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At least 235 records · Page 13Linked to original sources
USGS2016

Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)

Newcastle disease is caused by virulent forms of avian paramyxovirus of serotype 1 (APMV-1) and has global economic importance. The disease reached panzootic proportions within two decades after first being identified in 1926 in the United Kingdom and Indonesia and still remains endemic in many countries across the world. Here we review information on the host, temporal, and geographic distribution of APMV-1 genetic diversity based on the evolutionary systematics of the complete coding region of the fusion gene. Strains of APMV-1 are phylogenetically separated into two classes (class I and class II) and further classified into genotypes based on genetic differences. Class I viruses are genetically less diverse, generally present in wild waterfowl, and are of low virulence. Class II viruses are genetically and phenotypically more diverse, frequently isolated from poultry with occasional spillovers into wild birds, and exhibit a wider range of virulence. Waterfowl, cormorants, and pigeons are natural reservoirs of all APMV-1 pathotypes, except viscerotropic velogenic viruses for which natural reservoirs have not been identified. Genotypes I and II within class II include isolates of high and low virulence, the latter often being used as vaccines. Viruses of genotypes III and IX that emerged decades ago are now isolated rarely, but may be found in domestic and wild birds in China. Containing only virulent viruses and responsible for the majority of recent outbreaks in poultry and wild birds, viruses from genotypes V, VI, and VII, are highly mobile and have been isolated on different continents. Conversely, virulent viruses of genotypes XI (Madagascar), XIII (mainly Southwest Asia), XVI (North America) and XIV, XVII and XVIII (Africa) appear to have a more limited geographic distribution and have been isolated predominantly from poultry.

Infection, Genetics and Evolution↗
USGS2021

Coalescent methods reconstruct contributions of natural colonization and stocking to origins of Michigan inland Cisco (Coregonus artedi)

Fish population structure in previously glaciated regions is often influenced by natural colonization processes and human-mediated dispersal, including fish stocking. Endemic populations are of conservation interest because they may contain rare and unique genetic variation. While coregonines are native to certain Michigan inland lakes, some were stocked with fish from Great Lakes sources, calling into question the origin of extant populations. While most stocking targeted lake whitefish ( Coregonus clupeaformis ), cisco ( C. artedi ) were also stocked from the Great Lakes to inland waterbodies. We used population genetic data (microsatellite genotypes and mitochondrial (mt)DNA sequences), coalescent modeling, and approximate Bayesian computation to investigate the origins of 12 inland Michigan cisco populations. The spatial distribution of mtDNA haplotypes suggests Michigan is an introgression zone for two ancestral cisco lineages associated with separate glacial refugia. Low levels of genetic diversity and high levels of genetic divergence were observed for populations located well inland of the Great Lakes relative to populations occupying waterbodies near the Great Lakes. Estimates of recent Great Lakes gene flow ranged from 27 to 48% for populations near the Great Lakes shoreline but were substantially lower (under 8%) for populations further inland. Inland lakes with elevated recent gene flow estimates may have been recipients of stocked coregonine fry, including cisco. Low levels of genetic diversity paired with a high likelihood of endemism as indicated by strong genetic divergence and low Great Lakes population inputs suggest the analyzed cisco populations occupying southern Michigan kettle lakes are of elevated conservation interest.

Michigan↗
USGS2006

DNA damage and external lesions in brown bullheads (Ameiurus nebulosus) from contaminated habitats

The Comet assay was used to compare levels of DNA damage in brown bullheads ( Ameiurus nebulosus ) collected from three known contaminated locations, the Cuyahoga River (OH, USA), Ashtabula River (OH, USA; both tributaries to Lake Erie, USA), and Ashumet Pond (Cape Cod, MA, USA), with brown bullheads collected from three paired reference sites, Old Woman Creek (OH, USA), Conneaut River (OH, USA; both tributaries to Lake Erie), and Great Herring Pond (mainland MA, USA), respectively. Blood was sampled from each fish, and the Comet assay was conducted on erythrocytes. The assay results demonstrate that fish from the three contaminated sites each suffered higher DNA damage compared with fish from their respective reference sites. The results also show that the genetic damage was associated with the occurrence of external lesions and deformities in fish. The Comet assay is sufficiently sensitive to detect exposure of natural fish populations to environmental levels of genotoxic contaminants.

Environmental Toxicology and Chemistry↗
USGS2015

Connectivity among subpopulations of Louisiana black bears as estimated by a step selection function

Habitat fragmentation is a fundamental cause of population decline and increased risk of extinction for many wildlife species; animals with large home ranges and small population sizes are particularly sensitive. The Louisiana black bear ( Ursus americanus luteolus ) exists only in small, isolated subpopulations as a result of land clearing for agriculture, but the relative potential for inter-subpopulation movement by Louisiana black bears has not been quantified, nor have characteristics of effective travel routes between habitat fragments been identified. We placed and monitored global positioning system (GPS) radio collars on 8 female and 23 male bears located in 4 subpopulations in Louisiana, which included a reintroduced subpopulation located between 2 of the remnant subpopulations. We compared characteristics of sequential radiolocations of bears (i.e., steps) with steps that were possible but not chosen by the bears to develop step selection function models based on conditional logistic regression. The probability of a step being selected by a bear increased as the distance to natural land cover and agriculture at the end of the step decreased and as distance from roads at the end of a step increased. To characterize connectivity among subpopulations, we used the step selection models to create 4,000 hypothetical correlated random walks for each subpopulation representing potential dispersal events to estimate the proportion that intersected adjacent subpopulations (hereafter referred to as successful dispersals). Based on the models, movement paths for males intersected all adjacent subpopulations but paths for females intersected only the most proximate subpopulations. Cross-validation and genetic and independent observation data supported our findings. Our models also revealed that successful dispersals were facilitated by a reintroduced population located between 2 distant subpopulations. Successful dispersals for males were dependent on natural land cover in private ownership. The addition of hypothetical 1,000-m- or 3,000-m-wide corridors between the 4 study areas had minimal effects on connectivity among subpopulations. For females, our model suggested that habitat between subpopulations would probably have to be permanently occupied for demographic rescue to occur. Thus, the establishment of stepping-stone populations, such as the reintroduced population that we studied, may be a more effective conservation measure than long corridors without a population presence in between.

Louisiana↗
USGS2010

Population structure and plumage polymorphism: the intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani

Background Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. Results To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor ( Mc1r ) to investigate molecular genetic differentiation among three B. jamaicensis subspecies ( B. j. borealis , B. j. calurus , B. j. harlani ). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis . Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus , and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus , suggesting that Mc1r does not play a significant role in B. jamaicensis melanism. Conclusions These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.

BMC Evolutionary Biology↗
USGS2010

A summary of information on the rust Puccinia psidii Winter (guava rust) with emphasis on means to prevent introduction of additional strains to Hawaii

The neotropical rust fungus Puccinia psidii ( P. psidii ) was originally described from the host common guava in its native Brazil but has been found since on hosts throughout the myrtle family (Myrtaceae), including a dramatic host jump to nonnative Eucalyptus plantations. Most rust fungi are able to live only on a very narrow range of host species. P. psidii is unusual both for having a broad host range and for the intensity of its damage to susceptible young growth. This rust first got a foothold in the United States in Florida more than three decades ago. The U.S. Department of Agriculture (USDA) has since considered it a nonactionable, nonreportable pest. Hawaii and Florida are the only two states with native species in the myrtle family. Over a period of 30 years, this rust has done little damage to any of the scattered native Myrtaceae in Florida, although the host range of the rust has gradually grown to about 30 mostly nonnative species in the family, apparently because of increasing genetic variety of the rust by repeated introductions. However, Florida’s native Myrtaceae are among the roughly 1,100 neotropical species that are largely resistant to P. psidii . The 3,000 species of non-neotropical Myrtaceae of the Pacific, Australia, Asia, and Africa are expected to prove much more vulnerable to P. psidii . Little is known about the genetics or genetic strains of P. psidii , although existing literature shows that there are numerous strains that have differential ability to infect suites of host plants. The rust was first recorded in the state of Hawaii on Oahu in April 2005 and quickly spread throughout the Hawaiian Islands. The main concern in Hawaii became the potential threat to ohia, Metrosideros polymorpha (Myrtaceae), the endemic forest tree species overwhelmingly important in Hawaii’s nature and culture. The potential ecological consequences of a virulent strain of rust on ohia forests are immense, due to its role as a foundation tree species and the diversity of niches it fills in Hawaii. A single genetic strain of the rust is established in Hawaii, apparently composed of a single genotype lacking sexual reproduction. P. psidii has been found statewide in Hawaii attacking Myrtaceae from near sea level to about 1,200 m elevation in areas with rainfall ranging from 750–5,000 mm. Five of eight native Myrtaceae and at least 15 nonnative species have been observed as hosts of P. psidii in Hawaii. The federally endangered Eugenia koolauensis (nioi) and the nonendangered indigenous species Eugenia reinwardtiana are severely damaged. The introduced (an Asian species) and invasive rose apple, Syzygium jambos , is severely affected at a landscape scale, with widespread crown dieback and many instances of complete tree death. In spite of billions of wind-dispersed rust spores produced from rose apple infestations during 2006 to 2008, adjacent ohia have been little affected to date by the rust strain in Hawaii. Within the elevation range of the rust, P. psidii is found on less than 5 percent of the ohia trees in the wild; on those ohia trees on which the rust is found, it is normally found on less than 5 percent of the leaves. The strain in Hawaii has not attacked many of the species known to be infected by the rust elsewhere, including common guava. On the basis of the very substantial genetic diversity of the much-studied, crop-damaging species of the genus Puccinia , there is good reason to believe that there are at minimum dozens and likely hundreds or thousands of genotypes of P. psidii , likely concentrated in the core range in Brazil but with potential for dispersal by globalization. Multiple genotypes are believed already present in the United States and certain to spread freely in the absence of restrictions. The U.S. Forest Service has initiated a major collaborative project in Brazil to investigate the genetics of susceptibility of Hawaii’s ohia to P. psidii , but initial results will likely not be available for several years. If just one more strain reaches Hawaii, the consequences could be dire for ohia, with each new genotype arriving having an unknown likelihood of increasing damage to ohia; possibilities for mutation and (or) genetic mixing, even with asexual strains, are apparently substantial, based on what is known about other Puccinia species. Investigations are needed to clarify rust-nioi relationships. However, it is likely that keeping out new strains of P. psidii may be important for long-term survival of nioi as well as for the health of ohia forest. The source of Hawaii’s initial invasion by P. psidii is uncertain but is strongly suspected to have been decorative foliage of species in the myrtle family from the mainland United States, most likely California, where there had been outbreaks of this rust on cultivated myrtle in 2005. In 2006–7, Maui’s Hawaii Department of Agriculture (HDOA) inspectors intercepted several P. psidii infected shipments of foliage myrtle, shipped from several California counties. Recognizing the huge threat of the rust to Hawaii’s one million acres of ohia forests, and consequently to Hawaii’s watersheds and biodiversity, Hawaii’s Board of Agriculture unanimously approved an interim rule in August 2007 banning importation of plants in the myrtle family from “infested areas,” specified as South America, Florida, and California. However, the interim rule has not been made permanent by HDOA, and the department has stated that it needs further information to formulate a long-term rule that imposes appropriate measures. Rust spores can survive for 2 to 3 months, and the pathogen can be transported to Hawaii on Myrtaceae from anywhere in the world through the United States mainland. There is much geographic reshuffling of flowers and foliage among the far-flung firms in the trade, especially for bouquet making. Because P. psidii is a nonactionable and nonreportable pest in the United States, foliage and flowers of the myrtle family can move freely into the country (usually but not necessarily always through the ports of Miami or Los Angeles), and from state to state. Currently, the State of Hawaii regulates incoming plant material in the family Myrtaceae by visual inspection. Inspection capacity and latent (asymptomatic) infections limit the ability to detect the rust. New molecular tests could improve detection efficiency, but the cost and the time required to process samples currently precludes their routine use in ports of entry. Interdiction, which has effectively kept coffee rust ( Hemileia vastatrix ) out of Hawaii for 120 years, offers the strongest protection for Hawaii’s native ecosystems from P. psidii . Interdiction of Myrtaceae from the continental United States could have the important supplementary benefit of preventing establishment in Hawaii of other very significant pests of multiple species of Myrtaceae that are already in the country, including: the Eugenia psyllid Trioza eugeniae (Hemiptera: Psyllidae); Chrysophtharta m-fuscum , the Eucalyptus tortoise beetle (Coleoptera: Chrysomelidae); Leptocybe invasa , the blue gum chalcid wasp (Hymenoptera: Chalcidae); and the fungal pathogens Mycosphaerella molleriana (Ascomycota: Mycosphaerelliaceae, crinkle leaf disease of Eucalyptus spp.) and Neofusicoccum parvum (Ascomycota: Botryosphaeriaceae), currently causing serious damage to Syzygium paniculatum in south Florida nurseries. Each of these pests would be likely to cause very significant damage to native and (or) cultivated Myrtaceae in Hawaii. Each of these pests is a prime candidate for transport by the foliage and (or) nursery stock pathways from Florida and California into Hawaii. Hawaii Department of Agriculture has a clear mandate to protect Hawaii’s natural environment, forestry and cultivated Myrtaceae. Principles of the World Trade Organization’s Treaty on Sanitary and Phytosanitary Measures and the International Plant Protection Convention are consistent with the right of Hawaii to take action. The current threat of P. psidii and the other five serious threats to Myrtaceae are primarily posed by the importation of infected plants from the continental United States; however, that may change in the future. If Hawaii were to decide to take a stand (through State regulation) to protect its native and introduced Myrtaceae, there is a possibility that USDA would consider Federal regulation of Myrtaceae from foreign countries.

Hawaii↗
USGS2018

Adaptive population divergence and directional gene flow across steep elevational gradients in a climate‐sensitive mammal

The American pika is a thermally sensitive, alpine lagomorph species. Recent climate-associated population extirpations and genetic signatures of reduced population sizes range-wide indicate the viability of this species is sensitive to climate change. To test for potential adaptive responses to climate stress, we sampled pikas along two elevational gradients (each ~470 to 1640 m) and employed three outlier detection methods, BAYESCAN, LFMM, and BAYPASS, to scan for genotype-environment associations in samples genotyped at 30,763 SNP loci. We resolved 173 loci with robust evidence of natural selection detected by either two independent analyses or replicated in both transects. A BLASTN search of these outlier loci revealed several genes associated with metabolic function and oxygen transport, indicating natural selection from thermal stress and hypoxia. We also found evidence of directional gene flow primarily downslope from large high-elevation populations and reduced gene flow at outlier loci, a pattern suggesting potential impediments to the upward elevational movement of adaptive alleles in response to contemporary climate change. Finally, we documented evidence of reduced genetic diversity associated the south-facing transect and an increase in corticosterone stress levels associated with inbreeding. This study suggests the American pika is already undergoing climate-associated natural selection at multiple genomic regions. Further analysis is needed to determine if the rate of climate adaptation in the American pika and other thermally sensitive species will be able to keep pace with rapidly changing climate conditions.

Washington↗
USGS2020

Noble gases fingerprint the source and evolution of ore-forming fluids of Carlin-type gold deposits in the Golden Triangle, south China

Precise constraints on the source and evolution of ore-forming fluids of Carlin-type gold deposits in the Golden Triangle (south China) are of critical importance for a better understanding of the ore genesis and a refined genetic model for gold mineralization. However, constraints on the source of ore fluid components have long been a challenge due to the very fine grained nature of the ore and gangue minerals in the deposits. Here we present He, Ne, and Ar isotope data of fluid inclusion extracts from a variety of ore and gangue minerals (arsenian pyrite, realgar, quartz, calcite, and fluorite) representing the main and late ore stages of three well-characterized major gold deposits (Shuiyindong, Nibao, and Yata) to provide significant new insights into the source and evolution of ore-forming fluids of this important gold province. Measured He isotopes have R/R A ratios ranging from 0.01 to 0.4 that suggest a maximum of 5% mantle helium with an R/R A of 8. The Ne and Ar isotope compositions are broadly comparable to air-saturated water, with a few analyses indicating the presence of an external fluid containing nucleogenic 38 Ar and radiogenic 40 Ar. Plotted on the 20 Ne/ 4 He vs. helium R/R A and 3 He/ 20 Ne vs. 4 He/ 20 Ne diagrams, the results define two distinct arrays that emanate from a common sedimentary pore fluid or deeply sourced metamorphic fluid end-member containing crustal He. The main ore-stage fluids are interpreted as a mixture of magmatic fluid containing mantle He and sedimentary pore fluid or deeply sourced metamorphic fluid with predominantly crustal He, whereas the late ore-stage fluids are a mixture of sedimentary pore fluid or deeply sourced metamorphic fluid bearing crustal He and shallow meteoric groundwater containing atmospheric He. Results presented here, when combined with independent evidence, support a magmatic origin for the ore-forming fluids. The ascending magmatic fluid mixed with sedimentary pore fluid or deeply sourced metamorphic fluid in the ore stage and subsequently mixed with the meteoric groundwater in the late ore stage, eventually producing the Carlin-type gold deposits in the Golden Triangle.

Golden Triangle, south China↗
USGS2022

Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas

Background The fathead minnow ( Pimephales promelas ) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation. Methods Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950. Results We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow ( P. notatus ) as sister to fathead minnow, with the slim minnow ( P. tenellus ) and bullhead minnow ( P. vigilax ) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (F ST ) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.

PeerJ↗
USGS2008

Modest genetic differentiation among North American populations of Sarcocystic neurona may reflect expansion in its geographic range

Sarcocystis neurona is an important cause of neurological disease in horses (equine protozoal myeloencephalitis, EPM) and sea otters in the United States. In addition, EPM-like disease has been diagnosed in several other land and marine mammals. Opossums are its only definitive hosts. Little genetic diversity among isolates of S. neurona from different hosts has been reported. Here, we used 11 microsatellites to characterize S. neurona DNA isolated from natural infections in 22 sea otters (Enhydra lutris) from California and Washington and in 11 raccoons (Procyon lotor) and 1 striped skunk (Mephitis mephitis) from Wisconsin. By jointly analyzing these 34 isolates with 26 isolates previously reported, we determined that geographic barriers may limit S. neurona dispersal and that only a limited subset of possible parasite genotypes may have been introduced to recently established opossum populations. Moreover, our study confirms that diverse intermediate hosts share a common infection source, the opossum (Didelphis virginiana).

California, Washington↗
USGS2004

Natural selection of the major histocompatibility complex (Mhc) in Hawaiian honeycreepers (Drepanidinae)

The native Hawaiian honeycreepers represent a classic example of adaptive radiation and speciation, but currently face one the highest extinction rates in the world. Although multiple factors have likely influenced the fate of Hawaiian birds, the relatively recent introduction of avian malaria is thought to be a major factor limiting honeycreeper distribution and abundance. We have initiated genetic analyses of class II ?? chain Mhc genes in four species of honeycreepers using methods that eliminate the possibility of sequencing mosaic variants formed by cloning heteroduplexed polymerase chain reaction products. Phylogenetic analyses group the honeycreeper Mhc sequences into two distinct clusters. Variation within one cluster is high, with dN > d S and levels of diversity similar to other studies of Mhc (B system) genes in birds. The second cluster is nearly invariant and includes sequences from honeycreepers (Fringillidae), a sparrow (Emberizidae) and a blackbird (Emberizidae). This highly conserved cluster appears reminiscent of the independently segregating Rfp-Y system of genes defined in chickens. The notion that balancing selection operates at the Mhc in the honeycreepers is supported by transpecies polymorphism and strikingly high dN/dS ratios at codons putatively involved in peptide interaction. Mitochondrial DNA control region sequences were invariant in the i'iwi, but were highly variable in the 'amakihi. By contrast, levels of variability of class II ?? chain Mhc sequence codons that are hypothesized to be directly involved in peptide interactions appear comparable between i'iwi and 'amakihi. In the i'iwi, natural selection may have maintained variation within the Mhc, even in the face of what appears to a genetic bottleneck.

Molecular Ecology↗
USGS2018

Characterizing range-wide population divergence in an alpine-endemic bird: A comparison of genetic and genomic approaches

The delineation of intraspecific units that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Neutral genetic variation has served as the primary data source for delineating “evolutionarily significant units,” but with recent advances in genomic technology, we now have an unprecedented ability to utilize information about neutral and adaptive variation across the entire genome. Here, we use traditional genetic markers (microsatellites) and a newer reduced-representation genomic approach (single nucleotide polymorphisms) to delineate distinct groups of white-tailed ptarmigan (Lagopus leucura), an alpine-obligate species that is distributed in naturally fragmented habitats from Alaska to New Mexico. Five subspecies of white-tailed ptarmigan are currently recognized but their distinctiveness has not been verified with molecular data. Based on analyses of 436 samples at 12 microsatellite loci and 95 samples at 14,866 single nucleotide polymorphism loci, we provide strong support for treating two subspecies as distinct intraspecific units—L. l. altipetens, found in Colorado and neighboring states; and L. l. saxatilis, found on British Columbia’s Vancouver Island—but our findings reveal more moderate patterns of divergence within the remainder of the species’ range. Results based on genetic and genomic datasets generally agreed with one another, indicating that in many cases microsatellite loci may be sufficient for describing major patterns of genetic structure across species’ ranges. This work will inform future conservation and management decisions for the white-tailed ptarmigan, a species that may be vulnerable to future changes in climate.

Conservation Genetics↗
USGS2004

Differential propagation of the metazoan parasite Myxobolus cerebralis by Limnodrilus hoffmeisteri, Ilyodrilus templetoni, and genetically distinct strains of Tubifex tubifex

Whirling disease, caused by the parasite Myxobolus cerebralis, has infected rainbow trout (Oncorhynchus mykiss) and other salmonid fish in the western United States, often with devastating results to native populations but without a discernible spatial pattern. The parasite develops in a complex 2-host system in which the aquatic oligochaete Tubifex tubifex is an obligate host. Because substantial differences in whirling disease severity in different areas of North America did not seem explainable by environmental factors or features of the parasite or its fish host, we sought to determine whether ecological or genetic variation within oligochaete host populations may be responsible. We found large differences in compatibility between the parasite and various laboratory strains of T. tubifex that were established from geographic regions with different whirling disease histories. Moreover, 2 closely related species of tubificids, Limnodrilus hqffmeisteri and Ilyodrilus templetoni, which occur naturally in mixed species assemblages with T. tubifex, were incompatible with M. cerebralis. Virulence of the parasite was directly correlated with the numbers of triactinomyxon spores that developed within each strain of T. tubifex. Thus, the level of virulence was directly related to the compatibility between the host strain and the parasite. Genetic analyses revealed relationships that were in agreement with the level of parasite production. Differences in compatibilities between oligochaetes and M. cerebralis may contribute to the spatial variance in the severity of the disease among salmonid populations. ?? American Society of Parasitologists 2004.

Journal of Parasitology↗
USGS2020

Systematics, evolution, and genetics of bears

Molecular genetics are key to understanding current and historical relationships between isolated populations, including species’ colonizations during glacial–interglacial cycles, to determine viability of local populations, needs for habitat corridors, and other aspects of population management, especially where bears are harvested for sport, etc. As natural habitats shrink, some bear species will inevitably require high levels of management, perhaps combining captive and wild populations following the IUCN’s One Plan Approach. In this chapter we review the systematics of the Ursidae and its relationships with other Carnivora, the molecular phylogenetic of extant ursid species, the phylogeography of and morphological variation within each species, and the use of molecular genetics to monitor bear populations for management and conservation.

Book chapter↗
USGS2021

Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake

Genetic structuring of wild populations is dependent on environmental, ecological, and life-history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake ( Sistrurus catenatus ) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species’ range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population's genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.

Michigan↗
USGS2012

Differences in survival and growth in hatchery and stream environments, and in maturation of residuls in a stream, between progeny of hatchery and wild steelhead (Study sites: Brushy Fork Creek and Dworshak Hatchery; Stocks:Dworshak hatchery and Fish Creek wild; Year classes: 1992 and 1993)

Freshwater survival in hatchery and natural rearing environments was compared between progeny of hatchery (H) and wild (W) steelhead Oncorhynchus mykiss from the Clearwater River drainage in Idaho. Adults from Dworshak National Fish Hatchery and wild adults from Fish Creek fish were artificially spawned, and their progeny were genetically marked at the PEPA allozyme locus and released together as unfed fry in production facilities at the hatchery and in Brushy Fork Creek, also in the Clearwater River drainage, in a common garden design. Survival was higher for H than for W progeny at the hatchery but lower for H than for W progeny in Brushy Fork, indicating reduced fitness of the hatchery population for natural rearing and suggesting domestication as the cause. Survival at the hatchery was lower than is typical due to disease outbreaks. Survival of the first year-class of experimental fish to smolt release was only 18%. Survival of H fish was 3.8 times that of W fish under these poor survival conditions. All fish from the second year-class died halfway through the scheduled 10 month rearing period. Survival of H fish was 5.2 times that of W fish to when 1% of the initial fry were still alive indicating that W fish succumbed to the epizootic sooner than did H fish. Emigrants from the Brushy Fork study reach were sampled for three years and fish residing in the study reach were sampled for six years following fry release. Most emigrants were one or two years old and too small to be smolts (mean fork length at age-2 = 93 mm). Survival in Brushy Fork was lower for H than for W fish of the first year-class. Survival of the second year-class was higher for H than for W fish during the first two months in the stream but was lower for H than for W fish thereafter, and net survival from release to ages 3 and older was also lower for H than for W fish if our emigrant samples were representative (periods of inoperative emigrant traps prevented certainty about this). Differences between progeny groups were also found for growth (H>W) and condition (H>W) in the hatchery and downstream migration success of hatchery-reared fish after release (H>W), and for growth (H<W for one year-class; H>W for the other), condition (H>W), downstream dispersal (H>W for one year-class; H=W for the other), and maturation of residuals (ovaries weight was greater for H than for W females at ages 4 and 5; testes weight was less for H than for W age-3 males of one year-class) in Brushy Fork. A thunderstorm-induced power outage interrupted flow to the incubation trays at the hatchery and compromised a major tenet of the common garden design for the second year-class, possibly contributing to the inconsistency in relative survivals in Brushy Fork between year-classes. The storm caused the incubation environment to differ between the stocks as a result of reduced oxygen levels and substantially higher densities for H alevins. This difference was illustrated by a 55% loss for H fish during the event, about twice that for W fish.

Idaho↗
USGS2017

Juvenile salmonid monitoring in the White Salmon River, Washington, post-Condit Dam removal, 2016

Condit Dam, at river kilometer 5.3 on the White Salmon River, Washington, was breached in 2011 and removed completely in 2012, allowing anadromous salmonids access to habitat that had been blocked for nearly 100 years. A multi-agency workgroup concluded that the preferred salmonid restoration alternative was natural recolonization with monitoring to assess efficacy, followed by a management evaluation 5 years after dam removal. Limited monitoring of salmon and steelhead spawning has occurred since 2011, but no monitoring of juveniles occurred until 2016. During 2016, we operated a rotary screw trap at river kilometer 2.3 (3 kilometers downstream of the former dam site) from late March through May and used backpack electrofishing during summer to assess juvenile salmonid distribution and abundance. The screw trap captured primarily steelhead ( Oncorhynchus mykiss ; smolts, parr, and fry) and coho salmon ( O. kisutch ; smolts and fry). We estimated the number of steelhead smolts at 3,851 (standard error = 1,454) and coho smolts at 1,093 (standard error = 412). In this document, we refer to O. mykiss caught at the screw trap as steelhead because they were actively migrating, but because we did not know migratory status of O. mykiss caught in electrofishing surveys, we simply refer to them as O. mykiss or steelhead/rainbow trout. Steelhead and coho smolts tagged with passive integrated transponder tags were subsequently detected downstream at Bonneville Dam on the Columbia River. Few Chinook salmon ( O. tshawytscha ) fry were captured, possibly as a result of trap location or effects of a December 2015 flood. Sampling in Mill, Buck, and Rattlesnake Creeks (all upstream of the former dam site) showed that juvenile coho were present in Mill and Buck Creeks, suggesting spawning had occurred there. We compared O. mykiss abundance data in sites on Buck and Rattlesnake Creeks to pre-dam removal data. During 2016, age-0 O. mykiss were more abundant in Buck Creek than in 2009 or 2010, though age-1 and older O. mykiss abundance was similar. In Rattlesnake Creek, age-0 O. mykiss abundance during 2016 slightly exceeded the mean abundance from 2001 through 2005, although age-1 and older O. mykiss abundance was lower than from 2001 through 2005. These sampling efforts also provided the opportunity to collect genetic samples to investigate parental and stock origin, although funding to analyze the samples was not part of this grant. Juvenile salmonid sampling efforts during 2016 have shown that natural spawning produced steelhead and coho smolts and that coho were colonizing some tributaries. The 2016 efforts also provided the first post-dam juvenile abundance estimates. We hope to continue monitoring to better understand abundance trends, distribution, and life history patterns of recolonizing salmonids in the White Salmon River to assess efficacy of natural recolonization and to inform management decisions.

Washington↗
USGS2011

Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae)

Imperiled Okaloosa darters ( Etheostoma okaloosae ) are small, benthic fish limited to six streams that flow into three bayous of Choctawhatchee Bay in northwest Florida, USA. We analyzed the complete mitochondrial cytochrome b gene and 10 nuclear microsatellite loci for 255 and 273 Okaloosa darters, respectively. Bayesian clustering analyses and AMOVA reflect congruent population genetic structure in both mitochondrial and microsatellite DNA. This structure reveals historical isolation of Okaloosa darter streams nested within bayous. Most of the six streams appear to have exchanged migrants though they remain genetically distinct. The U.S. Fish and Wildlife Service recently reclassified Okaloosa darters from endangered to threatened status. Our genetic data support the reclassification of Okaloosa darter Evolutionary Significant Units (ESUs) in the larger Tom’s, Turkey, and Rocky creeks from endangered to threatened status. However, the three smaller drainages (Mill, Swift, and Turkey Bolton creeks) remain at risk due to their small population sizes and anthropogenic pressures on remaining habitat. Natural resource managers now have the evolutionary information to guide recovery actions within and among drainages throughout the range of the Okaloosa darter.

Florida↗