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Production of haploid gynogens to inform genomic resource development in the paleotetraploid pallid sturgeon (Scaphirhynchus albus)

Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of osteichthyan fishes (>200 million years old) with most extant species at conservation risk. A relatively basal species, the pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this study was to produce pallid sturgeon gynogens that contain 100% homozygous DNA contributed by only the maternal parent and have enough DNA for future SNP marker development. When homozygous gynogens are sequenced, heterozygosity at a locus within an individual indicates the presence of incorrectly aligned sequences that contain PSVs; accurate identification of these multi-locus contigs can facilitate their exclusion when developing disomic markers. In this study, we attempted to produce two types of pallid sturgeon gynogens: a) haploid gynogens produced from the activation of pallid sturgeon eggs with ultraviolet-irradiated sperm from the distantly related paddlefish (Polyodon spathula), and b) doubled haploids produced from the activation of pallid sturgeon eggs with irradiated paddlefish milt followed by thermal shock to suppress the first mitotic division. Production of doubled haploids, gynogens with 100% homozygous DNA and double the genome content of haploid gynogens, was pursued because it was originally unknown if haploid gyongens would survive long enough to attain enough genetic material for SNP marker development. We performed flow cytometry and microsatellite genotyping on the specimens in order to confirm haploid and doubled haploid status. Our study was unable to successfully yield doubled haploids; however, we successfully produced haploid gynogens that contained enough nuclear DNA for our future SNP marker development study. Interestingly, this study also produced paddlefish × pallid sturgeon hybrids in the control groups in two separate years; this is the first study to report viable offspring between the paddlefish and a Scaphirhynchus sturgeon species and reflects on the malleability of the genomes of the species in this order.

Louisiana, Arkansas, Missouri, Nebraska, North Dak↗

Polar bear management in Alaska 1997-2000

Since the Twelfth Working Meeting of the IUCN/SSC Polar Bear Specialist Group in 1997, a number of changes in the management of polar bears have occurred in Alaska. On October 16, 2000, the governments of the United States and the Russian Federation signed the “Agreement on the Conservation and Management of the Alaska-Chukotka Polar Bear Population.” This agreement provides substantial benefits for the effective conservation of polar bears shared between the U.S. and Russia. It will require enactment of enabling legislation by the U.S. Congress and other steps by Russia before the agreement has the force of law. A copy of the agreement is included as Appendix 1 to this report. Also, during this period, regulations were developed to implement 1994 amendments to the Marine Mammal Protection Act (MMPA), which allow polar bear trophies taken in approved Canadian populations by U.S. citizens to be imported into the U.S. A summary of the regulatory actions and a table listing populations approved for importation and the number of polar bears imported into the U.S. since 1997 is included in this report. Regarding oil and gas activities in polar bear habitat, three sets of regulations were published authorizing the incidental, non-intentional, taking of small numbers of polar bears concurrent to oil and gas activities. Cooperation continued with the Alaska Nanuuq Commission, representing the polar bear hunting communities in Alaska, as well as with the North Slope Borough and the Inuvialuit Game Council in their agreement for the management of the Southern Beaufort Sea polar bear population. Harvest summaries and technical assistance in designing and assistance in conducting a National Park Service/Alaska Nanuuq Commission study to collect traditional ecological knowledge of polar bear habitat use in Chukotka were provided. In addition, a long-range plan was developed to address and minimize polar bear-human conflicts in North Slope communities. We continued to monitor the harvest of polar bears in Alaska and collect and analyze specimens for presence and level of organochlorine compounds and trace elements. A paper on genetic assessment of hunter reported sex of harvested bears was recently published (Schliebe et al. 1999). Population status and trend assessment efforts continued. An aerial survey of polar bears in the Eastern Chukchi Sea and western portions of the Southern Beaufort Sea was conducted from the U.S. Coast Guard icebreaker “Polar Star” in August 2000. The first year of a multi-year survey of barrier islands and coastlines during the open water and freeze-up phase was conducted in the central Southern Beaufort Sea during fall 2000.

Alaska↗

Immigration does not offset harvest mortality in groups of a cooperatively breeding carnivore

The effects of harvest on cooperatively breeding species are often more complex than simply subtracting the number of animals that died from the group count. Changes in demographic rates, particularly dispersal, could offset some effects of harvest mortality in groups but this is rarely explored with cooperative breeders. We asked whether a cooperatively breeding species known for long-distance dispersal could compensate for the effect of harvest mortality on density by adopting immigrants into the group. We used genetic samples to estimate the minimum density of gray wolves ( Canis lupus ) and proportion of immigrants in groups in the northern US Rocky Mountains after an annual harvest regime was initiated and in the Canadian Rocky Mountains where wolves were managed consistently under an annual harvest regime. We tested whether immigration (1) compensated, (2) partially compensated or (3) did not compensate numerically for harvest mortality in groups and hypothesized immigration would increase with increasing harvest intensity. Density of wolves in groups declined after harvest was initiated whereas immigration into groups was consistently low and did not change with harvest in the US study area. Immigration into groups was similarly low and density even lower in the Canadian study area compared to the US study area. Our results indicate immigration did not compensate for harvest mortality in groups in two separate populations of a cooperatively breeding carnivore. We hypothesize the social structure of wolf groups may limit the potentially compensatory response of immigration in some populations.

Animal Conservation↗

A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus)

Background Previous work found that numerous genes positively selected within the hoary bat ( Lasiurus cinereus ) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. Methods A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo ( www.dnazoo.org ). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Results Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these ( Trpc4 ) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. Discussion This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.

PeerJ↗

Potential paths for male-mediated gene flow to and from an isolated grizzly bear population

For several decades, grizzly bear populations in the Greater Yellowstone Ecosystem (GYE) and the Northern Continental Divide Ecosystem (NCDE) have increased in numbers and range extent. The GYE population remains isolated and although effective population size has increased since the early 1980s, genetic connectivity between these populations remains a long-term management goal. With only ~110 km distance separating current estimates of occupied range for these populations, the potential for gene flow is likely greater now than it has been for many decades. We sought to delineate potential paths that would provide the opportunity for male-mediated gene flow between the two populations. We first developed step-selection functions to generate conductance layers using ecological, physical, and anthropogenic landscape features associated with non-stationary GPS locations of 124 male grizzly bears (199 bear-years). We then used a randomized shortest path (RSP) algorithm to estimate the average number of net passages for all grid cells in the study region, when moving from an origin to a destination node. Given habitat characteristics that were the basis for the conductance layer, movements follow certain grid cell sequences more than others and the resulting RSP values thus provide a measure of movement potential. Repeating this process for 100 pairs of random origin and destination nodes, we identified paths for three levels of random deviation (θ) from the least-cost path. We observed broad-scale concordance between model predictions for paths originating in the NCDE and those originating in the GYE for all three levels of movement exploration. Model predictions indicated that male grizzly bear movement between the ecosystems could involve a variety of routes, and verified observations of grizzly bears outside occupied range supported this finding. Where landscape features concentrated paths into corridors (e.g., because of anthropogenic influence), they typically followed neighboring mountain ranges, of which several could serve as pivotal stepping stones. The RSP layers provide detailed, spatially explicit information for land managers and organizations working with land owners to identify and prioritize conservation measures that maintain or enhance the integrity of potential areas conducive to male grizzly bear dispersal.

Montana↗

Developing an effective Agassiz's Desert Tortoise monitoring program: Final report to the Coachella Valley Conservation Commission

Agassiz’s desert tortoise (Gopherus agassizii) is a conservation-reliant species with populations north and west of the Colorado River protected as threatened under the Endangered Species Act (Averill-Murray et al. 2012). Since it was listed under this category in 1990, a great deal has been learned about the natural history of the species, and it is now one of the best-studied turtles in the United States (Lovich and Ennen 2013). However, the accumulated body of scientific data available for the species has not yet been translated into recovery or delisting of the species. Successful conservation of any species requires knowledge of their natural history and how vital rates affect their ability to maintain stable populations in the face of natural and anthropogenic stresses. Agassiz’s desert tortoises occur from southwestern Utah to near the Mexican border in California – a distance of over 450 km – but population densities vary greatly across this immense landscape (U.S. Fish and Wildlife Service 2015). Tortoises occur in the Sonoran Desert of California, including the eastern and western ends of the Coachella Valley, where it is one of 27 species covered under the Coachella Valley Multiple Species Habitat Conservation Plan and Natural Community Conservation Plan (CVMSHCP/NCCP). The southern portion of Joshua Tree National Park (JTNP) lies within this 1.1 million acre planning area, and was predicted to be an area of low-density tortoise populations using habitat suitability modeling (Barrows 2011). JTNP is near the southern distributional limit of G. agassizii, yet very little has been published regarding the ecology of tortoises in the Sonoran Desert of California. Reproductive output is an important gross measure of the ability of a population to persist. When integrated with data on fertility and survivorship, this information forms a foundation for assessing population status and formulating effective management strategies (e.g., Congdon et al. 1993, 1994), especially for imperiled species. One aspect of the biology of G. agassizii that has been particularly well-studied is reproductive output. However, most of what we know about this topic comes from research in the Mojave Desert portion of the species’ range (Ernst and Lovich 2009). Comparatively little has been published on the reproductive ecology of populations living in the Sonoran Desert ecosystem of California. Publications by Lovich et al. (1999, 2011, 2012, 2014, 2015) constitute the main body of literature on desert tortoise reproductive ecology in the Sonoran Desert of California, with one study population located at the western end of the CVMSHCP/NCCP area. Collecting data on Agassiz’s desert tortoise ecology in the Sonoran Desert ecosystem is important due to significant differences between the two adjacent desert ecosystems, especially the timing and amounts of annual precipitation, and their potential effects on reproductive output (e.g., Lovich et al. 5 2015). There are also differences in the vulnerability of tortoises to the effects of a warming, drying climate between the two deserts (Barrows 2011; Zylstra et al. 2012). The overall goal of this study was to collect data on demography, reproductive output, and genetic affinities at a study site in the Sonoran Desert portion of JTNP in the eastern end of the CVMSHCP/NCCP area. Specific objectives included: 1) Collect data to establish baselines on tortoise populations and/or their habitat suitability in core habitat within the CVNCCP area, including biotic and abiotic variables affecting persistence of tortoise populations; 2) Compare and contrast with data collected on desert tortoises at USGS/BLM study site near Palm Springs over 16 years; 3) Support long-term modeling efforts needed to determine tortoise population viability; 4) Refine modeled relationships with identified threats such as fire, invasive species and climate change; and 5) Prioritize adaptive management needs for the desert tortoise in and beyond the CVNCCP area. The data from this study will aid in determining baseline estimates of the desert tortoise population size within the planning area as well as establish a marked population of Agassiz’s desert tortoises for future monitoring. Data will be integrated with habitat modeling in order to refine model output. Genetic data will be collected on both the north and south sides of Interstate 10 to determine the potential effects of habitat fragmentation and genetic mixing. Analyses are ongoing and results beyond those presented in this report will be published in peer-reviewed scientific journals following inclusion of additional data collected on the south side of Shavers Valley in 2017-2018.

Report↗

Critical review of the phytohemagglutinin assay for assessing amphibian immunity

Infectious diseases are a major driver of the global amphibian decline. In addition, many factors, including genetics, stress, pollution, and climate change can influence the response to pathogens. Therefore, it is important to be able to evaluate amphibian immunity in the laboratory and in the field. The phytohemagglutinin (PHA) assay is an inexpensive and relatively non-invasive tool that has been used extensively to assess immunocompetence, especially in birds, and more recently in amphibians. However, there is substantial variation in experimental methodology among amphibian PHA studies in terms of species and life stages, PHA doses and injection sites, and use of experimental controls. Here, we compile and compare all known PHA studies in amphibians to identify knowledge gaps and develop best practices for future work. We found that research has only been conducted on a limited number of species, which may not reflect the diversity of amphibians. There is also a lack of validation studies in most species, so that doses and timing of PHA injection and subsequent swelling measurements may not effectively evaluate immunocompetence. Based on these and other findings, we put forward a set of recommendations to make future PHA studies more consistent and improve the ability to utilize this assay in wild populations, where immune surveillance is greatly needed.

Conservation Physiology↗

Vegetation projections for Wind Cave National Park with three future climate scenarios: Final report in completion of Task Agreement J8W07100052

Introduction The effects of climate change on the natural resources protected by Parks will likely be substantial, but geographically variable, due to local variation in climate trajectories and differences among ecosystems in their vulnerability to climate change. The projections of general circulation models (GCMs) indicate the possible magnitude and direction of future climate change for a region, but the utility of these projections for more local scales, those of individual National Park Service (NPS) units, are more uncertain because the coarse-scale GCMs lack much of the topographic detail that alters local climates. In addition, complex, interacting effects of temperature, precipitation, atmospheric CO 2 concentrations, fire, and herbivores on the vegetation that is the foundational natural resource of many NPS units present challenges in assessing the effects of projected future climates on plant and animal assemblages managed by the NPS. In spring 2009, Wind Cave National Park (WICA) served as a case study in a workshop assessing the use of scenario planning as a tool for park management planning in the face of rapidly changing climate. One outcome of the workshop was the recognized need for quantitative models to better understand the range of possible vegetation changes under different future climates and management decisions. This report addresses this need; it describes our adaptation of a dynamic global vegetation model (DGVM) to WICA vegetation and the resulting projections of future vegetation under three future climate scenarios and 11 management scenarios determined by Park natural resource managers. Wind Cave National Park lies along a narrow transition zone between the ponderosa pine (Pinus ponderosa) forests of the Black Hills and the mixed grass prairie that once extended with few interruptions over the lower, gentler terrain, subject to warmer, drier climate to the east and south of the Park. The location and character of this transition is strongly influenced by fire frequency and intensity (Brown and Sieg 1999). Furthermore, the mixed grass prairie occupies a broader transition zone between eastern tallgrass prairie and the shortgrass prairie of the western Great Plains. The dominance of species characteristic of these two prairie types varies with soil moisture availability, evaporative demand, and recent grazing history (Cogan et al. 1999). In addition, Wind Cave lies near the midpoint of a long gradient of C 3 (cool season) grass dominance to the north and C 4 (warm season) grass dominance to the south. The ecotonal position of WICA may make it particularly sensitive to climate change. For example, small changes in fire frequency and/or intensity and the vigor of trees vs. grass could dramatically shift the proportions of these two lifeforms. The Park hydrology is also sensitive to changes in the balance between infiltration of precipitation and evapotranspiration, as on average, only a small fraction of annual precipitation reaches the deeper soil layers that feed permanent streamflow. The resources at risk at Wind Cave NP include the Cave itself, as well as small backcountry caves, a genetically important bison herd, and other prairie species including the black-tailed prairie dog and endangered black-footed ferrets. All of these resources will be directly affected by climate change impacts on vegetation and hydrology. Natural resource management challenges at WICA are substantial, diverse, and intertwined. Aboveground, the park has been recognized as exemplary for its high quality vegetation (Marriot et al. 1999), though the park is relatively small for the diversity of vegetation types and species that it supports. Even without a changing climate, maintaining the integrity of the plant communities is complicated by the park’s legislated responsibility to maintain viable populations of bison, elk and pronghorn. In addition, the federally endangered black-footed ferret was recently re-introduced to the park. This species requires large extents of prairie dog towns for prey and habitat. Prairie dogs impact vegetation by constant clipping, grazing and soil disturbance, thereby affecting plant composition and productivity. Moreover, naturally high interannual climate variability and the strong influence of precipitation on grass productivity in this region combine to yield high interannual variability in the amount of forage available for the wildlife that the park is tasked to maintain. Finally, fire, which is now primarily controlled by WICA and NPS Northern Great Plains fire management programs, is intertwined with all other natural resource issues at WICA, as it can impact prairie dog colony and forest expansion, ungulate foraging behavior, invasive plant species, and hydrological processes. Although not capable of capturing all of these complexities, dynamic vegetation models do provide a means for quantitatively projecting vegetation futures in future climates under plausible fire and grazing regimes. Our work uses the DGVM MC1 to simulate the effects of future climate projections and management practices on the vegetation of WICA. MC1 is designed to project potential vegetation as influenced by natural processes and hence is appropriate for national parks, where conservation of native biota and ecosystems is of great importance. Since the initial application of MC1 to a small portion of WICA (Bachelet et al. 2000), the model has been altered to improve model performance with the inclusion of dynamic fire. Applying this improved version to WICA required substantial recalibration, during which we have made a number of improvements to MC1 that will be incorporated as permanent changes. In this report we document these changes and our calibration procedure following a brief overview of the model. We compare the projections of current vegetation to the current state of the park and present projections of vegetation dynamics under future climates downscaled from three GCMs selected to represent the existing range in available GCM projections. In doing so, we examine the consequences of different management options regarding fire and grazing, major aspects of biotic management at Wind Cave.

South Dakota↗

Success of restoration strategies in preventing extirpation of 2 critically endangered coral species

An unprecedented marine heatwave in 2023 caused widespread coral bleaching and mortality throughout the Caribbean. In the Florida Keys (USA), 2 foundation species, elkhorn coral ( Acropora palmata ) and staghorn coral ( Acropora cervicornis ), were severely affected. These species have been the primary focus of reef restoration in Florida for decades. Substantial losses of these species occurred in outplanted populations, in ocean-based nurseries, and among remnant wild colonies, leading to uncertainty over their future in the Florida Keys, given recent observed trends in climate conditions. However, the past 2 decades of restoration activity created a community of experts, a network of ocean-based and land-based coral-rearing infrastructure, and 2 independent land-based coral gene banks that prevented regional extirpation and preserved much of the genetic richness of these critically endangered coral species. Without the past decades of effort and the emergency response associated with the 2023 bleaching event, Florida acroporids would largely have been lost. This outcome afforded by the restoration network in Florida demonstrates the value of proactively establishing resources prior to major disturbances. We identified several critical strategies that, in the context of existing climate change, are preventing the extirpation of coral species in Florida, including extending collaborative restoration efforts to solidify a network of trained experts; establishing trust-focused relationships among management agencies and restoration groups; testing direct interventions to reduce light and temperature stress early during thermal anomalies; developing redundant ocean-based and land-based nurseries; and establishing living coral gene banks prior to major threats to prevent the extirpation of coral species.

Florida↗

Establishing an Agassiz’s Desert Tortoise monitoring program within the Coachella Valley multiple species habitat conservation plan area: Final report to the Coachella Valley conservation commission on work performed near the Orocopia Mountains

In support of the goals of the Coachella Valley Multiple Species Habitat Conservation Plan and Natural Community Conservation Plan (CVMSHCP/NCCP), a population of Agassiz’s desert tortoises ( Gopherus agassizii ) was marked and studied to establish a desert tortoise monitoring program near the Orocopia Mountains beginning in early 2017 and ending in the summer of 2018, following the epic drought of 2012‒2016. This effort compliments a similar effort in the nearby mouth of Cottonwood Canyon in 2015‒2016. Surveys were performed to locate tortoises, tortoise burrows, and tortoise remains at the eastern end of the CVMSHCP area north of the Orocopia Mountains and south of Interstate 10 in Riverside County, California. Although the area is considered Critical Habitat for the recovery of tortoise populations, it was heavily impacted by military training activities in the early 1940s and continues to be impacted by off-highway vehicle use. Data were collected from all live and dead tortoise specimens encountered. Only 22 live tortoises were found during transects covering approximately 21 km 2 of habitat surveyed. The sex ratio of live adult tortoises was strongly biased toward males and the sex ratio of recently (4‒5 years) dead carcasses during the long drought was strongly biased toward females. High female mortality may have resulted from the interaction of drought (including increased predation) and the reproductive strategy of tortoises. We located only one new live tortoise in the drought year of 2018 when there was no germination of winter annual food plants. A subsample of nine tortoises was outfitted with radio transmitters, and females (n = 4) were X-radiographed at approximately 10-day intervals from April–July. Mean clutch size was about 4 eggs as is typical for tortoises in this region. Additional tortoises were located opportunistically in and around the Santa Rosa Mountains (located in the southern end of the CVMSHCP area), and these tortoises were also marked for future identification. Blood samples were taken from adult tortoises and scute clips were taken from a subset of juveniles for ongoing studies to determine genetic diversity and relationships of desert tortoises within the CVMSHCP/NCCP area and beyond. The low tortoise density and high adult female mortality observed by us and others in the area may compromise the long-term viability of the population, especially given published predictions of the negative effects of future droughts on tortoises in the region.

California↗

Genetic analysis of the diet of red‐footed boobies (Sula sula) provisioning chicks at Ulupa'u Crater, O'ahu

The diet of red‐footed boobies ( Sula sula ) provisioning chicks was quantified using 106 regurgitations collected from 81 adults over two study years with contrasting oceanographic conditions: 2014 and 2015. A total of 1,049 prey items were sorted into three broad categories (fish, squid, and other, consisting of highly‐digested ‘mush’ and parasitic isopods) and assigned a categorical freshness value of 1 (perfect condition), 2 (superficial digestion), or 3 (highly digested and incomplete). A total of 492 undigested prey items (freshness 1 and 2) were measured and sampled for genetic identification with 401 (82%) successfully identified. Rarefaction analyses suggested robust diet sampling, with 32 documented species: 29 fishes and three squids. While the prey‐specific index of relative importance highlighted that fish dominated the diet in 2014 (32.3% fish, 15.1% squid) and in 2015 (29.9% fish, 22.3% squid), diet composition varied significantly between the two study years. The purpleback flying squid ( Stenoteuthis oulaniensis ) accounted for 98.7% (232 of 236) of the identified squid specimens. Mantle lengths were significantly longer in 2015 (7.2 ± 1.1 SD cm) than in 2014 (6.3 ± 1.7 SD cm). These results indicate a higher relative abundance and size of the epipelagic squids available to foraging red‐footed boobies in 2015, during warm‐water conditions associated with the positive phase of the El Niño Southern Oscillation. Due to their diverse diet, red‐footed boobies are useful bioindicators of epipelagic nekton assemblages during changing oceanographic conditions. Moreover, their reliance on the purpleback flying squid makes these seabirds ideal samplers of the juveniles of this poorly studied species. Understanding how interannual and longer‐term oceanographic variability affects central‐place foraging seabirds and the recruitment and abundance of their squid prey is critical for precautionary ecosystem‐based fisheries management of oceanic islands and the surrounding marine environment.

Hawaii↗

Geographic distribution of the mid-continent population of sandhill cranes and related management applications

The Mid-continent Population (MCP) of sandhill cranes ( Grus canadensis ) is widely hunted in North America and is separated into the Gulf Coast Subpopulation and Western Subpopulation for management purposes. Effective harvest management of the MCP requires detailed knowledge of breeding distribution of subspecies and subpopulations, chronology of their use of fall staging areas and wintering grounds, and exposure to and harvest from hunting. To address these information needs, we tagged 153 sandhill cranes with Platform Transmitting Terminals (PTTs) during 22 February–12 April 1998–2003 in the Central and North Platte River valleys of south-central Nebraska. We monitored PTT-tagged sandhill cranes, hereafter tagged cranes, from their arrival to departure from breeding grounds, during their fall migration, and throughout winter using the Argos satellite tracking system. The tracking effort yielded 74,041 useable locations over 49,350 tag days; median duration of tracking of individual cranes was 352 days and 73 cranes were tracked >12 months. Genetic sequencing of mitochondrial DNA (mtDNA) from blood samples taken from each of our random sample of tagged cranes indicated 64% were G. c. canadensis and 34% were Grus canadensis tabida . Tagged cranes during the breeding season settled in northern temperate, subarctic, and arctic North America (U.S. [23%, n = 35], Canada [57%, n = 87]) and arctic regions of northeast Asia (Russia [20%, n = 31]). Distribution of tagged cranes by breeding affiliation was as follows: Western Alaska–Siberia (WA–S, 42 ± 4% [SE]), northern Canada–Nunavut (NC–N, 21 ± 4%), west-central Canada–Alaska (WC–A, 23 ± 4%) and East-central Canada–Minnesota (EC–M, 14 ± 3%). All tagged cranes returned to the same breeding affiliation used during the previous year with a median distance of 1.60 km (range: 0.08–7.7 km, n = 53) separating sites used in year 1 and year 2. Fall staging occurred primarily in central and western Saskatchewan (69%), North Dakota (16%), southwestern Manitoba (10%), and northwestern Minnesota (3%). Space-use sharing indices showed that except for NC–N and WC–A birds, probability of finding a crane from one breeding affiliation within the home range of another breeding affiliation was low during fall staging. Tagged cranes from WC–A and EC–M breeding affiliations, on average, spent 25 and 20 days, respectively, longer on fall staging areas in the northern plains than did WA–S and NC–N birds. Cranes in the NC–N, WA–S, and WC–A affiliations spent 99%, 74%, and 64%, respectively, of winter in western Texas in Hunting Zone A; EC–M cranes spent 83% of winter along the Texas Gulf Coast in Hunting Zone C. Tagged cranes that settled within the breeding range of the Gulf Coast Subpopulation spent 28% and 42% of fall staging and winter within the range of the Western Subpopulation, indicating sufficient exchange of birds to potentially limit effectiveness of MCP harvest management. Harvests of EC–M and WC–A cranes during 1998–2003 were disproportionately high to their estimated numbers in the MCP, suggesting more conservative harvest strategies may be required for these subpopulations in the future, and for sandhill cranes to occupy major parts of their historical breeding range in the Prairie Pothole Region. Exceptionally high philopatry of MCP cranes of all 4 subpopulations to breeding sites coupled with strong linkages between crane breeding distribution, and fall staging areas and wintering grounds, provide managers guidance for targeting MCP crane harvest to meet management goals. Sufficient temporal or spatial separation exists among the 4 subpopulations on fall staging areas and wintering grounds to allow harvest to be targeted at the subpopulation level in all states and provinces (and most hunting zones within states and provinces) when conditions warrant. Knowledge gained from our study provides decision-makers in the United States, Canada, Mexico, and Russia with improved guidance for developing sound harvest regulations, focusing conservation efforts, and generating collaborative efforts among these nations on sandhill crane research and management to meet mutually important goals.

Nebraska↗

Roles of patch characteristics, drought frequency, and restoration in long-term trends of a widespread amphibian

Despite the high profile of amphibian declines and the increasing threat of drought and fragmentation to aquatic ecosystems, few studies have examined long-term rates of change for a single species across a large geographic area. We analyzed growth in annual egg-mass counts of the Columbia spotted frog (Rana luteiventris) across the northwestern United States, an area encompassing 3 genetic clades. On the basis of data collected by multiple partners from 98 water bodies between 1991 and 2011, we used state-space and linear-regression models to measure effects of patch characteristics, frequency of summer drought, and wetland restoration on population growth. Abundance increased in the 2 clades with greatest decline history, but declined where populations are considered most secure. Population growth was negatively associated with temporary hydroperiods and landscape modification (measured by the human footprint index), but was similar in modified and natural water bodies. The effect of drought was mediated by the size of the water body: populations in large water bodies maintained positive growth despite drought, whereas drought magnified declines in small water bodies. Rapid growth in restored wetlands in areas of historical population declines provided strong evidence of successful management. Our results highlight the importance of maintaining large areas of habitat and underscore the greater vulnerability of small areas of habitat to environmental stochasticity. Similar long-term growth rates in modified and natural water bodies and rapid, positive responses to restoration suggest pond construction and other forms of management can effectively increase population growth. These tools are likely to become increasingly important to mitigate effects of increased drought expected from global climate change.

Conservation Biology↗

Greater sage-grouse science (2015–17)—Synthesis and potential management implications

Executive Summary The greater sage-grouse ( Centrocercus urophasianus ; hereafter called “sage-grouse”), a species that requires sagebrush (Artemisia spp.), has experienced range-wide declines in its distribution and abundance. These declines have prompted substantial research and management investments to improve the understanding of sage-grouse and its habitats and reverse declines in distribution and population numbers. Over the past two decades, the U.S. Fish and Wildlife Service (USFWS) has responded to eight petitions to list the sage-grouse under the Endangered Species Act of 1973, with the completion of the most recent listing determination in September 2015. At that time, the USFWS determined that the sage-grouse did not warrant a listing, primarily because of the large scale science-based conservation and planning efforts completed or started by Federal, State, local agencies, private landowners, and other entities across the range. The planning efforts culminated in the development of the 2015 Bureau of Land Management (BLM) and U.S. Forest Service Land Use Plan Amendments, which provided regulatory certainty and commitment from Federal land-management agencies to limit, mitigate, and track anthropogenic disturbance and implement other sage-grouse conservation measures. After these policy decisions, the scientific community has continued to refine and expand the knowledge available to inform implementation of management actions, increase the efficiency and effectiveness of those actions, and continue developing an overall understanding of sage-grouse populations, habitat requirements, and their response to human activity and other habitat changes. The development of science has been driven by multiple prioritization documents including the “Greater Sage-Grouse National Research Strategy” (Hanser and Manier, 2013) and, most recently, the “Integrated Rangeland Fire Management Strategy Actionable Science Plan” (Integrated Rangeland Fire Management Strategy Actionable Science Plan Team, 2016). In October 2017, after a review of the 2015 Federal plans relative to State sage-grouse plans, in accordance with Secretarial Order 3353, the BLM issued a notice of intent to consider whether to amend some, all, or none of the 2015 land use plans. At that time, the BLM requested the U.S. Geological Survey (USGS) to inform this effort through the development of an annotated bibliography of sage-grouse science published since January 2015 and a report that synthesized and outlined the potential management implications of this new science. Development of the annotated bibliography resulted in the identification and summarization of 169 peer-reviewed scientific publications and reports. The USGS then convened an interagency team (hereafter referred to as the “team”) to develop this report that focuses on the primary topics of importance to the ongoing management of sage-grouse and their habitats. The team developed this report in a three-step process. First, the team identified six primary topic areas for discussion based on the members’ collective knowledge regarding sage-grouse, their habitats, and threats to either or both. Second, the team reviewed all the material in the “Annotated Bibliography of Scientific Research on Greater Sage-Grouse Published since January 2015” to identify the science that addressed the topics. Third, team members discussed the science related to each topic, evaluated the consistency of the science with existing knowledge before 2015, and summarized the potential management implications of this science. The six primary topics identified by the team were: Multiscale habitat suitability and mapping tools Discrete anthropogenic activities Diffuse activities Fire and invasive species Restoration effectiveness Population estimation and genetics

Open-File Report↗

Assessing historical and projected carbon balance of Alaska: A synthesis of results and policy/management implications

We summarize the results of a recent interagency assessment of land carbon dynamics in Alaska, in which carbon dynamics were estimated for all major terrestrial and aquatic ecosystems for the historical period (1950–2009) and a projection period (2010–2099). Between 1950 and 2009, upland and wetland (i.e., terrestrial) ecosystems of the state gained 0.4 Tg C/yr (0.1% of net primary production, NPP), resulting in a cumulative greenhouse gas radiative forcing of 1.68 × 10 −3 W/m 2 . The change in carbon storage is spatially variable with the region of the Northwest Boreal Landscape Conservation Cooperative (LCC) losing carbon because of fire disturbance. The combined carbon transport via various pathways through inland aquatic ecosystems of Alaska was estimated to be 41.3 Tg C/yr (17% of terrestrial NPP). During the projection period (2010–2099), carbon storage of terrestrial ecosystems of Alaska was projected to increase (22.5–70.0 Tg C/yr), primarily because of NPP increases of 10–30% associated with responses to rising atmospheric CO 2 , increased nitrogen cycling, and longer growing seasons. Although carbon emissions to the atmosphere from wildfire and wetland CH 4 were projected to increase for all of the climate projections, the increases in NPP more than compensated for those losses at the statewide level. Carbon dynamics of terrestrial ecosystems continue to warm the climate for four of the six future projections and cool the climate for only one of the projections. The attribution analyses we conducted indicated that the response of NPP in terrestrial ecosystems to rising atmospheric CO 2 (~5% per 100 ppmv CO 2 ) saturates as CO 2 increases (between approximately +150 and +450 ppmv among projections). This response, along with the expectation that permafrost thaw would be much greater and release large quantities of permafrost carbon after 2100, suggests that projected carbon gains in terrestrial ecosystems of Alaska may not be sustained. From a national perspective, inclusion of all of Alaska in greenhouse gas inventory reports would ensure better accounting of the overall greenhouse gas balance of the nation and provide a foundation for considering mitigation activities in areas that are accessible enough to support substantive deployment.

Alaska↗

Inter-population differences in salinity tolerance and osmoregulation of juvenile wild and hatchery-born Sacramento splittail

The Sacramento splittail ( Pogonichthys macrolepidotus ) is a minnow endemic to the highly modified San Francisco Estuary of California, USA and its associated rivers and tributaries. This species is composed of two genetically distinct populations, which, according to field observations and otolith strontium signatures, show largely allopatric distribution patterns as recently hatched juveniles. Juvenile Central Valley splittail are found primarily in the nearly fresh waters of the Sacramento and San Joaquin rivers and their tributaries, whereas San Pablo juveniles are found in the typically higher-salinity waters (i.e. up to 10‰) of the Napa and Petaluma Rivers. As the large salinity differences between young-of-year habitats may indicate population-specific differences in salinity tolerance, we hypothesized that juvenile San Pablo and Central Valley splittail populations differ in their response to salinity. In hatchery-born and wild-caught juvenile San Pablo splittail, we found upper salinity tolerances, where mortalities occurred within 336 h of exposure to 16‰ or higher, which was higher than the upper salinity tolerance of 14‰ for wild-caught juvenile Central Valley splittail. This, in conjunction with slower recovery of plasma osmolality, but not ion levels, muscle moisture or gill Na + ,K + -ATPase activity, in Central Valley relative to San Pablo splittail during osmoregulatory disturbance provides some support for our hypothesis of inter-population variation in salinity tolerance and osmoregulation. The modestly improved salinity tolerance of San Pablo splittail is consistent with its use of higher-salinity habitats. Although confirmation of the putative adaptive difference through further studies is recommended, this may highlight the need for population-specific management considerations.

California↗

A simulation test of the effectiveness of several methods for error-checking non-invasive genetic data

Non-invasive genetic sampling (NGS) is becoming a popular tool for population estimation. However, multiple NGS studies have demonstrated that polymerase chain reaction (PCR) genotyping errors can bias demographic estimates. These errors can be detected by comprehensive data filters such as the multiple-tubes approach, but this approach is expensive and time consuming as it requires three to eight PCR replicates per locus. Thus, researchers have attempted to correct PCR errors in NGS datasets using non-comprehensive error checking methods, but these approaches have not been evaluated for reliability. We simulated NGS studies with and without PCR error and 'filtered' datasets using non-comprehensive approaches derived from published studies and calculated mark-recapture estimates using CAPTURE. In the absence of data-filtering, simulated error resulted in serious inflations in CAPTURE estimates; some estimates exceeded N by ??? 200%. When data filters were used, CAPTURE estimate reliability varied with per-locus error (E??). At E?? = 0.01, CAPTURE estimates from filtered data displayed < 5% deviance from error-free estimates. When E?? was 0.05 or 0.09, some CAPTURE estimates from filtered data displayed biases in excess of 10%. Biases were positive at high sampling intensities; negative biases were observed at low sampling intensities. We caution researchers against using non-comprehensive data filters in NGS studies, unless they can achieve baseline per-locus error rates below 0.05 and, ideally, near 0.01. However, we suggest that data filters can be combined with careful technique and thoughtful NGS study design to yield accurate demographic information. ?? 2005 The Zoological Society of London.

Animal Conservation↗

Consequences of changes in vegetation and snow cover for climate feedbacks in Alaska and northwest Canada

Changes in vegetation and snow cover may lead to feedbacks to climate through changes in surface albedo and energy fluxes between the land and atmosphere. In addition to these biogeophysical feedbacks, biogeochemical feedbacks associated with changes in carbon (C) storage in the vegetation and soils may also influence climate. Here, using a transient biogeographic model (ALFRESCO) and an ecosystem model (DOS-TEM), we quantified the biogeophysical feedbacks due to changes in vegetation and snow cover across continuous permafrost to non-permafrost ecosystems in Alaska and northwest Canada. We also computed the changes in carbon storage in this region to provide a general assessment of the direction of the biogeochemical feedback. We considered four ecoregions, or Landscape Conservations Cooperatives (LCCs; including the Arctic, North Pacific, Western Alaska, and Northwest Boreal). We examined the 90 year period from 2010 to 2099 using one future emission scenario (A1B), under outputs from two general circulation models (MPI-ECHAM5 and CCCMA-CGCM3.1). We found that changes in snow cover duration, including both the timing of snowmelt in the spring and snow return in the fall, provided the dominant positive biogeophysical feedback to climate across all LCCs, and was greater for the ECHAM (+3.1 W m −2 decade −1 regionally) compared to the CCCMA (+1.3 W m −2 decade −1 regionally) scenario due to an increase in loss of snow cover in the ECHAM scenario. The greatest overall negative feedback to climate from changes in vegetation cover was due to fire in spruce forests in the Northwest Boreal LCC and fire in shrub tundra in the Western LCC (−0.2 to −0.3 W m −2 decade −1 ). With the larger positive feedbacks associated with reductions in snow cover compared to the smaller negative feedbacks associated with shifts in vegetation, the feedback to climate warming was positive (total feedback of +2.7 W m −2 decade regionally in the ECHAM scenario compared to +0.76 W m −2 decade regionally in the CCCMA scenario). Overall, increases in C storage in the vegetation and soils across the study region would act as a negative feedback to climate. By exploring these feedbacks to climate, we can reach a more integrated understanding of the manner in which climate change may impact interactions between high-latitude ecosystems and the global climate system.

Environmental Research Letters↗