Hypothesis testing for the genetic background of quantitative traits

The testing of Bayesian point null hypotheses on variance component models have resulted in a tough assignment for which no clear and generally accepted method exists. In this work we present what we believe is a succeeding approach to such a task. It is based on a simple reparameterization of the model in terms of the total variance and the proportion of the additive genetic variance with respect to it, as well as on the explicit inclusion on the prior probability of a discrete component at origin. The reparameterization was used to bypass an arbitrariness related to the impropriety of uninformative priors onto unbounded variables while the discrete component was necessary to overcome the zero probability assigned to sets of null measure by the usual continuous variable models. The method was tested against computer simulations with appealing results.     

Estimating the success of natural spawning of salmonids in streams

A new method is described to estimate the survival of salmonids in streams from fertilization of the eggs to the emergence of the fry. The method is compared to other techniques generally used to estimate the egg-to-fry survival: fry traps, excavation of redds, construction of artificial redds and laboratory experiments. Especially designed boxes filled with substratum and freshly fertilized eggs are buried in the stream bed. Survival is determined at three different embryological development stages: eyed stage, hatching and emergence. Boxes are planted inside the stream bed using a special injector, so that substratum alterations are minimal around the boxes. This method was tested successfully in two different studies, one in Switzerland on the brown trout, the other one in Sweden on the sea trout.     

Indirect genetic effects in a sex‐limited trait: the case of breeding time in red‐billed gulls

Female reproductive performance can be strongly affected by male care, so that breeding time, a trait expressed only by females, can be seen as one trait determined by both male and female genotypes. Animal model analyses of a 46‐year study of red‐billed gulls (Larus novaehollandiae scopulinus) revealed that laying date was not heritable in females (h² = 0.001 ± 0.030), but significantly so in males (h² = 0.134 ± 0.029). Heritability of breeding time in males probably reflects genetic variability in some other trait such as courtship feeding ability. In line with predictions of evolutionary models incorporating indirect genetic effects, the strong and consistent directional selection for advanced breeding time has not resulted in detectable selection response in males. Our results demonstrate that a female trait is largely determined by genetic characteristics of its mate, and hence, any evolutionary change in red‐billed gull breeding time depends critically on genetic variation in males.     

Big and beautiful? Quantitative genetic parameters for appearance of large rainbow trout

A quantitative genetic analysis of body condition, body shape, skin colour and spottiness of large, farmed rainbow trout Oncorhynchus mykiss showed that the traits can be modified through selective breeding. This was indicated by their high heritabilities ( h ² = 0·46–0·61 on the underlying liability scale and 0·29–0·50 on the observed scale). Correlations calculated using linear models showed that skin colour and the amount of spots displayed positive phenotypic ( r _P = 0·33) and genetic correlations ( r _A = 0·83), the relationship being advantageous for the genetic improvement of the traits. Body shape and condition factor displayed disadvantageous correlations with body mass at both ages, the genetic correlations between the traits ranging from 0·36 to 0·57. It was concluded that there are no strong genetic constraints for the genetic improvement of appearance, the only limitation being that rapidly growing fish become rotund.     

The genetic architecture of behavioral traits in a spider

The existence of consistent individual differences in behavior has been shown in a number of species, and several studies have found observable sex differences in these behaviors, yet their evolutionary implications remain unclear. Understanding the evolutionary dynamics of behavioral traits requires knowledge of their genetic architectures and whether this architecture differs between the sexes. We conducted a quantitative genetic study in a sexually size‐dimorphic spider, Larinioides sclopetarius, which exhibits sex differences in adult lifestyles. We observed pedigreed spiders for aggression, activity, exploration, and boldness and used animal models to disentangle genetic and environmental influences on these behaviors. We detected trends toward (i) higher additive genetic variances in aggression, activity, and exploration in males than females, and (ii) difference in variances due to common environment/maternal effects, permanent environment and residual variance in aggression and activity with the first two variances being higher in males for both behaviors. We found no sex differences in the amount of genetic and environmental variance in boldness. The mean heritability estimates of aggression, activity, exploration, and boldness range from 0.039 to 0.222 with no sizeable differences between females and males. We note that the credible intervals of the estimates are large, implying a high degree of uncertainty, which disallow a robust conclusion of sex differences in the quantitative genetic estimates. However, the observed estimates suggest that sex differences in the quantitative genetic architecture of the behaviors cannot be ruled out. Notably, the present study suggests that genetic underpinnings of behaviors may differ between sexes and it thus underscores the importance of taking sex differences into account in quantitative genetic studies.     

Heritability of life-history tactics and genetic correlation with body size in a natural population of brook charr (Salvelinus fontinalis)

A common dimorphism in life-history tactic in salmonids is the presence of an anadromous pathway involving a migration to sea followed by a freshwater reproduction, along with an entirely freshwater resident tactic. Although common, the genetic and environmental influence on the adoption of a particular life-history tactic has rarely been studied under natural conditions. Here, we used sibship-reconstruction based on microsatellite data and an 'animal model' approach to estimate the additive genetic basis of the life-history tactic adopted (anadromy vs. residency) in a natural population of brook charr, Salvelinus fontinalis. We also assess its genetic correlation with phenotypic correlated traits, body size and body shape. Significant heritability was observed for life-history tactic (varying from 0.52 to 0.56 depending on the pedigree scenario adopted) as well as for body size (from 0.44 to 0.50). There was also a significant genetic correlation between these two traits, whereby anadromous fish were genetically associated with bigger size at age 1 (r(G) = -0.52 and -0.61). Our findings thus indicate that life-history tactics in this population have the potential to evolve in response to selection acting on the tactic itself or indirectly via selection on body size. This study is one of the very few to have successfully used sibship-reconstruction to estimate quantitative genetic parameters under wild conditions.     

Climatic and temporal effects on the expression of secondary sexual characters: genetic and environmental components

Despite great interest in sexual selection, relatively little is known in detail about the genetic and environmental determinants of secondary sexual characters in natural populations. Such information is important for determining the way in which populations may respond to sexual selection. We report analyses of genetic and large-scale environmental components of phenotypic variation of two secondary sexual plumage characters (forehead and wing patch size) in the collared flycatcher Ficedula albicollis over a 22-year period. We found significant heritability for both characters but little genetic covariance between the two. We found a positive association between forehead patch size and a large-scale climatic index, the North Atlantic Oscillation (NAO) index, but not for wing patch. This pattern was observed in both cross-sectional and longitudinal data suggesting that the population response to NAO index can be explained as the result of phenotypic plasticity. Heritability of forehead patch size for old males, calculated under favorable conditions (NAO index > or = median), was greater than that under unfavorable conditions (NAO index < median). These changes occurred because there were opposing changes in additive genetic variance (VA) and residual variance (VR) under favorable and unfavorable conditions, with VA increasing and VR decreasing in good environments. However, no such effect was detected for young birds, or for wing patch size in either age class. In addition to these environmental effects on both phenotypic and genetic variances, we found evidence for a significant decrease of forehead patch size over time in older birds. This change appears to be caused by a change in the sign of viability selection on forehead patch size, which is associated with a decline in the breeding value of multiple breeders. Our data thus reveal complex patterns of environmental influence on the expression of secondary sexual characters, which may have important implications for understanding selection and evolution of these characters.     

Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations

Two commonly used techniques for estimating the effect of genes on traits in wild populations are the candidate gene approach and quantitative genetic analyses. However, whether these two approaches measure the same underlying processes remains unresolved. Here, we use these two methods to test whether they are alternative or complementary approaches to understanding genetic variation in the timing of reproduction - a key trait involved in adaptation to climate change - in wild tit populations. Our analyses of the candidate gene Clock show weak correlates with timing variables in blue tits, but no association in great tits, confirming earlier results. Quantitative genetic analyses revealed very low levels of both direct (female) and indirect (male) additive genetic variation in timing traits for both species, in contrast to previous studies on these traits, and much lower than generally assumed. Hence, neither method suggests strong genetic effects on the timing of breeding in birds, and further work should seek to assess the generality of these conclusions. We discuss how differences in the genetic control of traits, species life-history and confounding environmental variables may determine how useful integrating these two techniques is to understand the phenotypic variation in wild populations.     

Realized heritability and genetic gains of three generation for superior growth in the pearl oyster Pinctada martensii

The pearl oyster Pinctada martensii is an important economic shellfish species and mainly cultured in the southern provinces of China. The species is cultured for marine pearl production. However, pearl quality has recently decreased because the cultured stocks had slow growth and mass mortalities caused by inbreeding depression. We have initiated a selective breeding program to improve the cultivated stocks since 2002. In 2004, a base population was developed by collecting the breeders from Beibuwan and Liushagang stocks. During the period of 2005–2007, a two successive generation selection for shell length in the base population was carried out to produce the second generation selected and unselected lines. In May of 2008, three types of lines were produced by selecting the breeders from the second generation selected and unselected lines. The three types of lines were designated as SS (Selected for three generations), SC (selected for the two generations) and CC (unselected for three generations). Realized heritability for the third generation, cumulative (over three generation) and current (for the third generation) genetic gains were evaluated by comparing the growth performance of three types of lines at days 8, 16, 45, 75, 180 and 360. It was found that the SS lines had significant larger mean shell length and shell height than the SC and CC lines at all sampling ages (P < 0.05). The realized heritability estimate for adult shell length for the third generation was 0.41, similar with those detected for the first and second generation. The cumulative and current genetic gains for adult shell length were 20.94% and 13.27%, respectively. The present results indicate that there exists a high genetic variation in the population and mass selection is potential to improve pearl oyster stocks.     

Recording strategies and selection potential of feed intake measured using the X-ray method in rainbow trout

This study examines the way long-term feed intake should be recorded accurately for selective breeding purposes, and estimates selection potential in feed intake using the X-ray method to record individual daily feed intake in rainbow trout (Oncorhynchus mykiss). The analysis showed that the point estimates of daily feed intake displayed low repeatabilities (r = 0.09–0.32). This indicates that a minimum of three repeated records were needed to accurately record average feed intake at a fixed age. To effectively breed for feed intake over the whole growing period, it is necessary to determine average feed intake at different ages, since there were only moderate phenotypic and genetic correlations between average daily feed intake recorded at 140 g, 750 g and 2000 g wet mass. Heritability for average daily feed intake was low (average h² = 0.10), indicating that modest genetic changes can be obtained in response to selection. It was concluded that selection to genetically change long-term feed intake can be successful, yet repeated observations at several life stages are needed to ensure the accuracy of feed intake estimates and the efficiency of selection.     

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.     

Data depth, data completeness, and their influence on quantitative genetic estimation in two contrasting bird populations

Evolutionary biologists increasingly use pedigree‐based quantitative genetic methods to address questions about the evolutionary dynamics of traits in wild populations. In many cases, phenotypic data may have been collected only for recent parts of the study. How does this influence the performance of the models used to analyse these data? Here we explore how data depth (number of years) and completeness (number of observations) influence estimates of genetic variance and covariance within the context of an existing pedigree. Using long‐term data from the great tit Parus major and the mute swan Cygnus olor, species with different life‐histories, we examined the effect of manipulating the amount of data included on quantitative genetic parameter estimates. Manipulating data depth and completeness had little influence on estimated genetic variances, heritabilities, or genetic correlations, but (as expected) did influence confidence in these estimates. Estimated breeding values in the great tit were not influenced by data depth but were in the mute swan, probably because of differences in pedigree structure. Our analyses suggest the ‘rule of thumb’ that data from 3 years and a minimum of 100 individuals per year are needed to estimate genetic parameters with acceptable confidence, and that using pedigree data is worthwhile, even if phenotypes are only available toward the tips of the pedigree.     

Maternal genetic effects set the potential for evolution in a free-living vertebrate population

Heritable maternal effects have important consequences for the evolutionary dynamics of phenotypic traits under selection, but have only rarely been tested for or quantified in evolutionary studies. Here we estimate maternal effects on early-life traits in a feral population of Soay sheep (Ovis aries) from St Kilda, Scotland. We then partition the maternal effects into genetic and environmental components to obtain the first direct estimates of maternal genetic effects in a free-living population, and furthermore test for covariance between direct and maternal genetic effects. Using an animal model approach, direct heritabilities (h2) were low but maternal genetic effects (m2) represented a relatively large proportion of the total phenotypic variance for each trait (birth weight m2=0.119, birth date m2=0.197, natal litter size m2=0.211). A negative correlation between direct and maternal genetic effects was estimated for each trait, but was only statistically significant for natal litter size (ram= -0.714). Total heritabilities (incorporating variance from heritable maternal effects and the direct-maternal genetic covariance) were significant for birth weight and birth date but not for natal litter size. Inadequately specified models greatly overestimated additive genetic variance and hence direct h2 (by a factor of up to 6.45 in the case of birth date). We conclude that failure to model heritable maternal variance can result in over- or under-estimation of the potential for traits to respond to selection, and advocate an increased effort to explicitly measure maternal genetic effects in evolutionary studies.     

Variability in the distribution and abundance of stream salmonids, and the associated use of habitat models

The effective management of salmonid fisheries requires that the factors influencing variation in the abundance of stream populations are understood. The use of habitat models to explain the spatial component of population variance offers potential for management, but has not previously been set in the context of long term variation in population abundance because of the lack of suitable data sets. This paper examines contributions of spatial and temporal factors lo fish density variance using a 10-year data set from five tributaries of the River Conwy, North Wales. Recently developed habitat models were applied to the data to test their ability to explain nominal spatial variance. Spatial variance accounted for between 21 and 62% of the overall variance of salmonid abundance, and habitat models explained up to 95% of the spatial variance component. Synchrony in population variation amongst sites within and between tributaries is described, and some of the factors that may influence this are discussed.     

Ecological and life history characteristics predict population genetic divergence of two salmonids in the same landscape

Ecological and life history characteristics such as population size, dispersal pattern, and mating system mediate the influence of genetic drift and gene flow on population subdivision. Bull trout (Salvelinus confluentus) and mountain whitefish (Prosopium williamsoni) differ markedly in spawning location, population size and mating system. Based on these differences, we predicted that bull trout would have reduced genetic variation within and greater differentiation among populations compared with mountain whitefish. To test this hypothesis, we used microsatellite markers to determine patterns of genetic divergence for each species in the Clark Fork River, Montana, USA. As predicted, bull trout had a much greater proportion of genetic variation partitioned among populations than mountain whitefish. Among all sites, FST was seven times greater for bull trout (FST = 0.304 for bull trout, 0.042 for mountain whitefish. After removing genetically differentiated high mountain lake sites for each species FST, was 10 times greater for bull trout (FST = 0.176 for bull trout; FST = 0.018 for mountain whitefish). The same characteristics that affect dispersal patterns in these species also lead to predictions about the amount and scale of adaptive divergence among populations. We provide a theoretical framework that incorporates variation in ecological and life history factors, neutral divergence, and adaptive divergence to interpret how neutral and adaptive divergence might be correlates of ecological and life history factors.     

Caste-specific expression of genetic variation in the size of antibiotic-producing glands of leaf-cutting ants

Social insect castes represent some of the most spectacular examples of phenotypic plasticity, with each caste being associated with different environmental conditions during their life. Here we examine the level of genetic variation in different castes of two polyandrous species of Acromyrmex leaf-cutting ant for the antibiotic-producing metapleural gland, which has a major role in defence against parasites. Gland size increases allometrically. The small workers that play the main role in disease defence have relatively large glands compared with larger workers, while the glands of gynes are substantially larger than those of any workers, for their body size. The gland size of large workers varies significantly between patrilines in both Acromyrmex echinatior and Acromyrmex octospinosus. We also examined small workers and gynes in A. echinatior, again finding genetic variation in gland size in these castes. There were significant positive relationships between the gland sizes of patrilines in the different castes, indicating that the genetic mechanism underpinning the patriline variation has remained similar across phenotypes. The level of expressed genetic variation decreased from small workers to large workers to gynes. This is consistent with the hypothesis that there is individual selection on disease defence in founding queens and colony-level selection on disease defence in the worker castes.     

Genome‐wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral

Marine heat waves are increasing in magnitude, duration, and frequency as a result of climate change and are the principal global driver of mortality in reef‐building corals. Resilience‐based genetic management may increase coral heat tolerance, but it is unclear how temperature responses are regulated at the genome level and thus how corals may adapt to warming naturally or through selective breeding. Here we combine phenotypic, pedigree, and genomic marker data from colonies sourced from a warm reef on the Great Barrier Reef reproductively crossed with conspecific colonies from a cooler reef to produce combinations of warm purebreds and warm‐cool hybrid larvae and juveniles. Interpopulation breeding created significantly greater genetic diversity across the coral genome compared to breeding between populations and maintained diversity in key regions associated with heat tolerance and fitness. High‐density genome‐wide scans of single nucleotide polymorphisms (SNPs) identified alleles significantly associated with larval families reared at 27.5°C (87–2,224 loci), including loci putatively associated with proteins involved in responses to heat stress (cell membrane formation, metabolism, and immune responses). Underlying genetics of these families explained 43% of PCoA multilocus variation in survival, growth, and bleaching responses at 27.5°C and 31°C at the juvenile stage. Genetic marker contribution to total variation in fitness traits (narrow‐sense heritability) was high for survival but not for growth and bleaching in juveniles, with heritability of these traits being higher at 31°C relative to 27.5°C. While based on only a limited number of crosses, the mechanistic understanding presented here demonstrates that allele frequencies are affected by one generation of selective breeding, key information for the assessments of genetic intervention feasibility and modelling of reef futures.     

Strong artificial selection in the wild results in predicted small evolutionary change

Estimates of genetic variation and selection allow for quantitative predictions of evolutionary change, at least in controlled laboratory experiments. Natural populations are, however, different in many ways, and natural selection on heritable traits does not always result in phenotypic change. To test whether we were able to predict the evolutionary dynamics of a complex trait measured in a natural, heterogeneous environment, we performed, over an 8-year period, a two-way selection experiment on clutch size in a subdivided island population of great tits (Parus major). Despite strong artificial selection, there was no clear evidence for evolutionary change at the phenotypic level. Environmentally induced differences in clutch size among years are, however, large and can mask evolutionary changes. Indeed, genetic changes in clutch size, inferred from a statistical model, did not deviate systematically from those predicted. Although this shows that estimates of genetic variation and selection can indeed provide quantitative predictions of evolutionary change, also in the wild, it also emphasizes that demonstrating evolution in wild populations is difficult, and that the interpretation of phenotypic trends requires great care.     

Stability of genetic variance and covariance for reproductive characters in the face of climate change in a wild bird population

Global warming has had numerous effects on populations of animals and plants, with many species in temperate regions experiencing environmental change at unprecedented rates. Populations with low potential for adaptive evolutionary change and plasticity will have little chance of persistence in the face of environmental change. Assessment of the potential for adaptive evolution requires the estimation of quantitative genetic parameters, but it is as yet unclear what impact, if any, global warming will have on the expression of genetic variances and covariances. Here we assess the impact of a changing climate on the genetic architecture underlying three reproductive traits in a wild bird population. We use a large, long-term, data set collected on great tits (Parus major) in Wytham Woods, Oxford, and an 'animal model' approach to quantify the heritability of, and genetic correlations among, laying date, clutch size and egg mass during two periods with contrasting temperature conditions over a 40-year period (1965-1988 [cooler] vs. 1989-2004 [warmer]). We found significant additive genetic variance and heritability for all traits under both temperature regimes. We also found significant negative genetic covariances and correlations between clutch size and egg weight during both periods, and among laying date and clutch size in the colder years only. The overall G matrix comparison among periods, however, showed only a minor difference among periods, thus suggesting that genotype by environment interactions are negligible in this context. Our results therefore suggest that despite substantial changes in temperature and in mean laying date phenotype over the last decades, and despite the large sample sizes available, we are unable to detect any significant change in the genetic architecture of the reproductive traits studied.     

Realized heritability and genetic gains of three generation for superior growth in the pearl oyster Pinctada martensii

The pearl oyster Pinctada martensii is an important economic shellfish species and mainly cultured in the southern provinces of China. The species is cultured for marine pearl production. However, pearl quality has recently decreased because the cultured stocks had slow growth and mass mortalities caused by inbreeding depression. We have initiated a selective breeding program to improve the cultivated stocks since 2002. In 2004, a base population was developed by collecting the breeders from Beibuwan and Liushagang stocks. During the period of 2005–2007, a two successive generation selection for shell length in the base population was carried out to produce the second generation selected and unselected lines. In May of 2008, three types of lines were produced by selecting the breeders from the second generation selected and unselected lines. The three types of lines were designated as SS (Selected for three generations), SC (selected for the two generations) and CC (unselected for three generations). Realized heritability for the third generation, cumulative (over three generation) and current (for the third generation) genetic gains were evaluated by comparing the growth performance of three types of lines at days 8, 16, 45, 75, 180 and 360. It was found that the SS lines had significant larger mean shell length and shell height than the SC and CC lines at all sampling ages (P < 0.05). The realized heritability estimate for adult shell length for the third generation was 0.41, similar with those detected for the first and second generation. The cumulative and current genetic gains for adult shell length were 20.94% and 13.27%, respectively. The present results indicate that there exists a high genetic variation in the population and mass selection is potential to improve pearl oyster stocks.