Continued misuse of multiple testing correction methods in population genetics‐A wake‐up call?

Population geneticists often use multiple independent hypothesis tests of Hardy–Weinberg Equilibrium (HWE), Linkage Disequilibrium (LD), and population differentiation, to make broad inferences about their systems of choice. However, correcting for Family‐Wise Error Rates (FWER) that are inflated due to multiple comparisons, is sparingly reported in our current literature. In this issue of Molecular Ecology Resources, perform a meta‐analysis of 215 population genetics studies published between 2011 and 2013 to show (i) scarce use of FWER corrections across all three classes of tests, and (ii) when used, inconsistent application of correction methods with a clear bias towards less‐conservative corrections for tests of population differentiation, than for tests of HWE, and LD. Here we replicate this meta‐analysis using 205 population genetics studies published between 2013 and 2018, to show the same continued disuse, and inconsistencies. We hope that both studies serve as a wake‐up call to population geneticists, reviewers, and editors to be rigorous about consistently correcting for FWER inflation.     

Humans act against the natural process of breeder selection: A modern sickness for animal populations?

We present a new idea about the possible effects of human-induced mortality on different age cohorts (i.e., breeders vs. juveniles) in long-lived animals. Our hypothesis is based on Curios idea on the effect of natural selective processes on cohorts to explain age-related increases in fecundity (selection hypothesis). We believe that negative human pressure may modify such contribution to reproduction of good versus low quality phenotypes, altering the genetic structure of the population. Ecologists and environmental managers in general should be aware of how stochastic events provoked by humans may induce changes in the genetic structure of populations.     

How strong is natural selection?

The strength of selection in nature has long been a controversial subject, partly because there were few quantitative measurements of phenotypic selection available until recently. In a new paper, Kingsolver and colleagues reviewed 63 studies and found that the median standardized directional selection gradient (a measure of the strength of phenotypic selection) was 0.16. Whether this means selection in nature is strong or weak depends both on one's point of view and on the error in selection estimates.     

Does lethal control of top‐predators release mesopredators? A re‐evaluation of three Australian case studies

Top‐predators can sometimes be important for structuring fauna assemblages in terrestrial ecosystems. Through a complex trophic cascade, the lethal control of top‐predators has been predicted to elicit positive population responses from mesopredators that may in turn increase predation pressure on prey species of concern. In support of this hypothesis, many relevant research papers, opinion pieces and literature reviews identify three particular case studies as supporting evidence for top‐predator control‐induced release of mesopredators in Australia. However, many fundamental details essential for supporting this hypothesis are missing from these case studies, which were each designed to investigate alternative aims. Here, we re‐evaluate the strength of evidence for top‐predator control‐induced mesopredator release from these three studies after comprehensive analyses of associated unpublished correlative and experimental data. Circumstantial evidence alluded to mesopredator releases of either the European Red Fox (Vulpes vulpes) or feral Cat (Felis catus) coinciding with Dingo (Canis lupus dingo) control in each case. Importantly, however, substantial limitations in predator population sampling techniques and/or experimental designs preclude strong assertions about the effect of lethal control on mesopredator populations from these studies. In all cases, multiple confounding factors and plausible alternative explanations for observed changes in predator populations exist. In accord with several critical reviews and a growing body of demonstrated experimental evidence on the subject, we conclude that there is an absence of reliable evidence for top‐predator control‐induced mesopredator release from these three case studies. Well‐designed and executed studies are critical for investigating potential top‐predator control‐induced mesopredator release.     

Does natural selection organize ecosystems for the maintenance of high productivity and diversity?

Three types of evidence suggest that natural ecosystems are organized for high productivity and diversity: (i) changes not previously experienced by a natural ecosystem, such as novel human disturbances, tend to diminish its productivity and/or diversity, just as 'random' changes in a machine designed for a function usually impair its execution of that function; (ii) humans strive to recreate properties of natural ecosystems to enhance productivity of artificial ones, as farmers try to recreate properties of natural soils in their fields; and (iii) productivity and diversity have increased during the Earth's history as a whole, and after every major biotic crisis. Natural selection results in ecosystems organized to maintain high productivity of organic matter and diversity of species, just as competition among individuals in Adam Smith's ideal economy favours high production of wealth and diversity of occupations. In nature, poorly exploited energy attracts more efficient users. This circumstance favours the opening of new ways of life and more efficient recycling of resources, and eliminates most productivity-reducing 'ecological monopolies'. Ecological dominants tend to be replaced by successors with higher metabolism, which respond to more stimuli and engage in more varied interactions. Finally, increasingly efficient predators and herbivores favour faster turnover of resources.     

What was Fisher's fundamental theorem of natural selection and what was it for?

Fisher's 'fundamental theorem of natural selection' is notoriously abstract, and, no less notoriously, many take it to be false. In this paper, I explicate the theorem, examine the role that it played in Fisher's general project for biology, and analyze why it was so very fundamental for Fisher. I defend and Lessard (1997) in the view that the theorem is in fact a true theorem if, as Fisher claimed, 'the terms employed' are 'used strictly as defined' (1930, p. 38). Finally, I explain the role that projects such as Fisher's play in the progress of scientific inquiry.     

Flowering phenology: An example of relaxation of natural selection?

Flowering phenology has normally been viewed as fundamental to a plant species' reproductive ecology. Researchers in the field have emphasized the adaptive importance of flowering at a particular time relative to other individuals in the population, or other species in the community. An alternative view, however, is that flowering phenology is a trait that may not be under strong selection, and this may have allowed some variation to appear in populations by chance.     

Bottom‐up control in the benthos of ocean‐exposed sandy beaches?

Bottom‐up control is a fundamental structuring force in food webs. Food webs of ocean‐exposed sandy beaches are predicted to be bottom‐up controlled systems, underpinned by imported organic matter rather than in situ primary production. This ecological model of resource‐based regulation of biological assemblages is juxtaposed against a prevailing paradigm built around a dominance of physical drivers in sandy beach ecosystems. Surprisingly, given the apparently ubiquitous energetic subsidies of beach food webs, the central premise of bottom‐up control has not been tested. Here we experimentally manipulated in situ nutrient levels on a sandy beach to test food web responses at the levels of primary producers (benthic microalgae) and their grazers (meiofauna). The meiofauna community as a whole appeared most strongly influenced by the local physical environment, particularly changes in sediment grain size – this supports the traditional ‘environmental control paradigm’. We also detected a significant, positive response of two consumer groups of the meiofauna (nematodes, ostracods) to nutrient enrichment that supports a model of biological, bottom‐up control. Although the predicted response of elevated producer biomass following nutrient enrichment was not detected, intense grazing pressure on new, stimulated production may have masked positive responses by the primary producers. Multichannel regulation of food webs is likely for many exposed sandy beaches, albeit an often lower importance of in situ bottom‐up forces compared with stronger environmental control.     

Can limiting similarity increase invasion resistance? A meta‐analysis of experimental studies

Synthesis We used meta‐analyses to examine experimental evidence that functional similarity between invaders and resident communities reduces invasion. We synthesized evidence from studies that experimentally added seed to resident communities in which the functional group composition had been manipulated. We found communities containing functionally similar resident species reduced invasion of forb but not grass invaders. However, experimental design dramatically influenced the results – with evidence for limiting similarity only found in artificially assembled communities, and not when studies used functional group removal from more ‘natural communities’. We suggest that functional group similarity plays a limited role in biotic resistance in established communities. The principle of limiting similarity suggests that species must be functionally different to coexist; based on the assumption that inter‐specific competition should be greatest between functionally similar species. There has been controversy over the generality of this assembly rule for plant communities with some studies finding evidence for limiting similarity and others not. One approach to testing this is to examine the ‘invasion’ success of species into communities in which the functional group composition has been manipulated. Using a meta‐analysis approach, we examined the generality of limiting similarity for plant communities based on published experimental studies. We asked – is establishment of an invading species less successful if it belongs to a functional group that is already present in the community compared to a community in which that functional group is absent? We explored separately colonisation (i.e. germination, establishment or seedling survival) and performance (i.e. biomass, cover or growth) of different functional groups (forbs and grasses) and experimental designs (removal experiments of more or less natural communities and synthetic‐assemblage experiments). We found that communities containing functionally similar resident species did reduce invader colonisation and performance of forb invaders, but did not reduce colonisation or performance of grass invaders. Evidence in support of limiting similarity was only detected in synthetic‐assemblage experiments and not when studies used functional group removal from ‘natural’ communities. Functional similarity is an important aspect of biotic resistance for forb invaders, but was only found in artificial communities. This has implications for restoration ecology especially when communities are built de novo. However, we suggest that limiting similarity plays a limited role in biotic resistance, because no evidence was detected in established communities.     

Haldane’s view of natural selection

Among many things, J. B. S. Haldane is known for demonstrating how the principle of natural selection can be used to build a mathematical, and in particular quantitative, theory of evolution. However, to the end, he remained open to the idea of other evolutionary mechanisms. In his late writings, he repeatedly drew attention to situations in which natural selection did not operate, was hemmed in by constraints, or worked in a surprising manner. In this respect Haldane stands out among the architects of the Modern Synthesis.     

Managed care or managed inequality? A call for critiques of market-based medicine

This review article critiques the growing dominance of market-based medicine in the United States against the background of existing problems with quality of care, rising costs, devaluation of doctor-patient relationships, and, especially, persistent inequalities of access and outcomes. It summarizes the present state of health care delivery by focusing on the concurrent trends of growth in managed care, expanding profits, increasing proportion of those uninsured, and widening racial, ethnic, and class disparities in access to care. Allowing market forces to dictate the shape of health care delivery in this country ensures that inequalities will continue to grow and modern medicine will become increasingly adept at managing inequality rather than managing (providing) care. The article challenges anthropology to become more involved in critiquing these developments and suggests how anthropologists can expand on and contextualize debates surrounding the market's role in medicine, here and abroad.     

Do males pay for sex? Sex‐specific selection coefficients suggest not

Selection acting on males can reduce mutation load of sexual relative to asexual populations, thus mitigating the twofold cost of sex, provided that it seeks and destroys the same mutations as selection acting on females, but with higher efficiency. This could happen due to sexual selection—a potent evolutionary force that in most systems predominantly affects males. We used replicate populations of red flour beetles (Tribolium castaneum) to study sex‐specific selection against deleterious mutations introduced with ionizing radiation. We found no evidence for selection being stronger in males than in females; in fact, we observed a nonsignificant trend in the opposite direction. This suggests that selection on males does not reduce mutation load below the level expected under the (hypothetical) scenario of asexual reproduction. Additionally, we employed a novel approach, based on a simple model, to quantify the relative contributions of sexual and offspring viability selection to the overall selection observed in males. We found them to be similar in magnitude; however, only the offspring viability component was statistically significant. In summary, we found no support for the hypothesis that selection on males in general, and sexual selection in particular, contributes to the evolutionary maintenance of sex.     

Probabilistic optimization of phenotype distributions: a general solution for the effects of uncertainty on natural selection?

Summary Explorations of optimizing selection often find discrepancies between the theoretically expected and observed phenotypes. Such discrepancies are usually attributed to a variety of potential constraints. We suggest that one common constraint, environmental uncertainty, may reduce the applicability of traditional deterministic or stochastic optimization methods and that many apparent discrepancies might be artifacts of these methods. Since natural selection is essentially a statistical process, we propose that a probabilistic optimization procedure, that includes all of the variability in phenotype distributions and associated fitness potential functions might offer better results. The traditional methods define an optimal gene or genotype as that which produces a phenotype distribution with a mean or other measure of central tendency that equals the value yielding the maximum fitness potential. Our method defines the optimal gene or genotype as that which produces the phenotype distribution that maximizes fitness summed or integrated over its associated fitness potential function. Often the central tendency of the phenotype distribution yielding the probabilistic optimum will differ from the deterministic expectation. This method is an extension of utility theory to any phenotypic character. We illustrate our method using an example based on Price and Waser's (1979) notion of optimal inbreeding via optimal pollen dispersal.     

Trophic control of mesopredators in terrestrial ecosystems: top‐down or bottom‐up?

It has been argued that widespread extinctions of top predators have changed terrestrial ecosystem structures through mesopredator release, where increased abundances of medium-sized predators have detrimental effects on prey communities. This top-down concept has received much attention within conservation biology, but few studies have demonstrated the phenomenon. The concept has been criticized since alternative explanations involving bottom-up impacts from bioclimatic effects on ecosystem productivity and from anthropogenic habitat change are rarely considered. We analyse the response of a mesopredator (the red fox) to declines in top predators (wolf and Eurasian lynx) and agricultural expansion over 90 years in Sweden, taking bioclimatic effects into account. We show a top-down mesopredator release effect, but ecosystem productivity determined its strength. The impacts of agricultural activity were mediated by their effects on top predator populations. Thus, both top-down and bottom-up processes need to be understood for effective preservation of biodiversity in anthropogenically transformed ecosystems.     

Phenotypic selection in natural populations: what limits directional selection?

Studies of phenotypic selection document directional selection in many natural populations. What factors reduce total directional selection and the cumulative evolutionary responses to selection? We combine two data sets for phenotypic selection, representing more than 4,600 distinct estimates of selection from 143 studies, to evaluate the potential roles of fitness trade-offs, indirect (correlated) selection, temporally varying selection, and stabilizing selection for reducing net directional selection and cumulative responses to selection. We detected little evidence that trade-offs among different fitness components reduced total directional selection in most study systems. Comparisons of selection gradients and selection differentials suggest that correlated selection frequently reduced total selection on size but not on other types of traits. The direction of selection on a trait often changes over time in many temporally replicated studies, but these fluctuations have limited impact in reducing cumulative directional selection in most study systems. Analyses of quadratic selection gradients indicated stabilizing selection on body size in at least some studies but provided little evidence that stabilizing selection is more common than disruptive selection for most traits or study systems. Our analyses provide little evidence that fitness trade-offs, correlated selection, or stabilizing selection strongly constrains the directional selection reported for most quantitative traits.     

MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?

Elucidating how natural selection promotes local adaptation in interaction with migration, genetic drift and mutation is a central aim of evolutionary biology. While several conceptual and practical limitations are still restraining our ability to study these processes at the DNA level, genes of the major histocompatibility complex (MHC) offer several assets that make them unique candidates for this purpose. Yet, it is unclear what general conclusions can be drawn after 15 years of empirical research that documented MHC diversity in the wild. The general objective of this review is to complement earlier literature syntheses on this topic by focusing on MHC studies other than humans and mice. This review first revealed a strong taxonomic bias, whereby many more studies of MHC diversity in natural populations have dealt with mammals than all other vertebrate classes combined. Secondly, it confirmed that positive selection has a determinant role in shaping patterns of nucleotide diversity in MHC genes in all vertebrates studied. Yet, future tests of positive selection would greatly benefit from making better use of the increasing number of models potentially offering more statistical rigour and higher resolution in detecting the effect and form of selection. Thirdly, studies that compared patterns of MHC diversity within and among natural populations with neutral expectations have reported higher population differentiation at MHC than expected either under neutrality or simple models of balancing selection. Fourthly, several studies showed that MHC-dependent mate preference and kin recognition may provide selective factors maintaining polymorphism in wild outbred populations. However, they also showed that such reproductive mechanisms are complex and context-based. Fifthly, several studies provided evidence that MHC may significantly influence fitness, either by affecting reproductive success or progeny survival to pathogens infections. Overall, the evidence is compelling that the MHC currently represents the best system available in vertebrates to investigate how natural selection can promote local adaptation at the gene level despite the counteracting actions of migration and genetic drift. We conclude this review by proposing several directions where future research is needed.     

Centenarians – a useful model for healthy aging? A 29‐year follow‐up of hospitalizations among 40 000 Danes born in 1905

Centenarians surpass the current human life expectancy with about 20–25 years. However, whether centenarians represent healthy aging still remains an open question. Previous studies have been hampered by a number of methodological shortcomings such as a cross-sectional design and lack of an appropriate control group. In a longitudinal population-based cohort, it was examined whether the centenarian phenotype may be a useful model for healthy aging. The study was based on a complete follow up of 39 945 individuals alive in the Danish 1905 birth cohort on January 1, 1977 identified through the Danish Civil Registration System (DCRS). Data from the Danish Demographic Database and The Danish National Patient Register (in existence since 1977) were used. The 1905 cohort was followed up from 1977 through 2004 with respect to hospitalizations and number of hospital days. Survival status was available until December 2006. Danish centenarians from the 1905 cohort were hospitalized substantially less than their shorter-lived contemporaries at the same point in time during the years 1977 through 2004. For example, at age 71–74, the proportion of nonhospitalized centenarians was 80.5% compared with 68.4% among individuals who died in their early 80s. This trend was evident in both sexes. As a result of their lower hospitalization rates and length of stay in hospital compared with their contemporaries, who died at younger ages, Danish centenarians represent healthy agers. Centenarians constitute a useful study population in the search for fixed traits associated with exceptional longevity, such as genotype.