A flexible Bayesian hierarchical approach for analyzing spatial and temporal variation in the fecal corticosterone levels in birds when there is imperfect knowledge of individual identity.

Population cycles have long interested biologists. The ruffed grouse, Bonasa umbellus, is one such species whose populations cycle over most of their range. Thus, much effort has been expended to understand the mechanisms that might control cycles in this and other species. Corticosterone metabolites are widely used in studies of animals to measure physiological stress. We evaluated corticosterone metabolites in feces of territorial male grouse as a potential tool to study mechanisms governing grouse cycles. However, like most studies of corticosterone in wild animals, we did not know the identity of all individuals for which we had fecal samples. This presented an analytical problem that resulted in either pseudoreplication or confounding. Therefore, we derived an analytical approach that accommodated for uncertainty in individual identification. Because we had relatively low success capturing birds, we estimated turnover probabilities of birds on territorial display sites based on capture histories of a limited number of birds we captured. Hence, we developed a study design and modeling approach to quantify variation in corticosterone levels among individuals and through time that would be applicable to any field study of corticosterone in wild animals. Specifically, we wanted a sampling design and model that was flexible enough to partition variation among individuals, spatial units, and years, while incorporating environmental covariates that would represent potential mechanisms. We conducted our study during the decline phase of the grouse cycle and found high variation among corticosterone samples (11.33-443.92 ng/g [x=113.99 ng/g, SD=69.08, median=99.03 ng/g]). However, there were relatively small differences in corticosterone levels among years, but levels declined throughout each breeding season, which was opposite our predictions for stress hormones correlating with a declining population. We partitioned the residual variation into site, bird, and repetition (i.e., multiple samples collected from the same bird on the same day). After accounting for years and three general periods within breeding seasons, 42% of the residual variation among observations was attributable to differences among individual birds. Thus, we attribute little influence of site on stress level of birds in our study, but disentangling individual from site effects is difficult because site and bird are confounded. Our model structures provided analytical approaches for studying species having different ecologies. Our approach also demonstrates that even incomplete information on individual identity of birds within samples is useful for analyzing these types of data.

Population and individual elephant response to a catastrophic fire in Pilanesberg National Park.

In predator-free large herbivore populations, where density-dependent feedbacks occur at the limit where forage resources can no longer support the population, environmental catastrophes may play a significant role in population regulation. The potential role of fire as a stochastic mass-mortality event limiting these populations is poorly understood, so too the behavioural and physiological responses of the affected animals to this type of large disturbance event. During September 2005, a wildfire resulted in mortality of 29 (18% population mortality) and injury to 18, African elephants in Pilanesberg National Park, South Africa. We examined movement and herd association patterns of six GPS-collared breeding herds, and evaluated population physiological response through faecal glucocorticoid metabolite (stress) levels. We investigated population size, structure and projected growth rates using a simulation model. After an initial flight response post-fire, severely injured breeding herds reduced daily displacement with increased daily variability, reduced home range size, spent more time in non-tourist areas and associated less with other herds. Uninjured, or less severely injured, breeding herds also shifted into non-tourist areas post-fire, but in contrast, increased displacement rate (both mean and variability), did not adjust home range size and formed larger herds post-fire. Adult cow stress hormone levels increased significantly post-fire, whereas juvenile and adult bull stress levels did not change significantly. Most mortality occurred to the juvenile age class causing a change in post-fire population age structure. Projected population growth rate remained unchanged at 6.5% p.a., and at current fecundity levels, the population would reach its previous level three to four years post-fire. The natural mortality patterns seen in elephant populations during stochastic events, such as droughts, follows that of the classic mortality pattern seen in predator-free large ungulate populations, i.e. mainly involving juveniles. Fire therefore functions in a similar manner to other environmental catastrophes and may be a natural mechanism contributing to population limitation. Welfare concerns of arson fires, burning during "hot-fire" conditions and the conservation implications of fire suppression (i.e. removal of a potential contributing factor to natural population regulation) should be integrated into fire management strategies for conservation areas.

Large-scale generation and analysis of expressed sequence tags from porcine ovary.

One method to identify the factors that control ovarian function is to characterize the genes that are expressed in ovary. In the present study, cDNA libraries from fetal, neonatal, and prepubertal porcine ovaries, pubertal ovaries on different days of the estrous cycle (Days 0 [follicle], 5, and 12 [follicle and corpus luteum]), and follicles isolated from weaned sows (diameter, 2, 4, 6, and 8 mm) were constructed and sequenced. A total of 22 176 cDNAs were sequenced, of which 15 613 were of sufficient quality for clustering. Clustering of cDNAs resulted in 8507 contigs, 6294 (74%) of which were comprised of a single sequence. Sixty-eight percent of the contigs had consensus sequences that were homologous to existing Tentative Consensus (TC) sequences or mature transcripts (ET) in The Institute for Genomic Research Porcine Gene Index. The consensus sequences were classified according to the Gene Ontology Index. Most cDNA-encoded proteins were components of the nucleus, ribosome, or mitochondrion. The proteins primarily functioned in binding, catalysis, and transport. Nearly 75% of the proteins were involved in metabolism and cell growth and/or maintenance. Analysis of the cDNA frequency across different libraries demonstrated differential gene expression within different-size follicles, between follicles and corpora lutea, and across developmental time-points. The expression of selected genes (analyzed by ribonuclease protection assay and Northern blotting) was consistent with the frequency of their respective cDNA in the individual libraries. This porcine ovary unigene set will be useful for identifying factors and mechanisms controlling ovarian follicular development in a variety of species.

EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human.

A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3' end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14.