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USGS1983

Intrusive rocks and plutonic belts of southeastern Alaska, U.S.A

About 30 percent of the 175,000-km 2 area of southeastern Alaska is underlain by intrusive igneous rocks. Compilation of available information on the distribution, composition, and ages of these rocks indicates the presence of six major and six minor plutonic belts. From west to east, the major belts are: the Fairweather-Baranof belt of early to mid-Tertiary granodiorite; the Muir-Chichagof belt of mid-Cretaceous tonalite and granodiorite; the Admiralty-Revillagigedo belt of porphyritic granodiorite, quartz diorite, and diorite of probable Cretaceous age; the Klukwan-Duke belt of concentrically zoned or Alaskan-type ultramafic-mafic plutons of mid-Cretaceous age within the Admiralty-Revillagigedo belt; the Coast Plutonic Complex sill belt of tonalite of unknown, but perhaps mid-Cretaceous, age; and the Coast Plutonic Complex belt I of early to mid-Tertiary granodiorite and quartz monzonite. The minor belts are distributed as follows: the Glacier Bay belt of Cretaceous and(or) Tertiary granodiorite, tonalite, and quartz diorite lies within the Fair-weather-Baranof belt; layered gabbro complexes of inferred mid-Tertiary age lie within and are probably related to the Fairweather-Baranof belt; the Chilkat-Chichagof belt of Jurassic granodiorite and tonalite lies within the Muir-Chichagof belt; the Sitkoh Bay alkaline, the Kendrick Bay pyroxenite to quartz monzonite, and the Annette and Cape Fox trondhjemite plutons, all interpreted to be of Ordovician(?) age, together form the crude southern southeastern Alaska belt within the Muir-Chichagof belt; the Kuiu-Etolin mid-Tertiary belt of volcanic and plutonic rocks extends from the Muir-Chichagof belt eastward into the Admiralty-Revillagigedo belt; and the Behm Canal belt of mid- to late Tertiary granite lies within and next to Coast Plutonic Complex belt II. In addition, scattered mafic-ultramafic bodies occur within the Fairweather-Baranof, Muir-Chichagof, and Coast Plutonic Complex belts I and II. Palinspastic reconstruction of 200 km of right-lateral movement on the Chatham Strait fault does not significantly change the pattern of the major belts but does bring parts of the minor mid-Tertiary and Ordovician(?) belts closer together. The major belts are related to the stratigraphic-tectonic terranes of Berg, Jones, and Coney (1978) as follows: the Fairweather-Baranof belt is largely in the Chugach, Wrangell (Wrangellia), and Alexander terranes; the Muir-Chichagof belt is in the Alexander and Wrangell terranes; the Admiralty-Revillagigedo belt is in the Gravina and Taku terranes; the Klukwan-Duke belt is in the Gravina, Taku, and Alexander terranes; the Coast Plutonic Complex sill belt is probably between the Taku and Tracy Arm terranes; and the Coast Plutonic Complex belts I and II are in the Tracy Arm and Stikine terranes. Significant metallic-mineral deposits are spatially related to certain of these belts, and some deposits may be genetically related. Gold, copper, and molybdenum occurrences may be related to granodiorites of the Fairweather-Baranof belt. Magmatic copper-nickel deposits occur in the layered gabbro within that belt. The Juneau gold belt, which contains gold, silver, copper, lead, and zinc occurrences, parallels and lies close to the Coast Plutonic Complex sill belt; iron deposits occur in the Klukwan-Duke belt; and porphyry molybdenum deposits occur in the Behm Canal belt. The Muir-Chichagof belt of mid-Cretaceous age and the Admiralty-Revillagigedo belt of probable Cretaceous age are currently interpreted as possible magmatic arcs associated with subduction events. In general, the other belts of intrusive rocks are spatially related to structural discontinuities, but genetic relations, if any, are not yet known. The Coast Plutonic Complex sill belt is probably related to a post-Triassic, pre-early Tertiary suture zone that nearly corresponds to the boundary between the Tracy Arm and Taku terranes. The boundary between the Admiralty-Revillagigedo and Muir-Chichagof belts coincides nearly with the Seymour Canal-Clarence Strait lineament and also is probably a major post-Triassic suture.

Alaska↗

USGS2024

Wintering grounds leave their mark: Where birds winter influences genomic structure in Arctic nesting common eiders

Information about the distribution of genomic variation within and between nesting locations of waterfowl can aid in defining populations and conservation plans and inform harvest management. Identification of locations where shifts in allelic diversity occur is particularly important for Arctic nesting species nesting, a region currently experiencing rapid change associated with climate and other factors. Here, we build upon previous investigations on spatial patterns of genetic variation in a largely migratory, circumpolar breeding sea duck, the common eider ( Somateria mollissima ) through inclusion of additional sample locations and genomic markers. We analyzed double-digest restriction site-associated DNA sequences from 309 common eiders to estimate genetic variation within, and differentiation among, 21 nesting locations across North America. Our results corroborate previous evidence of four genetic groups that coincide with colonies that share similar winter areas. We found deeper genomic differences between common eiders wintering in the west (Pacific Ocean) versus the east (Atlantic Ocean and Hudson Bay). We also identified subtle structure, not previously recognized, within Hudson Bay nesting common eiders. Our findings add to evidence linking wintering areas and genomic differentiation in waterfowl, offering further insights for management of this culturally important sea duck species.

Conservation Genetics↗

USGS2015

Developing a conservation strategy to maximize persistence of an endangered freshwater mussel species while considering management effectiveness and cost

We used a structured decision-making process to develop conservation strategies to increase persistence of Dwarf Wedgemussel ( Alasmidonta heterodon ) in North Carolina, USA, while accounting for uncertainty in management effectiveness and considering costs. Alternative conservation strategies were portfolios of management actions that differed by location of management actions on the landscape. Objectives of the conservation strategy were to maximize species persistence, maintain genetic diversity, maximize public support, and minimize management costs. We compared 4 conservation strategies: 1) the ‘status quo’ strategy represented current management, 2) the ‘protect the best’ strategy focused on protecting the best populations in the Tar River basin, 3) the ‘expand the distribution’ strategy focused on management of extant populations and establishment of new populations in the Neuse River basin, and 4) the ‘hybrid’ strategy combined elements of each strategy to balance conservation in the Tar and Neuse River basins. A population model informed requirements for population management, and experts projected performance of alternative strategies over a 20-y period. The optimal strategy depended on the relative value placed on competing objectives, which can vary among stakeholders. The protect the best and hybrid strategies were optimal across a wide range of relative values with 2 exceptions: 1) if minimizing management cost was of overriding concern, then status quo was optimal, or 2) if maximizing population persistence in the Neuse River basin was emphasized, then expand the distribution strategy was optimal. The optimal strategy was robust to uncertainty in management effectiveness. Overall, the structured decision process can help identify the most promising strategies for endangered species conservation that maximize conservation benefit given the constraint of limited funding.

North Carolina↗

USGS2005

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using θ values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest θ (0.13-0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (θ = 0.04-0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Nino Southern Oscillation (ENSO) events along the Pacific coast.

Molecular Ecology↗

USGS2024

Phylogenomics, male internal genitalia, a new species, and other notes on New World Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

Based on past and expanded DNA sampling, the orthopteran families Stenopelmatidae and Anostostomatidae, as currently structured, are shown to be non-monophyletic. The splay-footed cricket genus Comicus is confirmed to be genetically distinct from all Stenopelmatidae. We add two specimens to our previously published phylogenetic tree for New World Stenopelmatus Jerusalem cricket species and report the first multilocus DNA recovery for S. ater from Costa Rica. Male internal genitalia may be of systematic value in Jerusalem crickets, but we believe they should be analyzed when in their unfolded, “physiologically functional” configuration, where morphological characters can be seen in more detail when compared to their preserved, folded state. We describe Stenopelmatus nuevoguatemalae n. sp. from Guatemala.

Zootaxa↗

USGS2012

High shrew diversity on Alaska's Seward Peninsula: Community assembly and environmental change

In September 2010, 6 species of shrews (genus: Sorex ) were collected at a single locality on the Seward Peninsula of Alaska. Such high sympatric diversity within a single mammalian genus is seldom realized. This phenomenon at high latitudes highlights complex Arctic community dynamics that reflect significant turnover through time as a consequence of environmental change. Each of these shrew species occupies a broad geographic distribution collectively spanning the entire Holarctic, although the study site lies within Eastern Beringia, near the periphery of all individual ranges. A review of published genetic evidence reflects a depauperate shrew community within ice-free Beringia through the last glaciation, and recent assembly of current diversity during the Holocene.

Alaska↗

USGS2012

Modeling the mesozoic-cenozoic structural evolution of east texas

The U.S. Geological Survey (USGS) recently assessed the undiscovered technically recoverable oil and gas resources within Jurassic and Cretaceous strata of the onshore coastal plain and State waters of the U.S. Gulf Coast. Regional 2D seismic lines for key parts of the Gulf Coast basin were interpreted in order to examine the evolution of structural traps and the burial history of petroleum source rocks. Interpretation and structural modeling of seismic lines from eastern Texas provide insights into the structural evolution of this part of the Gulf of Mexico basin. Since completing the assessment, the USGS has acquired additional regional seismic lines in east Texas; interpretation of these new lines, which extend from the Texas-Oklahoma state line to the Gulf Coast shoreline, show how some of the region's prominent structural elements (e.g., the Talco and Mount Enterprise fault zones, the East Texas salt basin, and the Houston diapir province) vary along strike. The interpretations also indicate that unexplored structures may lie beneath the current drilling floor. Structural restorations based upon interpretation of these lines illustrate the evolution of key structures and show the genetic relation between structural growth and movement of the Jurassic Louann Salt. 1D thermal models that integrate kinetics and burial histories were also created for the region's two primary petroleum source rocks, the Oxfordian Smackover Formation and the Cenomanian-Turonian Eagle Ford Shale. Integrating results from the thermal models with the structural restorations provides insights into the distribution and timing of petroleum expulsion from the Smackover Formation and Eagle Ford Shale in eastern Texas.

Texas↗

USGS2003

Update COSEWIC status report on the shortjaw cisco, Coregonus zenithicus, in Canada

Extirpated in most of the Great Lakes, the shortjaw cisco, Coregonus zenithicus, is currently found in Lakes Superior and Nipigon in addition to at least 22 Canadian lakes. The species exhibits morphological and genetic variability throughout its range and may consist of more than one distinct taxon. However, a common morph is widely distributed from the Great Lakes to the Northwest Territories, consistent with a hypothesis of preglacial origin for the species. Shortjaw ciscoes have declined because of excessive exploitation by food fisheries, habitat degradation, and predation and competition with introduced and exotic species such as alewife, Alosa pseudoharengus, and rainbow smelt, Osmerus mordax. The status of the species in most Canadian lakes is unknown, but continuing declines in those lakes that have been monitored suggest that the shortjaw cisco should be considered as threatened throughout its range.

Report↗

USGS2012

Variation in clinical phenotype of human infection among genetic groups of Blastomyces dermatitidis

Background. Blastomyces dermatitidis, the etiologic agent of blastomycosis, has 2 genetic groups and shows varied clinical presentation, ranging from silent infections to fulminant respiratory disease and dissemination. The objective of this study was to determine whether clinical phenotype and outcomes vary based on the infecting organism's genetic group. Methods. We used microsatellites to genotype 227 clinical isolates of B. dermatitidis from Wisconsin patients. For each isolate, corresponding clinical disease characteristics and patient demographic information were abstracted from electronic health records and Wisconsin Division of Health reportable disease forms and questionnaires. Results. In univariate analysis, group 1 isolates were more likely to be associated with pulmonary-only infections ( P < .0001) and constitutional symptoms such as fever ( P < .0001). In contrast, group 2 isolates were more likely to be associated with disseminated disease ( P < .0001), older patient age ( P < .0001), and comorbidities ( P = .0019). In multivariate analysis, disease onset to diagnosis of >1 month ( P < .0001), older age at diagnosis ( P < .0001), and current smoking status ( P = .0001) remained predictors for group 2 infections. Conclusions. This study identified previously unknown associations between clinical phenotype of human infection and genetic groups of B. dermatitidis and provides a framework for further investigations of the genetic basis for virulence in B. dermatitidis .

Journal of Infectious Diseases↗

USGS2015

Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape

Amphibian species persisting in isolated streams and wetlands in desert environments can be susceptible to low connectivity, genetic isolation, and climate changes. We evaluated the past (1900–1930), recent (1981–2010), and future (2071–2100) climate suitability of the arid Great Basin (USA) for the Columbia spotted frog ( Rana luteiventris ) and assessed whether changes in surface water may affect connectivity for remaining populations. We developed a predictive model of current climate suitability and used it to predict the historic and future distribution of suitable climates. We then modeled changes in surface water availability at each time period. Finally, we quantified connectivity among existing populations on the basis of hydrology and correlated it with interpopulation genetic distance. We found that the area of the Great Basin with suitable climate conditions has declined by approximately 49% over the last century and will likely continue to decline under future climate scenarios. Climate conditions at currently occupied locations have been relatively stable over the last century, which may explain persistence at these sites. However, future climates at these currently occupied locations are predicted to become warmer throughout the year and drier during the frog's activity period (May – September). Fall and winter precipitation may increase, but as rain instead of snow. Earlier runoff and lower summer base flows may reduce connectivity between neighboring populations, which is already limited. Many of these changes could have negative effects on remaining populations over the next 50–80 years, but milder winters, longer growing seasons, and wetter falls might positively affect survival and dispersal. Collectively, however, seasonal shifts in temperature, precipitation, and stream flow patterns could reduce habitat suitability and connectivity for frogs and possibly other aquatic species inhabiting streams in this arid region.

Ecology and Evolution↗

USGS2002

Age and origin of base and precious metal veins of the Coeur d'Alene mining district, Idaho

Ore-bearing quartz-carbonate veins of the Coeur d'Alene mining district yield 87Sr/86Sr ratios of 0.74 to >1.60 for low Rb/Sr, carbonate gangue minerals, similar to current ranges measured in Middle Proterozoic, high Rb/Sr rocks of the Belt Supergroup. Stable isotope and fluid inclusion studies establish a genetic relationship between vein formation and metamorphic-hydrothermal systems of the region. These extraordinary 87Sr/86Sr ratios require accumulation of radiogenic 87Sr in a high Rb/Sr system over an extended period prior to incorporation of Sr into the hydrothermal veins. Evaluation of the age and composition of potential sources of highly radiogenic Sr indicates that the ore-bearing veins of the Coeur d'Alene district formed during the Cretaceous from components scavenged from rocks of the Belt Supergroup, the primary host rocks of the district. Proterozoic Pb isotope ratios observed in galena from many Coeur d'Alene veins were established when Pb separated from uranium during deposition or diagenesis of the Belt Supergroup at 1400 to 1500 Ma, possibly as disseminated syngenetic deposits. K-Ar and Rb-Sr apparent ages and ??18O values of Belt Supergroup rocks decrease from the Coeur d'Alene district toward the Idaho and Kaniksu batholiths, approximately normal to the trends of metamorphic isograds, fold axes, foliation, and the major reverse faults of the district. Isoclinal folding, thrust faulting, high-temperature metamorphism, granitic plutonism, and regional-scale metamorphic-hydrothermal activity is documented in the region between 140 and 45 Ma, representing the only such combination of events in the Coeur d'Alene region subsequent to about 1300 Ma. The Sr and oxygen results and geologic evidence favor formation of the ore-bearing carbonate veins by fluids related to a complex metamorphic-hydrothermal system during the Cretaceous. Pb with Proterozoic isotopic compositions was probably mobilized and incorporated like other metals into the hydrothermal veins during this event. The ore-bearing veins were sheared and displaced during early Tertiary northwest-trending dextral strike-slip faulting along the Osburn fault and related structures of the Lewis and Clark line.

Economic Geology↗

USGS2003

Arsenic in midwestern glacial deposits — Occurrence and relation to selected hydrogeologic and geochemical factors

Ground-water-quality data collected as part of 12 U.S. Geological Survey National Water-Quality Assessment studies during 1996-2001 were analyzed to (1) document arsenic occurrence in four types of gla-cial deposits that occur in large areas of the Midwest, (2) identify hydrogeologic or geochemical factors asso-ciated with elevated arsenic concentrations, and (3) search for clues as to arsenic source(s) or mechanism(s) of mobilization that could be useful for designing future studies. Arsenic and other water-quality constituents were sampled in 342 monitor and domestic wells in parts of Illinois Indiana Ohio Michigan and Wisconsin. Arsenic was detected (at a concentration >1 ?g/L) in one-third of the samples. The maximum concentration was 84 ?g/L, and the median was less than 1 ?g/L. Eight percent of samples had arsenic concentrations that exceeded the U.S. Environmental Protection Agency Maximum Contaminant Level (MCL) of 10?g/L. Samples were from four aquifer types?confined valley fill, unconfined valley fill, outwash plain, and till with sand lenses. Highest arsenic concentrations were found in reducing waters from valley-fill depos-its. In confined valley fill, all waters were reducing and old (recharged before 1953), and almost half of sam-ples had arsenic concentrations greater than the MCL. In unconfined valley fill, redox conditions and ages were varied, and elevated arsenic concentrations were sporadic. In both types of valley fill, elevated arsenic concentrations are linked to the underlying bedrock on the basis of spatial relations and geochemical correla-tions. In shallow (<50 ft) till with sand lenses, arsenic was detected in oxic or mixed waters, but concentra-tions were rarely greater than the MCL. In shallow out-wash-plain deposits, arsenic concentrations greater than the MCL were detected in waters that were reduc-ing and young (recharged after 1953). Although arsenic concentrations were signifi-cantly higher in deep wells (>150 ft), all deep wells were from a distinctive aquifer type (confined valley fill). It is not known whether wells at similar depths in other aquifer types would produce waters with simi-larly high arsenic concentrations. Correlations of arsenic with fluoride, strontium, and barium suggest that arsenic might be related to epi-genetic (Mississippi Valley-type) sulfide deposits in Paleozoic bedrock. Arsenic is typically released from sulfides by oxidation, but in the current study, the highest arsenic concentrations in glacial deposits were detected in reducing waters. Therefore, a link between epigenetic sulfides and elevated arsenic concentrations in glacial deposits would probably require a multi-step process.

Illinois, Indiana, Ohio↗

USGS2000

Revision of middle Proterozoic Yellowjacket Formation, central Idaho, and revision of Cretaceous Slim Sam Formation, Elkhorn Mountains area, Montana

The Yellowjacket Formation is restricted to the strata originally assigned to it by Ross (1934). The Yellowjacket, the conformably overlying Hoodoo Quartzite, and succeeding unnamed argillaceous quartzite unit form a genetically related sequence that lies in a structural block delimited on the northeast by the Iron Lake fault. Directly northeast of the fault, strata currently assigned by others to the lower subunit of the Yellowjacket are correlated with the Apple Creek Formation in the Lemhi Range. Mapping in the western part of the Lemhi Range shows that the Apple Creek Formation lies depositionally above the Big Creek Formation and that no rocks of the Yellowjacket-Hoodoo unnamed unit stratigraphic sequence are present. In contrast, in the area of the Yellowjacket mapped by Ross (1934) and the area directly northeast of the Iron Lake Fault, the Big Creek Formation is absent, even though it is 2,700 m thick in the Lemhi Range. These data indicate that the Iron Lake Fault juxtaposed the Yellowjacket-Hoodoo-unnamed unit sequence against non-Yellowjacket strata to the northeast. The Upper Cretaceous Slim Sam Formation of the Elkhorn Mountains area is revised. Strata of the lower part are correlated with the regionally recognized marine Telegraph Creek Formation and the overlying marine to marginal marine Eagle Sandstone. Only lower strata of the Eagle are present in the study area and they are preserved discontinously. The nonmarine volcanic and volcaniclastic rocks of the upper part of the Slim Sam as originally defined retain the name Slim Sam Formation. These rocks, mainly of sedimentary origin, are genetically related to the Elkhorn Mountains Volcanics. The lower contact of the Slim Sam (restricted) is unconformable above the Eagle Sandstone or more commonly above the Telegraph Creek Formation. The upper contact is conformable with the Elkhorn Mountains Volcanics.

Idaho, Montana↗

USGS1998

Impact of alternative regeneration methods on genetic diversity in coastal Douglas-fir

Genetic implications of natural and artificial regeneration following three regeneration methods (group selection, shelterwood, and clearcut) were investigated in coastal Douglas-fir ( Pseudotsuga menziesii var. menziesii [Mirb.] Franco) using genetic markers (17 allozyme loci). In general, harvesting followed by either natural or artificial regeneration resulted in offspring populations little altered from those in the previous generation. Cutting the smallest trees to form shelterwoods, however, resulted in the removal of rare, presumably deleterious, alleles, such that slightly fewer alleles per locus were observed among residual trees (2.76) and natural regeneration (2.75) than found in uncut (control) stands (2.86). Thus, although the shelterwood regime appears quite compatible with gene conservation, it would be best to leave parent trees of a range of sizes in shelterwoods designated as gene conservation reserves, in order to maximize the number of alleles (regardless of current adaptive value) in naturally regenerated offspring. Seedling stocks used for artificial regeneration in clearcut, shelterwood, and group selection stands (7 total) had significantly greater levels of genetic diversity, on average, than found in natural regeneration. This is probably because the seeds used in artificial seedling stocks came from many wild stands and thus, sampled more diversity than found in single populations. For. Sci. 44(3): 390-396.

Forest Science↗

USGS2017

Novel RAD sequence data reveal a lack of genomic divergence between dietary ecotypes in a landlocked salmonid population

Preservation of heritable ecological diversity within species and populations is a key challenge for managing natural resources and wild populations. Salmonid fish are iconic and socio-economically important species for commercial, aquaculture, and recreational fisheries across the globe. Many salmonids are known to exhibit ecological divergence within species, including distinct feeding ecotypes within the same lakes. Here we used 5559 SNPs, derived from RAD sequencing, to perform population genetic comparisons between two dietary ecotypes of sockeye salmon ( Oncorhynchus nerka ) in Jo-Jo Lake, Alaska (USA). We tested the standing hypothesis that these two ecotypes are currently diverging as a result of adaptation to distinct dietary niches; results support earlier conclusions of a single panmictic population. The RAD sequence data revealed 40 new SNPs not previously detected in the species, and our sequence data can be used in future studies of ecotypic diversity in salmonid species.

Alaska↗

USGS2021

Trade-offs between suppression and eradication of sea lampreys from the Great Lake

Ecosystem managers confronted with newly invasive species may respond with a program of suppression or eradication. Suppression of an invasive species refers to management of a species such that its effect on other biota in the local ecosystem is acceptable. Eradication is the removal of all individuals of a species from a defined region. We examine the cost and benefit trade-offs between suppression and eradication of Laurentian Great Lakes sea lampreys ( Petromyzon marinus ) based on discussions at the 3rd Sea Lamprey International Symposium (held in 2019). Substantial effort has been expended annually since the 1960s to suppress sea lampreys in the Great Lakes basin. Choosing between suppression and eradication is a value judgement, ideally made jointly by scientists, decision-makers, stakeholders, and society. Successful large-scale eradications have been limited to a small number of cases for which the cost to human society justified and supported the long-term commitment necessary for success. The greatest challenge to successful eradication of sea lampreys from the Great Lakes may be a suitable social, political, legal, and institutional environment. Preparations could be made now for a transition in which public pushback on current control methods (pesticide applications and barriers to fish passage) leads to more extensive use of an alternative control method, such as genetic control.

Great Lakes and Saint Lawrence River areas↗

USGS2025

Geographic determination of Pinus ponderosa using DART TOFMS, ICP-MS, and LIBS handheld analyzer

Due to legal requirements on international imports, it is important for law enforcement and regulatory agencies to identify the geographical provenance of timber. Current methods for geographic identification utilize data generated by direct analysis in real time time-of-flight mass spectrometry (DART TOFMS), genetics, and isotope-ratio mass spectrometry (IRMS), but identification methods based on genetics and IRMS data require months to years to create usable databases. This study used machine learning algorithms to compare the results of DART TOFMS, inductively coupled plasma mass spectrometry (ICP-MS), and a handheld laser-induced breakdown spectroscopy (LIBS) analyzer for use in geographic identification of five populations of Pinus ponderosa spaced between 14 to 72 km apart. The results of the study showed comparable performances from machine learning algorithms applied to the ICP-MS and LIBS data with accuracy and kappa values over 90% while the DART TOFMS had an accuracy of 76% and a kappa value of 70%. This study demonstrated that data from the LIBS handheld analyzer is a viable and intriguing alternative to ICP-MS and DART TOFMS analyses in generating training databases and further indicates that trace elemental analysis via ICP-MS is a promising method for generating databases used to identify the origin of timber.

California, Oregon↗

USGS2008

Genetic characterization of Hawaiian isolates of Plasmodium relictum reveals mixed-genotype infections

Background: The relatively recent introduction of a highly efficient mosquito vector and an avian pathogen (Plasmodium relictum) to an isolated island ecosystem with nai??ve, highly susceptible avian hosts provides a unique opportunity to investigate evolution of virulence in a natural system. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct impacts on virulence. Toward further understanding of how host-parasite and parasite-parasite relationships may impact virulence, this study characterizes within-host diversity of malaria parasite populations based on genetic analysis of the trap (thrombospondin-related anonymous protein) gene in isolates originating from Hawaii, Maui and Kauai Islands. Methods: A total of 397 clones were produced by nested PCR amplification and cloning of a 1664 bp fragment of the trap gene from two malarial isolates, K1 (Kauai) and KV115 (Hawaii) that have been used for experimental studies, and from additional isolates from wild birds on Kauai, Maui and Hawaii Islands. Diversity of clones was evaluated initially by RFLP-based screening, followed by complete sequencing of 33 selected clones. Results: RFLP analysis of trap revealed a minimum of 28 distinct RFLP haplotypes among the 397 clones from 18 birds. Multiple trap haplotypes were detected in every bird evaluated, with an average of 5.9 haplotypes per bird. Overall diversity did not differ between the experimental isolates, however, a greater number of unique haplotypes were detected in K1 than in KV115. We detected high levels of clonal diversity with clear delineation between isolates K1 and KV115 in a haplotype network. The patterns of within-host haplotype clustering are consistent with the possibility of a clonal genetic structure and rapid within-host mutation after infection. Conclusion: Avian malaria (P. relictum) and Avipoxvirus are the significant infectious diseases currently affecting the native Hawaiian avifauna. This study shows that clonal diversity of Hawaiian isolates of P. relictum is much higher than previously recognized. Mixed infections can significantly contribute to the uncertainty in host-pathogen dynamics with direct implications for host demographics, disease management strategies, and evolution of virulence. The results of this study indicate a widespread presence of multiple-genotype malaria infections with high clonal diversity in native birds of Hawaii, which when coupled with concurrent infection with Avipoxvirus, may significantly influence evolution of virulence. ?? 2008 Jarvi et al; licensee BioMed Central Ltd.

Biology Direct↗