SNP-based heritability estimation using a Bayesian approach

Heritability is a central element in quantitative genetics. New molecular markers to assess genetic variance and heritability are continually under development. The availability of molecular single nucleotide polymorphism (SNP) markers can be applied for estimation of variance components and heritability on population, where relationship information is unknown. In this study, we evaluated the capabilities of two Bayesian genomic models to estimate heritability in simulated populations. The populations comprised different family structures of either no or a limited number of relatives, a single quantitative trait, and with one of two densities of SNP markers. All individuals were both genotyped and phenotyped. Results illustrated that the two models were capable of estimating heritability, when true heritability was 0.15 or higher and populations had a sample size of 400 or higher. For heritabilities of 0.05, all models had difficulties in estimating the true heritability. The two Bayesian models were compared with a restricted maximum likelihood (REML) approach using a genomic relationship matrix. The comparison showed that the Bayesian approaches performed equally well as the REML approach. Differences in family structure were in general not found to influence the estimation of the heritability. For the sample sizes used in this study, a 10-fold increase of SNP density did not improve precision estimates compared with set-ups with a less dense distribution of SNPs. The methods used in this study showed that it was possible to estimate heritabilities on the basis of SNPs in animals with direct measurements. This conclusion is valuable in cases when quantitative traits are either difficult or expensive to measure.     

An experimental comparison of selection alternatives to plateaued response

Three alternative selection methods for extending selection limits or breaking response plateaus were compared over ten generations in a replicated model experiment using two unrelated populations of Drosophila melanogaster that no longer responded to purebred selection for high egg number, a heterotic polygenic trait. The three methods were: (1) reciprocal recurrent selection (RRS) with selection within each of the plateaued populations based solely on crossbred performance, (2) a modification of reciprocal recurrent selection (MRRS) with selection within each population based on both purebred and crossbred performance, and (3) purebred selection within a new synthetic population formed by crossing the two plateaued populations.--Conflicting estimates were obtained for heritability of purebred egg number in each of the plateaued populations. The realized heritability values and estimates from diallel analyses indicated an absence of additive genetic variation for both populations; however, estimates from conventional intraclass correlation methods were positive. The diallel analyses revealed significant amounts of nonadditive gene effects for purebred egg number in each population, while the significant gene effects for crossbred egg numbers were additive. Estimates of the genetic correlation between purebred and crossbred egg number were negative (-0.85 +/- 0.68 and -0.32 +/- 0.25) for the two base populations.--All three alternatives to continued purebred selection gave significant responses, with the average gain per generation from MRRS being significantly superior to the other two methods. Observed purebred and crossbred responses under RRS were in agreement with quantitative genetic theory. Such was not the case for MRRS, which suggested the possibility of major gene segregation.--Evidence supporting a negative genetic correlation between purebred and crossbred performance and the possibility of overdominance is presented and discussed.     

Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex

The well-documented Floridian 'Gulf/Atlantic' marine genetic disjunction provides an influential example of vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. We are engaged in a two-part study that aims to place this disjunction into a regional Caribbean Basin phylogenetic perspective using the scorched mussel Brachidontes exustus as an exemplar. Our first step, documented here, is to thoroughly characterize the genetic structure of Floridian scorched mussel populations using mitochondrial (mt) and nuclear markers. Both sets of markers recovered the expected disjunction involving sister clades distributed on alternate flanks of peninsular Florida and lineage-specific mt molecular clocks placed its origin in the Pliocene. The two sister clades had distinct population genetic profiles and the Atlantic clade appears to have experienced an evolutionarily recent bottleneck, although plots of the relative estimates of N through time are consistent with its local persistence through the last Ice Age Maximum. Our primary novel result, however, was the discovery that the Gulf/Atlantic disjunction represents but one of three cryptic, nested genetic discontinuities represented in Floridian scorched mussel populations. The most pronounced phylogenetic split distinguished the Gulf and Atlantic sister clades from two additional nested cryptic sister clades present in samples taken from the southern Florida tropical marine zone. Floridian populations of B. exustus are composed of four cryptic taxa, a result consistent with the hypothesis that the Gulf/Atlantic disjunction in this morphospecies is but one of multiple latent regional genetic breakpoints.     

不同利用方式和载畜率对内蒙古典型草原群落初级生产力和植物补偿性生长的影响

基于2005年6月开始的放牧控制实验, 研究了不同草地利用方式和放牧强度对内蒙古典型羊草(Leymus chinensis)草原群落初级生产力和补偿性生长的影响。草地利用方式包括: 传统放牧、传统割草和放牧与割草轮换利用(混合利用)。结果表明: 传统放牧和混合利用方式下, 羊草群落地上生物量均随放牧强度增加逐渐降低。高载畜率下, 羊草群落地上净初级生产力表现为: 混合利用>传统割草>传统放牧, 说明混合利用方式优于传统放牧和传统割草利用方式; 而低载畜率则有利于草原的可持续利用和植物的补偿性生长。这一实验结果在一定程度上验证了放牧优化假说。在不同利用方式、地形因素的影响和采用不同的群落净生长量计算方法时, 随着放牧强度的变化, 等补偿、超补偿和欠补偿效应都可能出现。在低载畜率下, 群落大多表现出等补偿生长, 在高载畜率下, 群落大多表现出欠补偿生长。植物群落的补偿性生长与载畜率的关系可以用开口向下的二次函数或者斜率为负的线性函数模拟。说明随着载畜率的增加, 一些系统表现为欠补偿生长, 而另一些系统则表现为超补偿生长, 这可能与植物群落组成、地形部位(平地、坡地)和载畜率以及净生长量的计算方法有关。     

Heritability of sperm length in the bumblebee Bombus terrestris

Sperm length is highly variable, both between and within species, but the evolutionary significance of this variation is poorly understood. Sexual selection on sperm length requires a significant additive genetic variance, but few studies have actually measured this. Here we present the first estimates of narrow sense heritability of sperm length in a social insect, the bumblebee Bombus terrestris. In spite of a balanced and straightforward rearing design of colonies, and the possibility to replicate measurements of sperm within single males nested within colonies, the analysis proved to be complex. Several appropriate statistical models were derived, each depending on different assumptions. The heritability estimates obtained ranged from h ² = 0.197 ± 0.091 to h ² = 0.429 ± 0.154. All our estimates were substantially lower than previous estimates of sperm length heritability in non-social insects and vertebrates.     

松嫩平原光稃茅香无性系种群的营养繁殖特征

光稃茅香是典型的无性系禾草 .分蘖节可繁殖 2个世代 ,最多存活 3个年度 .根茎最多存活 2个年度 .无性系种群的分蘖株和根茎均有 2个龄级 ,并均以 1龄级占较大比重 .无性系潜在种群由冬性苗和根茎芽所组成 .以潜在种群的数量估计 ,在割草场混生群落中将保持现有的地位和作用 ,在放牧场的优势种群落中将增强其地位和作用 .     

Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long‐term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation‐derived maternal links and microsatellite‐derived paternal links; (ii) Pedigree 2, using SNP‐derived assignment of both maternity and paternity; and (iii) whole‐genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.     

Heritability of resting metabolic rate in a wild population of blue tits

We report the first study with the aim to estimate heritability in a wild population, a nest box breeding population of blue tits. We estimated heritability as well as genetic and phenotypic correlations of resting metabolic rate (RMR), body mass and tarsus length with an animal model based on data from a split cross‐fostering experiment with brood size manipulations. RMR and body mass, but not tarsus length, showed significant levels of explained variation but for different underlying reasons. In body mass, the contribution to the explained variation is mainly because of a strong brood effect, while in RMR it is mainly because of a high heritability. The additive variance in RMR was significant and the heritability was estimated to 0.59. The estimates of heritability of body mass (0.08) and tarsus length (0.00) were both low and based on nonsignificant additive variances. Thus, given the low heritability (and additive variances) in body mass and tarsus length the potential for direct selection on RMR independent of the two traits is high in this population. However, the strong phenotypic correlation between RMR and mass (0.643 ± 0.079) was partly accounted for by a potentially strong, although highly uncertain, genetic correlation (1.178 ± 0.456) between the two traits. This indicates that the additive variance of body mass, although low, might still somewhat constrain the independent evolvability of RMR.     

放牧干扰对根茎冰草无性系种群年龄结构的影响

根茎冰草（Agropyron michnoi)是典型的无性系禾草。在松嫩平原,根茎冰草的分蘖节最老为４龄,可存活５个年度。不同季节的放牧干扰可导致根茎冰草无性系种群分蘖株的年龄结构发生变化,全年放牧样地和夏秋休牧样地均为稳定型年龄结构,两个冬季放牧样地均为增长型年龄结构。１龄分蘖株的生产力和营养繁殖力力均最大。４龄分蘖株均已丧失了营养繁殖力。营养繁殖芽的年龄结构可以更好地预测预报无性系种群和群落的未来。全年放牧可保护稳定型年龄结构,冬季放牧可保持增长型年龄结构,夏秋休牧可使种群发展为增长型年龄结构,两个冬季放牧样地将仍然保持单优势种群落,全年放牧地将仍为混生群落,夏季林牧样地具有向着单优势种群落演替的潜在趋势。     

Is cladogenesis heritable?

The heritability of speciation rates and extinction risks is a crucial parameter in models of macroevolution, but little direct evidence has been available to assess the occurrence, strength, or generality of this heritability. We tested for heritability using correlations between ancestral and descendent branch lengths in phylogenetic trees, an approach first applied to a bird phylogeny by Harvey et al. (1991, pages 123-137 in Genes in ecology [R. J. Berry et al., eds.], Blackwell Scientific, Oxford). We applied Harvey et al.'s test to some of the largest DNA sequence-based phylogenetic analyses published to date for plants, insects, fungi, and bacteria. If one of two parent lineages splits first and if this is the case for any heritable reason, then on average we expect its daughter lineages to also split first. We also used a randomization procedure to assess significance of branch length heritability. Using maximum parsimony and maximum likelihood branch lengths and trees made ultrametric after nonparametric rate smoothing or by enforcing a molecular clock, we found a pattern for most clades consistent with heritable net cladogenesis. Heritability of cladogenesis may be a general phenomenon, detectable across a large number of lineages and a broad range of taxa.     

Burning and Grazing Management in a California Grassland: Growth, Mortality, and Recruitment of Nassella pulchra

Abstract Annual grasslands in California are often managed with seasonal grazing and prescribed burning on the assumption that such practices have long‐term benefits for native species. Mature native perennial bunchgrasses, particularly Nassella pulchra (purple needlegrass), are often the focal species, although very little is known about responses at different life history stages. Thus, important questions remain about long‐term population dynamics of both mature plants and seedling recruitment. In plots receiving repeated grazing and burning events over 7 years, mortality of mature plants was threefold higher on mounds than on intermounds and likely reflected increased competition intensity associated with increased resource availability in deeper soil. Burning and grazing treatments had strong positive effects on basal area of mature N. pulchra. However, plants in grazed plots that were not burned contained considerable standing dead biomass. Topographic location strongly influenced growth as intermound plants grew relatively more than mound plants, but the effects on growth of burning and grazing did not vary with topographic location. In mapped plots N. pulchra recruitment was very low, and overall density dropped an average of 31%. However, a significant time‐by‐burning effect indicated that survival was significantly higher in burned plots. After 7 years of repeated treatments, effects of burning and grazing management on mature N. pulchra were positive but not for all phenological stages. Understanding long‐term influence of management on bunchgrass populations may not be easy to determine because short‐term results may not reflect long‐term responses and some life cycle dynamics may be observed only over very long periods.     

Indirect effects of cattle grazing on shrub spatial pattern in a mediterranean scrub community

Identifying the mechanisms and interactions that influence the spatial structure of vegetation is important for both scientific and practical purposes. Grazing is one of the most fundamental interactions in ecology but so far its effect on vegetation spatial pattern received little attention. In this study we propose a conceptual model that can be used to predict the effect of grazing on shrub spatial pattern in water-limited ecosystems where shrubs grow within a matrix of annual vegetation. According to the model, grazing may increase or decrease clumping in shrub distribution, depending on (1) the relative palatability of shrubs vs. annual plants to the herbivores, and (2) the manner (negative or positive) by which adult shrubs and annual plants affect the establishment of shrub seedlings. We tested our model in a Mediterranean scrub ecosystem by analyzing the development of shrub spatial pattern over a period of 40 years in plots characterized by contrasting intensities of cattle grazing. As predicted by the model, all plots showed a clumped pattern of shrub distribution in the absence of cattle grazing while intense cattle grazing reduced the clumpiness of the vegetation and generated a more random pattern of shrub distribution. Interestingly, plots representing the two grazing regimes did not differ significantly in their shrub cover, suggesting that shrub spatial pattern may be more sensitive to grazing than overall shrub cover.     

Investigating the interaction between ungulate grazing and resource effects on Vaccinium myrtillus populations with integral projection models

Dense ungulate populations in forest accompanied by high grazing intensities have the potential to affect plant population dynamics, and such herbivory effects on populations are hypothesised to differ along environmental gradients. We investigated red deer grazing and resource interaction effects on the performance and dynamics of the functionally important boreal shrub Vaccinium myrtillus using integral projection models (IPMs). We sampled data from 900 V. myrtillus ramets in 30 plots in two consecutive years across the boreo-nemoral pine forest on the island Svanøy, western Norway. The plots spanned two environmental gradients: a red deer grazing intensity gradient (assessed by Cervus elaphus faecal pellets), and a relative resource gradient (DCA-ordination of species composition). The use of IPMs enabled projections of population growth rate (λ) using continuous plant size instead of forcing stage division upon the demographic data. We used the environmental gradients as continuous variables to explain the dynamics of V. myrtillus populations and found that both increasing grazing intensity and resource levels negatively affected λ of the V. myrtillus populations. Interestingly, these factors interacted: the negative effects of grazing were strongest in the resource-rich vegetation, and higher resource levels reduced λ more strongly than at low resource levels when grazing intensities became higher. Populations with λ > 1 were projected if the grazing intensity was less than or equal to the mean grazing intensity on the island, and indicated that V. myrtillus is relatively tolerant of grazing. Variance decomposing showed that the decrease of λ along the grazing gradient, both at low and high resource levels, was largely caused by reductions in plant growth. The use of IPMs together with important environmental gradients offered novel possibilities to study the synthesised effect of different factors on plant population dynamics. Here, we show that the population response of an abundant boreal shrub to ungulate grazing depends on resource level.     

How does selfing affect the genetic variance of quantitative traits? An updated meta‐analysis on empirical results in angiosperm species

Most theoretical works predict that selfing should reduce the level of additive genetic variance available for quantitative traits within natural populations. Despite a growing number of quantitative genetic studies undertaken during the last two decades, this prediction is still not well supported empirically. To resolve this issue and confirm or reject theoretical predictions, we reviewed quantitative trait heritability estimates from natural plant populations with different rates of self‐fertilization and carried out a meta‐analysis. In accordance with models of polygenic traits under stabilizing selection, we found that the fraction of additive genetic variance is negatively correlated with the selfing rate. Although the mating system explains a moderate fraction of the variance, the mean reduction of narrow‐sense heritability values between strictly allogamous and predominantly selfing populations is strong, around 60%. Because some nonadditive components of genetic variance become selectable under inbreeding, we determine whether self‐fertilization affects the relative contribution of these components to genetic variance by comparing narrow‐sense heritability estimates from outcrossing populations with broad‐sense heritability estimated in autogamous populations. Results suggest that these nonadditive components of variance may restore some genetic variance in predominantly selfing populations; it remains, however, uncertain how these nonadditive components will contribute to adaptation.     

Heritability of eleven metabolic phenotypes in Danish and Chinese twins: A cross‐population comparison

Objectives : A twin‐based comparative study on the genetic influences in metabolic endophenotypes in two populations of substantial ethnic, environmental, and cultural differences was performed. Design and Methods : Data on 11 metabolic phenotypes including anthropometric measures, blood glucose, and lipids levels as well as blood pressure were available from 756 pairs of Danish twins (309 monozygotic and 447 dizygotic twin pairs) with a mean age of 38 years (range: 18‐67) and from 325 pairs of Chinese twins (183 monozygotic and 142 dizygotic twin pairs) with a mean age of 40.5 years (range: 18‐69). Twin modeling was performed on full and nested models with the best fitting models selected. Results : Heritability estimates were compared between Danish and Chinese samples to identify differential genetic influences on each of the phenotypes. Except for hip circumference, all other body measures exhibited similar heritability patterns in the two samples with body weight showing only a slight difference. Higher genetic influences were estimated for fasting blood glucose level in Chinese twins, whereas the Danish twins showed more genetic regulation over most lipids phenotypes. Systolic blood pressure was more genetically controlled in Danish than in Chinese twins. Conclusions : Metabolic endophenotypes show disparity in their genetic determinants in populations under distinct environmental conditions.     

Effects of livestock exclusion on density,survival and biomass of the perennial sagebrush grass Hymenachne pernambucense (Poaceae) from a temperate fluvial wetland

In Argentina, the intensification of soybean production has displaced a substantial proportion of cattle ranching to fluvial wetlands such as those in the Delta of the Paraná River. Cattle grazing affects structure and dynamics of native forage plants but there is little information on this impact in populations from fluvial wetlands. This study addresses the effect of cattle ranching on density, survival, mean life-span and aerial biomass of Hymenachne pernambucense (Poaceae), an important forage species in the region. The study was carried out monthly for one year in permanents plots subject to continuous grazing and plots excluded from grazing in the Middle Delta of the Paraná River. In plots excluded from grazing, tillers showed significantly higher population density and survival, and a two-fold increase in mean life-span, while continuous grazing decreased survival of cohorts. The largest contribution to tiller density in ungrazed and grazed populations was made by spring and summer cohorts, respectively. Total and green biomass were significantly higher in the ungrazed population, with highest differences in late spring-early summer. Cattle grazing affected the relationship between tiller density and green biomass suggesting that cattle prefer sprouts because they are more palatable and nutritious than older tissue.     

Field heritability of a plant adaptation to fire in heterogeneous landscapes

The strong association observed between fire regimes and variation in plant adaptations to fire suggests a rapid response to fire as an agent of selection. It also suggests that fire‐related traits are heritable, a precondition for evolutionary change. One example is serotiny, the accumulation of seeds in unopened fruits or cones until the next fire, an important strategy for plant population persistence in fire‐prone ecosystems. Here, we evaluate the potential of this trait to respond to natural selection in its natural setting. For this, we use a SNP marker approach to estimate genetic variance and heritability of serotiny directly in the field for two Mediterranean pine species. Study populations were large and heterogeneous in climatic conditions and fire regime. We first estimated the realized relatedness among trees from genotypes, and then partitioned the phenotypic variance in serotiny using Bayesian animal models that incorporated environmental predictors. As expected, field heritability was smaller (around 0.10 for both species) than previous estimates under common garden conditions (0.20). An estimate on a subset of stands with more homogeneous environmental conditions was not different from that in the complete set of stands, suggesting that our models correctly captured the environmental variation at the spatial scale of the study. Our results highlight the importance of measuring quantitative genetic parameters in natural populations, where environmental heterogeneity is a critical aspect. The heritability of serotiny, although not high, combined with high phenotypic variance within populations, confirms the potential of this fire‐related trait for evolutionary change in the wild.     

Alternative spatial sampling in studies of plant demography: consequences for estimates of population growth rate

Ecologists commonly use matrix models to study the population dynamics of plants. Most studies of plant demography use plot-based methods to collect data, in part, because mapped individuals are easier to relocate in subsequent surveys and survey methods can be standardized among sites. However, there is tremendous variation among studies, both in terms of plot arrangement and the total area sampled. In addition, there has been little discussion of how alternative sampling arrangements influence estimates of population growth rates (λ) calculated with matrix models. We surveyed the literature to determine what sampling designs are most used in studies of plant demography using matrix models. We then used simulations of three common sampling techniques—using a single randomly placed plot, multiple randomly placed plots, and systematically distributed plots—to evaluate how these alternative strategies influenced the precision of estimates of λ. These simulations were based on long-term demographic data collected on 13 populations of the Amazonian understory herb Heliconia acuminate (Heliconiaceae). We found that the method used to collect data did not affect the bias or precision of estimates in our system—a surprising result, since the advantage in efficiency that is gained from systematic sampling is a well-known result from sampling theory. Because the statistical advantage of systematic sampling is most evident when there is spatial structure in demographic vital rates, we attribute this result to the lack of spatially structured vital rates in our focal populations. Given the likelihood of spatial autocorrelation in most ecological systems, we advocate sampling with a systematic grid of plots in each study site, as well as that researchers ensure that enough area is sampled—both within and across sites—to encompass the range of spatial variation in plant survival, growth, and reproduction.     

Genetic background,and not ontogenetic effects,affects avian seasonal timing of reproduction

Avian seasonal timing is a life‐history trait with important fitness consequences and which is currently under directional selection due to climate change. To predict micro‐evolution in this trait, it is crucial to properly estimate its heritability. Heritabilities are often estimated from pedigreed wild populations. As these are observational data, it leaves the possibility that the resemblance between related individuals is not due to shared genes but to ontogenetic effects; when the environment for the offspring provided by early laying pairs differs from that by late pairs and the laying dates of these offspring when they reproduce themselves is affected by this environment, this may lead to inflated heritability estimates. Using simulation studies, we first tested whether and how much such an early environmental effect can inflate heritability estimates from animal models, and we showed that pedigree structure determines by how much early environmental effects inflate heritability estimates. We then used data from a wild population of great tits (Parus major) to compare laying dates of females born early in the season in first broods and from sisters born much later, in second broods. These birds are raised under very different environmental conditions but have the same genetic background. The laying dates of first and second brood offspring do not differ when they reproduce themselves, clearly showing that ontogenetic effects are very small and hence, family resemblance in timing is due to genes. This finding is essential for the interpretation of the heritabilities reported from wild populations and for predicting micro‐evolution in response to climate change.