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USGS1961

Graphic and algebraic solutions of the discordant lead-uranium age problem

Uranium-bearing minerals that give lead-uranium and lead—lead ages that are essentially in agreement, i.e. concordant, generally are considered to have had a relatively simple geologic history and to have been unaltered since their deposition. The concordant ages obtained on such materials are, therefore, assumed to approach closely the actual age of the minerals. Many uranium-bearing samples, particularly uranium ores, give the following discordant age sequences; Pb 206 U 238 < Pb 207 U 235 ⪡ Pb 207 Pb 206 "> Pb 206 U 238 <Pb 207 U 235 ⪡Pb 207 Pb 206 or, less frequently, Pb 207 Pb 206 ⪡ Pb 207 U 235 < Pb 206 U 238 "> Pb 207 Pb 206 ⪡Pb 207 U 235 <Pb 206 U 238 . These discordant age sequences have been attributed most often to uncertainties in the common lead correction, selective loss of radio-active daughter products, loss or gain of lead or uranium, or contamination by an older generation of radiogenic lead. The evaluation of discordant lead isotope age data may be separated into two operations. The first operation, with which this paper is concerned, is mechanical in nature and involves the calculation of the different possible concordant ages corresponding to the various processes assumed to have produced the discordant ages. The second operation is more difficult to define and requires, in part, some personal judgement. It includes a synthesis of the possible concordant age solutions with other independent geologic and isotopic evidence. The concordant age ultimately chosen as most acceptable should be consistent not only with the known events in the geologic history of the area, the age relations of the enclosing rocks, and the mineralogic and paragenetic evidence, but also with other independent age measurements and the isotopic data obtained on the lead in related or associated non-radioactive minerals. The calculation of the possible concordant ages from discordant age data has been greatly simplified by Wetherill's graphical method of plotting the mole ratios of radiogenic Pb 206 U 238 "> Pb 206 U 238 ( N 206 N 238 "> N 206 N 238 ) vs. radiogenic Pb 207 U 235 "> Pb 207 U 235 ( N 207 N 235 "> N 207 N 235 ) after correcting for the contaminating common Pb 206 and Pb 207 . The linear relationships noted in this graphical procedure have been extended to plots of the mole ratios of total Pb 206 U 238 "> Pb 206 U 238 ( t N 206 N 238 "> t N 206 N 238 ) vs. total Pb 207 U 235 "> Pb 207 U 235 ( t N 207 N 235 "> t N 207 N 235 ). This modification permits the calculation of concordant ages for unaltered samples using only the Pb 207 Pb 206 "> Pb 207 Pb 206 ratio of the contaminating common lead. If isotopic data are available for two samples of the same age, x and y , from the same or related deposits or outcrops, graphs of the normalized difference ratios [ ( N 206 N 204 )x − ( N 206 N 204 )y ( N 238 N 204 )x −( N 238 N 204 )y ] vs. [ ( N 207 N 204 )x − ( N 207 N 204 )y ( N 235 N 204 )x −( N 235 N 204 )y ] "> [(N 206 N 204 )x − (N 206 N 204 )y(N 238 N 204 )x −(N 238 N 204 )y] vs. [(N 207 N 204 )x − (N 207 N 204 )y(N 235 N 204 )x −(N 235 N 204 )y] can give concordant ages corrected for unknown amounts of a common lead with an unknown Pb 207 / Pb 206 ratio. (If thorium is absent the difference ratios may be normalized with the more abundant index isotope, Pb 208 .) Similar plots of tho normalized, difference ratios for three genetically related samples ( x − y ) and( x − z ), will give concordant ages corrected, in addition, for either one unknown period of past alteration or initial contamination by an older generation of radiogenic lead of unknown Pb 207 /Pb 206 ratio. Practical numerical solutions for many of tho concordant age calculations are not currently available. However, the algebraic equivalents of these new graphical methods give equations which may be programmed for computing machines. For geologically probable parameters the equations of higher order have two positive real roots that rapidly converge on the exact concordant ages corrected for original radiogenic lead and for loss or gain of lead or uranium. Modifications of these general age equations expanded only to the second degree have been derived for use with desk calculators. These graphical and algebraic methods clearly suggest both the type and minimum number of samples necessary for adequate mathematical analysis of discordant lead isotope age data. This mathematical treatment also makes it clear that discordant lead isotope data alone cannot provide the basis for the choice of one of the possible concordant age solutions. The new equations, in particular, provide an incentive to improve our physical constants, analytical techniques and sampling methods in order that we may derive all of the useful geologic information that is available in a comprehensive lead isotope age study.

Geochimica et Cosmochimica Acta↗

USGS2001

Artificial insemination in captive Whooping Cranes: Results from genetic analyses

Artificial insemination has been used frequently in the captive whooping crane (Grus americana) population. In the 1980s, it was necessary at times to inseminate females with semen from several males during the breeding season or with semen from multiple males simultaneously due to unknown sperm viability of the breeding males. The goals of this study were to apply microsatellite DNA profiles to resolve uncertain paternities and to use these results to evaluate the current paternity assignment assumptions used by captive managers. Microsatellite DNA profiles were successful in resolving 20 of 23 paternity questions. When resolved paternities were coupled with data on insemination timing, substantial information was revealed on fertilization timing in captive whooping cranes. Delayed fertilization from inseminations 6+ days pre-oviposition suggests capability of sperm storage.

Zoo Biology↗

USGS2007

Sperm cryopreservation in fish and shellfish

Initial success in sperm cryopreservation came at about the same time for aquatic species and livestock. However, in the 50-plus years since then cryopreserved sperm of livestock has grown into a billion-dollar global industry, while despite work in some 200 species with well over 200 published reports, cryopreservation of aquatic species sperm remains essentially a research activity with little commercial application. Most research has focused on large-bodied culture and sport fishes, such as salmonids, carps, and catfishes, and mollusks such as commercially important oyster and abalone species. However, only a handful of studies have addressed sperm cryopreservation in small fishes, such as zebrafish, and in endangered species. Overall, this work has yielded techniques that are being applied with varying levels of success around the world. Barriers to expanded application include a diverse and widely distributed literature base, technical problems, small sperm volumes, variable results, a general lack of access to the technology, and most importantly, the lack of standardization in practices and reporting. The benefits of cryopreservation include at least five levels of improvements for existing industries and for creation of new industries. First, cryopreservation can be used to improve existing hatchery operations by providing sperm on demand and simplifying the timing of induced spawning. Second, frozen sperm can enhance efficient use of facilities and create new opportunities in the hatchery by eliminating the need to maintain live males, potentially freeing resources for use with females and larvae. Third, valuable genetic lineages such as endangered species, research models, or improved farmed strains can be protected by storage of frozen sperm. Fourth, cryopreservation opens the door for rapid genetic improvement. Frozen sperm can be used in breeding programs to create improved lines and shape the genetic resources available for aquaculture. Finally, cryopreserved sperm of aquatic species will at some point become an entirely new industry itself. A successful industry will require integrated practices for sample collection, refrigerated storage, freezing, thawing, rules for use and disposal, transfer agreements, and database development. Indeed the development of this new industry is currently constrained by factors including the technical requirements for scaling-up to commercial operations during the transition from research, and the absence of uniform quality control practices, industry standards, marketing and price structures, and appropriate biosecurity safeguards.

Society for Reproduction and Fertility Supplement↗

USGS2021

Mangroves and people: Impacts and interactions

Mangroves have long been associated with human populations, as coastal communities rely on the various ecosystem services that mangroves provide. However, human degradation and destruction of mangrove forests is common, despite and because of our reliance on them as valuable ecosystems. Mangrove research and management must elucidate and reconcile these conflicts to maintain mangrove forests and the services that humans depend on. To better understand the complex dynamics, interactions and relationships that exist between mangroves and coastal communities, the 5th Mangrove Macrobenthos and Management (MMM5) conference was held in Singapore in July 2019, with the theme “ Mangroves and People: Impacts and Interactions”. This theme was chosen because Southeast Asia is the epicentre of ongoing mangrove loss, and a large number of coastal communities in the region rely on the ecosystem services that mangroves provide. The 32 papers published in this Special Issue represent the breadth of mangrove research presented at MMM5, including topics in faunal biology, ecosystem ecology, genetics, physical geography, biogeochemistry, remote sensing and the social sciences. The articles are characterized under the following topics: 1) mangrove ecosystem functioning; 2) range expansion of mangroves; 3) ecosystem services of mangroves; 4) anthropogenic and natural threats to mangroves; and 5) the management and social-ecology of mangroves. This Special Issue highlights the current state of the art of mangrove research and application, and describes a number of emerging new ideas and research opportunities that will continue to advance mangrove ecosystem science into the future.

Estuarine, Coastal and Shelf Science↗

USGS2012

Analysis of the trap gene provides evidence for the role of elevation and vector abundance in the genetic diversity of Plasmodium relictum in Hawaii

Background: The avian disease system in Hawaii offers an ideal opportunity to investigate host-pathogen interactions in a natural setting. Previous studies have recognized only a single mitochondrial lineage of avian malaria (Plasmodium relictum) in the Hawaiian Islands, but cloning and sequencing of nuclear genes suggest a higher degree of genetic diversity. Methods: In order to evaluate genetic diversity of P. relictum at the population level and further understand host-parasite interactions, a modified single-base extension (SBE) method was used to explore spatial and temporal distribution patterns of single nucleotide polymorphisms (SNPs) in the thrombospondin-related anonymous protein (trap) gene of P. relictum infections from 121 hatch-year amakihi (Hemignathus virens) on the east side of Hawaii Island. Results: Rare alleles and mixed infections were documented at three of eight SNP loci; this is the first documentation of genetically diverse infections of P. relictum at the population level in Hawaii. Logistic regression revealed that the likelihood of infection with a rare allele increased at low-elevation, but decreased as mosquito capture rates increased. The inverse relationship between vector capture rates and probability of infection with a rare allele is unexpected given current theories of epidemiology developed in human malarias. Conclusions: The results of this study suggest that pathogen diversity in Hawaii may be driven by a complex interaction of factors including transmission rates, host immune pressures, and parasite-parasite competition.

Hawai'i↗

USGS2021

The Boreal-Arctic Wetland and Lake Dataset (BAWLD)

Methane emissions from boreal and arctic wetlands, lakes, and rivers are expected to increase in response to warming and associated permafrost thaw. However, the lack of appropriate land cover datasets for scaling field-measured methane emissions to circumpolar scales has contributed to a large uncertainty for our understanding of present-day and future methane emissions. Here we present the Boreal–Arctic Wetland and Lake Dataset (BAWLD), a land cover dataset based on an expert assessment, extrapolated using random forest modelling from available spatial datasets of climate, topography, soils, permafrost conditions, vegetation, wetlands, and surface water extents and dynamics. In BAWLD, we estimate the fractional coverage of five wetland, seven lake, and three river classes within 0.5 × 0.5∘ grid cells that cover the northern boreal and tundra biomes (17 % of the global land surface). Land cover classes were defined using criteria that ensured distinct methane emissions among classes, as indicated by a co-developed comprehensive dataset of methane flux observations. In BAWLD, wetlands occupied 3.2 × 106 km2 (14 % of domain) with a 95 % confidence interval between 2.8 and 3.8 × 106 km2. Bog, fen, and permafrost bog were the most abundant wetland classes, covering ∼ 28 % each of the total wetland area, while the highest-methane-emitting marsh and tundra wetland classes occupied 5 % and 12 %, respectively. Lakes, defined to include all lentic open-water ecosystems regardless of size, covered 1.4 × 106 km2 (6 % of domain). Low-methane-emitting large lakes (>10 km2) and glacial lakes jointly represented 78 % of the total lake area, while high-emitting peatland and yedoma lakes covered 18 % and 4 %, respectively. Small (<0.1 km2) glacial, peatland, and yedoma lakes combined covered 17 % of the total lake area but contributed disproportionally to the overall spatial uncertainty in lake area with a 95 % confidence interval between 0.15 and 0.38 × 106 km2. Rivers and streams were estimated to cover 0.12 × 106 km2 (0.5 % of domain), of which 8 % was associated with high-methane-emitting headwaters that drain organic-rich landscapes. Distinct combinations of spatially co-occurring wetland and lake classes were identified across the BAWLD domain, allowing for the mapping of “wetscapes” that have characteristic methane emission magnitudes and sensitivities to climate change at regional scales. With BAWLD, we provide a dataset which avoids double-accounting of wetland, lake, and river extents and which includes confidence intervals for each land cover class. As such, BAWLD will be suitable for many hydrological and biogeochemical modelling and upscaling efforts for the northern boreal and arctic region, in particular those aimed at improving assessments of current and future methane emissions. Data are freely available at https://doi.org/10.18739/A2C824F9X (Olefeldt et al., 2021).

Earth System Science Data↗

USGS2016

Historical habitat barriers prevent ring-like genetic continuity throughout the distribution of threatened Alameda Striped Racers ( Coluber lateralis euryxanthus )

We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We used cluster assignments to characterize population genetic structuring with respect to land management units and approximate Bayesian analysis to rank the ability of five alternative evolutionary hypotheses to explain the inferred structure. Then, we estimated rates of contemporary and historical migration among the major clusters and measured the fit of different historical migration models to better understand the formation of the current population structure. Our results reveal a ring-like pattern of historical connectivity around the Tri-Valley area of the East Bay (i.e., San Ramon, Amador, and Livermore valleys), with clusters largely corresponding to different management units. We found no evidence of continuous gene flow throughout the ring, however, and that the main gap in continuity is centered across the Livermore Valley. Historical migration models support higher rates of gene flow away from the terminal ends of the ring on the north and south sides of the Valley, compared with rates into those areas from western sites that border the interior San Francisco Bay. We attribute the break in ring-like connectivity to the presence of unsuitable habitat within the Livermore Valley that has been reinforced by 20th century urbanization, and the asymmetry in gene flow rates to spatial constraints on movement and east–west environmental gradients influenced by the proximity of the San Francisco Bay.

California↗

USGS2017

Multiple-source tracking: Investigating sources of pathogens, nutrients, and sediment in the Upper Little River Basin, Kentucky, water years 2013–14

The South Fork Little River (SFLR) and the North Fork Little River (NFLR) are two major headwater tributaries that flow into the Little River just south of Hopkinsville, Kentucky. Both tributaries are included in those water bodies in Kentucky and across the Nation that have been reported with declining water quality. Each tributary has been listed by the Kentucky Energy and Environment Cabinet—Kentucky Division of Water in the 303(d) List of Waters for Kentucky Report to Congress as impaired by nutrients, pathogens, and sediment for contact recreation from point and nonpoint sources since 2002. In 2009, the Kentucky Energy and Environment Cabinet—Kentucky Division of Water developed a pathogen total maximum daily load (TMDL) for the Little River Basin including the SFLR and NFLR Basins. Future nutrient and suspended-sediment TMDLs are planned once nutrient criteria and suspended-sediment protocols have been developed for Kentucky. In this study, different approaches were used to identify potential sources of fecal-indicator bacteria (FIB), nitrate, and suspended sediment; to inform the TMDL process; and to aid in the implementation of effective watershed-management activities. The main focus of source identification was in the SFLR Basin. To begin understanding the potential sources of fecal contamination, samples were collected at 19 sites for densities of FIB ( E. coli ) in water and fluvial sediment and at 11 sites for Bacteroidales genetic markers (General AllBac, human HF183, ruminant BoBac, canid BacCan, and waterfowl GFD) during the recreational season (May through October) in 2013 and 2014. Results indicated 34 percent of all E. coli water samples ( n =227 samples) did not meet the U.S. Environmental Protection Agency 2012 recommended national criteria for primary recreational waters. No criterion currently exists for E. coli in fluvial sediment. By use of the Spearman’s rank correlation test, densities of FIB in fluvial sediments were observed to have a statistically significant positive correlation with drainage area. As drainage area increased, so did the densities of FIB in the fluvial sediments. There was no statistically significant correlation between drainage area and FIB in water. The human-associated marker (HF183) was found above the detection limit in 26 percent of the samples ( n =120 samples); a higher proportion of positive samples was in the NFLR Basin. The ruminant-associated marker (BoBac) was above the detection limit in 65 percent of samples; a higher proportion of positive samples was in the headwaters of the SFLR Basin. Nutrient yields differed between the SFLR and NFLR Basins. Comparatively, the SFLR Basin produced the largest estimated mean yields of total nitrogen (16,000 pounds per year per square mile (lb/yr/mi 2 ) and nitrite plus nitrate nitrogen (12,500 lb/yr/mi 2 ), and the NFLR Basin produced the largest estimated mean yields of ammonia plus organic nitrogen (4,700 lb/yr/mi 2 ), total phosphorus (1,100 lb/yr/mi 2 ), and orthophosphorus (590 lb/yr/mi 2 ). Nitrate sources in surface water were assessed in both basins using dual-nitrate isotope (nitrogen and oxygen) ratios. Data from the different land uses in the SFLR Basin showed differences in nitrate concentrations and overlapping, but moderately distinct, isotopic signatures. Predominantly forested sites consistently had low nitrate concentrations (median = 0.233 milligrams per liter) with minimal variability, and agricultural sites had the highest nitrate concentrations (median = 7.55 milligrams per liter) with the greatest variability. The median nitrate concentration for sites with mixed land use was 2.66 milligrams per liter. Dual-isotope data for forested sites plotted within ranges characteristic of soil-derived nitrate with possible but minimal influence from recycled atmospheric nitrate. Ranges of dual-isotope data for sites with agricultural and mixed land uses were characteristic of possible mixtures of chemical fertilizer, soil-derived nitrate, and manure and septic wastes. In the NFLR Basin, a positive linear relation was observed between nitrate concentrations and nitrogen isotope ratios (δ 15 N NO3 ) (R 2 =0.56; p -value <0.001) that potentially suggests the NFLR Basin has a higher proportion of δ 15 N NO3 -enriched sources, such as manure and sewage. However, mixing of other nitrate-derived sources cannot be excluded, because many values of δ 15 N NO3 and concentrations of nitrate showed minimal variation and plotted within dual-nitrate isotope ranges characteristic of fertilizer and soil-derived nitrate sources. A sediment-fingerprinting approach was used to quantify the relative contribution of four upland sources in the SFLR Basin (agricultural, pasture, riparian/forest, and streambank) to understand how land management affects suspended-sediment concentration. Carbon isotope ratios (δ 13 C), together with calcium and carbon concentrations, were the best indicators of sediment source; the uncertainty was less than 11 percent. Fine-sediment samples collected at the SFLR Basin outlet indicated streambanks as the largest source of the fine sediment to the stream followed by cropland and riparian/forest-source areas, respectively; pasture was a minor contributing source. Streambanks and cropland were essentially equal contributors of fine sediment at the NFLR Basin outlet.

Kentucky↗

USGS2021

Modeling distribution of endemic Bartram’s Bass Micropterus sp. cf. coosae: Disturbance and proximity to invasion source increase hybridization with invasive Alabama Bass

“Bartram’s Bass” Micropterus sp. cf. coosae is endemic to the upper Savannah River basin of the southeastern United States and is threatened by hybridization with invasive Alabama Bass Micropterus henshalli . Bartram’s Bass have been functionally extirpated from reservoirs, and hybrid individuals have been detected in several tributaries. However, the extent of introgression in tributaries is currently unknown. Our objectives were to (1) assess the distribution of Bartram’s Bass, native Largemouth Bass M . salmoides , invasive Alabama Bass, and their hybrids in streams of the upper Savannah River basin and (2) quantify effects of abiotic variables on the distribution of each species. We sampled 154 locations in 2017 and 2018 and assigned genetic identity using hydrolysis probes and microsatellites. We used conditional inference trees to quantify variables affecting the occurrence of each species and hybrids. We observed widespread hybridization across the basin. Pure Bartram’s Bass were collected at 27% (42) of sites, among which only 12 sites contained pure Bartram’s Bass and no other congeners. Thirty sites where pure Bartram’s Bass were collected contained hybrids. In the montane Blue Ridge ecoregion, occurrence of pure Bartram’s Bass was negatively affected by low levels of local-scale developed land cover. In the lower-relief Piedmont ecoregion, pure Bartram’s Bass were positively associated with watershed-scale forest land cover and stream gradient. Distance from a reservoir was positively associated with occurrence of pure Bartram’s Bass in both ecoregions. Pure Bartram’s Bass are likely to occur with high probability in only 16% of nonimpounded stream segments; this represents a conservative estimate, and the true number is likely lower. However, future work accounting for incomplete detection of Bartram’s Bass will help to improve confidence in true extirpations. Conservation efforts may be more successful if implemented on stream segments farther from reservoirs or upstream of dispersal barriers preventing colonization of Alabama Bass.

Georgia, North Carolina, South Carolina↗

USGS2008

Molecular epidemiology of eastern equine encephalitis Virus, New York

Perpetuation, overwintering, and extinction of eastern equine encephalitis virus (EEEV) in northern foci are poorly understood. We therefore sought to describe the molecular epidemiology of EEEV in New York State during current and past epizootics. To determine whether EEEV overwinters, is periodically reintroduced, or both, we sequenced the E2 and partial NSP3 coding regions of 42 EEEV isolates from New York State and the Eastern Seaboard of the United States. Our phylogenetic analyses indicated that derived subclades tended to contain southern strains that had been isolated before genetically similar northern strains, suggesting southern to northern migration of EEEV along the Eastern Seaboard. Strong clustering among strains isolated during epizootics in New York from 2003–2005, as well as from 1974–1975, demonstrates that EEEV has overwintered in this focus. This study provides molecular evidence for the introduction of southern EEEV strains to New York, followed by local amplification, perpetuation, and overwintering.

New York↗

USGS1999

Hybridization and the phylogenetic relationship between polecats and domestic ferrets in Britain

Ferrets ( Mustela furo ) were domesticated from polecats ( M. putorius, M. eversmannii ) over 2000 years ago. Following their introduction to Britain, they escaped and hybridized with native European polecats ( M. putorius ). Native polecats declined to the point of near extinction prior to World War I, but have recently begun to expand from a Welsh refugium. Concern has arisen as to the extent of polecat/ferret introgression, and in particular, whether the expanding population is of mainly hybrid origin. Therefore, mitochondrial DNA sequencing was used to investigate polecat genetic diversity in Britain. Two geographically distinct lineages were found, where one may be ancestral to the British polecat, and the other to the domestic ferret. The ancestral distribution of each lineage, or assortative mating is sufficient to explain the observed pattern. A further comparison between the distribution of the polecat phenotype and mitochondrial haplotype implies that the current population expansion may be mediated by dispersing male polecats hybridizing with female feral ferrets. However, the wild source of the ferret remains obscure. Relatively recent speciation from European mink ( M. lutreola ) and black-footed ferrets ( M. nigripes ), and/or the effects of hybridization result in an unresolved molecular phylogeny.

Biological Conservation↗

USGS2008

Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization

Spatial genetic structure in populations of mosquitofish ( Gambusia ) sampled throughout the south-eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south-eastern Mississippi to north-eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrooki to the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species-specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.

Molecular Ecology↗

USGS2001

Ages and Origins of Calcite and Opal in the Exploratory Studies Facility Tunnel, Yucca Mountain, Nevada

Deposits of calcite and opal are present as coatings on open fractures and lithophysal cavities in unsaturated-zone tuffs at Yucca Mountain, Nevada, site of a potential high-level radioactive waste repository. Outermost layers of calcite and opal have radiocarbon ages of 16,000 to 44,000 years before present and thorium-230/uranium ages of 28,000 to more than 500,000 years before present. These ages are young relative to the 13-million-year age of the host rocks. Multiple subsamples from the same outer layer typically show a range of ages with youngest ages from the thinnest subsamples. Initial uranium-234/uranium-238 activity ratios between 1 and 9.5 show a distinct negative correlation with thorium-230/uranium age and are greater than 4 for all but one sample younger than 100,000 years before present. These data, along with micrometer-scale layering and distinctive crystal morphologies, are interpreted to indicate that deposits formed very slowly from water films migrating through open cavities. Exchanges of carbon dioxide and water vapor probably took place between downward-migrating liquids and upward-migrating gases at low rates, resulting in oversaturation of mineral constituents at crystal extremities and more or less continuous deposition of very thin layers. Therefore, subsamples represent mixtures of older and younger layers on a scale finer than sampling techniques can resolve. Slow, long-term rates of deposition (less than about 5 millimeters of mineral per million years) are inferred from subsamples of outermost calcite and opal. These growth rates are similar to those calculated assuming that total coating thicknesses of 10 to 40 millimeters accumulated over 12 million years. Calcite has a wide range of delta carbon-13 values from about -8.2 to 8.5 per mil and delta oxygen-18 values from about 10 to 21 per mil. Systematic microsampling across individual mineral coatings indicates basal (older) calcite tends to have the largest delta carbon-13 values and smallest delta oxygen-18 values compared to calcite from intermediate and outer positions. Basal calcite has relatively small strontium-87/strontium-86 ratios, between 0.7105 and 0.7120, that are similar to the initial isotopic compositions of the strontium-rich tuff units, whereas outer calcite has more radiogenic strontium-87/strontium-86 ratios between 0.7115 and 0.7127. Isotopic compositions of strontium, oxygen, and carbon in the outer (youngest) unsaturated-zone calcite are coincident with those measured in Yucca Mountain calcrete, which formed by pedogenic processes. The physical and isotopic data from calcite and opal indicate that they formed from solutions of meteoric origin percolating through a limited network of connected fracture pathways in the unsaturated zone rather than by inundation from ascending ground water originating in the saturated zone. Mineral assemblages, textures, and distributions within the unsaturated zone are distinctly different from those deposited below the water table at Yucca Mountain. The calcite and opal typically are present only on footwall surfaces of a small fraction of fractures and only on floors of a small fraction of lithophysal cavities. The similarities in the carbon, oxygen, and strontium isotopic compositions between fracture calcite and soil-zone calcite, as well as the gradation of textures from detritus-rich micrite in the soil to detritus-free spar 10 to 30 meters below the surface, also support a genetic link between the two depositional environments. Older deposits contain oxygen isotope compositions that indicate elevated temperatures of mineral formation during the early stages of deposition; however, in the youngest deposits these values are consistent with deposition under geothermal gradients similar to modern conditions. Correlations between mineral ages and varying Pleistocene climate conditions are not apparent from the current data. Cumulative evidence from calcite and opal deposits indicate

Water-Resources Investigations Report↗

USGS2021

Optimization of a suite of flathead catfish (Pylodictis olivaris) microsatellite markers for understanding the population genetics of introduced populations in the northeast United States

Flathead catfish are rapidly expanding into nonnative waterways throughout the United States. Once established, flathead catfish may cause disruptions to the local ecosystem through consumption and competition with native fishes, including species of conservation concern. Flathead catfish often become a popular sport fish in their introduced range, and so management strategies must frequently balance the need to protect native and naturalized fauna while meeting the desire to maintain or enhance fisheries. However, there are currently few tools available to inform management of invasive flathead catfish ( Pylodictis olivaris ). We describe a suite of microsatellite loci that can be used to characterize population structure, predict invasion history, and assess potential mitigation strategies for flathead catfish.

Pennsylvania↗

USGS2002

Mitochondrial phylogeography of moose ( Alces alces ): Late Pleistocene divergence and population expansion

We examined phylogeographic relationships of moose ( Alces alces ) worldwide to test the proposed existence of two geographic races and to infer the timing and extent of demographic processes underpinning the expansion of this species across the Northern Hemisphere in the late Pleistocene. Sequence variation within the left hypervariable domain of the control region occurred at low or moderate levels worldwide and was structured geographically. Partitioning of genetic variance among regions indicated that isolation by distance was the primary agent for differentiation of moose populations but does not support the existence of distinct eastern and western races. Levels of genetic variation and structure of phylogenetic trees identify Asia as the origin of all extant mitochondrial lineages. A recent coalescence is indicated, with the most recent common ancestor dating to the last ice age. Moose have undergone two episodes of population expansion, likely corresponding to the final interstade of the most recent ice age and the onset of the current interglacial. Timing of expansion for the population in the Yakutia–Manchuria region of eastern Asia indicates that it is one of the oldest populations of moose and may represent the source of founders of extant populations in North America, which were colonized within the last 15,000 years. Our data suggest an extended period of low population size or a severe bottleneck prior to the divergence and expansion of extant lineages and a recent, less-severe bottleneck among European lineages. Climate change during the last ice age, acting through contraction and expansion of moose habitat and the flooding of the Bering land bridge, undoubtedly was a key factor influencing the divergence and expansion of moose populations.

Alaska, Colorado↗

USGS2023

Survival, cause-specific mortality, and population growth of white-tailed deer in western Virginia

Understanding the role of recruitment in population dynamics of white-tailed deer ( Odocoileus virginianus ) is important for management. In the central Appalachian Mountains, deer are part of a largely forested ecosystem that supports 3 carnivore species thought to be capable of influencing white-tailed deer recruitment: black bears ( Urus americanus ), coyotes ( Canis latrans ), and bobcats ( Lynx rufus ). Yet little is known about predation, how other environmental factors influence recruitment, or the importance of neonate survival to white-tailed deer population performance in the region. Our objectives were to identify causes of mortality for neonates, analyze effects of landscape attributes on survival of neonates, estimate survival rates for neonates and adult female white-tailed deer, and to model population growth trends based on current vital rates and hypothetical harvest and neonate survival scenarios. During 2019–2020, we captured 57 neonate deer in Bath County, Virginia, USA, by monitoring 38 pregnant females equipped with global positioning system collars and vaginal implant transmitters and by conducting transect searches for recently born neonates. We observed 37 neonate mortalities and identified cause of death using field and genetic evidence. Mortalities included 28 predation events and 9 deaths from other causes (e.g., abandonment, malnutrition, disease). Black bears accounted for 48.6% of neonate mortalities, and 64.2% of predation events ( n = 18), followed by bobcats ( n = 5) and coyotes ( n = 3). Annual survival for adult female deer was 0.871 and neonate survival to 12 weeks old was 0.310. Elevation was a significant predictor of neonate survival; mortality risk increased 20% for every 100-m increase in elevation. Models of annual population growth using observed vital rates predicted an increasing population (λ = 1.10). A 10% increase in female harvest would still result in a potential population increase of 2% (λ = 1.02), but a 20% increase in harvest rate would result in a potential 7% decline (λ = 0.93). Neonate survival was higher near fertile valley bottoms and lower along forested ridges characterized by shallow, infertile soils and limited edge or early successional forests. While predation, largely influenced by black bears, was the leading cause of neonate mortality and contributed to low neonate survival, we observed little evidence of population decline, and suggest there is opportunity for a modest increase in harvest of female deer.

Virginia↗

USGS2022

Tracking the desert's edge with a Pleistocene relict

In addition to the Sky Islands of the southwestern U.S. and northwestern Mexico, a series of 900–1200 m desert peaks surrounded by arid lowlands support temperate affiliated species at their summits. The presence of disjunct long-lived plant taxa on under-explored desert mountains, especially Isla Tiburón at 29° latitude in the Gulf of California, suggests a more southerly extent of Ice Age woodlands than previously understood. The phylogeography of the desert edge species Canotia holacantha (Celastraceae) was investigated to test the hypothesis that insular desert peak populations represent remnants of Pleistocene woodlands rather than recent dispersal events. Sequences of four chloroplast DNA regions totaling 2032 bp were amplified from 74 individuals of 14 populations across the entire range of C. holacantha as well as nine individuals that represented the other two species in its clade ( C. wendtii and Acanthothamnus aphyllus ) and two outgroups. Results suggest that a Canotia common ancestor occurred on the landscape, which underwent a population contraction ca. 15 kya. The Isla Tiburón C. holacantha population and the Chihuahuan Desert microendemic C. wendtii have the greatest genetic differentiation, are sister to one another, and basal to all other Canotia populations. Three haplotypes within C. holacantha were recovered, which correspond to regional geography and thus identified as the Arizona, Sonora, and Tiburón haplotypes, within which Acanthothamnus aphyllus is nested rather than as a sister genus. These results indicate a once broad distribution of Canotia / Acanthothamnus when the current peripheral desert ecotone habitat was more widespread during the Pleistocene, now present in relict populations on the fringes of the southern desert, in the Chihuahuan Desert, with scattered populations on desert peaks, and a common or abundant distribution at the northern boundary of the Sonoran Desert. These results suggest Canotia has tracked the shift of the desert's edge both in latitude and elevation since the end of the last Ice Age.

Journal of Arid Environments↗

USGS2006

Autoinducer 2: a concentration-dependent signal for mutualistic bacterial biofilm growth

4,5-dihydroxy-2,3-pentanedione (DPD), a product of the LuxS enzyme in the catabolism of S -ribosylhomocysteine, spontaneously cyclizes to form autoinducer 2 (AI-2). AI-2 is proposed to be a universal signal molecule mediating interspecies communication among bacteria. We show that mutualistic and abundant biofilm growth in flowing saliva of two human oral commensal bacteria, Actinomyces naeslundii T14V and Streptococcus oralis 34, is dependent upon production of AI-2 by S. oralis 34. A luxS mutant of S. oralis 34 was constructed which did not produce AI-2. Unlike wild-type dual-species biofilms, A. naeslundii T14V and an S. oralis 34 luxS mutant did not exhibit mutualism and generated only sparse biofilms which contained a 10-fold lower biomass of each species. Restoration of AI-2 levels by genetic or chemical (synthetic AI-2 in the form of DPD) complementation re-established the mutualistic growth and high biomass characteristic for the wild-type dual-species biofilm. Furthermore, an optimal concentration of DPD was determined, above and below which biofilm formation was suppressed. The optimal concentration was 100-fold lower than the detection limit of the currently accepted AI-2 assay. Thus, AI-2 acts as an interspecies signal and its concentration is critical for mutualism between two species of oral bacteria grown under conditions that are representative of the human oral cavity.

Molecular Microbiology↗