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Open Access Publications from the University of California

Scholarly Works (4 results)

  • Article
  • Peer Reviewed
San Francisco Estuary and Watershed Science, Volume 14, Issue 2 (2016)

The Sacramento–San Joaquin Delta (Delta) is a heterogeneous, highly modified aquatic system. I reviewed relevant predator–prey theory, and described extant data on predator–prey relationships of Delta fishes. I ranked predator consumption rates as occasional, moderate, and common, based on frequency-of-occurrence data, and evaluated the frequency, and hypothesized the effects of predation on native and invasive species. I identified 32 different predator categories and 41 different prey categories. Most predators were occasional consumers of individual prey species, although I also observed moderate and common consumption of some prey types. My analysis yielded few generalizations regarding predator–prey interactions for Delta fishes; most predators consumed a variety of both native and invasive fishes. The only evidence for predator specialization on either native or invasive fishes occurred in Prickly Sculpin which, when it consumed fishes, ate mostly native species. Both Striped and Largemouth Bass exhibited wide dietary breadth, preying upon 32 and 28 categories of fish prey respectively. Sacramento Pikeminnow, a native predator, also displayed wide dietary breadth of piscine prey, with 14 different prey categories consumed. Data for reptilian, avian, and mammalian predators were sparse; however, these predators may be significant fish predators in altered habitats or when hatchery salmonids are released. The database for predators and their fish prey was not strong, and I recommend long-term dietary studies combined with prey availability and behavioral and experimental studies to establish predator preferences and anti-predator behaviors, rather than just consumption. The behavioral effects of contaminants on prey species also warrant further examination. Although it has been suggested that a reduction in the Striped Bass population be implemented to reduce predation mortality of Chinook Salmon, the large number of salmon predators in the Delta make it unlikely that this effort will significantly affect salmon mortality.

    Cover page: Predation on Fishes in the Sacramento–San Joaquin Delta: Current Knowledge and Future DirectionsCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2007)
    Understanding how variation in reproductive success is related to demography is a critical component in understanding the life history of an organism. Parentage analysis using molecular markers can be used to estimate the reproductive success of different groups of individuals in natural populations. Previous models have been developed for cases where offspring are random samples from the population but these models do not account for the presence of full- and half-sibs commonly found in large clutches of many organisms. Here we develop a model for comparing reproductive success among different groups of individuals that explicitly incorporates within-nest relatedness. Inference for the parameters of the model is done in a Bayesian framework, where we sample from the joint posterior of parental assignments and fertility parameters. We use computer simulations to determine how well our model recovers known parameters and investigate how various data collection scenarios (varying the number of nests or the number of offspring) affect the estimates. We then apply our model to compare reproductive success among different age groups of mottled sculpin, Cottus bairdi, from a natural population. We demonstrate that older adults are more likely to contribute to a nest and that females in the older age groups contribute more eggs to a nest than younger individuals.
      Cover page: Estimating Differential Reproductive Success From Nests of Related Individuals, With Application to a Study of the Mottled Sculpin, Cottus bairdiCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2002)
      Most genetic surveys of parentage in nature sample only a small fraction of the breeding population. Here we apply microsatellite markers to deduce the genetic mating system and assess the reproductive success of females and males in an extensively collected, semi-closed stream population of the mottled sculpin fish, Cottus bairdi. In this species, males guard nest rocks where females deposit the eggs for fertilization. The potential exists for both males and females to mate with multiple partners and for males to provide parental care to genetically unrelated offspring. Four hundred and fifty-five adults and subadults, as well as 1,259 offspring from 23 nests, were genotyped at five polymorphic microsatellite loci. Multilocus maternal genotypes, deduced via genetic analyses of embryos, were reconstructed for more than 90% of the analysed nests, thus allowing both male and female reproductive success to be estimated accurately. There was no genetic evidence for cuckoldry, but one nest probably represents a takeover event. Successful males spawned with a mean of 2.8 partners, whereas each female apparently deposited her entire clutch of eggs in a single nest (mean fecundity = 66 eggs/female). On average, genetically deduced sires and dams were captured 1.6 and 9.3 metres from their respective nests, indicating little movement by breeders during the spawning season. Based on a 'genetic mark-recapture' estimate, the total number of potentially breeding adults (c. 570) was an order-of-magnitude larger than genetically based estimates of the effective number of breeders (c. 54). In addition, significantly fewer eggs per female were deposited in single than in multidam nests. Not only were perceived high-quality males spawning with multiple partners, but they were receiving more eggs from each female.
        Cover page: Intensive genetic assessment of the mating system and reproductive success in a semi‐closed population of the mottled sculpin, Cottus bairdiCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2018)

        Motivation

        The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

        Main types of variables included

        The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

        Spatial location and grain

        BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

        Time period and grain

        BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

        Major taxa and level of measurement

        BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

        Software format

        .csv and .SQL.
          Cover page: BioTIME: A database of biodiversity time series for the Anthropocene
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