Local Adaptation and Genetics of Acid-Stress Tolerance in the Moor Frog, Rana arvalis

As potential to adapt to environmental stress can be essential for population persistence, knowledge on the genetic architecture of local adaptation is important for conservation genetics. We investigated the relative importance of additive genetic, dominance and maternal effects contributions to acid stress tolerance in two moor frog (Rana arvalis) populations originating from low and neutral pH habitats. Experiments with crosses obtained from artificial matings revealed that embryos from the acid origin population were more tolerant to low pH than embryos from the neutral origin population in embryonic survival rates, but not in terms of developmental stability, developmental and growth rates. Strong maternal effect and small additive genetic contributions to variation were detected in all traits in both populations. In general, dominance contributions to variance in different traits were of similar magnitude to the additive genetic effects, but dominance effects outweighed the additive genetic and maternal effects contributions to early growth in both populations. Furthermore, the expression of additive genetic variance was independent of pH treatment, suggesting little additive genetic variation in acid stress tolerance. The results suggest that although local genetic adaptation to acid stress has taken place, the current variation in acid stress tolerance in acidified populations may owe largely to non-genetic effects. However, low but significant heritabilities (h ² 0.07–0.22) in all traits – including viability itself – under a wide range of pH conditions suggests that environmental stress created by low pH is unlikely to lower moor frog populations' ability to respond to selection in the traits studied. Nevertheless, acid conditions could lower populations' ability to respond to selection in the long run through reduction in effective population size.     

Demographic factors and genetic variation influence population persistence under environmental change

Population persistence has been studied in a conservation context to predict the fate of small or declining populations. Persistence models have explored effects on extinction of random demographic and environmental fluctuations, but in the face of directional environmental change they should also integrate factors affecting whether a population can adapt. Here, we examine the population‐size dependence of demographic and genetic factors and their likely contributions to extinction time under scenarios of environmental change. Parameter estimates were derived from experimental populations of the rainforest species, Drosophila birchii, held in the lab for 10 generations at census sizes of 20, 100 and 1000, and later exposed to five generations of heat‐knockdown selection. Under a model of directional change in the thermal environment, rapid extinction of populations of size 20 was caused by a combination of low growth rate (r) and high stochasticity in r. Populations of 100 had significantly higher reproductive output, lower stochasticity in r and more additive genetic variance (V_A) than populations of 20, but they were predicted to persist less well than the largest size class. Even populations of 1000 persisted only a few hundred generations under realistic estimates of environmental change because of low V_A for heat‐knockdown resistance. The experimental results document population‐size dependence of demographic and adaptability factors. The simulations illustrate a threshold influence of demographic factors on population persistence, while genetic variance has a more elastic impact on persistence under environmental change.     

Estimates of direct and indirect effects for early juvenile survival in captive populations maintained for conservation purposes: the case of Cuvier's gazelle

Together with the avoidance of any negative impact of inbreeding, preservation of genetic variability for life‐history traits that could undergo future selective pressure is a major issue in endangered species management programmes. However, most of these programmes ignore that, apart from the direct action of genes on such traits, parents, as contributors of offspring environment, can influence offspring performance through indirect parental effects (when parental genotype and phenotype exerts environmental influences on offspring phenotype independently of additive genetic effects). Using quantitative genetic models, we estimated the additive genetic variance for juvenile survival in a population of the endangered Cuvier's gazelle kept in captivity since 1975. The dataset analyzed included performance recording for 700 calves and a total pedigree of 740 individuals. Results indicated that in this population juvenile survival harbors significant additive genetic variance. The estimates of heritability obtained were in general moderate (0.115–0.457) and not affected by the inclusion of inbreeding in the models. Maternal genetic contribution to juvenile survival seems to be of major importance in this gazelle's population as well. Indirect genetic and indirect environmental effects assigned to mothers (i.e., maternal genetic and maternal permanent environmental effects) roughly explain a quarter of the total variance estimated for the trait analyzed. These findings have major evolutionary consequences for the species as show that offspring phenotypes can evolve strictly through changes in the environment provided by mothers. They are also relevant for the captive breeding programme of the species. To take into account, the contribution that mothers have on offspring phenotype through indirect genetic effects when designing pairing strategies might serve to identify those females with better ability to recruit, and, additionally, to predict reliable responses to selection in the captive population.     

Evolution of Adaptation and Mate Choice: Parental Relatedness Affects Expression of Phenotypic Variance in a Natural Population

Mating between relatives generally results in reduced offspring viability or quality, suggesting that selection should favor behaviors that minimize inbreeding. However, in natural populations where searching is costly or variation among potential mates is limited, inbreeding is often common and may have important consequences for both offspring fitness and phenotypic variation. In particular, offspring morphological variation often increases with greater parental relatedness, yet the source of this variation, and thus its evolutionary significance, are poorly understood. One proposed explanation is that inbreeding influences a developing organism’s sensitivity to its environment and therefore the increased phenotypic variation observed in inbred progeny is due to greater inputs from environmental and maternal sources. Alternatively, changes in phenotypic variation with inbreeding may be due to additive genetic effects alone when heterozygotes are phenotypically intermediate to homozygotes, or effects of inbreeding depression on condition, which can itself affect sensitivity to environmental variation. Here we examine the effect of parental relatedness (as inferred from neutral genetic markers) on heritable and nonheritable components of developmental variation in a wild bird population in which mate choice is often constrained, thereby leading to inbreeding. We found greater morphological variation and distinct contributions of variance components in offspring from highly related parents: inbred offspring tended to have greater environmental and lesser additive genetic variance compared to outbred progeny. The magnitude of this difference was greatest in late-maturing traits, implicating the accumulation of environmental variation as the underlying mechanism. Further, parental relatedness influenced the effect of an important maternal trait (egg size) on offspring development. These results support the hypothesis that inbreeding leads to greater sensitivity of development to environmental variation and maternal effects, suggesting that the evolutionary response to selection will depend strongly on mate choice patterns and population structure.     

Is my study system good enough? A case study for identifying maternal effects

In this paper, we demonstrate how simulation studies can be used to answer questions about identifiability and consequences of omitting effects from a model. The methodology is presented through a case study where identifiability of genetic and/or individual (environmental) maternal effects is explored. Our study system is a wild house sparrow (Passer domesticus) population with known pedigree. We fit pedigree‐based (generalized) linear mixed models (animal models), with and without additive genetic and individual maternal effects, and use deviance information criterion (DIC) for choosing between these models. Pedigree and R‐code for simulations are available. For this study system, the simulation studies show that only large maternal effects can be identified. The genetic maternal effect (and similar for individual maternal effect) has to be at least half of the total genetic variance to be identified. The consequences of omitting a maternal effect when it is present are explored. Our results indicate that the total (genetic and individual) variance are accounted for. When an individual (environmental) maternal effect is omitted from the model, this only influences the estimated (direct) individual (environmental) variance. When a genetic maternal effect is omitted from the model, both (direct) genetic and (direct) individual variance estimates are overestimated.     

The nature of nurture in a wild mammal's fitness

Genetic variation in fitness is required for the adaptive evolution of any trait but natural selection is thought to erode genetic variance in fitness. This paradox has motivated the search for mechanisms that might maintain a population''s adaptive potential. Mothers make many contributions to the attributes of their developing offspring and these maternal effects can influence responses to natural selection if maternal effects are themselves heritable. Maternal genetic effects (MGEs) on fitness might, therefore, represent an underappreciated source of adaptive potential in wild populations. Here we used two decades of data from a pedigreed wild population of North American red squirrels to show that MGEs on offspring fitness increased the population''s evolvability by over two orders of magnitude relative to expectations from direct genetic effects alone. MGEs are predicted to maintain more variation than direct genetic effects in the face of selection, but we also found evidence of maternal effect trade-offs. Mothers that raised high-fitness offspring in one environment raised low-fitness offspring in another environment. Such a fitness trade-off is expected to maintain maternal genetic variation in fitness, which provided additional capacity for adaptive evolution beyond that provided by direct genetic effects on fitness.     

Demographic inference from whole‐genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age

We investigated how population changes and fluctuations in the pink‐footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, demographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100–1,000 individuals) that split into the current populations at the end of the last glacial maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human‐related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink‐footed geese, (2) the decline inferred during the Middle Ages is due to human persecution, and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.     

Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon

An approach frequently used to demonstrate a genetic basis for population-level phenotypic differences is to employ common garden rearing designs, where observed differences are assumed to be attributable to primarily additive genetic effects. Here, in two common garden experiments, we employed factorial breeding designs between wild and domestic, and among wild populations of Chinook salmon (Oncorhynchus tshawytscha). We measured the contribution of additive (V(A)) and maternal (V(M)) effects to the observed population differences for 17 life history and fitness-related traits. Our results show that, in general, maternal effects contribute more to phenotypic differences among populations than additive genetic effects. These results suggest that maternal effects are important in population phenotypic differentiation and also signify that the inclusion of the maternal source of variation is critical when employing models to test population differences in salmon, such as in local adaptation studies.     

Genetic and maternal effect influences on viability of common frog tadpoles under different environmental conditions

The influence of environmental stress on the expression of genetic and maternal effects on the viability traits has seldom been assessed in wild vertebrates. We have estimated genetic and maternal effects on the viability (viz probability of survival, probability of being deformed, and body size and shape) of common frog, Rana temporaria, tadpoles under stressful (low pH) and nonstressful (neutral pH) environmental conditions. A Bayesian analysis using generalized linear mixed models was applied to data from a factorial laboratory experiment. The expression of additive genetic variance was independent of pH treatments, and all traits were significantly heritable (survival: h2 approximately 0.08; deformities: h2 approximately 0.26; body size: h2 approximately 0.12; body shape: h2 approximately 0.14). Likewise, nonadditive genetic contributions to variation in all traits were significant, independent of pH treatments and typically of magnitude similar to the additive genetic effects. Maternal effects were large for all traits, especially for viability itself, and their expression was partly dependent on the environment. In the case of body size, the maternal effects were mediated largely through egg size. In general, the results give little evidence for the conjecture that environmental stress created by low pH would impact strongly on the genetic architecture of fitness-related traits in frogs, and hamper adaptation to stress caused by acidification. The low heritabilities and high dominance contributions conform to the pattern typical for traits subject to relatively strong directional selection.     

Genetic architecture and maternal contributions of early‐life survival in lake trout Salvelinus namaycush

The influences of additive, non‐additive and maternal effects on early survival (uneyed embryo survival, eyed embryo survival, alevin survival and overall survival to first feeding) were quantified in lake trout Salvelinus namaycush using a 7 × 7 full‐factorial breeding design. Maternal effects followed by non‐additive genetic effects explained around one third of the phenotypic variance of the survival traits. Although the amount of additive genetic effects were low (<1%), suggesting a limited potential of the traits to respond to new selection pressures, how maternal and non‐additive genetic effects may respond to selection under certain circumstances are discussed.     

Body size divergence in nine‐spined sticklebacks: disentangling additive genetic and maternal effects

Interpopulation differences in body size are of common occurrence in vertebrates, but the relative importance of genetic, maternal, and environmental effects as causes of observed differentiation have seldom been assessed in the wild. Gigantism in pond nine‐spined sticklebacks (Pungitius pungitius Linnaeus, 1758) has been repeatedly observed, but the quantitative genetic basis of population divergence in size has remained unstudied. We conducted a common garden experiment – using ‘pure’ and reciprocal crosses between two populations (‘giant’ pond versus ‘normal’ marine) – to test for the relative importance of additive genetic, non‐additive genetic, and maternal effects on body size after 11 months of growth in the laboratory. We found that body size difference between the two populations in laboratory conditions owed mainly to additive genetic effects, and only to a minor degree to maternal effects. Furthermore, the weak maternal effects were seen only in the offspring of ‘giant’ mothers, and appeared to be mediated through differences in egg size. Thus, the results suggest that gigantism in pond populations of P. pungitius is based on the effects of additively acting genes, rather than to direct environmental induction, or maternal or non‐additive gene action. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 521–528.     

Mass‐dependent reproductive strategies in wild bighorn ewes: a quantitative genetic approach

In the Ram Mountain bighorn sheep (Ovis canadensis) population, ewes differing by more than 30% in body mass weaned lambs with an average mass difference of only 3%. Variability in adult body mass was partly due to additive genetic effects, but inheritance of weaning mass was weak. Maternal effects could obscure genetic effects in the phenotypic expression of weaning mass, particularly if they reflected strategies of maternal expenditure that varied according to ewe mass. We performed a quantitative genetic analysis to assess genetic and environmental influences on ewe mass and on maternal expenditure. We used the mean daughters/mother regression method and Derivative Free Restricted Maximum Likelihood models to estimate heritability (h²) of ewe mass and indices of maternal expenditure. We found additive genetic effects on phenotypic variation in maternal mass, in lamb mass at weaning (absolute maternal expenditure) and in weaning mass relative to maternal mass at weaning (relative maternal expenditure). Heritability suggests that maternal expenditure has the potential to evolve. The genetic correlation of ewe mass and absolute maternal expenditure was weak, while ewe mass and relative maternal expenditure were strongly negatively correlated. These results suggest additive genetic effects on mass‐dependent reproductive strategies in bighorn ewes. Mass‐dependent reproductive strategies could affect lamb survival and phenotypic variation in adult mass. As population density increased and reproduction became costlier, small females reduced maternal expenditure more than large females. Constraints on reproductive strategy imposed by variations in resource availability are therefore likely to differ according to ewe mass. A general trend for a decrease in maternal expenditure relative to maternal size in mammals suggests that size‐dependent negative maternal effects may be common.     

Heritability of flight and resting metabolic rates in the Glanville fritillary butterfly

Dispersal capacity is a key life‐history trait especially in species inhabiting fragmented landscapes. Evolutionary models predict that, given sufficient heritable variation, dispersal rate responds to natural selection imposed by habitat loss and fragmentation. Here, we estimate phenotypic variance components and heritability of flight and resting metabolic rates (RMRs) in an ecological model species, the Glanville fritillary butterfly, in which flight metabolic rate (FMR) is known to correlate strongly with dispersal rate. We modelled a two‐generation pedigree with the animal model to distinguish additive genetic variance from maternal and common environmental effects. The results show that FMR is significantly heritable, with additive genetic variance accounting for about 40% of total phenotypic variance; thus, FMR has the potential to respond to selection on dispersal capacity. Maternal influences on flight metabolism were negligible. Heritability of flight metabolism was context dependent, as in stressful thermal conditions, environmentally induced variation dominated over additive genetic effects. There was no heritability in RMR, which was instead strongly influenced by maternal effects. This study contributes to a mechanistic understanding of the evolution of dispersal‐related traits, a pressing question in view of the challenges posed to many species by changing climate and fragmentation of natural habitats.     

Human‐modified habitats change patterns of population genetic structure and group relatedness in Peter's tent‐roosting bats

Although coloniality is widespread among mammals, it is still not clear what factors influence composition of social groups. As animals need to adapt to multiple habitat and environmental conditions throughout their range, variation in group composition should be influenced by adaptive adjustment to different ecological factors. Relevant to anthropogenic disturbance, increased habitat modification by humans can alter species’ presence, density, and population structure. Therefore, it is important to understand the consequences of changes to landscape composition, in particular how habitat modification affects social structure of group‐forming organisms. Here, we combine information on roosting associations with genetic structure of Peter's tent‐roosting bats, Uroderma bilobatum to address how different habitat characteristics at different scales affect structure of social groups. By dividing analyses by age and sex, we determined that genetic structure was greater for adult females than adult males or offspring. Habitat variables explained 80% of the variation in group relatedness (mainly influenced by female relatedness) with roost characteristics contributing the most explained variation. This suggests that females using roosts of specific characteristics exhibit higher relatedness and seem to be philopatric. These females mate with more males than do more labile female groups. Results describe ecological and microevolutionary processes, which affect relatedness and social structure; findings are highly relevant to species distributions in both natural and human‐modified environments.     

Are there indirect fitness benefits of female extra-pair reproduction? Lifetime reproductive success of within-pair and extra-pair offspring

The forces driving extra-pair reproduction by socially monogamous females, and the resulting genetic polyandry, remain unclear. A testable prediction of the hypothesis that extra-pair reproduction partly reflects indirect selection on females is that extra-pair young (EPY) will be fitter than their within-pair young (WPY) maternal half-siblings. This prediction has not been comprehensively tested in a wild population, requiring data on the lifetime reproductive success (LRS) of maternal half-sib EPY and WPY. We used 17 years of genetic parentage data from song sparrows, Melospiza melodia, to compare the LRS of hatched EPY and WPY maternal half-siblings measured as their lifetime number of hatched offspring, recruited offspring, and hatched grandoffspring. EPY hatchlings were not significantly fitter than WPY hatchlings for any of three measures of LRS. Furthermore, opposite to prediction, EPY hatchlings tended to have lower LRS than their maternal half-sibling WPY hatchlings on average. EPY also tended to be less likely to survive to hatch than their maternal half-sibling WPY. Taken together, these results fail to support one key hypothesis explaining the evolution of genetic polyandry by socially monogamous females and suggest there may be weak indirect selection against female extra-pair reproduction in song sparrows.     

The quantitative genetic basis of adaptive divergence in the moor frog (Rana arvalis) and its implications for gene flow

Knowledge on the relative contribution of direct genetic, maternal and environmental effects to adaptive divergence is important for understanding the drivers of biological diversification. The moor frog (Rana arvalis) shows adaptive divergence in embryonic and larval fitness traits along an acidification gradient in south-western Sweden. To understand the quantitative genetic basis of this divergence, we performed reciprocal crosses between three divergent population pairs and reared embryos and larvae at acid and neutral pH in the laboratory. Divergence in embryonic acid tolerance (survival) was mainly determined by maternal effects, whereas the relative contributions of maternal, additive and nonadditive genetic effects in larval life-history traits differed between traits, population pairs and rearing environments. These results emphasize the need to investigate the quantitative genetic basis of adaptive divergence in multiple populations and traits, as well as different environments. We discuss the implications of our findings for maintenance of local adaptation in the context of migrant and hybrid fitness.     

Pedigree‐free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer

Assessing the evolutionary potential of animal populations in the wild is crucial to understanding how they may respond to selection mediated by rapid environmental change (e.g. habitat loss and fragmentation). A growing number of studies have investigated the adaptive role of behaviour, but assessments of its genetic basis in a natural setting remain scarce. We combined intensive biologging technology with genome‐wide data and a pedigree‐free quantitative genetic approach to quantify repeatability, heritability and evolvability for a suite of behaviours related to the risk avoidance‐resource acquisition trade‐off in a wild roe deer (Capreolus capreolus) population inhabiting a heterogeneous, human‐dominated landscape. These traits, linked to the stress response, movement and space‐use behaviour, were all moderately to highly repeatable. Furthermore, the repeatable among‐individual component of variation in these traits was partly due to additive genetic variance, with heritability estimates ranging from 0.21 ± 0.08 to 0.70 ± 0.11 and evolvability ranging from 1.1% to 4.3%. Changes in the trait mean can therefore occur under hypothetical directional selection over just a few generations. To the best of our knowledge, this is the first empirical demonstration of additive genetic variation in space‐use behaviour in a free‐ranging population based on genomic relatedness data. We conclude that wild animal populations may have the potential to adjust their spatial behaviour to human‐driven environmental modifications through microevolutionary change.     

Habitat use and hybridisation between the Rocky Mountain sculpin (Cottus sp.) and slimy sculpin (Cottus cognatus)

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Quantitative genetic and translocation experiments reveal genotype‐by‐environment effects on juvenile life‐history traits in two populations of Chinook salmon (Oncorhynchus tshawytscha)

Understanding the genetic architecture of phenotypic plasticity is required to assess how populations might respond to heterogeneous or changing environments. Although several studies have examined population‐level patterns in environmental heterogeneity and plasticity, few studies have examined individual‐level variation in plasticity. Here, we use the North Carolina II breeding design and translocation experiments between two populations of Chinook salmon to detail the genetic architecture and plasticity of offspring survival and growth. We followed the survival of 50 800 offspring through the larval stage and used parentage analysis to examine survival and growth through freshwater rearing. In one population, we found that additive genetic, nonadditive genetic and maternal effects explained 25%, 34% and 55% of the variance in larvae survival, respectively. In the second population, these effects explained 0%, 24% and 61% of the variance in larvae survival. In contrast, fry survival was regulated primarily by additive genetic effects, which indicates a shift from maternal to genetic effects as development proceeds. Fry growth also showed strong additive genetic effects. Translocations between populations revealed that offspring survival and growth varied between environments, the degree of which differed among families. These results indicate genetic differences among individuals in their degree of plasticity and consequently their ability to respond to environmental variation.     

Natural selection on the genetical component of variance in body condition in a wild bird population

Although there is substantial evidence that skeletal measures of body size are heritable in wild animal populations, it is frequently assumed that the nonskeletal component of body weight (or ‘condition’) is determined primarily by environmental factors, in particular nutritional state. We tested this assumption by quantifying the genetic and environmental components of variance in fledgling body condition index (=relative body weight) in a natural population of collared flycatchers (Ficedula albicollis), and compared the strength of natural selection on individual breeding values with that on phenotypic values. A mixed model analysis of the components of variance, based on an ‘animal model’ and using 18 years of data on 17 717 nestlings, revealed a significant additive genetic component of variance in body condition, which corresponded to a narrow sense heritability (h²) of 0.30 (SE=0.03). Nongenetic contributions to variation in body condition were large, but there was no evidence of dominance variance nor of contributions from early maternal or common environment effects (pre‐manipulation environment) in condition at fledging. Comparison of pre‐ and post‐selection samples revealed virtually identical h² of body condition index, despite the fact that there was a significant decrease (35%) in the levels of additive genetic variance from fledging to breeding. The similar h² in the two samples occurred because the environmental component of variance was also reduced by selection, suggesting that natural selection was acting on both genotypic and environmental variation. The effects of selection on genetic variance were confirmed by calculation of the selection differentials for both phenotypic values and best linear unbiased predictor (BLUP) estimates of breeding values: there was positive directional selection on condition index both at the phenotypic and the genotypic level. The significant h² of body condition index is consistent with data from human and rodent populations showing significant additive genetic variance in relative body mass and adiposity, but contrasts with the common assumption in ecology that body condition reflects an individual’s nongenetic nutritional state. Furthermore, the substantial reduction in the additive genetic component of variance in body condition index suggests that selection on environmental deviations cannot alone explain the maintenance of additive genetic variation in heritable traits, but that other mechanisms are needed to explain the moderate to high heritabilities of traits under consistent and strong directional selection.