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At least 1,333 records · Page 74Linked to original sources

Origin and identity of Fejervarya (Anura: Dicroglossidae) on Guam

We used morphological and molecular data to infer the identity and origin of frogs in the genus Fejervarya that have been introduced to the island of Guam. Mensural and meristic data were collected from 96 specimens from throughout their range on the island and a principal component analysis was used to investigate the distribution of these data in morphological space. We also amplified a fragment of the 16S ribosomal ribonucleic acid mitochondrial gene from 27 of these specimens and compared it to 63 published sequences of Fejervarya and the morphologically similar Zakerana. All examined Fejervarya from Guam are morphologically indistinguishable and share an identical haplotype. The molecular data identify them as Fejervarya cancrivora with a haplotype identical to F. cancrivora from Taiwan.

Guam↗

A morphological review of the Cuora flavomarginata complex (Testudines: Geoemydidae)

A reevaluation of the morphometric and color pattern differences within the Asiatic box turtle, Cuora flavomarginata sensu latu, was conducted in view of determining the taxonomic position of the three currently recognized subspecies: C. f. flavomarginata (Taiwan), C. f. sinensis (southern mainland China), and C. f. evelynae (Ryukyu Islands, Japan). Recent analyses indicate that the allopatric population of C. f. evelynae is the most divergent of the three taxa and shares little possibility for gene exchange with the other two populations. In contrast, the populations of C. f. flavomarginata and C. f. sinensis share many characters. We recommend the recognition of the Ryukyu population as a full species, C. evelynae.

Proceedings of the Biological Society of Washingto↗

Rocky Mountain Center for Conservation Genetics and Systematics

The use of molecular genetic tools has become increasingly important in addressing conservation issues pertaining to plants and animals. Genetic information can be used to augment studies of population dynamics and population viability, investigate systematic, refine taxonomic definitions, investigate population structure and gene flow, and document genetic diversity in a variety of plant and animal species. Further, genetic techniques are being used to investigate mating systems through paternity analysis, and analyze ancient DNA samples from museum specimens, and estimate population size and survival rates using DNA as a unique marker. Such information is essential for the sound management of small, isolated populations of concern and is currently being used by universities, zoos, the U.S. Fish and Wildlife Service, and numerous state fish and wildlife agencies.

Fact Sheet↗

Genetics/Genomics Research in the Central Region

Genetics-based research within the Biological Resources Discipline (BRD) Science Centers in the Central Region incorporates many aspects of the field of genetics. Research activities range from documenting patterns of genetic variation in order to investigate relationships among species, populations and individuals to investigating the structure, function and expression of genes and their response to environmental stressors. Research in the broad areas of genetics requires multidisciplinary expertise and specialized equipment and instrumentation. Brief summaries of the capabilities of the five BRD Centers are given below.

Fact Sheet↗

Genetic analyses of captive Alala (Corvus hawaiiensis) using AFLP analyses

Population level studies of genetic diversity can provide information about population structure, individual genetic distinctiveness and former population size. They are especially important for rare and threatened species like the Alala, where they can be used to assess extinction risks and evolutionary potential. In an ideal situation multiple methods should be used to detect variation, and these methods should be comparable across studies. In this report, we discuss AFLP (Amplified Fragment Length Polymorphism) as a genetic approach for detecting variation in the Alala , describe our findings, and discuss these in relation to mtDNA and microsatellite data reported elsewhere in this same population. AFLP is a technique for DNA fingerprinting that has wide applications. Because little or no prior knowledge of the particular species is required to carry out this method of analysis, AFLP can be used universally across varied taxonomic groups. Within individuals, estimates of diversity or heterozygosity across genomes may be complex because levels of diversity differ between and among genes. One of the more traditional methods of estimating diversity employs the use of codominant markers such as microsatellites. Codominant markers detect each allele at a locus independently. Hence, one can readily distinguish heterozygotes from homozygotes, directly assess allele frequencies and calculate other population level statistics. Dominant markers (for example, AFLP) are scored as either present or absent (null) so heterozygotes cannot be directly distinguished from homozygotes. However, the presence or absence data can be converted to expected heterozygosity estimates which are comparable to those determined by codominant markers. High allelic diversity and heterozygosity inherent in microsatellites make them excellent tools for studies of wild populations and they have been used extensively. One limitation to the use of microsatellites is that heterozygosity estimates are affected by the mutation rate at microsatellite loci, thus introducing a bias. Also, the number of loci that can be studied is frequently limited to fewer than 10. This theoretically represents a maximum of one marker for each of 10 chromosomes. Dominant markers like AFLP allow a larger fraction of the genome to be screened. Large numbers of loci can be screened by AFLP to resolve very small individual differences that can be used for identification of individuals, estimates of pairwise relatedness and, in some cases, for parentage analyses. Since AFLP is a dominant marker (can not distinguish between +/+ homozygote versus +/- heterozygote), it has limitations for parentage analyses. Only when both parents are homozygous for the absence of alleles (-/-) and offspring show a presence (+/+ or +/-) can the parents be excluded. In this case, microsatellites become preferable as they have the potential to exclude individual parents when the other parent is unknown. Another limitation of AFLP is that the loci are generally less polymorphic (only two alleles/locus) than microsatellite loci (often >10 alleles/locus). While generally fewer than 10 highly polymorphic microsatellite loci are enough to exclude and assign parentage, it might require up to 100 or more AFLP loci. While there are pros and cons to different methodologies, the total number of loci evaluated by AFLP generally offsets the limitations imposed due to the dominant nature of this approach and end results between methods are generally comparable. Overall objectives of this study were to evaluate the level of genetic diversity in the captive population of Alala, to compare genetic data with currently available pedigree information, and to determine the extent of relatedness of mating pairs and among founding individuals.

Open-File Report↗

Use of DNA markers for investigating sources of bacteria in contaminated ground water: Wooster Township, Wayne County, Ohio

In 2004, a public-health nuisance was declared by the Wayne County Board of Health in the Scenic Heights Drive-Batdorf Road area of Wooster Township, Wayne County, Ohio, because of concerns about the safety of water from local wells. Repeated sampling had detected the presence of fecal-indicator bacteria and elevated nitrate concentrations. In June 2006, the U.S. Geological Survey (USGS), in cooperation with the Ohio Environmental Protection Agency (Ohio EPA), collected and analyzed samples from some of the affected wells to help investigate the possibility of human-origin bacterial contamination. Water samples from 12 wells and 5 home sewage-treatment systems (HSTS) were collected. Bromide concentrations were determined in samples from the 12 wells. Samples from 5 of the 12 wells were analyzed for wastewater compounds. Total coliform, enterococci and Escherichia coli (E. coli) bacteria concentrations were determined for samples from 8 of the 12 wells. In addition, two microbial source-tracking tools that employ DNA markers were used on samples from several wells and a composite sample of water from five septic tanks. The DNA markers from the Enterococcus faecium species and the order Bacteroidales are associated with specific sources, either human or ruminant sources. Bromide concentrations ranged from 0.04 to 0.18 milligrams per liter (mg/L). No wastewater compounds were detected at concentrations above the reporting limits. Samples from the 12 wells also were collected by Ohio EPA and analyzed for chloride and nitrate. Chloride concentrations ranged from 12.6 to 61.6 mg/L and nitrate concentrations ranged from 2.34 to 11.9 mg/L (as N). Total coliforms and enterococci were detected in samples from 8 wells, at concentrations from 2 to 200 colony-forming units per 100 milliliters (CFU/100 mL) and 0.5 to 17 CFU/100 mL, respectively. E. coli were detected in samples from three of the eight wells, at concentrations of 1 or 2 CFU/100 mL. Tests for the human-specific marker of enterococci, the esp gene, were negative in the seven samples tested, including the composite sample of HSTS water. DNA with the general Bacteroidales marker was detected in samples from four wells, but the tests for both the human- and ruminant-associated markers were negative. The presence of the PCR (polymerase chain reaction) -detectable DNA for the general fecal Bacteroidales marker is indicative of fecal contamination and recently recharged water.

Ohio↗

Using Molecular Genetic Markers to Resolve a Subspecies Boundary: The Northern Boundary of the Southwestern Willow Flycatcher in the Four-Corner States

*Executive Summary* The northern boundary of the endangered Southwestern Willow Flycatcher (Empidonax traillii extimus) is currently approximated as running through southern Colorado and Utah, but the exact placement is uncertain because this subspecies shares a border with the more northern and non-endangered E. t. adastus. To help resolve this issue, we evaluated the geographic distribution of mitochondrial and nuclear DNA by sampling breeding sites across the four-corner states (Arizona, Colorado, New Mexico, and Utah). We found that breeding sites clustered into two major groups generally consistent with the currently designated boundary, with the exception of three sites situated along the current boundary. However, delineating a precise boundary that would separate the two subspecies is made difficult because (1) we found evidence for a region of intergradation along the boundary area, suggesting the boundary is not discreet, and (2) the boundary region is sparsely populated, with too few extant breeding populations to precisely locate a boundary. The boundary region encompasses an area where elevation changes markedly over relatively short distances, with low elevation deserts to the south and more mesic, higher elevation habitats to the north. We hypothesized that latitudinal and elevational differences and their concomitant ecological effects could form an ecological barrier that inhibited gene flow between the subspecies, forming the basis for the subspecies boundary. We modeled changes in geographic patterns of genetic markers as a function of latitude and elevation finding significant support for this relationship. The model was brought into a GIS environment to create multiple subspecies boundaries, with the strength of each predicted boundary evaluated on the basis of how much genetic variation it explained. The candidate boundary that accounted for the most genetic variation was situated generally near the currently recognized subspecies boundary, but should be more biologically meaningful because it incorporates the landscape features that may be driving separation of the subspecies. Even so, we caution that using any narrow boundary line as an indicator of subspecies identity could be misleading because biologically the boundary is a region of intergradation rather than a discrete line. Designating, a boundary ultimately becomes a regulatory and management decision based on how much of the genetic variation unique to a subspecies should be protected. We discuss how the results of this study can help guide this decision process by wildlife policy makers.

Open-File Report↗

Comparison of three DNA extraction kits to establish maximum yield and quality of coral-associated microbial DNA

Coral microbiology is an expanding field, yet there is no standard DNA extraction protocol. Although many researchers depend on commercial extraction kits, no specific kit has been optimized for use with coral samples. Both soil and plant DNA extraction kits from MO BIO Laboratories, Inc., have been used by many research groups for this purpose. MO BIO recently replaced their PowerPlant® kit with an improved PowerPlantPro kit, but it was unclear how these changes would affect the kit’s use with coral samples. In order to determine which kit produced the best results, we conducted a comparison between the original PowerPlant kit, the new PowerPlantPro kit, and an alternative kit, PowerSoil, using samples from several different coral genera. The PowerPlantPro kit had the highest DNA yields, but the lack of 16S rRNA gene amplification in many samples suggests that much of the yield may be coral DNA rather than microbial DNA. The most consistent positive amplifications came from the PowerSoil kit.

Open-File Report↗

Bull trout in the Boundary System: managing connectivity and the feasibility of a reintroduction in the lower Pend Oreille River, northeastern Washington

Many of the World’s rivers are influenced by large dams (>15 m high) most of which have fragmented formerly continuous habitats, and significantly altered fish passage, natural flow, temperature, and sediment fluxes (Nilsson and others, 2005; Arthington, 2012; Liermann and others, 2012). In the Pacific Northwest, dams on major rivers have been a major focus for fishery managers, primarily in regard to passage of anadromous salmonids (principally Pacific salmon and steelhead trout [ Oncorhynchus mykiss ], for example, Ferguson and others, 2011), but more recently other species, such as Pacific lamprey ( Entosphenus tridentatus ) and resident (non-anadromous) salmonids, are receiving more attention (Neraas and Spruell, 2001; Moser and others, 2002; Muhlfeld and others, 2012). In the case of resident salmonids, fish can adopt a wide range of migratory behaviors that often bring them into mainstem rivers where they can come into direct contact with large dams. When this occurs, some of the most important direct effects of dams on salmonids include barriers to upstream and downstream movement and mortality associated with entrainment within the dam or spill over dams. Biologically, these direct impacts can lead to (1) disruption of natural historical (pre-dam) genetic and demographic connectivity among local populations, (2) loss of access to historically used migratory destinations, (3) loss of individuals to the population through mortality associated with entrainment. In this report, we address these issues for the case of Boundary Dam, located immediately south of the Canadian border on the lower Pend Oreille River in northeastern Washington (fig. 1). Specifically, we addressed the following objectives: Evaluate the justification for bull trout ( Salvelinus confluentus ) passing over Boundary Dam in the context of likely historical patterns of gene flow that occurred prior to dam construction, current patterns of movement, and status of existing populations. Assess the role of passage over Boundary Dam, in the context of other factors in the system that may influence the feasibility of establishing a self-sustaining bull trout population in the Boundary system.

Washington↗

Validation of eDNA markers for New Zealand mudsnail surveillance and initial eDNA monitoring at Mississippi River Basin sites

The performance of newly developed New Zealand mudsnail ( Potamopyrgus antipodarum ; NZMS) genetic markers for environmental (eDNA) analysis of water were compared across two laboratories. The genetic markers were tested in four quantitative polymerase chain reaction assays targeting two regions of the NZMS mitochondrial genome, specifically the cytochrome c oxidase subunit 1 (coi) and cytochrome b (cytb) genes. In a blind study, analysts tested each sample eight times with each assay. There were 10 expected-negative samples from the Black River in La Crosse, Wisconsin, 10 expected-positive samples from the Black Earth Creek in Black Earth, Wisconsin, and 10 known-positive samples from the Black River spiked with NZMS DNA. Previously extracted samples, kept at the Upper Midwest Environmental Sciences Center, were pooled by sample location and then equal quantities were distributed between the Upper Midwest Environmental Sciences Center and the Molecular Conservation Genetics Laboratory at the University of Wisconsin-Stevens Point for analysis. The assays tested were (1) the assay targeting cytb with a minor groove binder probe described by Goldberg and others (2013), (2) the cytb assay with a modified double-quenched probe, (3) an assay targeting coi with a double-quenched probe, and (4) a duplex reaction combining the modified cytb assay and the coi assay. Samples were considered positive for the presence of NZMS DNA when quantitative polymerase chain reaction amplification and probe signal was higher than the normalized threshold value above baseline fluorescence. For the duplex assay, samples were considered positive only when both probe signals were higher than the normalized threshold value above baseline fluorescence. Positive results were then confirmed by sequencing the products. All four assays detected the DNA of NZMS in all expected-positive and known-positive samples in both labs. The modified cytb assay, the coi assay, and the duplex assay all failed to detect the DNA of NZMS in all expected-negative samples in both labs. The cytb assay, as described by Goldberg and others (2013), failed to detect the DNA of NZMS in all expected-negative samples for the Molecular Conservation Genetics Laboratory, but some reactions resulted in positive detection in late cycles for 9 of the 10 expected-negative samples at the Upper Midwest Environmental Sciences Center. Amplicons for expected-negative samples with positive reactions were sent for sequencing, and none were confirmed as NZMS. Six amplicons failed to give readable sequences, and three gave sequences without similarity to any known sequence in GenBank. Amplicons from each assay for one representative positive sample were sequenced and identified as NZMS with greater than 99 percent identity. The duplex assay was chosen as the most efficient assay and was used at the Upper Midwest Environmental Sciences Center to analyze triplicate samples from 29 streams in Wisconsin, 8 streams in Illinois, and 8 streams in Iowa. In order to verify results, additional triplicate samples were collected from two of the streams in Iowa and two of the streams in Wisconsin for analysis at the Molecular Conservation Genetics Laboratory. All samples at all sites were negative for NZMS DNA.

Illinois, Iowa, Wisconsin↗

Jaguar taxonomy and genetic diversity for southern Arizona, United States, and Sonora, Mexico

Executive Summary The jaguar is the largest Neotropical felid and the only extant representative of the genus Panthera in the Americas. In recorded history, the jaguars range has extended from the Southern United States, throughout Mexico, to Central and South America, and they occupy a wide variety of habitats. A previous jaguar genetic study found high historical levels of gene flow among jaguar populations over broad areas but did not include any samples of jaguar from the States of Arizona, United States, or Sonora, Mexico. Arizona and Sonora have been part of the historical distribution of jaguars; however, poaching and habitat fragmentation have limited their distribution until they were declared extinct in the United States and endangered in Sonora. Therefore, a need was apparent to have this northernmost (Arizona/Sonora) jaguar population included in an overall jaguar molecular taxonomy and genetic diversity analyses. In this study, we used molecular genetic markers to examine diversity and taxonomy for jaguars in the Northwestern Jaguar Recovery Unit (NJRU; Sonora, Sinaloa, and Jalisco, Mexico; and southern Arizona and New Mexico, United States) relative to jaguars in other parts of the jaguar range (Central and South America). The objectives of this study were to: Collect opportunistic jaguar samples (hide, blood, hair, saliva, and scat), from historical and current individuals, that originated in NJRU areas of Arizona, New Mexico, and Sonora; Use these samples to assess molecular taxonomy of NJRU jaguars compared to data from a previous study of jaguars rangewide; and Develop suggestions for conservation of NJRU jaguars based on the results.

Arizona, Jalisco, New Mexico, Sonora, Sinaloa↗

Genetic diversity and population structure in the threatened Oregon silverspot butterfly ( Speyeria zerene hippolyta ) in western Oregon and northwestern California— Implications for future translocations and the establishment of new populations

Executive Summary We present results of population genetic analyses performed on Oregon silverspot butterflies (OSB; Speyeria zerene hippolyta ) in western Oregon and northwestern California. We used DNA sequences from a 561-base pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene for a dataset comprised of 112 S. z. hippolyta and 32 S. z. gloriosa individuals collected at 9 locations in western Oregon and northwestern California. The most pertinent findings thus far are summarized as follows: Among OSB populations, genetic diversity is lowest at Mount Hebo and highest at Rock Creek and Bray Point. Of the 32 haplotypes detected in OSB, only 2 were shared among populations (1 shared by Mount Hebo, Cascade Head, Bray Point, and Rock Creek, and 1 shared by Rock Creek and Lake Earl). The remaining 30 haplotypes were identified in individual populations, highlighting the strong differentiation among sites. It is unclear if the shared haplotypes represent widespread, naturally occurring genetic variation or if allele sharing among populations is due to translocation history. Using full siblings of individuals that were released at Rock Creek and Bray Point in 2012 as comparison standards, the analyses suggest that 54 percent of the sampled individuals from Bray Point were naturally recruited into the population and were not originating from the 2012 release of captive reared individuals. Likewise, 33 percent of the analyzed individuals from Rock Creek were naturally recruited. Both of these estimates may be underestimates if the shared alleles that we identified among populations are naturally occurring and not a product of the 2012 translocations. The results suggest that there are about 12–13 COI haplotypes in the Mount Hebo population. The U.S. Fish and Wildlife Service anticipates using Mount Hebo as the source of individuals when establishing new populations in the future. Nonlinear regression models based on a series of rarefaction analyses suggest that progeny from 12, 37, 109, and 326 female individuals would be required to respectively capture 25, 50, 75, and 90 percent of the allelic diversity from Mount Hebo. Phylogenetic analyses identified two different haplotype groups, but the two groups did not correspond to the different subspecies used in the analysis. One group included 22 S. z. hippolyta haplotypes and 7 haplotypes identified in S. z. gloriosa . The second group included eight haplotypes from S. z. hippolyta, three haplotypes from S. z. gloriosa , and one haplotype that was detected in both subspecies.

California, Oregon↗

DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) in North San Diego County, California (2018-19)

Throughout the western United States, efforts are underway to better understand and preserve migration and movement corridors for mule deer and other big game and to minimize the impacts of development and other land-use change on populations. San Diego County is home to a unique non-migratory subspecies of mule deer, the Southern mule deer ( Odocoileus hemionus fuliginatus ; herein referred to as “mule deer”). Because it is the only large herbivorous mammal in San Diego, connectivity among mule deer groups is an important indicator of functional connectivity throughout San Diego County urban preserves and has therefore been monitored within central and eastern San Diego County using DNA fingerprinting since 2005. To continue this effort and to assess genetic connectivity in north San Diego County (herein “North County”), we genotyped scat samples from preserves in the area and tissue samples from Marine Corps Base Camp Pendleton (MCBCP). We used non-invasive capture/recapture analyses and pedigree analyses for assessing short-term movement and population clustering analyses to assess gene flow in North County. Additionally, we performed similar analyses on the combined San Diego County dataset, which was composed of the North County dataset collected for this study and a previously collected dataset from central and eastern San Diego County. Using recapture data, we found multiple instances of mule deer crossing roads in urban North County preserves, with several of these events occurring in areas where there are underpasses and culverts known to be used by mule deer. Corroborating previous studies in the region and statewide, pedigree and population structure analyses support the presence of two genetic clusters for mule deer in San Diego County—the “Coastal” and “Inland/Mountain” clusters. Low estimates of effective population size, especially in the Coastal cluster, suggest that to further understand potential vulnerabilities of mule deer in this region, it is important to continue to monitor connectivity, in particular, at the boundary between these two clusters.

California↗

Genetic structure and diversity in wild populations of the Light-footed Ridgway’s Rail reflect 20 years of augmentation through captive breeding and release

Captive breeding and release programs aimed at recovery of rare species can be informed by genetic data to help select high-diversity source populations, make pairing decisions to minimize inbreeding, and manage release strategies. We developed a set of 54 microsatellite loci to assess genetic structure and diversity across the United States range of the Light-footed Ridgway’s Rail ( Rallus obsoletus levipes ), a federally endangered marsh bird for which populations have been augmented by a captive breeding program annually since 2001. We identified three regional genetic clusters, with the highest genetic diversity reported in the central cluster, which included all sampled wetlands in north San Diego County. Recent (2019–24) captive-breeding adults all clustered within the northernmost cluster (Orange and Ventura Counties), which was expected given that this cluster included the source wetland for the captive breeding program. Gene flow rates, which approximate the proportions of individuals in a population originating from other populations, were relatively high among clusters (4–24 percent) and may have been enhanced through the release of captive-bred rails. Based on the genetic data analyzed in a genetic rescue decision framework, sourcing new breeding birds from the north San Diego County cluster could provide the greatest genetic diversity benefits. The northernmost cluster, which included Mugu Lagoon and all sampled Orange County wetlands, was considered the most in need of genetic rescue. Recent breeding pairs in the captive breeding program have comparatively low diversity and high interrelatedness. Sourcing birds from wetlands with high genetic diversity and population sizes, assessing genetic relatedness before pairing, and focusing releases in areas that have low estimates of genetic diversity could improve the distribution of genetic diversity across wild populations in the future.

California↗

Behavioral and catastrophic drift of invertebrates in two streams in northeastern Wyoming

Invertebrate drift samples were collected in August 1977 from two streams in the Powder River structural basin in northeastern Wyoming. The streams are Clear Creek, a mountain stream, and the Little Powder River, a plains stream. Two major patterns of drift were recognized. Clear Creek was sampled during a period of normal seasonal conditions. High drift rates occurred during the night indicating a behavioral drift pattern that is related to the benthic invertebrate density and carrying capacity of the stream substrates. The mayfly genes Baetis, a common drift organism, dominated the peak periods of drift in Clear Creek. The Little Powder River has a high discharge during the study period. Midge larvae of the families Chironomidae and Ceratopogonidae, ususally not common in drift, dominated the drift community. The dominance of midge larvae, the presence of several other organisms not common in drift, and the high discharge during the study period caused a catastrophic drift pattern. (USGS)

Open-File Report↗

Evaluation of potential sources and transport mechanisms of fecal indicator bacteria to beach water, Murphy Park Beach, Door County, Wisconsin

Fecal Indicator Bacteria (FIB) concentrations in beach water have been used for many years as a criterion for closing beaches due to potential health concerns. Yet, current understanding of sources and transport mechanisms that drive FIB occurrence remains insufficient for accurate prediction of closures at many beaches. Murphy Park Beach, a relatively pristine beach on Green Bay in Door County, Wis., was selected for a study to evaluate FIB sources and transport mechanisms. Although the relatively pristine nature of the beach yielded no detection of pathogenic bacterial genes and relatively low FIB concentrations during the study period compared with other Great Lakes Beaches, its selection limited the number of confounding FIB sources and associated transport mechanisms. The primary sources of FIB appear to be internal to the beach rather than external sources such as rivers, storm sewer outfalls, and industrial discharges. Three potential FIB sources were identified: sand, swash-zone groundwater, and Cladophora mats. Modest correlations between FIB concentrations in these potential source reservoirs and FIB concentrations at the beach from the same day illustrate the importance of understanding transport mechanisms between FIB sources and the water column. One likely mechanism for transport and dispersion of FIB from sand and Cladophora sources appears to be agitation of Cladophora mats and erosion of beach sand due to storm activity, as inferred from storm indicators including turbidity, wave height, current speed, wind speed, sky visibility, 24-hour precipitation, and suspended particulate concentration. FIB concentrations in beach water had a statistically significant relation (p-value ‹0.05) with the magnitude of these storm indicators. In addition, transport of FIB in swash-zone groundwater into beach water appears to be driven by groundwater recharge associated with multiday precipitation and corresponding increased swash-zone groundwater discharge at the beach, as indicated by an increase in the specific conductance of beach water. Understanding the dynamics of FIB sources (sand, swash-zone groundwater, and Cladophora ) and transport mechanisms (dispersion and erosion from storm energy, and swash-zone groundwater discharge) is important for improving predictions of potential health risks from FIB in beach water.

Wisconsin↗

Anatomical and genetic variation of western Oxyloma (Pulmonata: Succineidae) concerning the endangered Kanab ambersnail ( Oxyloma haydeni kanabense ) in Arizona and Utah

The land snail genus Oxyloma (Pulmonata: Succineidae) includes the Federally endangered Kanab ambersnail (Oxyloma haydeni kanabense Pilsbry), which is known at the time of this study from only two locations in the United States: Three Lakes, Utah, and Vaseys Paradise, Arizona, on the Colorado River in Grand Canyon National Park. Since 1994, the Kanab ambersnail has received much attention because its presence at Vaseys Paradise has implications for the ecosystem-wide management of the Colorado River. This attention is primarily because an experimental high-flow release of water from Glen Canyon Dam in 1996 destroyed or degraded Kanab ambersnail habitat at Vaseys Paradise. This experimental high flow was designed to replicate natural flow regimes throughout the Grand Canyon river corridor. However, as a result of the habitat destruction at Vaseys Paradise, in 1996, the U.S. Fish and Wildlife Service ruled that no further experimental high-discharge floods could be carried out until additional Kanab ambersnail populations were discovered or established. This mandate created a situation where the management of a single endangered species conflicted directly with the management of an entire ecosystem. Although since 1996, the U.S. Fish and Wildlife Service has permitted the use of flows as high as stage heights equivalent to 44,000 cubic feet per second, higher flows were requested by various Grand Canyon stakeholders and scientists but were not possible owing to low storage of Lake Powell. Adding to the controversy about Oxyloma and the Kanab ambersnail were previous anatomical and genetic analyses of the genus, which showed that genetic characteristics of specimens did not correspond with their identifications based on traditional taxonomic criteria, raising questions about the validity of the taxonomy of Oxyloma and the protected status of Kanab ambersnails. Specifically, a previous study suggested that the endangered Kanab ambersnail population at Three Lakes was more closely related to other, non-endangered ambersnail populations across the Southwest. In contrast, the Kanab ambersnail population at Vaseys Paradise appeared to be genetically distinct from all other ambersnail populations studied. Management options for the ambersnail population at Vaseys Paradise, at the time of this study, conflict with ecosystem-wide measures proposed to benefit other natural resources in the Grand Canyon. The U.S. Fish and Wildlife Service will not revise the 1995 Kanab Ambersnail Recovery Plan until further genetic and anatomical analyses provide more fine-scale taxonomic resolution of the identity of Oxyloma populations on the Colorado Plateau and elsewhere in the American Southwest. Likewise, interagency cooperators cannot revise down-listing criteria for the Kanab ambersnail until substantial evidence is provided identifying distinct Oxyloma taxa or a larger group of conspecifics that reasonably could be managed as one species. Therefore, given the current controversy about the taxonomy of Oxyloma and the endangered Kanab ambersnail, new detailed analyses were completed of morphological and genetic variation from many Oxyloma specimens collected at 12 western North American locations. These new data have allowed us to evaluate many issues related to Kanab ambersnail taxonomy. Using this dataset, the study of shells and anatomy indicates that the holotype of Oxyloma haydeni kanabense plausibly can be regarded as a member of the same species as the populations of Oxyloma analyzed in this study. Additionally, the presence of gene flow among all populations is evidence that they are members of the same species. Almost all the observed genetic diversity can be accounted for by short-distance or long-distance dispersal events between populations in this study. Our major taxonomic conclusion is that all samples collected for this study were drawn from populations of the same species.

Arizona;Utah↗

Using high-throughput DNA sequencing, genetic fingerprinting, and quantitative PCR as tools for monitoring bloom-forming and toxigenic cyanobacteria in Upper Klamath Lake, Oregon, 2013 and 2014

Monitoring the community structure and metabolic activities of cyanobacterial blooms in Upper Klamath Lake, Oregon, is critical to lake management because these blooms degrade water quality and produce toxic microcystins that are harmful to humans, domestic animals, and wildlife. Genetic tools, such as DNA fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analysis, high-throughput DNA sequencing (HTS), and real-time, quantitative polymerase chain reaction (qPCR), provide more sensitive and rapid assessments of bloom ecology than traditional techniques. The objectives of this study were (1) to characterize the microbial community at one site in Upper Klamath Lake and determine changes in the cyanobacterial community through time using T-RFLP and HTS in comparison with traditional light microscopy; (2) to determine relative abundances and changes in abundance over time of toxigenic Microcystis using qPCR; and (3) to determine relative abundances and changes in abundance over time of Aphanizomenon , Microcystis , and total cyanobacteria using qPCR. T-RFLP analysis of total cyanobacteria showed a dominance of only one or two distinct genotypes in samples from 2013, but results of HTS in 2013 and 2014 showed more variations in the bloom cycle that fit with the previous understanding of bloom dynamics in Upper Klamath Lake and indicated that potentially toxigenic Microcystis was more prevalent in 2014 than in years prior. The qPCR-estimated copy numbers of all target genes were higher in 2014 than in 2013, when microcystin concentrations also were higher. Total Microcystis density was shown with qPCR to be a better predictor of late-season increases in microcystin concentrations than the relative proportions of potentially toxigenic cells. In addition, qPCR targeting Aphanizomenon at one site in Upper Klamath Lake indicated a moderate bloom of this species (corresponding to chlorophyll a concentrations between approximately 75 and 200 micrograms per liter) from mid-June to mid-August, 2014. After August 18, the Aphanizomenon bloom was overtaken by Microcystis late in the season as microcystin concentrations peaked. Overall, results of this study showed how DNA-based, genetic methods may provide rapid and sensitive diagnoses for the presence of toxigenic cyanobacteria and that they are useful for general monitoring or ecological studies and identification of cyanobacterial community members in complex aquatic habitats. These same methods can also be used to simultaneously address spatial (horizontal and vertical) and temporal variation and under different conditions. Additionally, with some modifications, the same techniques can be applied to different sample types, including water, sediment, and tissue.

Oregon↗