Geology topics

Tim L. King

Publications and source records attributed to Tim L. King.

34 records · Page 2Linked to original sources

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↗

USGS2015

Origin of Atlantic Sturgeon collected off the Delaware coast during spring months

Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus was federally listed under the U.S. Endangered Species Act as five distinct population segments (DPS). Currently, at least 18 estuaries coastwide host spawning populations and the viability of these vary, requiring differing levels of protection. Subadults emigrate from their natal estuaries to marine waters where they are vulnerable to bycatch; one of the major threats to the rebuilding of populations. As a result, identifying the population origin of Atlantic Sturgeon in coastal waters is critical to development of management plans intended to minimize interactions of the most imperiled populations with damaging fisheries. We used mitochondrial DNA control region sequencing and microsatellite DNA analyses to determine the origin of 261 Atlantic Sturgeon collected off the Delaware coast during the spring months. Using individual-based assignment (IBA) testing and mixed stock analysis, we found that specimens originated from all nine of our reference populations and the five DPSs used in the listing determination. Using IBA, we found that the Hudson River population was the largest contributor (38.3%) to our coastal collection. The James (19.9%) and Delaware (13.8%) river populations, at one time thought to be extirpated or nearly so, were the next largest contributors. The three populations combined in the South Atlantic DPS contributed 21% of specimens; the Altamaha River, the largest population in the South Atlantic DPS, only contributed a single specimen to the collection. While the origin of specimens collected on the Delaware coast was most likely within rivers of the New York Bight DPS (52.1%), specimens that originated elsewhere were also well represented. Genetic analyses provide a robust tool to identify the population origin of individual sturgeon outside of their natal estuaries and to determine the quantitative contributions of individual populations to coastal aggregations that are vulnerable to bycatch and other anthropogenic threats.

Delaware↗

USGS2015

Designation of a neotype for brook trout, Salvelinus fontinalis

The taxonomic status of Salvelinus fontinalis (Mitchill) is problematic. Difficulties in comparison of populations are exacerbated by the lack of type material. Here we designate a neotype from Connetquot River, Long Island, New York. We provide genetic and morphological data for the neotype, conspecifics, and other populations (Swan Creek, Nissequogue Creek) from Long Island, New York. We demonstrate, using molecular markers, that the population from Connetquot River most likely has not been influenced by the major broodstock strains utilized in the Northeast for supplemental and restorative stocking programs. We distinguish the above populations morphologically from lower interior basin populations, represented by fishes from the Pigeon-French Broad drainage, North Carolina and Tennessee. Finally, we position populations from Long Island, New York, within six distinct lineages of S. fontinalis .

Proceedings of the Biological Society of Washingto↗

USGS2014

Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection

We characterized variation within the mitochondrial genomes of the invasive silver carp ( Hypophthalmichthys molitrix ) and bighead carp ( H. nobilis ) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis . The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.

Conservation Genetics Resources↗

USGS2014

A nuclear DNA perspective on delineating evolutionarily significant lineages in polyploids: the case of the endangered shortnose sturgeon ( Acipenser brevirostrum )

The shortnose sturgeon, Acipenser brevirostrum , oft considered a phylogenetic relic, is listed as an “endangered species threatened with extinction” in the US and “Vulnerable” on the IUCN Red List. Effective conservation of A. brevirostrum depends on understanding its diversity and evolutionary processes, yet challenges associated with the polyploid nature of its nuclear genome have heretofore limited population genetic analysis to maternally inherited haploid characters. We developed a suite of polysomic microsatellite DNA markers and characterized a sample of 561 shortnose sturgeon collected from major extant populations along the North American Atlantic coast. The 181 alleles observed at 11 loci were scored as binary loci and the data were subjected to multivariate ordination, Bayesian clustering, hierarchical partitioning of variance, and among-population distance metric tests. The methods uncovered moderately high levels of gene diversity suggesting population structuring across and within three metapopulations (Northeast, Mid-Atlantic, and Southeast) that encompass seven demographically discrete and evolutionarily distinct lineages. The predicted groups are consistent with previously described behavioral patterns, especially dispersal and migration, supporting the interpretation that A. brevirostrum exhibit adaptive differences based on watershed. Combined with results of prior genetic (mitochondrial DNA) and behavioral studies, the current work suggests that dispersal is an important factor in maintaining genetic diversity in A. brevirostrum and that the basic unit for conservation management is arguably the local population.

PLoS ONE↗

USGS2014

River mainstem thermal regimes influence population structuring within an Appalachian brook trout population

Brook trout ( Salvelinus fontinalis ) often exist as highly differentiated populations, even at small spatial scales, due either to natural or anthropogenic sources of isolation and low rates of dispersal. In this study, we used molecular approaches to describe the unique population structure of brook trout inhabiting the Shavers Fork watershed, located in eastern West Virginia, and contrast it to nearby populations in tributaries of the upper Greenbrier River and North Fork South Branch Potomac Rivers. Bayesian and maximum likelihood clustering methods identified minimal population structuring among 14 collections of brook trout from throughout the mainstem and tributaries of Shavers Fork, highlighting the role of the cold-water mainstem for connectivity and high rates of effective migration among tributaries. In contrast, the Potomac and Greenbrier River collections displayed distinct levels of population differentiation among tributaries, presumably resulting from tributary isolation by warm-water mainstems. Our results highlight the importance of protecting and restoring cold-water mainstem habitats as part of region-wide brook trout conservation efforts. In addition, our results from Shavers Fork provide a contrast to previous genetic studies that characterize Appalachian brook trout as fragmented isolates rather than well-mixed populations. Additional study is needed to determine whether the existence of brook trout as genetically similar populations among tributaries is truly unique and whether connectivity among brook trout populations can potentially be restored within other central Appalachian watersheds.

West Virginia↗

USGS2014

The history of sturgeon in the Baltic Sea

Aim Migrants of the Atlantic sturgeon, Acipenser oxyrinchus, from North America are thought to have founded the Baltic sturgeon population during the Little Ice Age around 1200 years ago, replacing the European sturgeon, Acipenser sturio. To test this hypothesis and to further elucidate the colonization of the Baltic Sea by A. oxyrinchus, we carried out DNA analyses of ancient and contemporary populations of both species. Location We analysed DNA from 188 specimens of sturgeons collected from archaeological sites and museums in Poland and of 225 contemporary specimens from North American and European populations. Methods Several mitochondrial DNA fragments were sequenced and eight microsatellite loci were genotyped for species identification, polymorphism and population structure analyses. Approximate Bayesian computation was used to estimate when the Baltic Sea was colonized. Results Of 125 ancient sturgeon specimens from the Baltic Sea, only four were classified as A. sturio, the remainder being A. oxyrinchus oxyrinchus. The ancient A. o. oxyrinchus population over two different time periods was highly polymorphic and genetically distant from contemporary populations of this taxon. The time of entry into the Baltic Sea was estimated to be 4000–5000 years ago. We also detected introgression of A. sturio into the A. o. oxyrinchus gene pool, caused by a prior hybridization event. Main conclusions For the past 2000 years at least, A. o. oxyrinchus has been the dominant sturgeon in the Baltic Sea, indicating a much earlier origin than previously suggested. The most similar extant sturgeon populations to the extinct Baltic stock are those from the St John and St Lawrence rivers in Canada. These populations should be considered the best source of breeding material for the ongoing sturgeon restitution programmes in Poland and Germany.

Journal of Biogeography↗

USGS2014

Regional differentiation among populations of the Diamondback terrapin ( Malaclemys terrapin )

The Diamondback terrapin (Malaclemys terrapin) is a brackish-water turtle species whose populations have been fragmented due to anthropogenic activity such as development of coastal habitat and entrapment in commercial blue crab (Callinectes sapidus) fishing gear. Genetic analyses can improve conservation efforts for the long-term protection of the species. We used microsatellite DNA analysis to investigate levels of gene flow among and genetic variability within 21 geographically separate collections of the species distributed from Massachusetts to Texas. Quantified levels of genetic variability (allelic diversity, genotypic frequencies, and heterozygosity) revealed three zones of genetic discontinuity, resulting in four discrete populations: Northeast Atlantic, Coastal Mid-Atlantic, Florida and Texas/Louisiana. The average number of alleles and expected heterozygosity for the four genetic clusters were N A = 6.54 and H E = 0.050, respectively. However, the geographic boundaries of the populations did not correspond to accepted terrapin subspecies limits. Our results illuminate not only the need to sample terrapins in additional sites, specifically in the southeast, but also the necessity for allowing uninterrupted gene flow among population groupings to preserve current levels of genetic diversity.

Conservation Genetics↗

USGS2014

Genetic evidence of local exploitation of Atlantic salmon in a coastal subsistence fishery in the Northwest Atlantic

Fisheries targeting mixtures of populations risk the over utilization of minor stock constituents unless harvests are monitored and managed. We evaluated stock composition and exploitation of Atlantic salmon in a subsistence fishery in coastal Labrador, Canada using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 11 829 individuals, 12 regional groups) encompassing the species western Atlantic range. Bayesian and maximum likelihood mixture analyses of fishery samples over six years (2006-2011; 1 772 individuals) indicate contributions of adjacent stocks of 96-97%. Estimates of fishery associated exploitation were highest for Labrador salmon (4.2-10.6% per year) and generally < 1% for other regions. Individual assignment of fishery samples indicated non-local contributions to the fishery (e.g., Quebec, Newfoundland) were rare and primarily in southern Labrador, consistent with migration pathways utilizing the Strait of Belle Isle. This work illustrates how genetic analysis of mixed stock Atlantic salmon fisheries in the northwest Atlantic using this new baseline can disentangle exploitation and reveal complex migratory behaviours.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2013

Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis ( Myotis septentrionalis ) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

Acta Theriologica↗

USGS2012

Puerto Rico and Florida manatees represent genetically distinct groups

The West Indian manatee ( Trichechus manatus ) populations in Florida ( T. m. latirostris ) and Puerto Rico ( T. m. manatus ) are considered distinct subspecies and are listed together as endangered under the United States Endangered Species Act. Sustained management and conservation efforts for the Florida subspecies have led to the suggested reclassification of the species to a threatened or delisted status. However, the two populations are geographically distant, morphologically distinct, and habitat degradation and boat strikes continue to threaten the Puerto Rico population. Here, 15 microsatellite markers and mitochondrial control region sequences were used to determine the relatedness of the two populations and investigate the genetic diversity and phylogeographic organization of the Puerto Rico population. Highly divergent allele frequencies were identified between Florida and Puerto Rico using microsatellite (F ST = 0.16; R ST = 0.12 (P < 0.001)) and mitochondrial (F ST = 0.66; Φ ST = 0.50 (P < 0.001)) DNA. Microsatellite Bayesian cluster analyses detected two populations (K = 2) and no admixture or recent migrants between Florida (q = 0.99) and Puerto Rico (q = 0.98). The microsatellite genetic diversity values in Puerto Rico (H E = 0.45; N A = 3.9), were similar, but lower than those previously identified in Florida (H E = 0.48, N A = 4.8). Within Puerto Rico, the mitochondrial genetic diversity values (π = 0.001; h = 0.49) were slightly lower than those previously reported (π = 0.002; h = 0.54) and strong phylogeographic structure was identified (F ST global = 0.82; Φ ST global = 0.78 (P < 0.001)). The genetic division with Florida, low diversity, small population size (N = 250), and distinct threats and habitat emphasize the need for separate protections in Puerto Rico. Conservation efforts including threat mitigation, migration corridors, and protection of subpopulations could lead to improved genetic variation in the endangered Puerto Rico manatee population.

Florida↗

USGS2010

Genetic structure and diversity among brook trout from Isle Royale, Lake Nipigon, and three Minnesota tributaries of Lake Superior

Brook trout Salvelinus fontinalis from Isle Royale, Michigan, three Minnesota tributaries of Lake Superior, and Lake Nipigon in Ontario were analyzed for genetic variation at 12 microsatellite DNA loci. Analysis of molecular variance, genetic distance measures, and cluster analysis were used to examine the diversity, gene flow, and relatedness among the samples. The diversity estimates for the samples from Isle Royale were similar to those for the samples collected from Minnesota tributaries of Lake Superior, and all estimates were lower than those reported in other studies of brook trout from eastern North America. Genetic differences were detected among the brook trout at Isle Royale, Lake Nipigon, and the Minnesota tributaries of Lake Superior. Further, the population in Tobin Harbor at the eastern end of Isle Royale was distinct from the populations from tributaries at the southwestern end of the island. The Minnesota tributary population formed a group that was genetically distinct from those from Isle Royale and Lake Nipigon. The Isle Royale population should be managed to preserve the genetic and phenotypic variation that distinguishes it from the other brook trout populations analyzed to date.

Michigan, Minnesota, Ontario↗

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↗

USGS2006

Comprehensive genetic analyses reveal evolutionary distinction of a mouse ( Zapus hudsonius preblei ) proposed for delisting from the US Endangered Species Act

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius. ?? 2006 The Authors.

Molecular Ecology↗

USGS2003

Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers

The Recovery Plan for the federally threatened Louisiana black bear ( Ursus americanus luteolus ) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km 2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao M h to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km 2 . We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

Louisiana↗

USGS1999

Targeted stock identification using multilocus genotype 'familyprinting'

We present an approach to stock identification of small, targeted populations that uses multilocus microsatellite genotypes of individual mating adults to uniquely identify first- and second-generation offspring in a mixture. We call the approach ‘familyprinting’; unlike DNA fingerprinting where tissue samples of individuals are matched, offspring from various families are assigned to pairs of parents or sets of four grandparents with known genotypes. The basic unit of identification is the family, but families can be nested within a variety of stock units ranging from naturally reproducing groups of fish in a small tributary or pond from which mating adults can be sampled to large or small collections of families produced in hatcheries and stocked in specific locations. We show that, with as few as seven alleles per locus using four loci without error, first-generation offspring can be uniquely assigned to the correct family. For second-generation applications in a hatchery more alleles per locus (10) and loci (10) are required for correct assignment of all offspring to the correct set of grandparents. Using microsatellite DNA variation from an Atlantic salmon ( Salmo solar ) restoration river (Connecticut River, USA), we also show that this population contains sufficient genetic diversity in sea-run returns for 100% correct first-generation assignment and 97% correct second-generation assignment using 14 loci. We are currently using first- and second-generation familyprinting in this population with the ultimate goal of identifying stocking tributary. In addition to within-river familyprinting, there also appears to be sufficient genetic diversity within and between Atlantic salmon populations for identification of ‘familyprinted’ fish in a mixture of multiple populations. We also suggest that second-generation familyprinting with multiple populations may also provide a tool for examining stock structure. Familyprinting with microsatellite DNA markers is a viable method for identification of offspring of randomly mating adults from small, targeted stocks and should provide a useful addition to current mixed stock analyses with genetic markers.

Fisheries Research↗