The population growth consequences of variation in individual heterozygosity

Heterozygosity has been associated with components of fitness in numerous studies across a wide range of taxa. Because heterozygosity is associated with individual performance it is also expected to be associated with population dynamics. However, investigations into the association between heterozygosity and population dynamics have been rare because of difficulties in linking evolutionary and ecological processes. The choice of heterozygosity measure is a further issue confounding such studies as it can be biased by individual differences in the frequencies of the alleles studied, the number of alleles at each locus as well as the total number of loci typed. In this study, we first examine the differences between the principal metrics used to calculate heterozygosity using long-term data from a marked population of Soay sheep (Ovis aries). Next, by means of statistical transformation of the homozygosity weighted by loci index, we determine how heterozygosity contributes to population growth in Soay sheep by modelling individual contributions to population growth (p(t(i))) as a function of several covariates, including sex, weight and faecal egg count--a surrogate of parasitic nematode burden in the gut. We demonstrate that although heterozygosity is associated with some components of fitness, most notably adult male reproductive success, in general it is only weakly associated with population growth.     

Approaches to mapping genetically correlated complex traits

Our Markov chain Monte Carlo (MCMC) methods were used in linkage analyses of the Framingham Heart Study data using all available pedigrees. Our goal was to detect and map loci associated with covariate-adjusted traits log triglyceride (lnTG) and high-density lipoprotein cholesterol (HDL) using multipoint LOD score analysis, Bayesian oligogenic linkage analysis and identity-by-descent (IBD) scoring methods. Each method used all marker data for all markers on a chromosome. Bayesian linkage analysis detected a linkage signal on chromosome 7 for lnTG and HDL, corroborating previously published results. However, these results were not replicated in a classical linkage analysis of the data or by using IBD scoring methods.We conclude that Bayesian linkage analysis provides a powerful paradigm for mapping trait loci but interpretation of the Bayesian linkage signals is subjective. In the absence of a LOD score method accommodating genetically complex traits and linkage heterogeneity, validation of these signals remains elusive.     

Multilocus heterozygosity, parental relatedness and individual fitness components in a wild mountain goat, Oreamnos americanus population

Matings between relatives lead to a decrease in offspring genetic diversity which can reduce fitness, a phenomenon known as inbreeding depression. Because alpine ungulates generally live in small structured populations and often exhibit a polygynous mating system, they are susceptible to inbreeding. Here, we used marker-based measures of pairwise genetic relatedness and inbreeding to investigate the fitness consequences of matings between relatives in a long-term study population of mountain goats ( Oreamnos americanus ) at Caw Ridge, Alberta, Canada. We first assessed whether individuals avoided mating with kin by comparing actual and random mating pairs according to their estimated genetic relatedness, which was derived from 25 unlinked polymorphic microsatellite markers and reflected pedigree relatedness. We then examined whether individual multilocus heterozygosity H , used as a measure of inbreeding, was predicted by parental relatedness and associated with yearling survival and the annual probability of giving birth to a kid in adult females. Breeding pairs identified by genetic parentage analyses of offspring that survived to 1 year of age were less genetically related than expected under random matings. Parental relatedness was negatively correlated with offspring H , and more heterozygous yearlings had higher survival to 2 years of age. The probability of giving birth was not affected by H in adult females. Because kids that survived to yearling age were mainly produced by less genetically related parents, our results suggest that some individuals experienced inbreeding depression in early life. Future research will be required to quantify the levels of gene flow between different herds, and evaluate their effects on population genetic diversity and dynamics.     

Novel polymorphisms of goat growth hormone and growth hormone receptor genes and their effects on growth traits

In this study, the polymorphisms of growth hormone (GH) gene 5' promoter region and intron 8, exons 4 and 10 of growth hormone receptor (GHR) gene were analyzed in Xinong Saanen goats (SG) and Boer goats (BG). Two alleles (A and B) and three genotypes (AA, AB and BB) were detected at P1 locus of GH gene, and two alleles (G and T) and two genotypes (GG and GT) were detected at P4 locus of GHR gene by PCR-SSCP analysis. In addition, two single nucleotide polymorphisms (SNPs)-A73C (P1 locus) and G114T (P4 locus), were identified by DNA sequencing. The frequencies of alleles A and B in the two goat breeds were 0.61-0.62, and 0.39-0.38, respectively, and the frequencies of alleles G and T in the two goat breeds were 0.82-0.86, and 0.18-0.14, respectively. The SNP loci were in Hardy-Weinberg disequilibrium in both goat breeds (P<0.05). Polymorphisms of GH and GHR genes were shown to be associated with growth traits in BG breed. AA and GG genotypes were associated with superior growth traits in 1-, 2- and 3-month old individuals. Hence, AA and GG genotypes are suggested to be a molecular marker for superior growth traits in BG breed.     

genhet: an easy-to-use R function to estimate individual heterozygosity

genhet is an R function which calculates the five most used estimates of individual heterozygosity. The advantage of this program is that it can be applied to any diploid genotype dataset, without any limitation in the number of individuals, loci or alleles. Its detailed manual should allow people who have never used R before to make the function work quite easily. The program is freely available at http://www.aureliecoulon.net/research/ac-computer-programs.html.     

Relationships between individual behavioural traits and post-weaning growth in segregated early-weaned piglets

Piglets' individual behavioural traits have been studied in the last decade but no report has linked these traits with growth. This experiment was conducted to determine if behavioural traits of segregated early-weaned piglets could be good predictors of their post-weaning growth and, thus, help to predict their adaptation to early weaning. Following segregated early weaning at 17+/-1 days old, 252 piglets were submitted to three tests between 20 and 25 days of age: open-field, reaction to humans and rank order based on competition for a restricted-access feeder. The body weight of each piglet was measured the day before weaning and once a week for the next 4 weeks. A principal component analysis yielded five factors with an Eigenvalue higher than 0.90 that accounted for 81% of the total variation between individuals: reaction to humans (25%), active response to stress (21%), passive response to stress (14%), feeding behaviour (10%) and rank order (9%). Passive reaction to stress was associated with better weight gain during the first week post-weaning (r=0.18; P=0.01), and a positive correlation was found between social status and weight gain during the 4 weeks following weaning (-0.15相似文献   

Estimating genetic and phenotypic diversity in a northern hoverfly reveals lack of heterozygosity correlated with significant fluctuating asymmetry of wing traits

The genetic structure and phenotypic diversity of a population of Cheilosia naruska Haarto and Kerppola, 2007 (Diptera, Syrphidae) from Lapland, Finland, was examined through allozyme electrophoresis and wing morphometrics. The morphological identification of the species was verified molecularly using partial sequences of mitochondrial COI and the nuclear ribosomal ITS2 genes comparing with corresponding sequences of a paratype of the taxon. Based on protein electrophoresis, out of 12 analyzed allozyme loci, only one locus (Me) was found to be polymorphic. The low genetic variability was further evidenced by the absence of heterozygote genotypes. Fluctuating asymmetry was used as a measure of developmental stability. For this we used different wing traits that were estimated using both wing landmark positions and metric traits. Procrustes ANOVA and Canonical variate analysis revealed asymmetry in wing metric and wing shape and size, and within each sex considered separately. Principal component analysis revealed similar multivariate patterns of landmark covariation between within-individual variability (fluctuating asymmetry) and variation among individuals. Finally, the observed association between lack of heterozygosity and high level of asymmetry is discussed in light of conservation.     

Factors affecting placental traits and relationships of placental traits with neonatal behaviour in goat

The relationships between placental characteristics and litter weight, factors affecting these characteristics, and the relationship between these characteristics and neonatal behaviour of goat kids were investigated in this study. The study was carried out over three consecutive years and animal material consisted of total 152 Turkish Saanen goats and their 230 kids. The results of the study demonstrated that there were positive correlations between litter weight (LW), cotyledon number (CN), placental weight (PW) (r=0.64 and 0.76, P<0.01), but there was negative correlation between LW and cotyledon density (CD) (r=-0.42, P<0.01). CD was negatively correlated with PW (r=-0.61, P<0.01). CN and PW were influenced by the parity of doe, birth type-sex combination, buck within years and year of the study. On the other hand, parity and birth type-sex combination had no effect on PE (P>0.05), but buck within year affected placental efficiency (P<0.01). CD was only influenced by the parity of doe (P<0.01). Duration of birth (D) was not significantly related with CD, but if CD declined, it prolonged (r=-0.23, P>0.05). There were strong relationships between CD and birth-to-standing (B-St), and CD and birth-to-suckling (B-Su) (r=-0.42 and -0.51, P=0.01 and P<0.01).The results of the present study have shown similarities to the findings of the studies in sheep. Further studies are required to investigate the basis of the relationship between CD and neonatal behaviour.     

Variance in quantitative traits due to linked dominant genes and variance in heterozygosity in small populations

The influence of small population size (N) on the genetic variance within and between randomly bred unselected lines, with selfing permitted, is investigated for a model of a quantitative trait determined by linked genes that show dominance within loci but are additive over loci. Formulae for within-line variance include terms in linkage disequilibrum, which occurs by chance in the lines and these are evaluated in terms of N, map length and gene number.—The expected variance within lines is increased by this disequilibrium, quite substantially if there are many loci, with most of the increase being between or within full-sib families and almost no change expected between half-sib families or in the covariance of offspring and parent. If all loci are unlinked, there is no increase in variance within full-sib families. The variance between lines is little affected by disequilibrum generated by chance.—Expressions for the variance between individuals in heterozygosity over the whole genome are special cases of those for the variance due to linked dominated genes, and formulae are given and evaluated. The coefficient of variation of heterozygosity is at least (see PDF) and can be much higher for species with few chromosomes.     

Inbreeding,microsatellite heterozygosity,and morphological traits in Lipizzan horses

While the negative effects of inbreeding and reduced heterozygosity on fecundity and survival are well established, only a few investigations have been carried out concerning their influence on morphological traits. This topic is of particular interest for a small and closed population such as the Lipizzan horse. Thus, 27 morphological traits were measured in 360 Lipizzan mares and were regressed on the individual inbreeding coefficients, as well as on the individual heterozygosity and mean squared distances (mean d(2)) between microsatellite alleles within an individual. Both individual heterozygosity and mean d(2) were based on 17 microsatellite loci dispersed over 14 chromosomes. The results obtained by multivariate analysis reveal significant effects of stud (P <.0001), age at measurement (P <.0001), and mean d(2) (P =.0143). In univariate analyses, significant associations were obtained between length of pastern-hindlimbs and inbreeding coefficient (P <.01), length of cannons-hindlimb and mean d(2) (P <.01), and length of neck and mean d(2) (P <.001). After adjustment of single-test P values for multiple tests (Hochberg's step-up Bonferroni method), only the association of the length of neck and mean d(2) remained significant (P =.0213). Thus, no overall large effects of inbreeding, microsatellite heterozygosity, and mean d(2) on morphological traits were observed in the Lipizzan horse.     

Fluorescence contributions of the individual Trp residues in goat alpha-lactalbumin

Goat alpha-lactalbumin (GLA) contains four tryptophan (Trp) residues. In order to obtain information on the fluorescence contribution of the individual Trp residues in native GLA, we recorded the fluorescence spectra of four GLA mutants, W26F, W60F, W104F, and W118F, in each of which a single Trp residue was replaced with phenylalanine (Phe). Comparison of the fluorescence spectra of the four mutants with that of wild-type GLA indicated that, in native GLA, three Trp residues (Trp60, Trp104, and Trp118) are strongly quenched and account for the partial indirect quenching of Trp26. As a consequence, the fluorescence of wild-type GLA and of the mutants W60F, W104F, and W118F mainly results from Trp26. An inspection of the crystal structure indicated that, in addition to the disulfide bonds that are in direct contact with the indole groups of Trp60 and Trp118, backbone peptide bonds that are in direct contact with the indole groups of Trp60, Trp104, and Trp118, contribute to the direct quenching effects. Interestingly, the lack of direct quenching of Trp26 explains why the cleavage of disulfide bonds by UV light is mediated more by the highly fluorescent Trp26 than by the less fluorescent Trp104 and Trp118.     

Realized correlated responses to artificial selection on pre-adult life-history traits in a butterfly

We use artificial selection experiments targeted on egg size, development time or pupal mass within a single butterfly population followed by a common-garden experiment to explore the interactions among these life-history traits. Relationships were predicted to be negative between egg size and development time, but to be positive between development time and body size and between egg size and body size. Correlated responses to selection were in part inconsistent with these predictions. Although there was evidence for a positive genetic correlation between egg and body size, there was no support for genetic correlations between larval development time and either egg size or pupal mass. Phenotypic correlations among the three target traits of selection gave comparable results for the relationships between egg mass and development time (no association) as well as between egg mass and pupal mass (positive association), but not for the relation between development time and pupal mass (negative phenotypic correlation). In summary, correlated responses to selection as well as phenotypic correlations were rather unpredictable. The impact of variation in acquisition and allocation of energy as well as of the benign conditions used deserve further investigation.     

Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations

Using multilocus individual heterozygosity, a method is developed to estimate the outcrossing rates of a population over a few previous generations. Considering that individuals originate either from outcrossing or from n successive selfing generations from an outbred ancestor, a maximum-likelihood (ML) estimator is described that gives estimates of past outcrossing rates in terms of proportions of individuals with different n values. Heterozygosities at several unlinked codominant loci are used to assign n values to each individual. This method also allows a test of whether populations are in inbreeding equilibrium. The estimator's reliability was checked using simulations for different mating histories. We show that this ML estimator can provide estimates of outcrossing rates for the final generation outcrossing rate (t(0)) and a mean of the preceding rates (t(p)) and can detect major temporal variation in the mating system. The method is most efficient for low to intermediate outcrossing levels. Applied to nine populations of wheat, this method gave estimates of t(0) and t(p). These estimates confirmed the absence of outcrossing t(0) = 0 in the two populations subjected to manual selfing. For free-mating wheat populations, it detected lower final generation outcrossing rates t(0) = 0-0.06 than those expected from global heterozygosity t = 0.02-0.09. This estimator appears to be a new and efficient way to describe the multilocus heterozygosity of a population, complementary to Fis and progeny analysis approaches.     

Influence of mother's heterozygosity on the variation of anthropometric traits in newborns]

The relationship between mother's heterozygosity as revealed by 14 polymorphic loci and variation of the set of anthropometric traits were studied in normal singleton newborns (174 boys, 127 girls). Statistically significant negative correlation between mother's heterozygosity and the index of fluctuating asymmetry was found in girls. Variances of four traits--body weight, body length, circumference of head and breast measured by first principal component, and mean number of minor deviations from development (stigma) are shown to be minimal in the children born by mothers with the average level of heterozygosity. The groups of newborns with different level of mother's heterozygosity are characterized by different combinations of first principal component, stigma, and the index of fluctuating asymmetry. It is concluded from the whole set of data that children born by mothers with the average level of heterozygosity have the highest level of viability.     

Effect of selection on genetic parameters of correlated traits

Summary Changes in genetic parameters of correlated traits due to the buildup of linkage (gametic phase) disequilibrium from repeated truncation selection on a single trait are studied. After several generations of selection, an equilibrium is approached where there are no further changes in genetic parameters and limiting values are reached. Formulae are derived under an infinitesimal model for these limiting values of genetic variances and covariances, heritabilities, and genetic correlations between traits directly and indirectly selected. Changes from generation zero to the limit in all these parameters become greater as heritability of the trait under direct selection increases and, to a lesser extent, as intensity of selection increases. Change in heritability of a trait under indirect selection also increases as the absolute value of the correlation between the trait under indirect and the trait under direct selection increases. The change is maximum when the initial value of heritability is close to 0.5 and insignificant when the initital value is close to zero or one. Change in the genetic correlation between the trait under direct selection and the trait under indirect selection is maximum when its initial value is close to ±0.6 and insignificant when its initial value is close to zero or ±1. Heritability of the trait indirectly selected and genetic correlation between that trait and the trait directly selected always decrease in absolute value, whereas genetic correlation between two traits indirectly selected can either decrease or increase in absolute value. It is suggested that use be made of formulae at selection equilibrium in the prediction of correlated responses after several generations of selection.     

Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex

Heterozygosity–fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways.     

Natural selection and the traits of individual organisms

It has recently been argued that origin essentialism regarding individual organisms entails that natural selection does not explain why individual organisms have the traits that they do. This paper defends this and related theses against Mohan Matthens recent objections.