Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models.

Quantifying patterns of temporal trends in species assemblages is an important analytical challenge in community ecology. We describe methods of analysis that can be applied to a matrix of counts of individuals that is organized by species (rows) and time-ordered sampling periods (columns). We first developed a bootstrapping procedure to test the null hypothesis of random sampling from a stationary species abundance distribution with temporally varying sampling probabilities. This procedure can be modified to account for undetected species. We next developed a hierarchical model to estimate species-specific trends in abundance while accounting for species-specific probabilities of detection. We analysed two long-term datasets on stream fishes and grassland insects to demonstrate these methods. For both assemblages, the bootstrap test indicated that temporal trends in abundance were more heterogeneous than expected under the null model. We used the hierarchical model to estimate trends in abundance and identified sets of species in each assemblage that were steadily increasing, decreasing or remaining constant in abundance over more than a decade of standardized annual surveys. Our methods of analysis are broadly applicable to other ecological datasets, and they represent an advance over most existing procedures, which do not incorporate effects of incomplete sampling and imperfect detection.

Estimating differential reproductive success from nests of related individuals, with application to a study of the mottled sculpin, Cottus bairdi.

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.

Form and performance: body shape and prey-capture success in four drift-feeding minnows.

Identifying links between morphology and performance for ecologically relevant tasks will help elucidate the relationships between organismal design and fitness. We conducted a laboratory study to quantify the relationship between variation in body shape and prey-capture success in four drift-feeding minnow species. We offered drifting prey to individual fish in a test flume, counted successful strikes to measure prey-capture success and recorded the position (X, Y coordinates) of ten landmarks on each fish's outline to delineate the specimen's form. We then quantified shape variation among species and related it to capture performance through thin-plate spline analysis. Body shape varied significantly among species and with specimen size and was the major determinant of capture success, explaining 45-47% of its variability. Prey-capture success at differing velocities differed among species, but once the effects of shape and size were accounted for, those differences were no longer significant. Allometric shape changes appeared responsible for most of the ontogenetic variation in capture performance, although other size-related, non-shape factors also seemed relevant. Fishes with deeper, shorter bodies, more caudally placed median fins and larger, more upward-pointing mouths exhibited greater capture success than more fusiform fish, suggesting that streamlining, which is energetically advantageous for sustained swimming, entails a cost in terms of prey-capture ability. Our findings demonstrate a strong connection between organismal shape and performance and provide empirical evidence of the cost of morphological specialization for fishes in the drift-feeding functional guild.

Intensive genetic assessment of the mating system and reproductive success in a semi-closed population of the mottled sculpin, Cottus bairdi.

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.

Ecological aspects of ontogenetic shifts in prey size utilization in the bay goby (Pisces: Gobiidae).

Two age classes (0+ to 3+ and 4+ to 7+) of bay gobies (Lepidogobius lepidus Girard) differed in the sizes of whole prey (except polychaetes) recovered from the digestive tract. Although older fish consumed greater amounts of larger prey they did not capture larger individuals of a given prey type for seven of nine prey classes. The remaining two, harpacticoid copepods and ostracods contribute minimally to ontogenetic differences. The switch to larger prey appears to either decrease exposure to predation through a reduction in foraging time or increase energy intake. This is facilitated through older fishes greater size and/or superiority in intraspecific competition. These differences can probably be viewed as adaptations to selective pressures imposed by fluctuating food resources on predation levels in bays and estuaries.

Food, fights, and burrows: The adaptive significance of intraspecific aggression in the bay goby (Pisces: Gobiidae).

The effects of size, sex, bout initiation, past experience, and prior residence were examined with respect to the outcome of intraspecific agonistic contests in the bay goby (Lepidogobius lepidus). In addition, the adaptive significance of this behavior was examined by investigating the relationship between dominance and access to two potentially limiting resources; food and the burrows of invertebrate symbionts.For heterosexual and male homosexual contests, size and initiation significantly affected bout outcome. Gender did not affect heterosexual encounters. In female homosexual bouts initiation played a significant role in determining contest outcome while size did not. Both past experience and prior residency had significant effects on the outcome of intraspecific encounters.Dominant gobies had increased access to simulated invertebrate burrows and limited food. It appears that intraspecific aggression is an adaptive phenomenon through which access to limiting resources may be mediated.