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At least 271 records · Page 15Linked to original sources
USGS2014

Tick control: Trapping, bio-control, host management and other alternative strategies

Biology of Ticks is the most comprehensive work on tick biology and tick-borne diseases. This second edition is a multi-authored work, featuring the research and analyses of renowned experts across the globe. Spanning two volumes, the book examines the systematics, biology, structure, ecological adaptations, evolution, genomics and the molecular processes that underpin the growth, development and survival of these important disease-transmitting parasites. Also discussed is the remarkable array of diseases transmitted (or caused) by ticks, as well as modern methods for their control. This book should serve as a modern reference for students, scientists, physicians, veterinarians and other specialists. Volume II includes chapters on the ecology of non-nidicolous and nidicolous ticks, genetics and genomics (including the genome of the Lyme disease vector Ixodes scapularis) and immunity, including host immune responses to tick feeding and tick-host interactions, as well as the tick's innate immune system that prevents and/or controls microbial infections. Six chapters cover in depth the many diseases caused by the major tick-borne pathogens, including tick-borne protozoa, viruses, rickettsiae of all types, other types of bacteria (e.g., the Lyme disease agent) and diseases related to tick paralytic agents and toxins. The remaining chapters are devoted to tick control using vaccines, acaricides, repellents, biocontrol, and, finally, techniques for breeding ticks in order to develop tick colonies for scientific study.

Book chapter↗
USGS2025

Diversity of polyomaviruses and papillomaviruses in penguins from eastern and western Antarctica

Polyomaviruses and papillomaviruses are icosahedral viruses with small circular dsDNA genomes. Limited information on their diversity and evolution in avian hosts is available, with even less known regarding Antarctic penguins. Prior to this study, only one polyomavirus and two papillomaviruses had been identified in Adélie penguins ( Pygoscelis adeliae ). To expand our knowledge of these viruses in Antarctic penguins, we collected faecal and cloacal swab samples from 246 Adélie penguins over 3 breeding seasons (2021–2024) and 10 emperor penguins ( Aptenodytes forsteri ) during the 2023–2024 season on Ross Island (Ross Sea). Additionally, we sampled 66 Adélie, 40 chinstrap ( Pygoscelis antarcticus ) and 71 gentoo ( Pygoscelis papua ) penguins during the 2022–2023 season across various sites on the Antarctic Peninsula. All samples were screened for papillomaviruses and polyomaviruses. We identified 31 polyomaviruses in Adélie, gentoo and chinstrap penguins and 4 papillomaviruses in Adélie penguins sampled in both eastern and western Antarctica. The 31 penguin polyomaviruses belong to a single species but form four distinct variants that are host species specific with strong geographic clustering. The four papillomaviruses represent three different types, of which two are new types from Adélie penguins sampled on Yalour Island in the West Antarctic Peninsula. Co-occurrence of two polyomavirus variants was identified in two individual gentoo penguins. Both of these variants appear to be circulating in gentoo penguins at Cierva Cove, Hope Bay in Trinity Peninsula along the Antarctic Peninsula, and at Hannah Point on Livingstone Island and Stranger Point on King George Island in the South Shetland Islands. Here, we expand the known diversity, host and geographical ranges of penguin polyomaviruses and, together with a previously identified polyomavirus on Ross Island from 2012 to 2013, show that they form five distinct lineages. The four papillomaviruses identified in this study, together with two previously identified from Ross Island in 2012 and 2013 breeding seasons, show substantial diversity reflecting four papillomavirus types across three viral species and two distinct genera. Continued surveillance and viral genomic analysis across a larger geographical framework will help understand the evolution, transmission and incidence rates of these viruses.

Microbial Genomics↗
USGS2020

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

Background Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted. Results Here we used microsatellite and SNP data generated from Gunnison sage-grouse ( Centrocercus minimus ) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity ( H O , H E , F IS , A R ) and differentiation ( F ST , G ST , D Jost ). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for H E , F IS , A R , and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data. Conclusion We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.

Arizona, Colorado, New Mexico, Utah↗
USGS2021

Species and population specific gene expression in blood transcriptomes of marine turtles

Background Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. Results We generated high quality blood transcriptome assemblies for hawksbill ( Eretmochelys imbricata ) , loggerhead ( Caretta caretta ), green ( Chelonia mydas ), and leatherback ( Dermochelys coriacea ) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. Conclusions Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

BMC Genomics↗
USGS1977

Virion RNA polymerases of two salmonid rhabdoviruses

RNA-dependent RNA polymerases were found to be associated with two salmonid rhabdoviruses: infectious hematopoietic necrosis (IHN) virus and the virus of hemorrhagic septicemia (VHS). The protein composition of these rhabdoviruses closely resembles that of rabies virus rather than that of vesicular stomatitis virus (McAllister and Wagner, 1975). The optimal temperature for in vitro transcription was found to be approximately 18 degrees C for IHN virus and approximately 15 degrees for VHS, closely approximating optimal temperatures for growth of these viruses in salmonid cells. Unlike vesicular stomatitis virus, manganese ion (1 mM) could be used as a divalent cation substitute for magnesium ion (5 mM). The in vitro transcription products of IHN and VHS viruses hybridized completely to the homologous genome but not at all to the heterologous genome.

Journal of Virology↗
USGS2024

Development and validation of a GT-seq panel for genetic monitoring in a threatened species using minimally invasive sampling

Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping-in-thousands by sequencing (GT-seq) is a powerful amplicon sequencing method that can genotype large numbers of variable-quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and F ST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative F IS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT-seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT-seq for minimally invasive DNA sampling techniques in other rare animals.

Ecology and Evolution↗
USGS2024

Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic

Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish ( Bagre marinus , Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.

Alabama, Florida, Louisiana, Mississippi, Texas↗
USGS2024

Influence of dams on sauger population structure and hybridization with introduced walleye

Dams have negatively affected freshwater biodiversity throughout the world. These negative effects tend to be exacerbated for aquatic taxa with migratory life histories, and for taxa whose habitat is fundamentally altered by the formation of large reservoirs. Sauger ( Sander candadensis ; Percidae), large-bodied migratory fishes native to North America, have seen population declines over much of the species' range, and dams are often implicated for their role in blocking access to spawning habitat and otherwise negatively affecting river habitat. Furthermore, hybridization appears to be more frequent between sauger and walleye in the reservoirs formed by large dams. In this study, we examine the role of dams in altering sauger population connectivity and facilitating hybridization with introduced walleye in Wyoming's Wind River and Bighorn River systems. We collected genomic data from individuals sampled over a large spatial scale and replicated sampling throughout the spawning season, with the intent to capture potential variation in hybridization prevalence or genomic divergence between sauger with different life histories. The timing of sampling was not related to hybridization prevalence or population divergence, suggesting limited genetic differences between sauger spawning in different time and places. Overall, there was limited hybridization detected, however, hybridization was most prevalent in Boysen Reservoir (a large impounded section of the Wind River). Dams in the lower Wind River and upper Bighorn River were associated with population divergence between sauger upstream and downstream of the dams, and demographic models suggest that this divergence has occurred in concordance with the construction of the dam. Sauger upstream of the dams exhibited substantially lower estimates of genetic diversity, which implies that disrupted connectivity between Wind River and Bighorn River sauger populations may already be causing negative demographic effects. This research points towards the importance of considering the evolutionary consequences of dams on fish populations in addition to the threats they pose to population persistence.

Wyoming↗
USGS2020

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

Genomic tools are lacking for invasive and native populations of sea lamprey ( Petromyzon marinus ). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site‐associated DNA sequencing (RAD‐Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00–0.018) were concordant with previous microsatellite‐based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age‐1 and age‐2 families of full and half‐siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non‐native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.

Michigan, Ontario, Wisconsin↗
USGS2025

Development of a genotyping-in-thousands by sequencing (GT-seq) panel for identifying individuals and estimating relatedness among Alaska black bears (Ursus americanus)

The management and conservation of large mammals, such as black bears ( Ursus americanus ), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as ‘genotyping-in-thousands-by sequencing’ (GT-seq), now enable the efficient and cost-effective genotyping of hundreds of loci and individuals in the same sequencing run. Here, we develop a GT-seq panel for individual identification and kinship inference in Alaska black bears. Using genomic data from restriction site-associated DNA sequencing of hunter-harvested bears from Southcentral Alaska ( n = 85), we identified 170 microhaplotype and single nucleotide polymorphism (SNP) loci that were highly heterozygous in local populations. To enable sexing of individuals, we also included a previously published sex-linked locus in the GT-seq panel. We empirically validated the GT-seq panel using samples collected at different spatial scales. These samples included tissues ( n = 82) obtained from bears within a small geographic area in Anchorage, Alaska, which were likely to be relatives as well as the hunter-harvested samples collected from geographically widespread locations throughout Southcentral Alaska. Empirical validation indicated high genotyping success and genotype reproducibility across replicate subsamples. Computer simulations demonstrated that the GT-seq panel had ample statistical power for distinguishing distinct individuals and first-order relatives (parent-offspring and full-sibling pairs) from unrelated individuals. As a final proof of concept, the panel was used to identify individual bears and close kin sampled from urban and wild habitats in Anchorage, Alaska. We anticipate that the GT-seq panel will be a useful genomic resource for the monitoring and management of Alaska black bear populations. ons.

Alaska↗
USGS2021

Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska

Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char ( Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha -1 ), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.

Alaska↗
USGS2021

Establishing conservation units to promote recovery of two threatened freshwater mussel species (Bivalvia: Unionida: Potamilus)

Population genomics has significantly increased our ability to make inferences about microevolutionary processes and demographic histories, which have the potential to improve protection and recovery of imperiled species. Freshwater mussels (Bivalvia: Unionida) represent one of the most imperiled groups of organisms globally. Despite systemic decline of mussel abundance and diversity, studies evaluating spatiotemporal changes in distribution, demographic histories, and ecological factors that threaten long-term persistence of imperiled species remain lacking. In this study, we use genotype-by-sequencing (GBS) and mitochondrial sequence data (mtDNA) to define conservation units (CUs) for two highly imperiled freshwater mussel species, Potamilus amphichaenus and Potamilus streckersoni . We then synthesize our molecular findings with details from field collections spanning from 1901 to 2019 to further elucidate distributional trends, contemporary status, and other factors that may be contributing to population declines for our focal species. We collected GBS and mtDNA data for individuals of P. amphichaenus and P. streckersoni from freshwater mussel collections in the Brazos, Neches, Sabine, and Trinity drainages ranging from 2012 to 2019. Molecular analyses resolved disputing number of genetic clusters within P. amphichaenus and P. streckersoni ; however, we find defensible support for four CUs, each corresponding to an independent river basin. Evaluations of historical and recent occurrence data illuminated a generally increasing trend of occurrence in each of the four CUs, which were correlated with recent increases in sampling effort. Taken together, these findings suggest that P. amphichaenus and P. streckersoni are likely rare throughout their respective ranges. Because of this, the establishment of CUs will facilitate evidence-based recovery planning and ensure potential captive propagation and translocation efforts are beneficial. Our synthesis represents a case study for conservation genomic assessments in freshwater mussels and provides a model for future studies aimed at recovery planning for these highly imperiled organisms.

Ecology and Evolution↗
USGS2021

Intraspecific variation mediates density dependence in a genetically diverse plant species

Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant–plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush ( Artemisia tridentata ), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata , we ask how intraspecific variation, environment, and stand age mediate neighbor effects on plant growth and survival. Spatially explicit models revealed that ploidy variation and subspecies identity can mediate plant–plant interactions but that the effect size varied in time and across experimental sites. We found that demographic impacts of neighbor effects were strongest during early stages of stand development and in sites with greater growth rates. Within subspecies, tetraploid populations showed greater tolerance to neighbor crowding compared to their diploid variants. Our findings provide evidence that intraspecific variation related to genome size and subspecies identity impacts spatial demography in a genetically diverse plant species. Accounting for intraspecific variation in studies of conspecific density dependence will improve our understanding of how local populations will respond to novel genotypes and biotic interaction regimes. As introduction of novel genotypes into local populations becomes more common, quantifying demographic processes in genetically diverse populations will help predict long-term consequences of plant–plant interactions.

Idaho, Utah↗
USGS2019

Great Lakes Cladophora harbors phylogenetically diverse nitrogen-fixing microorganims

Abstract Nitrogen‐fixing microorganisms are among the epiphytic communities in Cladophora, potentially benefitting the algae in nutrient‐deficient waters, but their abundance and diversity remain unexplored. In this study, we determined the abundance and taxonomic composition of these nitrogen‐fixing microorganisms in Cladophora growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan (N = 33) during the summer 2015, using two complementary genomic techniques: quantitative PCR (qPCR) and shotgun metagenomic sequencing. Genomic DNA was extracted from processed algal pellets, and the nitrogen‐fixing microbes were quantified by qPCR by targeting the nifH gene. Mean nifH concentrations (log10 copy numbers/gram algae fresh weight ± SE) were 5.54 ± 0.09, ranging from 4.31 to 6.57. Mean nifH concentrations in water samples (log10 copy numbers/milliliter of water ± SE) were: 3.25 ± 0.06, ranging from 2.41 to 3.90. Shotgun sequencing of a subset of algal samples representing the four sampling locations (N = 10) revealed as many as 267 nifH reads from among the sequences of the 10 shotgun metagenomes (averaging 27 reads per metagenome), ranging from 5 to 91 reads from Jeorse Park (September) and North Beach (September) locations. Taxonomic assignment of nifH sequences identified members from bacteria and archaea domains showing a clear separation of reads at domain and lower taxonomic levels. Bacteria were relatively more abundant than archaea. Anabaena, Bradyrhizobium, Geobacter, Methylocystis, Oscillatoria sp., and Skermanella (all bacteria), and Methanoregula, Methanothrix, and Methanosarcina (archaea) were among the nitrogen‐fixing genera identified by the MEGAN Community Edition program. Collectively, these findings show that phylogenetically diverse nitrogen‐fixing microbial communities are part of the Cladophora microbiome, likely contributing to the algal nitrogen needs.

Environmental DNA↗
USGS2012

Gene expression, glutathione status and indicators of hepatic oxidative stress in laughing gull (Larus atricilla) hatchlings exposed to methylmercury

Despite extensive studies of methylmercury (MeHg) toxicity in birds, molecular effects on birds are poorly characterized. To improve our understanding of toxicity pathways and identify novel indicators of avian exposure to Hg, the authors investigated genomic changes, glutathione status, and oxidative status indicators in liver from laughing gull (Larus atricilla) hatchlings that were exposed in ovo to MeHg (0.05–1.6 µg/g). Genes involved in the transsulfuration pathway, iron transport and storage, thyroid-hormone related processes, and cellular respiration were identified by suppression subtractive hybridization as differentially expressed. Quantitative polymerase chain reaction (qPCR) identified statistically significant effects of Hg on cytochrome C oxidase subunits I and II, transferrin, and methionine adenosyltransferase RNA expression. Glutathione-S-transferase activity and protein-bound sulfhydryl levels decreased, whereas glucose-6-phosphate dehydrogenase activity increased dose-dependently. Total sulfhydryl concentrations were significantly lower at 0.4 µg/g Hg than in controls. T ogether, these endpoints provided some evidence of compensatory effects, but little indication of oxidative damage at the tested doses, and suggest that sequestration of Hg through various pathways may be important for minimizing toxicity in laughing gulls. This is the first study to describe the genomic response of an avian species to Hg. Laughing gulls are among the less sensitive avian species with regard to Hg toxicity, and their ability to prevent hepatic oxidative stress may be important for surviving levels of MeHg exposures at which other species succumb.

Environmental Toxicology and Chemistry↗
USGS2020

RAD-seq refines previous estimates of genetic structure in Lake Erie walleye

Delineating population structure helps fishery managers to maintain a diverse “portfolio” of local spawning populations (stocks), as well as facilitate stock-specific management. In Lake Erie, commercial and recreational fisheries for Walleye Sander vitreus exploit numerous local spawning populations, which cannot be easily differentiated using traditional genetic data (e.g., microsatellites). Here, we used genomic information (12,264 polymorphic loci) generated using restriction site-associated DNA sequencing to investigate stock structure in Lake Erie Walleye. We found low genetic divergence (genetic differentiation index F ST = 0.0006–0.0019) among the four Lake Erie western basin stocks examined, which resulted in low classification accuracies for individual samples (40–60%). However, more structure existed between western and eastern Lake Erie basin stocks ( F ST = 0.0042–0.0064), resulting in greater than 95% classification accuracy of samples to a lake basin. Thus, our success in using genomics to identify stock structure varied with spatial scale. Based on our results, we offer suggestions to improve the efficacy of this new genetic tool for refining stock structure and eventually determining relative stock contributions in Lake Erie Walleye and other Great Lakes populations.

Michigan, New York, Ohio, Ontario, Pennsylvania↗
USGS1993

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. Hae III digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

Experimental Mycology↗
USGS1994

Factors affecting the efficient transformation of Colletotrichum species

Factors affecting the efficient transformation of Colletotrichum species. Experimental Mycology , 18, 230-246. Twelve isolates representing four species of Colletotrichum were transformed either by enhanced protoplast, restriction enzyme-mediated integration (REMI), or electroporation-mediated protocols. The enhanced protoplast transformation protocol resulted in 100- and 50-fold increases in the transformation efficiencies of Colletotrichum lindemuthianum and C. magna , respectively. REMI transformation involved the use of Hin dIII and vector DNA linearized with Hin dIII to increase the number of integration events and potential gene disruptions in the fungal genome. Combining the enhanced protoplast and the REMI protocols resulted in a 22-fold increase in the number of hygromycin/nystatin-resistant mutants in C. lindemuthianum . Electroporation-mediated transformation was performed on mycelial fragments and spores of four Colletotrichum species, resulting in efficiencies of up to 1000 transformants/μg DNA. The pHA1.3 vector which confers hygromycin resistance contains telomeric sequences from Fusarium oxysporum , transforms by autonomous replication and genomic integration, and was essential for elevated transformation efficiencies of 100 to 10,000 transformants/μg DNA. Modifications of pHA1.3 occurred during bacterial amplification and post fungal transformation resulting in plasmids capable of significantly elevated transformation efficiencies in C. lindemuthianum.

Experimental Mycology↗