The aunt and uncle effect: an empirical evaluation of the confounding influence of full sibs of parents on pedigree reconstruction.

This study used simulations and a known two-generation pedigree of chinook salmon (Oncorhynchus tshawytscha) to evaluate the effect of full sibs of parents on pedigree reconstruction. Parentage analysis was conducted on 100 parent pair-offspring relationships from pedigrees with unrelated (simulation) and related (chinook salmon) candidate parents. Parentage assignment success for the chinook salmon was lower than in the simulated populations. For example, the six most variable loci (mean H(E) = 0.87) provided a mean of 97% unambiguous assignments in the simulated population and 67% unambiguous assignments for the chinook salmon. Estimates of the pairwise relatedness coefficient ((xy)) for most nonexcluded false parents and true parents of chinook salmon offspring exceeded 0.50. These results support the conclusion that closely related candidate parents decrease the power of genetic markers for pedigree reconstruction based on exclusion. Ambiguous parentage may be resolved using single parent- and parent pair-offspring likelihood analysis, however, these methods should be used with caution and they are not replacements for using more loci when many candidate parents are full sibs.     

Relative accuracy of three common methods of parentage analysis in natural populations

Parentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioural processes in natural populations. However, a number of different assignment methods have emerged in common use and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents and the presence of genotyping errors. Here, we examine how these factors affect the accuracy of three popular parentage inference methods (colony , famoz and an exclusion‐Bayes’ theorem approach by Christie (Molecular Ecology Resources, 2010a, 10, 115) to resolve true parent–offspring pairs using simulated data. Our findings demonstrate that accuracy increases with the number and diversity of loci. These were clearly the most important factors in obtaining accurate assignments explaining 75–90% of variance in overall accuracy across 60 simulated scenarios. Furthermore, the proportion of candidate parents sampled had a small but significant impact on the susceptibility of each method to either false‐positive or false‐negative assignments. Within the range of values simulated, colony outperformed FaMoz, which outperformed the exclusion‐Bayes’ theorem method. However, with 20 or more highly polymorphic loci, all methods could be applied with confidence. Our results show that for parentage inference in natural populations, careful consideration of the number and quality of markers will increase the accuracy of assignments and mitigate the effects of incomplete sampling of parental populations.     

Comparing parentage inference software: reanalysis of a red deer pedigree

Knowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent–offspring relationships. However, Cervus does not make use of all available information: additional phenotypic information may exist predicting parent–offspring relationships, and additional genetic information may be exploited by simultaneously considering multiple types of relationships rather than just pairwise or just parent–offspring relationships. Here we reanalyse data from a wild red deer population using two programs capable of using this additional information, MasterBayes and COLONY2, and quantify the impact of these alternative approaches by comparison with a ‘known pedigree’ estimated using a larger suite of microsatellite makers for a subset of the population. The use of phenotypic information and multiple relationships increased the number of correct assignments. We highlight the differences between programs, particularly the use of population‐ rather than individual‐level statistical confidence in Cervus. We conclude that the use of additional information allows MasterBayes and COLONY2 to assign more correct paternities, whereas their use of individual‐ rather than population‐level confidence generates fewer erroneous assignments. We suggest that maximal information may be gained by combining outputs from different programs. Higher accuracy and completeness of pedigree information will improve parameters estimated from pedigree information in studies of natural populations.     

Detection of linkage between marker loci and loci affecting quantitative traits in crosses between segregating populations

Summary By making use of pedigree information and information on marker-genotypes of the parent and F-1 individuals crossed to form an F-2 population, it is possible to carry out a linkage analysis between marker loci and loci affecting quantitative traits in a cross between segregating parent populations that are at fixation for alternative alleles at the QTL, but share the same alleles at the marker loci. For two-allele systems, depending on marker allele frequencies in the parent populations, 2–4 times as many F-2 offspring will have to be raised and scored for markers and quantitative traits in order to provide power equivalent to that obtained in a cross between fully inbred lines. Major savings in number of F-2 offspring raised can be achieved by scoring each parent pair for a large number of markers in each chromosomal region and scoring F-1 and F-2 offspring only for those markers for which the parents were homozygous for alternative alleles. For multiple allele systems, particularly when dealing with hypervariable loci, only 10%–20% additional F-2 offspring will have to be raised and scored to provide power equivalent to that obtained in a cross between inbred lines. When a resource population contains novel favorable alleles at quantitative trait loci that are not present (or rare) in a commercial population, analyses of this sort will enable the loci of interest to be identified, mapped and manipulated effectively in breeding programs.Contribution no. 2124-E, 1987 series from The Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel     

Genetic variation and relationship of alfalfa populations and their progenies based on RAPD markers

The aim of investigation was to evaluate genetic variation and relationship among alfalfa populations and their offspring, with minimal cost, by using DNA marker analysis. RAPD analysis was performed on bulked DNA samples of five alfalfa parental populations and their progenies: 20 F1 populations from reciprocal diallel crosses and five S1 populations from self-pollination. Twenty primers generated 217 bands, ranging in size from 300 to 6000 bp, with the average number of bands per primer of 10.85 and polymorphism information content of 0.246. Percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Higher diversity was observed in F1 progeny populations, while genetic variation in parental populations and S1 progenies remained similar. The genetic relatedness of alfalfa populations was analysed by UPGMA and Bayesian model-based clustering approach. In both types of analysis selfpollinated progenies were grouped. Furthermore, the hybrid offspring where Zuzana, and RSI 20 were maternal parents were placed in separate groups. The results indicate that use of RAPD markers on bulked DNA samples can be fast and cost-effective way for differentiation of alfalfa parental populations and their offspring, as well as for evaluation of their genetic relationships.     

Consanguinity and prereproductive mortality in the Utah Mormon population

To test the effects of parental consanguinity on mortality among offspring, inbreeding coefficients were estimated for 303,675 members of the Utah Mormon population who were born between 1847 and 1945. Although consanguinity has been relatively rare in this population, the large sample size permitted the identification of more than 3,500 inbred offspring. Among the offspring of unrelated parents, 13.2% died before the age of 16. Significant elevations in prereproductive mortality were seen among the offspring of first-cousin marriages (22%) and among the offspring of closer unions (32%). The cor- responding relative risks are 1.70 (95% confidence limits = 1.52, 1.91) and 2.41 (95% confidence limits = 1.59, 3.41), respectively. Other categories of relationship did not produce significant elevations in offspring mortality. Similar results were obtained when a case-control approach was used to remove the effects of socioeconomic variation. Consistent with many other studies of populations with low consanguinity rates, this population experienced a relatively high absolute increase in mortality among the offspring of first-cousin marriages (9%). Preliminary evidence is offered for the hypothesis that mortality differentials are larger in populations with low inbreeding and low mortality because nongenetic causes of death do not obscure the effects of consanguinity.     

Determining colony densities in wild honeybee populations (<Emphasis Type="Italic">Apis mellifera</Emphasis>) with linked microsatellite DNA markers

Estimating the population size of social bee colonies in the wild is often difficult because nests are highly cryptic. Because of the honeybee (Apis mellifera) mating behaviour, which is characterized by multiple mating of queens at drone congregation areas (DCA), it is possible to use genotypes of drones caught at these areas to infer the number of colonies in a given region. However, DCAs are difficult to locate and we assess the effectiveness of an alternative sampling technique to determine colony density based on inferring male genotypes from queen offspring. We compare these methods in the same population of wild honeybees, Apis mellifera scutellata. A set of linked microsatellite loci is used to decrease the frequency of recombination among marker loci and therefore increase the precision of the estimates. Estimates of population size obtained through sampling of queen offspring is significantly larger than that obtained by sampling drones at DCAs. This difference may be due to the more extensive flying range of queens compared with drones on mating flights. We estimate that the population size sampled through queen offspring is about double that sampled through drones.     

Interannual genetic heterogeneity of pollen pools accepted by Quercus salicina individuals

Since flowering often varies among years in wind-pollinated woody species, the genetic composition of pollen pools accepted by seed parents can differ between years. The interannual heterogeneity of pollen flow may be important for maintaining genetic diversity within populations because it can increase genetic variation within populations and the effective sizes of the populations. In this study we examined heterogeneity, using paternity analysis and analysis of molecular variance, in the genetic composition of pollen pools among different reproductive years for six Quercus salicina seed parents in an 11.56-ha plot in a temperate old-growth evergreen broadleaved forest. The genotypes at seven microsatellite loci were determined for 111 adult trees and 777 offspring of the six seed parents in 2-5 reproductive years. Genetic differentiation of pollen pools among different reproductive years for each seed parent was significant over all seed parents and for each of four seed parents that were analysed for more than 2 years, but not for either of the other two seed parents (analysed for 2 years). For both the pollen pools originating from inside the plot and those originating from outside it, genetic differentiation among different reproductive years for each seed parent was significant over all seed parents. However, among-year genetic differentiation in the pollen pools originating from within the plot was detected for all four of the seed parents that were analysed for more than 2 years, but for only one of the four in the pools originating from outside the plot. Genetic diversity (estimated as allelic richness and gene diversity) was higher for pollen pools over all reproductive years than for pollen pools in single years. These results indicate that the year-to-year genetic variation of pollen pools increases genetic diversity in offspring and is strongly affected by the variation in pollen parents within the plot because of their high pollination contributions. The high year-to-year variation in pollen parents within the plot and overall supports the hypothesis that the offspring produced across years represent a larger genetic neighbourhood.     

Genetic correlation and response to selection in simulated populations

Summary Effects of truncation selection of a primary trait upon genetic correlation with a secondary trait were examined over 30 generations in genetic populations simulated by computer. Populations were 24 males and 24 females mated randomly with replacement; number of offspring was determined by intensity of selection. Each trait was controlled by 48 loci segregating independently, effects were equal at every locus, and gene frequency was arbitrarily set at 0.5 at each locus in the initial generation. All combinations of three genetic correlations, three intensities of selection, and three environmental variances were simulated. Gene action was additive. Genetic correlation was set by number of loci which affected both traits and was measured each generation as the product-moment correlation of genotypic values and estimated by two methods of combining phenotypic covariances between parent and offspring.Genetic correlations in each offspring generation remained consistently near initial correlations for all environmental variances when fraction of offspring saved as parents was as large as one-half. When the fraction of offspring saved was as small as one-fifth, genetic correlations decreased but most rapidly with heritability high and after the 15th generation of selection. Truncation selection caused genetic correlation to decrease in those offspring selected to become parents of the next generation. Amount of reduction depended on heritability of the selected trait rather than on degree of truncation selection. Estimates of genetic correlation from phenotypic covariances between parent and offspring fluctuated markedly from real correlations in the small populations simulated.Michigan Agricultural Experiment Station Journal Article 4836. Part of North Central Regional Project NC-2.     

Food-supplementing parents reduces their sons' song repertoire size

Food-supplemented parents typically produce more offspring, as numerous experiments on vertebrate populations have shown. ‘Propagule’ (egg or neonate) size and parental care may also be affected, with implications concerning the adult quality of offspring, although few experiments have addressed whether food-supplementing one generation affects adult quality in the next. We conducted a food supplementation experiment on song sparrows (Melospiza melodia) and tested whether song repertoire size, a demonstrated indicator of male quality, differed between the adult sons of fed (food-supplemented) and unfed (non-food-supplemented) parents. Counterintuitively, fed parents produced sons with smaller adult song repertoires, who may thus be expected to contribute fewer offspring, and fewer grand-offspring, to the population. Fed and unfed parents invested equally in the total biomass of their clutches and broods, and average nestling condition was comparable, but because fed parents produced more offspring, average egg and nestling sizes were reduced. Fed and unfed parents apportioned care differently within their broods, and we suggest compensatory growth of offspring emerging from light eggs, or egg size itself, may have affected adult repertoire size. Conceivably, the conservation benefits of food-supplementing populations could attenuate over time if fed parents produce offspring of poorer quality than themselves.     

Assessing the roles of population density and predation risk in the evolution of offspring size in populations of a placental fish

Population density is an ecological variable that is hypothesized to be a major agent of selection on offspring size. In high-density populations, high levels of intraspecific competition are expected to favor the production of larger offspring. In contrast, lower levels of intraspecific competition and selection for large offspring should be weaker and more easily overridden by direct selection for increased fecundity in low-density populations. Some studies have found associations between population density and offspring size consistent with this hypothesis. However, their interpretations are often clouded by a number of issues. Here, we use data from a 10-year study of nine populations of the least killifish, Heterandria formosa, to describe the associations of offspring size with habitat type, population density, and predation risk. We found that females from spring populations generally produced larger offspring than females from ponds; however, the magnitude of this difference varied among years. Across all populations, larger offspring were associated with higher densities and lower risks of predation. Interestingly, the associations between the two ecological variables (density and predation risk) and offspring size were largely independent of one another. Our results suggest that previously described genetic differences in offspring size are due to density-dependent natural selection.     

Patterns of pollen flow in a dense population of the insect-pollinated canopy tree species Castanopsis sieboldii

Insect pollinations of tree species with high-density populations have rarely been studied. Since the density of adults can affect effective pollen dispersal, short-distance pollination, even by insects, may frequently occur in high-density populations. To test this prediction, we investigated pollination patterns in a high-density population of the insect-pollinated canopy tree species Castanopsis sieboldii by paternity analysis using genotypes at 8 microsatellite loci of 145 adult trees and 439 seeds from 11 seed parents in a 4-ha plot. We then explored their genetic effects on the population by calculating other population genetics parameters. Although C. sieboldii has high potential for long-distance dispersal of pollen (as indicated by a fat-tailed dispersal kernel), the cumulative pollination at the local scale was spatially limited and strongly dependent on the distance between parents due to the high density of adults. Genetic diversity estimates for pollen pools accepted by each seed parent converged on a maximum as the effective number of pollen parents increased. The genetic diversity of pollen pool bulked over all the seed parents from inside the plot did not differ from that of the total pollen pools. Therefore, although pollen flow from distant pollen parents may help to maintain the genetic diversity of offspring, pollen parents neighboring seed parents may be the main contributors to the genetic diversity of the offspring at the seed stage.     

Power calculations for the transmission/disequilibrium and affected sib pair tests using elementary probability methods

The transmission/disequilibrium test (TDT) and the affected sib pair test (ASP) both test for the association of a marker allele with some conditions. Here, we present methods for calculating the probability of detecting the association (power) for a study examining a fixed number of families for suitability for the study and for calculating the number of such families to be examined. Both calculations use a genetic model for the association. The model considered posits a bi-allelic marker locus that is linked to a bi-allelic disease locus with a possibly nonzero recombination fraction between the loci. The penetrance of the disease is an increasing function of the number of disease alleles. The TDT tests whether the transmission by a heterozygous parent of a particular allele at a marker locus to an affected offspring occurs with probability greater than 0.5. The ASP tests whether transmission of the same allele to two affected sibs occurs with probability greater than 0.5. In either case, evidence that the probability is greater than 0.5 is evidence for association between the marker and the disease. Study inclusion criteria (IC) can greatly affect the necessary sample size of a TDT or ASP study. IC considered by us include a randomly selected parent at least one parent or both parents required to be heterozygous. It also allows a specified minimum number of affected offspring to be required (TDT only). We use elementary probability calculations rather than complex mathematical manipulations or asymptotic methods (large sample size approximations) to compute power and requisite sample size for a proposed study. The advantages of these methods are simplicity and generality.     

Geographic variation in offspring size of a widespread lizard (Takydromus septentrionalis): importance of maternal investment

Geographic variation in offspring size is widespread, but the proximate causes of this variation have not yet been explicitly determined. We compared egg size and egg contents among five populations of a lizard (Takydromus septentrionalis, Günther, 1864) along a latitudinal gradient, and incubated eggs at two temperatures to determine the influence of maternal investment and incubation temperature on offspring size. The mean values for female size and egg size were both greater in the two northern populations (Chuzhou and Anji) than in the three southern populations (Lishui, Dongtou, and Ningde). The larger eggs were entirely attributable to the body size of females in the Anji population, but their increased size also stemmed from further enlargement of egg size relative to female body size in Chuzhou, the northernmost population sampled in this study. Eggs of the Chuzhou population contained more yolk and less water than those of southern populations. Despite the lower lipid content in the yolk, eggs from the Chuzhou population had higher energy contents than those from the two southern populations, owing to the larger egg size and increased volume of yolk. Hatchling size was not affected by incubation temperature, but differed significantly among populations, with hatchlings being larger in the Chuzhou population than in the other populations. Our data provide an inference that oviparous reptiles from cold climates may produce larger offspring, not only by increasing egg size but also by investing more energy into their eggs. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 59–67.     

Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo.

When populations are separated for long periods and then brought into contact for a brief episode in part of their range, this can result in genetic admixture. To analyze this type of event we considered a simple model under which two parental populations (P1 and P2) mix and create a hybrid population (H). After that event, the three populations evolve under pure drift without exchange during T generations. We developed a new method, which allows the simultaneous estimation of the time since the admixture event (scaled by the population size t(i) = T/N(i), where N(i) is the effective population size of population i) and the contribution of one of two parental populations (which we call p1). This method takes into account drift since the admixture event, variation caused by sampling, and uncertainty in the estimation of the ancestral allele frequencies. The method is tested on simulated data sets and then applied to a human data set. We find that (i) for single-locus data, point estimates are poor indicators of the real admixture proportions even when there are many alleles; (ii) biallelic loci provide little information about the admixture proportion and the time since admixture, even for very small amounts of drift, but can be powerful when many loci are used; (iii) the precision of the parameters' estimates increases with sample size n = 50 vs. n = 200 but this effect is larger for the t(i)'s than for p1; and (iv) the increase in precision provided by multiple loci is quite large, even when there is substantial drift (we found, for instance, that it is preferable to use five loci than one locus, even when drift is 100 times larger for the five loci). Our analysis of a previously studied human data set illustrates that the joint estimation of drift and p1 can provide additional insights into the data.     

Inbreeding depression and mating-distance dependent offspring fitness in large and small populations of Lychnis flos-cuculi (Caryophyllaceae)

The spatial structure of four Lychnis flos-cuculi populations, varying in size and degree of isolation, was studied by comparing the fitness of offspring resulting from self-pollination and pollinations by neighbouring plants, plants within the same population, and plants from other populations. Selfed offspring had the lowest fitness of the four offspring groups. No significant difference was found between the performance of offspring from pollinations by neighbouring plants and offspring pollinated by plants further apart but within the same population. A lower fitness of offspring from pollinations between neighbours would be expected if these matings, on average, yielded inbred offspring which suffered from inbreeding depression. These results imply that either a tight neighbourhood structuring is not present, or that the inbreeding depression for offspring by neighbours is too low to detect, although these are inbred. Crossings between populations produced offspring with a significantly higher fitness than offspring sired within populations. There were no significant differences in response to inbreeding among the populations, and differences in mean fitness among populations had no clear relation to the population size or degree of isolation. A reduced fitness of small populations due to inbreeding depression or a less severe response to experimental inbreeding due to purging of deleterious alleles is therefore not supported by our results.     

Do honest signalling models of offspring solicitation apply to insects?

Honest signalling models predict that the intensity of solicitation by offspring influences the level of provisioning provided by parents and reflects offspring need. The empirical evidence supporting these predictions primarily comes from studies of birds or mammals. Thus, although parental care of altricial offspring is taxonomically widespread, the generality of these models is not well known. To investigate whether honest signalling models apply to insects, we manipulated parent and offspring behaviour in the burying beetle Nicrophorus orbicollis, a species with advanced parental care. First, within biparental care, we manipulated the brood size to alter the parents'' perception of offspring need. We measured the care giving behaviour of male and female parents to examine whether either adjusts its level of care according to offspring need. In the second experiment, because two parents together provision the brood more often than single parents, we manipulated the number of care givers (uniparental and biparental care) and measured offspring solicitation to assess whether offspring change their behaviour in response to need. Our results show that parent behaviour is broadly consistent with the first prediction of the models; both sexes provisioned larger broods more often than smaller broods. Larval solicitation was also consistent with the second prediction; larvae that were provisioned less often begged more. Our results provide evidence that honest signalling models can be applied to insects as well as vertebrates, although there are also subtle differences in care giving behaviour that may be important.     

Statistical confidence in parentage analysis with incomplete sampling: how many loci and offspring are needed?

We have recently presented models to estimate parentage in breeding systems with multiple mating and incomplete sampling of the candidate parents. Here we provide formulas to calculate the statistical confidence and the optimal trade-off between the number of loci and offspring. These calculations allow an understanding of the statistical significance of the parentage estimates as well as the appropriate sampling regime required to obtain a desired level of confidence. We show that the trade-off generally depends on the parentage of the putative parents. When parentage is low, sampling effort should concentrate on increasing the number of loci. Otherwise, there are similar benefits from increasing the number of loci or offspring. We demonstrate these methods using genetic data from a nest of the bluegill sunfish (Lepomis macrochirus).     

Estimation of migration rates from marker‐based parentage analysis

Coupled with rapid developments of efficient genetic markers, powerful population genetic methods were proposed to estimate migration rates (m) in natural populations in much broader spatial and temporal scales than the traditional mark‐release‐recapture (MRR) methods. Highly polymorphic (e.g. microsatellites) and genomic‐wide (e.g. SNPs) markers provide sufficient information to assign individuals to their populations or parents of origin and thereby to estimate directly m in a way similar to MRR. Such direct estimates of current migration rates are particularly useful in understanding the ecology and microevolution of wild populations and in managing the populations in the future. In this study, I proposed and implemented, in the software MigEst, a likelihood method to use marker‐based parentage assignments in jointly estimating m and candidate parent sampling proportions (x) in a subset of populations, investigated its power and accuracy using data simulated in various scenarios of population properties (e.g. the actual m, number, size and differentiation of populations) and sampling properties (e.g. the numbers of sampled parent candidates, offspring and markers), compared it with the population assignment approach implemented in the software BayesAss and demonstrated its usefulness by analysing a microsatellite data set from three natural populations of Brazilian bats. Simulations showed that MigEst provides unbiased and accurate estimates of m and performs better than BayesAss except when populations are highly differentiated with very small and ecologically insignificant migration rates. A valuable property of MigEst is that in the presence of unsampled populations, it gives good estimates of the rate of migration among sampled populations as well as of the rate of migration into each sampled population from the pooled unsampled populations.     

Parental condition affects early life-history of a coral reef fish

Parents can exert a range of non-genetic effects on the growth and survival of their offspring. In particular, parents may modify the size or condition of their offspring depending on the amount of energy they have available for reproduction. In this study, the body condition of breeding pairs of the coral reef fish Acanthochromis polyacanthus was experimentally manipulated to test the effects of parental condition on reproductive output and offspring life history traits. Parents in good condition commenced breeding earlier, had higher reproductive output, and their eggs exhibited increased survival during embryogenesis, compared to parents in poorer condition. Increased reproductive output was attained through more reproductive bouts over the breeding season that contained both a greater number and an increased size of eggs. The offspring from parents in good condition were larger at hatching, with larger yolk reserves and increased survival on endogenous reserves. Larger size is expected to provide benefits to offspring through reduced susceptibility to size-selective mortality. The range of offspring characteristics modified by parental condition could result in a greater proportion of offspring from good condition parents recruiting to the population.