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USGS2026

Advancing ecosystem recovery with diverse species plantings in tropical forest restoration

Tropical forest restoration has increased in the past decades, with possible advancements given the UN declaration of the “Decade of Ecosystem Restoration”. However, robust assessments to compare ecosystem functions among restored forest stages are essential. We evaluated 13 actively restored forest stands ranging from 3 to 21 years of age and compared measures of forest biodiversity, structure, and ecosystem function to four 70+ year old “reference” stands that serve as restoration “targets” in the study region of the Premontane wet forest of Costa Rica. The restored stands were planted with an average of 13 tree species on abandoned pastures that were fallow for at least two years. Sixteen tree-stand attributes and six ecosystem function estimates were assessed, including: annual biomass (C) accumulation, N-fixation potential, threatened species conservation, and the provision of avian frugivore forage, insect habitat, and insect pollination. Using Principal Component Analysis, linear modeling, and Mahalanobis distance analyses, we learned that planting a diversity of tree species sets the stage for forest recovery at early restoration ages, with an inflection point at 15 years towards older reference forest characteristics and functions. Given that all restoration ages provided tree diversity and some level of ecosystem functions, the value of all restored stands in the landscape is notable. The assessment methods are easily employed, thereby providing an accessible tool to restoration practitioners.

Monteverde↗

USGS2016

Distribution and diversity of tunicates utilizing eelgrass as substrate in the western North Atlantic between 39° and 47° north latitude (New Jersey to Newfoundland)

Seagrass meadows are ecologically important habitats that are declining globally at an accelerating rate due to natural and anthropogenic stressors. Their decline is a serious concern as this habitat provides many ecosystem services. Eelgrass ( Zostera marina ) is the dominant seagrass species in the western North Atlantic. It has recently been established that invasive tunicate species possibly threaten the health of eelgrass beds. Colonization of eelgrass leaves by tunicates can inhibit eelgrass growth and may cause shoot mortality. To document the distribution and diversity of tunicate species that attach to eelgrass in the western North Atlantic, we surveyed twenty-one eelgrass sites from New Jersey to Newfoundland. Eight species of tunicates were found to be colonizing eelgrass, of which 6 are considered invasive. Botrylloides violaceus and Botryllus schlosseri were most commonly attached to eelgrass, with B. schlosseri having the largest latitudinal range of any species. Tunicate faunas attached to eelgrass were less diverse north of Gloucester, Massachusetts, where individual survey sites exhibited two species at most and only 4 of the 8 species observed in this study. Percent tunicate cover on eelgrass tended to fall within the 1–25 range, with occasional coverage up to >75–100. Density of eelgrass was highly variable among sites, ranging from <1 to 820 shoots/m². The solitary tunicate Ciona intestinalis was only found on eelgrass at the highest latitude sampled, in Newfoundland, where it is a new invader. The tunicates observed in this study, both solitary and colonial, are viable when attached to eelgrass and pose a potential threat to overgrow and weaken seagrass shoots and reduce the sustainability of seagrass meadows.

Management of Biological Invasions↗

USGS2015

Structure, diversity, and biophysical properties of old-growth forestsin the Klamath region, USA

The diverse old-growth forests in Klamath region of northern California and southern Oregon provide valuable ecosystem services (e.g., maintaining watersheds, wildlife habitat, recreation), but may be vulnerable to a wide range of stressors, including invasive species, disrupted disturbance regimes, and climatic change. Yet our understanding of how forest structure in the Klamath region relates to the current physical environment is limited. Here we provide present-day benchmarks for old-growth forest structure across a climatic gradient ranging from coastal to dry interior sites. We established 16 large (1 ha) forest plots where all stems > 5 cm in diameter were identified to species and mapped. Climate across these sites was highly variable, with estimated actual evapotranspiration correlated to several basic measures of forest structure, including plot basal area, stem size-class inequality, tree species diversity and, to a lesser extent, tree species richness. Analyses of the spatial arrangement of stems indicated a high degree of non-uniformity, with 75% of plots showing significant stem clumping at small spatial scales (0 to 10 m). Downscaled predictions of future site water balance suggest changes will be dominated by rapidly increasing climatic water deficit (D, a biologically meaningful index of drought). While these plots give a picture of current conditions, continued monitoring of these stands is needed to describe forest dynamics and to detect forest responses to ongoing and future stressors.

Klamath region↗

USGS2026

A Lake Charr pangenome reveals highly conserved Ohnologs as drivers of phenotypic diversity

Whole-genome duplication (WGD) is hypothesized to spur evolutionary diversification by producing genome-wide duplicate gene sets (Ohnologs) that are initially functionally redundant but can diverge markedly as the effects of relaxed selection accumulate over time. However, the underlying mechanisms remain unclear, in part because genomic studies often reconstruct Ohnolog evolution over millions of years, during which subsequent mutations can obscure deep-time signals. Investigating the relationship between Ohnolog evolution and diversification on a contemporary timescale offers clearer insights. We explore this relationship in Lake Charr ( Salvelinus namaycush ), where ∼10% of genes are retained highly conserved polyploid duplicates following the Salmonid-Specific Fourth Round WGD. Using 31 chromosome-level assemblies of Lake Charr from morphologically and ecologically diverse populations, joined into a pangenome graph, we characterized 189,555 structural variants (SVs) that were significantly less likely to affect genes retained as sequence-conserved Ohnolog pairs, nuancing the hypothesis that gene redundancy, relaxed selection, and functional diversification are intertwined. However, we found that SVs affecting such conserved Ohnologs may be potent drivers of adaptive evolution. Notably, we identified a putative 938-Kb interchromosomal translocation containing 25 genes with highly conserved Ohnologs in a paralogous (but untranslocated) genomic block. This putative translocation appears to have facilitated Ohnolog divergence in ankrd11 and hp , genes putatively linked to craniofacial and lipid metabolic diversity in sympatric Lake Superior morphs. This research reveals that conserved Ohnologs previously presumed to be redundant remain a reservoir for adaptive change.

BioRxiv↗

USGS1996

Measuring and monitoring biological diversity: Standard methods for mammals

Measuring and Monitoring Biological Diversity: Standard Methods for Mammals provides a comprehensive manual for designing and implementing inventories of mammalian biodiversity anywhere in the world and for any group, from rodents to open-country grazers. The book emphasizes formal estimation approaches, which supply data that can be compared across habitats and over time. Beginning with brief natural histories of the twenty-six orders of living mammals, the book details the field techniques—observation, capture, and sign interpretation—appropriate to different species. The contributors provide guidelines for study design, discuss survey planning, describe statistical techniques, and outline methods of translating field data into electronic formats. Extensive appendixes address such issues as the ethical treatment of animals in research, human health concerns, preserving voucher specimens, and assessing age, sex, and reproductive condition in mammals. Useful in both developed and developing countries, this volume and the Biological Diversity Handbook Series as a whole establish essential standards for a key aspect of conservation biology and resource management.

Book↗

USGS2008

Diverse deformation patterns of Aleutian volcanoes from InSAR

Interferometric synthetic aperture radar (InSAR) is capable of measuring ground-surface deformation with centimeter-to-subcentimeter precision at a spatial resolution of tens of meters over an area of hundreds to thousands of square kilometers. With its global coverage and all-weather imaging capability, InSAR has become an increasingly important measurement technique for constraining magma dynamics of volcanoes over remote regions such as the Aleutian Islands. The spatial pattern of surface deformation data derived from InSAR images enables the construction of detailed mechanical models to enhance the study of magmatic processes. This paper summarizes the diverse deformation patterns of the Aleutian volcanoes observed with InSAR and demonstrates that deformation patterns and associated magma supply mechanisms in the Aleutians are diverse and vary between volcanoes. These findings provide a basis for improved models and better understanding of magmatic plumbing systems.

Conference Paper↗

USGS1998

Impact of alternative regeneration methods on genetic diversity in coastal Douglas-fir

Genetic implications of natural and artificial regeneration following three regeneration methods (group selection, shelterwood, and clearcut) were investigated in coastal Douglas-fir ( Pseudotsuga menziesii var. menziesii [Mirb.] Franco) using genetic markers (17 allozyme loci). In general, harvesting followed by either natural or artificial regeneration resulted in offspring populations little altered from those in the previous generation. Cutting the smallest trees to form shelterwoods, however, resulted in the removal of rare, presumably deleterious, alleles, such that slightly fewer alleles per locus were observed among residual trees (2.76) and natural regeneration (2.75) than found in uncut (control) stands (2.86). Thus, although the shelterwood regime appears quite compatible with gene conservation, it would be best to leave parent trees of a range of sizes in shelterwoods designated as gene conservation reserves, in order to maximize the number of alleles (regardless of current adaptive value) in naturally regenerated offspring. Seedling stocks used for artificial regeneration in clearcut, shelterwood, and group selection stands (7 total) had significantly greater levels of genetic diversity, on average, than found in natural regeneration. This is probably because the seeds used in artificial seedling stocks came from many wild stands and thus, sampled more diversity than found in single populations. For. Sci. 44(3): 390-396.

Forest Science↗

USGS2012

Primer for identifying cold-water refuges to protect and restore thermal diversity in riverine landscapes

In 2003, EPA issued Region 10 guidance for Pacific Northwest state and tribal temperature water quality standards. This document was the culmination of a multi-agency, multi-disciplinary effort to develop a temperature standard for the protection of salmon, steelhead, bull trout, and redband and Lahontan cutthroat trout (collectively termed coldwater salmonids). Since its release, the Oregon and Washington have adopted the temperature standard for their waters designated for protection of coldwater salmonids. One of the unique aspects of the temperature standard, which strived to integrate the physical nature of rivers and streams and the biological requirements of coldwater salmonids, is the requirement to protect and restore cold-water refuges. This requirement is incorporated into the temperature criterion for the protection of migration corridors in the Willamette, Columbia, and Snake rivers. The intent of this provision is the recognition that some coldwater salmonids migrate through waters during thermally stressful months of summer and most likely are able to do so by using features in the rivers that provide cold water spatially or temporally. The challenge is to ensure that these features are identified, protected, and restored in order for these waters to meet the temperature standard. This primer is intended to assist Region 10 states, tribes, and local watershed groups in meeting this goal and thereby further the protection and restoration of coldwater salmonids. It provides an up-to-date summary with easily referenced information and illustrations on the scientific advances and management applications of research on cold-water refuges and can be used as a "roadmap" for identifying cold-water refuges and learning more about processes that create thermal diversity in riverine landscapes. The specific objectives are to 1. define cold-water refuge in scientific and management contexts. 2. outline an approach for identifying cold-water refuges to address water quality standards. 3. classify and characterize the types and physical processes that create cold-water refuges. 4. review methods and tools for identifying cold-water refuges in small streams to large rivers. 5. describe ecological perspectives and on-the-ground approaches for protecting and restoring thermal diversity in rivers.

Oregon↗

USGS2012

Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria , phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

Atacama Desert↗

USGS1977

Miospore diversity and its relationship to lithology in the Coker Formation (Upper Cretaceous) of western Alabama

A multiple-regression procedure was applied to samples from two cores of the Coker Formation (Upper Cretaceous) of western Alabama in an attempt to characterize the relationship between the diversity of miospore species and selected lithologic factors. The resulting prediction equations suggest that the number of miospore species in these samples is inversely related to changes in median grain size and to other as yet undefined factors not reflected by lithology. In addition, it appears that the degree of sorting of the sediment has no effect on species diversity. A plot of these prediction equations shows that changes in the number of miospore species are negligible in samples of clay and silt size but that the number of species decreases rapidly in sediments of fine sand size or coarser. The results presented here agree with those presented by other workers for the relationship between grain size and the absolute abundance of miospores.

Alabama↗

USGS2013

Field trial of a pulsed limestone diversion well

The use of limestone diversion wells to treat acid mine drainage (AMD) is well-known, but in many cases, acid neutralization is not as complete as would be desired. Reasons for this include channeling of the water through the limestone bed, and the slow reaction rate of the limestone gravel. A new approach to improve the performance of the diversion well was tested in the field at the Jennings Environmental Education Center, near Slippery Rock, PA. In this approach, a finer size distribution of limestone was used so as to allow fluidization of the limestone bed, thus eliminating channeling and increasing particle surface area for faster reaction rates. Also, water flow was regulated through the use of a dosing siphon, so that consistent fluidization of the limestone sand could be achieved. Testing began late in the summer of 2010, and continued through November of 2011. Initial system performance during the 2010 field season was good, with the production of net alkaline water, but hydraulic problems involving air release and limestone sand retention were observed. In the summer of 2011, a finer size of limestone sand was procured for use in the system. This material fluidized more readily, but acid neutralization tapered off after several days. Subsequent observations indicated that the hydraulics of the system was compromised by the formation of iron oxides in the pipe leading to the limestone bed, which affected water distribution and flow through the bed. Although results from the field trial were mixed, it is believed that without the formation of iron oxides and plugging of the pipe, better acid neutralization and treatment would have occurred. Further tests are being considered using a different hydraulic configuration for the limestone sand fluidized bed.

Pennsylvania↗

USGS2016

Effects of Climate and land use on diversity, prevalence, and seasonal transmission of avian hematozoa in American Samoa

The indigenous forest birds of American Samoa are increasingly threatened by changing patterns of rainfall and temperature that are associated with climate change as well as environmental stressors associated with agricultural and urban development, invasive species, and new introductions of avian diseases and disease vectors. Long term changes in their distribution, diversity, and population sizes could have significant impacts on the ecological integrity of the islands because of their critical role as pollinators and seed dispersers. We documented diversity of vector borne parasites on Tutuila and Ta‘u Islands over a 10-year period to expand earlier observations of Plasmodium, Trypanosoma , and filarial parasites, to provide better parasite identifications, and to create a better baseline for detecting new parasite introductions. We also identified potential mosquito vectors of avian Plasmodium and Trypanosoma , determined whether land clearing and habitat alterations associated with subsistence farming within the National Park of American Samoa can influence parasite prevalence, and determined whether parasite prevalence is correlated with seasonal changes in rainfall, temperature and wind speed. Three taxonomically distinct lineages of Plasmodium were identified from mosquito vectors and forest birds based on partial sequence data from parasite mitochondrial genes. All three have been described from passerine and galliform birds in Australasia. Two lineages, SCEDEN01 and ORW1, had elongate gametocytes and large schizonts that were consistent with species of Plasmodium in the subgenus Giavannolaia, but were taxonomically distinct from known morphological species of Plasmodium based on a Bayesian phylogenetic analysis of a 478 bp region of the parasite cytochrome b gene. Both are candidates for description as new species. The third lineage (GALLUS02) was detected only in mosquito vectors on Tutuila and was similar in cytochrome b sequence to P. juxtanucleare , a pathogenic species of Plasmodium from chickens and other galliform birds from Australasia, Africa, and South America. Plasmodium relictum , the malarial parasite that has had such a devastating impact on Hawaiian forest birds, was not detected. We observed large, striated trypanosomes in avian hosts from both Tutuila and Ta‘u Islands that fell within the same taxonomic clade as T. corvi and T. culicavium based on 18S ribosomal DNA sequence. We also observed sheathed microfilariae with pointed tails that had some morphological similarities to microfilaria from species of Pelecitus, Struthiofilaria and Eulimdana , but identification will require recovery and examination of adult filarial worms from the connective tissue or body cavities of infected birds. We also observed one or more species of haemococcidians (Isospora, synonym = Atoxoplasma ) within circulating lymphocytes from multiple avian host species. Overall prevalence of Plasmodium was higher on Ta‘u (22%, 75/341) than Tutuila (9.2%, 27/294), with most infections occurring in Polynesian starlings, Samoan starlings, Wattled honeyeaters, and Cardinal honeyeaters. Prevalence was relatively constant from year to year and between seasons at individual study sites, but varied among study sites, with highest rates of infection in areas with agricultural activity at Faleasao (37.4%, 73/195, Ta‘u Island) and Amalau Valley (9.7%, 21/216, Tutuila Island). Prevalence in more remote areas of the National Park of American Samoa was lower, ranging from 1.4% (2/146) at Laufuti and Luatele on Ta‘u to 7.7% (6/78) at Olo Ridge on Tutuila. Similar trends were evident for infections with Trypanosoma and filarial worms. Overall prevalence was not influenced significantly by warmer, wet (summer) or cooler, dry (winter) season. We detected Plasmodium infections in Culex sitiens and C. quinquefasciatus through either salivary gland and midgut dissections or PCR amplification of parasite cytochrome b genes in pooled or individual samples of mosquitoes that were collected on Tutuila. Pooled or individual Aedes oceanicus, A. polynesiensis, A. tutuilae, A. upolensis, A. nocturnus, Aedes (Finlaya) (mixed pools of A. samoanus, A. oceanicus, A. tutuilae), Aedes (Stegomyia) (mixed pools of A. aegypti, A. upolensis, A. polynesiensis ), and C. annulirostris were negative for Plasmodium , but we detected infections with Trypanosoma through midgut and salivary gland dissections in a single C. sitiens from Amalau Valley, Tutuila and three A. oceanicus from Faleasao, Ta‘u. Two of the A. oceanicus from Faleasao amplified successfully with Trypanosoma primers, but sequences were distinctly different from those obtained from avian hosts. We found a strong association between land use and prevalence of mosquito-transmitted parasites on Ta‘u Island with odds of being infected more than 20 times greater in agricultural plots than more remote native forest. This relationship was evident on Tutuila Island but not statistically significant because of the close proximity of study sites and observed movement of birds between native forest and agricultural land. Our data support previous studies that have suggested that Plasmodium and other vector-borne parasites are part of the indigenous parasite fauna in American Samoa. Transmission dynamics appear to be affected by environmental changes associated with land use practices.

HI↗

USGS2016

Genetic diversity of Wolbachia endosymbionts in Culex quinquefasciatus from Hawai`i, Midway Atoll, and Samoa

Incompatible insect techniques are potential methods for controlling Culex quinquefasciatus and avian disease transmission in Hawai‘i without the use of pesticides or genetically modified organisms. The approach is based on naturally occurring sperm-egg incompatibilities within the Culex pipiens complex that are controlled by different strains of the bacterial endosymbiont Wolbachia pipientis (wPip). Incompatibilities can be unidirectional (crosses between males infected with strain A and females infected with strain B are fertile, while reciprocal crosses are not) or bidirectional (reciprocal crosses between sexes with different wPip strains are infertile). The technique depends on release of sufficient numbers of male mosquitoes infected with an incompatible wPip strain to suppress mosquito populations and reduce transmission of introduced avian malaria ( Plasmodium relictum ) and Avipoxvirus in native forest bird habitats. Both diseases are difficult to manage using more traditional methods based on removal and treatment of larval habitats and coordination of multiple approaches may be needed to control this vector. We characterized the diversity of Wolbachia strains in C. quinquefasciatus from Hawai‘i, Kaua‘i, Midway Atoll, and American Samoa with a variety of genetic markers to identify compatibility groups and their distribution within and between islands. We confirmed the presence of wPip with multilocus sequence typing, tested for local genetic variability using 16 WO prophage genes, and identified similarities to strains from other parts of the world with a transposable element (tr1). We also tested for genetic differences in ankyrin motifs (ank2 and pk1) which have been used to classify wPip strains into five worldwide groups (wPip1–wPip5) that vary in compatibility with each other based on experimental crosses. We found a mixture of both widely distributed and site specific genotypes based on presence or absence of WO prophage and transposable element markers on Hawai‘i Island (Volcano, Pu‘u Wa‘awa‘a, Laupāhoehoe, Kaumana, Kahuku, Nīnole, and Maulua Gulch), Kaua‘i Island (Kawaikōī, Mōhihi, Kalāheo, Lāwa‘i and Hanapepe) and Midway Atoll. Genotypes from American Samoa were unique and formed their own clade. Based on analysis of ankyrin motifs, wPip strains from Hawai‘i, Kaua‘i, and Midway Atoll were most similar to wPip5 strains of Australasian origin. By contrast, Wolbachia strains from Culex quinquefasciatus collected in American Samoa were most similar to wPip3 strains of American origin. We detected a single Culex mosquito from Pu‘u Wa‘awa‘a on Hawai‘i Island that was infected with a unique wPip3 genotype. This discovery, plus a rarefaction analysis of genotypes from Kaua‘i and Hawai‘i Islands suggests that limited sampling may have underestimated diversity of wPip in our study. Mosquitoes infected with wPip5 and wPip3 are bidirectionally compatible with each other based on prior studies, which would support their ability to coexist within the same population on Hawai‘i Island. Available evidence from prior studies suggests that genotype wPip4 from Africa, the Middle East, Europe, and Asia is bidirectionally incompatible with genotype wPip5 and varies in compatibility with genotype wPip3 depending on geographic origin. Since wPip5 appears to be the most common compatibility group in Hawai‘i based on limited sampling, logical next steps are to 1) expand the current survey to include additional islands and localities, 2) infect a laboratory colony of Hawaiian Culex with wPip4 through tetracycline treatment of Hawaiian mosquitoes and backcross with Culex from Europe, North Africa, and the Middle East that are naturally infected with wPip4, 3) conduct cage trials to confirm bidirectional incompatibilities between Hawaiian Culex infected with wPip4 and wPip5, and 4) conduct field trials to evaluate whether release of incompatible males can be applied at small scales to suppress local populations.

American Samoa, Hawaii↗

USGS2016

Undergraduate research projects help promote diversity in the geosciences

A workforce that draws from all segments of society and mirrors the ethnic, racial, and gender diversity of the United States population is important. The geosciences (geology, hydrology, geospatial sciences, environmental sciences) continue to lag far behind other science, technology, engineering and mathematical (STEM) disciplines in recruiting and retaining minorities (Valsco and Valsco, 2010). A report published by the National Science Foundation in 2015, “Women, Minorities, and Persons with Disabilities in Science and Engineering” states that from 2002 to 2012, less than 2% of the geoscience degrees were awarded to African-American students. Data also show that as of 2012, approximately 30% of African-American Ph.D. graduates obtained a bachelor’s degree from a Historic Black College or University (HBCU), indicating that HBCUs are a great source of diverse students for the geosciences. This paper reviews how an informal partnership between Tennessee State University (a HBCU), the U.S. Geological Survey, and Mammoth Cave National Park engaged students in scientific research and increased the number of students pursuing employment or graduate degrees in the geosciences.

Conference Paper↗

USGS1994

Genetic diversity in Arctic-nesting geese: Implications for management and conservation

The North Pacific Rim harbors breeding populations of many unique wildlife resources, of which waterfowl are among the most abundant and taxonomically diverse. Arctic nesting geese in particular are wide-spread in distribution (Figure 1), and though only seasons residents, they have evolved many unique adaptations for breeding in northern latitudes. This diversity has been recognized and managed at many taxonomic and geographic levels (Figure 2). Populations are spatially structured on macro- and micro-geographic scales reflecting taxon-specific migratory tendencies, and breeding and winter site fidelity.

Transactions of the North American Wildlife and Na↗

USGS2025

Amphibian diversity of the western Colorado canyonlands including potential threats from nonnative bullfrogs and disease

Throughout the canyons of the Colorado and Uncompahgre Plateaus, water is a limited resource for wildlife, with patchy distribution and seasonal availability. Tributary creeks within these canyons drain into mainstem rivers, providing habitat and breeding sites for native amphibians. Yet, little is known about the diversity and distribution of amphibians that live in these harsh, dynamic environments. In addition, the rivers that border these canyon tributaries may serve as corridors for nonnative species and disease. The American Bullfrog ( Lithobates catesbeianus ) is a nonnative species in western Colorado known to prey on native amphibians and act as a reservoir for pathogens such as Batrachochytrium dendrobatidis ( Bd ). From 2019 to 2022, we surveyed for amphibians using visual encounter surveys (VES) and environmental DNA (eDNA) surveys throughout the McInnis Canyons National Conservation Area (MCNCA), the Dominguez–Escalante National Conservation Area (DENCA), and the Dolores River Canyon Wilderness Study Area (DRCWSA). Our primary goals were to document the diversity and distribution of native amphibians in the canyonlands and evaluate potential threats to these species from bullfrogs and Bd . We confirmed that sensitive species, such as the Great Basin Spadefoot ( Spea intermontana ) and the Northern Leopard Frog ( Lithobates pipiens ), inhabit these protected areas. In most cases, bullfrogs were not detected within ephemeral tributaries, but bullfrog DNA was detected in some tributaries at the confluence with the mainstem rivers. In Mee Canyon (MCNCA), however, bullfrogs were found within the tributary, up to 3 km from the Colorado River. A bullfrog individual removed from this canyon tested positive for Bd , and diet contents suggested that native amphibians are potential prey in this system. Nonnative predators and disease pose a threat to native amphibians, alongside environmental changes such as drought and hydrological shifts driven by ongoing climate change.

Colorado↗

USGS2025

A model for regional-scale oak savanna management: The roles of fire, canopy, and soils for understory plant diversity

Predicting the outcomes of land management on biodiversity is difficult without a mechanistic understanding of how management approaches, ecosystem structure, environmental conditions, and biodiversity interact. Management effects may be direct or indirect, context- or scale-dependent, or obscured by local environmental conditions. Resolving these relationships at the regional scale may be difficult, given heterogeneity in local environmental conditions, yet understanding broad-scale patterns can elucidate context dependencies and improve restoration outcomes. We confronted these challenges within globally rare oak savannas in the midwestern United States, which have been altered by fire exclusion and resulting woody encroachment. By modeling direct and indirect pathways by which management influences diversity, we test a general framework for savanna restoration. Across 100 oak savannas spanning five US states, management by prescribed fire and mechanical thinning of woody vegetation affected groundlayer plant species richness through changes to ecosystem structure (canopy openness and litter depth), and these effects were both context- and scale-dependent. Frequent prescribed fires and canopy thinning promoted greater canopy openness, which in turn increased richness at small (1 m 2 ), but not larger (1000 m 2 ) scales. Frequent fire additionally increased richness at small and larger scales through effects independent of ecosystem structure. While management effects were large relative to the influence of local edaphic conditions, soil productivity had two largely offsetting effects on small-scale richness, increasing richness directly but decreasing richness indirectly by promoting closed canopy structure. These results suggest using a combination of fire and canopy thinning to reverse the effects of decades of fire exclusion. However, management effects were also context-dependent, emphasizing that management outcomes vary regionally. Here, 1-m 2 plant species richness increased with both fire frequency and canopy thinning under low, but not high, productivity soil conditions. By demonstrating how specific management practices influence savanna structure and biodiversity by manipulating ecological processes across broad geographic and edaphic gradients, our findings provide a framework for understanding management outcomes at short and medium intervals (e.g., within and between decades, respectively), in the form of a model that can be refined by testing additional hypotheses to better predict savanna restoration outcomes.

Illinois, Indiana, Michigan, Ohio, Wisconsin↗

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↗