Geology topics

Joseph E. Kirsch

Publications and source records attributed to Joseph E. Kirsch.

6 recordsLinked to original sources

USGS2026

Who needs closure? Estimating abundance with a Markovian availability model for geographically open removal sampling

Removal sampling is an important method for estimating abundance, but nearly all removal models assume closure during sampling. Yet, closure may be difficult to assume, evaluate, or enforce in many settings. To address situations where populations are geographically open between each removal sample, we incorporated a Markovian availability process into an N-mixture model framework. This model relates local abundance available for sampling to a superpopulation through recruitment of new individuals to the sampling area. To test the model, we (1) conducted parameter identifiability analysis, (2) fit the model to removal data generated from a random walk movement model, and (3) analyzed a case study of empirical removal data. Parameters were increasingly identifiable as capture probability exceeded 0.25 and removal samples increased from 3 to 6. Abundance estimates were unbiased when parameters were identifiable, except for scenarios that simulated a behavioral response to sampling. For our case study, the model estimated negligible recruitment for benthic-oriented fishes, indicating closure, but we found evidence against closure for juvenile Chinook salmon, a highly mobile species. Our removal model allows researchers to formally test closure assumptions, to estimate the degree of closure, and to estimate abundance without bias when closure is violated.

California↗

USGS2023

Imperfect detection and misidentification affect inferences from data informing water operation decisions

Objective Managers can modify river flow regimes using fish monitoring data to minimize impacts from water management infrastructure. For example, operation of the gate-controlled Delta Cross Channel (DCC) in California can negatively affect the endangered Sacramento River winter-run Chinook Salmon Oncorhynchus tshawytscha . Although guidelines have been developed for DCC operations by using real-time juvenile fish sampling count data, there is uncertainty about how environmental conditions influence fish occupancy and the extent to which those relationships are affected by sampling and identification error. Methods We evaluated the effect of environmental conditions, imperfect detection, and misidentification error on salmon occupancy by analyzing data using hierarchical multistate occupancy models. A total of 14,147 trawl tows and beach seine hauls were conducted on 1058 sampling days between October and December from 1996 to 2019. During these surveys, 2803 juvenile winter-run Chinook Salmon were identified, and approximately 29% of the sampling days had at least one winter-run juvenile detected. Result The probability of misidentifying an individual juvenile winter-run Chinook Salmon in the field was estimated to be 0.056 based on fish identification examinations and genetic sampling. Occupancy varied considerably and was related to flow characteristics, water clarity, weather, time of year, and whether occupancy was detected during the previous sampling day. However, these relationships and their significance changed considerably when accounting for imperfect detection and the probability of misidentifying individual juvenile salmon. Detection was <0.3 under average sampling conditions during a single sample and was influenced by flow, water clarity, site, and volume sampled. Conclusion Our modeling results indicate that DCC gate closure decisions could occur on fewer days when imperfect detection and misidentification error are not accounted for. These findings demonstrate the need to account for identification and detection error while using monitoring data to assess factors influencing fish occupancy and inform future management decisions.

North American Journal of Fisheries Management↗

USGS2021

Recruitment dynamics of non-native largemouth bass within the Sacramento-San Joaquin delta

Largemouth bass (LMB; Micropterus salmoides ) recruitment is limited by a critical developmental period during early life stages, but this mechanism may be less important within non-native habitats. We conducted boat electrofishing surveys in four tidal lakes of California’s Sacramento–San Joaquin Delta (SSJD) from 2010 to 2011 to describe introduced LMB recruitment dynamics. We evaluated growth, proximate composition, and health indices of young-of-the-year (YOY) LMB among tidal lakes and developed an integrated count model to determine how factors known to affect LMB recruitment shape SSJD population structure. Our results show a mismatch among growth, nutrition, and YOY abundance, where the tidal lake with the most abundant and fastest-growing LMB had the poorest nutritional status. The warm winter water temperatures and lack of a hatching-cohort growth advantage suggests overwinter starvation plays a less important role in SSJD LMB recruitment than in many native LMB habitats. Collectively, our results suggest that habitat characteristics (submerged aquatic vegetation) and not overwinter mortality shapes SSJD LMB population structure, a mechanism consistent with contemporary hypotheses about the altered fish community structure of the SSJD.

California↗

USGS2021

Mixed evidence for biotic homogenization of southern Appalachian fish communities

Anthropogenic impacts on the landscape can drive biotic homogenization, whereby distinct biological communities become more similar to one another over time. Land-use change in the Southern Appalachian region is expected to result in homogenization of the highly diverse freshwater fish communities as in-stream habitat alterations favor widespread cosmopolitan species at the expense of more narrowly distributed highland endemic species. We compiled four datasets spanning 25 years to (1) evaluate the effects of environmental factors on relative abundance and richness of highland endemic vs. cosmopolitan species in this region and (2) test for taxonomic homogenization, measured as a change in beta diversity over time. We found that several environmental factors differentially affected highland endemic and cosmopolitan species, with the proportion of forested land cover in a watershed most strongly predicting higher relative abundance and richness of highland endemic species. Our analysis of beta diversity change, however, shows mixed evidence of taxonomic homogenization, depending on how common species are weighted. Shifts in community composition, with or without homogenization, may warrant attention in biodiversity conservation planning.

Georgia, North Carolina↗

USGS2017

Science advancements key to increasing management value of life stage monitoring networks for endangered Sacramento River winter-run Chinook salmon in California

A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winterrun Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California’s Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within- and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity, abundance, and condition diminishes, despite the juvenile monitoring enterprise. We identified six system-wide recommended actions to strengthen the value of data generated from the existing monitoring network to assess resource management actions: (1) incorporate genetic run identification; (2) develop juvenile abundance estimates; (3) collect data for life history diversity metrics at multiple life stages; (4) expand and enhance real-time fish survival and movement monitoring; (5) collect fish condition data; and (6) provide timely public access to monitoring data in open data formats. To illustrate how updated technologies can enhance the existing monitoring to provide quantitative data on SRWRC, we provide examples of how each recommendation can address specific management issues.

California↗

USGS2016

Estimating juvenile Chinook salmon ( Oncorhynchus tshawytscha ) abundance from beach seine data collected in the Sacramento–San Joaquin Delta and San Francisco Bay, California

Resource managers rely on abundance or density metrics derived from beach seine surveys to make vital decisions that affect fish population dynamics and assemblage structure. However, abundance and density metrics may be biased by imperfect capture and lack of geographic closure during sampling. Currently, there is considerable uncertainty about the capture efficiency of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) by beach seines. Heterogeneity in capture can occur through unrealistic assumptions of closure and from variation in the probability of capture caused by environmental conditions. We evaluated the assumptions of closure and the influence of environmental conditions on capture efficiency and abundance estimates of Chinook salmon from beach seining within the Sacramento–San Joaquin Delta and the San Francisco Bay. Beach seine capture efficiency was measured using a stratified random sampling design combined with open and closed replicate depletion sampling. A total of 56 samples were collected during the spring of 2014. To assess variability in capture probability and the absolute abundance of juvenile Chinook salmon, beach seine capture efficiency data were fitted to the paired depletion design using modified N-mixture models. These models allowed us to explicitly test the closure assumption and estimate environmental effects on the probability of capture. We determined that our updated method allowing for lack of closure between depletion samples drastically outperformed traditional data analysis that assumes closure among replicate samples. The best-fit model (lowest-valued Akaike Information Criterion model) included the probability of fish being available for capture (relaxed closure assumption), capture probability modeled as a function of water velocity and percent coverage of fine sediment, and abundance modeled as a function of sample area, temperature, and water velocity. Given that beach seining is a ubiquitous sampling technique for many species, our improved sampling design and analysis could provide significant improvements in density and abundance estimation.

California↗