Geology topics

Julie L. Yee

Publications and source records attributed to Julie L. Yee.

At least 19 recordsLinked to original sources

USGS2026

Black abalone surveys at Naval Base Ventura County, San Nicolas Island, California—2023 annual report

The U.S. Geological Survey monitors a suite of intertidal black abalone ( Haliotis cracherodii ) sites at San Nicolas Island, California, in cooperation with the U.S. Navy, which owns the island. The nine rocky intertidal sites were established in 1980 to study the potential effect of translocated sea otters on the intertidal black abalone population at the island. The sites were monitored from 1981 to 1997, typically annually or biennially. Monitoring resumed in 2001 and has been completed annually thereafter. Since 2018, the work has been carried out by the U.S. Geological Survey Western Ecological Research Center. The study sites became particularly important, from a management perspective, after a virulent disease decimated black abalone populations throughout southern California beginning in the mid-1980s. The disease, withering syndrome ( Candidatus Xenohaliotis californiensis ), was first observed on San Nicolas Island in 1992 and over the next few years, withering syndrome reduced the black abalone population on San Nicolas Island by more than 99 percent. In 2009, the black abalone subsequently was listed as endangered under the Endangered Species Act. The subject of this report is the 2023 survey of the sites and the status of the measured population in comparison to long-term patterns (based on data collected since 1981) at San Nicolas Island. Between the years 2000 and 2023, the total monitored black abalone population at the island has grown from roughly 200 to more than 2,500 abalone following disease-related decline. Since it was first consistently measured in 2005, the average distance between adjacent black abalone has decreased substantially from approximately 50 centimeters to less than 15 centimeters, indicating that abalone are sufficiently close together at several of the sites to reproduce successfully. The total abalone count in 2023 was 2,570, which was 19.2 percent higher than in 2022 and the highest count since 1993. All nine sites had higher counts in 2023 than in the previous year. Over 25 percent of the black abalone counted in 2023 were classified as recruits, defined as having a shell length of 3 centimeters or less.

California↗

USGS2026

Quantifying southern sea otter (Enhydra lutris nereis) reactions to a quadcopter drone in central California

Drones are useful for wildlife research and management, but they can cause disturbance and harassment to wildlife. Sea otters ( Enhydra lutris ) are candidates for drone-based observation and monitoring but are vulnerable to disturbance. No studies have evaluated drone effects on sea otter behavior, but based on prior disturbance studies, we hypothesized: (1) sea otters would exhibit behaviors indicating higher reactivity in the presence of drones than when drones were absent and (2) drone disturbance to sea otters would be greater when drones were closer. At two sites in Monterey Bay, CA, we conducted 37 observational sessions, recording behavior codes for focal sea otters during a baseline (no drone) period and three consecutive drone flights. Data were analyzed using ANOVA and ordinal logistic regression models. At both locations, focal sea otters had higher behavior codes during drone trials compared to baseline, and behavior codes increased with descending drone altitude. Pup presence, group size, flight trial number, and gull presence were significant covariables. We calculated multipliers to predict drone-mediated behavioral responses at a range of drone altitudes. Our findings can inform best practices for a variety of uses of drones around sea otters, including population monitoring, oil spill response, and drone photography/videography.

California↗

USGS2026

Non-native invasive beetle alters structure of a riparian bird community in a biodiversity hotspot

A serious emerging threat to southern California riparian ecosystems is the invasive shot hole borer ( Euwallacea spp.; SHB), a non-native beetle that cultivates a pathogenic fungus that kills trees of 66 reproductive host species. We examined the response of the bird community at the Tijuana River, California, to a massive SHB infestation in 2015 using data from a Monitoring Avian Productivity and Survivorship (MAPS) station operated during 7 pre-infestation (2009-15) and 7 post-infestation (2017-23) years. Species richness did not change between pre- and immediate (2017-18) post-SHB periods, but average annual adult captures declined by 27%. Among the species making up ≥ 5% of the total individuals caught in any one year (n=15), abundance declined by up to 76% in 10 species, including those most abundant at the station (Bushtit ( Psaltriparus minimus ), Song Sparrow ( Melospiza melodia ), Common Yellowthroat ( Geothlypis trichas ), Orange-crowned Warbler ( Leiothlypis celata ), and Wilson’s Warbler ( Cardellina pusilla )). Mean annual abundance increased slightly for the endangered Least Bell’s Vireo ( Vireo bellii pusillus ) and Northern Yellow Warbler ( Setophaga aestiva ) and doubled for House Finch ( Haemorhous mexicanus ) and Western Warbling-Vireo ( V. swainsoni ). We compared species trends at the Tijuana River to those at a nearby uninfested MAPS station on the Santa Margarita River to isolate the effect of SHB from other factors influencing annual abundance. The contribution of SHB to changes in abundance post-SHB was high (63-80%) for 7 declining species, moderate (22-45%) for 4 species, and weakly to moderately positive (18-40%) for 3 species. By 2019, the SHB infestation at the Tijuana River had abated and canopy cover was recovering through resprouting of mature willows ( Salix spp.) and seedling establishment. Bird abundance tracked this regrowth, with all of the species strongly affected by SHB increasing between 2019-23. The rapid recovery of the Tijuana River habitat and the associated response by the bird community are encouraging signs that the threat of the invasive shot hole borer to regional biodiversity may not be as great as originally anticipated.

California↗

USGS2025

Black abalone surveys at Naval Base Ventura County, San Nicolas Island, California—2022 annual report

The U.S. Geological Survey monitors a suite of intertidal black abalone ( Haliotis cracherodii ) sites at San Nicolas Island, California, in cooperation with the U.S. Navy, which owns the island. The nine rocky intertidal sites were established in 1980 to study the potential effect of translocated southern sea otters ( Enhydra lutris nereis ) on the intertidal black abalone population at San Nicolas Island. The sites were monitored, typically annually or biennially, from 1981 to 1997. Monitoring resumed in 2001 and has been completed annually thereafter. Since 2018, the monitoring has been carried out by the U.S. Geological Survey Western Ecological Research Center. The study sites became particularly important from a management perspective after a virulent disease decimated black abalone populations throughout southern California beginning in the mid-1980s. The disease, withering syndrome, was first observed on San Nicolas Island in 1992, and during the next few years, withering syndrome reduced the black abalone population on San Nicolas Island by more than 99 percent. The black abalone was subsequently listed as endangered under the Endangered Species Act in 2009. The subject of this report is the 2022 survey of the sites and the status of the measured population of black abalone in comparison to long-term patterns (based on data collected since 1981) at San Nicolas Island. Between the years 2000 and 2022, the total monitored black abalone population on the island has grown from roughly 200 to more than 2,000, approximately a ten-fold increase following the disease-related decline. Since it was first consistently measured in 2005, the distance between adjacent black abalone has decreased substantially from approximately 50 centimeters to less than 15 centimeters, indicating that black abalone are sufficiently close together at several of the sites to reproduce successfully. The total black abalone count in 2022 was 2,156, which was 7.9 percent lower than the total count in 2020 but 6.6 percent higher than in 2021. There were increases and decreases among the sites and transects within each site in 2022, but six of the nine sites had higher counts than in the previous year. The 2022 count is one of the highest since 1993, second only to the 2020 count. In 2022, the annual recruitment rate, defined as the percentage of measured black abalone with a shell length of 3 centimeters or less, was the second highest recorded, only slightly less than in 2017.

California↗

USGS2025

Black abalone (Haliotis cracherodii) population density, recruitment, size structure, and population growth at Naval Base Ventura County, San Nicolas Island, California, 2013–22

The range of the endangered black abalone ( Haliotis cracherodii ) is divided into the North Central California region, the Central California region, the Southern California Mainland region, the Channel Islands region, and the Baja California region by the National Marine Fisheries Service for management purposes. San Nicolas Island is one of eight subregions of the Channel Islands region. The black abalone recovery plan establishes five demographic criteria for the possible delisting or downlisting of the species. The U.S. Geological Survey monitors nine long-term intertidal black abalone sites at San Nicolas Island, California, in cooperation with the U.S. Navy, which owns the island. This report uses data collected between 2013 and 2022 and the delisting criteria to analyze and describe the density, recruitment, size structure, and population trends at the nine U.S. Geological Survey monitoring sites at San Nicolas Island.

California↗

USGS2024

Foraging ecology of southern sea otters at the northern range extent informs regional population dynamics

Sea otters Enhydra lutris are vital keystone predators throughout the North Pacific that were nearly extirpated during the maritime fur trade. Recovery of southern sea otters E. l. nereis has proceeded slowly, with much of their historical range remaining unoccupied, resulting in reduced ecosystem functioning. Numerous studies have used foraging metrics to assess the population status of southern sea otters throughout their current range, but little is known about the northern range extent, where a stall in expansion has limited recovery. Thus, we collected census and foraging data of sea otters at Año Nuevo State Park, California, from 2019 to 2021 to determine sea otter abundance, diet composition, diet diversity, and average energy intake rate at the northern range edge. We then assessed regional population status by comparing values from Año Nuevo with previously collected data from other locations in California, including high-density, range center sites and low-density, range periphery sites. We found that sea otter density at Año Nuevo was greater than surrounding areas at the northern range periphery, and the average (±95% CI) energy intake (9.51 ± 0.91 kcal min -1 ) more closely resembled values observed at high-density sites. Further, dietary diversity (using the Shannon-Wiener index, H ) was intermediate between previously studied high- and low-density populations ( H = 1.81), with crabs making up the largest proportion of the diet (~56%). Overall, this study highlights possible effects of occupation time and range stagnation, identifies unique aspects of the prey resource base at Año Nuevo, and provides insight into the ongoing lack of northern range expansion.

California↗

USGS2024

Methylmercury effects on birds: A review, meta-analysis, and development of toxicity reference values for injury assessment based on tissue residues and diet

Birds are used as bioindicators of environmental mercury (Hg) contamination, and toxicity reference values are needed for injury assessments. We conducted a comprehensive review, summarized data from 168 studies, performed a series of Bayesian hierarchical meta-analyses, and developed new toxicity reference values for the effects of methylmercury (MeHg) on birds using a benchmark dose analysis framework. Lethal and sublethal effects of MeHg on birds were categorized into nine biologically relevant endpoint categories and three age classes. Effective Hg concentrations where there was a 10% reduction (EC10) in the production of juvenile offspring (0.55 µg/g wet wt adult blood-equivalent Hg concentrations, 80% credible interval: [0.33, 0.85]), histology endpoints (0.49 [0.15, 0.96] and 0.61 [0.09, 2.48]), and biochemical markers (0.77 [<0.25, 2.12] and 0.57 [0.35, 0.92]) were substantially lower than those for survival (2.97 [2.10, 4.73] and 5.24 [3.30, 9.55]) and behavior (6.23 [1.84, >13.42] and 3.11 [2.10, 4.64]) of juveniles and adults, respectively. Within the egg age class, survival was the most sensitive endpoint (EC10 = 2.02 µg/g wet wt adult blood-equivalent Hg concentrations [1.39, 2.94] or 1.17 µg/g fresh wet wt egg-equivalent Hg concentrations [0.80, 1.70]). Body morphology was not particularly sensitive to Hg. We developed toxicity reference values using a combined survival and reproduction endpoints category for juveniles, because juveniles were more sensitive to Hg toxicity than eggs or adults. Adult blood-equivalent Hg concentrations (µg/g wet wt) and egg-equivalent Hg concentrations (µg/g fresh wet wt) caused low injury to birds (EC1) at 0.09 [0.04, 0.17] and 0.04 [0.01, 0.08], moderate injury (EC5) at 0.6 [0.37, 0.84] and 0.3 [0.17, 0.44], high injury (EC10) at 1.3 [0.94, 1.89] and 0.7 [0.49, 1.02], and severe injury (EC20) at 3.2 [2.24, 4.78] and 1.8 [1.28, 2.79], respectively. Maternal dietary Hg (µg/g dry wt) caused low injury to juveniles at 0.16 [0.05, 0.38], moderate injury at 0.6 [0.29, 1.03], high injury at 1.1 [0.63, 1.87], and severe injury at 2.4 [1.42, 4.13]. We found few substantial differences in Hg toxicity among avian taxonomic orders, including for controlled laboratory studies that injected Hg into eggs. Our results can be used to quantify injury to birds caused by Hg pollution.

Environmental Toxicology and Chemistry↗

USGS2024

Modeling coupled dynamics of an empirical predator-prey system to predict top predator recovery

Limited data, time, and funding lead conservation managers to make difficult choices in managing species recovery. Coupled dynamical models are relied upon for decision support, but their application to empirical predator-prey systems has generally been restricted to small, tractable species. To broaden their use in conservation decision-making, we developed a model suitable for predicting the population dynamics of a larger apex carnivore and its prey. We selected southern sea otters ( Enhydra lutris nereis ) and their primary estuarine prey as our case study and parameterized the dynamical model with data on sea otter, clam, and crab abundances; predator-prey interactions; and sea otter bioenergetics collected from Elkhorn Slough, CA. Our model, having integrated all these salient factors, was able to successfully reproduce trends in taxa abundance as well as shifts in sea otter diet composition and energy intake rates. Rich data inputs allow the model to predict population dynamics over realistic temporal scales not only for the site of data collection, but also for similar estuaries uncolonized by sea otters. Based on model projections parameterized with prey survey data from two such estuaries, Tomales Bay and Drakes Estero, we predict the sites could support over 160 sea otters and may hold potential to further species recovery. In systems with good data availability, the model has high predictive power and can provide multi-taxa projections useful for making informed management decisions.

California↗

USGS2023

Southern (California) sea otter population status and trends at San Nicolas Island, 2020–2023

The population of southern sea otters ( Enhydra lutris nereis ) at San Nicolas Island, California, has been monitored annually since the translocation of 140 southern sea otters to the island was completed in 1990. Monitoring efforts have varied in frequency and type across years. In 2017, the U.S. Navy and the U.S. Fish and Wildlife Service initiated a southern sea otter monitoring and research plan to determine the effects of military readiness activities on the growth or decline of the southern sea otter population at San Nicolas Island. The southern sea otter is the only subspecies of sea otter in California (hereafter, “sea otter"). The monitoring program, at its basic level, includes seasonal surveys of population abundance, distribution, and foraging activity. From 2020 to 2023, we measured a 10-percent per annum increase in population abundance (95-percent confidence interval =0–20 percent), with 146 total individuals as of April 2023. Coinciding with the recent population growth, the sea otter distribution, which previously tended to concentrate on the island’s west end during 2003–2006 before shifting toward more use in the north and south sides during 2017–2019, appears to have shifted again during 2020–2023 to concentrate at the island’s east end. Forage data were collected between February 2020 and April 2023. There was a total of 773 forage dives in 60 forage bouts, with most of the identified prey on successful dives (n=401) recorded as sea urchins (66 percent), followed by bivalves (15 percent), snails (12 percent), and crabs (5.2 percent). Two lobsters and three abalone also were identified among the sea otter prey. Estimates of energy intake rates averaged 14.0 kilocalories per minute (95-percent confidence interval =10.8–17.2 kilocalories per minute). Monitoring data from the past two decades indicate that sea otters at San Nicolas Island have maintained a steady pattern of energy intake and population growth characteristic of a robust population, including a sixfold growth between 2000 and 2023. There was no conclusive evidence of density-dependent effects based on these patterns; however, estimates of energy intake rates for 2020–2023 were slightly lower than previous estimates from 2017 to 2019. Additionally, subtidal monitoring results at four sites around San Nicolas Island indicated that counts of purple sea urchins ( Strongylocentrotus purpuratus ) have increased between 2003 and 2023, whereas sea otter foraging surveys completed during the same period revealed that some sea otters have shifted toward higher consumption of purple sea urchins and bivalves compared to red sea urchins ( S. fransicanus ), which generally are the preferred larger prey of sea otters. These results contribute to the understanding of population dynamics and to the conservation and planning of future monitoring and research of sea otters at San Nicolas Island.

California↗

USGS2023

Gene expression and wildlife health: Varied interpretations based on perspective

We evaluated wildlife population health from the perspective of statistical means vs. variances. We outlined the choices necessary to provide the framework for our study. These consisted of spatial and temporal boundaries (e.g., choice of sentinel species, populations, time frame), measurement techniques (molecular to population level), and appropriate statistical analyses. We chose to assess the health of 19 sea otter populations, located in the north Pacific from the Aleutian Islands, AK, to Santa Barbara, CA, and varying in population growth rates and length of occupancy. Our focal metric was gene expression (i.e., mRNA transcripts) data that we had previously generated across sea otter populations as a measure of population health. We used statistical methods with different approaches (i.e., means vs. variances) and examined the subsequent interpretive outcomes and how these influence our assessment of “health.” Interpretations based on analyses using variances versus means overlapped to some degree. In general, sea otter populations with low variation in gene expression were limited by food resources and at or near carrying capacity. In populations where the variation in gene expression was moderate or high, four out of five populations were increasing in abundance, or had been recently increasing. Where we had additional information on sources of stressors at the level of the population, we were able to draw inferences from those stressors to specific gene expression results. For example, gene expression patterns of sea otters from Western Prince William Sound were consistent with long term exposure to petroleum hydrocarbons, whereas in Kachemak Bay, patterns were consistent with exposure to algal toxins. Ultimately, determination of population or ecosystem health will be most informative when multiple metrics are examined across disciplines in the context of specific scenarios and goals.

Alaska, British Columbia, California, Oregon, Wash↗

USGS2022

Black Abalone surveys at Naval Base Ventura County, San Nicolas Island, California—2021, annual report

The U.S. Geological Survey monitors a suite of intertidal black abalone sites at San Nicolas Island, California, in cooperation with the U.S. Navy, which owns the island. The nine rocky intertidal sites were established in 1980 to study the potential effect of translocated sea otters on the intertidal black abalone population at the island. The sites were monitored from 1981 to 1997, usually annually or biennially. Monitoring resumed in 2001 and has been completed annually since then. Since 2018, the work has been carried out by the U.S. Geological Survey Western Ecological Research Center. The study sites became particularly important, from a management perspective, after a virulent disease decimated black abalone populations throughout southern California beginning in the mid-1980s. The disease, withering syndrome, was first observed on San Nicolas Island in 1992 and during the next few years, it reduced the population there by more than 99 percent. The species was subsequently listed as endangered under the Endangered Species Act in 2009. The subject of this report is the 2021 survey of the sites and how the measured population status compares to the long-term data (collected over several decades) at San Nicolas Island. During the last two decades, the total monitored black abalone population at the island has grown approximately ten-fold after the disease related decline, from about 200 to more than 2,000 abalone. Since it was first consistently measured in 2005, the mean distance between adjacent black abalone has decreased substantially from approximately 50 centimeters to less than 15 centimeters, indicating that abalone are close enough together at several of the sites to reproduce successfully. The 2021 counts were the first since 2016 to indicate a possible decline in the monitored population at San Nicolas Island. Although still more than ten times the population counted in 2001, counts on the transects dropped by 13.6 percent from the survey count in 2020. The most significant decline was the loss of 341 abalone, from the previous count of 547, on a transect that since 2002 had the highest count of all 44 transects. Between 2020 and 2021, there were increases and decreases at the sites and the transects at each site. Although the 2021 count was lower than the 2020 count, it was the second highest since 1997. Based on the number of small abalone counted, recruitment rates were similar to most years since 2008 and higher than the rates observed before the population declines resulting from withering syndrome.

California↗

USGS2022

Sea otters in a California estuary: Detecting temporal and spatial dynamics with volunteer monitoring

Volunteer monitoring can support conservation of imperiled wildlife, by providing higher resolution data in space and time than those available from professional scientists. However, concerns have been raised that data collected by amateurs are inaccurate or inconsistent and thus do not allow for robust detection of spatial or temporal trends. We evaluated the rigor and value of volunteer monitoring data for one iconic wildlife species, the southern sea otter ( Enhydra lutris nereis ), in Elkhorn Slough estuary in central California, USA, and explored whether volunteer monitoring could provide added value to complement limited professional surveys. First, we compiled and analyzed sea otter counts taken on daily ecotourist boat trips along the estuary, and then compared temporal patterns to data collected by professional scientists tasked with monitoring this federally listed species. Second, we analyzed data on sea otter abundance, habitat use, and behavior collected by a team of trained volunteers, the Elkhorn Slough Reserve Otter Monitoring Program. Overall, we demonstrated the ability to detect important ecological patterns relevant to sea otter conservation and wetland habitat management using volunteer-derived datasets. Long-term trends and inter-annual variability were similar between professional agency monitoring data and volunteer datasets. Moreover, the much higher frequency of volunteer observations allowed for seasonal and tidal dynamics to be detected that could not be revealed by less frequent professional monitoring. We found higher sea otter abundance in the estuary in spring–summer, indicating seasonality in use of the estuary. We detected differences in habitat use of the estuary between higher and lower tides, and greater frequency of foraging at low tide and in certain areas. Volunteer observations revealed fine-scale differences in habitat use: eelgrass beds were used much more heavily than adjacent areas only a few meters away. Volunteer data can thus provide critical information about coastal habitat use and behavior that can improve conservation strategies for threatened wildlife species.

California↗

USGS2022

Vulnerability of avian populations to renewable energy production

Renewable energy production can kill individual birds, but little is known about how it affects avian populations. We assessed the vulnerability of populations for 23 priority bird species killed at wind and solar facilities in California, USA. Bayesian hierarchical models suggested that 48% of these species were vulnerable to population-level effects from added fatalities caused by renewables and other sources. Effects of renewables extended far beyond the location of energy production to impact bird populations in distant regions across continental migration networks. Populations of species associated with grasslands where turbines were located were most vulnerable to wind. Populations of nocturnal migrant species were most vulnerable to solar, despite not typically being associated with deserts where the solar facilities we evaluated were located. Our findings indicate that addressing declines of North American bird populations requires consideration of the effects of renewables and other anthropogenic threats on both nearby and distant populations of vulnerable species.

California↗

USGS2022

Kelp-forest dynamics controlled by substrate complexity

The factors that determine why ecosystems exhibit abrupt shifts in state are of paramount importance for management, conservation, and restoration efforts. Kelp forests are emblematic of such abruptly shifting ecosystems, transitioning from kelp-dominated to urchin-dominated states around the world with increasing frequency, yet the underlying processes and mechanisms that control their dynamics remain unclear. Here, we analyze four decades of data from biannual monitoring around San Nicolas Island, CA, to show that substrate complexity controls both the number of possible (alternative) states and the velocity with which shifts between states occur. The superposition of community dynamics with reconstructions of system stability landscapes reveals that shifts between alternative states at low-complexity sites reflect abrupt, high-velocity events initiated by pulse perturbations that rapidly propel species across dynamically unstable state–space. In contrast, high-complexity sites exhibit a single state of resilient kelp–urchin coexistence. Our analyses suggest that substrate complexity influences both top-down and bottom-up regulatory processes in kelp forests, highlight its influence on kelp-forest stability at both large (island-wide) and small (<10 m) spatial scales, and could be valuable for holistic kelp-forest management.

PNAS↗

USGS2022

Spatial effects in relation to reproductive performance of Common Murres (Uria aalge) at a re-established colony

A main goal of seabird colony restoration is for the colony to become self-sustaining. To do so, elevated rates must be attained in (1) reproductive success and (2) recruitment by immigrants and birds produced at the colony. Thus, an understanding of the factors affecting reproductive success and recruitment at restoration sites is vital. We examined how spatial features at the colony level affected reproductive success of Common Murres Uria aalge (hereafter, murres) over a six-year period at Devil's Slide Rock, California, a colony re-established using social attraction techniques. Clusters of sites with similar egg-laying dates, as well as high hatching and breeding success, occurred in the densest portion of the colony, which was also the last area occupied by murres at the time of extirpation and the first area to be re-colonized. Clusters of sites with low success occurred in outlying, low-density portions of the colony. Breeding success, influenced largely by high fledging success, averaged > 60% most years. Reproductive success was greatest at breeding sites with earlier egg-laying dates, those in closest proximity to the breeding sites of other murres and the Brandt's Cormorant Urile penicillatus , and those outside Brown Pelican Pelecanus occidentalis disturbance zones. Based on our findings, for future murre restoration projects in the California Current System, we suggest (1) placing social attraction equipment in the area(s) last utilized by murres prior to extirpation, (2) attempting to establish two dense breeding groups, (3) targeting sites already utilized regularly by nesting Brandt's Cormorants, and (4) avoiding sites or habitats prone to disturbance by larger and aggressive species such as Brown Pelicans, Bald Eagles Haliaeetus leucocephalus , or Common Ravens Corvus corax .

California↗

USGS2021

Development of demographic models to analyze populations with multi-year data—Using Agassiz’s Desert Tortoise (Gopherus agassizii) as a case study

We developed a model for analyzing multi-year demographic data for long-lived animals and used data from a population of Agassiz’s desert tortoise ( Gopherus agassizii ) at the Desert Tortoise Research Natural Area in the western Mojave Desert of California as a case study. The study area was 7.77 square kilometers and included two locations: inside and outside the fenced boundary. The wildlife-permeable, protective fence was designed to prevent entry from vehicle users and sheep grazing. We collected mark-recapture data from 1,123 tortoises during seven annual surveys consisting of two censuses each over a 34-year period. Additional data were collected when marked tortoises were recovered dead and removed between survey years. We used a Bayesian modeling framework to develop a multistate Jolly-Seber model because of its ability to handle unobserved (latent) states and modified this model to incorporate the additional data from non-survey years. Three size-age states (juvenile, immature, adult), sex (female, male), two location states (inside and outside the fenced boundary), and three survival states (not-yet-entered, entered/alive, and dead/removed) were incorporated into the model. We calculated population densities and estimated probabilities of growth of the tortoises from one size-age state to a larger size-age state, survival after 1 year and 5 years, and detection. Our results show a declining population with low estimates for survival after 1 year and 5 years. The probability for tortoises to move from outside to inside the boundary fence was greater than for tortoises to move from inside the fence to outside. The probability for detecting tortoises differed by size-age state and was lowest for the smallest tortoises and highest for the adult tortoises. The framework for the model can be used to analyze other animal populations where vital rates are expected to vary depending on multiple individual states.

Open-File Report↗

USGS2021

An integrated population model for southern sea otters

Southern sea otters ( Enhydra lutris nereis ) have recovered slowly from their near extinction a century ago, and their continued recovery has been challenged by multiple natural and anthropogenic factors. Development of an integrated population model (IPM) for southern sea otters has been identified as a management priority, to help in evaluating the relative impacts of known threats and guide best management options for species recovery. An IPM represents an analytical modeling framework where various types of data relevant to animal health, population trends, and survival can be evaluated collectively to project future population dynamics under different resource management scenarios. Here, we describe the development of a spatially explicit IPM for southern sea otters that is fit by using Bayesian methods to multiple datasets including a time series of range-wide survey counts, estimated survival rates of tagged animals from telemetry-based population studies, and cause-of-death data from comprehensive necropsies of beach-cast carcasses. The core of the model is a stage-structured matrix, in which survival rates for a given life history stage, year, and location are computed as the outcome of multiple ‘competing risks,’ or hazards, allowing for spatiotemporal variation in each hazard, density-dependence, and stochasticity. The parameterized IPM was used to (1) examine how age and sex-specific hazards vary over space and time, (2) gain insights into density-dependent variation in specific hazards, (3) assess population-level effects of known mortality hazards in the past and in future projections, and (4) evaluate the relative benefits of various potential management actions to address these hazards. Our results indicated that different types of hazards have variable impacts at different life history stages of sea otters; for example, shark-bite mortality had a strong impact on mortality of subadult females but relatively low impacts on aged adult female survival, whereas End Lactation Syndrome showed just the opposite age-based pattern. There also was spatial and temporal variation in exposure to different hazards; for example, shark-bite mortality generally was highest at the north and south ends of the sea otter range, End Lactation Syndrome and cardiac disease were highest in the center part of the range, and harmful algal bloom intoxication and protozoal infection mortalities were highest around Morro Bay. The relative impacts of hazards depended on population density; for example, shark-bite mortality had the greatest effect on male survival when population abundance was low, but as densities increased the impacts of cardiac disease (for aged adults) and acanthocephalan peritonitis (for subadults) exceeded the effects of shark-bite mortality. Sensitivity analyses showed that modifying certain hazard rates can have substantial impacts on future population growth; for example, if the shark-bite hazard rate were to decrease by 20 percent, projected abundance after 50 years is predicted to be 18-percent higher, on average, than under baseline conditions. We used the IPM to evaluate the possible impacts of a potential management action: the reintroduction of sea otters to currently unoccupied parts of their historical range. We found that there were large increases in expected growth potential associated with reintroduction programs to various locations to the north and south of the currently occupied range, although a reintroduction to San Francisco Bay was projected to have the greatest potential impacts on future population growth. The IPM for southern sea otters presented here provides resource managers with a useful tool for evaluating the impacts of specific hazards, forecasting future population dynamics and range expansion, and evaluating alternative management scenarios.

California↗

USGS2021

Waterfowl use of wetland habitats informs wetland restoration designs for multi‐species benefits

Extensive global estuarine wetland losses have prompted intensive focus on restoration of these habitats. In California, substantial tracts of freshwater, brackish and tidal wetlands have been lost. Given the anthropogenic footprint of development and urbanization in this region, wetland restoration must rely on conversion of existing habitat types rather than adding new wetlands. These restorations can cause conflicts among stakeholders and species that win or lose depending on identified restoration priorities. Suisun Marsh on the San Francisco Bay Estuary is the largest brackish marsh on the U.S. Pacific coast. To understand how conversion of brackish managed wetlands to tidal marsh would impact waterfowl populations and whether future tidal marsh restorations could provide suitable habitat for dabbling ducks, we examined waterfowl wetland use with a robust GPS‐GSM tracking dataset (442,017 locations) from six dabbling duck species (N=315). Managed wetlands, which comprise 47% of Suisun Marsh, were consistently and strongly selected by waterfowl over tidal marshes, with use ~98% across seasons and species. However, while use of tidal marsh (only 14% of Suisun Marsh) was generally <2%, almost half our ducks (~44%) spent some time in this habitat and exhibited strong utilization of pond‐like features. Ponds only comprise ~10% of this habitat but attracted 44% use (~4.5 times greater than availability). Synthesis and applications : Managed wetlands were vital to dabbling ducks, but losses from conversion of these habitats may be partially mitigated by incorporating pond features that are more attractive to waterfowl, and likely to offer multi‐species benefits, into tidal marsh restoration designs. While waterfowl are presently a common taxon, previously seen calamitous population declines can be avoided through informed ecosystem‐based management that promotes species richness, biodiversity and helps “keep common species common”.

California↗