Reconstruction of Parentage in a Band of Captive Hamadryas Baboons

The male leaders of free-ranging harem groups of hamadryas baboons are believed to mate exclusively with the female members of their harems, which typically contain no more than 2–3 females. Using no-parent parentage exclusion analysis (PEA) we identified the paternity of 25 offspring born in a captive band of hamadryas baboons (Papio hamadryas hamadryas) containing five adult males, each with a stable harem of about five females. Nine of 13 microsatellite (SSR) loci known to be highly polymorphic in rhesus macaques (Macaca mulatta) were successful in identifying the sires of all but two offspring without knowledge of the dams' genotypes, and we were able to determine the sires of all offspring when the dams' genotypes were considered. Mating success of the males ranged between 2 and 7 offspring and bore no clear relationship to the males' ages, ranks or the number of females in their harems. The males sired 7 of the 25 offspring with females outside their own harems, with higher-ranking males exhibiting greater success monopolizing access to females in their harem than lower-ranking males did. More surprisingly, the females assigned as the dams of 14 of the 25 offspring could be unequivocally excluded from parentage. The identity of the true dam could be determined for each of these 14 offspring using single-parent PEA and was uncorrelated with the ranks of these offsprings' sires and whether the offspring were born to dams outside the sires' harem groups. The combined effect of this extraharem mating and kidnapping was that only 12 of the 25 offspring were raised within their sires' harem groups. A second group of hamadryas baboons of identical structure exhibited the same high incidences of infant kidnapping and mating outside the harem group. It is unclear whether these behaviors provide an adaptive advantage or represent aberrant behavior resulting from captivity or other circumstances.     

Sires influence fetal death in pigtailed macaques (Macaca nemestrina)

Computerized colony records were used to identify dams and sires whose reproductive histories while breeding in harem groups indicated high or low risk for producing fetal deaths. The monkeys were then singly caged and bred within and between risk conditions during 24- to 72-hour matings. Although the low- and high-risk sires did not differ in ability to achieve conceptions, the results revealed that reproductive history predicted subsequent fetal death rates, and sires made a substantial contribution. Overall, high-risk sires had a 4.86 times higher relative risk of producing fetal death than low-risk sires. Compared with this figure, high-risk dams had only a 2.64 times higher risk for fetal death than low-risk dams. The male effect was most evident in comparisons of between- and within-risk matings. Females with excellent reproductive histories experienced a threefold increase in fetal deaths when mated with high-risk males, whereas females with poor reproductive histories experienced almost a 50% reduction in fetal deaths when mated with low-risk males. The results show that male factors beyond fertility need to be considered when examining the causes of reproductive failure in captive primates.     

Minimizing inbreeding by managing genetic contributions across generations

Here we present the strategy that achieves the lowest possible rate of inbreeding (DeltaF) for a population with unequal numbers of sires and dams with random mating. This new strategy results in a DeltaF as much as 10% lower than previously achieved. A simple and efficient approach to reducing inbreeding in small populations with sexes of unequal census number is to impose a breeding structure where parental success is controlled in each generation. This approach led to the development of strategies for selecting replacements each generation that were based upon parentage, e.g., a son replacing its sire. This study extends these strategies to a multigeneration round robin scheme where genetic contributions of ancestors to descendants are managed to remove all uncertainties about breeding roles over generations; i.e., male descendants are distributed as equally as possible among dams. In doing so, the sampling variance of genetic contributions within each breeding category is eliminated and consequently DeltaF is minimized. Using the concept of long-term genetic contributions, the asymptotic DeltaF of the new strategy for random mating, M sires and d dams per sire, is phi/(12M), where phi = [1 + 2((1)/(4))(d)]. Predictions were validated using Monte Carlo simulations. The scheme was shown to achieve the lowest possible DeltaF using pedigree alone and showed that further reductions in DeltaF below that obtained from random mating arise from preferential mating of relatives and not from their avoidance.     

Intensive genetic assessment of the mating system and reproductive success in a semi-closed population of the mottled sculpin,Cottus bairdi

Most genetic surveys of parentage in nature sample only a small fraction of the breeding population. Here we apply microsatellite markers to deduce the genetic mating system and assess the reproductive success of females and males in an extensively collected, semi-closed stream population of the mottled sculpin fish, Cottus bairdi. In this species, males guard nest rocks where females deposit the eggs for fertilization. The potential exists for both males and females to mate with multiple partners and for males to provide parental care to genetically unrelated offspring. Four hundred and fifty-five adults and subadults, as well as 1,259 offspring from 23 nests, were genotyped at five polymorphic microsatellite loci. Multilocus maternal genotypes, deduced via genetic analyses of embryos, were reconstructed for more than 90% of the analysed nests, thus allowing both male and female reproductive success to be estimated accurately. There was no genetic evidence for cuckoldry, but one nest probably represents a takeover event. Successful males spawned with a mean of 2.8 partners, whereas each female apparently deposited her entire clutch of eggs in a single nest (mean fecundity = 66 eggs/female). On average, genetically deduced sires and dams were captured 1.6 and 9.3 metres from their respective nests, indicating little movement by breeders during the spawning season. Based on a 'genetic mark-recapture' estimate, the total number of potentially breeding adults (c. 570) was an order-of-magnitude larger than genetically based estimates of the effective number of breeders (c. 54). In addition, significantly fewer eggs per female were deposited in single than in multidam nests. Not only were perceived high-quality males spawning with multiple partners, but they were receiving more eggs from each female.     

Imputation of non-genotyped sheep from the genotypes of their mates and resulting progeny

Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys’ dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams’) genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam’s genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire’s mate (i.e. dam of the progeny).     

Reproductive and Mating Success in the Small-Mouthed Salamander (Ambystoma texanum) Estimated via Microsatellite Parentage Analysis

Bateman’s principles of sexual selection predict that the sex with “cheaper” gametes may maximize reproductive efforts by mating multiply and so display greater positive covariance between reproductive and mating success. We conducted a semi-controlled breeding experiment to genetically quantify sexual selection in adult Ambystoma texanum, a sexually monomorphic salamander with simple courtship behaviors. We used four polymorphic microsatellite loci to genotype 57 adults enclosed in a breeding wetland and compared their multilocus profiles to that of 862 embryos collected from the enclosure. The molecular data were used to assign parentage, investigate the mating system, and measure sexual selection intensity. Parentage analyses indicated 36% of dams and 93% of sires were genetically sampled via their gametes but physically unsampled, suggesting that a large number of breeders over-wintered within the enclosure and/or some females released into the enclosure were already inseminated. We used the genetic data to generate estimates of individual reproductive and mating success and we interpret these in light of salamander behavior and sexual selection theory. The incidence of multiple mating in females (86%) was considerably higher than in males (32%) and the standardized variance in mating success was significantly greater in females. The correlations between reproductive and mating success were significant and of similar magnitude between the sexes, indicating that both sexes increased reproductive success through increased mating success. This pattern may be a function of differential opportunities for mating success between the sexes. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Moving from QTL experimental results to the utilization of QTL in breeding programmes

Results from quantitative trait loci studies cannot be readily implemented into breeding schemes through marker assisted selection because of uncertainty about whether the quantitative trait loci identified are real and whether the identified quantitative trait loci are segregating in the breeding population. The present paper outlines and discusses strategies to reduce uncertainty in the results from quantitative trait loci studies. One strategy to confirm results from quantitative trait loci studies is to combine P -values from many quantitative trait loci experiments, while another is to establish a confirmation study. The power of a confirmation study must be high to ensure that the postulated quantitative trait loci can be verified. In the calculation of the experimental power, there are many issues that have to be addressed: size of the quantitative trait loci to be detected, significance level required, experimental design and expected heterozygosity for the design. To ensure marker assisted selection can be quickly implemented once quantitative trait loci are confirmed, DNA samples should be retained from daughters, and the sires and dams of elite sires.     

Detection of QTL for milk production on Chromosomes 1 and 6 of Holstein cattle

Seventy to 75 sons of each of six Holstein sires were assayed for genotypes at a number of microsatellite loci spanning Chromosomes (Chrs) 1 and 6. The number of informative loci varied from three to eight on each chromosome in different sire families. Linkage order and map distance for microsatellite loci were estimated using CRI-MAP. Estimates of QTL effect and location were made by using a least squares interval mapping approach based on daughter yield deviations of sons for 305-d milk, fat, protein yield, and fat and protein percentage. Thresholds for statistical significance of QTL effects were determined from interval mapping of 10,000 random permutations of the data across the bull sire families and within each sire family separately. Across-sire analyses indicated a significant QTL for fat and protein yield, and fat percentage on Chr 1, and QTL effects on milk yield and protein percentage that might represent one or two QTL on Chr 6. Analyses within each sire family indicated significant QTL effects in five sire families, with one sire possibly being heterozygous for two QTLs. Statistically significant estimates of QTL effects on breeding value ranged from 340 to 640 kg of milk, from 15.6 to 28.4 kg of fat, and 14.4 to 17.6 kg of protein. Received: 19 November 1999 / Accepted: 31 August 2000     

Heritability and Y-chromosome influence in the jack male life history of chinook salmon (Oncorhynchus tshawytscha)

Jacking in chinook salmon (Oncorhynchus tshawytscha) is an alternative reproductive strategy in which males sexually mature at least 1 year before other members of their year class. We characterize the genetic component of this reproductive strategy using two approaches; hormonal phenotypic sex manipulation, and a half-sib breeding experiment. We 'masculinized' chinook salmon larvae with testosterone, reared them to first maturation, identified jacks and immature males based on phenotype, and genotyped all fish as male ('XY') or female ('XX') using PCR-based Y-chromosome markers. The XY males had a much higher incidence of jacking than the XX males (30.8% vs 9.9%). There was no difference in body weight, gonad weight, and plasma concentrations of testosterone and 17beta-estradiol between the two jack genotypes, although XY jacks did have a higher gonadosomatic index (GSI) than XX jacks. In the second experiment, we bred chinook salmon in two modified half-sib mating designs, and scored the number of jacks and immature fish at first maturation. Heritability of jacking was estimated using two ANOVA models: dams nested within sires, and sires nested within dams with one-half of the half-sib families common to the two models. The sire component of the additive genetic variance yielded a high heritability estimate and was significantly higher than the dam component (h(2)(sire) = 0.62 +/- 0.21; h(2)(dam) = -0.14 +/- 0.12). Our experiments both indicated a strong sex-linked component (Y-chromosome) to jacking in chinook salmon, although evidence for at least some autosomal contribution was also observed.     

Prediction of rates of inbreeding in populations selected on best linear unbiased prediction of breeding value

Predictions for the rate of inbreeding (DeltaF) in populations with discrete generations undergoing selection on best linear unbiased prediction (BLUP) of breeding value were developed. Predictions were based on the concept of long-term genetic contributions using a recently established relationship between expected contributions and rates of inbreeding and a known procedure for predicting expected contributions. Expected contributions of individuals were predicted using a linear model, u(i)(()(x)()) = alpha + betas(i), where s(i) denotes the selective advantage as a deviation from the contemporaries, which was the sum of the breeding values of the individual and the breeding values of its mates. The accuracy of predictions was evaluated for a wide range of population and genetic parameters. Accurate predictions were obtained for populations of 5-20 sires. For 20-80 sires, systematic underprediction of on average 11% was found, which was shown to be related to the goodness of fit of the linear model. Using simulation, it was shown that a quadratic model would give accurate predictions for those schemes. Furthermore, it was shown that, contrary to random selection, DeltaF less than halved when the number of parents was doubled and that in specific cases DeltaF may increase with the number of dams.     

Multiple paternity in an aggregate breeding amphibian: the effect of reproductive skew on estimates of male reproductive success

Aggregate, or explosive, breeding is widespread among vertebrates and likely increases the probability of multiple paternity. We assessed paternity in seven field-collected clutches of the explosively breeding spotted salamander (Ambystoma maculatum) using 10 microsatellite loci to determine the frequency of multiple paternity and the number of males contributing to a female's clutch. Using the Minimum Method of allele counts, multiple paternity was evident in 70% of these egg masses. Simple allele counts underestimate the number of contributing males because this method cannot distinguish multiple fathers with common or similar alleles. Therefore, we used computer simulations to estimate from the offspring genotypes the most likely number of contributing fathers given the distributions of allele frequencies in this population. We determined that two to eight males may contribute to A. maculatum clutches; therefore, multiple paternity is a common strategy in this aggregate breeding species. In aggregate mating systems competition for mates can be intense, thus differential reproductive success (reproductive skew) among males contributing to a female's clutch could be a probable outcome. We use our data to evaluate the potential effect of reproductive skew on estimates of the number of contributing males. We simulated varying scenarios of differential male reproductive success, ranging from equal contribution to high reproductive skew among contributing sires in multiply sired clutches. Our data suggest that even intermediate levels of reproductive skew decrease confidence substantially in estimates of the number of contributing sires when parental genotypes are unknown.     

Prediction of expected genetic variation within groups of offspring for innovative mating schemes

Background

Experience from progeny-testing indicates that the mating of popular bull sires that have high estimated breeding values with excellent dams does not guarantee the production of offspring with superior breeding values. This is explained partly by differences in the standard deviation of gamete breeding values (SDGBV) between animals at the haplotype level. The SDGBV depends on the variance of the true effects of single nucleotide polymorphisms (SNPs) and the degree of heterozygosity. Haplotypes of 58 035 Holstein animals were used to predict and investigate expected SDGBV for fat yield, protein yield, somatic cell score and the direct genetic effect for stillbirth.

Results

Differences in SDGBV between animals were detected, which means that the groups of offspring of parents with low SDGBV will be more homogeneous than those of parents with high SDGBV, although the expected mean breeding values of the progeny will be the same. SDGBV was negatively correlated with genomic and pedigree inbreeding coefficients and a small loss of SDGBV over time was observed. Sires that had relatively low mean gamete breeding values but high SDGBV had a higher probability of producing extremely positive offspring than sires that had a high mean gamete breeding value and low SDGBV.

Conclusions

An animal’s SDGBV can be estimated based on genomic information and used to design specific genomic mating plans. Estimated SDGBV are an additional tool for mating programs, which allows breeders to identify and match mating partners using specific haplotype information.     

Power analysis of QTL detection in half-sib families using selective DNA pooling

Individual loci of economic importance (QTL) can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers). Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams.     

The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods

In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing gene-assisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD-LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD-LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD-LA was larger than when all animals had phenotypes. Missing gene contents were predicted with higher accuracy using multiple-marker iterative peeling than with using mixed model methodology, but the difference in accuracy of total EBV was negligible and mixed model methodology was computationally much faster than multiple iterative peeling. For large livestock populations it can be concluded that gene-assisted breeding value estimation can be practically best performed by regression on gene contents, using mixed model methodology to predict missing marker genotypes, combining phenotypic information of genotyped and ungenotyped animals in one evaluation. This technique would be, in principle, also feasible for genomic selection. It is expected that genomic selection for ungenotyped animals using predicted single nucleotide polymorphism gene contents might be beneficial especially for low heritable traits.     

No association between the ovine leucocyte antigen (OLA) system in the Australian merino and susceptibility to Haemonchus contortus infection

A genetic analysis has been made of the Ovine Leucocyte Antigenic (OLA) system in Australian merinos. The animals consisted of sires, dams and their progeny. The typing data were consistent with previous findings of a high degree of polymorphism. At least two closely linked loci with several alleles at each are necessary to explain the data. No evidence was found for an association between OLA types and three measures of susceptibility to infection by the blood-sucking parasite Haemonchus contortus. Attention is drawn to the utility of half-sib data for analysis of the genetic control of resistance to parasites in sheep and other animals with a similar breeding structure.     

Retrotransposon Insertional Polymorphism in Iranian Bread Wheat Cultivars and Breeding Lines Revealed by IRAP and REMAP Markers

Inter-retrotransposon amplified polymorphisms (IRAPs) and retrotransposon-microsatellite amplified polymorphisms (REMAPs) were used to detect retrotransposon integration events and genetic diversity in 101 Iranian bread wheat (Triticum aestivum L.) cultivars and breeding lines. The 9 IRAP primers amplified 128 loci, and 20 REMAP primers amplified 263 loci. Percentage of polymorphic loci, average expected heterozygosity, number of effective alleles, and Shannon’s information index for the REMAP markers were slightly higher than those for the IRAP markers. The same estimated parameters calculated for native and nonnative retrotransposons were not considerably different. A Mantel test between IRAP and REMAP cophenetic matrices evidenced no significant correlation. Cluster analysis based on the Dice similarity coefficient and complete linkage algorithm using IRAP+REMAP loci identified five groups among the genotypes studied that could be applied as crossing parents in T. aestivum breeding programs.     

Insights into the mating habits of the tiger salamander (Ambystoma tigrinum tigrinum) as revealed by genetic parentage analyses

Among urodeles, ambystomatid salamanders are particularly amenable to genetic parentage analyses because they are explosive aggregate breeders that typically have large progeny arrays. Such analyses can lead to direct inferences about otherwise cryptic aspects of salamander natural history, including the rate of multiple mating, individual reproductive success, and the spatial distribution of clutches. In 2002, we collected eastern tiger salamander (Ambystoma tigrinum tigrinum) egg masses (> 1000 embryos) from a approximately 80 m linear transect in Indiana, USA. Embryos were genotyped at four variable microsatellite loci and the resulting progeny array data were used to reconstruct multilocus genotypes of the parental dams and sires for each egg mass. UPGMA analysis of genetic distances among embryos resolved four instances of egg mass admixture, where two or more females had oviposited at exactly the same site resulting in the mixing of independent cohorts. In total, 41 discrete egg masses were available for parentage analyses. Twenty-three egg masses (56%) consisted exclusively of full-siblings (i.e. were singly sired) and 18 (44%) were multiply sired (mean 2.6 males/clutch). Parentage could be genetically assigned to one of 17 distinct parent pairs involving at least 15 females and 14 different males. Reproductive skew was evident among males who sired multiply sired clutches. Additional evidence of the effects of sexual selection on male reproductive success was apparent via significant positive correlations between male mating and reproductive success. Females frequently partitioned their clutches into multiple discrete egg masses that were separated from one another by as many as 43 m. Collectively, these data provide the first direct evidence for polygynandry in a wild population of tiger salamanders.     

The association of two single nucleotide polymorphisms (SNPs) in growth hormone (GH) gene with litter size and superovulation response in goat-breeds

Two active mutations (A 781 G and A 1575 G) in growth hormone (GH) gene, and their associations with litter size (LS), were investigated in both a high prolificacy (Matou, n = 182) and a low prolificacy breed (Boer, n = 352) by using the PCR-RFLP method. Superovulation experiments were designed in 57 dams, in order to evaluate the effect of different genotypes of the GH gene on superovulation response. Two genotypes (AA and AB, CC and CD) in each mutation were detected in these two goat breeds. Neither BB nor DD homozygous genotypes were observed. The genotypic frequencies of AB and CC were significantly higher than those of AA and CD. In the third parity, Matou dams with AB or CC genotypes had significantly larger litter sizes than those with AA and CD (p < 0.05). On combining the two loci, both Matou and Boer dams with ABCD genotype had the largest litter sizes when compared to the other genotypes (p < 0.05). When undergoing like superovulation treatments, a significantly higher number of corpora lutea and ova, with a lower incidence of ovarian cysts, were harvested in the AB and CC genotypes than in AA and CD. These results show that the two loci of GH gene are highly associated with abundant prolificacy and superovulation response in goat breeds.     

Linkage disequilibrium among commonly genotyped SNP variants detected from bull sequence,

Genomic prediction utilizing causal variants could increase selection accuracy above that achieved with SNPs genotyped by currently available arrays used for genomic selection. A number of variants detected from sequencing influential sires are likely to be causal, but noticeable improvements in prediction accuracy using imputed sequence variant genotypes have not been reported. Improvement in accuracy of predicted breeding values may be limited by the accuracy of imputed sequence variants. Using genotypes of SNPs on a high‐density array and non‐synonymous SNPs detected in sequence from influential sires of a multibreed population, results of this examination suggest that linkage disequilibrium between non‐synonymous and array SNPs may be insufficient for accurate imputation from the array to sequence. In contrast to 75% of array SNPs being strongly correlated to another SNP on the array, less than 25% of the non‐synonymous SNPs were strongly correlated to an array SNP. When correlations between non‐synonymous and array SNPs were strong, distances between the SNPs were greater than separation that might be expected based on linkage disequilibrium decay. Consistently near‐perfect whole‐genome linkage disequilibrium between the full array and each non‐synonymous SNP within the sequenced bulls suggests that whole‐genome approaches to infer sequence variants might be more accurate than imputation based on local haplotypes. Opportunity for strong linkage disequilibrium between sequence and array SNPs may be limited by discrepancies in allele frequency distributions, so investigating alternate genotyping approaches and panels providing greater chances of frequency‐matched SNPs strongly correlated to sequence variants is also warranted. Genotypes used for this study are available from https://www.animalgenome.org/repository/pub/ ;USDA2017.0519/.     

SEXUAL SELECTION IN AMERICAN TOADS: A TEST OF A GOOD-GENES HYPOTHESIS

Adaptive mate choice in species lacking male resource control and/or paternal care might be maintained by selection because preferred males sire genetically superior offspring. For such a process to occur, some male phenotypic trait(s) must both reliably indicate male genetic quality and influence the pattern of mate choice by females. In American toads, Bufo americanus, male body length has been documented to influence female mating patterns: females usually mate with males that are larger than average. However, the relationship between male size and male genetic quality is unknown. We conducted a controlled breeding experiment using 48 sires and 19 dams to determine if larger males sire offspring with superior larval performance characteristics (greater survival to metamorphosis, larger mass at metamorphosis, and earlier metamorphosis). We also aged each sire to test the hypothesis that older males are, on average, genetically superior to younger males. We crossed each female with three sires representing three body size categories (mean and 1 SD ± mean snout-ischium length). Hatchlings (500 from each cross) were reared to metamorphosis in seminatural ponds in the field. Metamorph weight (log transformed) and age at metamorphosis showed significant heritability and were genetically correlated with each other. Hence, sires differed in genetic quality. However, none of the three measures of offspring performance was correlated with sire body size or age. Thus, we obtained no support for the prediction that sire body size or age is related to genetic quality.