Spatial-temporal stratifications in natural populations and how they affect understanding and estimation of effective population size

The concept of effective population size (N(e) ) is based on an elegantly simple idea which, however, rapidly becomes very complex when applied to most real-world situations. In natural populations, spatial and temporal stratifications create different classes of individuals with different vital rates, and this in turn affects (generally reduces) N(e) in complex ways. I consider how these natural stratifications influence our understanding of effective size and how to estimate it, and what the consequences are for conservation and management of natural populations. Important points that emerge include the following: 1 The relative influences of local vs metapopulation N(e) depend on a variety of factors, including the time frame of interest. 2 Levels of diversity in local populations are strongly influenced by even low levels of migration, so these measures are not reliable indicators of local N(e) . 3 For long-term effective size, obtaining a reliable estimate of mutation rate is the most important consideration; unless this is accomplished, estimates can be biased by orders of magnitude. 4 At least some estimators of contemporary N(e) appear to be robust to relatively high (approximately 10%) equilibrium levels of migration, so under many realistic scenarios they might yield reliable estimates of local N(e) . 5 Age structure probably has little effect on long-term estimators of N(e) but can strongly influence contemporary estimates. 6 More research is needed in several key areas: (i) to disentangle effects of selection and drift in metapopulations connected by intermediate levels of migration; (ii) to elucidate the relationship between N(b) (effective number of breeders per year) and N(e) per generation in age-structured populations; (iii) to perform rigorous sensitivity analyses of new likelihood and coalescent-based methods for estimating demographic and evolutionary histories.     

Quantitative traits in relation to population structure: why and how are they used and what do they imply?

I describe the basic ingredients of a population structure analysis and the rationale for using polygenic quantitative traits in such analyses. The complexity of inheritance and the population dynamics of quantitative traits, however, imply that inferences regarding population structure based on such traits must be evaluated with appropriate cautions. Although many studies of quantitative traits in relation to population structure analysis underscore the importance of gene flow between subpopulations, I show that the role of selection in the evolution of a quantitative trait and its relationship to the inferred population structure cannot be overlooked. Finally, I review some recent advances in human quantitative genetic methodologies that can be used profitably in population structure analysis.     

Opportunistic mothers: female marmosets (Callithrix kuhlii) reduce their investment in offspring when they have to, and when they can

All female primates incur energetic costs associated with producing and caring for offspring, but females belonging to the New World primate family Callitrichidae, the marmosets and tamarins, appear to face even further demands. In fact, the energetic demands of rearing callitrichid infants are thought to have led to the evolution of cooperative infant care in these species. If this explanation is true, then one might expect that natural selection should also have shaped patterns of maternal behavior to be sensitive to the costs of reproduction and equipped females to reduce their investment in offspring under certain conditions. Therefore, we examined the maternal effort and postpartum endocrine profiles of individual female marmosets (Callithrix kuhlii) across conditions that represented two hallmarks of callitrichid reproduction-conception during the early postpartum period and alloparental assistance. When females conceived during the early postpartum period and faced the upcoming demands of caring for their newly conceived litters (Study 1), they significantly reduced their caregiving effort and had significantly higher postpartum levels of estradiol relative to breeding attempts in which conception occurred later in the postpartum period. Postpartum estradiol was negatively correlated with maternal carrying effort. When experienced alloparents were present (Study 2), females again reduced their caregiving effort relative to breeding attempts in which experienced alloparents were not present. Postpartum cortisol, however, did not vary as a function of experienced alloparental assistance. The results of these studies suggest that female marmosets have been subjected to similar selection pressures as females of other primate taxa--to maximize their reproductive success by reducing their investment in offspring under the worst and best of conditions--and suggest that hormones may mediate within-female variation in maternal care. These studies also provide support for the notion that mothers are "flexible opportunists" when it comes to providing care to their young.     

Plant size,flowering synchrony and edge effects: What,how and where they affect the reproductive success of a Neotropical tree species

Plant reproductive success is supposedly influenced by phenology and individual size, which may be modified under edge effects. We tested if reproductive success, estimated by fruit set, in Senefeldera verticillata (Euphorbiaceae) is related to flowering synchrony and tree size, including plant height and circumference at breast height. The study was carried out in the interior and in edges of clearings for gas pipelines and electric lines of a lowland rainforest in south‐eastern Brazil. Monthly observations were performed during one reproductive season, of 19 individuals that grew at edges of electric lines and gas pipelines and at forest interior. Reproductive success was significantly higher at forest interior than at gas pipeline area; there was no significant difference between gas pipeline and electric line areas or between forest interior and electric line area. In the forest edges, only plant height was positively related to plant reproductive success. This is probably related to crown exposure to sunlight, which enhances flower production. At forest interior, reproductive success was positively influenced by the synchrony of flowering activity among neighbouring individuals. In contrast, flowering synchrony based on phenophase intensity negatively impacted reproductive success. Senefeldera verticillata shows temporal dioecy and is mainly pollinated by small social bees, and the high degree of flowering synchrony at low intensity may increase the number of mating partners and therefore enhance its reproductive success. Inside the forest fragments, individuals with thicker trunks showed lower reproductive success, which may be related to a loss of reproductive capacity of older individuals. Our results evidenced the complexity of responses experienced by tropical plants subjected to forest fragmentation because of linear clearings.     

Interaction rates,vital rates,background fitness and replicator dynamics: how to embed evolutionary game structure into realistic population dynamics

In this paper we are concerned with how aggregated outcomes of individual behaviours, during interactions with other individuals (games) or with environmental factors, determine the vital rates constituting the growth rate of the population. This approach needs additional elements, namely the rates of event occurrence (interaction rates). Interaction rates describe the distribution of the interaction events in time, which seriously affects the population dynamics, as is shown in this paper. This leads to the model of a population of individuals playing different games, where focal game affected by the considered trait can be extracted from the general model, and the impact on the dynamics of other events (which is not neutral) can be described by an average background fertility and mortality. This leads to a distinction between two types of background fitness, strategically neutral elements of the focal games (correlated with the focal game events) and the aggregated outcomes of other interactions (independent of the focal game). The new approach is useful for clarification of the biological meaning of concepts such as weak selection. Results are illustrated by a Hawk–Dove example.     

Sensitivity of comparative analyses to population variation in trait values: clutch size and cavity excavation tendencies

Importance of within-species (population) variation in trait values to correlations of traits among species has received very little attention in comparative analyses. We use randomization and bootstrapping techniques to provide a sensitivity analysis of the influence of population variation on correlations between clutch size and propensity to excavate. These traits are predicted to be negatively correlated under the limited breeding opportunities hypothesis, but opposing results have been found by two studies using different population estimates for western Palearctic Paridae. Our analyses support the limited breeding opportunities hypothesis and suggest low sensitivity to within-species variation in trait values. Yet, a small proportion of population data provide non-significant results. Checking for the effects of this variation on the postulated association between traits is necessary in comparative studies if one wishes to avoid type I and type II errors.     

The relocation of starch metabolism to chloroplasts: when, why and how

Plastid endosymbiosis was accompanied by the appearance of a novel type of semi-cristalline storage polysaccharide (starch). Interestingly, starch is found in the cytoplasm of Rhodophyceae and Glaucophyta but is localized to the chloroplast stroma of Chloroplastida. The pathway is presumed to have been cytosolic in the common ancestor of the three Archaeplastida lineages. The means by which in green plants and algae an entire suite of nuclear-encoded starch-metabolism genes could have had their protein products rewired simultaneously to plastids are unclear. This opinion article reviews the timing and the possible reasons underlying this rewiring and proposes a hypothesis that explains its mechanism. The consequences of this mechanism on the complexity of starch metabolism in Chloroplastida are discussed.     

Reproductive responses to varying food supply in a population of Darwin's finches: Clutch size,growth rates and hatching synchrony

Summary I show how food shortage affects reproduction in a population of Darwin's Medium Ground Finches, Geospiza fortis. Despite the common occurrence of starvation and absence of nest predation, hatching is typically nighly synchronous and adaptive brood reductionappears to be absent. Variation in both growth rates and clutch size in association with the varying conditions is documented. This variation is interpreted as being a direct response to environmental conditions rather than adaptive phenotypic plasticity. I conclude that selection pressures to raise one or two chicks during times of food shortage, or to delay growth rates, are weak or absent.     

Parental and genetic factors rather than nesting forest patch size affect physiological traits of offspring in an area‐sensitive passerine: an experimental study

Our understanding of the effects of habitat loss on individual performance is limited due to a lack of experimental studies that take the potential genetic and parental effects producing phenotypic variation into consideration. To assess the relative role of habitat loss on offspring phenotype while controlling for the confounding effects of genetic and parental variation we performed a partial cross‐fostering experiment using the Eurasian Treecreeper Certhia familiaris. The experiment was carried out by swapping half the nestlings in a brood between small and large nesting forest patches to determine the effect of nesting forest patch size on five nestling traits reflecting morphological size, body condition, physiological stress and inflammation status. There was no effect of nesting forest patch size on the offspring traits examined. Instead, we found evidence of genetic and early parental effects on all traits except inflammation status, as well as parental effects after cross‐fostering for all of the measured offspring traits. Our results suggest that genetic and parental effects should be taken into account when making inferences about species’ responses to habitat loss.     

Functional traits of epiphytic lichen communities in a Temperate-Mediterranean fragmented landscape: Importance of patch size,tree diameter and summer rainfall

Functional traits have become important tools for evaluating the response of epiphytic lichens to environmental changes. In this study, we evaluated which predictors related to fragmentation, habitat quality and climate were driving the richness and cover of lichen growth form, type of photobiont and reproduction traits, at both fragment and plot levels in a Temperate-Mediterranean area dominated by Quercus forests. At fragment level, patch size and summer rainfall positively contributed to richness in most of the traits, while tree diameter and slope were the most important drivers, especially for the type of reproduction and growth form at plot scale. High coverage of growth forms especially sensitive to fragmentation were indicative of high values of total species richness, while early-colonizers indicated the opposite. These results provide important information on how lichen traits respond to environmental conditions in an ecotone area where a shift towards a drier climate is more likely to occur.     

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

Background  

During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.     

The approach to mutation-selection balance in an infinite asexual population, and the evolution of mutation rates

A method is described for calculating the dynamics of the distribution of fitness in an infinite asexual population which is subject to unconditionally deleterious mutations with independent effects. This method is applied to the problem of calculating the frequency of a mutator subpopulation, at equilibrium between mutation and indirect selection due to association with deleterious mutations. Many mutator alleles are produced by loss-of-function mutations in polymerase or mismatch repair genes. Previous calculations have ignored the fact that this creates a flux of higher fitness individuals into the mutator subpopulation. This flux raises the mean fitness of the mutator subpopulation, and when this factor is taken into account, the frequency of the mutator may be more than an order of magnitude greater than recent theoretical work has suggested.     

Filtration and ingestion rates of Salpa fusiformis Cuvier (Tunicata : Thaliacea): Effects of size,individual weight and algal concentration

Filtration and ingestion rates of Salpa fusiformis Cuvier were determined while fed Phaeodactylumtricomutum Bohlin at concentrations of 2?64 × 10³ cells·ml^?1. Filtration and ingestion rates increase exponentially with increasing length and body protein. The relations between protein content and body length, and between filtration rate and weight are similar for blastozooids and oozooids. A capture efficiency of the order of 6–32% is calculated: Salpa fusiformis seems to have a low retention efficiency, but its very high filtration rate gives it pride of place amongst filter-feeders. Specific filtration rates are independent of weight; specific ingestion rates are independent of weight for blastozooids, but for oozooids they seem to diminish with increasing weight. The mean daily ration (μg C ingested · μg body C^?1) is 107% for a blastozooid and 117% for an oozooid. Specific filtration rates decrease exponentially as particle concentration rises, as for many other filter-feeders, and the specific ingestion rate follows an Ivlev relation.