Standardising terminology and notation for the analysis of demographic processes in marked populations

The development of statistical methods for the analysis of demographic processes in marked animal populations has brought with it the challenges of communication between the disciplines of statistics, ecology, evolutionary biology and computer science. In order to aid communication and comprehension, we sought to root out a number of cases of ambiguity, redundancy and inaccuracy in notation and terminology that have developed in the literature. We invited all working in this field to submit topics for resolution and to express their own views. In the ensuing discussion forum it was then possible to establish a series of general principles which were, almost without exception, unanimously accepted. Here we set out the background to the areas of confusion, how these were debated and the conclusions which were reached in each case. We hope that the resulting guidelines will be widely adopted as standard terminology in publications and in software for the analysis of demographic processes in marked animal populationspostprin

Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA

The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a high amplification success rate (89%) by storing faeces in 70% ethanol and using the guanidine thiocyanate/silica method for extraction. Using 70% ethanol as a storage agent had the advantage of it being an antiseptic. In order to obtain reliable genotypes with fewer amplification reactions than the standard multiple-tubes approach, we devised a comparative approach in which genetic profiles were compared and replication directed at similar, but not identical, genotypes. This modified method achieved a reduction in polymerase chain reactions comparable with the maximumlikelihood model when just using reliability criteria, and was slightly better when using reliability criteria with the additional proviso that alleles must be observed twice to be considered reliable. Our comparative approach would be best suited for studies that include multiple faeces from each individual. We utilized our approach in a well-studied population of badgers from which individuals had been sampled and reliable genotypes obtained. In a study of 53 faeces sampled from three social groups over 10 days, we found that direct enumeration could not be used to estimate population size, but that the application of mark–recapture models has the potential to provide more accurate results

Evaluation of Two Methods to Estimate and Monitor Bird Populations

Background: Effective management depends upon accurately estimating trends in abundance of bird populations over time, and in some cases estimating abundance. Two population estimation methods, double observer (DO) and double sampling (DS), have been advocated for avian population studies and the relative merits and short-comings of these methods remain an area of debate. Methodology/Principal Findings: We used simulations to evaluate the performances of these two population estimation methods under a range of realistic scenarios. For three hypothetical populations with different levels of clustering, we generated DO and DS population size estimates for a range of detection probabilities and survey proportions. Population estimates for both methods were centered on the true population size for all levels of population clustering and survey proportions when detection probabilities were greater than 20%. The DO method underestimated the population at detection probabilities less than 30 % whereas the DS method remained essentially unbiased. The coverage probability of 95 % confidence intervals for population estimates was slightly less than the nominal level for the DS method but was substantially below the nominal level for the DO method at high detection probabilities. Differences in observer detection probabilities did not affect the accuracy and precision of population estimates of the DO method. Population estimates for the DS method remained unbiased as the proportion of units intensively surveyed changed, but the variance of th

Modeling Trap-Awareness and Related Phenomena in Capture-Recapture Studies

Trap-awareness and related phenomena whereby successive capture events are not independent is a feature of the majority of capture-recapture studies. This phenomenon was up to now difficult to incorporate in open population models and most authors have chosen to neglect it although this may have damaging consequences. Focusing on the situation where animals exhibit a trap response at the occasion immediately following one where they have been trapped but revert to their original naïve state if they are missed once, we show that trap-dependence is more naturally viewed as a state transition and is amenable to the current models of capture-recapture. This approach has the potential to accommodate lasting or progressively waning trap effects

How Does Spatial Study Design Influence Density Estimates from Spatial Capture-Recapture Models?

When estimating population density from data collected on non-invasive detector arrays, recently developed spatial capture-recapture (SCR) models present an advance over non-spatial models by accounting for individual movement. While these models should be more robust to changes in trapping designs, they have not been well tested. Here we investigate how the spatial arrangement and size of the trapping array influence parameter estimates for SCR models. We analysed black bear data collected with 123 hair snares with an SCR model accounting for differences in detection and movement between sexes and across the trapping occasions. To see how the size of the trap array and trap dispersion influence parameter estimates, we repeated analysis for data from subsets of traps: 50% chosen at random, 50% in the centre of the array and 20% in the South of the array. Additionally, we simulated and analysed data under a suite of trap designs and home range sizes. In the black bear study, we found that results were similar across trap arrays, except when only 20% of the array was used. Black bear density was approximately 10 individuals per 100 km2. Our simulation study showed that SCR models performed well as long as the extent of the trap array was similar to or larger than the extent of individual movement during the study period, and movement was at least half the distance between traps. SCR models performed well across a range of spatial trap setups and animal movements. Contrary to non-spatial capture-recapture models, they do not require the trapping grid to cover an area several times the average home range of the studied species. This renders SCR models more appropriate for the study of wide-ranging mammals and more flexible to design studies targeting multiple species

A strong conditional mutualism limits and enhances seed dispersal and germination of a tropical palm

Seed predation and seed dispersal can have strong effects on early life history stages of plants. These processes have often been studied as individual effects, but the degree to which their relative importance co-varies with seed predator abundance and how this influences seed germination rates is poorly understood. Therefore, we used a combination of observations and field experiments to determine the degree to which germination rates of the palm Astrocaryum mexicanum varied with abundance of a small mammal seed predator/disperser, Heteromysdesmarestianus, in a lowland tropical forest. Patterns of abundance of the two species were strongly related; density of H. desmarestianus was low in sites with low density of A. mexicanum and vice versa. Rates of predation and dispersal of A. mexicanum seeds depended on abundance of H. desmarestianus; sites with high densities of H. desmarestianus had the highest rates of seed predation and lowest rates of seed germination, but a greater total number of seeds were dispersed and there was greater density of seedlings, saplings, and adults of A. mexicanum in these sites. When abundance of H. desmarestianus was experimentally reduced, rates of seed predation decreased, but so did dispersal of A. mexicanum seeds. Critically, rates of germination of dispersed seeds were 5 times greater than undispersed seeds. The results suggest that the relationship between A. mexicanum and H. desmarestianus is a conditional mutualism that results in a strong local effect on the abundance of each species. However, the magnitude and direction of these effects are determined by the relative strength of opposing, but related, mechanisms. A. mexicanum nuts provide H. desmarestianus with a critical food resource, and while seed predation on A. mexicanum nuts by H. desmarestianus is very intense, A. mexicanum ultimately benefits because of the relatively high germination rates of its seeds that are dispersed by H. desmarestianus

Estimating Animal Abundance in Ground Beef Batches Assayed with Molecular Markers

Estimating animal abundance in industrial scale batches of ground meat is important for mapping meat products through the manufacturing process and for effectively tracing the finished product during a food safety recall. The processing of ground beef involves a potentially large number of animals from diverse sources in a single product batch, which produces a high heterogeneity in capture probability. In order to estimate animal abundance through DNA profiling of ground beef constituents, two parameter-based statistical models were developed for incidence data. Simulations were applied to evaluate the maximum likelihood estimate (MLE) of a joint likelihood function from multiple surveys, showing superiority in the presence of high capture heterogeneity with small sample sizes, or comparable estimation in the presence of low capture heterogeneity with a large sample size when compared to other existing models. Our model employs the full information on the pattern of the capture-recapture frequencies from multiple samples. We applied the proposed models to estimate animal abundance in six manufacturing beef batches, genotyped using 30 single nucleotide polymorphism (SNP) markers, from a large scale beef grinding facility. Results show that between 411∼1367 animals were present in six manufacturing beef batches. These estimates are informative as a reference for improving recall processes and tracing finished meat products back to source

A Mitochondrial Kinase Complex Is Essential to Mediate an ERK1/2-Dependent Phosphorylation of a Key Regulatory Protein in Steroid Biosynthesis

ERK1/2 is known to be involved in hormone-stimulated steroid synthesis, but its exact roles and the underlying mechanisms remain elusive. Both ERK1/2 phosphorylation and steroidogenesis may be triggered by cAMP/cAMP-dependent protein kinase (PKA)-dependent and-independent mechanisms; however, ERK1/2 activation by cAMP results in a maximal steroidogenic rate, whereas canonical activation by epidermal growth factor (EGF) does not. We demonstrate herein by Western blot analysis and confocal studies that temporal mitochondrial ERK1/2 activation is obligatory for PKA-mediated steroidogenesis in the Leydig-transformed MA-10 cell line. PKA activity leads to the phosphorylation of a constitutive mitochondrial MEK1/2 pool with a lower effect in cytosolic MEKs, while EGF allows predominant cytosolic MEK activation and nuclear pERK1/2 localization. These results would explain why PKA favors a more durable ERK1/2 activation in mitochondria than does EGF. By means of ex vivo experiments, we showed that mitochondrial maximal steroidogenesis occurred as a result of the mutual action of steroidogenic acute regulatory (StAR) protein –a key regulatory component in steroid biosynthesis-, active ERK1/2 and PKA. Our results indicate that there is an interaction between mitochondrial StAR and ERK1/2, involving a D domain with sequential basic-hydrophobic motifs similar to ERK substrates. As a result of this binding and only in the presence of cholesterol, ERK1/2 phosphorylates StAR at Ser232. Directed mutagenesis of Ser232 to a non-phosphorylable amino acid such as Ala (StAR S232A) inhibited in vitro StAR phosphorylation by active ERK1/2. Transient transfection of MA-10 cells with StAR S232A markedly reduced the yield of progesterone production. In summary, here we show that StAR is a novel substrate of ERK1/2, and that mitochondrial ERK1/2 is part of a multimeric protein kinase complex that regulates cholesterol transport. The role of MAPKs in mitochondrial function is underlined

Glutamine-to-glutamate ratio in the nucleus accumbens predicts effort-based motivated performance in humans

Substantial evidence implicates the nucleus accumbens in motivated performance, but very little is known about the neurochemical underpinnings of individual differences in motivation. Here, we applied 1H magnetic resonance spectroscopy (1H-MRS) at ultra-high-field in the nucleus accumbens and inquired whether levels of glutamate (Glu), glutamine (Gln), GABA or their ratios predict interindividual differences in effort-based motivated task performance. Given the incentive value of social competition, we also examined differences in performance under self-motivated or competition settings. Our results indicate that higher accumbal Gln-to-Glu ratio predicts better overall performance and reduced effort perception. As performance is the outcome of multiple cognitive, motor and physiological processes, we applied computational modeling to estimate best-fitting individual parameters related to specific processes modeled with utility, effort and performance functions. This model-based analysis revealed that accumbal Gln-to-Glu ratio specifically relates to stamina; i.e., the capacity to maintain performance over long periods. It also indicated that competition boosts performance from task onset, particularly for low Gln-to-Glu individuals. In conclusion, our findings provide novel insights implicating accumbal Gln and Glu balance on the prediction of specific computational components of motivated performance. This approach and findings can help developing therapeutic strategies based on targeting metabolism to ameliorate deficits in effort engagement