Collision between biological process and statistical analysis revealed by mean centring.

Animal ecologists often collect hierarchically structured data and analyse these with linear mixed-effects models. Specific complications arise when the effect sizes of covariates vary on multiple levels (e.g. within vs. among subjects). Mean centring of covariates within subjects offers a useful approach in such situations, but is not without problems. A statistical model represents a hypothesis about the underlying biological process. Mean centring within clusters assumes that the lower level responses (e.g. within subjects) depend on the deviation from the subject mean (relative) rather than on the absolute scale of the covariate. This may or may not be biologically realistic. We show that mismatch between the nature of the generating (i.e. biological) process and the form of the statistical analysis produce major conceptual and operational challenges for empiricists. We explored the consequences of mismatches by simulating data with three response-generating processes differing in the source of correlation between a covariate and the response. These data were then analysed by three different analysis equations. We asked how robustly different analysis equations estimate key parameters of interest and under which circumstances biases arise. Mismatches between generating and analytical equations created several intractable problems for estimating key parameters. The most widely misestimated parameter was the among-subject variance in response. We found that no single analysis equation was robust in estimating all parameters generated by all equations. Importantly, even when response-generating and analysis equations matched mathematically, bias in some parameters arose when sampling across the range of the covariate was limited. Our results have general implications for how we collect and analyse data. They also remind us more generally that conclusions from statistical analysis of data are conditional on a hypothesis, sometimes implicit, for the process(es) that generated the attributes we measure. We discuss strategies for real data analysis in face of uncertainty about the underlying biological process.

Track and dive-based movement metrics do not predict the number of prey encountered by a marine predator.

BACKGROUND: Studying animal movement in the context of the optimal foraging theory has led to the development of simple movement metrics for inferring feeding activity. Yet, the predictive capacity of these metrics in natural environments has been given little attention, raising serious questions of the validity of these metrics. The aim of this study is to test whether simple continuous movement metrics predict feeding intensity in a marine predator, the southern elephant seal (SES; Mirounga leonine), and investigate potential factors influencing the predictive capacity of these metrics. METHODS: We equipped 21 female SES from the Kerguelen Archipelago with loggers and recorded their movements during post-breeding foraging trips at sea. From accelerometry, we estimated the number of prey encounter events (nPEE) and used it as a reference for feeding intensity. We also extracted several track- and dive-based movement metrics and evaluated how well they explain and predict the variance in nPEE. We conducted our analysis at two temporal scales (dive and day), with two dive profile resolutions (high at 1 Hz and low with five dive segments), and two types of models (linear models and regression trees). RESULTS: We found that none of the movement metrics predict nPEE with satisfactory power. The vertical transit rates (primarily the ascent rate) during dives had the best predictive performance among all metrics. Dive metrics performed better than track metrics and all metrics performed on average better at the scale of days than the scale of dives. However, the performance of the models at the scale of days showed higher variability among individuals suggesting distinct foraging tactics. Dive-based metrics performed better when computed from high-resolution dive profiles than low-resolution dive profiles. Finally, regression trees produced more accurate predictions than linear models. CONCLUSIONS: Our study reveals that simple movement metrics do not predict feeding activity in free-ranging marine predators. This could emerge from differences between individuals, temporal scales, and the data resolution used, among many other factors. We conclude that these simple metrics should be avoided or carefully tested a priori with the studied species and the ecological context to account for significant influencing factors.

Sex, body size, and boldness shape the seasonal foraging habitat selection in southern elephant seals.

Selecting foraging habitat is a fundamental behavior in the life of organisms as it directly links resource acquisition to fitness. Differences in habitat selection among individuals may arise from several intrinsic and extrinsic factors, and yet, their interaction has been given little attention in the study of wild populations. We combine sex, body size, and boldness to explain individual differences in the seasonal foraging habitat selection of southern elephant seals (Mirounga leonina) from the Kerguelen Archipelago. We hypothesize that habitat selection is linked to the trade-off between resource acquisition and risk, and that individuals differ in their position along this trade-off because of differences in reproductive strategies, life stages, and metabolic requirements. Before the post-molt foraging trip, we used a novel object approach test to quantify the boldness of 28 subadult and adult females and 42 subadult males and equipped them with data loggers to track their movements at sea. Subadult males selected neritic and oceanic habitats, whereas females mostly selected less productive oceanic habitats. Both sexes showed a seasonal shift from Antarctic habitats in the south in the summer to the free of ice subantarctic and subtropical habitats in the north in the winter. Males avoided oceanic habitats and selected more productive neritic and Antarctic habitats with body size mostly in the winter. Bolder males selected northern warmer waters in winter, while shyer ones selected the Kerguelen plateau and southern colder oceanic waters. Bolder females selected the Kerguelen plateau in the summer when prey profitability is assumed to be the highest. This study not only provides new insights into the spatiotemporal foraging ecology of elephant seals in relation to personality but also emphasizes the relevance of combining several intrinsic and extrinsic factors in understanding among-individual variation in space use essential in wildlife management and conservation.

Data on the diets of Salish Sea harbour seals from DNA metabarcoding.

Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal (Phoca vitulina) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon (Oncorhynchus spp.). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.

Indirect genetic and environmental effects on behaviors, morphology, and life-history traits in a wild Eastern chipmunk population.

Additive genetic variance in a trait reflects its potential to respond to selection, which is key for adaptive evolution in the wild. Social interactions contribute to this genetic variation through indirect genetic effects-the effect of an individual's genotype on the expression of a trait in a conspecific. However, our understanding of the evolutionary importance of indirect genetic effects in the wild and of their strength relative to direct genetic effects is limited. In this study, we assessed how indirect genetic effects contribute to genetic variation of behavioral, morphological, and life-history traits in a wild Eastern chipmunk population. We also compared the contribution of direct and indirect genetic effects to traits evolvabilities and related these effects to selection strength across traits. We implemented a novel approach integrating the spatial structure of social interactions in quantitative genetic analyses, and supported the reliability of our results with power analyses. We found indirect genetic effects for trappability and relative fecundity, little direct genetic effects in all traits and a large role for direct and indirect permanent environmental effects. Our study highlights the potential evolutionary role of social permanent environmental effects in shaping phenotypes of conspecifics through adaptive phenotypic plasticity.