isotracer: An R package for the analysis of tracer addition experiments

Tracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. However, performing rigorous statistical analyses to gain reliable quantitative insights from these experiments often remains challenging. We present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. The isotracer package is capable of handling a variety of tracer study designs, inc…

Territorial defense, territory size, and population regulation.

The carrying capacity of an environment is determined partly by how individuals compete over the available resources. To territorial animals, space is an important resource, leading to conflict over its use. We build a model where the carrying capacity for an organism in a given environment results from the evolution of territorial defense effort and the consequent space use. The same evolutionary process can yield two completely different modes of population regulation. Density dependence arises through expanding and shrinking territories if fecundity is low, breeding success increases gradually with territory size, and/or defense is cheap. By contrast, when fecundity is high, breeding suc…

Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies

Genetic rescue, an increase in population growth owing to the infusion of new alleles, can aid the persistence of small populations, but its use as a management tool is limited by a lack of empirical data geared towards predicting effects of gene flow on local adaptation and demography. Experimental translocations provide an ideal opportunity to monitor the demographic consequences of gene flow. In this study we take advantage of two experimental introductions of Trinidadian guppies to test the effects of gene flow on downstream native populations. We individually marked guppies from the native populations to monitor population dynamics for 3 months before and 26 months after gene flow. We …

Evolutionary conservation advice for despotic populations: habitat heterogeneity favours conflict and reduces productivity in Seychelles magpie robins

Individual preferences for good habitat are often thought to have a beneficial stabilizing effect for populations. However, if individuals preferentially compete for better-quality territories, these may become hotspots of conflict. We show that, in an endangered species, this process decreases the productivity of favoured territories to the extent that differences in productivity between territories disappear. Unlike predictions from current demographic theory on site-dependent population regulation (ideal despotic distribution), we show that population productivity is reduced if resources are distributed unevenly in space. Competition for high-quality habitat can thus have detrimental con…

Estimating the abundance of burrow-nesting species through the statistical analysis of combined playback and visual surveys

Can adaptation lead to extinction?

Ever since J.B.S. Haldane proposed the idea, evolutionary biologists are aware that individual level adaptations do not necessarily lead to optimal population performance. A few deeply mathematical models, drawing from a diverse range of systems, even predict that individual selection can lead to the extinction of the whole population, a phenomenon which has become known as evolutionary suicide. Due to the complexity of both following adaptation and determining the exact cause of an extinction, evolutionary suicide has remained untested empirically. However, three recent empirical studies suggest that it may occur, and that suicide should be taken seriously as a potentially important evolut…

Species-level selection reduces selfishness through competitive exclusion.

Adaptation does not necessarily lead to traits which are optimal for the population. This is because selection is often the strongest at the individual or gene level. The evolution of selfishness can lead to a ‘tragedy of the commons’, where traits such as aggression or social cheating reduce population size and may lead to extinction. This suggests that species-level selection will result whenever species differ in the incentive to be selfish. We explore this idea in a simple model that combines individual-level selection with ecology in two interacting species. Our model is not influenced by kin or trait-group selection. We find that individual selection in combination with competitive ex…

Beyond lifetime reproductive success: the posthumous reproductive dynamics of male Trinidadian guppies

In semelparous populations, dormant germ banks (e.g. seeds) have been proposed as important in maintaining genotypes that are adaptive at different times in fluctuating environments. Such hidden storage of genetic diversity need not be exclusive to dormant banks. Genotype diversity may be preserved in many iteroparous animals through sperm-storage mechanisms in females. This allows males to reproduce posthumously and increase the effective sizes of seemingly female-biased populations. Although long-term sperm storage has been demonstrated in many organisms, the understanding of its importance in the wild is very poor. We here show the prevalence of male posthumous reproduction in wild Trini…

DOES ENVIRONMENTAL ROBUSTNESS PLAY A ROLE IN FLUCTUATING ENVIRONMENTS?

Fluctuating environments are expected to select for individuals that have highest geometric fitness over the experienced environments. This leads to the prediction that genetically determined environmental robustness in fitness, and average fitness across environments should be positively genetically correlated to fitness in fluctuating environments. Because quantitative genetic experiments resolving these predictions are missing, we used a full-sib, half-sib breeding design to estimate genetic variance for egg-to-adult viability in Drosophila melanogaster exposed to two constant or fluctuating temperatures that were above the species' optimum temperature, during development. Viability in t…

Spatio-temporal dynamics of density-dependent dispersal during a population colonisation

Predicting population colonisations requires understanding how spatio‐temporal changes in density affect dispersal. Density can inform on fitness prospects, acting as a cue for either habitat quality, or competition over resources. However, when escaping competition, high local density should only increase emigration if lower‐density patches are available elsewhere. Few empirical studies on dispersal have considered the effects of density at the local and landscape scale simultaneously. To explore this, we analyze 5 years of individual‐based data from an experimental introduction of wild guppies Poecilia reticulata. Natal dispersal showed a decrease in local density dependence as density at…

isotracer: An R package for the analysis of tracer addition experiments

AbstractTracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels.We present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer.The isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments, and pulse-chase experiments. It can also take into account tracer decay when radio…

Selection analysis on the rapid evolution of a secondary sexual trait

Evolutionary analyses of population translocations (experimental or accidental) have been important in demonstrating speed of evolution because they subject organisms to abrupt environmental changes that create an episode of selection. However, the strength of selection in such studies is rarely measured, limiting our understanding of the evolutionary process. This contrasts with long-term, mark–recapture studies of unmanipulated populations that measure selection directly, yet rarely reveal evolutionary change. Here, we present a study of experimental evolution of male colour in Trinidadian guppies where we tracked both evolutionary change and individual-based measures of selection. Guppie…

REPLICATED ORIGIN OF FEMALE-BIASED ADULT SEX RATIO IN INTRODUCED POPULATIONS OF THE TRINIDADIAN GUPPY (POECILIA RETICULATA)

There are many theoretical and empirical studies explaining variation in offspring sex ratio but relatively few that explain variation in adult sex ratio. Adult sex ratios are important because biased sex ratios can be a driver of sexual selection and will reduce effective population size, affecting population persistence and shapes how populations respond to natural selection. Previous work on guppies (Poecilia reticulata) gives mixed results, usually showing a female-biased adult sex ratio. However, a detailed analysis showed that this bias varied dramatically throughout a year and with no consistent sex bias. We used a mark-recapture approach to examine the origin and consistency of fema…

From individual dispersal to species ranges: perspectives for a changing world.

Dispersal is often risky to the individual, yet the long-term survival of populations depends on having a sufficient number of individuals that move, find each other, and locate suitable breeding habitats. This tension has consequences that rarely meet our conservation or management goals. This is particularly true in changing environments, which makes the study of dispersal urgently topical in a world plagued with habitat loss, climate change, and species introductions. Despite the difficulty of tracking mobile individuals over potentially vast ranges, recent research has revealed a multitude of ways in which dispersal evolution can either constrain, or accelerate, species' responses to en…

The ecogenetic link between demography and evolution: can we bridge the gap between theory and data?

Calls to understand the links between ecology and evolution have been common for decades. Population dynamics, i.e. the demographic changes in populations, arise from life history decisions of individuals and thus are a product of selection, and selection, on the contrary, can be modified by such dynamical properties of the population as density and stability. It follows that generating predictions and testing them correctly requires considering this ecogenetic feedback loop whenever traits have demographic consequences, mediated via density dependence (or frequency dependence). This is not an easy challenge, and arguably theory has advanced at a greater pace than empirical research. Howeve…

Reproductive conflict delays the recovery of an endangered social species

1. Evolutionary theory predicts that individuals, in order to increase their relative fitness, can evolve behaviours that are detrimental for the group or population. This mismatch is particularly visible in social organisms. Despite its potential to affect the population dynamics of social animals, this principle has not yet been applied to real-life conservation. 2. Social group structure has been argued to stabilize population dynamics due to the buffering effects of nonreproducing subordinates. However, competition for breeding positions in such species can also interfere with the reproduction of breeding pairs. 3. Seychelles magpie robins, Copsychus sechellarum, live in social groups w…

Rapid Changes in the Sex Linkage of Male Coloration in Introduced Guppy Populations

Theory predicts that the sex linkage of sexually selected traits can influence the direction and rate of evolution and should itself evolve in response to sex-specific selection. Some studies have found intraspecific differences in sex linkage associated with differences in selection pressures, but we know nothing about how fast these differences can evolve. Here we show that introduced guppy populations showing rapid evolution of male coloration also show rapid changes in sex-linkage patterns. A comparison, using hormonal manipulations in females, of introduced populations of different ages suggests a consistent increase of autosomal or X-linked coloration 2 years after introduction from h…