Geology topics

Robert N. Fisher

Publications and source records attributed to Robert N. Fisher.

At least 37 records · Page 2Linked to original sources

USGS2024

2023-2024 Coastal sage scrub and chaparral community monitoring for western San Diego County

Western San Diego County is dominated by shrublands supporting biologically diverse native plant and animal communities. Widespread urbanization has led to regional habitat loss and fragmentation, and many species in these shrubland communities are rare, threatened, or endangered. Large-scale, multiple-species conservation planning has resulted in a regional preserve system that focuses on these shrubland communities. Several large-scale threats are leading to type conversion from shrub-dominated to non-native invasive annual grass-dominated vegetation. To understand the changes that are occurring to native shrublands, we have developed a vegetation monitoring program with several components at multiple spatial scales, focused on quantifying coastal sage scrub (CSS) and chaparral vegetation community characteristics. Several drivers of change associated with type conversion of native shrubland to non-native annual grassland have been identified by previous research including increasing fire frequency, nitrogen deposition from air pollution, and prolonged and intense drought associated with changing climate. Loss of ecological integrity indices have been proposed as useful measures of the threat of degradation and type conversion of shrublands in San Diego County. For this study, ecological integrity is defined as a system’s ability to maintain species’ relationships and functions comparable to natural habitat in the region. Previous studies have identified the percent cover of invasive non-native annual grasses as a proxy for overall ecological degradation (loss of integrity) that is consistent across native taxonomic groups. Increased cover of non-native grass is associated with lower integrity of the shrubland vegetation community as shrub-associated plant and animal species are replaced by species preferring grassy and disturbed habitats. The objectives of this CSS and chaparral vegetation community monitoring plan are to: 1) Determine the distribution, composition, structure, and integrity of CSS and chaparral vegetation communities on conserved lands in western San Diego County, 2) Identify whether these attributes of the vegetation communities are changing over time, and 3) Evaluate relationships of known drivers of change (threats) and environmental factors in association with changes in vegetation community attributes. The CSS and chaparral vegetation community monitoring program is divided into four components: 1) vegetation mapping, 2) GIS/remote sensing office analysis of landscape-scale data, 3) permanent field plots using Unmanned Aerial Systems (UAS) and field data collections, and 4) animal and target species surveys and rapid assessment protocols. The first component, which is not detailed in this vegetation monitoring plan, aims to map vegetation communities every 10-15 years based on a classification developed for western San Diego County. High resolution aerial imagery will be used to update the 2012 vegetation map and expand it across the entire study area. The second component uses remote sensing models to annually track ecological integrity of shrublands across the study area and will include a map of areas of change and areas of stability over several decades. These landscape-scale integrity classifications will be used to analyze ecological processes, threats, and abiotic factors relative to changes to shrubland ecological integrity over time and space. The third component includes field surveys of 100 permanent plots across areas historically mapped as shrublands. Surveys in the 1930s mapped vegetation types using plot data. By using this historical classification map, we included areas that have already type-converted from shrubland to non-native annual grassland. The plots were split between CSS (55 plots) and chaparral (45 plots) and stratified into four geographical eco-subregions to guarantee coverage over small patches of habitat along the heavily developed coast. Surveys will include the collection of UAS imagery at a very high resolution. Species-level identifications will be made from the imagery based on a plant list compiled of all species detected in the plot during a thorough field survey by botanists, combined with geo-referenced samples of plant species locations. In addition, herbaceous cover will be estimated in the field using nine 1-m diameter circles (one per subplot) to obtain ocular estimates of cover for each plant species within the circle frame. Soil samples will be collected and analyzed for important element compositions. These data will be analyzed to evaluate plot-level ecological integrity based on species composition and cover. Repeated monitoring will allow evaluation of changes in vegetation attributes over time with known drivers or threats and other environmental factors. In addition, analyses will focus on indicator species and various measures of biological diversity for the vegetation communities. Finally, animal species and rare plants will be assessed using either taxa-based rapid assessment protocols or specialized species-specific protocols for rarer species. The purpose of these assessments is to document the status, habitat, and threat covariates of specific species and confirm the species composition and diversity of animal taxonomic groups (e.g., pollinators). Diversity and abundance of animal species at vegetation plots will be used to refine measures and thresholds of ecological integrity. Rapid assessment protocols for animal taxonomic groups can include multiple detection methods such as, camera traps, cover boards, and bird point counts. Pollinators will be monitored at plots using a protocol currently being developed in conjunction with but separately from this plan. Target rare plant species will be monitored using the regional Inspect and Manage (IMG) protocol that measures the status of rare plant occurrences and habitat and threat covariates over time. Species-specific animal survey methods will be refined as these species are prioritized for future monitoring. The goal of this monitoring program is to classify CSS and chaparral vegetation community integrity, identify areas of degradation across western San Diego County, and characterize drivers, and environmental factors associated with loss of ecological integrity. A combination of vegetation mapping, landscape-scale remote sensing, and field plots will be used to address all the aspects of our research questions. Data compiled and collected will be available to conservation partners to help inform future management decisions.

California↗

USGS2023

Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard

Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334–127 Mb) representing macrochromosomes and 8 small scaffolds (63–22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.

Genome Biology and Evolution↗

USGS2023

Broad-scale assessment of methylmercury in adult amphibians

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg bioaccumulation in 3,241 juvenile and adult amphibians during 2017–2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R 2 ≥ 0.67), whereas total Hg in sediment was not (R 2 ≤ 0.04). Our study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential threats of MeHg to amphibians.

Environmental Science and Technology↗

USGS2023

Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods

Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.

California↗

USGS2023

Fecal metabarcoding of the endangered Pacific pocket mouse (Perognathus longimembris pacificus) reveals a diverse and forb rich diet that reflects local habitat availability

Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long-term study plots in two populations on Marine Corps Base Camp Pendleton, San Diego County, CA. Fecal samples ( n = 221) were collected between spring 2016 and fall 2017 during monthly live-trap surveys. Concurrently, percent cover and plant phenology were measured in plots centered on trap locations. Fecal samples were sequenced with paired-end reads of the internal transcribed spacer 2 region of the nuclear ribosomal gene, and the resulting amplicons were matched to a regionally specific database. Seventy-three plant taxa were detected, which were mostly forbs and perennial herbs (70–90%). Diet composition differed between populations, years, seasons, and plots. Overall, diet and local habitat composition in plots were significantly correlated. However, we detected some differences in above-ground seed availability and proportion in fecal samples that indicate diet preferences for some forbs, perennial herbs, and native bunch grasses over perennial shrubs and non-native grasses. This is the first study of PPM to pair plant phenology surveys with diet metabarcoding to estimate resource selection, and results suggest that managing habitat for diverse native forb communities and reducing non-native grass cover may be beneficial for this critically endangered species.

California↗

USGS2023

Native amphibian toxin reduces invasive crayfish feeding with potential benefits to stream biodiversity

Background Biodiversity is generally reduced when non-native species invade an ecosystem. Invasive crayfish, Procambarus clarkii , populate California freshwater streams, and in the Santa Monica Mountains (Los Angeles, USA), their introduction has led to trophic cascades due to omnivorous feeding behavior and a rapid rate of population growth. The native California newt, Taricha torosa , possesses a neurotoxin, tetrodotoxin (TTX), that affects freshwater animal behavior. Given P. clarkii has a limited evolutionary history with TTX, we hypothesized that TTX may affect crayfish feeding behaviors. To determine if TTX affects P. clarkii behavior, we measured cumulative movement and various feeding behaviors of P. clarkii exposed to (i) waterborne, ecologically realistic concentrations of TTX (~ 3.0 × 10 − 8 moles/L), (ii) an anuran chemical cue to account for intraguild cues, or (iii) a T. torosa chemical cue with quantitated TTX in it (~ 6.2 × 10 − 8 moles/L). Results We found that the presence of TTX in any form significantly reduced crayfish movement and decreased the amount of food consumed over time. Crayfish responses to the anuran treatment did not significantly differ from controls. Conclusion Our laboratory results show that naturally occurring neurotoxin from native California newts limits invasive crayfish foraging and feeding rates, which may play a role in preserving local stream ecosystems by limiting invasive crayfish behaviors that are detrimental to biodiversity.

California↗

USGS2023

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus , has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed “ring species” around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis , as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Journal of Heredity↗

USGS2023

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake ( Crotalus oreganus ) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus , in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

California↗

USGS2023

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Spiny lizards (genus Sceloporus ) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis , is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis , the species status of the California endemic island fence lizard ( S. becki ), and the spectacular radiation of Sceloporus lizards.

California↗

USGS2023

Elevated road segment (ERS) passage design may provide enhanced connectivity for amphibians, reptiles, and small mammals

Introduction: Designs for safe and effective road crossing structures for small animals are typically under-road microtunnels and culverts which have varying levels of effectiveness reported in the scientific literature. Many species, particularly migratory amphibians, may have limited ability to find and use passages if they are too far apart, resulting in substantial barrier effects. Methods: We designed a novel open elevated passage (elevated road segment: ERS), similar to a low terrestrial bridge, that could theoretically be built to any length based upon species needs and movement characteristics. A 30 m length prototype ERS was installed along a forest road with a history of amphibian road mortality in Sierra National Forest, Fresno County, CA, USA. From 2018 to 2021, we monitored small animal activity under the ERS in relation to surrounding roadside and forest habitats using active infrared cameras. Results: We documented a total of 8,815 unique use events, using species specific independence criteria, across 22 species of amphibians (3), reptiles (4), and small mammals (15). Poisson regression modeling of taxonomic group activity under the ERS, roadside and forest, showed that amphibian activity was highest in the forest habitat, no differences were observed for reptiles, and small mammal activity was highest under the ERS. However, mean activity estimates under the ERS were equal to or greater than the open roadside habitat for all 22 species, suggesting that adding cover objects, such as downed logs and vegetation may further enhance passage use. Discussion: Overall, results showed that the design of the ERS crossing has potential to provide high connectivity for a wide range of amphibian, reptile, and small mammal species while reducing road mortality. ERS systems can also be used in areas with challenging terrain and other hydrological and environmental constraints. Incorporating current road ecology science, we provide supplemental ERS concept designs for secondary roads, primary roads and highways to help increase the options available for road mitigation planning for small animals.

California↗

USGS2023

Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii

Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville’s horned lizard, Phrynosoma blainvillii , due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.

California↗

USGS2023

Protocol for the reintroduction of California red-legged frogs to Santa Monica Mountains National Recreation Area

Once common and widespread in Southern California, California red-legged frogs ( Rana draytonii ) began declining sometime in the middle of the 20th century. They were listed as threatened under the Endangered Species Act in 1996. Three small and isolated populations remained in Los Angeles and Ventura Counties by the start of the 21st century. The nearest population of California red-legged frogs to Santa Monica Mountains National Recreation Area is critically small, located 15 km to the north, yet there is evidence of persistence, including successful reproduction each year it has been measured. A potential solution to alleviate small population size and isolation is to reintroduce a species back to habitable historical locations nearby. In 2011, we initiated a project to reintroduce California red-legged frogs back to the Santa Monica Mountains, where historical records showed they were once widespread. We developed a procedure to transfer partial egg masses into tadpole rearing pens located within streams determined to be suitable for the species. This translocation protocol outlines our procedure and results for the first five years of the project. It is our hope that this protocol will guide and inform similar conservation efforts for California red-legged frogs in other parts of their range as well as other amphibian conservation efforts throughout the world.

California↗

USGS2023

Taxonomic reassessment of the Little pocket mouse, Perognathus longimembris (Rodentia, Heteromyidae) of southern California and northern Baja California

The Little pocket mouse ( Perognathus longimembris ) encompasses 15 to 16 currently recognized subspecies, six of which are restricted to southern California and adjacent northern Baja California. Using cranial geomorphometric shape parameters and dorsal color variables we delineate six regional groups of populations from this area that we recognize as valid, but these differ in name combination and geographic range from the current taxonomy. We resurrect two names from their current placement in synonymies, synonymize two currently recognized subspecies, and we reassign a third. Importantly, we restrict the U. S. Federally endangered Pacific pocket mouse ( P. l. pacificus Mearns) to the vicinity of its type locality at the mouth of the Tijuana River in the southwestern corner of San Diego County and resurrect P. l. cantwelli von Bloeker for the other two population segments along the coast, those that span the northwestern corner of San Diego County and adjacent Orange County and that in coastal Los Angeles County. The name cantwelli would now apply to the only extant populations of the Pacific pocket mouse, a reassignment with obvious management implications. Our taxonomic decisions also reconfigure the ranges of other subspecies of conservation concern, notably P. l. bangsi Mearns and P. l. brevinasus Osgood.

California↗

USGS2023

Skinks of Oceania, New Guinea, and Eastern Wallacea: An underexplored biodiversity hotspot

Context: Skinks comprise the dominant component of the terrestrial vertebrate fauna in Oceania, New Guinea, and Eastern Wallacea (ONGEW). However, knowledge of their diversity is incomplete, and their conservation needs are poorly understood. Aims: To explore the diversity and threat status of the skinks of ONGEW and identify knowledge gaps and conservation needs. Methods: We compiled a list of all skink species occurring in the region and their threat categories designated by the International Union for Conservation of Nature. We used available genetic sequences deposited in the National Center for Biotechnology Information’s GenBank to generate a phylogeny of the region’s skinks. We then assessed their diversity within geographical sub-divisions and compared to other reptile taxa in the region. Key results: Approximately 300 species of skinks occur in ONGEW, making it the second largest global hotspot of skink diversity following Australia. Many phylogenetic relationships remain unresolved, and many species and genera are in need of taxonomic revision. One in five species are threatened with extinction, a higher proportion than almost all reptile families in the region. Conclusions: ONGEW contain a large proportion of global skink diversity on <1% of the Earth’s landmass. Many are endemic and face risks such as habitat loss and invasive predators. Yet, little is known about them, and many species require taxonomic revision and threat level re-assessment. Implications: The skinks of ONGEW are a diverse yet underexplored group of terrestrial vertebrates, with many species likely facing extreme risks in the near future. Further research is needed to understand the threats they face and how to protect them.

Pacific Conservation Biology↗

USGS2023

Interactions among rainfall, fire, forbs and non-native grasses predict occupancy dynamics for the endangered Pacific pocket mouse (Perognathus longimembris pacificus) in a Mediterranean-type ecosystem

It is important to understand species-habitat relationships to implement effective adaptive management for rare species. However, it can be challenging to assess habitat associations and their relationships to abiotic stressors in dynamic habitats without the insights that can be gained from long-term monitoring. We report results from the first six years of extensive track tube monitoring of the largest two of three remaining extant populations of federally endangered Pacific pocket mouse ( Perognathus longimembris pacificus ) in a coastal Mediterranean-type ecosystem on Marine Corps Base, Camp Pendleton in southern California, USA. We used dynamic occupancy and structural equation modeling to assess potential drivers of population trends that included habitat, fire history, rainfall, disturbance, and the presence of other small mammals. We found that the variables that best predicted mouse occupancy were moderate to high forb and perennial herb cover (40–80%), and moderate to high open ground (20–70%) and low non-native grass cover (<20%), Non-native grass cover (>20%) was also a strong predictor of lower PPM colonization and increased extinction probabilities, with the extent of non-native grass cover being strongly influenced by annual rainfall and recency of fire. Our study adds to the growing literature on effects of invasive annual grasses on native species in Mediterranean-type ecosystems. We suggest that habitat management could be based upon promotion of open forb and perennial herb dominated habitats with reduction of non-native grasses by prescribed fire and other methods. These types of spatial and temporal monitoring programs can support land managers by creating a monitoring and management feedback loop. They can reveal landscape and environmental variables associated with species persistence, inform habitat management goals, and help managers to assess the success of management actions on populations of conservation concern.

California↗

USGS2023

On the origin and current distribution of the Oceania Snake-Eyed Skink (Cryptoblepharus poecilopleurus) in the Hawaiian archipelago

Because of its extreme isolation and lack of historical connection to a mainland, the Hawaiian Archipelago is thought to have no native nonvolant terrestrial reptiles. Several squamate species have been introduced to the archipelago, likely starting with early Polynesian contact, and increasing as human traffic in the Pacific has amplified. Of the earlier introductions, one species of skink, Cryptoblepharus poecilopleurus , belongs to a genus known for its ability to naturally disperse long distances, even across oceans. The earliest herpetofaunal surveys from Hawai‘i describe the skink as widespread and abundant across the archipelago. A recent phylogenetic analysis reveals substantial haplotype divergence between Hawaiian individuals and other known populations in the Pacific, raising the possibility that this species was an early and natural arrival to the archipelago before human contact. Recent surveys suggest that the species has undergone a dramatic reduction in range across the archipelago, possibly due to the invasion of highly competitive species. Given this information, we aim to further assess the origin of C. poecilopleurus in Hawai‘i, determine its current range, and suggest specific needs for future work. Here, we review the earliest European voyages in the Pacific that are known to have sampled C. poecilopleurus , review literature and museum specimens to develop an understanding of this species’ history in the islands, survey the island of O‘ahu to characterize its current range, and provide preliminary genetic analyses to show the relationship of the Hawai’i populations to the rest of the Pacific.

Hawaii↗

USGS2023

Prioritizing the risk and management of introduced species in a landscape with high indigenous biodiversity

Risk analysis protocols for prioritizing the management of non-native species are numerous, yet few incorporate risk and management in the same analysis or accommodate a broad diversity of taxa outside of a specific geographic area. We adapted a protocol that accounts for these factors to address non-native animal species in the Southern California/Northern Baja California Coast Ecoregion near the international border in San Diego County, an area with high indigenous biodiversity and high numbers of species of conservation concern. This stepwise, semi-quantitative protocol is applicable to any animal group in any predefined geographic area, relies on consensus-building among taxonomic experts, and has been vetted through previous use and in peer-reviewed literature. Our results show that the final prioritization was driven mainly by management feasibility, with top-ranked species having multitrophic effects that favor other non-native invaders over native residents. Conditions within the assessment area required some modification to the protocol as it was originally designed, namely a shift in emphasis from eradication to control, given that eradication is implausible for most non-native species in the assessment area. We call attention to taxon-specific issues that surfaced during the analysis, identify areas for improvement in this first-ever risk assessment for invasive animal species in the Natural Communities Conservation Plan/Habitat Conservation Plan (NCCP/HCP) reserve system of San Diego County, and provide suggestions for further refinement of the protocol. This study builds on the effort to standardize risk analysis for invasive species globally, given that many of the same invaders present threats to indigenous biodiversity worldwide.

California↗

USGS2022

Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore

Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIV Lru ) genetic variation and spread among bobcats ( Lynx rufus ) sampled from coastal southern California. We found evidence for increased rates of FIV Lru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIV Lru sequences was associated with host genetic distances and geographic location, with FIV Lru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIV Lru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIV Lru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.

California↗