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USGS2022

Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex

The Neosho Bass ( Micropterus velox ), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass ( M. dolomieu ), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.

Ecology and Evolution↗

USGS2013

Fluvial rainbow trout contribute to the colonization of steelhead ( Oncorhynchus mykiss ) in a small stream

Life history polymorphisms provide ecological and genetic diversity important to the long term persistence of species responding to stochastic environments. Oncorhynchus mykiss have complex and overlapping life history strategies that are also sympatric with hatchery populations. Passive integrated transponder (PIT) tags and parentage analysis were used to identify the life history, origin (hatchery or wild) and reproductive success of migratory rainbow/steelhead for two brood years after barriers were removed from a small stream. The fluvial rainbow trout provided a source of wild genotypes to the colonizing population boosting the number of successful spawners. Significantly more parr offspring were produced by anadromous parents than expected in brood year 2005, whereas significantly more parr offspring were produced by fluvial parents than expected in brood year 2006. Although hatchery steelhead were prevalent in the Methow Basin, they produced only 2 parr and no returning adults in Beaver Creek. On average, individual wild steelhead produced more parr offspring than the fluvial or hatchery groups. Yet, the offspring that returned as adult steelhead were from parents that produced few parr offspring, indicating that high production of parr offspring may not be related to greater returns of adult offspring. These data in combination with other studies of sympatric life histories of O. mykiss indicate that fluvial rainbow trout are important to the conservation and recovery of steelhead and should be included in the management and recovery efforts.

Washington↗

USGS2020

A multifaceted reconstruction of the population structure and life history expressions of a remnant metapopulation of Bonneville Cutthroat Trout: Implications for maintaining intermittent connectivity

Fishes that evolutionarily demonstrated a fluvial life history expression and migrated to spawning and rearing habitat by using lotic corridors are increasingly impacted by fragmentation. The overall goal of this study was to identify the contemporary importance of main-stem connectivity and tributaries for maintaining life history expression, population structure, and viability of a large metapopulation of Bonneville Cutthroat Trout (BCT) Oncorhynchus clarkii utah persisting in the highly fragmented Weber River, Utah. We used a multifaceted approach, including active sampling, mark–recapture, passive PIT tag detection, otolith microchemistry, and genetics. We collected BCT in all tributaries and the main stem, encountering age-0 fish in three tributaries, indicating successful reproduction. In tributaries, the size structure was bimodal and consisted of smaller fish that were classified as resident and larger fish that were deemed to be fluvial, whereas all sizes and ages (age ≥ 1) were present in the main stem. We identified up to eight age-classes; tributaries were dominated by ages 2 and 8, and the main stem was dominated by ages 2, 5, 6, and 7. Tributary BCT had lower growth rates than BCT in the main stem. We observed a surprising degree of fluvial life history expression, and fish also demonstrated very complex movement patterns across their life span. Average apparent survival (33%) was within the range estimated in similar studies for BCT, and the resight rate was best explained by angler management regulations. The fact that BCT in the Weber River and tributaries still reproduce successfully in most years and are still able to grow into large, fluvial fish suggests that connectivity must be occasionally available despite considerable fragmentation. Therefore, this metapopulation may need little further human intervention if barriers to fish passage can be removed, thereby improving connectivity, and it represents a high-priority metapopulation for conservation, thus highlighting the utility of our approach.

Utah↗

USGS2019

Environmental DNA (eDNA) detection of nonnative bullseye snakehead in southern Florida

Bullseye Snakehead Channa marulius (Hamilton 1822) was first detected in the southern Florida town of Tamarac in 2000 and has been expanding its geographic range since. Environmental DNA (eDNA) analysis is a newly-developed technique used to noninvasively detect cryptic or low-density species or those that are logistically difficult-to-study. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of target species eDNA. To help delineate Bullseye Snakehead’s geographic range, we developed and validated a species-specific eDNA assay for both quantitative and droplet digital PCR (ddPCR). We then used ddPCR to assess 16 locations in southeast Florida using 222 water samples collected from 2015 to 2018. Positive eDNA detections were obtained at all six locations that were within the known geographic range of Bullseye Snakehead. Furthermore, eDNA was detected in six of 10 locations that were previously thought to be outside the periphery of the range but hydrologically connected through the extensive canal system. Over the four years of sampling, estimated occurrence rates (ψ) remained stable and relatively high (ψ = 0.67 [95% credible interval (CI) 0.33–0.95]) near Tamarac, Florida, as compared to the most southern sampling locations (ψ = 0.0–0.37). Bulls- eye Snakehead eDNA estimated occurrence rates in the middle region increased between 2016 (0.28 [95% CI 0.03–0.94]) and 2017 (0.66 [95% CI 0.24–0.98]), potentially reflecting eDNA detections related to a growing or expanding population. Bullseye Snakehead eDNA was detected at low concentrations on the northern and eastern borders of Everglades National Park, which is an important conservation area and UNESCO World Heritage Site. Despite extensive sampling via electrofishing, no Bullseye Snakehead were visually detected in several locations that yielded positive eDNA samples. It is unclear whether eDNA was transported through flowing water or another vector. To date, collection records for this species are confined to urban canals; however, Bullseye Snakehead may use the interconnected system of canals to disperse to natural conservation areas such as Everglades National Park, Big Cypress National Preserve, and Water Conservation Areas, where it may impact native species via predation and competition.

Florida↗

USGS2020

An evaluation of noninvasive sampling techniques for Malayan sun bears

Traditional mark–recapture studies to estimate abundance and trends of Malayan sun bear ( Helarctos malayanus ) populations are impeded by logistics of live-trapping wild individuals. The development of noninvasive sampling techniques for monitoring sun bear populations is therefore crucial for targeted conservation action. Sun bears have short fur, and conventional hair-snagging devices are ineffective. Moreover, scats are rapidly decomposed by the warm, humid environment, as well as by invertebrates. In combination with camera-sampling, we tested 2 designs of hair traps ( n = 45) in situ at Tabin Wildlife Reserve in Sabah, Malaysia, during April–October 2017, to obtain hair samples from wild sun bears. We also deployed 4 types of hair traps in rainforest enclosures with captive sun bears to evaluate hair-capture success and the effects of weathering, lure, and adhesive on polymerase chain reaction (PCR) amplification success. Wild adult male sun bears displayed back-rubbing behavior at hair traps and 6 individuals were identified based on unique chest marks. We collected 30 hair samples from wild sun bears, including 15 chest mark images of 6 individuals over 1,260 trap-nights. We detected adult males at hair traps more frequently than females and subadults. We obtained 39 hair samples in the captive trials. Extracted DNA from hair roots successfully amplified with mitochondrial (wild bears: 95%; captive bears: 97%) and microsatellite primers (wild bears: 100%; captive bears 87%). Adhesive and lure type did not affect PCR amplification, but weathering reduced amplification of microsatellite loci. This study is the first successful attempt to obtain genetic samples from wild sun bears using inexpensive, readily available materials such as duct tape, polybutyl glue, and locally sourced lures. The quality of genetic material from these genetic samples should be suitable for studies of population size and gene flow.

Sabah↗

USGS2020

Using movement to inform conservation corridor design for Mojave desert tortoise

Background Preserving corridors for movement and gene flow among populations can assist in the recovery of threatened and endangered species. As human activity continues to fragment habitats, characterizing natural corridors is important in establishing and maintaining connectivity corridors within the anthropogenic development matrix. The Mojave desert tortoise ( Gopherus agassizii ) is a threatened species occupying a variety of habitats in the Mojave and Colorado Deserts. Desert tortoises have been referred to as corridor-dwellers, and understanding how they move within suitable habitat can be crucial to defining corridors that will sustain sufficient gene flow to maintain connections among populations amidst the increases in human development. Methods To elucidate how tortoises traverse available habitat and interact with potentially inhospitable terrain and human infrastructure, we used GPS dataloggers to document fine-scale movement of individuals and estimate home ranges at ten study sites along the California/Nevada border. Our sites encompass a variety of habitats, including mountain passes that serve as important natural corridors connecting neighboring valleys, and are impacted by a variety of linear anthropogenic features. We used path selection functions to quantify tortoise movements and develop resistance surfaces based on landscape characteristics including natural features, anthropogenic alterations, and estimated home ranges with autocorrelated kernel density methods. Using the best supported path selection models and estimated home ranges, we determined characteristics of known natural corridors and compared them to mitigation corridors (remnant habitat patches) that have been integrated into land management decisions in the Ivanpah Valley. Results Tortoises avoided areas of high slope and low perennial vegetation cover, avoided moving near low-density roads, and traveled along linear barriers (fences and flood control berms). Conclusions We found that mitigation corridors designated between solar facilities should be wide enough to retain home ranges and maintain function. Differences in home range size and movement resistance between our two natural mountain pass corridors align with differences in genetic connectivity, suggesting that not all natural corridors provide the same functionality. Furthermore, creation of mitigation corridors with fences may have unintended consequences and may function differently than natural corridors. Understanding characteristics of corridors with different functionality will help future managers ensure that connectivity is maintained among Mojave desert tortoise populations.

California, Nevada↗

USGS2015

Arctic biodiversity: Increasing richness accompanies shrinking refugia for a cold-associated tundra fauna

As ancestral biodiversity responded dynamically to late-Quaternary climate changes, so are extant organisms responding to the warming trajectory of the Anthropocene. Ecological predictive modeling, statistical hypothesis tests, and genetic signatures of demographic change can provide a powerful integrated toolset for investigating these biodiversity responses to climate change, and relative resiliency across different communities. Within the biotic province of Beringia, we analyzed specimen localities and DNA sequences from 28 mammal species associated with boreal forest and Arctic tundra biomes to assess both historical distributional and evolutionary responses and then forecasted future changes based on statistical assessments of past and present trajectories, and quantified distributional and demographic changes in relation to major management regions within the study area. We addressed three sets of hypotheses associated with aspects of methodological, biological, and socio-political importance by asking (1) what is the consistency among implications of predicted changes based on the results of both ecological and evolutionary analyses; (2) what are the ecological and evolutionary implications of climate change considering either total regional diversity or distinct communities associated with major biomes; and (3) are there differences in management implications across regions? Our results indicate increasing Arctic richness through time that highlights a potential state shift across the Arctic landscape. However, within distinct ecological communities, we found a predicted decline in the range and effective population size of tundra species into several discrete refugial areas. Consistency in results based on a combination of both ecological and evolutionary approaches demonstrates increased statistical confidence by applying cross-discipline comparative analyses to conservation of biodiversity, particularly considering variable management regimes that seek to balance sustainable ecosystems with other anthropogenic values. Refugial areas for cold-adapted taxa appear to be persistent across both warm and cold climate phases and although fragmented, constitute vital regions for persistence of Arctic mammals.

Ecosphere↗

USGS2022

Evolutionary dynamics inform management interventions of a hanging garden obligate, Carex specuicola

Uncovering the historical and contemporary processes shaping rare species with complex distributions is of growing importance due to threats such as habitat destruction and climate change. Species restricted to specialized, patchy habitat may persist by virtue of life history characteristics facilitating ongoing gene flow and dispersal, but they could also reflect the remnants of formerly widespread, suitable habitat that existed during past climate regimes. If formerly widespread species did not rely upon traits facilitating high dispersibility to persist, contemporary populations could be at high risk of extirpation or extinction. Fortunately, genomic investigations provide an opportunity to illuminate such alternative scenarios while simultaneously offering guidance for future management interventions. Herein, we test the role of these mechanisms in shaping patterns of genomic diversity and differentiation across a highly restricted and rare ecosystem: desert hanging gardens. We focus on Carex specuicola (Cyperaceae), a hanging garden obligate narrowly distributed in the Four Corners region of the southwestern United States that is listed as Threatened under the United States Endangered Species Act. Population structure and diversity analyses reveal that hanging garden populations are shaped by strong genetic drift, but that individuals in gardens are occasionally more closely related to individuals at other gardens than to individuals within the same garden. Similarly, gardens separated by long geographic distances may contain individuals that are more closely related compared to individuals in gardens separated by short geographic distances. Demographic modeling supports historical gene flow between some contemporary garden pairs, which is corroborated by low estimates of inbreeding coefficients and recent divergence times. As such, multiple lines of evidence support dispersal and gene flow across C. specuicola populations at both small and large spatial scales, indicating that even if C. specuicola was formerly more widespread, it may be well suited to persist in hanging gardens so long as suitable habitat remains available. Analyses like those demonstrated herein may be broadly applicable for understanding the short- and long-term evolutionary processes influencing rare species, and especially those having complex distributions across heterogeneous landscapes.

Arizona, Utah↗

USGS2025

Feeding habits of sympatric aoudad (Ammotragus lervia) and desert bighorn sheep (Ovis canadensis mexicana) in West Texas

Aoudad ( Ammotragus lervia ), native to northern Africa, were introduced as exotic game animals to the Chihuahuan Desert in West Texas, USA, and have become invasive. Aoudad and bighorn sheep ( Ovis canadensis mexicana ) are adapted to rugged terrain in arid climates, and both persist in desert regions with low primary productivity and limited perennial water availability, which suggests potential for competition for food and water resources. Aoudad are highly adaptable, which could make them more resilient to a changing environment with extreme conditions, providing a competitive edge over bighorn sheep. To evaluate the potential for exploitative competition between invasive aoudad and endemic desert bighorn sheep, we used genetic metabarcoding to assess diet composition using fecal samples collected from adults of each species in the Sierra Vieja Mountains in West Texas. We collected 32 composite samples from aoudad and 27 composite samples for bighorn sheep and identified 88 genera consumed. Bighorn sheep and aoudad diets (as inferred by genera) were most different during the warm-wet season (16 June–15 October; Kulczynski similarity index = 0.81) and most similar during the warm-dry season (16 February–15 June; Kulczynski similarity index = 1.05). During the warm-wet season, the 2 herbivores tended to consume different genera, suggesting the possibility of resource partitioning, with less likelihood of resource partitioning during the warm-dry season when forage was more limited and diets were similar. Diet diversity, measured by Shannon's diversity index, did not vary substantially between species, but for aoudad it was highest during the warm-wet season (1.1 ± 0.0.1 [SE]) and lowest during the cool-dry season (16 October–15 February, 0.9 ± 0.0.1). For bighorn sheep, diet richness was highest during the cool-dry season (1.1 ± 0.2) and lowest during the warm-dry season (0.8 ± 0.10). Bighorn sheep may specialize on high-quality forage species, particularly during the warm-wet season, while aoudad have a more generalist foraging strategy, although temporal windows for increased competition for food resources likely occur. Aoudad are well-adapted to low-quality forage and arid climates, which could increase their competitive ability and compromise bighorn sheep conservation efforts in areas of sympatry.

Texas↗

USGS2021

Impact of "non-lethal" tarsal clipping on bumble bees (Bombus vosnesenskii) may depend on queen stage and worker size

Recent bumble bee declines have prompted the development of novel population monitoring tools, including the use of putatively non-lethal tarsal clipping to obtain genetic material. However, the potential side effects of tarsal clipping have only been tested in the worker caste of a single domesticated species, prompting the need to more broadly test whether tarsal clipping negatively affects sampled individuals. To determine if tarsal clipping reduces queen survivorship and colony establishment, we collected wild queens of Bombus vosnesenskii and clipped tarsi from a single leg of half the individuals. We reared captive queens and estimated survivorship and nest establishment success. We also clipped tarsi of workers from a subset of colonies across a range of body sizes. We found no consistent negative effect of clipping on queen survival. In the first year, clipped nest-searching queens suffered heavy mortality, but there was no effect on foraging queens. The following year, we found no effect of clipping on queen survival or establishment. Clipping did not reduce overall worker survival but reduced survivorship for those in the smallest size quartile.

Journal of Insect Conservation↗

USGS2014

A hierarchical integrated population model for greater sage-grouse ( Centrocercus urophasianus ) in the Bi-State Distinct Population Segment, California and Nevada

Greater sage-grouse ( Centrocercus urophasianus , hereafter referred to as “sage-grouse”) are endemic to sagebrush ( Artemisia spp.) ecosystems throughout Western North America. Populations of sage-grouse have declined in distribution and abundance across the range of the species (Schroeder and others, 2004; Knick and Connelly, 2011), largely as a result of human disruption of sagebrush communities (Knick and Connelly, 2011). The Bi-State Distinct Population Segment (DPS) represents sage-grouse populations that are geographically isolated and genetically distinct (Benedict and others, 2003; Oyler-McCance and others, 2005) and that are present at the extreme southwestern distribution of the sage-grouse range (Schroeder and others, 2004), straddling the border of California and Nevada. Subpopulations of sage-grouse in the DPS may be at increased risk of extirpation because of a substantial loss of sagebrush habitat and lack of connectivity (Oyler-McCance and others, 2005). Sage-grouse in the Bi-State DPS represent small, localized breeding populations distributed across 18,325 km 2 . The U.S. Fish and Wildlife Service currently (2014) is evaluating the Bi-State DPS as threatened or endangered under the Endangered Species Act of 1973, independent of other sage-grouse populations. This DPS was designated as a higher priority for listing than sage-grouse in other parts of the species’ range (U.S. Department of the Interior, 2010). Range-wide population analyses for sage-grouse have included portions of the Bi-State DPS (Sage and Columbian Sharp-tailed Grouse Technical Committee 2008; Garton and others, 2011). Although these analyses are informative, the underlying data only represent a portion of the DPS and are comprised of lek count observations only. A thorough examination of population dynamics and persistence that includes multiple subpopulations and represents the majority of the DPS is largely lacking. Furthermore, fundamental information on population growth rate (i.e., finite rate of change, λ) and specific demographic parameters that explain sources of variation in λ within different subpopulations would be valuable for making conservation and management decisions for this DPS. During 2003–12, agencies and universities collaborated to conduct extensive monitoring of sage-grouse populations within the Bi-State DPS. Data regarding lek attendance, movement, and survival of sage-grouse across multiple life stages were documented. Specifically, sage-grouse from nearly all subpopulations were marked and tracked across multiple seasons using radio-telemetry techniques. A hierarchical integrated population modeling (IPM) approach was used to derive demographic parameters for the Bi-State DPS using the large amount of data collected over a 10-year period. This modeling approach allows integration of multiple data sources to inform population growth rates and population vital rates for the Bi-State DPS overall, as well as for individual subpopulations. These models are more informative than other models because they integrate inputs of demographic data (for example, survival and fecundity rates) and survey data (for example, lek observations). The findings here will help characterize population growth rates within the Bi-State DPS.

California;Nevada↗

USGS2021

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↗

USGS2002

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↗

USGS2020

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↗

USGS2024

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↗

USGS2017

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↗

USGS2017

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↗

USGS2023

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↗