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At least 1,531 records · Page 85Linked to original sources

USGS2009

Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure

A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare ( F ST msat = 0.43, Φ STmtDNA = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1–3.9 alleles/locus; H e = 0.06–0.53) and mtDNA ( h = 0.00 for most drainages; π = 0.000–0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

Gulf of Mexico↗

USGS2011

Comparative mitochondrial genetics of North American and Eurasian mergansers with an emphasis on the endangered scaly-sided merganser (Mergus squamatus)

The scaly-sided merganser, Mergus squamatus , is considered one of the most threatened sea duck species in the Palearctic with limited breeding and wintering distribution in China and Russia. To provide information for future conservation efforts, we sequenced a portion of the mitochondrial (mt) DNA control region in four species of mergansers and three additional sea duck taxa to characterize the evolutionary history of the scaly-sided merganser, infer population trends that may have led to its limited geographic distribution, and to compare indices of genetic diversity among species of mergansers. Scaly-sided mergansers exhibit substantially lower levels of mtDNA genetic diversity ( h = 0.292, π = 0.0007) than other closely related sea ducks and many other avian taxa. The four haplotypes observed differed by a single base pair suggesting that the species has not experienced a recent population decline but has instead been at a low population level for some time. A phylogenetic analysis placed the scaly-sided merganser basal to North American and European forms of the common merganser, M. merganser . Our inclusion of a small number of male samples doubled the number of mtDNA haplotypes observed, suggesting that additional genetic variation likely exists within the global population if there is immigration of males from unsampled breeding areas.

Conservation Genetics↗

USGS2011

Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi : implications for conservation

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei’s DS, populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention.

Idaho, Montana↗

USGS2011

Demographic and genetic status of an isolated population of bog turtles (Glyptemys muhlenbergii): Implications for managing small populations of long-lived animals

In this study, we sought to determine the population stability and genetic diversity of one isolated population of the federally-threatened bog turtle ( Glyptemys muhlenbergii ) in North Carolina. Using capture–recapture data, we estimated adult survival and population growth rate from 1992 to 2007. We found that the population decreased from an estimated 36 adult turtles in 1994 to approximately 11 adult turtles in 2007. We found a constant adult survival of 0.893 (SE = 0.018, 95% confidence interval, 0.853–0.924) between 1992 and 2007. Using 18 microsatellite markers, we compared the genetic status of this population with five other bog turtle populations. The target population displayed allelic richness (4.8 ± 0.5) and observed heterozygosity (0.619 ± 0.064) within the range of the other bog turtle populations. Coalescent analysis of population growth rate, effective population size, and timing of population structuring event also indicated the genetics of the target population were comparable to the other populations studied. Estimates of effective population size were a proportion of the census size in all populations except the target population, in which the effective population size was larger than the census size (30 turtles vs. 11 turtles). We attribute the high genetic diversity in the target population to the presence of multiple generations of old turtles. This study illustrates that the demographic status of populations of long-lived species may not be reflected genetically if a decline occurred recently. Consequently, the genetic integrity of populations of long-lived animals experiencing rapid demographic bottlenecks may be preserved through conservation efforts effective in addressing demographic problems.

Conservation Genetics↗

USGS2014

Regional differentiation among populations of the Diamondback terrapin ( Malaclemys terrapin )

The Diamondback terrapin (Malaclemys terrapin) is a brackish-water turtle species whose populations have been fragmented due to anthropogenic activity such as development of coastal habitat and entrapment in commercial blue crab (Callinectes sapidus) fishing gear. Genetic analyses can improve conservation efforts for the long-term protection of the species. We used microsatellite DNA analysis to investigate levels of gene flow among and genetic variability within 21 geographically separate collections of the species distributed from Massachusetts to Texas. Quantified levels of genetic variability (allelic diversity, genotypic frequencies, and heterozygosity) revealed three zones of genetic discontinuity, resulting in four discrete populations: Northeast Atlantic, Coastal Mid-Atlantic, Florida and Texas/Louisiana. The average number of alleles and expected heterozygosity for the four genetic clusters were N A = 6.54 and H E = 0.050, respectively. However, the geographic boundaries of the populations did not correspond to accepted terrapin subspecies limits. Our results illuminate not only the need to sample terrapins in additional sites, specifically in the southeast, but also the necessity for allowing uninterrupted gene flow among population groupings to preserve current levels of genetic diversity.

Conservation Genetics↗

USGS2019

Temporal variation in genetic structure within the threatened spectacled eider

We examined the genetic structure of the threatened spectacled eider 14–18 years after the initial assessment to evaluate the influence of population recovery on diversity. Concordant with the initial assessment, spectacled eiders were highly structured at mitochondrial (mt) DNA and lacked differentiation at microsatellite loci. The degree and spatial pattern of structure has changed at mtDNA; a 33.0–40.3% reduction in overall FST and ΦST, respectively, and a marked reduction in pairwise FST (-83.1 to -91.4%) among Alaska sites. Reduction in genetic structure is suggestive of increased female dispersal within Alaska. These findings highlight the importance of reevaluating genetic diversity as species recover from declines as microevolutionary and demographic processes are dynamic and continually shape associations among populations.

Alaska↗

USGS2021

Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States

Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose ( Alces alces ) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.

Conservation Genetics↗

USGS2022

Population genetics of three at-risk tiger beetles Habroscelimorpha dorsalis dorsalis, H. d. media, and Ellipsoptera puritana

Many tiger beetles (Family Cicindelidae ) are critically imperiled due to their dependence on small patches of suitable habitat that are frequently threatened by natural and anthropogenic disturbances. In the eastern United States, conservation of three tiger beetles - Habroscelimorpha dorsalis dorsalis , H. dorsalis media , and Ellipsoptera puritana - has been inhibited by the absence of population genetic information that is needed for effective recovery planning and potential reintroductions. Using microsatellite panels, we performed population genetic analyses and compared patterns in diversity and differentiation within and between taxa. Nearly all collections of the three taxa had less observed heterozygosity than expected under Hardy-Weinberg Equilibrium, and there was a strong latitudinal gradient in genetic diversity in H. d. dorsalis distributed along the eastern and western shores of the Chesapeake Bay. We also found clear spatial patterns of genetic differentiation which reflected strong isolation-by-distance within all three taxa and between collections of H. d. dorsalis and H. d. media. However, there was evidence of admixture in current (mouth of the Chesapeake Bay) and former (coastal New Jersey) contact zones of H. d. dorsalis and H. d. media . Taken together, our study suggests that relatively few adult tiger beetles may maintain many populations, and that gene flow among nearby habitat patches is common in all three taxa – a characteristic that may help tiger beetles persist in dynamic coastal environments. Results of our analyses can be used to support conservation and management by identifying the spatial scale of metapopulation connectivity and locating populations at the greatest risk of extirpation.

Maryland, Virginia↗

USGS2005

Benthic invertebrate community structure is influenced by forest succession after clearcut logging in southeastern Alaska

To assess the effects of timber harvesting on headwater streams in upland forests, benthic community structure was contrasted among four dominant forest management types (old growth, red alder-dominated young growth, conifer-dominated young growth, clearcut) and instream habitats (woody debris, cobble, gravel) in southeastern Alaska. Benthos in streams of previously harvested areas resulted in increased richness, densities and biomass relative to old growth types, particularly in young growth stands with a red alder-dominated riparian canopy. Woody debris and gravel habitats supported a combination of higher densities and biomass of invertebrates than cobble habitats. In addition, woody debris also supported a richer and more diverse invertebrate fauna than either cobble or gravel substrates. Maintaining both a woody debris source and a red alder component in regenerating riparian forests following timber harvesting should support greater invertebrate densities and diversity following clearcutting. ?? Springer 2005.

Hydrobiologia↗

USGS2010

Challenges in merging fisheries research and management: The Upper Mississippi River experience

The Upper Mississippi River System (UMRS) is a geographically diverse basin extending 10?? north temperate latitude that has produced fishes for humans for millennia. During European colonization through the present, the UMRS has been modified to meet multiple demands such as navigation and flood control. Invasive species, notably the common carp, have dominated fisheries in both positive and negative ways. Through time, environmental decline plus reduced economic incentives have degraded opportunities for fishery production. A renewed focus on fisheries in the UMRS may be dawning. Commercial harvest and corresponding economic value of native and non-native species along the river corridor fluctuates but appears to be increasing. Recreational use will depend on access and societal perceptions of the river. Interactions (e. g., disease and invasive species transmission) among fish assemblages within the UMRS, the Great Lakes, and other lakes and rivers are rising. Data collection for fisheries has varied in intensity and contiguousness through time, although resources for research and management may be growing. As fisheries production likely relies on the interconnectivity of fish populations and associated ecosystem processes among river reaches (e. g., between the pooled and unpooled UMRS), species-level processes such as genetics, life-history interactions, and migratory behavior need to be placed in the context of broad ecosystem- and landscape-scale restoration. Formal communication among a diverse group of researchers, managers, and public stakeholders crossing geographic and disciplinary boundaries is necessary through peer-reviewed publications, moderated interactions, and the embrace of emerging information technologies. ?? Springer Science+Business Media B.V. 2010.

Hydrobiologia↗

USGS2025

Responses of larval fish and zooplankton to whole-lake 2,4-D herbicide treatments used to control Eurasian watermilfoil in northern Wisconsin lakes

In North America, Eurasian watermilfoil Myriophyllum spicatum is one of the most widespread non-native aquatic plant species in freshwater ecosystems. Applications of 2,4-dichlorophenoxyacetic acid (2,4-D) herbicides are often utilized to control Eurasian watermilfoil. Herbicide applications may have unintended effects on non-target organisms like zooplankton and fish, but these effects are poorly understood. Our objectives were to determine if whole-lake 2,4-D herbicide treatments (epilimnetic target rate = 0.3 ppm) used to control Eurasian watermilfoil affected (1) density, diversity, and size of zooplankton and (2) density, diversity, and growth of larval fishes in three northern Wisconsin lakes when compared to trends observed in three untreated reference lakes. Average peak concentrations of 2,4-D following applications ranged from 0.152 to 0.257 ppm. We found no statistically significant evidence that the applications influenced the zooplankton and larval fish metrics we examined, but subtle responses to the herbicides may not have been detected given the inherent variation in our response metrics. Additional replication and research are needed to assess responses to higher concentrations and repeated applications over time and to document responses across a broader range of lake types and fish communities.

Wisconsin↗

USGS2007

Influence of landscape structure on reef fish assemblages

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

Landscape Ecology↗

USGS2015

Climate-induced lake drying causes heterogeneous reductions in waterfowl species richness

Context Lake size has declined on breeding grounds for international populations of waterfowl. Objectives Our objectives were to (1) model the relationship between waterfowl species richness and lake size; (2) use the model and trends in lake size to project historical, contemporary, and future richness at 2500+ lakes; (3) evaluate mechanisms for the species–area relationship (SAR); and (4) identify species most vulnerable to shrinking lakes. Methods Monte Carlo simulations of the richness model were used to generate projections. Correlations between richness and both lake size and habitat diversity were compared to identify mechanisms for the SAR. Patterns of nestedness were used to identify vulnerable species. Results Species richness was greatest at lakes that were larger, closer to rivers, had more wetlands along their perimeters and were within 5 km of a large lake. Average richness per lake was projected to decline by 11 % from 1986 to 2050 but was heterogeneous across sub-regions and lakes. Richness in sub-regions with species-rich lakes was projected to remain stable, while richness in the sub-region with species-poor lakes was projected to decline. Lake size had a greater effect on richness than did habitat diversity, suggesting that large lakes have more species because they provide more habitat but not more habitat types. The vulnerability of species to shrinking lakes was related to species rarity rather than foraging guild. Conclusions Our maps of projected changes in species richness and rank-ordered list of species most vulnerable to shrinking lakes can be used to identify targets for conservation or monitoring.

Landscape Ecology↗

USGS2022

Effects of an early mass-flowering crop on wild bee communities and traits in power line corridors vary with blooming plants and landscape context

Context Power line corridors have been repeatedly assessed as habitat for wild bees; however, few studies have examined them as bee habitat relative to nearby crop fields and surrounding landscape context. Objectives We surveyed bee communities in power line corridors near to and isolated from lowbush blueberry fields in two landscape contexts in Maine, U.S.A. We examined the influences of blooming plant abundance and diversity and bee life-history traits including sociality, nesting preference, and body size. Methods We surveyed wild bees and blooming plants in power line corridors from 2013 to 2015. We calculated landscape composition surrounding sites at multiple scales and gathered bee trait information from the literature. We assessed differences in bee communities owing to landscape context with generalized linear models. Results We collected 125 wild bee species and observed a rare plant-pollinator relationship within power line corridors. We found greater bee abundance and species richness throughout a complex, resource-rich landscape, while mass-flowering lowbush blueberry fields enhanced bee species richness only in a simple, resource-poor landscape. Landscape composition and blooming plant diversity varied with landscape context, though only landscape composition influenced bee communities. Solitary and ground-nesting species were more sensitive to landscape context than social or cavity-nesting species. Conclusions Power line corridors provide crucial refugia for crop pollinating wild bees in agricultural landscapes with resource-poor natural habitat, while bees may selectively forage in power line corridors within agricultural landscapes containing resource-rich natural habitat. We found high-quality forage within corridors; quantifying nesting resources could clarify corridor use by wild bees.

Maine↗

USGS2021

Machine learning can assign geologic basin to produced water samples using major ion geochemistry

Understanding the geochemistry of waters produced during petroleum extraction is essential to informing the best treatment and reuse options, which can potentially be optimized for a given geologic basin. Here, we used the US Geological Survey’s National Produced Waters Geochemical Database (PWGD) to determine if major ion chemistry could be used to classify accurately a produced water sample to a given geologic basin based on similarities to a given training dataset. Two datasets were derived from the PWGD: one with seven features but more samples (PWGD7), and another with nine features but fewer samples (PWGD9). The seven-feature dataset, prior to randomly generating a training and testing (i.e., validation) dataset, had 58,541 samples, 20 basins, and was classified based on total dissolved solids (TDS), bicarbonate (HCO 3 ), Ca, Na, Cl, Mg, and sulfate (SO 4 ). The nine-feature dataset, prior to randomly splitting into a training and testing (i.e., validation) dataset, contained 33,271 samples, 19 basins, and was classified based on TDS, HCO 3 , Ca, Na, Cl, Mg, SO 4 , pH, and specific gravity. Three supervised machine learning algorithms—Random Forest, k-Nearest Neighbors, and Naïve Bayes—were used to develop multi-class classification models to predict a basin of origin for produced waters using major ion chemistry. After training, the models were tested on three different datasets: Validation7, Validation9, and one based on data absent from the PWGD. Prediction accuracies across the models ranged from 23.5 to 73.5% when tested on the two PWGD-based datasets. A model using the Random Forest algorithm predicted most accurately compared to all other models tested. The models generally predicted basin of origin more accurately on the PWGD7-based dataset than on the PWGD9-based dataset. An additional dataset, which contained data not in the PWGD, was used to test the most accurate model; results suggest that some basins may lack geochemical diversity or may not be well described, while others may be geochemically diverse or are well described. A compelling result of this work is that a produced water basin of origin can be determined using major ions alone and, therefore, deep basinal fluid compositions may not be as variable within a given basin as previously thought. Applications include predicting the geochemistry of produced fluid prior to drilling at different intervals and assigning historical produced water data to a producing basin.

Natural Resources Research↗

USGS2018

Thiamine deficiency in fishes: Causes, consequences, and potential solutions

Thiamine deficiency complex (TDC) is a disorder resulting from the inability to acquire or retain thiamine (vitamin B 1 ) and has been documented in organisms in aquatic ecosystems ranging from the Baltic Sea to the Laurentian Great Lakes. The biological mechanisms leading to TDC emergence may vary among systems, but in fishes, one common outcome is high mortality among early life stages. Here, we review the causes and consequences of thiamine deficiency in fishes and identify potential solutions. First, we examine the biochemical and physiological roles of thiamine in vertebrates and find that thiamine deficiency consistently results in impaired neurological function across diverse taxa. Next, we review natural producers of thiamine, which include bacteria, fungi, and plants, and suggest that thiamine is not currently limiting for most animal species inhabiting natural aquatic environments. A survey of historic occurrences of thiamine deficiency identifies consumption of a thiamine-degrading enzyme, thiaminase, as the primary explanation for low levels of thiamine in individuals and subsequent onset of TDC. Lastly, we review conservation and management strategies for TDC mitigation ranging from evolutionary rescue to managing for a diverse forage base. As recent evidence suggests occurrences of thiamine deficiency may be increasing in frequency, increased awareness and a better mechanistic understanding of the underlying causes associated with thiamine deficiency may help prevent further population declines.

Reviews in Fish Biology and Fisheries↗

USGS2023

Towards vibrant fish populations and sustainable fisheries that benefit all: Learning from the last 30 years to inform the next 30 years

A common goal among fisheries science professionals, stakeholders, and rights holders is to ensure the persistence and resilience of vibrant fish populations and sustainable, equitable fisheries in diverse aquatic ecosystems, from small headwater streams to offshore pelagic waters. Achieving this goal requires a complex intersection of science and management, and a recognition of the interconnections among people, place, and fish that govern these tightly coupled socioecological and sociotechnical systems. The World Fisheries Congress (WFC) convenes every four years and provides a unique global forum to debate and discuss threats, issues, and opportunities facing fish populations and fisheries. The 2021 WFC meeting, hosted remotely in Adelaide, Australia, marked the 30th year since the first meeting was held in Athens, Greece, and provided an opportunity to reflect on progress made in the past 30 years and provide guidance for the future. We assembled a diverse team of individuals involved with the Adelaide WFC and reflected on the major challenges that faced fish and fisheries over the past 30 years, discussed progress toward overcoming those challenges, and then used themes that emerged during the Congress to identify issues and opportunities to improve sustainability in the world's fisheries for the next 30 years. Key future needs and opportunities identified include: rethinking fisheries management systems and modelling approaches, modernizing and integrating assessment and information systems, being responsive and flexible in addressing persistent and emerging threats to fish and fisheries, mainstreaming the human dimension of fisheries, rethinking governance, policy and compliance, and achieving equity and inclusion in fisheries. We also identified a number of cross-cutting themes including better understanding the role of fish as nutrition in a hungry world, adapting to climate change, embracing transdisciplinarity, respecting Indigenous knowledge systems, thinking ahead with foresight science, and working together across scales. By reflecting on the past and thinking about the future, we aim to provide guidance for achieving our mutual goal of sustaining vibrant fish populations and sustainable fisheries that benefit all. We hope that this prospective thinking can serve as a guide to (i) assess progress towards achieving this lofty goal and (ii) refine our path with input from new and emerging voices and approaches in fisheries science, management, and stewardship.

Reviews in Fish Biology and Fisheries↗

USGS2012

Surface properties of the Mars Science Laboratory candidate landing sites: characterization from orbit and predictions

This work describes the interpretation of THEMIS-derived thermal inertia data at the Eberswalde, Gale, Holden, and Mawrth Vallis Mars Science Laboratory (MSL) candidate landing sites and determines how thermophysical variations correspond to morphology and, when apparent, mineralogical diversity. At Eberswalde, the proportion of likely unconsolidated material relative to exposed bedrock or highly indurated surfaces controls the thermal inertia of a given region. At Gale, the majority of the landing site region has a moderate thermal inertia (250 to 410 J m -2 K -1 s -1/2 ), which is likely an indurated surface mixed with unconsolidated materials. The primary difference between higher and moderate thermal inertia surfaces may be due to the amount of mantling material present. Within the mound of stratified material in Gale, layers are distinguished in the thermal inertia data; the MSL rover could be traversing through materials that are both thermophysically and compositionally diverse. The majority of the Holden ellipse has a thermal inertia of 340 to 475 J m -2 K -1 s -1/2 and consists of bed forms with some consolidated material intermixed. Mawrth Vallis has a mean thermal inertia of 310 J m -2 K -1 s -1/2 and a wide variety of materials is present contributing to the moderate thermal inertia surfaces, including a mixture of bedrock, indurated surfaces, bed forms, and unconsolidated fines. Phyllosilicates have been identified at all four candidate landing sites, and these clay-bearing units typically have a similar thermal inertia value (400 to 500 J m -2 K -1 s -1/2 ), suggesting physical properties that are also similar.

Space Science Reviews↗