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At least 217 records · Page 12Linked to original sources
USGS2010

An overview of marine biodiversity in United States waters

Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise.

Arctic Ocean, Atlantic Ocean, Pacific Ocean↗
USGS2021

International importance of Percids: Summary and looking forward

Research presented in the preceding chapters emphasizes recent advancements in the research, management, and aquaculture of Walleye, Sauger, and Yellow Perch in North America. These percid fishes, along with the European Perch and Pikeperch, are economically and ecologically important fishes in their native geographic range. Advances in techniques to evaluate current habitat and predict future habitat conditions provide managers with detailed baseline information and biophysical models useful for evaluating adaptive management practices. Current habitat use and movement assessments have improved substantially with technological advancements in acoustic tags and extensive receiver array networks, which, combined with genetic and genomic tools, are improving percid stock assessments and management. Advances in percid aquaculture techniques have improved growth, survival, and disease resistance, enhancing percid stocking efforts and the production of marketable fish. The exchange of information between researchers and managers will continue to advance techniques of percid management for commercial and recreational exploitation and improve aquaculture practices to provide a lucrative commercial aquaculture industry.

Book chapter↗
USGS2001

Representation of natural vegetation in protected areas: Capturing the geographic range

Current conservation strategies for plant and animal species rarely address the need to protect the species throughout its geographic range thereby capturing potential genetic and ecological variation. We examined the degree that existing protected areas in the western United States satisfied this goal for four widespread vegetation cover types. We used latitude and longitude to stratify the distribution of these types into 16 cells, each of which was further stratified by up to five elevation classes. While protection of some vegetation types was high in parts of their range, it was minimal to nonexistent in other parts. While it is yet to be shown that protecting a given species throughout its geographic range is essential for its long-term existence, in the face of often unpredictable environmental changes, it seems a prudent course to follow. Our results suggest that if full range protection is a conservation goal, the existing network of protected areas may be inadequate for the task.

Biodiversity and Conservation↗
USGS2017

Between hot rocks and dry places: The status of the Dixie Valley toad

In Dixie Valley, Nevada, an isolated population of toads has been the subject of proactive conservation measures by the Nevada Department of Wildlife and the U.S. Fish and Wildlife Service since 2008 due to concerns about potential habitat degradation resulting from exploitation of nearby geothermal energy resources. These toads appear to belong within the Anaxyrus boreas species group but are commonly referred to as Dixie Valley toads (DVTs). The DVT is currently confined to an extremely narrow habitat range (370 ha) that is geographically isolated from any other A. boreas population. In this study, genetic variations in mitochondrial genes and 11 microsatellite loci were used to assess the affinities of DVTs in relation to members of the A. boreas species group. We compared results from DVTs with previously published data spanning much of the range of A. boreas in the United States and new data from a nearby toad population within Dixie Valley. Data from both mitochondrial DNA and microsatellites placed DVTs inside the A. boreas species group. In particular, DVTs fell into a cluster of A. boreas from Washington and California, along with other species from the A. boreas species group, namely A. nelsoni, A. canorus, and A. exsul. Genetic differentiation of DVTs was lowest between A. boreas populations in Washington and California. However, allele frequencies were significantly different between DVTs and all other populations, including a nearby locality within Dixie Valley. This genetic differentiation, along with the DVT's geographical isolation and restricted habitat, warrants recognition of the DVT as a distinct management unit.

Nevada↗
USGS2007

Research to support sterile-male-release and genetic alteration techniques for sea lamprey control

Integrated pest management of sea lampreys in the Laurentian Great Lakes has recently been enhanced by addition of a sterile-male-release program, and future developments in genetic approaches may lead to additional methods for reducing sea lamprey reproduction. We review the development, implementation, and evaluation of the sterile-male-release technique (SMRT) as it is being applied against sea lampreys in the Great Lakes, review the current understanding of SMRT efficacy, and identify additional research areas and topics that would increase either the efficacy of the SMRT or expand its geographic potential for application. Key areas for additional research are in the sterilization process, effects of skewed sex ratios on mating behavior, enhancing attractiveness of sterilized males, techniques for genetic alteration of sea lampreys, and sources of animals to enhance or expand the use of sterile lampreys.

Journal of Great Lakes Research↗
USGS2023

Genetic structure of the Silver Chub indicates distinctiveness of Lake Erie population

Objective Silver Chub Macrhybopsis storeriana is a small riverine minnow endemic to North American fresh waters. Its range extends from the southern USA to southcentral Canada; the latter includes a rare lacustrine population in Lake Erie. Anthropogenic activities pose an immediate threat to several Silver Chub populations, currently categorized from special concern to threatened at the state level in the USA and federally and provincially not-at-risk to endangered in Canada. Several studies have examined the anthropogenic causes for the decline of Silver Chub populations, but conservation efforts have been hindered by the lack of knowledge of the population genetics of this species. Methods Here, we provide an assessment of the genetic diversity of Silver Chub populations across the USA and Canada using a fast-evolving mitochondrial gene, with particular focus on the Lake Erie population. Result We found the Lake Erie population to be divergent from all other populations, with nearly all the haplotypes sampled there being private. Conclusion Our study provides genetic evidence that the Silver Chub population in Lake Erie could be considered a separate conservation unit.

Lake Erie↗
USGS2019

North-facing slopes and elevation shape asymmetric genetic structure in the range-restricted salamander Plethodon shenandoah

Species with narrow environmental preferences are often distributed across fragmented patches of suitable habitat, and dispersal among subpopulations can be difficult to directly observe. Genetic data collected at population centers can help quantify gene flow, which is especially important for vulnerable species with a disjunct range. Plethodon shenandoah is a Federally Endangered salamander known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture for all three populations and found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genome indicated a deep split between the most southern population and the combined central and northern population. Although there was some mitochondrial haplotype-splitting between the central and northern populations, there was complete admixture in nuclear markers. This is indicative of either a recent split or current male-biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north-facing slopes at mid-elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of landscape features in understanding and predicting movement and fragmentation of salamanders across space.

Ecology and Evolution↗
USGS2014

Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina (displaying low genetic divergence and greater than average levels of genetic diversity) . Our results show the utility o f genetic data sets for identifying cross - species patterns of genetic diversity and divergence (i.e., evolutionary hotspots) in aquatic and terrestrial environments for use in conservation design and delivery across the southeastern United States.

Alabama, Florida, Georgia, North Carolina, South C↗
USGS2015

Shoal basses: A clade of cryptic identity

Shoal basses are a cryptic clade composed of Micropterus spp. restricted to the Apalachicola River system and three southeastern Atlantic slope river drainages in the southeastern United States. This reciprocally monophyletic clade includes the Shoal Bass M. cataractae (endemic to the Apalachicola River system), the Chattahoochee Bass M. chattahoochae, and two undescribed forms from the Altamaha, Ogeechee, and Savannah River drainages. Members of the shoal bass clade can be distinguished from all other species of Micropterus basses using 20 diagnostic characters (characteristic attributes) found in mitochondrial DNA (NADH dehydrogenase subunit 2) gene sequences. Each member of the clade additionally possesses unique characteristic attributes, which along with morphological and meristic characters can be used to diagnose this cryptic biodiversity. Biologists and managers have previously regarded the shoal basses in the Chattahoochee, Savannah, Altamaha and Ogeechee River systems as belonging to a single taxon synonymous with the Redeye Bass M. coosae, which is endemic to the Mobile River drainage. With these and previous analyses (including description of the Shoal Bass), we now recognize that what was once considered a single taxon actually comprises seven species, each of which is endemic to a single southeastern drainage. Recognizing and documenting the actual diversity of Micropterus spp. provides important information for managers who may wish to avoid stocking or translocations that could compromise the genetic integrity of native bass populations. Introductions of nonnative basses, including Alabama Bass M. henshalli, Spotted Bass M. punctulatus, and Smallmouth Bass M. dolomieu currently threaten the integrity of native shoal bass species in streams of the Chattahoochee, Altamaha, Ogeechee, and Savannah River systems.

Conference Paper↗
USGS2025

Widespread dispersal of a human commensal across the Pacific: Reconstructing the human-mediated invasion history of the house gecko (Hemidactylus frenatus)

The spread of human commensal species is intricately tied to human movements and historical events. Through waves of human migrations, colonization, trade routes, commercial activities, and war, humans have redistributed species from their native ranges to widely scattered areas across the Pacific. Deciphering the invasion history of recent human-mediated introductions is challenging due to similar genetic signatures arising from these factors, which complicates the identification of specific pathways or sources. The extensive timeline of human events in the Pacific further compounds this challenge, potentially leading to numerous introductions from various regions over an extended period. The house gecko ( Hemidactylus frenatus ), a human commensal native to Southeast Asia, is now widespread in the Pacific region. While its current range is often attributed to activities during and following World War II (WWII), its invasion history necessitates a finer-scale dissection given the dynamic and extensive history of human-mediated introductions in the Pacific. We combine population genetics, phylogenetics, and approximate Bayesian computation to infer the invasion history of the house gecko from its native to its introduced range in the Pacific. Patterns of differentiation across native and introduced populations align with the extent of each region’s wartime involvement and the invasion history reconstruction supports the predicted chronology of introductions given a war-induced spread. This marks the first comprehensive genetic assessment of the house gecko’s invasion history in the Pacific and provides evidence in support of an initial spread across the Pacific consistent with WWII activities.

Biological Invasions↗
USGS2022

Stream macroinvertebrate reintroductions: A cautionary approach for restored urban streams

Macroinvertebrate assemblages often remain depauperate in physically restored urban streams despite efforts to improve habitat conditions and increase species abundance and diversity. The lack of biological recovery may be due to a lack of a natural, nearby source of colonists, and this has inspired researchers and practitioners to reintroduce macroinvertebrates in otherwise restored urban streams to jump start the recovery process. However, without standardized guidelines that describe reintroduction best practices, some reintroduction programs may create additional problems (e.g., disease spread, genetic homogenization, population loss). To reduce these risks and limit a potential waste of resources, a cautionary approach is warranted. In this paper we summarize current stream reintroduction knowledge and detail best practices for aquatic macroinvertebrate reintroduction in restored urban streams. We provide criteria that managers can use to determine whether reintroduction is appropriate and demonstrate how researchers can use reintroduction as a tool to test hypotheses regarding factors limiting recolonization. We provide guidance for how to set clear reintroduction goals, select donor sites, determine the number of organisms required, establish reintroduction frequency and timing, and overcome challenges associated with monitoring. This framework can help managers create more successful reintroduction programs that can benefit urban stream restoration.

Freshwater Science↗
USGS2024

Helpers show plasticity in their responses to breeder turnover

Nonbreeding helpers can greatly improve the survival of young and the reproductive fitness of breeders in many cooperatively breeding species. Breeder turnover, in turn, can have profound effects on dispersal decisions made by helpers. Despite its importance in explaining group size and predicting the population demography of cooperative breeders, our current understanding of how individual traits influence animal behavior after disruptions to social structure is incomplete particularly for terrestrial mammals. We used 12 yr of genetic sampling and group pedigrees of gray wolves ( Canis lupus ) in Idaho, USA, to ask questions about how breeder turnover affected the apparent decisions by mature helpers (≥2-yr-old) to stay or leave a group over a 1-yr time interval. We found that helpers showed plasticity in their responses to breeder turnover. Most notably, helpers varied by sex and appeared to base dispersal decisions on the sex of the breeder that was lost as well. Male and female helpers stayed in a group slightly more often when there was breeder turnover of the same sex, although males that stayed were often recent adoptees in the group. Males, however, appeared to remain in a group less often when there was breeding female turnover likely because such vacancies were typically filled by related females from the males’ natal group (i.e. inbreeding avoidance). We show that helpers exploit instability in the breeding pair to secure future breeding opportunities for themselves. The confluence of breeder turnover, helper sex, and dispersal and breeding strategies merge to influence group composition in gray wolves.

Idaho↗
USGS2012

SYBR green-based real-time reverse transcription-PCR for typing and subtyping of all hemagglutinin and neuraminidase genes of avian influenza viruses and comparison to standard serological subtyping tests

Continuing outbreaks of H5N1 highly pathogenic (HP) avian influenza virus (AIV) infections of wild birds and poultry worldwide emphasize the need for global surveillance of wild birds. To support the future surveillance activities, we developed a SYBR green-based, real-time reverse transcriptase PCR (rRT-PCR) for detecting nucleoprotein (NP) genes and subtyping 16 hemagglutinin (HA) and 9 neuraminidase (NA) genes simultaneously. Primers were improved by focusing on Eurasian or North American lineage genes; the number of mixed-base positions per primer was set to five or fewer, and the concentration of each primer set was optimized empirically. Also, 30 cycles of amplification of 1:10 dilutions of cDNAs from cultured viruses effectively reduced minor cross- or nonspecific reactions. Under these conditions, 346 HA and 345 NA genes of 349 AIVs were detected, with average sensitivities of NP, HA, and NA genes of 10 1.5 , 10 2.3 , and 10 3.1 50% egg infective doses, respectively. Utility of rRT-PCR for subtyping AIVs was compared with that of current standard serological tests by using 104 recent migratory duck virus isolates. As a result, all HA genes and 99% of the NA genes were genetically subtyped, while only 45% of HA genes and 74% of NA genes were serologically subtyped. Additionally, direct subtyping of AIVs in fecal samples was possible by 40 cycles of amplification: approximately 70% of HA and NA genes of NP gene-positive samples were successfully subtyped. This validation study indicates that rRT-PCR with optimized primers and reaction conditions is a powerful tool for subtyping varied AIVs in clinical and cultured samples.

Journal of Clinical Microbiology↗
USGS2020

Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease

Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases. We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white-tailed deer ( Odocoileus virginianus ) in the Mid-Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units. Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle ( F ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however. Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity. These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.

Maryland, Pennsylvania, Virginia↗
USGS2005

Phylogeographic patterns of Hawaiian Megalagrion damselflies (Odonata: Coenagrionidae) correlate with Pleistocene island boundaries

The Pleistocene geological history of the Hawaiian Islands is becoming well understood. Numerous predictions about the influence of this history on the genetic diversity of Hawaiian organisms have been made, including the idea that changing sea levels would lead to the genetic differentiation of populations isolated on individual volcanoes during high sea stands. Here, we analyse DNA sequence data from two closely related, endemic Hawaiian damselfly species in order to test these predictions, and generate novel insights into the effects of Pleistocene glaciation and climate change on island organisms. Megalagrion xanthomelas and Megalagrion pacificum are currently restricted to five islands, including three islands of the Maui Nui super-island complex (Molokai, Lanai, and Maui) that were connected during periods of Pleistocene glaciation, and Hawaii island, which has never been subdivided. Maui Nui and Hawaii are effectively a controlled, natural experiment on the genetic effects of Pleistocene sea level change. We confirm well-defined morphological species boundaries using data from the nuclear EF-1?? gene and show that the species are reciprocally monophyletic. We perform phylogeographic analyses of 663 base pairs (bp) of cytochrome oxidase subunit II (COII) gene sequence data from 157 individuals representing 25 populations. Our results point to the importance of Pleistocene land bridges and historical island habitat availability in maintaining inter-island gene flow. We also propose that repeated bottlenecks on Maui Nui caused by sea level change and restricted habitat availability are likely responsible for low genetic diversity there. An island analogue to northern genetic purity and southern diversity is proposed, whereby islands with little suitable habitat exhibit genetic purity while islands with more exhibit genetic diversity. ?? 2005 Blackwell Publishing Ltd.

Molecular Ecology↗
USGS2016

Available data support protection of the Southwestern Willow Flycatcher under the Endangered Species Act

Zink (2015) argued there was no evidence for genetic, morphological, or ecological differentiation between the federally endangered Southwestern Willow Flycatcher ( Empidonax traillii extimus ) and other Willow Flycatcher subspecies. Using the same data, we show there is a step-cline in both the frequency of a mtDNA haplotype and in plumage variation roughly concordant with the currently recognized boundary between E. t. extimus and E. t adastus, the subspecies with which it shares the longest common boundary. The geographical pattern of plumage variation is also concordant with previous song analyses differentiating those 2 subspecies and identified birds in one low-latitude, high-elevation site in Arizona as the northern subspecies. We also demonstrate that the ecological niche modeling approach used by Zink yields the same result whether applied to the 2 flycatcher subspecies or to 2 unrelated species, E. t. extimus and Yellow Warbler ( Setophaga petechia ). As a result, any interpretation of those results as evidence for lack of ecological niche differentiation among Willow Flycatcher subspecies would also indicate no differentiation among recognized species and would therefore be an inappropriate standard for delineating subspecies. We agree that many analytical techniques now available to examine genetic, morphological, and ecological differentiation would improve our understanding of the distinctness (or lack thereof) of Willow Flycatcher subspecies, but we argue that currently available evidence supports protection of the Southwestern Willow Flycatcher under the Endangered Species Act.

The Condor↗
USGS2021

Increasing comparability among coral bleaching experiments

Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross-study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldwide.

Ecological Applications↗
USGS2014

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

PLoS ONE↗