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At least 163 records · Page 9Linked to original sources
USGS2021

Genetic structure and diversity of the endemic Carolina Madtom and conservation implications

Identification and conservation of genetic diversity within and among freshwater fish populations are important to better manage and conserve imperiled species. The Carolina Madtom Noturus furiosus is a small, nongame catfish that is endemic to the Tar and Neuse River basins of North Carolina. Genetic structure has not been studied in the species, and given recent population declines in both basins, identification of remaining genetic diversity within the species is vital for informing conservation efforts. To assess the status and trends of Carolina Madtom genetic structure, we analyzed genetic markers from 173 individuals to (1) define population genetic structure, (2) assess intra- and interbasin genetic differentiation in the Tar and Neuse River basins, and (3) present management implications to guide conservation efforts. Using 10 microsatellite primers developed for the related Yellowfin Madtom N. flavipinnis , we observed low genetic diversity in Carolina Madtoms. Genotype frequencies within samples were not in Hardy–Weinberg equilibrium, with a deficit of heterozygotes that could be due to family structure, inbreeding, or segregation of null alleles. Mean (±SD) M -ratios for the Tar River (0.414 ± 0.117) and Neuse River (0.117 ± 0.102) basin collections indicated that both populations have experienced recent demographic bottlenecks, with that in the Neuse River basin population being more severe. Effective population size estimates for the respective populations were small, on the order of tens of individuals, driving low genetic diversity within populations. However, the multilocus population differentiation metrics (mean ± SE = 0.135 ± 0.031) and D EST (0.125 ± 0.029) were significantly different from zero ( P < 0.001), indicating significant genetic differentiation between the Tar and Neuse River basin populations. Our findings will inform managers on the status of genetic variation in the Carolina Madtom and will guide conservation toward protective listing and management decisions to maintain the viability of this important endemic species.

North Carolina↗
USGS2001

Difficulties with estimating and interpreting species pools and the implications for understanding patterns of diversity

Evidence has been accumulating that species pools play a major role in regulating variations in small-scale diversity. However, our ability to unambiguously estimate and interpret species pools remains a major impediment to understanding the processes that control patterns of diversity. Two main approaches have been employed to evaluate the relationships between species pools and species diversity. The direct approach has been to estimate the actual sizes of species pools by sampling discrete areas at larger spatial scales and then relating these estimates to samples taken at smaller scales. The indirect approach has been to search for correlations between abiotic environmental factors and patterns of diversity that are indicative of gradients in species pools. Both of these approaches have substantial predictive capability but also have limitations that impair our ability to draw unambiguous interpretations about causal factors. A primary difficulty for the direct approach is in deciding which species in the larger pool of potential species are actually capable of living in a sample. In this regard, the indirect approach requires fewer assumptions and has the ability to detect previously unsuspected gradients in species pools. As with the direct approach, assessing the causes for observed gradients in species pools remains a limitation for the indirect approach. Consideration of experimental studies of potential niches suggests that it may be valuable to distinguish between potential and observed species pools if the role of competitive exclusion is to be fully assessed. This paper concludes by arguing for (1) an increased use of multivariate studies that examine the effects of species pools indirectly and (2) further experimental studies designed to determine potential species pools.

Folia Geobotanica↗
USGS2005

Consequences of harvesting for genetic diversity in American ginseng (Panax quinquefolius L.): A simulation study

American ginseng, Panax quinquefolius L., is one of the most heavily traded medicinal plants in North America. The effect of harvest on genetic diversity in ginseng was measured with a single generation culling simulation program. Culling scenarios included random harvest at varying levels, legal limit random harvest and legal limit mature plant harvest. The legal limit was determined by the proportion of legally harvestable plants per population (% mature plants per population). Random harvest at varying levels resulted in significant loss of genetic diversity, especially allelic richness. Relative to initial levels, average within-population genetic diversity (H e) was significantly lower when plants were culled randomly at the legal limit (Mann-Whitney U = 430, p < 0.001) or when only mature plants were culled (Mann-Whitney U = 394, p < 0.01). Within-population genetic diversity was significantly higher with legal limit mature plant harvest (H e = 0.068) than when plants were culled randomly at the legal limit (H e = 0.064; U = 202, p < 0.01). Based on these simulations of harvest over one generation, we recommend that harvesting fewer than the proportion of mature plants could reduce the negative genetic effects of harvest on ginseng populations. ?? Springer 2005.

Biodiversity and Conservation↗
USGS2010

Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations. ?? 2010 US Government.

Conservation Genetics↗
USGS2018

Rare long-distance dispersal of the Island Night Lizard, Xantusia riversiana, maintains high diversity in a fragmented environment

The Island Night Lizard ( Xantusia riversiana ) is endemic to three of the Channel Islands off the coast of California, USA. Introduced species such as goats, sheep, and cats have profoundly affected the fauna and flora of the islands for over 150 years, but most of these non-native species have been recently removed. We measured the distribution of genetic diversity in Island Night Lizards across San Nicolas Island using DNA microsatellites to assess the impacts of historical habitat change on effective population size, gene flow, and population divergence; to provide baseline data for future monitoring of genetic diversity; and to provide recommendations to inform the restoration of degraded habitat. Despite a history of profound anthropogenic habitat disturbance, genetic diversity was high within sites, and there was no evidence of population bottlenecks. Divergence between sites was extraordinarily high, as expected for this sedentary species. Landscape resistance modeling using circuit theory showed that unsuitable habitat is relatively permeable to gene flow compared to suitable habitat, and yet populations separated by very short geographic distances remain genetically distinct. We found no evidence of a need for short-term intervention such as artificial translocations to maintain genetic diversity. Instead, we suggest that management should focus on maintaining, improving, and increasing habitat, especially in creating patches of habitat to link existing sites.

California↗
USGS2021

Authors’ reply to letter to the editor: Continued improvement to genetic diversity indicator for CBD

We appreciate the encouraging response to our call for indicators for genetic diversity within the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity, CBD (Laikre et al. 2020 ; Hoban et al. 2020 ). In agreement with us, Frankham ( 2021 ) highlights the urgent necessity for the CBD to include an indicator that tracks the maintenance of genetic diversity within populations of all species—wild and domestic. Draft CBD Headline indicators (which all CBD Parties will need to report) do not include genetic diversity within populations of wild species (CBD/SBSTTA/24/3Add.1).

Conservation Genetics↗
USGS2008

Loss of genetic connectivity and diversity in urban microreserves in a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus n. sp. "santa monica")

Microreserves may be useful in protecting native arthropod diversity in urbanized landscapes. However, species that do not disperse through the urban matrix may eventually be lost from these fragments. Population extinctions may be precipitated by an increase in genetic differentiation among fragments and loss of genetic diversity within fragments, and these effects should become stronger with time. We analyzed population genetic structure in the dispersal limited Jerusalem cricket Stenopelmatus n. sp. "santa monica" in the Santa Monica Mountains and Simi Hills north of Los Angeles, California (CA), to determine the impacts of fragmentation over the past 70 years. MtDNA divergence was greater among urban fragments than within contiguous habitat and was positively correlated with fragment age. MtDNA genetic diversity within fragments increased with fragment size and decreased with fragment age. Genetic divergence across 38 anonymous nuclear Inter-Simple Sequence Repeat (ISSR) loci was influenced by the presence of major highways and highway age, but there was no effect of additional urban fragmentation. ISSR diversity was not correlated with fragment size or age. Differing results between markers may be due to male-biased dispersal, or different effective population sizes, sorting rates, or mutation rates among sampled genes. Results suggest that genetic connectivity among populations has been disrupted by highways and urban development, prior to declines in local population sizes. We emphasize that genetic connectivity can rapidly erode in fragmented landscapes and that flightless arthropods can serve as sensitive indicators for these effects. ?? Springer Science+Business Media B.V. 2008.

Journal of Insect Conservation↗
USGS2023

The effects of landscape and yard features on mammal diversity in residential yards within Northwest Arkansas, USA

The human footprint is rapidly expanding, and wildlife habitat is continuously being converted to human residential properties. Surviving wildlife that reside in developing areas are displaced to nearby undeveloped areas. However, some animals can co-exist with humans and acquire the necessary resources (food, water, shelter) within the human environment. This ability to coexist may be particularly true when development is low intensity, as in residential suburban yards. Yards are individually managed “greenspaces” that can provide a range of food (e.g., bird feeders, compost, gardens), water (bird baths and garden ponds), and shelter (e.g., brush-piles, outbuildings) resources and are surrounded by varying landscape cover. To evaluate which residential landscape and yard features influence the richness and diversity of mammalian herbivores and mesopredators; we deployed wildlife game cameras throughout Northwestern Arkansas, USA in 46 residential yards in summer 2021 and 96 yards in summer 2022. We found that mesopredator diversity had a negative relationship with fences and was positively influenced by the number of bird feeders present in a yard. Mesopredator richness increased with the amount of forest within 400 m of the camera. Herbivore diversity and richness were positively correlated to the area of forest within 400 m surrounding yard and by garden area within yards, respectively. Our results suggest that while landscape does play a role in the presence of wildlife in a residential area, homeowners also have agency over the richness and diversity of mammals using their yards based on the features they create or maintain on their properties.

Arkansas↗
USGS2022

The role of organic matter diversity on the Re-Os systematics of organic-rich sedimentary units: Insights into the controls of isochron age determinations from the lacustrine Green River Formation

The range of 187 Re/ 188 Os values measured from samples of five organic-rich lacustrine mudstones units in the Eocene Green River Formation in the easternmost Uinta Basin covaries with organic matter diversity driven by changing water column conditions. A set of samples from the Douglas Creek Member has the highest pristane/phytane ratio and lowest β-carotane/ n -C 30 ratio compared to overlying units, indicating deposition in an oxic-anoxic environment with low salinity that would have allowed for the accumulation of a diverse assemblage of aquatic organisms. These samples define the broadest 187 Re/ 188 Os range of 1504. In contrast, samples from the R6 and Mahogany zones possess lower pristane/phytane ratios and higher β-carotane/ n -C 30 ratios indicating deposition in a more restricted lacustrine environment with elevated salinities and alkalinities that would have limited aquatic organic matter diversity. The R6 and Mahogany zones have the narrowest range of 187 Re/ 188 Os values measured in this study of 254.9 and 154.6, respectively. As noted by previous workers, these results suggest that organic matter diversity plays a primary role in determining the range of 187 Re/ 188 Os ratios in a sample set, and in turn the uncertainty of Re-Os age determinations from organic-rich sedimentary rocks. The Re-Os data from the R3 zone and R6 zone yield ages of 49.7 ± 3.4 Ma and 42.0 ± 18 Ma, respectively, which are statistically indistinguishable based on 2σ uncertainty from three previously reported Re-Os age determinations and those provided by 40 Ar/ 39 Ar geochronology of interbedded volcanic ash beds. Although the age uncertainty is high, these findings further highlight the importance of Re-Os geochronology in lacustrine basins, particularly those with thick mudstone successions that lack volcanic ash layers, reliable biostratigraphy , or magnetostratigraphic control. In these cases, even ages with large uncertainties can be useful to constrain burial history and thermal history models. Together, the initial 187 Os/ 188 Os ratios of five sets of samples analyzed from the Uinta Basin define the largest Os isotope stratigraphic record from any lacustrine basin compiled to date and record a shift from a value of 1.40 to 1.48 between the R3 and R4 zones in the lower part of the Parachute Creek Member. This small shift may signify a change in the chemical weathering products that entered the lake preserved 20 to 50 m above the contact between the Douglas Creek and the lower Parachute Creek members during a period when the basin transitioned from a shallow lake with mostly open hydrology to an alkaline lake with more frequent basin restrictions.

Colorado, Utah, Wyoming↗
USGS2019

Hydrodynamic controls on sediment retention in an emerging diversion-fed delta

The morphodynamics of river-dominated deltas are largely controlled by the supply and retention of sediment within deltaic wetlands and the rate of relative sea-level rise. Yet, sediment budgets for deltas are often poorly constrained. In the Mississippi River Delta, a system rapidly losing land due to natural and anthropogenic causes, restoration efforts seek to build new land through the use of river diversions. At the Davis Pond Freshwater Diversion, a new crevasse splay has emerged since construction was completed in 2002. Here, we use beryllium-7 activity in sediment cores and USGS measurements of discharge and turbidity to calculate seasonal sediment input, deposition, and retention within the vegetated Davis Pond receiving basin. In winter/spring 2015, which included an experimental period of high discharge through the diversion, Davis Pond received 106,800 metric tons of sediment, 44% of which was retained within the basin. During this time, mean flow velocity was 0.21 m s −1 and mean turbidity was 56 formazin nephelometric units (FNU). In summer/fall 2015, the Davis Pond basin received 35,900 metric tons of sediment, 81% of which was retained. Mean flow velocity in summer/fall was 0.10 m s −1 and mean turbidity was 55 FNU. The increase in sediment retention from winter/spring 2015 to summer/fall 2015 may be due in part to the corresponding drop in water flow velocity, which allowed more sediment to settle out of suspension. Although high water discharge increases sediment input and deposition, increased turbulence associated with higher current velocity appears to increase sediment throughput and thereby decrease the sediment trapping efficiency. Sediment retention in Davis Pond is on the high end of the range seen in deltaic wetlands, perhaps due to the enclosed geometry of the receiving basin. Future diversion design and operation should target moderate water discharge and flow velocities in order to jointly maximize sediment deposition and retention and provide optimal conditions for delta growth.

Louisiana↗
USGS2017

Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

Lake Takvatn↗
USGS2010

Genetic diversity of lake whitefish in lakes Michigan and Huron: sampling, standardization, and research priorities

We combined data from two laboratories to increase the spatial extent of a genetic data set for lake whitefish Coregonus clupeaformis from lakes Huron and Michigan and saw that genetic diversity was greatest between lakes, but that there was also structuring within lakes. Low diversity among stocks may be a reflection of relatively recent colonization of the Great Lakes, but other factors such as recent population fluctuation and localized stresses such as lamprey predation or heavy exploitation may also have a homogenizing effect. Our data suggested that there is asymmetrical movement of lake whitefish between Lake Huron and Lake Michigan; more genotypes associated with Lake Michigan were observed in Lake Huron. Adding additional collections to the calibrated set will allow further examination of diversity in other Great Lakes, answer questions regarding movement among lakes, and estimate contributions of stocks to commercial yields. As the picture of genetic diversity and population structure of lake whitefish in the Great Lakes region emerges, we need to develop methods to combine data types to help identify important areas for biodiversity and thus conservation. Adding genetic data to existing models will increase the precision of predictions of the impacts of new stresses and changes in existing pressures on an ecologically and commercially important species.

Journal of Great Lakes Research↗
USGS2017

The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

Virus Research↗
USGS2012

GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

Oklahoma↗
USGS2000

Monitoring shifts in plant diversity in response to climate change: A method for landscapes

Improved sampling designs are needed to detect, monitor, and predict plant migrations and plant diversity changes caused by climate change and other human activities. We propose a methodology based on multi-scale vegetation plots established across forest ecotones which provide baseline data on patterns of plant diversity, invasions of exotic plant species, and plant migrations at landscape scales in Rocky Mountain National Park, Colorado, USA. We established forty two 1000-m 2 plots in relatively homogeneous forest types and the ecotones between them on 14 vegetation transects. We found that 64% of the variance in understory species distributions at landscape scales were described generally by gradients of elevation and under-canopy solar radiation. Superimposed on broad-scale climatic gradients are small-scale gradients characterized by patches of light, pockets of fertile soil, and zones of high soil moisture. Eighteen of the 42 plots contained at least one exotic species; monitoring exotic plant invasions provides a means to assess changes in native plant diversity and plant migrations. Plant species showed weak affinities to overstory vegetation types, with 43% of the plant species found in three or more vegetation types. Replicate transects along several environmental gradients may provide the means to monitor plant diversity and species migrations at landscape scales because: (1) ecotones may play crucial roles in expanding the geophysiological ranges of many plant species; (2) low affinities of understory species to overstory forest types may predispose vegetation types to be resilient to rapid environmental change; and (3) ecotones may help buffer plant species from extirpation and extinction.

Biodiversity and Conservation↗
USGS2001

Rapid assessment of butterfly diversity in a montane landscape

We present the results of a rapid assessment of butterfly diversity in the 754 ha Beaver Meadows study area in Rocky Mountain National Park, Larimer County, Colorado. We measured butterfly species richness and relative abundance as part of a landscape-scale investigation of diversity patterns involving several groups of organisms. A stratified random sampling design was used to include replication in both rare and common vegetation types. We recorded 49 butterfly species from the twenty-four 0.1 ha plots that were sampled four times during June, July, and August 1996. Butterfly species richness, diversity, and uniqueness were highest in quaking aspen ( Populus tremuloides Michaux) groves and wet meadows, which occupy only a small proportion of the studied landscape. This result supports the suggestion that aspen areas represent ‘hotspots’ of biological diversity in this montane landscape. Patterns of butterfly species richness were positively correlated with total vascular plant species richness ( r = 0.69; P < 0.001), and native plant species richness ( r = 0.64; P < 0.001). However, exotic plant species richness ( r = 0.70; P < 0.001) and the cover of exotic plant species ( r = 0.70; P < 0.001) were the best predictors of butterfly species richness.

Colorado↗
USGS2014

Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish ( Lepomis cyanellus ) and Creek Chub ( Semotilus atromaculatus ) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

West Virginia↗
USGS2023

Reduction of genetic diversity in ‘Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the ‘Alalā, or Hawaiian crow ( Corvus hawaiiensis ), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if ‘Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when ‘Alalā were more numerous, to samples taken between 1973 and 1998, when ‘Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.

Hawaii↗