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At least 343 records · Page 19Linked to original sources

USGS2013

Evidence of Hybridization between Common Gartersnakes ( Thamnophis sirtalis ) and Butler’s Gartersnakes ( Thamnophis butleri ) in Wisconsin (USA).

Snakes within the genus Thamnophis (Gartersnakes and Ribbonsnakes) are often found in sympatry throughout their geographic distributions. Past work has indicated that some sympatric species within this genus may hybridize, but research of this nature is limited. We attempted to determine whether hybridization occurs between two Thamnophis species native to the upper midwestern United States: Common Gartersnake ( Thamnophis sirtalis ) and the Butler's Gartersnake ( Thamnophis butleri ). We sampled snakes ( n = 411) across 26 locations in Wisconsin, including sites where both species coexist and sites where only Common Gartersnakes are found. We conducted genetic analyses on tissue collected from individuals field-identified as Common Gartersnakes or Butler's Gartersnakes. To verify the results of our field-collected data, we analyzed tissues from juvenile snakes ( n = 4) suspected to be the offspring of a Common Gartersnake and a Butler's Gartersnake that were housed together in a captive situation. Of the field-collected snakes analyzed, eight snakes were consistent with expected Common × Butler's Gartersnake hybrids. All four of the captive offspring analyzed resolved as putative hybrids, corresponding with our field-collected samples. Butler's Gartersnake is a globally rare species, endemic only to the upper midwestern United States. Studies involving the potential for hybridization between common and uncommon species are useful from a conservation perspective. The low incidence of hybridization we observed would indicate that hybridization between these species is uncommon. Further research investigating rates of hybridization would help assess any potential threat posed by outbreeding between common and rare gartersnakes in this region of the United States.

Wisconsin↗

USGS2003

Projecting the success of plant restoration with population viability analysis

Conserving viable populations of plant species requires that they have high probabilities of long-term persistence within natural habitats, such as a chance of extinction in 100 years of less than 5% (Menges 1991, 1998; Brown 1994; Pavlik 1994; Chap. 1, this Vol.). For endangered and threatened species that have been severely reduces in range and whose habitats have been fragmented, important species conservation strategies may include augmenting existing populations or restoring new viable populations (Bowles and Whelan 1994; Chap. 2, this Vol.). Restoration objectives may include increasing population numbers to reduce extinction probability, deterministic manipulations to develop a staged cohort structure, or more complex restoration of a desired genetic structure to allow outcrossing or increase effective population size (DeMauro 1993, 1994; Bowles et al. 1993, 1998; Pavlik 1994; Knapp and Dyer 1998; Chap. 2, this Vol.). These efforts may require translocation of propagules from existing (in situ) populations, or from ex situ botanic gardens or seed storage facilities (Falk et al. 1996; Guerrant and Pavlik 1998; Chap. 2, this Vol.). Population viability analysis (PVA) can provide a critical foundation for plant restoration, as it models demographic projections used to evaluate the probability of population persistence and links plant life history with restoration strategies. It is unknown how well artificially created populations will meet demographic modeling requirements (e.g., due to artificial cohort transitions) and few, if any, PVAs have been applied to restorations. To guide application of PVA to restored populations and to illustrate potential difficulties, we examine effects of planting different life stages, model initial population sizes needed to achieve population viability, and compare demographic characteristics between natural and restored populations. We develop and compare plant population restoration viability analysis (PRVA) case studies of two plant species listed in the USA for which federal recovery planning calls for population restoration: Cirsium pitcheri , a short-lived semelparous herb, and Asclepias meadii , a long-lived iteroparous herb.

Book chapter↗

USGS2018

Large-scale variation in density of an aquatic ecosystem indicator species

Monitoring indicator species is a pragmatic approach to natural resource assessments, especially when the link between the indicator species and ecosystem state is well justified. However, conducting ecosystem assessments over representative spatial scales that are insensitive to local heterogeneity is challenging. We examine the link between polychlorinated biphenyl (PCB) contamination and population density of an aquatic habitat specialist over a large spatial scale using non-invasive genetic spatial capture-recapture. Using American mink (Neovison vison), a predatory mammal and an indicator of aquatic ecosystems, we compared estimates of density in two major river systems, one with extremely high levels of PCB contamination (Hudson River), and a hydrologically independent river with lower PCB levels (Mohawk River). Our work supports the hypothesis that the mink densities are substantially (1.64-1.67 times) lower in the contaminated river system. We demonstrate the value of coupling the indicator species concept with well-conceived and spatially representative monitoring protocols. PCBs have demonstrable detrimental effects on aquatic ecosystems, including mink, and these effects are likely to be profound and long-lasting, manifesting as population-level impacts. Through integrating non-invasive data collection, genetic analysis, and spatial capture-recapture methods, we present a monitoring framework for generating robust density estimates across large spatial scales.

New York↗

USGS2021

Review of the invasive Asian clam Corbicula spp. (Bivalvia: Cyrenidae) distribution in North America, 1924–2019

The bivalve Corbicula is one of the most successful aquatic mollusk invaders in the world. Since being introduced to North America from its native range in Asia, it has dispersed widely over a large portion of the continent from southern Canada to Panama. The first evidence of its introduction in the Western Hemisphere was discovered in 1924 in British Columbia, Canada. A review of distribution records from natural history museums, scientific literature, Federal and State agencies, universities, and oral and written communications with scientists has shown the continued dispersal of Corbicula in North America. Since the most recent comprehensive review of its distribution information through the mid-1980s, Corbicula has been found in an additional 2 Canadian Provinces, 10 U.S. States and Puerto Rico, 9 Mexican States, Cuba, and Panama. The known distribution in North America now includes 47 U.S. States, District of Columbia, Puerto Rico, 3 Canadian Provinces, 16 Mexican States, Cuba, and Panama. Corbicula has been found in three of the Laurentian Great Lakes (Erie, Michigan, Superior) primarily associated with industrial warmwater effluent refugia. Problems associated with Corbicula populations were widely realized not long after its arrival and included negative impacts to power generation, industrial water supply operations, and agricultural water conveyance. In natural settings, impacts on native mussels such as altering nutrient cycling, food webs, and sediment distribution dynamics have occurred. In past decades, control of established open water populations had not been a management priority. With a relatively recent interest in eradication of small, newly established populations, several attempts were made in the United States but were unsuccessful. Recent molecular genetic analyses provide evidence of multiple species and (or) genetically and morphologically distinguishable “forms” in North America. However, the number and identification of Corbicula species in North America remain unresolved. It appears likely that more than one species of Corbicula has been introduced into U.S. waters.

Scientific Investigations Report↗

USGS2003

A special issue devoted to gold deposits in northern Nevada: Part 2. Carlin-type Deposits

This is the second of two special issues of Economic Geology devoted to gold deposits in northern Nevada. Readers interested in a general overview of these deposits, their economic significance, their context within the tectonic evolution of the region, and synoptic references on each gold deposit type are directed to the preface of the first special issue (John et al., 2003). Volume 98, issue 2, contains five papers that address regional aspects important to the genesis of gold deposits in northern Nevada and five papers that present detailed studies of epithermal deposits and districts. All of the regional papers are pertinent to Carlin-type gold deposits, because they address the age of mineralization (Arehart et al., 2003), origin and evolutionary history of the northwest-striking mineral belts that localize many deposits (Grauch et al., 2003), nature of the middle and lower crust below these mineral belts (Howard, 2003), district- to deposit-scale stream sediment and lithogeochemical anomalies (Theodore et al., 2003), and stratigraphy and structure of a district located along a northeast-striking lineament (Peters et al., 2003). The nine papers in this second special issue focus on an array of problems pertinent to genetic and exploration models for Carlin-type deposits in northern Nevada (Fig. 1). These investigations sort out and characterize the sequence of deformational, igneous, and hydrothermal events in mining districts, constrain the age of mineralization, map paleothermal gradients, identify structures and lithologies that are preferentially mineralized, ascertain processes of ore formation, determine sources of ore fluid components, and define fluid flow paths. A common theme among these papers is inheritance, whereby older features in the mineral belts influence ore formation in subsequent Carlin-type hydrothermal systems. Three types of inheritance are inferred by one or more of these investigations: (1) structural inheritance, where older faults are reactivated during subsequent contractional and/or extensional tectonic events producing permeable fracture systems that focused flow of ore fluids; (2) alteration inheritance, where one or more preore alteration events produced reactive host rocks that are preferentially mineralized; and (3) geochemical inheritance, in which Au and other elements are recycled from older mineralization into younger Carlin-type deposits. Despite the similar age, tectonic setting, alteration types, mineral parageneses, and geochemical signatures of the deposits studied, these papers do not lead to consensus regarding genetic models for Carlin-type deposits. Rather, the separate investigations by different workers, utilizing both similar and unlike approaches, result in markedly different conclusions. Some of this disparity probably is due to real differences in the origin of different districts; however, the opposing conclusions arrived at by investigations on neighboring deposits in a single district are more problematic and most likely are due to difficulties resulting from the superposition of different types and ages of gold mineralization or to substantial variations in the hydrology and proportions of fluid components derived from deep and shallow sources in each deposit. Further work is needed to validate and understand the significance of these differences.

Nevada↗

USGS2018

Genetic integrity, population status, and long-term viability of isolated populations of shoal bass in the upper Chattahoochee River basin, Georgia

This report characterizes the status of multiple isolated Shoal Bass ( Micropterus cataractae ) populations in the upper Chattahoochee River basin (UCRB), Georgia. The Shoal Bass, a sport fish endemic to the Apalachicola-Chattahoochee-Flint River (ACF) basin, is a fluvial-specialist species considered vulnerable to local extirpations and extinction due to habitat fragmentation and introgression with non-native congeners. Perhaps one of the most isolated populations of Shoal Bass exists in a 2-km reach of Big Creek, a tributary of the Chattahoochee River located near Roswell, Georgia. Big Creek is partially contained within the Chattahoochee River National Recreation Area, although the Big Creek watershed is riddled with urban land cover. Roswell Mill Dam limits the upstream extent of the Shoal Bass population at Big Creek, and the downstream extent is presumably limited to the confluence of Big Creek and the Chattahoochee River. This reach of the Chattahoochee River is thermally depressed because of coldwater releases from Lake Lanier, and is considered unsuitable for Shoal Bass. Herein, we examine the genetic integrity, population status, and long-term viability of the Shoal Bass population in Big Creek. We also examine two additional Shoal Bass populations that occur in the UCRB, specifically the Chestatee River and the upper Chattahoochee River, both of which are impounded at Lake Lanier. Together, the Shoal Bass inhabiting these three stream systems comprise a distinct genetic stock of Shoal Bass (Taylor 2017), underscoring the importance of conserving these populations towards maintaining the overall diversity and adaptive potential of the species. We assessed genetic diversity and estimated effective population sizes within these three rivers by genotyping fish with 16 microsatellite DNA markers. Results demonstrated that the Shoal Bass population in Big Creek has experienced high rates of introgression with non-native Smallmouth Bass (M. dolomieu), purportedly introduced into the Chattahoochee River in the past 10-15 years. Alarmingly, only 24% (15 of 62) of putative Shoal Bass collected from Big Creek were genetically pure Shoal Bass, whereas the majority of fish were first-filial (F1) generation hybrids and unidirectional backcrosses towards Shoal Bass. Fleeting opportunity may remain to conserve the native genome of the Shoal Bass population in Big Creek. High hybridization rates prevented genetic diversity analysis for the Big Creek population. Shoal Bass populations in the Chestatee and Chattahoochee rivers displayed levels of genetic diversity similar to populations that persist in other rivers in the ACF basin, namely the Flint and Chipola rivers. Effective population sizes of 93.8– 197.4 for the Chestatee and Chattahoochee rivers (combined) suggest that the conservation status of these populations is stable for the short-term, but may be at risk of losing genetic diversity and adaptive potential in the long-term. To estimate age and mortality of the three populations, we used fish scales and capture-markrecapture (CMR) as complementary, non-lethal methods for age estimation. Estimated ages of phenotypic Shoal Bass ranged from 1-12 years in all three populations, demonstrating increased longevity compared to populations elsewhere within the native range. Catch-curve estimates of annual mortality ranged from 18.4-23.7%, which are markedly lower than those observed in other Shoal Bass populations in the ACF basin. These differences in life-history characteristics underscore the need for the development of population-specific management and conservation strategies for Shoal Bass in the UCRB. The lowest recruitment variability (i.e., the variation in year-class strength) was observed in the Chestatee River, a forested watershed, whereas the highest variability was observed in Big Creek, an urbanized watershed. Recruitment strength in Big Creek was negatively influenced by discharge variability in the summer months, suggesting that flashy, sediment-laden flows hinder survival of recently hatched young. Other statistically significant models from Big Creek and the Chattahoochee River indicated that over-winter survival could be an important pinch-point for recruitment in UCRB populations. A multi-agency sampling effort was conducted from May 2013-May 2016 to estimate the population size of Shoal Bass occupying the 1-km of wadeable shoal habitats in Big Creek. Using CMR models, we estimated that approximately 219-348 Shoal Bass (≥ 70 mm total length) occupied the area throughout the duration of our study. These estimates largely reflect abundance of individuals aged 0-2 years, as only 9% (36 of 408) tagged fish were aged ≥ 7 years. Local abundance appeared similar to that reported for a population that inhabited Little Uchee Creek, a similar-sized tributary of the Chattahoochee River, prior to its recent functional extirpation. The low abundance of large, adult Shoal Bass further suggests the long-term viability of the Big Creek population may be in jeopardy. Perhaps most importantly, CMR estimates reflect abundance of phenotypic Shoal Bass – genetic analyses suggest the abundance of pure Shoal Bass could be an order of magnitude smaller. To evaluate the potential for adult Shoal Bass to emigrate from Big Creek into the mainstem Chattahoochee River, we tagged eight adults with acoustic telemetry tags and assessed their seasonal residency at two stationary receiver locations located in increasing proximity to the confluence with the Chattahoochee River. Fish took up residency near the confluence during the fall and winter months, during which time water temperatures in Big Creek were periodically colder than the Chattahoochee River. Although we were unable to document emigration, we conclude that the potential for emigration is highest during the winter months when the Chattahoochee River may be warmer than Big Creek. Two of the tagged fish were caught by anglers near the confluence, suggesting that angling pressure at Big Creek may be higher than previously suspected. Overall, this study observed unique life-history characteristics and characterized the population status of multiple Shoal Bass populations in the UCRB. Populations in the Chestatee and Chattahoochee rivers appear stable at present and likely represent the last remaining strongholds for pure Shoal Bass in the UCRB. Efforts to preserve forested watershed conditions, natural hydrology, and shoal habitats would contribute to the long-term persistence of Shoal Bass populations in these two rivers. Additionally, the detection of non-native Alabama Bass and their associated hybrids in both rivers is cause for concern. Diligent monitoring of hybridization dynamics between Alabama Bass and Shoal Bass is warranted, along with an assessment of Alabama Bass invasion extent upstream of Lake Lanier. The Shoal Bass population in Big Creek is threatened by elevated levels of introgression with nonnative Smallmouth Bass, recruitment variability, low abundance of adults, and isolation from other populations. Conservation intervention is urgently needed to restore and preserve this genetically distinct population, which would contribute to preservation of range wide genetic diversity and adaptability of the species. Additionally, an urban sport fishery for Shoal Bass at Big Creek has the potential to serve as a tool for increasing public awareness, engagement, and support of Shoal Bass conservation efforts in the UCRB. We suggest strategies for conservation of the remnant shoal habitats and Shoal Bass population in Big Creek, including potential development of a supplemental stocking program, selective removal of non-native congeners, and delivery of environmental education programs that could bolster awareness and appreciation.

Georgia↗

USGS2017

Conservation genetics of American crocodile, Crocodylus acutus , populations in Pacific Costa Rica

Maintaining genetic diversity is crucial for the survival and management of threatened and endangered species. In this study, we analyzed genetic diversity and population genetic structure at neutral loci in American crocodiles, Crocodylus acutus, from several areas (Parque Nacional Marino Las Baulas, Parque Nacional Santa Rosa, Parque Nacional Palo Verde, Rio Tarcoles, and Osa Conservation Area) in Pacific Costa Rica. We genotyped 184 individuals at nine microsatellite loci to describe the genetic diversity and conservation genetics between and among populations. No population was at Hardy-Weinberg Equilibrium (HWE) over all loci tested and a small to moderate amount of inbreeding was present. Populations along the Pacific coast had an average heterozygosity of 0.572 across all loci. All populations were significantly differentiated from each other with both FST and RST measures of population differentiation with a greater degree of molecular variance (81%) found within populations. Our results suggest C. acutus populations in Pacific Costa Rica were not panmictic with moderate levels of genetic diversity. An effective management plan that maintains the connectivity between clusters is critical to the success of C. acutus in Pacific Costa Rica.

Nature Conservation↗

USGS1985

Crystalline gold in soil and the problem of supergene nugget formation: Freezing and exclusion as genetic mechanisms

Many of the world's richest gold placer deposits now occur in cold regions despite differences in their climatic history. It therefore seems possible that there may be some fundamental connection between freezing climates and the local chemical behavior of gold in the weathering cycle. This hypothesis, along with the problematical occurrence of gold as euhedral crystals in arctic gravel and soil placers, has led me to review low temperature phenomena that may bear on the geochemistry of gold. Several effects which may influence the weathering of natural gold-bearing rocks, the chemical complexation of gold, and its subsequent mobility and deposition appear to be strongly connected with freeze action. The exclusion of dissolved solutes, solute gases, and particles from ice, subjects rock and soil minerals to increased corrosion from thin, unfrozen, adsorbed water films which remain at particle surfaces throughout the freezing of rocks and soils. The preferential exclusion of cations (over anions) from growing ice crystals creates charge separations and measurable current flow across waterice phase boundaries in freezing soil — a phenomenon which leads to troublesome seasonal electrolytic corrosion of pipelines buried in soil; this phenomenon may also favor the dissolution of normally insoluble metals such as gold during geologic time periods. The ice-induced accumulation of clays, organic acids, bacteria, and other organic matter at mineral surfaces may also speed chemical attack by providing a nearby sink of alternate cation-binding sites and hence rapid removal of liberated cations from solution. The latter mechanism may be operative in both the dissolution and redeposition of gold. These physical, chemical, and electrical effects are favorable to the dissolution of rocks (in addition to frost shattering) and to the dissolution, mobilization, and redeposition of gold and other noble metals and must therefore contribute significantly to the behavior of gold at low temperatures. The occurrence of large numbers of gold placer deposits in northern Canada, Alaska, and Siberia may thus be due in part to the low temperatures common to these regions.

Precambrian Research↗

USGS2007

Sequence analysis of the msp4 gene of Anaplasma ovis strains

Anaplasma ovis (Rickettsiales: Anaplasmataceae) is a tick-borne pathogen of sheep, goats and wild ruminants. The genetic diversity of A. ovis strains has not been well characterized due to the lack of sequence information. In this study, we evaluated bighorn sheep ( Ovis canadensis ) and mule deer (Odocoileus hemionus ) from Montana for infection with A. ovis by serology and sequence analysis of the msp4 gene. Antibodies to Anaplasma spp. were detected in 37% and 39% of bighorn sheep and mule deer analyzed, respectively. Four new msp4 genotypes were identified. The A. ovis msp4 sequences identified herein were analyzed together with sequences reported previously for the characterization of the genetic diversity of A. ovis strains in comparison with other Anaplasma spp. The results of these studies demonstrated that although A. ovis msp4 genotypes may vary among geographic regions and between sheep and deer hosts, the variation observed was less than the variation observed between A. marginale and A. phagocytophilum strains. The results reported herein further confirm that A. ovis infection occurs in natural wild ruminant populations in Western United States and that bighorn sheep and mule deer may serve as wildlife reservoirs of A. ovis . ?? 2006.

Veterinary Microbiology↗

USGS2012

Spatial segregation of spawning habitat limits hybridization between sympatric native Steelhead and Coastal Cutthroat Trout

Native Coastal Cutthroat Trout Oncorhynchus clarkii clarkii and Coastal Steelhead O. mykiss irideus hybridize naturally in watersheds of the Pacific Northwest yet maintain species integrity. Partial reproductive isolation due to differences in spawning habitat may limit hybridization between these species, but this process is poorly understood. We used a riverscape approach to determine the spatial distribution of spawning habitats used by native Coastal Cutthroat Trout and Steelhead as evidenced by the distribution of recently emerged fry. Molecular genetic markers were used to classify individuals as pure species or hybrids, and individuals were assigned to age-classes based on length. Fish and physical habitat data were collected in a spatially continuous framework to assess the relationship between habitat and watershed features and the spatial distribution of parental species and hybrids. Sampling occurred in 35 reaches from tidewaters to headwaters in a small (20 km 2 ) coastal watershed in Washington State. Cutthroat, Steelhead, and hybrid trout accounted for 35%, 42%, and 23% of the fish collected, respectively. Strong segregation of spawning areas between Coastal Cutthroat Trout and Steelhead was evidenced by the distribution of age-0 trout. Cutthroat Trout were located farther upstream and in smaller tributaries than Steelhead were. The best predictor of species occurrence at a site was the drainage area of the watershed that contributed to the site. This area was positively correlated with the occurrence of age-0 Steelhead and negatively with the presence of Cutthroat Trout, whereas hybrids were found in areas occupied by both parental species. A similar pattern was observed in older juveniles of both species but overlap was greater, suggesting substantial dispersal of trout after emergence. Our results offer support for spatial reproductive segregation as a factor limiting hybridization between Steelhead and Coastal Cutthroat Trout.

Washington↗

USGS2015

Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus

Since 1998, cyclic mortality events in common eiders ( Somateria mollissima ), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, Massachusetts, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of the Quaranjavirus genus within the family Orthomyxoviridae . Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein, which was demonstrated to have fusion activity, and also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated as VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity to Quaranfil virus and Johnston Atoll virus , the original members of the Quaranjavirus genus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined. Importance The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.

Massachusets↗

USGS2015

USGS role and response to highly pathogenic avian influenza

Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These viruses generally do not cause illness in wild birds, however, when spread to poultry they can be highly pathogenic and cause illness and death in backyard and commercial farms. Outbreaks may cause devastating agricultural economic losses and some viral strains have the potential to infect people directly. Furthermore, the combination of avian influenza viruses with mammalian viruses can result in strains with the ability to transmit from person to person, possibly leading to viruses with pandemic potential. All known pandemic influenza viruses have had some genetic material of avian origin. Since 1996, a strain of highly pathogenic avian influenza (HPAI) virus, H5N1, has caused infection in wild birds, losses to poultry farms in Eurasia and North Africa, and led to the deaths of several hundred people. Spread of the H5N1 virus and other influenza strains from China was likely facilitated by migratory birds. In December 2014, HPAI was detected in poultry in Canada and migratory birds in the United States. Since then, HPAI viruses have spread to large parts of the United States and will likely continue to spread through migratory bird flyways and other mechanisms throughout North America. In the United States, HPAI viruses have severely affected the poultry industry with millions of domestic birds dead or culled. These strains of HPAI are not known to cause disease in humans; however, the Centers for Disease Control and Prevention (CDC) advise caution when in close contact with infected birds. Experts agree that HPAI strains currently circulating in wild birds of North America will likely persist for the next few years. This unprecedented situation presents risks to the poultry industry, natural resource management, and potentially human health. Scientific knowledge and decision support tools are urgently needed to understand factors affecting the persistence of HPAI in wild birds, to forecast future spread of HPAI by wild birds, and to detect novel strains of HPAI that may emerge.

Fact Sheet↗

USGS2015

USGS highly pathogenic avian influenza research strategy

Fact Sheet↗

USGS2020

Spatial capture–recapture with random thinning for unidentified encounters

Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear ( Ursus arctos ) density in Oriental Cantabrian Mountains (North Spain). Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.

Ecology & Evolution↗

USGS2012

Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured--exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

California↗

USGS2005

Bioremediation of petroleum hydrocarbon-contaminated ground water: The perspectives of history and hydrology

Bioremediation, the use of microbial degradation processes to detoxify environmental contamination, was first applied to petroleum hydrocarbon-contaminated ground water systems in the early 1970s. Since that time, these technologies have evolved in some ways that were clearly anticipated early investigators, and in other ways that were not foreseen. The expectation that adding oxidants and nutrients to contaminated aquifers would enhance biodegradation, for example, has been born out subsequent experience. Many of the technologies now in common use such as air sparging, hydrogen peroxide addition, nitrate addition, and bioslurping, are conceptually similar to the first bioremediation systems put into operation. More unexpected, however, were the considerable technical problems associated with delivering oxidants and nutrients to heterogeneous ground water systems. Experience has shown that the success of engineered bioremediation systems depends largely on how effectively directions and rates of ground water flow can be controlled, and thus how efficiently oxidants and nutrients can be delivered to contaminated aquifer sediments. The early expectation that injecting laboratory-selected or genetically engineered cultures of hydrocarbon-degrading bacteria into aquifers would be a useful bioremediation technology has not been born out subsequent experience. Rather, it appears that petroleum hydrocarbon-degrading bacteria are ubiquitous in ground water systems and that bacterial addition is usually unnecessary. Perhaps the technology that was least anticipated early investigators was the development of intrinsic bioremediation. Experience has shown that natural attenuation mechanisms - biodegradation, dilution, and sorption - limit the migration of contaminants to some degree in all ground water systems. Intrinsic bioremediation is the deliberate use of natural attenuation processes to treat contaminated ground water to specified concentration levels at predetermined points in the aquifer. In current practice, intrinsic bioremediation of petroleum hydrocarbons requires a systematic assessment to show that ambient natural attenuation mechanisms are efficient enough to meet regulatory requirements and a monitoring program to verify that performance requirements are met in the future.

Ground Water↗

USGS2019

Genetic and morphological differences between water chestnut (Myrtales: Lythraceae: Trapa) populations in the northeastern United States, Japan, and South Africa

This Special Report (SR) outlines preliminary work conducted under the Aquatic Plant Control Research Program (APCRP) to investigate genetic and morphological differences of Trapa taxa (water chestnut) in the Northeastern (NE) US. Comparisons of morphological characteristics and genetics were made between Trapa populations from the native region of Eurasia and Africa versus the NE US. Unpublished data suggests a new introduction of Trapa (herein referred to as Trapa sp.) has occurred in the Commonwealth of Virginia, US with unknown biology and life history. Observations of morphological and phenological characteristics of this potential new taxon of Trapa differ from those typically found with naturalized Trapa natans reported in the NE US. A better understanding of the biology and ecology of Trapa sp. is warranted to identify control strategies that would benefit water resource managers tasked with management of water chestnut.

Technical Report↗

USGS2023

Historical DNA reveals climate adaptation in an endangered songbird

To cope with climate change, species may shift their distributions or adapt in situ to changing environmental conditions. However, clear examples of genetic changes via adaptation are limited. We explore evolutionary responses to climate change in the endangered southwestern willow flycatcher ( Empidonax traillii extimus ) through whole-genome comparisons between historical specimens, collected from 1888 to 1909 near San Diego, California, United States, and contemporary individuals from across the breeding range. Genomic analyses revealed that introgression into San Diego increased adaptive potential over time and shifted genome-wide population structure towards that of neighbouring populations. In contrast, loci linked to climate (dew point temperature and precipitation) shifted away from neighbouring populations and in a direction consistent with adaptation to climate change in southern California. This research highlights the role of admixture in facilitating adaptive shifts through its impact on genome-wide genetic variation and represents one of the few studies to document climate adaptation in a wild population.

Nature Climate Change↗