USGS Science⌕ Search

SEARCH · USGS Science

Results for “Diversity”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources
USGS2010

Effects of littoral habitat complexity and sunfish composition on fish production

Habitat complexity is a key driver of food web dynamics because physical structure dictates resource availability to a community. Changes in fish diversity can also alter trophic interactions and energy pathways in food webs. Few studies have examined the direct, indirect, and interactive effects of biodiversity and habitat complexity on fish production. We explored the effects of habitat complexity (simulated vegetation), sunfish diversity (intra‐ vs. inter‐specific sunfish), and their interaction using a mesocosm experiment. Total fish production was examined across two levels of habitat complexity (low: 161 strands m −2 and high: 714 strands m −2 ) and two sunfish diversity treatments: bluegill only ( Lepomis macrochirus ) and bluegill, redear sunfish ( Lepomis microlophus ), and green sunfish ( Lepomis cyanellus ) combination. We also measured changes in total phosphorus, phytoplankton, periphyton, and invertebrates to explain patterns in fish production. Bluegill and total fish production were unaffected by the sunfish treatments. Habitat complexity had a large influence on food web structure by shifting primary productivity from pelagic to a more littoral pathway in the high habitat treatments. Periphyton was higher with dense vegetation, leading to reductions in total phosphorus, phytoplankton, cladoceran abundance and fish biomass. In tanks with low vegetation, bluegill exhibited increased growth. Habitat complexity can alter energy flow through food webs ultimately influencing higher trophic levels. The lack of an effect of sunfish diversity on fish production does not imply that conserving biodiversity is unimportant; rather, we suggest that understanding the context in which biodiversity is important to food web dynamics is critical to conservation planning

Ecology of Freshwater Fish↗
USGS2011

Hierarchical spatial structure of stream fish colonization and extinction

Spatial variation in extinction and colonization is expected to influence community composition over time. In stream fish communities, local species richness (alpha diversity) and species turnover (beta diversity) are thought to be regulated by high extinction rates in headwater streams and high colonization rates in downstream areas. We evaluated the spatiotemporal structure of fish communities in streams originally surveyed by Burton and Odum 1945 (Ecology 26: 182-194) in Virginia, USA and explored the effects of species traits on extinction and colonization dynamics. We documented dramatic changes in fish community structure at both the site and stream scales. Of the 34 fish species observed, 20 (59%) were present in both time periods, but 11 (32%) colonized the study area and three (9%) were extirpated over time. Within streams, alpha diversity increased in two of three streams but beta diversity decreased dramatically in all streams due to fish community homogenization caused by colonization of common species and extirpation of rare species. Among streams, however, fish communities differentiated over time. Regression trees indicated that reproductive life-history traits such as spawning mound construction, associations with mound-building species, and high fecundity were important predictors of species persistence or colonization. Conversely, native fishes not associated with mound-building exhibited the highest rates of extirpation from streams. Our results demonstrate that stream fish colonization and extinction dynamics exhibit hierarchical spatial structure and suggest that mound-building fishes serve as keystone species for colonization of headwater streams.

Oikos↗
USGS2021

Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms

Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level genetic diversity and estimates of the number of genetic contributors in a sample. Using a panel of microsatellite loci, we evaluated intraspecific genetic diversity in the round goby (Neogobius melanostomus) using eDNA samples from experimental mesocosms. First, we tested the similarity between eDNA and individual tissue-based estimates of allele frequencies. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in mesocosm eDNA samples and in simulated mixtures of alleles. Allele frequencies from eDNA accurately reflected allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples under controlled conditions. DNA mixture analyses were able to estimate the number of genetic contributors from eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. This study is the first to document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in mesocosms. With proper validation, this approach has the potential to advance non-invasive survey methods to characterize populations and broadens the application of eDNA methodologies to inform population-level management objectives.

New York↗
USGS2023

Timing of reproduction underlies fitness tradeoffs for a salmonid fish

Life history diversity is generated and maintained in part by density-dependent fitness tradeoffs that inhibit a single trait value from reaching fixation. While central to our understanding of evolution, demonstrating density dependence in the strength of fitness tradeoffs is difficult in natural systems. The timing of reproduction is a key life history trait that determines access to breeding habitat and exposure of offspring to competitive interactions and environmental conditions. Understanding the processes underlying diversity in reproductive timing will aid efforts to increase adaptive capacity under global environmental change. Here, we used detailed field studies, genetic parentage assignment, and simulation modeling to evaluate the fitness tradeoffs associated with the timing of reproduction for Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri in groundwater-dominated tributaries to the upper Snake River, Wyoming, USA. We conducted our study across two years to understand how the strength of tradeoffs changes with population density. We found that early breeders experienced reduced reproductive success relative to later breeders due to the negative impact of nest superimposition (where later breeders construct nests overlapping those constructed previously) on embryo survival. However, as the risk of superimposition declined in the low-density year and early breeders experienced fewer losses, reproductive success became more similar among individuals breeding at different times. Further, in the spring following the critical period for growth and survival, offspring of early breeders had experienced longer growing seasons, attained larger body sizes, and were equally abundant relative to those of later breeders, suggesting that fitness losses due to superimposition may be offset by size-dependent competitive ability and overwinter survival. Our results illustrate a mechanism underlying diversity in the timing of reproduction for salmonids. This type of life history diversity will help to ensure the resilience and stability of salmonid populations attempting to adapt to changing local stressors associated with global climate change.

Oikos↗
USGS2001

Genetic and morphologic variation in Phyllodoce empetriformis and Phyllodoce glanduliflora (Ericaceae) in Mount Rainier National Park, Washington

Genetic and morphological diversity of Phyllodoce empetriformis (Sw.) D. Don and Phyllodoce glanduliflora (hook.) Cov. were surveyed in Mount Rainier National Park in the Cascade Mountains of Washington State. Paired populations at high and low elevations were sampled at three study areas between 1720- and 2451-m elevation. Allozyme analysis of four polymorphic loci indicates high levels of genetic diversity within populations ( P. empetriformis = 94.2% and P. glanduliflora = 93.4% of total diversity) and significant differences in allele frequencies among populations and study areas. Individual populations are composed of multiple clones with high ratios of local to widespread genotypes. The proportion of distinguishable clones ranges from 32 to 83% within individual populations. Within individual populations, 18-67% of genotypes were restricted to one population. Patterns of morphologic variation, estimated through measurements of leaf width, leaf length, stem extension, and plant height paralleled those displayed by allozyme analysis. Significant differences were found in leaf width and stem length for P. empetriformis and among greenhouse populations for leaf width ( P. empetriformis ) and leaf length ( P. glanduliflora ). Species conservation strategies for Phyllodoce should concentrate on the maintenance of within-population levels of diversity, protection of adjacent populations, and protection of safe sites for recruitment of new populations.

Washington↗
USGS2009

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer. ?? 2009 Pearson et al; licensee BioMed Central Ltd.

BMC Biology↗
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↗
USGS2009

The needs of salmon and steelhead in balancing their conservation and use

Over the past 100 years, Pacific salmon Oncorhynchus spp. and steelhead trout O. mykiss populations in the Pacific Northwest have experienced dramatic declines as a result of human population growth and associated development of the region's natural resources. Any strategy to reverse those declines will depend on achieving consensus among a diverse group of stakeholders willing to (1) restore damaged habitats and watersheds; (2) consider the biological needs of salmonid fishes; and (3) understand, conserve, and manage existing levels of biodiversity within an ecosystem context. The objective of this chapter is to review and summarize the needs of Pacific salmon and steelhead trout from perspectives that promote their sustainability and perpetuity, and, within that context, provide a framework, for the development of a sustainable fisheries strategy. Although volumes of information are available on the life histories and habitat requirements of Pacific salmonids, new concepts have begun to address the importance of habitat complexity, genetic diversity among locally adapted populations, and the need for appropriate units of conservation. Habitat variability and complexity are the templates that produce diverse, locally adapted populations of Pacific salmon and steelhead trout. Molded by conditions in the environments they colonized, salmon and steelhead have unique adaptations they may have taken hundred i?? perhaps thousands i?? of years to evolve. Any strategy to reverse the declines of salmon and steelhead must focus on conserving both current levels of genetic diversity as well as restoration and maintenance of habitats compatible with the specific needs of individual populations. An argument can be made that we know enough already about the needs of our salmon and steelhead to allow us to make appropriate decisions. There is strong need to integrate what we know about local salmonid adaptations and habitat needs with conservation and management strategies that address the problems we have created. It may be possible to have healthy, sustainable salmonid populations coastwide if we do not wait too long to make up our minds.

Book chapter↗
USGS2012

Molecular detection of hematozoa infections in tundra swans relative to migration patterns and ecological conditions at breeding grounds

Tundra swans ( Cygnus columbianus ) are broadly distributed in North America, use a wide variety of habitats, and exhibit diverse migration strategies. We investigated patterns of hematozoa infection in three populations of tundra swans that breed in Alaska using satellite tracking to infer host movement and molecular techniques to assess the prevalence and genetic diversity of parasites. We evaluated whether migratory patterns and environmental conditions at breeding areas explain the prevalence of blood parasites in migratory birds by contrasting the fit of competing models formulated in an occupancy modeling framework and calculating the detection probability of the top model using Akaike Information Criterion (AIC). We described genetic diversity of blood parasites in each population of swans by calculating the number of unique parasite haplotypes observed. Blood parasite infection was significantly different between populations of Alaska tundra swans, with the highest estimated prevalence occurring among birds occupying breeding areas with lower mean daily wind speeds and higher daily summer temperatures. Models including covariates of wind speed and temperature during summer months at breeding grounds better predicted hematozoa prevalence than those that included annual migration distance or duration. Genetic diversity of blood parasites in populations of tundra swans appeared to be relative to hematozoa prevalence. Our results suggest ecological conditions at breeding grounds may explain differences of hematozoa infection among populations of tundra swans that breed in Alaska.

Alaska↗
USGS2019

Morphology and genetics of Lythrum salicaria from latitudinal gradients of the Northern Hemisphere grown in cold and hot common gardens

The aim of this project was to compare the phenotypic responses of global populations of Lythrum salicaria in cold/dry and hot/humid environments to determine if phenotypic plasticity varied between the native and invasive ranges, and secondarily if this variation was linked to genetic diversity. Common garden studies were conducted in Třeboň, Czech Republic, and Lafayette, Louisiana, USA (cold/dry vs. hot/humid garden, respectively), using populations from latitudinal gradients in Eurasia and North America. Lythrum salicaria seeds collected from the same maternal plants across these latitudinal gradients were germinated and grown in Třeboň and Lafayette. Tissue masses (above-, below-ground, inflorescence and total) of these individuals were assessed at the end of each growing season (2006–2008). Worldwide field measurements of L . salicaria height were made by volunteers from 2004–2016. Biomass and height data were analyzed using the General Linear Model framework and multivariate techniques. Molecular markers (amplified fragment length polymorphisms) of individuals used in the common garden study were analyzed using traditional genetic diversity metrics and Bayesian clustering algorithms in STRUCTURE. Reaction norms were developed from differences in maternal plant responses in Třeboň versus Lafayette. In the common garden studies, stem/leaf, root and total biomass generally were highest for individuals grown from seeds collected in the southern part of the range in the cold garden, particularly by the third year of the study. In contrast, inflorescence biomass in the cold garden was higher by the third year in individuals from mid-latitude populations. As measured by volunteers, plants were taller in Eurasia than in North America moving from north to south with the pattern switching southward of 40°N latitude. Genetic diversity was similar between native and non-native invasive populations regardless of geographical origin of the seed and was not significantly different in the GLM Select model (p > 0.05). Reaction norm slopes showed that Eurasia had larger values than North America for reaction norms for above-ground and total biomass. Plants from the seeds of mother plants from Turkey had wide variation in total biomass when grown in Třeboň versus Lafayette; this variation in response within certain populations may have contributed to the lack of population-level differences in plasticity. These results indicate no loss of genetic diversity for L . salicaria during its North American invasion, nor reduction in plastic tissue allocation responses to a varying environment, which may help explain some of its invasive qualities and which could be of adaptive value under changing future environments.

PLoS ONE↗
USGS2020

Combining genetic and demographic monitoring better informs conservation of an endangered urban snake

Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species’ ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake ( Thamnophis sirtalis tetrataenia ), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T . s . tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T . s . tetrataenia populations could promote persistence of this endangered snake.

California↗
USGS2005

Genetics of Central Valley, O. mykiss, populations: Drainage and watershed scale analyses

Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M < 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts.

California↗
USGS2024

Bird habitat value and management priorities of the California Winter Rice Habitat Incentive Program

Flooding rice ( Oryza sativa ) agricultural fields during winter to facilitate rice straw decomposition has mitigated the loss of some of the natural wetlands in California’s Central Valley. We conducted bird surveys in 253 rice checks (2,158 ha) within 177 rice fields in the Sacramento Valley during the fall and winter of 2021-2022 and 2022-2023 to evaluate factors influencing bird use of winter-flooded, post-harvest rice fields enrolled in the California Winter Rice Habitat Incentive Program. We counted 143,932 birds from 57 species, including dabbling ducks (86.4%), geese (8.0%), shorebirds (0.9%), wading birds (0.7%), and other birds (4.0%). Extrapolating from the lowest densities observed in rice fields during the 70-day mandatory flooding period, we estimated that properties enrolled in this public-private partnership provided habitat for at least 271,312 birds day-1 (16,248 ha; 2021-2022) and 147,315 birds day-1 (8,448 ha; 2022-2023), totaling >10 million bird-use-days each winter. Water depth had the greatest influence on bird abundance and diversity. Relatively shallow water depths (≤13 cm) had greater abundance of shorebirds, wading birds, and geese, and higher diversity, whereas intermediate depths (~23 cm) resulted in the greatest dabbling duck abundance. Duck, goose, and wading bird abundances were greatest and species richness and family diversity were highest 8 days after the onset of flooding in rice fields (typically late October), followed by a decline in bird use until 65-87 days post flooding, after which bird use increased slightly. Bird abundance and species diversity were lowest in rice fields with the greatest hunting intensity (≥3 days week-1). We identified several habitat variables that could be managed and prioritized by landowner incentive programs to increase bird use of winter-flooded rice, including water depth, variation in emergent vegetation height, mudflat habitat availability, rice check shape, hunting intensity, and post-harvest treatment of residual rice straw.

California↗
USGS2002

Genetic characterization of infectious hematopoietic necrosis virus of coastal salmonid stocks in Washington State

Infectious hematopoietic necrosis virus (IHNV) is a pathogen that infects many Pacific salmonid stocks from the watersheds of North America. Previous studies have thoroughly characterized the genetic diversity of IHNV isolates from Alaska and the Hagerman Valley in Idaho. To enhance understanding of the evolution and viral transmission patterns of IHNV within the Pacific Northwest geographic range, we analyzed the G gene of IHNV isolates from the coastal watersheds of Washington State by ribonuclease protection assay (RPA) and nucleotide sequencing. The RPA analysis of 23 isolates indicated that the Skagit basin IHNV isolates were relatively homogeneous as a result of the dominance of one G gene haplotype (S). Sequence analysis of 303 bases in the middle of the G gene (midG region) of 61 isolates confirmed the high frequency of a Skagit River basin sequence and identified another sequence commonly found in isolates from the Lake Washington basin. Overall, both the RPA and sequence analysis showed that the Washington coastal IHNV isolates are genetically homogeneous and have little genetic diversity. This is similar to the genetic diversity pattern of IHNV from Alaska and contrasts sharply with the high genetic diversity demonstrated for IHNV isolates from fish farms along the Snake River in Idaho. The high degree of sequence and haplotype similarity between the Washington coastal IHNV isolates and those from Alaska and British Columbia suggests that they have a common viral ancestor. Phylogenetic analyses of the isolates we studied and those from different regions throughout the virus's geographic range confirms a conserved pattern of evolution of the virus in salmonid stocks north of the Columbia River, which forms Washington's southern border.

Washington↗
USGS2008

Field-based evaluations of horizontal flat-plate fish screens

Diversions from streams are often screened to prevent the loss of or injury to fish. Hydraulic criteria meant to protect fish that encounter screens have been developed, but primarily for screens that are vertical to the water flow rather than horizontal. For this reason, we measured selected hydraulic variables and released wild rainbow trout Oncorhynchus mykiss over two types of horizontal flat-plate fish screens in the field. Our goal was to assess the efficacy of these screens under a variety of conditions in the field and provide information that could be used to develop criteria for safe fish passage. We evaluated three different invertedweir screens over a range of stream (0.24-1.77 m3/s) and diversion flows (0.10-0.31 m3/s). Approach velocities (AVs) ranged from 3 to 8 cm/s and sweeping velocities (SVs) from 69 to 143 cm/s. We also evaluated a simple backwatered screen over stream flows of 0.23-0.79 m3/s and diversion flows of 0.08-0.32 m3/s. The mean SVs for this screen ranged from 15 to 66 cm/s and the mean AVs from 1 to 5 cm/s. The survival rates of fish held for 24 h after passage over these screens exceeded 98%. Overall, the number of fish-screen contacts was low and the injuries related to passage were infrequent and consisted primarily of minor fin injuries. Our results indicate that screens of this type have great potential as safe and effective fish screens for small diversions. Care must be taken, however, to avoid operating conditions that produce shallow or no water over the screen surface, situations of high AVs and low SVs at backwatered screens, and situations producing a localized high AV with spiraling flow. ?? Copyright by the American Fisheries Society 2008.

North American Journal of Fisheries Management↗
USGS2011

Spatial variation in fish species richness of the upper Mississippi River system

Important natural environmental gradients, including the connectivity of off-channel aquatic habitats to the main-stem river, have been lost in many reaches of the upper Mississippi River system, and an understanding of the consequences of this isolation is lacking in regard to native fish communities. The objectives of this study were to describe patterns of fish species richness, evenness, and diversity among representative habitats and river reaches and to examine the relationship between fish species richness and habitat diversity. Each year (1994-1999) fish communities of main-channel borders (MCB), side channel borders (SCB), and contiguous backwater shorelines (BWS) were sampled using boat-mounted electrofishing, mini-fyke-nets, tyke nets, hoop nets, and seines at a standardized number of sites. A total of 0.65 million fish were collected, representing 106 species from upper Mississippi River Pools 4, 8, 13, and 26; the open (unimpounded) river reach; and the La Grange Reach of the Illinois River. Within pools, species richness based on rarefaction differed significantly among habitats and was highest in BWS and lowest in MCB (P < 0.0001). At the reach scale, Pools 4, 8, and 13 consistently had the highest species richness and Pool 26, the open-river reach, and the La Grange Reach were significantly lower (P < 0.0001). Species evenness and diversity indices showed similar trends. The relationship between native fish species richness and habitat diversity was highly significant (r(2) = 0.85; P = 0.0091). These results support efforts aimed at the conservation and enhancement of connected side channels and backwaters. Although constrained by dams, pools with high native species richness could serve as a relative reference. The remnants of natural riverine dynamics that remain in these reaches should be preserved and enhanced; conditions could be used to guide restoration activities in more degraded reaches.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗
USGS2017

Short-term vegetation response following mechanical control of saltcedar ( Tamarix spp.) on the Virgin River, Nevada, USA

Tamarisk (a.k.a. saltcedar, Tamarix spp.) is an invasive plant species that occurs throughout western riparian and wetland ecosystems. It is implicated in alterations of ecosystem structure and function and is the subject of many local control projects, including removal using heavy equipment. We evaluated short-term vegetation responses to mechanical Tamarix spp. removal at sites ranging from 2 to 5 yr post-treatment along the Virgin River in Nevada, USA. Treatments resulted in lower density and cover (but not eradication) of Tamarix spp., increased cover of the native shrub Pluchea sericia (arrow weed), decreased density and cover of all woody species combined, increased density of both native annual forbs and the nonnative annual Salsola tragus (prickly Russian-thistle), and lower density of nonnative annual grasses. The treated plots had lower mean woody species richness, but greater herbaceous species richness and diversity. Among herbaceous species, native taxa increased in richness whereas nonnative species increased in both species richness and diversity. Thus, efforts to remove Tamarix,/i> spp. at the Virgin River reduced vegetative cover contributing to fuel loads and probability of fire, and resulted in positive effects for native plant diversity, with mixed effects on other nonnative species. However, absolute abundances of native species and species diversity were very low, suggesting that targets of restoring vegetation to pre-invasion conditions were not met. Longer evaluation periods are needed to adequately evaluate how short-term post-treatment patterns translate to long-term patterns of plant community dynamics.

Nevada↗