshwater mussels Amblema and Megalonaias

Freshwater bivalves are among the most endangered groups of organisms in North America. Efforts to protect the declining mussel fauna are confounded by ambiguities associated with recognition of distinct evolutionary entities or species. This, in part, is due to the paucity of reliable morphological characters for differentiating taxa. We have employed allozymes and DNA sequence data to search for diagnosably distinct evolutionary entities within two problematic genera of unionid mussels, Amblema and Megalonaias. Within the genus Amblema three species are recognized based on our DNA sequence data for the mitochondrial 16S rRNA and allozyme data (Amblema neislerii, A. plicata, and A. elliotti). Only one taxonomically distinct entity is recognized within the genus Megalonaias—M. nervosa. Megalonaias boykiniana of the Apalachicolan Region is not diagnosable and does not warrant specific taxonomic status. Interestingly, Megalonaias from west of the Mississippi River, including the Mississippi, exhibited an allozyme and mtDNA haplotype frequency shift suggestive of an east-west dichotomy. The results of this study eliminate one subspecies of Amblema and increase the range of A. plicata. This should not affect the conservation status of “currently stable” assigned to A. plicata by Williams et al. (1993). The conservation status of A. elliotti needs to be reexamined because its distribution appears to be limited to the Coosa River System in Alabama and Georgia.

Conservation Biology↗