The genetic architecture of maternal effects across ontogeny in the red deer

Maternal effects, either environmental or genetic in origin, are an underappreciated source of phenotypic variance in natural populations. Maternal genetic effects have the potential to constrain or enhance the evolution of offspring traits depending on their magnitude and their genetic correlation with direct genetic effects. We estimated the maternal effect variance and its genetic component for 12 traits expressed over the life history in a pedigreed population of wild red deer (morphology, survival/longevity, breeding success). We only found support for maternal genetic effect variance in the two neonatal morphological traits: birth weight ( = 0.31) and birth leg length ( = 0.17). For these two traits, the genetic correlation between maternal and direct additive effects was not significantly different from zero, indicating no constraint to evolution from genetic architecture. In contrast, variance in maternal genetic effects enhanced the additive genetic variance available to respond to natural selection. Maternal effect variance was negligible for late-life traits. We found no evidence for sex differences in either the direct or maternal genetic architecture of offspring traits. Our results suggest that maternal genetic effect variance declines over the lifetime, but also that this additional heritable genetic variation may facilitate evolutionary responses of early-life traits.     

An estimator of the Opportunity for Selection that is independent of mean fitness

Variation among individuals in number of offspring (fitness, k) sets an upper limit to the evolutionary response to selection. This constraint is quantified by Crow's Opportunity for Selection (I), which is the variance in relative fitness (I = σ²_k/(u_k)²). Crow's I has been widely used but remains controversial because it depends on mean offspring number in a sample (). Here, I used a generalized Wright-Fisher model that allows for unequal probabilities of producing offspring to evaluate behavior of Crow's I and related indices under a wide range of sampling scenarios. Analytical and numerical results are congruent and show that rescaling the sample variance (s²_k) to its expected value at a fixed removes dependence of I on mean offspring number, but the result still depends on choice of . A new index is introduced, Δ_I = Π– E(Î_drift) = Π– 1/, which makes Î independent of sample without the need for variance rescaling. Δ_I has a straightforward interpretation as the component of variance in relative fitness that exceeds that expected under a null model of random reproductive success. Δ_I can be used to directly compare estimates of the Opportunity for Selection for samples from different studies, different sexes, and different life stages.     

THE MAINTENANCE OF POLYGENIC VARIATION IN FINITE POPULATIONS

Models of the maintenance of genetic variance in a polygenic trait have usually assumed that population size is infinite and that selection is weak. Consequently, they will overestimate the amount of variation maintained in finite populations. I derive approximations for the equilibrium genetic variance, in finite populations under weak stabilizing selection for triallelic loci and for an infinite “rare alleles” model. These are compared to results for neutral characters, to the “Gaussian allelic” model, and to Wright's approximation for a biallelic locus under arbitrary selection pressures. For a variety of parameter values, the three-allele, Gaussian, and Wrightian approximations all converge on the neutral model when population size is small. As expected, far less equilibrium genetic variance can be maintained if effective population size, N, is on the order of a few hundred than if N is infinite. All of the models predict that comparisons among populations with N less than about 10⁴ should show substantial differences in . While it is easier to maintain absolute when alleles interact to yield dominance or overdominance for fitness, less additivity also makes more susceptible to differences in N. I argue that experimental data do not seem to reflect the predicted degree of relationship between N and . This calls into question the ability of mutation-selection balance or simple balancing selection to explain observed . The dependence of on N could be used to test the adequacy of mutation-selection balance models.     

Quantitative genetics of temperature performance curves of Neurospora crassa

Earth's temperature is increasing due to anthropogenic CO emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organism's physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation to higher temperatures, therefore we studied the quantitative genetics of growth rates in different temperatures that make up the thermal performance curve of the fungal model system Neurospora crassa. We studied the amount of genetic variation for thermal performance curves and examined possible genetic constraints by estimating the G -matrix. We observed a substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions, we did not find strong evidence for genetic trade-offs for growth between hotter and colder temperatures. We also simulated short-term evolution of thermal performance curves of N. crassa, and suggest that they can have versatile responses to selection.     

RISK OF POPULATION EXTINCTION FROM FIXATION OF NEW DELETERIOUS MUTATIONS

The fixation of new deleterious mutations is analyzed for a randomly mating population of constant size with no environmental or demographic stochasticity. Mildly deleterious mutations are far more important in causing loss of fitness and eventual extinction than are lethal and semilethal mutations in populations with effective sizes, N_e, larger than a few individuals. If all mildly deleterious mutations have the same selection coefficient, s against heterozygotes and 2s against homozygotes, the mean time to extinction, , is asymptotically proportional to for 4N_es > 1. Nearly neutral mutations pose the greatest risk of extinction for stable populations, because the magnitude of selection coefficient that minimizes is about ? = 0.4/N_e. The influence of variance in selection coefficients among mutations is analyzed assuming a gamma distribution of s, with mean and variance . The mean time to extinction increases with variance in selection coefficients if is near ?, but can decrease greatly if is much larger than ?. For a given coefficient of variation of , the mean time to extinction is asymptotically proportional to for . When s is exponentially distributed, (c = 1) is asymptotically proportional to . These results in conjunction with data on the rate and magnitude of mildly deleterious mutations in Drosophila melanogaster indicate that even moderately large populations, with effective sizes on the order of N_e = 10³, may incur a substantial risk of extinction from the fixation of new mutations.     

Evidence of linked selection on the Z chromosome of hybridizing hummingbirds*

Levels of genetic differentiation vary widely along the genomes of recently diverged species. What processes cause this variation? Here, I analyze geographic population structure and genome-wide patterns of variation in the Rufous, Allen's, and Calliope Hummingbirds (Selasphorus rufus/Selasphorus sasin/Selasphorus calliope) and assess evidence that linked selection on the Z chromosome drives patterns of genetic differentiation in a pair of hybridizing species. Demographic models, introgression tests, and genotype clustering analyses support a reticulate evolutionary history consistent with divergence during the late Pleistocene followed by gene flow across migrant Rufous and Allen's Hummingbirds during the Holocene. Relative genetic differentiation () is elevated, and within-population diversity (π) is depressed on the Z chromosome in all interspecific comparisons. The ratio of Z to autosomal within-population diversity is much lower than that expected from population size effects alone, and Tajima's D is depressed on the Z chromosome in S. rufus and S. calliope. These results suggest that conserved structural features of the genome play a prominent role in shaping genetic differentiation through the early stages of speciation in northern Selasphorus hummingbirds, and that the Z chromosome is a likely site of genes underlying behavioral and morphological variation in the group.     

Reversal of response to artificial selection on body size in a wild passerine

A general assumption in quantitative genetics is the existence of an intermediate phenotype with higher mean individual fitness in the average environment than more extreme phenotypes. Here, we investigate the evolvability and presence of such a phenotype in wild bird populations from an eleven‐year experiment with four years of artificial selection for long and short tarsus length, a proxy for body size. The experiment resulted in strong selection in the imposed directions. However, artificial selection was counteracted by reduced production of recruits in offspring of artificially selected parents. This resulted in weak natural selection against extreme trait values. Significant responses to artificial selection were observed at both the phenotypic and genetic level, followed by a significant return toward preexperimental means. During artificial selection, the annual observed phenotypic response closely followed the predicted response from quantitative genetic theory ( = 0.96, = 0.56). The rapid return to preexperimental means was induced by three interacting mechanisms: selection for an intermediate phenotype, immigration, and recombination between selected and unselected individuals. The results of this study demonstrates the evolvability of phenotypes and that selection may favor an intermediate phenotype in wild populations.     

THE EFFECT OF SOFT SELECTION ON THE VARIABILITY OF A QUANTITATIVE TRAIT

The equilibrium phenotypic variance of a normally distributed quantitative character P under soft selection is studied. This character is assumed to undergo Gaussian stabilizing selection W(p, x) = exp[–(p – x)²/2w²]. The environmentally determined optimum (x) is a normal variable with variance s². A stable equilibrium with is found, so that increases both with increasing environmental heterogeneity and with increasing local intensity of stabilizing selection. It is shown that both genetic and environmental components of the variance are selected until this equilibrium is reached. Habitat selection, supposed to be normal (with variance H²) around the optimum, also increases the value. Nevertheless, relatively intense local stabilizing selection (w < s) and accurate habitat choice (H < s) are required for the initial spread and the evolutionary stability of this habitat selection.     

EPISTASIS,PLEIOTROPY, AND THE MUTATION LOAD IN SEXUAL AND ASEXUAL POPULATIONS

Mutation may impose a substantial load on populations, which varies according to the reproductive mode of organisms. Over the past years, various authors used adaptive landscape models to predict the long‐term effect of mutation on mean fitness; however, many of these studies assumed very weak mutation rates, so that at most one mutation segregates in the population. In this article, we derive several simple approximations (confirmed by simulations) for the mutation load at high mutation rate (U), using a general model that allows us to play with the number of selected traits (n), the degree of pleiotropy of mutations, and the shape of the fitness function (which affects the average sign and magnitude of epistasis among mutations). When mutations have strong fitness effects, the equilibrium fitness of sexuals and asexuals is close to ; under weaker mutational effects, sexuals reach a different regime where is a simple function of U and of a parameter describing the shape of the fitness function. Contrarily to weak mutation results showing that is an increasing function of population size and a decreasing function of n, these parameters may have opposite effects in sexual populations at high mutation rate.     

Additive genetic variance for lifetime fitness and the capacity for adaptation in an annual plant

The immediate capacity for adaptation under current environmental conditions is directly proportional to the additive genetic variance for fitness, V_A(W). Mean absolute fitness, , is predicted to change at the rate , according to Fisher's Fundamental Theorem of Natural Selection. Despite ample research evaluating degree of local adaptation, direct assessment of V_A(W) and the capacity for ongoing adaptation is exceedingly rare. We estimated V_A(W) and in three pedigreed populations of annual Chamaecrista fasciculata, over three years in the wild. Contrasting with common expectations, we found significant V_A(W) in all populations and years, predicting increased mean fitness in subsequent generations (0.83 to 6.12 seeds per individual). Further, we detected two cases predicting “evolutionary rescue,” where selection on standing V_A(W) was expected to increase fitness of declining populations (< 1.0) to levels consistent with population sustainability and growth. Within populations, inter‐annual differences in genetic expression of fitness were striking. Significant genotype‐by‐year interactions reflected modest correlations between breeding values across years, indicating temporally variable selection at the genotypic level that could contribute to maintaining V_A(W). By directly estimating V_A(W) and total lifetime , our study presents an experimental approach for studies of adaptive capacity in the wild.     

The effects of hurricanes on the stochastic population growth of the endemic epiphytic orchid Broughtonia cubensis living in Cuba

We carried out a posthurricane evaluation of Broughtonia cubensis (Lindl.) Cogn., an endemic Cuban epiphytic orchid, after Hurricane Ivan (2004). We studied the transient responses in the stochastic dynamics of the species at three different sites over 13 successive years (2006–2019), monitored plot inventories (464 individuals in 10 transects) and built stochastic population models. The deterministic stochastic growth rate values () did not significantly differ (F = 2.76; p > 0.076) among the three sites over the 2006–2019 period. The long-term stochastic growth rate was 0.973 [0.932, 1.034]. The matrix elements that had the largest effect on were the transition to and stasis within the largest size class. Transient responses explained an average of 86% of the variation in the observed population growth rates , compared to 4% of the variation in the vital rates . Because transient dynamics are dependent on the population size composition, we ran extinction risk analyses under two scenarios: a population composed mainly of juveniles and another composed mainly of adults. There was little risk of falling below the quasi-extinction threshold before 25 year for both juveniles and adults. However, the risk of quasi-extinction was almost certain for both size classes by 80 year. We also simulated the effect of increasing the hurricane occurrence probability over 80 year on the population. There was little risk of extinction before 20 year in the baseline model, but there was a significant risk of extinction within 5 year when 90% of the individuals were affected by a new hurricane event.     

EXTINCTION-RECOLONIZATION DYNAMICS IN THE MYCOPHAGOUS BEETLE PHALACRUS SUBSTRIATUS

The population structure of the mycophagous beetle Phalacrus substriatus is characterized by many small, local populations interconnected by migration over a small spatial scale (10 × 75 m²). Each local P. substriatus population has a relatively short expected persistence time, but persistence of the species occurs due to a balance between frequent local extinctions and recolonizations. This nonequilibrium population structure can have profound effects on how the genetic variation is structured between and within populations. Theoretical models have stated that the genetic differentiation among local populations will be enhanced relative to an island model at equilibrium if the number of colonizers is less than approximately twice the number of migrants among local populations. To study these effects, a set of 50 local P. substriatus populations were surveyed over a four-year period to record any naturally occurring extinctions and recolonizations. The per population colonization and extinction rate were 0.237 and 0.275, respectively. Mark-recapture techniques were used to estimate a number of demographic parameters: local population size (N = 11.1), migration rate , number of colonizers (k = 4.0), and the probability of common origin of colonizers (φ = 0.5). The theoretically predicted level of differentiation among local populations (measured as Wright's F_ST) was 0.070. Genetic data obtained from an electrophoretic survey of seven polymorphic loci gave an estimated degree of differentiation of 0.077. There was thus a good agreement between the empirical results and the theoretical predictions. Young populations had significantly higher levels of differentiation than old, more established populations . The extinction-recolonization dynamics resulted in an overall increase in the genetic differentiation among local populations by c. 40%. The global effective population size was also reduced by c. 55%. The results give clear evidence to how nonequilibrium processes shape the genetic structure of populations.     

INBREEDING DEPRESSION IN PARTIALLY SELF-FERTILIZING DECODON VERTICILLATUS (LYTHRACEAE): POPULATION-GENETIC AND EXPERIMENTAL ANALYSES

Inbreeding depression is a major selective force favoring outcrossing in flowering plants. Some self-fertilization, however, should weaken the harmful effects of inbreeding by exposing genetic load to selection. This study examines the maintenance of inbreeding depression in partially self-fertilizing populations of the long-lived, herbaceous wetland plant, Decodon verticillatus (L.) Ell. (Lythraceae). Estimates from ten populations indicate that 30% of offspring are produced through self-fertilization. Population-genetic estimates of inbreeding depression (δ = 1 – relative mean fitness of selfed progeny) based on changes in the inbreeding coefficient for the same ten populations were uniformly high, ranging from 0.49 to 1.79 and averaging 1.11 ± 0.29 SE. Although confidence intervals of individual population estimates were large, estimates were significantly greater than 0 in six populations and greater than 0.5 in four. Inbreeding depression was also estimated by comparing growth, survival, and flowering of experimentally selfed and outcrossed offspring from two of these populations in a 1-yr glasshouse experiment involving three density regimes; after which offspring were transplanted into garden arrays and two field sites and monitored for two consecutive growing seasons. Overall for survival averaged 0.27 ± 0.01 in the glasshouse, 0.33 ± 0.04 in the garden, and 0.46 ± 0.04 in the field. The glasshouse experiment also revealed strong inbreeding depression for growth variables, especially above-soil dry weight ( = 0.42 ± 0.03). The fitness consequences of inbreeding depression for these growth variables approximately doubles if survival to maturity is determined by severe truncation selection. Despite substantial selfing, inbreeding depression appears to be a major selective force favoring the maintenance of outcrossing in D. verticillatus.     

SEX RATIO AND DENSITY AFFECT SEXUAL SELECTION IN A SEX‐ROLE REVERSED FISH

Understanding how demographic processes influence mating systems is important to decode ecological influences on sexual selection in nature. We manipulated sex ratio and density in experimental populations of the sex‐role reversed pipefish Syngnathus typhle. We quantified sexual selection using the Bateman gradient (), the opportunity for selection (I), and sexual selection (I_s), and the maximum standardized sexual selection differential (). We also measured selection on body length using standardized selection differentials (s′) and mating differentials (m′), and tested whether the observed I and I_s differ from values obtained by simulating random mating. We found that I, I_s, and , but not , were higher for females under female than male bias and the opposite for males, but density did not affect these measures. However, higher density decreased sexual selection (m′ but not s′) on female length, but selection on body length was not affected by sex ratio. Finally, I_s but not I was higher than expected from random mating, and only for females under female bias. This study demonstrates that both sex ratio and density affect sexual selection and that disentangling interrelated demographic processes is essential to a more complete understanding of mating behavior and the evolution of mating systems.     

MATERNAL INHERITANCE AND ITS EFFECT ON ADAPTIVE EVOLUTION: A QUANTITATIVE GENETIC ANALYSIS OF MATERNAL EFFECTS IN A NATURAL PLANT POPULATION

A mother can influence a trait in her offspring both by the genes she transmits (Mendelian inheritance) and by maternal attributes that directly affect that trait in her offspring (maternal inheritance). Maternal inheritance can alter the direction, rate, and duration of adaptive evolution from standard Mendelian models and its impact on adaptive evolution is virtually unexplored in natural populations. In a hierarchical quantitative genetic analysis to determine the magnitude and structure of maternal inheritance in the winter annual plant, Collinsia verna, I consider three potential models of inheritance. These range from a standard Mendelian model estimating only direct (i.e., Mendelian) additive and environmental variance components to a maternal inheritance model estimating six additive and environmental variance components: direct additive and environmental variances; maternal additive and environmental variances; and the direct-maternal additive () and environmental covariances. The structure of maternal inheritance differs among the 10 traits considered at four stages in the life cycle. Early in the life cycle, seed weight and embryo weight display substantial , a negative , and a positive . Subsequently, cotyledon diameter displays and of roughly the same magnitude and negative . For fall rosettes, leaf number and length are best described by a Mendelian model. In the spring, leaf length displays maternal inheritance with significant and and a negative . All maternally inherited traits show significant negative . Predicted response to selection under maternal inheritance depends on and as well as . Negative results in predicted responses in the opposite direction to selection for seed weight and embryo weight and predicted responses near zero for all subsequent maternally inherited traits. Maternal inheritance persists through the life cycle of this annual plant for a number of size-related traits and will alter the direction and rate of evolutionary response in this population.     

SMALL POPULATION GENETIC VARIABILITY AT LOCI UNDER STABILIZING SELECTION

Genetic variability at a locus under stabilizing selection in a finite population is investigated using analytic methods and computer simulations. Three measures are examined: the number of alleles k, heterozygosity H, and additive genetic variance Vg. A nearly-neutral theory results. The composite parameter S = NV_M/V_s (where N is the population size, V_M the variance of new mutant allelic effects and V_s the weakness of stabilizing selection) figures prominently in the results. The equilibrium heterozygosity is similar to that of strictly neutral theory, H = 4N_μc/ (1 + 4N_μc), except that μ_c = where c is about 0.5. Simulations corroborate except for very low N. Genetic variability attains similar equilibrium values at both a “lone” locus and at an “embedded” locus. This agrees with my earlier work concerning molecular clock rates. These results modify the neutralist interpretation of data concerning genetic variability and genetic distances between populations. Low H values are proportional not to N but to . This may explain the narrow observed range of H among species. Heterozygosities need not be highly correlated to genetic variances. Genetic variances are not highly dependent on population size except in very small populations which are difficult to sample without bias because the smallest populations go extinct the fastest. Nearly neutral evolution will not be easily distinguished from strictly neutral theory under the Hudson-Kreitman-Aguade inter-/intraspecific variation ratio test, since a similar effective mutation rate holds for genetic distances and D = 2μ_ct, where . As with strictly neutral theory, comparisons across loci should show D and H to be positively correlated because of the shared μ_c. But unlike neutral theory, for a given locus, comparisons across species should show D and H to be negatively correlated. There is no obvious threshold of population size below which genetic variability inevitably declines. Extinction depends on both genetic variation and natural selection. Neither theory nor observation presently indicates the measure of genetic variability (k, H, V_G or other) that best indicates vulnerability of a small population to extinction.     

Mean growth rate when rare is not a reliable metric for persistence of species

The coexistence of many species within ecological communities poses a long‐standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, , is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on and show that it fails to capture the effect of temporal random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in , since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as increases.     

Life‐history evolution under fluctuating density‐dependent selection and the adaptive alignment of pace‐of‐life syndromes

We present a novel perspective on life‐history evolution that combines recent theoretical advances in fluctuating density‐dependent selection with the notion of pace‐of‐life syndromes (POLSs) in behavioural ecology. These ideas posit phenotypic co‐variation in life‐history, physiological, morphological and behavioural traits as a continuum from the highly fecund, short‐lived, bold, aggressive and highly dispersive ‘fast’ types at one end of the POLS to the less fecund, long‐lived, cautious, shy, plastic and socially responsive ‘slow’ types at the other. We propose that such variation in life histories and the associated individual differences in behaviour can be explained through their eco‐evolutionary dynamics with population density – a single and ubiquitous selective factor that is present in all biological systems. Contrasting regimes of environmental stochasticity are expected to affect population density in time and space and create differing patterns of fluctuating density‐dependent selection, which generates variation in fast versus slow life histories within and among populations. We therefore predict that a major axis of phenotypic co‐variation in life‐history, physiological, morphological and behavioural traits (i.e. the POLS) should align with these stochastic fluctuations in the multivariate fitness landscape created by variation in density‐dependent selection. Phenotypic plasticity and/or genetic (co‐)variation oriented along this major POLS axis are thus expected to facilitate rapid and adaptively integrated changes in various aspects of life histories within and among populations and/or species. The fluctuating density‐dependent selection POLS framework presented here therefore provides a series of clear testable predictions, the investigation of which should further our fundamental understanding of life‐history evolution and thus our ability to predict natural population dynamics.     

THE EFFECT OF INBREEDING IN DIPLOID AND TETRAPLOID POPULATIONS OF EPILOBIUM ANGUSTIFOLIUM (ONAGRACEAE): IMPLICATIONS FOR THE GENETIC BASIS OF INBREEDING DEPRESSION

The partial dominance model for the evolution of inbreeding depression predicts that tetraploids should exhibit less inbreeding depression than their diploid progenitors. We tested this prediction by comparing the magnitude of inbreeding depression in tetraploid and diploid populations of the herbaceous perennial Epilobium angustifolium (Onagraceae). Inbreeding depression was estimated in the greenhouse for three tetraploid and two diploid populations at four life stages. The mating system of a tetraploid population was estimated and compared to a previous estimate for diploids. Tetraploids showed less inbreeding depression than diploids at all life history stages, and these differences were significant for seed-set and cumulative fitness, but not for germination, survival, or plant dry mass at nine weeks. This result suggests that the genetic basis of inbreeding depression may differ among life stages. The primary selfing rate of the tetraploid population was r = 0.43, which is nearly identical to that of a diploid population (r = 0.45), indicating that differences in inbreeding depression between diploids and tetraploids are probably not due to differences in the mating system. Cumulative inbreeding depression, calculated from the four life history stages, was significantly higher for diploids () than for tetraploids (), supporting the partial dominance model of inbreeding depression.     

Effective size of density‐dependent populations in fluctuating environments

Reliable estimates of effective population size are of central importance in population genetics and evolutionary biology. For populations that fluctuate in size, harmonic mean population size is commonly used as a proxy for (multi‐) generational effective size. This assumes no effects of density dependence on the ratio between effective and actual population size, which limits its potential application. Here, we introduce density dependence on vital rates in a demographic model of variance effective size. We derive an expression for the ratio in a density‐regulated population in a fluctuating environment. We show by simulations that yearly genetic drift is accurately predicted by our model, and not proportional to as assumed by the harmonic mean model, where N is the total population size of mature individuals. We find a negative relationship between and N. For a given N, the ratio depends on variance in reproductive success and the degree of resource limitation acting on the population growth rate. Finally, our model indicate that environmental stochasticity may affect not only through fluctuations in N, but also for a given N at a given time. Our results show that estimates of effective population size must include effects of density dependence and environmental stochasticity.