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USGS2011

Minnesota wolf ear lengths as possible indicators of taxonomic differences

Genetic findings suggest that 2 types of wolves, Canis lupus (Gray Wolf) and C. lycaon (Eastern Wolf), and/or their hybrids occupy Minnesota (MN), and this study examines adult wolf ear lengths as a possible distinguisher between these two. Photographic evidence suggested that the Eastern Wolf possesses proportionately longer ears than Gray Wolves. Ear lengths from 22 northwestern MN wolves from the early 1970s and 22 Alaskan wolves were used to represent Gray Wolves, and the greatest length of the sample (12.8 cm) was used as the least length to demarcate Eastern Wolf from Gray Wolf influence in the samples. Twenty-three percent of 112 adult wolves from Algonquin Park in eastern Ontario and 30% of 106 recent adult wolves in northeastern MN possessed ears >12.8 cm. The northeastern MN sample differed significantly from that of current and past northwestern MN wolves. Ear-lengths of wolves in the eastern half of the northeastern MN wolf population were significantly longer than those in the western half of that study area, even though the mean distance between the 2 areas was only 40 km, and the mean length of my 2004–2009 sample was significantly longer than that of 1999–2003. These findings support the hypothesis that Eastern Wolves tend to possess longer ears than do Gray Wolves and suggest a dynamic hybridization process is still underway in MN.

Minnesota↗

USGS2002

Phylogeography and history of giant Galápagos tortoises

We examined the phylogeography and history of giant Galápagos tortoise populations based on mitochondrial DNA sequence data from 161 individuals from 21 sampling sites representing the 11 currently recognized extant taxa. Molecular clock and geological considerations indicate a founding of the monophyletic Galápagos lineage around 2–3 million years ago, which would allow for all the diversification to have occurred on extant islands. Founding events generally occurred from geologically older to younger islands with some islands colonized more than once. Six of the 11 named taxa can be associated with monophyletic maternal lineages. One, Geochelone porteri on Santa Cruz Island, consists of two distinct populations connected by the deepest node in the archipelago-wide phylogeny, whereas tortoises in northwest Santa Cruz are closely related to those on adjacent Pinzón Island. Volcan Wolf, the northernmost volcano of Isabela Island, consists of both a unique set of maternal lineages and recent migrants from other islands, indicating multiple colonizations possibly due to human transport or multiple colonization and partial elimination through competition. These genetic findings are consistent with the mixed morphology of tortoises on this volcano. No clear genetic differentiation between two taxa on the two southernmost volcanoes of Isabela was evident. Extinction of crucial populations by human activities confounds whether domed versus saddleback carapaces of different populations are mono- or polyphyletic. Our findings revealed a complex phylogeography and history for this tortoise radiation within an insular environment and have implications for efforts to conserve these endangered biological treasures.

Galápagos Islands↗

USGS2019

Primarily resident grizzly bears respond to late-season elk harvest

Autumn ungulate hunting in the Greater Yellowstone Ecosystem carries the risk of hunter–grizzly bear ( Ursus arctos ) conflict and creates a substantial challenge for managers. For Grand Teton National Park, Wyoming, USA, a key information need is whether increased availability of elk ( Cervus canadensis ) carcasses during a late autumn (Nov–Dec) harvest within the national park attracts grizzly bears and increases the potential for conflict with hunters. Using a robust design analysis with 6 primary sampling periods during 2014–2015, we tested the hypothesis that the elk harvest resulted in temporary movements of grizzly bears into the hunt areas, thus increasing bear numbers. We detected 31 unique individuals (6 F, 25 M) through genetic sampling and retained 26 encounter histories for analysis. Markovian movement models had more support than a null model of no temporary movement. Contrary to our research hypothesis, temporary movements into the study area occurred between the July–August (no hunt; N̄ 2014–2015 = 5) and September–October (no hunt; N̄ 2014–2015 = 24) primary periods each year, rather than during the transition from September–October (no hunt) to November–December (hunt; N̄ 2014–2015 = 15). A post hoc analysis indicated that September–October population estimates were biased high by detections of transient bears. Grizzly bear presence during the elk hunt was limited to approximately 15 resident bears that specialized in accessing elk carcasses. The late timing of the elk hunt likely moderated the effect of carcasses as a food attractant because it coincides with the onset of hibernation. From a population response perspective, the current timing of the elk harvest likely represents a scenario of low relative risk of hunter–bear conflicts. The risk of hunter–grizzly bear encounters remains, but may be more a function of factors that operate at the level of individual bears and hunters, such as hunter movements and bear responses to olfactory cues.

Wyoming↗

USGS2010

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

PNAS↗

USGS2016

Ecological requirements for pallid sturgeon reproduction and recruitment in the Missouri River—A synthesis of science, 2005 to 2012

This report is intended to synthesize the state of the scientific understanding of pallid sturgeon ecological requirements to provide recommendations for future science directions and context for Missouri River restoration and management decisions. Recruitment of pallid sturgeon has been low to non-existent throughout its range. Emerging understanding of the genetic structure of pallid sturgeon populations sets a broad framework for species and river management decisions, including decisions about managing the future genetic diversity of the species, but also decisions about where and what type of river restoration actions will be effective for subpopulations of this highly migratory species. Adult pallid sturgeon may migrate hundreds of kilometers (km) to spawn and their progeny may disperse even greater distances downstream as drifting free embryos. As a result of their complex life history pallid sturgeon naturally exploit a wide range of habitats during their life cycles. The construction of dams and reservoirs has fragmented habitats and may have shifted Missouri River subpopulations downstream. Research has not identified one primary biological or ecological constraint that appears to limit populations of the pallid sturgeon. With the present (2013) state of knowledge many life stages and life-stage transitions cannot be ruled out as contributing to recruitment failure. Biological opinions in 2000 (and amended in 2003) presented the dominant hypotheses for recruitment failure that existed at that time. Emphasis was on the role of the flow regime, specifically spring flow pulses (“spring rises”), to condition spawning substrate and cue reproductive aggregations and migrations, and on low flows and additional slow, shallow-water area to serve as rearing habitat for age-0 to juvenile pallid sturgeon. Studies on spawning habitat dynamics have documented that habitat patches selected for spawning by fish in the Lower Missouri River (Missouri River downstream from Gavins Point Dam to the confluence with the Mississippi River) are dominantly on outside, revetted bends in the deepest, fastest, and most turbulent water. Studies in more natural habitat on the Yellowstone River have documented spawning in convergent flow in the middle of the channel on discrete patches of gravel within a sand-dominated channel, an arrangement that may be more effective in attracting aggregations of reproductive fish compared to the nearly continuous revetment on the Lower Missouri River. Pallid sturgeon spawn in the spring and early summer during periods of increasing day length. Water temperature consistently exerts a threshold effect for spawning at 16–18 °C. In addition, the role of water temperature is indicated by pauses and reversals in upstream migrations that have been associated with cold weather fronts that create a transient decrease in water temperature. From 2005 to 2012 on the Lower Missouri River, no obvious relations between flow pulses and fish movements and spawning behaviors have been apparent. However, pallid sturgeon tracking at the Upper Missouri–Yellowstone confluence indicates that in most years, most telemetered pallid sturgeon migrate out of the Missouri River and into the Yellowstone River in the June–July timeframe in association with the spring pulse. This pattern was disrupted in 2011 when a high flow pulse with warm temperatures and high turbidity emanated from the Milk River, followed by record releases from Fort Peck Dam, and 36–39 percent of the telemetered population migrated up the Upper Missouri. This result supports the hypothesis that sufficiently large flow pulses may trigger migration and aggregation but it is not clear that functional pulses are within reservoir management authorities. Notably, a pallid sturgeon free embryo was captured on the Upper Missouri River in 2011 and another single, genetically confirmed embryo was captured on the Yellowstone River in 2012. Research on free-embryo drift has indicated the potential for hundreds of miles of downstream dispersal. Lack of distance to accommodate the extended downstream dispersal period of free embryos on the Upper Missouri and Yellowstone Rivers is the predominant hypothesis for recruitment failure in the upper basin. Long drift distances in the Lower Missouri River may be responsible for shifting Lower Missouri River sub-populations further into the Middle Mississippi River. Physical understanding of drift processes indicates that mean velocities could be slowed through decreased discharges or increased channel hydraulic radius (width and topographic diversity) to reduce free-embryo dispersal distances. In addition, the probability that free embryos are transported into and retained in channel-margin habitats is theoretically amenable to channel re-engineering that would increase cross-channel secondary currents in bends or channel expansions. Considerable uncertainty persists, however, about whether extended drift of Lower Missouri River larvae is responsible for recruitment failure. If drift distance is limiting, it is important to discern whether it would be advisable to retain larvae within the Missouri River, and where along the river restoration projects should be placed to optimize survival and growth of age-0 and juvenile sturgeon. Longitudinal differences in female pallid sturgeon fecundity lend support to the hypothesis that recruitment failure may be due, in part, to fish having insufficient nutrition to produce the numbers of gametes needed for the population to grow, perhaps because of simultaneous declines in prey-fish populations and their habitats. Establishing a chain of causality from habitat decline, to prey-fish populations, to sturgeon diets, to sturgeon fecundity, and to pallid sturgeon population growth presents a considerable scientific challenge. In addition to the dominant hypotheses relating pallid sturgeon populations to changes in flow regime and channel morphology, other factors have been identified that might be sources of stress and contribute to recruitment failure. Among these are water quality and contaminants. Ambient water-quality monitoring on the Missouri River has demonstrated summer episodes when dissolved oxygen dips below 5 milligrams per liter, a threshold that may be stressful especially to age-0 and juvenile sturgeon. Documented cases of intersex in shovelnose and pallid sturgeon indicate that agricultural and municipal sources of endocrine disrupting chemicals also may have a role in pallid sturgeon recruitment failure. Scientific understanding of the ecological requirements of pallid sturgeon has increased almost exponentially in the last two decades, and efforts are now turning from understanding fundamental biology of the species to quantifying how population dynamics relate to potential management actions. Progress in developing the science needed to inform management actions on the Missouri River may benefit from continuation of monitoring of reproductive cycles, reproductive movements, growth, and survival of telemetry tagged adults, increased emphasis on focused, complementary field and laboratory studies of factors influencing early life history, implementation of studies to resolve the role of food limitations in growth, survival, and reproductive condition, and implementation of studies designed specifically to parameterize models linking management to populations.

Missouri River↗

USGS2023

Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States

Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E ( mcyE ) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis . Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.

Scientific Reports↗

USGS2017

Molecular systematics of the critically-endangered North American spinymussels (Unionidae: Elliptio and Pleurobema ) and description of Parvaspina gen. nov.

Despite being common in numerous marine bivalve lineages, lateral spines are extremely rare among freshwater bivalves (Bivalvia: Unionidae), with only three known species characterized by the presence of spines: Elliptio spinosa, Elliptio steinstansana , and Pleurobema collina . All three taxa are endemic to the Atlantic Slope of southeastern North America, critically endangered, and protected by the US Endangered Species Act. Currently, these species are recognized in two genera and remain a source of considerable taxonomic confusion. Because spines are rare in freshwater mussels and restricted to a small region of North America, we hypothesized that spinymussels represent a monophyletic group. We sequenced two mtDNA gene fragments ( COI and ND1 ) and a fragment of the nuclear ITS-1 locus from >70 specimens. Bayesian and maximum-likelihood phylogenetic reconstructions suggest that the spinymussels do not comprise a monophyletic group. Elliptio steinstansana is sister to P. collina , forming a monophyletic clade that was estimated to have diverged from its most recent ancestor in the late Miocene and is distinct from both Elliptio and Pleurobema ; we describe a new genus ( Parvaspina gen. nov.) to reflect this relationship. Additionally, E. spinosa forms a monophyletic clade that diverged from members of the core Elliptio lineage in the mid-Pliocene. Furthermore, E. spinosa is genetically divergent from the other spinymussel species, suggesting that spines, while extremely rare in freshwater mussels worldwide, may have evolved independently in two bivalve lineages. Recognizing the genetic distinctiveness and inter-generic relationships of the spinymussels is an important first step towards effectively managing these imperiled species and lays the groundwork for future conservation genetics studies.

Conservation Genetics↗

USGS2023

Evaluating the utility of effective breeding size estimates for monitoring sea lamprey spawning abundance

Sea lamprey ( Petromyzon marinus ) is an invasive species that is a significant source of mortality for populations of valued fish species across the North American Great Lakes. Large annual control programs are needed to reduce the species' impacts; however, the number of successfully spawning adults cannot currently be accurately assessed. In this study, effective breeding size ( N b ) and the minimum number of spawning adults ( N s ) were estimated for larval cohorts from 17 tributaries across all five Great Lakes using single nucleotide polymorphisms (SNP) genotyped via RAD-capture sequencing. Reconstructed larval pedigrees showed substantial variability in the size and number of full- and half-sibling groups, N b (<1–367), and N s (5–545) among streams. Generalized linear models examining the effects of stream environmental characteristics and aspects of sampling regimes on N b and N s estimates identified sample size, the number of sampling sites, and drainage area as important factors predicting N b and N s . Correlations between N b , N s , and capture–mark–recapture estimates of adult census size ( N c ) increased when streams with small sample sizes ( n < 50) were removed. Results collectively indicate that parameters estimated from genetic data can provide valuable information on spawning adults in a river system, especially if sampling regimes are standardized and physical stream covariates are included.

Ecology and Evolution↗

USGS2020

Spatial capture–recapture with random thinning for unidentified encounters

Spatial capture–recapture (SCR) models have increasingly been used as a basis for combining capture–recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark–resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of “marked” and “unmarked” individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites. Here we describe a “random thinning” SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE. We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low‐density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear ( Ursus arctos ) density in Oriental Cantabrian Mountains (North Spain). Our model can improve density estimation for noninvasive sampling studies for low‐density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.

Ecology & Evolution↗

USGS1999

Professional conduct of scientists during volcanic crises

Stress during volcanic crises is high, and any friction between scientists can distract seriously from both humanitarian and scientific effort. Friction can arise, for example, if team members do not share all of their data, if differences in scientific interpretation erupt into public controversy, or if one scientist begins work on a prime research topic while a colleague with longer-standing investment is still busy with public safety work. Some problems arise within existing scientific teams; others are brought on by visiting scientists. Friction can also arise between volcanologists and public officials. Two general measures may avert or reduce friction: (a) National volcanologic surveys and other scientific groups that advise civil authorities in times of volcanic crisis should prepare, in advance of crises, a written plan that details crisis team policies, procedures, leadership and other roles of team members, and other matters pertinent to crisis conduct. A copy of this plan should be given to all current and prospective team members. (b) Each participant in a crisis team should examine his or her own actions and contribution to the crisis effort. A personal checklist is provided to aid this examination. Questions fall generally in two categories: Are my presence and actions for the public good? Are my words and actions collegial, i.e., courteous, respectful, and fair? Numerous specific solutions to common crisis problems are also offered. Among these suggestions are: (a) choose scientific team leaders primarily for their leadership skills; (b) speak publicly with a single scientific voice, especially when forecasts, warnings, or scientific disagreements are involved; (c) if you are a would-be visitor, inquire from the primary scientific team whether your help would be welcomed, and, in general, proceed only if the reply is genuinely positive; (d) in publications, personnel evaluations, and funding, reward rather than discourage teamwork. Models are available from the fields of particle physics and human genetics, among others.

Bulletin of Volcanology↗

USGS2014

Conserving Prairie Pothole Region wetlands and surrounding grasslands: evaluating effects on amphibians

The maintenance of viable and genetically diverse populations of amphibians in the Prairie Pothole Region of the United States depends on upland as well as wetland over-wintering and landscape level habitat features. Prairie pothole wetlands provide important amphibian breeding habitat while grasslands surrounding these wetlands provide foraging habitat for adults, overwintering habitat for some species, and important connectivity among breeding wetlands. Grasslands surrounding wetlands were found to be especially important for wood frogs and northern leopard frogs, while croplands dominated habitat utilized by Great Plains toads and Woodhouse’s toads. Habitat suitability mapping highlighted (1) the influence of deep-water overwintering wetlands on suitable habitat for four of five anuran species encountered; (2) the lack of overlap between areas of core habitat for both the northern leopard frog and wood frog compared to the core habitat for both toad species; and (3) the importance of conservation programs in providing grassland components of northern leopard frog and wood frog habitat. Currently, there are approximately 7.2 million acres (2.9 million hectares, ha) of habitat in the PPR identified as suitable for amphibians. WRP and CRP wetland and grassland habitats accounted for approximately 1.9 million acres (0.75 million ha) or 26 percent of this total area. Continued loss of amphibian habitat resulting from an ongoing trend of returning PPR conservation lands to crop production, will likely have significant negative effects on the region’s ability to maintain amphibian biodiversity. Conversely, increases in conservation wetlands and surrounding grasslands on the PPR landscape have great potential to positively influence the region’s amphibian populations.

Report↗

USGS2015

USGS role and response to highly pathogenic avian influenza

Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These viruses generally do not cause illness in wild birds, however, when spread to poultry they can be highly pathogenic and cause illness and death in backyard and commercial farms. Outbreaks may cause devastating agricultural economic losses and some viral strains have the potential to infect people directly. Furthermore, the combination of avian influenza viruses with mammalian viruses can result in strains with the ability to transmit from person to person, possibly leading to viruses with pandemic potential. All known pandemic influenza viruses have had some genetic material of avian origin. Since 1996, a strain of highly pathogenic avian influenza (HPAI) virus, H5N1, has caused infection in wild birds, losses to poultry farms in Eurasia and North Africa, and led to the deaths of several hundred people. Spread of the H5N1 virus and other influenza strains from China was likely facilitated by migratory birds. In December 2014, HPAI was detected in poultry in Canada and migratory birds in the United States. Since then, HPAI viruses have spread to large parts of the United States and will likely continue to spread through migratory bird flyways and other mechanisms throughout North America. In the United States, HPAI viruses have severely affected the poultry industry with millions of domestic birds dead or culled. These strains of HPAI are not known to cause disease in humans; however, the Centers for Disease Control and Prevention (CDC) advise caution when in close contact with infected birds. Experts agree that HPAI strains currently circulating in wild birds of North America will likely persist for the next few years. This unprecedented situation presents risks to the poultry industry, natural resource management, and potentially human health. Scientific knowledge and decision support tools are urgently needed to understand factors affecting the persistence of HPAI in wild birds, to forecast future spread of HPAI by wild birds, and to detect novel strains of HPAI that may emerge.

Fact Sheet↗

USGS2015

USGS highly pathogenic avian influenza research strategy

Fact Sheet↗

USGS2022

Biofilms as potential reservoirs of stony coral tissue loss disease

Since 2014, corals throughout Florida’s Coral Reef have been plagued by an epizootic of unknown etiology, colloquially termed stony coral tissue loss disease (SCTLD). Although in Florida the movement of this waterborne coral disease has been consistent with natural transport via water currents, outbreaks in the Caribbean have been more sporadic, with infections occurring in locations inconsistent with spread via natural means. Often Caribbean outbreaks have been clustered near ports, potentially implicating ships as mediators of SCTLD into new regions. Biofilms attached to ship hulls, ballast tank walls, or other surfaces could represent a possible vector for the disease. We investigated whether bacteria shed by healthy and SCTLD-diseased corals would form distinct biofilms, and whether a SCTLD signal would be detectable within biofilm bacterial communities. Stainless steel plates serving as proxies for ship hulls, ballast tank walls, and other colonizable surfaces were incubated for three days in filtered seawater mesocosms containing healthy or SCTLD-infected corals. Resulting biofilm bacterial communities were characterized through sequencing of the V4 region of the 16S rRNA gene. We determined that bacteria shed by healthy and diseased corals formed significantly different biofilms consisting of highly diverse taxa. Comparison with 16S data from previous SCTLD investigations spanning different coral species, collection locations, years, and source material revealed the presence of numerous genetically identical sequences within the biofilm bacterial communities formed during exposure to SCTLD-infected corals, including several previously identified as possible SCTLD bioindicators. These results suggest ship-associated biofilms may have the potential to be vectors for the transmission of SCTLD into new regions.

Frontiers in Marine Science↗

USGS2022

Speciation with gene flow in a narrow endemic West Virginia cave salamander (Gyrinophilus subterraneus)

Due to their limited geographic distributions and specialized ecologies, cave species are often highly endemic and can be especially vulnerable to habitat degradation within and surrounding the cave systems they inhabit. We investigated the evolutionary history of the West Virginia Spring Salamander ( Gyrinophilus subterraneus) , estimated the population trend from historic and current survey data, and assessed the current potential for water quality threats to the cave habitat. Our genomic data (mtDNA sequence and ddRADseq-derived SNPs) reveal two, distinct evolutionary lineages within General Davis Cave corresponding to G. subterraneus and its widely distributed sister species, Gyrinophilus porphyriticus , that are also differentiable based on morphological traits. Genomic models of evolutionary history strongly support asymmetric and continuous gene flow between the two lineages, and hybrid classification analyses identify only parental and first generation cross (F1) progeny. Collectively, these results point to a rare case of sympatric speciation occurring within the cave, leading to strong support for continuing to recognize G. subterraneus as a distinct and unique species. Due to its specialized habitat requirements, the complete distribution of G. subterraneus is unresolved, but using survey data in its type locality (and currently the only known occupied site), we find that the population within General Davis Cave has possibly declined over the last 45 years. Finally, our measures of cave and surface stream water quality did not reveal evidence of water quality impairment and provide important baselines for future monitoring. In addition, our unexpected finding of a hybrid zone and partial reproductive isolation between G. subterraneus and G. porphyriticus warrants further attention to better understand the evolutionary and conservation implications of occasional hybridization between the species.

West Virginia↗

USGS2002

History of pronghorn population monitoring, research, and management in Yellowstone National Park

Pronghorn antelope in Yellowstone National Park (YNP) persist in a small population that historically has experienced recurrent, sometimes dramatic declines. They apparently are isolated from other pronghorns, depend partly on private lands for winter range, experience heavy predation of fawns, and concentrate during winter in a relatively small area, thereby increasing their vulnerability to factors like disease or locally extreme weather. Overall, the situation raises serious concerns about the long-term viability of this population. Although such concerns are not new, evidence of a dramatic population decline since 1991 and continued poor recruitment has created a renewed sense of urgency. Recent efforts to revitalize pronghorn research in YNP began with fawn recruitment and habitat use studies, initiated in 1999 and 2000. With those studies drawing to a close, YNP is reviewing the status and direction of its pronghorn program. The Yellowstone Pronghorn Conservation Assessment Workshop was convened in YNP in January, 2002, to appraise the current state of knowledge about this pronghorn population and make recommendations about future management and research needs. A review of pronghorn population change, management, and research in YNP was commissioned in May, 2001, to provide historical background for workshop participants. Following is a written summary of that review. The process of locating materials for this review was limited to 3 months. Not all relevant materials were discovered or reviewed in that time. In particular, it was not possible to find and review all original sources of information. Also, except for occasional anecdotal accounts, weather records were not reviewed, leaving a potentially serious gap in our understanding of the forces driving changes in pronghorn population counts and estimates 2 over time. Despite these deficiencies, considerable information was reviewed, earlier summaries of population classification and count data were updated, and previously uncited sources of information were identified that challenge important aspects of previous interpretations of the history of pronghorns and pronghorn management in YNP. Information is grouped into 4 major subject areas: distribution and habitat use, demographics and management, genetics, and disease.

Wyoming↗

USGS2009

Natural offshore oil seepage and related tarball accumulation on the California coastline — Santa Barbara Channel and the southern Santa Maria Basin; source identification and inventory

Oil spillage from natural sources is very common in the waters of southern California. Active oil extraction and shipping is occurring concurrently within the region and it is of great interest to resource managers to be able to distinguish between natural seepage and anthropogenic oil spillage. The major goal of this study was to establish the geologic setting, sources, and ultimate dispersal of natural oil seeps in the offshore southern Santa Maria Basin and Santa Barbara Basins. Our surveys focused on likely areas of hydrocarbon seepage that are known to occur between Point Arguello and Ventura, California. Our approach was to 1) document the locations and geochemically fingerprint natural seep oils or tar; 2) geochemically fingerprint coastal tar residues and potential tar sources in this region, both onshore and offshore; 3) establish chemical correlations between offshore active seeps and coastal residues thus linking seep sources to oil residues; 4) measure the rate of natural seepage of individual seeps and attempt to assess regional natural oil and gas seepage rates; and 5) interpret the petroleum system history for the natural seeps. To document the location of sub-sea oil seeps, we first looked into previous studies within and near our survey area. We measured the concentration of methane gas in the water column in areas of reported seepage and found numerous gas plumes and measured high concentrations of methane in the water column. The result of this work showed that the seeps were widely distributed between Point Conception east to the vicinity of Coal Oil Point, and that they by in large occur within the 3-mile limit of California State waters. Subsequent cruises used sidescan and high resolution seismic to map the seafloor, from just south of Point Arguello, east to near Gaviota, California. The results of the methane survey guided the exploration of the area west of Point Conception east to Gaviota using a combination of seismic instruments. The seafloor was mapped by sidescan sonar, and numerous lines of high -resolution seismic surveys were conducted over areas of interest. Biomarker and stable carbon isotope ratios were used to infer the age, lithology, organic matter input, and depositional environment of the source rocks for 388 samples of produced crude oil, seep oil, and tarballs mainly from coastal California. These samples were used to construct a chemometric fingerprint (multivariate statistics) decision tree to classify 288 additional samples, including tarballs of unknown origin collected from Monterey and San Mateo County beaches after a storm in early 2007. A subset of 9 of 23 active offshore platform oils and one inactive platform oil representing a few oil reservoirs from the western Santa Barbara Channel were used in this analysis, and thus this model is not comprehensive and the findings are not conclusive. The platform oils included in this study are from west to east: Irene, Hildago, Harvest, Hermosa, Heritage, Harmony, Hondo, Holly, Platform A, and Hilda (now removed). The results identify three “tribes” of 13 C-rich oil samples inferred to originate from thermally mature equivalents of the clayey-siliceous, carbonaceous marl, and lower calcareous-siliceous members of the Monterey Formation. Tribe 1 contains four oil families having geochemical traits of clay-rich marine shale source rock deposited under suboxic conditions with substantial higher-plant input. Tribe 2 contains four oil families with intermediate traits, except for abundant 28,30-bisnorhopane, indicating suboxic to anoxic marine marl source rock with hemipelagic input. Tribe 3 contains five oil families with traits of distal marine carbonate source rock deposited under anoxic conditions with pelagic but little or no higher-plant input. Tribes 1 and 2 occur mainly south of Point Conception in paleogeographic settings where deep burial of the Monterey Formation source rock favored generation from all three members or their equivalents. In this area, oil from the clayey-siliceous and carbonaceous marl members (Tribes 1 and 2) may overwhelm that from the lower calcareous-siliceous member (Tribe 3) because the latter is thinner and less oil-prone than the overlying members. Tribe 3 occurs mainly north of Point Conception, where shallow burial caused preferential generation from the underlying lower calcareous-siliceous member or another unit with similar characteristics. It is very desirable to be able to clearly distinguish the naturally occurring seep oils from the anthropogenically derived platform oils. Within the “training set” of oils and tars (388 samples), the biomarker parameters are sometimes sufficient to allow unique discrimination of individual platform oils. More often however, platform samples and seep samples with sources geographically close to each other are too similar to each other, with respect to the biomarker parameters, to definitively differentiate them on that basis alone. In some cases other parameters can be helpful. These other parameters are related to the degree of biogeochemical degradation or weathering that the oils or tars have experienced. These components include the typical oil distribution of n-alkane hydrocarbons and isoprenoids pristane and phytane. All of the platform oils in our sample set contain these components. On the other hand, the seep oils or tars have been exposed to significant biodegradation while in the near subsurface. The majority, but not all of seep oils or tars have been biodegraded up to or beyond the loss of n-alkanes and isoprenoids. Seep oils found in the vicinity of Coal Oil Point or Arroyo Burro are apparently the least weathered and are particularly likely to retain significant n-alkanes and isoprenoids. Therefore the combination of chemometric fingerprinting and the presence or absence of n-alkanes and isoprenoids help to differentiate anthropogenic production oils versus natural seeps oils and tars. The differentiation is not always definitive because of the close chemical similarity of some samples and the variability in the biodegradation progression. This is the case near Coal Oil Point, and near Platform A (Dos Cuadros Field) where seep oils and Platform Holly and Platform A oils are genetically very similar and cannot be definitively distinguished after a period of a few days of weathering. In contrast, oils from the Point Conception platforms can be distinguished on the basis of chemometric fingerprinting alone. In the middle of this spectrum are oils from Platforms Harmony, Heritage, and Hondo, where it is expected that oil weathering would take on the order of two weeks to a month to produce tarballs similar to those seen near Point Conception. In this case there is a much greater degree of weathering needed to proceed from produced oil to the biodegraded tar characteristic of tarball stranded on the beach. Tar deposition on beaches was monitored as part of cooperative with the County of Santa Barbara Energy Division and the U.S. Geological Survey during 2001-2003. We found tar deposition varies on a seasonal basis. In general, tarballs accumulate at a faster rate or remain longer on all beaches during the summer and fall months. The reasons for this are unclear based on our limited observations, however we speculate that factors such as prevailing winds and currents combined with more quiescent wave conditions favors the accumulation and preservation of tarballs on the beach during the summer and fall months. In contrast, winter storms, with much greater wave action remove beach sand and other materials, and stormy seas tend to break up oil that might weather into tarballs. Natural seepage is affected by the spring/neap tidal cycle; however, the link to tar deposition is unclear. Longer periods of monitoring are needed to address the variability in the data and provide a more robust statistical analysis.

California↗

USGS2012

Lead and strontium isotopes and related trace elements as genetic tracers in the Upper Cenozoic rhyolite-basalt association of the Yellowstone Plateau volcanic field

Supported by various field geologic and petrologic data, the contents of Pb, U, Th, Rb, and Sr and the isotopic compositions of Pb and Sr for upper Cenozoic volcanic rocks of the Yellowstone Plateau volcanic field are consistent with the hypothesis of derivation of the basaltic and rhyolitic magmas by partial melting of distinct source regions in the upper mantle and lower crust, respectively. All the basalt samples analyzed but one have systematically lower values of 207 Pb/ 204 Pb and 87 Sr/ 86 Sr than the rhyolites. The values of 206 Pb/ 204 Pb are smaller, and 87 Sr/ 86 Sr are mostly larger than known values in oceanic basalts. In all but one case, the values of 207 Pb/ 204 Pb are higher than expected from an extrapolation of known values in oceanic basalts to less radiogenic values of 206 Pb/ 204 Pb. Because there are no xenoliths, phenocrysts are only moderate to sparse in abundance, REE patterns are low and flat at the radiogenic end of lead isotopic compositions, several values of Rb/Sr are low, and 80% of the basalt samples form a well-developed secondary isochron separate from the rhyolites, we favor an interpretation for basalt genesis wherein isotopic signatures of most mafic magmas were attained in a continental ‘keel’ of mantlelike character about 2.6 b.y. old or somewhat older attached to the crust, and these signatures were unaltered by magma passage through the crust. At the very least, the current data continue to cast serious doubt as to the inevitability of crustal contamination for basaltic magma intruding the continental environment and postulate that much can be learned about the mantle under continents through the study of continental basalts. One basalt unit with an unusually low value of 207 Pb/ 204 Pb and an 87 Ar/ 86 Ar less than 0.704 may represent subcontinental ‘keel’-derived magma that rose unaltered to the surface. Our data also are not consistent with formation of this rhyolite-basalt association primarily by such processes as crystal fractionation, separation of immiscible silicate liquids from a common parental magma, or fractional melting of a homogeneous source. Rather as a conceptual model, we envision large mafic intrusions to have been injected into the lower crust resulting in rhyolite generation through partial anatexis of the adjacent wall rocks which probably had a 206 Pb/ 204 Pb < 17 and 87 Sr/ 86 Sr > 0.709; a model that has much in common with that proposed by Holmes (1931). All the other hypotheses listed have the necessary added complication that either the basalt or the rhyolite or both become contaminated after the two magma types separated, have problems accounting for the lack of igneous rocks of intermediate compositions or production of such large volumes of rhyolitic material (∼5000 km 3 ), and fail to explain why rhyolitic magma is not a more common occurrence in the ocean basin. We appeal to bouyancy of rhyolites to generate a barrier for basalt magma migration and account for the great preponderance of rhyolite relative to basalt at the surface. Furthermore, the complex isotopic picture in the rhyolites indicates that many of these magmas interacted with the upper crustal geologic units that they traversed. The interactions involved diverse processes, probably including reacton with hydrothermal fluids or hydrothermally altered rocks at high levels as well as by contamination with Phanerozoic sedimentary and Precambrian crystalline rocks at deeper levels. At the very least, we feel our study adds a cautionary note to the currently increasingly popular hypothesis that differentiation of basalt or gabbro magmas to rhyolite or granite (as distinct from tonalite or dacite) is a common occurrence and is therefore an important continential building process. Models for formation of rhyolite and granite predominantly by reworking of crust (anatexis) must still be considered. The primitive Archean mantle of the region was characterized by higher Rb/Sr, U/Pb, and Th/U values than are typical of modern suboceanic mantle. The mantle residuum within the continental subcrustal lithosperic ‘keel’ that resulted from the Archean crustal differentiation event probably was depleted in Rb/Sr and U/Pb, and the crust was correspondingly enriched in these ratios. The crust probably was further differentiated by an Archean high-grade metamorphism, during or after the primary event, into a granulitic lower crust depleted in U/Pb and Rb/Sr and a lower-grade upper crust enriched in these ratios.

Journal of Geophysical Research Solid Earth↗