NONPARAMETRIC ESTIMATION OF NATURAL SELECTION ON A QUANTITATIVE TRAIT USING MARK‐RECAPTURE DATA

Shell colour diversification induced by ecological release: A shift in natural selection after a migration event

Ecological release is often attributed to the rapid adaptive diversification of phenotypic traits. However, it is not well understood how natural selection changes its strength and direction through the process of ecological release. Herein, we demonstrated how shell colour of the Japanese land snail Euhadra peliomphala simodae has diversified via a shift in natural selection due to ecological release after migration from the mainland to an island. This snail's shell colour diversified on the island due to disruptive selection after migration from the mainland. We used trail camera traps to identify the cause of natural selection on both the mainland and the island. We then conducted a mark-recapture experiment while collecting microhabitat use data. In total, we captured and marked around 1,700 snails on the mainland, some of which were preyed upon by an unknown predator. The trail camera traps showed that the predator is the large Japanese field mouse Apodemus speciosus, and the predatory frequency was higher on the mainland than on the island. However, this predation did not correlate with shell colour. Microhabitat use on the island was more extensive than on the mainland, with snails on the island using both ground and arboreal microhabitats. A Bayesian estimation showed that the stabilizing selection on shell colour came from factors other than predation. Our results suggest that the course of natural selection was modified due to ecological release after migration from the mainland, explaining one cause of the phenotypic diversification.

Environmental change reduces body condition, but not population growth, in a high-arctic herbivore

Environmental change influences fitness-related traits and demographic rates, which in herbivores are often linked to resource-driven variation in body condition. Coupled body condition-demographic responses may therefore be important for herbivore population dynamics in fluctuating environments, such as the Arctic. We applied a transient Life-Table Response Experiment ('transient-LTRE') to demographic data from Svalbard barnacle geese (Branta leucopsis), to quantify their population-dynamic responses to changes in body mass. We partitioned contributions from direct and delayed demographic and body condition-mediated processes to variation in population growth. Declines in body condition (1980-2017), which positively affected reproduction and fledgling survival, had negligible consequences for population growth. Instead, population growth rates were largely reproduction-driven, in part through positive responses to rapidly advancing spring phenology. The virtual lack of body condition-mediated effects indicates that herbivore population dynamics may be more resilient to changing body condition than previously expected, with implications for their persistence under environmental change.

Disruptive selection of shell colour in land snails: a mark–recapture study of Euhadra peliomphala simodae

Many theoretical studies have suggested that disruptive selection plays an important role in phenotypic divergence, but few studies have determined the action of disruptive selection on phenotypic divergence via field studies. This study investigated the effect of disruptive selection on shell colour polymorphism in the Japanese land snail Euhadra peliomphala simodae to determine whether extreme phenotypes of snail shell colour are favoured over intermediate phenotypes. We conducted field surveys on an oceanic island with black, yellow and intermediate-coloured E. p. simodae snails. We captured and marked ~1800 individual snails and monitored their survival over 18 months. We quantified shell colours against images and examined the frequency distribution of shell colour variation. The variation exhibited a bimodal distribution with a far lower frequency of intermediate-coloured snails than of black or yellow snails. The population sizes of the three snail groups fluctuated synchronously with the changing seasons. Bayesian estimates showed lower survival rates for juvenile intermediate-coloured snails than for juvenile black and yellow snails, implying there was disruptive selection associated with shell colour. We suggest this disruptive selection may have resulted in the evolutionary divergence of the snail’s shell colour within the lineage having high shell colour variation.

Survival by genotype: patterns at Mc1r are not black and white at the White Sands ecotone

Measuring links among genotype, phenotype and survival in the wild has long been a focus of studies of adaptation. We conducted a 4-year capture-recapture study to measure survival by genotype and phenotype in the Southwestern Fence Lizard (Sceloporus cowlesi) at the White Sands ecotone (transition area between white sands and dark soil habitats). We report several unanticipated findings. First, in contrast with previous work showing that cryptic blanched coloration in S. cowlesi from the heart of the dunes is associated with mutations in the melanocortin-1 receptor gene (Mc1r), ecotonal S. cowlesi showed minimal association between colour phenotype and Mc1r genotype. Second, the frequency of the derived Mc1r allele in ecotonal S. cowlesi appeared to decrease over time. Third, our capture-recapture data revealed a lower survival rate for S. cowlesi individuals with the derived Mc1r allele. Thus, our results suggest that selection at the ecotone may have favoured the wild-type allele in recent years. Even in a system where a genotype-phenotype association appeared to be black and white, our study suggests that additional factors - including phenotypic plasticity, epistasis, pleiotropy and gene flow - may play important roles at the White Sands ecotone. Our study highlights the importance of linking molecular, genomic and organismal approaches for understanding adaptation in the wild. Furthermore, our findings indicate that dynamics of natural selection can be particularly complex in transitional habitats like ecotones and emphasize the need for future research that examines the patterns of ongoing selection in other ecological 'grey' zones.

The temporal distribution of directional gradients under selection for an optimum

Temporal variation in phenotypic selection is often attributed to environmental change causing movements of the adaptive surface relating traits to fitness, but this connection is rarely established empirically. Fluctuating phenotypic selection can be measured by the variance and autocorrelation of directional selection gradients through time. However, the dynamics of these gradients depend not only on environmental changes altering the fitness surface, but also on evolution of the phenotypic distribution. Therefore, it is unclear to what extent variability in selection gradients can inform us about the underlying drivers of their fluctuations. To investigate this question, we derive the temporal distribution of directional gradients under selection for a phenotypic optimum that is either constant or fluctuates randomly in various ways in a finite population. Our analytical results, combined with population- and individual-based simulations, show that although some characteristic patterns can be distinguished, very different types of change in the optimum (including a constant optimum) can generate similar temporal distributions of selection gradients, making it difficult to infer the processes underlying apparent fluctuating selection. Analyzing changes in phenotype distributions together with changes in selection gradients should prove more useful for inferring the mechanisms underlying estimated fluctuating selection.

Revisiting the effect of capture heterogeneity on survival estimates in capture-mark-recapture studies: does it matter?

Recently developed capture-mark-recapture methods allow us to account for capture heterogeneity among individuals in the form of discrete mixtures and continuous individual random effects. In this article, we used simulations and two case studies to evaluate the effectiveness of continuously distributed individual random effects at removing potential bias due to capture heterogeneity, and to evaluate in what situation the added complexity of these models is justified. Simulations and case studies showed that ignoring individual capture heterogeneity generally led to a small negative bias in survival estimates and that individual random effects effectively removed this bias. As expected, accounting for capture heterogeneity also led to slightly less precise survival estimates. Our case studies also showed that accounting for capture heterogeneity increased in importance towards the end of study. Though ignoring capture heterogeneity led to a small bias in survival estimates, such bias may greatly impact management decisions. We advocate reducing potential heterogeneity at the sampling design stage. Where this is insufficient, we recommend modelling individual capture heterogeneity in situations such as when a large proportion of the individuals has a low detection probability (e.g. in the presence of floaters) and situations where the most recent survival estimates are of great interest (e.g. in applied conservation).

Cormack-Jolly-Seber model with environmental covariates: a P-spline approach

In capture-recapture models, survival and capture probabilities can be modelled as functions of time-varying covariates, such as temperature or rainfall. The Cormack-Jolly-Seber (CJS) model allows for flexible modelling of these covariates; however, the functional relationship may not be linear. We extend the CJS model by semi-parametrically modelling capture and survival probabilities using a frequentist approach via P-splines techniques. We investigate the performance of the estimators by conducting simulation studies. We also apply and compare these models with known semi-parametric Bayesian approaches on simulated and real data sets.

Estimating demographic parameters using hidden process dynamic models

Structured population models are widely used in plant and animal demographic studies to assess population dynamics. In matrix population models, populations are described with discrete classes of individuals (age, life history stage or size). To calibrate these models, longitudinal data are collected at the individual level to estimate demographic parameters. However, several sources of uncertainty can complicate parameter estimation, such as imperfect detection of individuals inherent to monitoring in the wild and uncertainty in assigning a state to an individual. Here, we show how recent statistical models can help overcome these issues. We focus on hidden process models that run two time series in parallel, one capturing the dynamics of the true states and the other consisting of observations arising from these underlying possibly unknown states. In a first case study, we illustrate hidden Markov models with an example of how to accommodate state uncertainty using Frequentist theory and maximum likelihood estimation. In a second case study, we illustrate state-space models with an example of how to estimate lifetime reproductive success despite imperfect detection, using a Bayesian framework and Markov Chain Monte Carlo simulation. Hidden process models are a promising tool as they allow population biologists to cope with process variation while simultaneously accounting for observation error.

High hunting pressure selects for earlier birth date: wild boar as a case study

Exploitation by humans affects the size and structure of populations. This has evolutionary and demographic consequences that have typically being studied independent of one another. We here applied a framework recently developed applying quantitative tools from population ecology and selection gradient analysis to quantify the selection on a quantitative trait-birth date-through its association with multiple fitness components. From the long-term monitoring (22 years) of a wild boar (Sus scrofa scrofa) population subject to markedly increasing hunting pressure, we found that birth dates have advanced by up to 12 days throughout the study period. During the period of low hunting pressure, there was no detectable selection. However, during the period of high hunting pressure, the selection gradient linking breeding probability in the first year of life to birth date was negative, supporting current life-history theory predicting selection for early births to reproduce within the first year of life with increasing adult mortality.

Investigating evolutionary trade-offs in wild populations of atlantic salmon (salmo salar): incorporating detection probabilities and individual heterogeneity

Evolutionary trade-offs among demographic parameters are important determinants of life-history evolution. Investigating such trade-offs under natural conditions has been limited by inappropriate analytical methods that fail to address the bias in demographic estimates that can result when issues of detection (uncertain detection of individual) are ignored. We propose a new statistical approach to quantify evolutionary trade-offs in wild populations. Our method is based on a state-space modeling framework that focuses on both the demographic process of interest as well as the observation process. As a case study, we used individual mark-recapture data for stream-dwelling Atlantic salmon juveniles in the Scorff River (Southern Brittany, France). In freshwater, juveniles face two life-history choices: migration to the ocean and sexual maturation (for males). Trade-offs may appear with these life-history choices and survival, because all are energy dependent. We found a cost of reproduction on survival for fish staying in freshwater and a survival advantage associated with the "decision" to migrate. Our modeling framework opens up promising prospects for the study of evolutionary trade-offs when some life-history traits are not, or only partially, observable.

Individual heterogeneity in studies on marked animals using numerical integration: capture-recapture mixed models

In conservation and evolutionary ecology, quantifying and accounting for individual heterogeneity in vital rates of open populations is of particular interest. Individual random effects have been used in capture-recapture models, adopting a Bayesian framework with Markov chain Monte Carlo (MCMC) to carry out estimation and inference. As an alternative, we show how numerical integration via the Gauss-Hermite quadrature (GHQ) can be efficiently used to approximate the capture-recapture model likelihood with individual random effects. We compare the performance of the two approaches (MCMC vs. GHQ) and finite mixture models using two examples, including data on European Dippers and Sociable Weavers. Besides relying on standard statistical tools, GHQ was found to be faster than MCMC simulations. Our approach is implemented in program E-SURGE. Overall, capture recapture mixed models (CR2Ms), implemented either via a GHQ approximation or MCMC simulations, have potential important applications in population biology.

Estimating and visualizing fitness surfaces using mark-recapture data

Understanding how selection operates on a set of phenotypic traits is central to evolutionary biology. Often, it requires estimating survival (or other fitness-related life-history traits) which can be difficult to obtain for natural populations because individuals cannot be exhaustively followed. To cope with this issue of imperfect detection, we advocate the use of mark-recapture data and we provide a general framework for both the estimation of linear and nonlinear selection gradients and the visualization of fitness surfaces. To quantify the strength of selection, the standard second-order polynomial regression method is integrated in mark-recapture models. To visualize the form of selection, we use splines to display selection acting on multivariate phenotypes in the most flexible way. We employ Markov chain Monte Carlo sampling in a Bayesian framework to estimate model parameters, assessing traits relevance and calculating the optimal amount of smoothing. We illustrate our approach using data from a wild population of Common blackbirds (Turdus merula) to investigate survival in relation to morphological traits, and provide evidence for correlational selection using the new methodology. Overall, the framework we propose will help in exploring the full potential of mark-recapture data to study natural selection.

The risk of flawed inference in evolutionary studies when detectability is less than one

Addressing evolutionary questions in the wild remains a challenge. It is best done by monitoring organisms from birth to death, which is very difficult in part because individuals may or may not be resighted or recaptured. Although the issue of uncertain detection has long been acknowledged in ecology and conservation biology, in evolutionary studies of wild populations it is often assumed that detectability is perfect. We argue that this assumption may lead to flawed inference. We demonstrate that the form of natural selection acting on body mass of sociable weavers is altered and that the rate of senescence of roe deer is underestimated when not accounting for a value of detectability that is less than one. Because mark-recapture models provide an explicit way to integrate and reliably model the detection process, we strongly recommend their use to address questions in evolutionary biology.

Climate and the range dynamics of species with imperfect detection

Reliable predictions for species range changes require a mechanistic understanding of range dynamics in relation to environmental variation. One obstacle is that most current models are static and confound occurrence with the probability of detecting a species if it occurs at a site. Here we draw attention to recently developed occupancy models, which can be used to examine colonization and local extinction or changes in occupancy over time. These models further account for detection probabilities, which are likely to vary spatially and temporally in many datasets. Occupancy models require repeated presence/absence surveys, for example checklists used in bird atlas projects. As an example, we examine the recent range expansion of hadeda ibises (Bostrychia hagedash) in South African protected areas. Colonization exceeded local extinction in most biomes, and the probability of occurrence was related to local climate. Extensions of the basic occupancy models can estimate abundance or species richness. Occupancy models are an appealing additional tool for studying species' responses to global change.