Aquatic Soundscape Recordings Reveal Diverse Vocalizations and Nocturnal Activity of an Endangered Frog.

AbstractAutonomous sensors provide opportunities to observe organisms across spatial and temporal scales that humans cannot directly observe. By processing large data streams from autonomous sensors with deep learning methods, researchers can make novel and important natural history discoveries. In this study, we combine automated acoustic monitoring with deep learning models to observe breeding-associated activity in the endangered Sierra Nevada yellow-legged frog (Rana sierrae), a behavior that current surveys do not measure. By deploying inexpensive hydrophones and developing a deep learning model to recognize breeding-associated vocalizations, we discover three undocumented R. sierrae vocalization types and find an unexpected temporal pattern of nocturnal breeding-associated vocal activity. This study exemplifies how the combination of autonomous sensor data and deep learning can shed new light on species' natural history, especially during times or in locations where human observation is limited or impossible.

Patterns, timing, and environmental drivers of growth in two coexisting green-stemmed Mediterranean alpine shrubs species.

The Mediterranean alpine is one of the most vulnerable ecosystems under future environmental change. Yet, patterns, timing and environmental controls of plant growth are poorly investigated. We aimed at an improved understanding of growth processes, as well as stem swelling and shrinking patterns, by examining two common coexisting green-stemmed shrub species. Using dendrometers to measure daily stem diameter changes, we separated these changes into water-related shrinking and swelling and irreversible growth. Implementing correlation analysis, linear mixed effects models, and partial least squares regression on time series of stem diameter changes, with corresponding soil temperature and moisture data as environmental predictors, we found species-specific growth patterns related to different drought-adaptive strategies. We show that the winter-cold-adapted species Cytisus galianoi uses a drought tolerance strategy combined with a high ecological plasticity, and is, thus, able to gain competitive advantages under future climate warming. In contrast, Genista versicolor is restricted to a narrower ecological niche using a winter-cold escape and drought avoidance strategy, which might be of disadvantage in a changing climate. Pregrowth environmental conditions were more relevant than conditions during growth, controlling the species' resource availability. Thus, studies focusing on current driver constellations of growth may fail to predict a species' ecological niche and its potential future performance.

Effects of climate change on Lepidoptera pollen loads and their pollination services in space and time.

Shifts in flowering time among plant communities as a result of climate change, including extreme weather events, are a growing concern. These plant phenological changes may affect the quantity and quality of food sources for specialized insect pollinators. Plant-pollinator interactions are threatened by habitat alterations and biodiversity loss, and changes in these interactions may lead to declines in flower visitors and pollination services. Most prior research has focused on short-term plant-pollinator interactions, which do not accurately capture changes in pollination services. Here, we characterized long-term plant-pollinator interactions and identified potential risks to specialized butterfly species due to habitat loss, fragmented landscapes, and changes in plant assemblages. We used 21 years of historical data from museum specimens to track the potential effects of direct and indirect changes in precipitation, temperature, monsoons, and wildfires on plant-pollinator mutualism in the Great Basin and Sierra Nevada. We found decreased pollen richness associated with butterflies within sites, as well as an increase in pollen grain abundance of drought-tolerant plants, particularly in the past 10 years. Moreover, increased global temperatures and the intensity and frequency of precipitation and wildfires were negatively correlated with pollen diversity. Our findings have important implications for understanding plant-pollinator interactions and the pollination services affected by global warming.

Exploring the influence of activity participation on the economic value of nature-based recreation in the Sierra Nevada.

A more comprehensive understanding of how recreational values and forest visitation rates vary across different activities enables forest managers to tailor conservation and management strategies to align with preferences among visitors, ensuring more effective allocation of budgetary resources. However, current research often focuses on only a few recreational activities, resulting in limited insights for forest managers. This study aims to expand the nature-based activities considered so that management can better serve the broader public. We conduct a travel cost analysis using a large survey-based dataset to estimate the value of nature-based recreation in national forests in the Sierra Nevada region and assess how these values differ across main activities. We categorize recreational activities into five broad groups (Passive, Active, Camping, Winter, and Other) to offer a comprehensive view of recreational preferences. A truncated negative binomial regression accounting for endogenous stratification is used to analyze the relationship between the number of trips to the forests, travel cost, activity categories, and socio-demographic variables. Our results suggest a mean consumer surplus (CS) of $65 per visit per person to national forests in the Sierra Nevada. Aggregated over annual per person visits, the total CS is approximately $313.3 million per year. Our findings reveal variations in CS across activity groups, with winter activities (e.g., skiing, snowboarding) and active activities (e.g., hiking, fishing) attracting the highest number of visits, and the highest total CS. Our results provide valuable insights for national forest managers, facilitating the strategic allocation of limited resources to recreational activities that maximize societal welfare.

New hard tick (Acari: Ixodidae) reports and detection of Rickettsia in ticks from Sierra Nevada de Santa Marta, Colombia.

The Sierra Nevada de Santa Marta (SNSM), located in northern Colombia, is considered a geographical island with high levels of biodiversity and endemism. However, little is known about tick species and their associated microorganisms at the SNSM. In this study we sampled host-seeking ticks in areas of the town of Minca within the SNSM. We collected 47 ticks identified as Amblyomma pacae, Amblyomma longirostre, Amblyomma ovale, Amblyomma mixtum, Haemaphysalis juxtakochi, Ixodes sp. cf. Ixodes affinis and Ixodes sp. Of these ticks, we tested for Rickettsia spp. by amplifying the gltA, SCA1, and 16S rRNA genes via PCR. Rickettsia amblyommatis was detected in one pool of 3 larvae and in a female of A. pacae. Additonally, we isolated Rickettsia sp. belonging to the group of spotted fevers in larvae of A. longirostre. This study reports new findings of six species of ticks and two species of Rickettsia within the SNSM.

Candida auris Discovery through Community Wastewater Surveillance during Healthcare Outbreak, Nevada, USA, 2022.

Candida auris transmission is steadily increasing across the United States. We report culture-based detection of C. auris in wastewater and the epidemiologic link between isolated strains and southern Nevada, USA, hospitals within the sampled sewershed. Our results illustrate the potential of wastewater surveillance for containing C. auris.

Climate and fire impacts on tree recruitment in mixed conifer forests in northwestern Mexico and California.

Frequent-fire forests were once heterogeneous at multiple spatial scales, which contributed to their resilience to severe fire. While many studies have characterized historical spatial patterns in frequent-fire forests, fewer studies have investigated their temporal dynamics. We investigated the influences of fire and climate on the timing of conifer recruitment in old-growth Jeffrey pine-mixed conifer forests in the Sierra San Pedro Martir (SSPM) and the eastern slope of the Sierra Nevada. Additionally, we evaluated the impacts of fire exclusion and recent climate change on recruitment levels using statistical models with realized as well as fire suppression and climate change-free counterfactual scenarios. Excessive soil drying from anthropogenic climate change resulted in diminished recruitment in the SSPM but not in the Sierra Nevada. Longer fire-free intervals attributable to fire suppression and exclusion resulted in greater rates of recruitment across all sites but was particularly pronounced in the Sierra Nevada, where suppression began >100 years ago and recruitment was 28 times higher than the historical fire return interval scenario. This demonstrates the profound impact of fire's removal on tree recruitment in Sierra Nevada forests even in the context of recent climate change. Tree recruitment at the SSPM coincided with the early-20th-century North American pluvial, as well as a fire-quiescent period in the late 18th and early 19th centuries. Episodic recruitment occurred in the SSPM with no "average" recruitment over the last three centuries. We found that temporal heterogeneity, in conjunction with spatial heterogeneity, are critical components of frequent-fire-adapted forests. Episodic recruitment could be a desirable characteristic of frequent-fire-adapted forests, and this might be more amenable to climate change impacts that forecast more variable precipitation patterns in the future. One key to this outcome would be for frequent fire to continue to shape these forests versus continued emphasis on fire suppression in California.

Leveraging species richness and ecological condition indices to guide systematic conservation planning.

The global crises of biodiversity loss and climate change are interconnected in root cause and solutions. Targeted land conservation has emerged as a leading strategy to protect vulnerable species and buffer climate impacts, however, consistent methods to assess biodiversity and prioritize areas for protection have not yet been established. Recent landscape-scale planning initiatives in California present an opportunity to conserve biodiversity, but to enhance their effectiveness, assessment approaches should move beyond commonly used measures of terrestrial species richness. In this study, we compile publicly available datasets and explore how distinct biodiversity conservation indices - including indicators of terrestrial and aquatic species richness and of biotic and physical ecosystem condition - are represented in watersheds of the northern Sierra Nevada mountain region of California (n = 253). We also evaluate the extent to which the existing protected area network covers watersheds that support high species richness and intact ecosystems. Terrestrial and aquatic species richness showed unique spatial patterns (Spearman R = 0.27), with highest richness of aquatic species in the low-elevation watersheds of the study area and highest richness of terrestrial species in mid- and high-elevation watersheds. Watersheds with the highest ecosystem condition were concentrated in upper-elevations and were poorly correlated with those with the highest species richness (Spearman R = -0.34). We found that 28% of watersheds in the study area are conserved by the existing protected area network. Protected watersheds had higher ecosystem condition (mean rank-normalized score = 0.71) than unprotected areas (0.42), but species richness was generally lower (0.33 in protected versus 0.57 in unprotected watersheds). We illustrate how the complementary measures of species richness and ecosystem condition can be used to guide strategies for landscape-scale ecosystem management, including prioritization of watersheds for targeted protection, restoration, monitoring, and multi-benefit management. Though designed for California, application of these indices to guide conservation planning, design monitoring networks, and implement landscape-scale management interventions provides a model for other regions of the world.

Rapid Increase in Suspected SARS-CoV-2 Reinfections, Clark County, Nevada, USA, December 2021.

Genetic differences between SARS-CoV-2 variants raise concerns about reinfection. Public health authorities monitored the incidence of suspected reinfection in Clark County, Nevada, USA, during March 2020-March 2022. Suspected reinfections, defined as a second positive PCR test collected >90 days after an initial positive test, were monitored through an electronic disease surveillance system. We calculated the proportion of all new cases per week that were suspected reinfections and rates per 1,000 previously infected persons by demographic groups. The rate of suspected reinfection remained <2.7% until December 2021, then increased to ≈11%, corresponding with local Omicron variant detection. Reinfection rates were higher among adults 18-50 years of age, women, and minority groups, especially persons identifying as American Indian/Alaska Native. Suspected reinfection became more common in Clark County after introduction of the Omicron variant, and some demographic groups are disproportionately affected. Public health surveillance could clarify the SARS-CoV-2 reinfection burden in communities.

Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris).

Genetic structure and phenotypic variation among populations are affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD data set of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.

Changes in tree drought sensitivity provided early warning signals to the California drought and forest mortality event.

Climate warming in recent decades has negatively impacted forest health in the western United States. Here, we report on potential early warning signals (EWS) for drought-related mortality derived from measurements of tree-ring growth (ring width index; RWI) and carbon isotope discrimination (∆13 C), primarily focused on ponderosa pine (Pinus ponderosa). Sampling was conducted in the southern Sierra Nevada Mountains, near the epicenter of drought severity and mortality associated with the 2012-2015 California drought and concurrent outbreak of western pine beetle (Dendroctonus brevicomis). At this site, we found that widespread mortality was presaged by five decades of increasing sensitivity (i.e., increased explained variation) of both tree growth and ∆13 C to Palmer Drought Severity Index (PDSI). We hypothesized that increasing sensitivity of tree growth and ∆13 C to hydroclimate constitute EWS that indicate an increased likelihood of widespread forest mortality caused by direct and indirect effects of drought. We then tested these EWS in additional ponderosa pine-dominated forests that experienced varying mortality rates associated with the same California drought event. In general, drier sites showed increasing sensitivity of RWI to PDSI over the last century, as well as higher mortality following the California drought event compared to wetter sites. Two sites displayed evidence that thinning or fire events that reduced stand basal area effectively reversed the trend of increasing hydroclimate sensitivity. These comparisons indicate that reducing competition for soil water and/or decreasing bark beetle host tree density via forest management-particularly in drier regions-may buffer these forests against drought stress and associated mortality risk. EWS such as these could provide land managers more time to mitigate the extent or severity of forest mortality in advance of droughts. Substantial efforts at deploying additional dendrochronological research in concert with remote sensing and forest modeling will aid in forecasting of forest responses to continued climate warming.

Restoring function: Positive responses of carbon and nitrogen to 20 years of hydrologic restoration in montane meadows.

Montane meadows are highly productive ecosystems that contain high densities of soil carbon (C) and nitrogen (N). However, anthropogenic disturbances that have led to channel incision and disconnected floodplain hydrology have altered the C balance of many meadows, converting them from net C sinks to net sources of C to the atmosphere. Restoration efforts designed to reconnect floodplain hydrology may slow rates of soil C loss from degraded meadows and restore the conditions for C sequestration and N immobilization, yet questions remain about the long-term impact of such efforts. Here, we used a 22-year meadow restoration chronosequence to measure the decadal impact of hydrologic restoration on aboveground and belowground C and N stocks and concentrations. Increases in herbaceous vegetation biomass preceded changes in soil C stocks, with the largest gains occurring belowground. Root biomass (0-15 cm) increased at a rate of 270.3 g m-2 year-1 and soil C stocks (0-15 cm) increased by 232.9 g C m-2 year-1 across the chronosequence. Increases in soil C concentration (2.99 g C kg-1 year-1 ) were tightly coupled with increases in soil N concentration (0.21 g N kg-1 year-1 ) and soil C:N did not vary with time since restoration. Fourier transform infrared spectroscopy results showed that the fraction of labile aliphatic C-H and carboxylate C-O (COO) compounds in the soil increased with the age of restoration and were positively correlated with soil C and N concentrations. Our results demonstrate that restoration of floodplain hydrology in montane meadows has significant impacts on belowground C and N stocks, soil C and N concentration, and soil C chemistry within the first two decades following restoration.

Effects of Livestock Grazing On The Ecology Of Sierra Meadows: A Review of The Current State of Scientific Knowledge To Inform Meadow Restoration And Management.

Wet montane meadows are an important component of the Sierra Nevada, CA ecosystem that provide diverse ecological services when in functional condition. Efforts are underway to restore meadows that have been degraded from past and historic land uses. Livestock grazing is a common land use in meadows with the potential to impact Sierra meadow ecology and may be a critical determinant of restoration success. We used a systematic literature review (SLR) method to identify, review, and synthesize scientific literature about the ecological effects of livestock grazing on Sierra meadow ecology resource areas, including hydrologic function, water quality, plants, soil, fens, and fish and wildlife species. We found 47 studies that matched our search criteria for inclusion in this SLR. Livestock grazing was associated with predominantly negative effects for each resource area reviewed, suggesting that achieving functional ecological condition in Sierra meadows that are currently used for livestock grazing may be challenging. Nevertheless, there was some evidence for compatibility with certain resource areas and certain management regimes. We discuss livestock management options, ecological objectives, and research questions that emerge from the literature to help inform meadow restoration and management.

Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California.

The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e., on nunataks), while shallow divergence and limited genetic variation are assumed to result from expansion from large refugia at the edge of ice shields (i.e., massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their spatial and demographic response to glaciation, and such a simple dichotomy may obscure the localization of actual refugia. In this study, we use the Nebria ingens complex (Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test how drainage basins are linked to their observed population structure. By analysing mitochondrial COI gene sequences and genome-wide single nucleotide polymorphisms, we find that the major drainage systems of the Sierra Nevada Mountains in California best explain the population structure of the N. ingens complex. In addition, we find that an intermediate morphotype within the N. ingens complex is the product of historical hybridization of N. riversi and N. ingens in the San Joaquin basin during glaciation. This study highlights the importance of considering ecological preferences in how species respond to climate fluctuations and provides an explanation for discordances that are often observed in comparative phylogeographical studies.

Anthropogenic climate change has altered lake state in the Sierra Nevada (California, USA).

Climatic changes threaten freshwater resources and aquatic ecosystem health in the Sierra Nevada (California, USA), which has important consequences for millions of people and the world's fifth largest economy. However, the timing and magnitude of ecological changes driven by hydroclimate oscillations remain poorly understood in California's headwater region. Here, we develop a precisely dated, annually to decadally resolved lake sediment record of ecological change from the eastern Sierra Nevada that spans the last three millennia. Diatom paleoecology reveals a detailed history of abrupt limnologic transitions, best explained by modifications in water column stratification, mixing, and nutrient status in response to changing seasonality. Seasonally stratified conditions were registered during the Late Holocene Dry Period and the Medieval Climate Anomaly, illustrating the sensitivity of fossil diatoms to well-known periods of drought. Yet the most striking feature of the record is the uniqueness of ~1840-2016 CE: a period of singularly strong water column stratification, increased algal diversity, and reduced diatom productivity consistent with unprecedented "hot droughts." The data demonstrate that hot-dry conditions of the Industrial Era altered lake state to conditions unseen in the past ~3180 years, and suggest that regional trends identified by historical monitoring began far earlier than previously recognized. Our record illustrates the profound influence of anthropogenic climate warming on high-elevation lakes and the ecosystem services they provide in the Sierra Nevada, which hold implications for water quality and availability in California.

Low-intensity frequent fires in coniferous forests transform soil organic matter in ways that may offset ecosystem carbon losses.

The impact of shifting disturbance regimes on soil carbon (C) storage is a key uncertainty in global change research. Wildfires in coniferous forests are becoming more frequent in many regions, potentially causing large C emissions. Repeated low-intensity prescribed fires can mitigate wildfire severity, but repeated combustion may decrease soil C unless compensatory responses stabilize soil organic matter. Here, we tested how 30 years of decadal prescribed burning affected C and nitrogen (N) in plants, detritus, and soils in coniferous forests in the Sierra Nevada mountains, USA. Tree basal area and litter stocks were resilient to fire, but fire reduced forest floor C by 77% (-36.4 Mg C/ha). In mineral soils, fire reduced C that was free from minerals by 41% (-4.4 Mg C/ha) but not C associated with minerals, and only in depths ≤ 5 cm. Fire also transformed the properties of remaining mineral soil organic matter by increasing the proportion of C in a pyrogenic form (from 3.2% to 7.5%) and associated with minerals (from 46% to 58%), suggesting the remaining soil C is more resistant to decomposition. Laboratory assays illustrated that fire reduced microbial CO2 respiration rates by 55% and the activity of eight extracellular enzymes that degrade cellulosic and aromatic compounds by 40-66%. Lower decomposition was correlated with lower inorganic N (-49%), especially ammonium, suggesting N availability is coupled with decomposition. The relative increase in forms of soil organic matter that are resistant to decay or stabilized onto mineral surfaces, and the associated decline in decomposition suggest that low-intensity fires may promote mineral soil C storage in pools with long mean residence times in coniferous forests.

Mapping the vulnerability of giant sequoias after extreme drought in California using remote sensing.

Between 2012 and 2016, California suffered one of the most severe droughts on record. During this period Sequoiadendron giganteum (giant sequoias) in the Sequoia and Kings Canyon National Parks (SEKI), California, USA experienced canopy water content (CWC) loss, unprecedented foliage senescence, and, in a few cases, death. We present an assessment of the vulnerability of giant sequoia populations to droughts that is currently lacking and needed for management. We used a temporal trend of remotely sensed CWC obtained between 2015 and 2017, and recently georeferenced giant sequoia crowns to quantify the vulnerability of 7,408 individuals in 10 groves in the northern portion of SEKI. CWC is sensitive to changes in liquid water in tree canopies; therefore, it is a useful metric for quantifying the response of sequoia trees to drought. Temporal trends indicated that 9% of giant sequoias had a significant decline or consistently low CWC, suggesting these trees were likely operating at low photosynthetic capacity and potentially at high risk to drought stress. We also found that 20% of the giant sequoias had an increase or consistently high level of CWC, indicating these trees were at low risk to drought stress. These vulnerability categories were used in a random forest model with a combination of topographic, fire-related, and climate variables to generate high-resolution vulnerability risk maps. These maps show that higher risk is associated with lower elevation and higher climate water deficit. We also found that sequoias at higher elevations but located near meadows had higher vulnerability risk. These results and the vulnerability maps can identify vulnerable sequoias that may be difficult to save or locations of refugia to be protected, and thus may aid forest managers in preparation for future droughts.

Using an unmanned aerial vehicle water sampler to gather data in a pit-lake mining environment to assess closure and monitoring.

Residual pit lakes from mining are often dangerous to sample for water quality. Thus, pit lakes may be rarely (or never) sampled. This study developed new technology in which water-sampling devices, mounted on an unmanned aerial vehicle (UAV), were used to sample three pit lakes in Nevada, USA, during 1 week in 2017. Water-quality datasets from two of the three pit lakes on public lands, Dexter and Clipper, are presented here. The current conditions of the Dexter pit lake were assessed by examining cation and anion concentration changes that have occurred over a 17-year period since the pit lake was last sampled in 2000. Data gathered during this sampling campaign assessed 2017 conditions of the Dexter and Clipper pit lakes by comparing constituent concentrations to the Nevada Division of Environmental Protection (NDEP) pit lake water-quality requirements, indicating that selenium concentrations exceeded regulatory standards. We compared our sampling data for Dexter lake to prior water-quality data from the Dexter pit lake collected in 1999 and 2000. This comparison for the Dexter pit lake indicates that evapoconcentration may have caused increasing cation and anion concentrations. This UAV sampling approach can potentially incorporate the use of additional multiparameter probes: pH, oxygen concentration, turbidity, or chlorophyll. Some limitations of this UAV water-sampling methodology are battery duration, weather conditions, and payload capacity.

Local forest structure variability increases resilience to wildfire in dry western U.S. coniferous forests.

A 'resilient' forest endures disturbance and is likely to persist. Resilience to wildfire may arise from feedback between fire behaviour and forest structure in dry forest systems. Frequent fire creates fine-scale variability in forest structure, which may then interrupt fuel continuity and prevent future fires from killing overstorey trees. Testing the generality and scale of this phenomenon is challenging for vast, long-lived forest ecosystems. We quantify forest structural variability and fire severity across >30 years and >1000 wildfires in California's Sierra Nevada. We find that greater variability in forest structure increases resilience by reducing rates of fire-induced tree mortality and that the scale of this effect is local, manifesting at the smallest spatial extent of forest structure tested (90 × 90 m). Resilience of these forests is likely compromised by structural homogenisation from a century of fire suppression, but could be restored with management that increases forest structural variability.

Coyotes as Reservoirs for Onchocerca lupi, United States, 2015-2018.

The Onchocerca lupi nematode infects dogs, cats, and humans, but whether it can be spread by coyotes has been unknown. We conducted surveillance for O. lupi nematode infection in coyotes in the southwestern United States. We identified multiple coyote populations in Arizona and New Mexico as probable reservoirs for this species.