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At least 379 records · Page 21Linked to original sources

USGS2018

Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides

Codominant marker systems are better suited to analyze population structure and assess the source of an individual in admixture analyses. Currently, there is no codominant marker system using microsatellites developed for the sea sandwort, Honckenya peploides (L.) Ehrh., an early colonizer in island systems. We developed and characterized novel microsatellite loci from H. peploides , using reads collected from whole genome shotgun sequencing on a 454 platform. The combined output from two shotgun runs yielded a total of 62,669 reads, from which 58 loci were screened. We identified 12 polymorphic loci that amplified reliably and exhibited disomic inheritance. Microsatellite data were collected and characterized for the 12 polymorphic loci in two Alaskan populations of H. peploides : Fossil Beach, Kodiak Island ( n = 32) and Egg Bay, Atka Island ( n = 29). The Atka population exhibited a slightly higher average number of alleles (3.9) and observed heterozygosity (0.483) than the Kodiak population (3.3 and 0.347, respectively). The overall probability of identity values for both populations was PID = 2.892e −6 and PID sib = 3.361e −3 . We also screened the 12 polymorphic loci in Wilhelmsia physodes (Fisch. ex Ser.) McNeill, the most closely related species to H. peploides , and only one locus was polymorphic. These microsatellite markers will allow future investigations into population genetic and colonization patterns of the beach dune ruderal H. peploides on new and recently disturbed islands.

Alaska↗

USGS2024

Are threatened seabird colonies of the Pacific Ocean genetically vulnerable? The case of the red-tailed tropicbird, Phaethon rubricauda, as a model species

Oceanic seabirds have suffered population declines and extirpations due to human disturbance and still face multiple threats. Here, we assessed the potential genetic vulnerability of the red-tailed tropicbird, Phaethon rubricauda , a seabird species threatened by human disturbance and listed as ‘least concern’ by the IUCN. Using Single Nucleotide Polymorphisms (SNPs) we evaluated the genetic population structure of the red-tailed tropicbird throughout the Pacific Ocean using samples from 132 individuals from six islands. We sampled individuals from islands without human-related disturbance (non-impacted islands) and with human-related disturbance (impacted islands). Results of genome-wide SNP analyses were consistent with previous results using mitochondrial DNA sequences analyses. Genetic diversity did not differ between impacted and non-impacted islands, and low inbreeding estimates were detected for all colonies. The SNPs analyses confirmed a pattern of isolation by distance and significant inter-regional (Chile, Australasia, and Hawaiʻi) genetic structure, but revealed greater differentiation of tropicbirds in Hawaiʻi compared with Chile and Australasia. Within regions, our results further indicated significant differentiation between Rapa Nui and Salas & Gómez Island (Chile), and between Meyer and Phillip islands (Australasia) that was not detected using mitochondrial DNA analyses. Within Hawaiʻi, we found a lack of significant genetic differentiation between Oʻahu and Kauaʻi, separated by 200 km. Our findings indicated that red-tailed tropicbird colonies are at genetic risk due to limited dispersal among colonies which may reduce the fitness of the species in the long-term. We suggest that red-tailed tropicbird colonies are vulnerable to future population declines because recovery through immigration from other islands may be limited by geographic distance. Conservation actions will help preserve genetic diversity and discrete populations for this native seabird at colonies throughout the Pacific.

Biodiversity and Conservation↗

USGS2013

Are captive tortoises a reservoir for conservation? An assessment of genealogical affiliation of captive Gopherus agassizii to local, wild populations

The conservation of tortoises poses a unique situation because several threatened species are commonly kept as pets within their native ranges. Thus, there is potential for captive populations to be a reservoir for repatriation efforts. We assess the utility of captive populations of the threatened Agassiz’s desert tortoise ( Gopherus agassizii ) for recovery efforts based on genetic affinity to local areas. We collected samples from 130 captive desert tortoises from three desert communities: two in California (Ridgecrest and Joshua Tree) and the Desert Tortoise Conservation Center (Las Vegas) in Nevada. We tested all samples for 25 short tandem repeats and sequenced 1,109 bp of the mitochondrial genome. We compared captive genotypes to a database of 1,258 Gopherus samples, including 657 wild caught G. agassizii spanning the full range of the species. We conducted population assignment tests to determine the genetic origins of the captive individuals. For our total sample set, only 44 % of captive individuals were assigned to local populations based on genetic units derived from the reference database. One individual from Joshua Tree, California, was identified as being a Morafka’s desert tortoise, G. morafkai , a cryptic species which is not native to the Mojave Desert. Our data suggest that captive desert tortoises kept within the native range of G. agassizii cannot be presumed to have a genealogical affiliation to wild tortoises in their geographic proximity. Precautions should be taken before considering the release of captive tortoises into the wild as a management tool for recovery.

Conservation Genetics↗

USGS2018

Implications of introgression for wildlife translocations: the case of North American martens

The evolutionary consequences of natural introgression provide a rare opportunity to retrospectively evaluate how the introduction of exotics or genetic rescue efforts may impact endemic faunas. Phylogeographic structure among mainland, endemic insular, and introduced North American marten ( Martes americana and M. caurina ) populations have been shaped by a complex history of natural, post-glacial population expansion followed by a series of anthropogenic introductions. In some cases, both natural colonization and translocations facilitated secondary contact, offering a series of replicated experiments that demonstrate how introgression, in these cases following isolation (insular and refugial), shapes genetic diversity. We test whether genetic exchange is occurring between North American marten species using mitochondrial genomes and ten nuclear loci. We present evidence of biased nuclear introgression from M. caurina into M. americana across two natural hybrid zones (insular and mainland) and found no remnant evidence of M. caurina on islands that received M. americana translocations, suggesting prior absence, potential extirpation, or genetic swamping of M. caurina from these islands. Our results highlight the importance of understanding phylogeographic variation prior to identifying source populations for wildlife translocations and caution the use of genetic rescue for North American marten populations. Although previously managed as a single species, these two species show substantial genetic divergence. When the two are placed into contact, they exhibit unidirectional, asymmetric introgression with potentially negative consequences for M. caurina , underscoring the value of mindful consideration of introgression in wildlife management.

Conservation Genetics↗

USGS2023

Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America

Genetic diversity is critical to a population’s ability to overcome gradual environment change. Large-bodied wildlife existing in regions with relatively high human population density are vulnerable to isolation-induced genetic drift, population bottlenecks, and loss of genetic diversity. Moose ( Alces americanus americanus ) in eastern North America have a complex history of drastic population changes. Current and potential threats to moose populations in this region could be exacerbated by loss of genetic diversity and connectivity among subpopulations. Existing genetic diversity, gene flow, and population clustering and fragmentation of eastern North American moose are not well quantified, while physical and anthropogenic barriers to population connectivity already exist. Here, single nucleotide polymorphism (SNP) genotyping of 507 moose spanning five northeastern U.S. states and one southeastern Canadian province indicated low diversity, with a high proportion of the genomes sharing identity-by-state, with no consistent evidence of non-random mating. Gene flow estimates indicated bidirectionality between all pairs of sampled areas, with magnitudes reflecting clustering and differentiation patterns. A Discriminant Analysis of Principal Components analysis indicated that these genotypic data were best described with four clusters and indicated connectivity across the Saint Lawrence River and Seaway, a potential physical barrier to gene flow. Tests for genetic differentiation indicated restricted gene flow between populations across the Saint Lawrence River and Seaway, and between many sampled areas facing expanding human activity. These results document current genetic variation and connectivity of moose populations in eastern North America, highlight potential challenges to current population connectivity, and identify areas for future research and conservation.

New York, Vermont, New Hampshire, Maine, and Massa↗

USGS2023

A 37 K SNP array for the management and conservation of Golden Eagles (Aquila chrysaetos)

We describe the development of a custom 37 K Affymetrix Axiom myDesign single nucleotide polymorphism (SNP) array for a culturally and ecologically important apex predator, the golden eagle ( Aquila chrysaetos ). Using this SNP array, we performed population genomic analysis on 154 individuals of known natal localities and detected three genetic clusters that we designated as Taiga/High Arctic, Great Basin, and Rocky Mountains/Great Plains. Each of these clusters appears to display clinal variation within these geographic regions. After determining genetic structure, we performed an assignment test of 32 individuals, five of which were siblings of individuals used in the assessment of genetic structure, three had associated telemetry data, and the remaining individuals were of unknown natal locations. Using this array, four siblings were correctly assigned to the same geographic region as their sibling and the genetic assignment of the radio telemetered birds agreed with the expected movement patterns displayed by these individuals. For the remaining individuals, we were able to assign all but five individuals to one of the three genetic clusters. Our genetic assignments illustrates the utility of this SNP array to accurately assign most individuals to predesignated geographical regions. While further compiling genetic and other data types, we can increase the power of this tool for identifying those breeding populations that may need assistance due to anthropogenic stressors that negatively impact their population viability. The use of this genetic resource will help substantiate decisions by multiple conservation groups that seek to preserve the natural population structure of the golden eagle.

Conservation Genetics↗

USGS2024

Genetic Connectivity in the Arizona toad (Anaxyrus microscaphus): implications for conservation of a stream dwelling amphibian in the arid Southwestern U.S.

The Arizona Toad ( Anaxyrus microscaphus ) is restricted to riverine corridors and adjacent uplands in the arid southwestern United States. As with numerous amphibians worldwide, populations are declining and face various known or suspected threats, from disease to habitat modification resulting from climate change. The Arizona Toad has been petitioned to be listed under the U.S. Endangered Species Act and was considered “warranted but precluded” citing the need for additional information – particularly regarding natural history (e.g., connectivity and dispersal ability). The objectives of this study were to characterize population structure and genetic diversity across the species’ range. We used reduced-representation genomic sequencing to genotype 3,601 single nucleotide polymorphisms in 99 Arizona Toads from ten drainages across its range. Multiple analytical methods revealed two distinct genetic groups bisected by the Colorado River; one in the northwestern portion of the range in southwestern Utah and eastern Nevada and the other in the southeastern portion of the range in central and eastern Arizona and New Mexico. We also found subtle substructure within both groups, particularly in central Arizona where toads at lower elevations were less connected than those at higher elevations. The northern and southern parts of the Arizona Toad range are not well connected genetically and could be managed as separate units. Further, these data could be used to identify source populations for assisted migration or translocations to support small or potentially declining populations.

Arizona, Nevada, New Mexico↗

USGS2025

Population genetics of the endangered narrowly endemic Island Marble butterfly (Euchloe ausonides insulanus)

The Island Marble butterfly ( Euchloe ausonides insulanus ) is an endangered species endemic to the San Juan Islands off the coast of Washington State, United States, and British Columbia, Canada. The species was thought to be extinct for ~ 90 years before it was rediscovered at American Camp, San Juan Island National Historical Park in 1998. Here, we report the results of the first population genetic analyses for insulanus , using DNA collected non-invasively from individuals in the last known stronghold for the species. We used DNA extracted from meconium, larval exuviae, and natural mortalities to generate and test thirteen new microsatellite markers to estimate genetic diversity, population structure, and kinship. We assembled and annotated mitochondrial genomes, which were used alongside museum specimens of insulanus collected ~ 100 years ago from Vancouver Island, and other members of the E. ausonides species complex, to infer the evolutionary history of the species. The results indicated that insulanus experiences low heterozygosity, a small effective population size (N e ), and low allelic diversity. High levels of inbreeding were found in some individuals, but inbreeding was uneven across the population. No population structure or partitioning of genetic variation by host plant was detected. The mitogenomes of extant insulanus were all identical and modern samples showed a loss of allelic diversity compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management and genetic monitoring.

British Columbia, Washington↗

USGS2015

Population connectivity and genetic structure of burbot ( Lota lota ) populations in the Wind River Basin, Wyoming

Burbot ( Lota lota ) occur in the Wind River Basin in central Wyoming, USA, at the southwestern extreme of the species’ native range in North America. The most stable and successful of these populations occur in six glacially carved mountain lakes on three different tributary streams and one large main stem impoundment (Boysen Reservoir) downstream from the tributary populations. Burbot are rarely found in connecting streams and rivers, which are relatively small and high gradient, with a variety of potential barriers to upstream movement of fish. We used high-throughput genomic sequence data for 11,197 SNPs to characterize the genetic diversity, population structure, and connectivity among burbot populations on the Wind River system. Fish from Boysen Reservoir and lower basin tributary populations were genetically differentiated from those in the upper basin tributary populations. In addition, fish within the same tributary streams fell within the same genetic clusters, suggesting there is movement of fish between lakes on the same tributaries but that populations within each tributary system are isolated and genetically distinct from other populations. Observed genetic differentiation corresponded to natural and anthropogenic barriers, highlighting the importance of barriers to fish population connectivity and gene flow in human-altered linked lake-stream habitats.

Wyoming↗

USGS2022

Development of a ddPCR assay for the detection of the Smoky Madtom (Noturus baileyi) from eDNA in stream water samples

The Smoky Madtom Noturus baileyi is a federally endangered species, whose native distribution includes lower Abrams Creek in Great Smoky Mountains National Park (GRSM) and Citico Creek in nearby Cherokee National Forest. Due to challenges for bio-monitoring posed by its nocturnality and cryptic life history, an environmental DNA (eDNA)-based approach for detection would be useful to complement existing electrofishing and seining efforts to better understand the distribution of this species. We developed a probe-based droplet digital PCR (ddPCR) assay to detect Smoky Madtoms from non-invasively collected water samples. The assay was specific to N. baileyi and did not amplify concentrated genomic DNA of 16 co-occurring or regional fish species, including the yellowfin madtom N. flavipinnis and stonecat N. flavus . The assay limit of detection (LOD) was determined to be 4.18 copies (95% CI: 3.95, 4.41). Several 2 L water samples collected from throughout various streams in GRSM in 2016 and 2017 were tested for the presence of N. baileyi using the ddPCR assay. N. baileyi was detected at two different sites in 2016 and 2017 within Abrams Creek previously known to contain N. baileyi , but no novel detections in other sampled streams were observed. This assay should prove useful for continued surveys of N. baileyi in GRSM.

Great Smoky Mountains National Park↗

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↗

USGS2022

A critical review of bioaccumulation and biotransformation of organic chemicals in birds

A literature review of bioaccumulation and biotransformation of organic chemicals in birds was undertaken, aiming to support scoping and prioritization of future research. The objectives were to characterize available bioaccumulation/biotransformation data, identify knowledge gaps, determine how extant data can be used, and explore the strategy and steps forward. An intermediate approach balanced between expediency and rigor was taken given the vastness of the literature. Following a critical review of > 500 peer-reviewed studies, > 25,000 data entries and 2 million information bytes were compiled on > 700 organic compounds for ~ 320 wild species and 60 domestic breeds of birds. These data were organized into themed databases on bioaccumulation and biotransformation , field survey , microsomal enzyme activity , metabolic pathway , and bird taxonomy and diet . Significant data gaps were identified in all databases at multiple levels. Biotransformation characterization was largely fragmented over metabolite/pathway identification and characterization of enzyme activity or biotransformation kinetics. Limited biotransformation kinetic data constrained development of an avian biotransformation model. A substantial shortage of in vivo biotransformation kinetics has been observed as most reported rate constants were derived in vitro. No metric comprehensively captured all key contaminant classes or chemical groups to support broad-scope modeling of bioaccumulation or biotransformation. However, metrics such as biota-feed accumulation factor, maximum transfer factor, and total elimination rate constant were more readily usable for modeling or benchmarking than other reviewed parameters. Analysis demonstrated the lack of bioaccumulation/biotransformation characterization of shorebirds, seabirds, and raptors. In the study of bioaccumulation and biotransformation of organic chemicals in birds, this review revealed the need for greater chemical and avian species diversity, chemical measurements in environmental media, basic biometrics and exposure conditions, multiple tissues/matrices sampling, and further exploration on biotransformation. Limitations of classical bioaccumulation metrics and current research strategies used in bird studies were also discussed. Forward-looking research strategies were proposed: adopting a chemical roadmap for future investigations, integrating existing biomonitoring data, gap-filling with non-testing approaches, improving data reporting practices, expanding field sampling scopes, bridging existing models and theories, exploring biotransformation via avian genomics, and establishing an online data repository.

Reviews of Environmental Contamination and Toxicol↗

USGS1994

The genetic diversity and epizootiology of infectious hematopoietic necrosis virus

Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus which causes a serious disease in salmondd fish. The T1 ribonuclease fingerprinttin method was used to compare the RNA genomes of 26 isolates of IHNV recovered from sockeye salmon ( Oncorhynchus nerka ), chinook salmon ( O. tshawytscha ), and steelhead trout ( O. mykiss ) throughout the enzootic portion of western North America. Most of the isolates as a source of genetic variation. In from a single year (1987) to limit time of isolation as a source of genetic variation. In addition, isolates from different years collected at three sites were analyzed to investigate genetic drift or evolution of IHNV within specific locations. All of the isolates examined by T1 fingerprint analysis contained less than a 50% variation in spot location and were represented by a single fingerprint group. The observed variation was estimated to correspond to less than 5% variation in the nucleic acid sequence. However, sufficient variation was detected to separate the isolates into four subgroups which appeared to correlate to different geographic regions. Host species appeared not to be a significant source of variation. The evolutionary and epizootiologic significance of these findings and their relationship to other evidence of genetic variation in IHNV isolates are discussed.

Virus Research↗

USGS1996

The glycoprotein genes and gene junctions of the fish rhabdoviruses spring viremia of carp virus and hirame rhabdovirus: Analysis of relationships with other rhabdoviruses

The nucleotide sequences of the glycoprotein genes and all of the internal gene junctions of the fish pathogenic rhabdoviruses spring viremia of carp virus (SVCV) and hirame rhabdovirus (HIRRV) have been determined from cDNA clones generated from viral genomic RNA. The SVCV glycoprotein gene sequence is 1588 nucleotides (nt) long and encodes a 509 amino acid (aa) protein. The HIRRV glycoprotein gene sequence comprises 1612 nt, coding for a 508 aa protein. In sequence comparisons of 15 rhabdovirus glycoproteins, the SVCV glycoprotein gene showed the highest amino acid sequence identity (31.2-33.2%) with vesicular stomatitis New Jersey virus (VSNJV), Chandipura virus (CHPV) and vesicular stomatitis Indiana virus (VSIV). The HIRRV glycoprotein gene showed a very high amino acid sequence identity (74.3%) with the glycoprotein gene of another fish pathogenic rhabdovirus, infectious hematopoietic necrosis virus (IHNV), but no significant similarity with glycoproteins of VSIV or rabies virus (RABV). In phylogenetic analyses SVCV was grouped consistently with VSIV, VSNJV and CHPV in the Vesiculovirus genus of Rhabdoviridae. The fish rhabdoviruses HIRRV, IHNV and viral hemorrhagic septicemia virus (VHSV) showed close relationships with each other, but only very distant relationships with mammalian rhabdoviruses. The gene junctions are highly conserved between SVCV and VSIV, well conserved between IHNV and HIRRV, but not conserved between HIRRV/IHNV and RABV. Based on the combined results we suggest that the fish lyssa-type rhabdoviruses HIRRV, IHNV and VHSV may be grouped in their own genus within the family Rhabdoviridae. Aquarhabdovirus has been proposed for the name of this new genus.

Virus Research↗

USGS1977

Reassociation and hybridization properties of DNAs from several species of fish

Reassociation and hybridization properties from spectrophotometric studies of DNAs from 10 species of fish indicate: 1. Great diversity in the amounts of repeated sequences in the genomes of different species - more specialized fish had less redundancy. 2. Large differences in the complexities of the DNAs - more specialized fish had less information. 3. Little homology between sequences of remotely related species but substantial homology between sequences of closely related species.

Comparative Biochemistry and Physiology, Part B: C↗

USGS2013

Hormonal control of euryhalinity

Hormones play a critical role in maintaining body fluid balance in euryhaline fishes during changes in environmental salinity. The neuroendocrine axis senses osmotic and ionic changes, then signals and coordinates tissue-specific responses to regulate water and ion fluxes. Rapid-acting hormones, e.g. angiotensins, cope with immediate challenges by controlling drinking rate and the activity of ion transporters in the gill, gut, and kidney. Slow-acting hormones, e.g. prolactin and growth hormone/insulin-like growth factor-1, reorganize the body for long-term acclimation by altering the abundance of ion transporters and through cell proliferation and differentiation of ionocytes and other osmoregulatory cells. Euryhaline species exist in all groups of fish, including cyclostomes, and cartilaginous and teleost fishes. The diverse strategies for responding to changes in salinity have led to differential regulation and tissue-specific effects of hormones. Combining traditional physiological approaches with genomic, transcriptomic, and proteomic analyses will elucidate the patterns and diversity of the endocrine control of euryhalinity.

Book chapter↗

USGS2013

Smolt physiology and endocrinology

Book chapter↗

USGS2024

Hepeviruses of aquatic organisms

Originally reported in California, the cutthroat trout virus (CTV) has now been isolated from nine species of salmonids in North America. Early work focused on the replication and physical characteristics of the virus, but 20 years later was determined to be most closely related to the hepatitis E virus. The small genome is positive-sense, single-stranded RNA similar to other members of the family Hepeviridae , which now contains its own genus Piscihepevirus with two distinct genotypes, CTV-1 and CTV-2. While CTV has not been associated with acute disease in fish, the virus could form persistently infected cell cultures that may aid research in treating hepatitis E-like viruses affecting humans or other animals. Interestingly, trout exposed to CTV were protected for about a month against subsequent exposure to the infectious hematopoietic necrosis virus. Replicating agents suspected to be CTV can be confirmed by polymerase chain reaction (PCR), quantitative PCR, and sequencing. Other unclassified hepeviruses detected in fish using viral metagenomics include Wenling fish hepevirus, Wenling moray eel hepevirus, Murray–Darling carp hepevirus, and eastern mosquitofish hepevirus. The family Hepeviridae has been placed in the order Hepevirales together with the family Matonaviridae (rubella virus), with member viruses having amino acid homology in the helicase and replicase regions of the nonstructural proteins. In addition, using next-generation sequencing, a hepe-like sequence was characterized in diseased giant freshwater prawn Macrobrachium rosenbergii and named Crustacea hepe-like virus 1. Thus the family Hepeviridae continues to expand among aquatic animal hosts.

Book chapter↗