Exclusion probabilities for pedigree testing farm animals

Parentage exclusion of close relatives in haplodiploid species

Parentage exclusion probability is usually calculated to evaluate the informativeness of a set of markers for, and the statistical power of, a parentage analysis. Equations for parentage exclusion probability have been derived in various scenarios such as paternity exclusion when maternity is known or unknown or when candidate males are unrelated or loosely related (being from the same subpopulation) to the father. All previous work assumes a diploid species. Although marker-based parentage analyses have been conducted in haploidiploid species (such as ants, bees and wasps) for diploid offspring at the individual level or haploid offspring at the class level, rigorously derived formulations of parentage exclusion probability for haploid offspring at the individual level are lacking, which prevents the precise evaluation of the informativeness for and the statistical power of a parentage analysis. In this study we derive equations for the exclusion probability of maternity of a haploid male when multiple mother candidates (workers or queens) are unrelated or fullsibs to the mother. The usefulness of the equations is exemplified by numerical examples, and the results are discussed in the context of the study of worker reproductivity in eusocial haplodiploid species. The results are especially valuable for an optimal experimental design in determining sampling intensities (e.g. number of markers and number of individuals) to achieve satisfactory statistical power of a parentage analysis in investigating workers' reproductivity in eusocial haplodiploid species.

Paternity Analyses for the Planning of SIT Projects against the Red Palm Weevil

The red palm weevil Rhynchophorus ferrugineus is an invasive pest from southeastern Asia and Melanesia that has spread widely across the Middle East and the Mediterranean Basin over the last 30 years. Its endophagous larvae cause huge amounts of damage to several palm tree species from the Arecaceae family. Many of these palms are economically important for agricultural and ornamental purposes. Therefore, a lot of attention has recently been focused on studying this species with the aim of identifying sustainable and effective eradication strategies. Sterile insect techniques are biological control strategies that are currently being investigated for their potential to eradicate this pest in selected invasion areas. Mating system features (e.g., polyandry and related features) can affect the success and suitability of these approaches. The main goal of this research was to assess the performance of a previously developed microsatellite panel in terms of the paternity assignment of progeny from laboratory mating experiments. Using a simulation approach, we evaluated the reliability of the microsatellite markers in the paternity tests both in complex laboratory experiment scenarios and on the progeny of wild-caught gravid females to help future studies on the RPW mating system. As a case study of the simulation results, we performed two double-mating experiments, genotyped the progeny and estimated the P₂ values to compare to the expected progeny genotypes according to the crossing scheme of each experiment. The results of our simulations on laboratory experiments showed that it was possible to carry out paternity assignments for all progeny with reliable statistical confidence using our 13 microsatellites set. On the contrary the low genetic variability measured in red palm weevil populations in invaded areas made the resolution power of our loci too low to carry out paternity analyses on natural populations. Results of laboratory crossing were completely congruent with the expectations from the Mendelian laws.

Integer programming for selecting set of informative markers in paternity inference

Background

Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms.

Results

Here, for a closed half-sib population, we generalized the process of marker loci selection as a binary integer programming problem. The proposed systematic formulation considered marker localization and the family structure of the potential parental population, resulting in an accurate assignment with a small set of markers. We also proposed an efficient heuristic approach, which effectively improved the number of markers, localization, and tolerance to missing data of the set. Applying this method to the actual genotypes of apple (Malus × domestica) germplasm, we identified a set of 34 SNP markers that distinguished 300 potential parents crossed to a particular cultivar with a greater than 99% accuracy.

Conclusions

We present a novel approach for selecting informative markers based on binary integer programming. Since the data generated by high-throughput sequencing technology far exceeds the requirement for parentage assignment, a combination of the systematic marker selection with targeted SNP genotyping, such as KASP, allows flexibly enlarging the analysis up to a scale that has been unrealistic in various species. The method developed in this study can be directly applied to unsolved large-scale problems in breeding, reproduction, and ecological research, and is expected to lead to novel knowledge in various biological fields. The implementation is available at https://github.com/SoNishiyama/IP-SIMPAT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04801-z.

Spatial asymmetry of the paternity success in nests of a fish with alternative reproductive tactics

Guard-sneaker tactics are widespread among fish, where territorial males defend a nest and provide parental care while sneakers try to steal fertilizations. Territorials and sneakers adopt diverse pre- and post-mating strategies, adjusting their ejaculate investment and/or behavioural responses to the presence of competitors. The relative distance of competitors from the spawning female plays a major role in influencing male mating strategies and the resulting paternity share. However, territorial male quality and sneaking intensity do not fully account for the variability in the relative siring success occurring among species. An often neglected factor potentially affecting sneakers proximity to females is the nest structure. We conducted a field experiment using the black goby, whose nests show two openings of different size. We found that territorial males defend more and sneaking pressure is higher at the front, larger access of the nest than at the back, smaller one. Moreover, microsatellite paternity analysis shows that territorials sire more offspring at the back of their nest. Such a predictable spatial distribution of the paternity share suggests that nest structure might work as an indirect cue of male relative siring success, potentially influencing the territorial male investment in parental care and/or the female egg deposition strategy.

Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition

Genomic technologies have been increasingly applied in livestock production due to their utility in production management and animal genetic improvement. The current project aimed to develop genomic resources for the Canadian bison industry, specifically a parentage verification tool and a subspecies composition tool. Both products stand to help with building and maintaining purebred and crossbred bison populations, and in turn bison conservation and production. The development of this genomic toolkit proceeded in two stages. In the single-nucleotide polymorphism (SNP) discovery and selection stage, raw sequence information from 41 bison samples was analyzed, and approximately 52.5 million candidate biallelic SNPs were discovered from 21 samples with high sequence quality. A set of 19,954 SNPs (2,928 for parentage verification and 17,026 for subspecies composition) were then selected for inclusion on an Axiom myDesign custom array. In the refinement and validation stage, 480 bison were genotyped using the custom SNP panel, and the resulting genotypes were analyzed to further filter SNPs and assess tool performance. In various tests using real and simulated genotypes, the two genomic tools showed excellent performance for their respective tasks. Final SNP sets consisting of 191 SNPs for parentage and 17,018 SNPs for subspecies composition are described. As the first SNP-based genomic toolkit designed for the Canadian bison industry, our results may provide a new opportunity in improving the competitiveness and profitability of the industry in a sustainable manner.

Harvesting changes mating behaviour in European lobster

Removing individuals from a wild population can affect the availability of prospective mates and the outcome of competitive interactions, with subsequent effects on mating patterns and sexual selection. Consequently, the rate of harvest-induced evolution is predicted to be strongly dependent on the strength and dynamics of sexual selection, yet there is limited empirical knowledge on the interplay between selective harvesting and the mating systems of exploited species. In this study, we used genetic parentage assignment to compare mating patterns of the highly valued and overexploited European lobster (Homarus gammarus) in a designated lobster reserve and nearby fished area in southern Norway. In the area open to fishing, the fishery is regulated by a closed season, a minimum legal size and a ban on the harvest of egg-bearing females. Due to the differences in size and sex-specific fishing mortality between the two areas, males and females are of approximately equal average size in the fished area, whereas males tend to be larger in the reserve. Our results show that females would mate with males larger than their own body size, but the relative size difference was significantly larger in the reserve. Sexual selection acted positively on both body size and claw size in males in the reserve, while it was nonsignificant in fished areas. This strongly suggests that size truncation of males by fishing reduces the variability of traits that sexual selection acts upon. If fisheries continue to target large individuals (particularly males) with higher relative reproductive success, the weakening of sexual selection will likely accelerate fisheries-induced evolution towards smaller body size.

Development of a SNP panel dedicated to parentage assignment in French sheep populations

BACKGROUND

The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes. Both methods have major drawbacks, notably time-consuming tasks for breeders, and are thus used at varying levels in breeding programs. As a consequence, the percentage of known sires can be very low in some breeds and results in less accurate estimated breeding values.

RESULTS

In order to address this issue and offer an alternative strategy for obtaining parentage information, we designed a set of 249 SNPs for parentage assignment in French sheep breeds and tested its efficiency in one breed. The set was derived from the 54 K SNP chip that was used to genotype the thirty main French sheep populations. Only SNPs in Hardy-Weinberg equilibrium, displaying the highest Minor Allele Frequency across all the thirty populations and not associated with Mendelian errors in verified family trios were selected. The panel of 249 SNPs was successfully used in an on-farm test in the BMC breed and resulted in more than 95% of lambs being assigned to a unique sire.

CONCLUSION

In this study we developed a SNP panel for assignment that achieved good results in the on-farm testing. We also raised some conditions for optimal use of this panel: at least 180 SNPs should be used and a minute preparation of the list of candidate sires. Our panel also displays high levels of MAF in the SheepHapMap breeds, particularly in the South West European breeds.

Genetic evidence for prevalence of alloparental care in a socially monogamous biparental cichlid fish, Perissodus microlepis, from Lake Tanganyika supports the "selfish shepherd effect" hypothesis

Alloparental care – care for unrelated young – is rare in animals, and its ecological or evolutionary advantages or, alternative maladaptive nature, remain unclear. We investigate alloparental care in the socially monogamous cichlid fish Perissodus microlepis from Lake Tanganyika that exhibits bi‐parental care. In a genetic parentage analysis, we discovered a surprisingly high percentage of alloparental care represented by brood mixing, extra‐pair paternity and extra‐pair maternity in all broods that we investigated. The percentage of nondescendant juveniles of other parents, i.e., brood mixing, ranged from 5% to 57% (mean = 28%). The distribution of genetic parentage also suggests that this socially monogamous species has, in fact, polygamous mating system. The prevalence of genetically mixed broods can be best explained by two, not mutually exclusive hypotheses on farming‐out and fostering behaviors. In the majority of broods, the sizes of the parents’ own (descendant) offspring were significantly larger than those of the adopted (nondescendant) juveniles, supporting the ‘selfish shepherd effect’ hypothesis, i.e., that foster parents preferentially accept unrelated “smaller or not larger” young since this would tend to lower the predation risks for their own larger offspring. There was also a tendency for larger parents particularly mothers, more so than smaller parents, to care predominantly for their own offspring. Larger parents might be better at defending against cuckoldry and having foreign young dumped into their broods through farming‐out behavior. This result might argue for maladaptive effects of allopatric care for the foster parents that only larger and possibly more experienced pairs can guard against. It needs to be determined why, apparently, the ability to recognize one's own young has not evolved in this species.

Genotype Reconstruction of Paternity in European Lobsters (Homarus gammarus)

Decapod crustaceans exhibit considerable variation in fertilisation strategies, ranging from pervasive single paternity to the near-ubiquitous presence of multiple paternity, and such knowledge of mating systems and behaviour are required for the informed management of commercially-exploited marine fisheries. We used genetic markers to assess the paternity of individual broods in the European lobster, Homarus gammarus, a species for which paternity structure is unknown. Using 13 multiplexed microsatellite loci, three of which are newly described in this study, we genotyped 10 eggs from each of 34 females collected from an Atlantic peninsula in the south-western United Kingdom. Single reconstructed paternal genotypes explained all observed progeny genotypes in each of the 34 egg clutches, and each clutch was fertilised by a different male. Simulations indicated that the probability of detecting multiple paternity was in excess of 95% if secondary sires account for at least a quarter of the brood, and in excess of 99% where additional sire success was approximately equal. Our results show that multiple paternal fertilisations are either absent, unusual, or highly skewed in favour of a single male among H. gammarus in this area. Potential mechanisms upholding single paternal fertilisation are discussed, along with the prospective utility of parentage assignments in evaluations of hatchery stocking and other fishery conservation approaches in light of this finding.

Evidence of limited polyandry in a natural population of Aedes aegypti

The mosquito Aedes aegypti is a vector of yellow fever, dengue, and chikungunya. Control of the insect is crucial to stop the spread of dengue and chikungunya, so it is critically important to understand its mating behavior. Primarily, based on laboratory behavior, it has long been assumed that Ae. aegypti females mate once in their lifetime. However, multiple inseminations have been observed in semi-field and laboratory settings, and in closely related species. Here, we report the first evidence of polyandry in a natural population of Ae. aegypti. Female Ae. aegypti were captured around the New Orleans, LA, metropolitan area. They were offered a blood meal and allowed to lay eggs, which were reared to the third-instar larval stage. A parentage analysis using four microsatellite loci was performed. Out of 48 families, 3 showed evidence of multiple paternity. An expanded analysis of these three families found that one family group included offspring contributed by three fathers, and the other two included offspring from two fathers. This result establishes that polyandry can occur in a small proportion of Ae. aegypti females in a natural setting. This could complicate future genetic control efforts and has implications for sampling for population genetics.

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep

Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development- firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 “parentage SNP panel” was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test’s suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.

Molecular evidence for multiple paternity in a population of the Viviparous Tule Perch Hysterocarpus traski

Population density might be an important variable in determining the degree of multiple paternity. In a previous study, a high level of multiple paternity was detected in the shiner perch Cymatogaster aggregata, a species with high population density and a high mate encounter rate. The tule perch Hysterocarpus traski is phylogenetically closely related to C. aggregata, but it has relatively lower population density, which may result in distinct patterns of multiple paternity in these 2 species. To test the hypothesis that mate encounter rate may affect the rate of successful mating, we used polymorphic microsatellite markers to identify multiple paternity in the progeny arrays of 12 pregnant females from a natural population of tule perch. Multiple paternity was detected in 11 (92%) of the 12 broods. The number of sires per brood ranged from 1 to 4 (mean 2.5) but with no correlation between sire number and brood size. Although the brood size of tule perch is considerably larger than that of shiner perch (40.7 vs. 12.9, respectively), the average number of sires per brood in tule perch is much lower than that in shiner perch (2.5 vs. 4.6, respectively). These results are consistent with the hypothesis that mate encounter rate is an important factor affecting multiple mating.

An accurate formula to calculate exclusion power of marker sets in parentage assignment

In studies on parentage assignment with both parents unknown, the exclusion power of a marker set is generally computed under the hypothesis that the potential families tested are independent and unrelated samples. This tends to produce overly optimistic exclusion power estimates. In this work, we have developed a new formula that gives almost unbiased results at the population level.

Body size correlates with fertilization success but not gonad size in grass goby territorial males

In fish species with alternative male mating tactics, sperm competition typically occurs when small males that are unsuccessful in direct contests steal fertilization opportunities from large dominant males. In the grass goby Zosterisessor ophiocephalus, large territorial males defend and court females from nest sites, while small sneaker males obtain matings by sneaking into nests. Parentage assignment of 688 eggs from 8 different nests sampled in the 2003-2004 breeding season revealed a high level of sperm competition. Fertilization success of territorial males was very high but in all nests sneakers also contributed to the progeny. In territorial males, fertilization success correlated positively with male body size. Gonadal investment was explored in a sample of 126 grass gobies collected during the period 1995-1996 in the same area (61 territorial males and 65 sneakers). Correlation between body weight and testis weight was positive and significant for sneaker males, while correlation was virtually equal to zero in territorial males. That body size in territorial males is correlated with fertilization success but not gonad size suggests that males allocate much more energy into growth and relatively little into sperm production once the needed size to become territorial is attained. The increased paternity of larger territorial males might be due to a more effective defense of the nest in comparison with smaller territorial males.

Consistency statistics and genetic parameters for taste panel assessed meat quality traits and their relationship with carcass quality traits in a commercial population of Angus-sired beef cattle

Sensory traits, such as juiciness and tenderness, are known to be important to the consumer and thus will influence their consumption of meat, specifically beef. These traits are difficult to measure and often require the use of taste panels to assess the complex parameters involved in the eating experience. Such panels are potentially a large source of measurement error, which may reduce the effectiveness of breeding programmes based on the data they generate. The aim of this study was to assess the quality of such taste panel-derived sensory traits as well as calculating genetic parameters and residual correlations for these traits along with a further set of traditional carcass quality traits. The study examined a sample of 443 Aberdeen Angus-cross animals collected from 14 breeder-finisher farms throughout Scotland. To assess the quality of the taste panel measurements, three consistency statistics were calculated: (i) panel-member consistency, i.e. the extent to which an individual panel member varied in their scoring for a given trait over the period of the experiment; (ii) repeatability, i.e. the consistency with which an individual panel member was able to score a trait on repeated samples from the same animal; and (iii) reproducibility, i.e. the extent to which taste panel members agreed with each other when scoring a trait. These consistency statistics were moderately high, particularly for panel-member consistency and reproducibility, with values ranging from 0.48 to 0.81 and 0.43 to 0.73 respectively. Estimated heritabilities were low for most of the sensory taste-panel-evaluated traits where the maximum value was 0.16 for overall liking. Residual correlations were high between many of the closely related sensory traits, although few significant correlations were found between the carcass quality data and meat quality traits.

Variation in female reproductive quality and reproductive success of male Midland Painted Turtles (Chrysemys picta marginata)

Although mate number is perceived to be the primary factor affecting male reproductive success in polygynous systems, differences in female reproductive qualities may also influence variation in male reproductive success. We combined 32 years of data on variation in reproductive qualities (clutch size and clutch frequency) of female Midland Painted Turtles ( Chrysemys picta marginata Agassiz, 1857) with genetic data on patterns of repeated paternity (i.e., stored sperm use) and multiple paternity to examine the potential influence on male reproductive success. Over 24 years (1983–2006), the number of reproductive females each year averaged 84 (minimum–maximum = 62–106) and, on average, 23% (minimum–maximum = 6%–40%) produced two clutches (intraseasonally). Among females with reproductive histories spanning 5–24 years (N = 167), 26% of individuals produced only one clutch annually, whereas 74% produced two clutches within a season. Among just intraseasonally iteroparous females, second-clutch production varied from 7% to 50%. Repeated paternity was observed in 97.5% of 40 paired clutches and 44% of 9 among-year comparisons of clutches from consecutive years. The frequent use of stored sperm to fertilize sequential clutches within and potentially among years can substantially increase a male’s reproductive success, particularly if males can base mating decisions on phenotypic characteristics correlated with female quality.

Genetic mating system and population history of the endangered Western Yellow-breasted Chat (Icteria virens auricollis) in British Columbia, Canada

The Western Yellow-breasted Chat ( Icteria virens auricollis (Deppe, 1830)) is a Neotropical migrant, with a Canadian distribution restricted to breeding populations in southern British Columbia. Given its small population size and diminishing breeding habitat, Yellow-breasted Chats are federally endangered in Canada. We used genotypic data at eight microsatellite loci to assess genetic diversity, reconstruct population structure and demographic history, and characterize genetic mating system of Yellow-breasted Chats sampled across 60 nesting sites at five locations in the Okanagan Valley (n = 148). Microsatellite-based analyses indicated lack of significant genetic differentiation among breeding sites and no genetic evidence of population decline. Parentage assignments indicated moderate levels of extra-pair paternity, with 30.7% offspring not sired by attending males. Patterns of sibship among nestlings revealed 49.1% of the clutches were composed entirely of full-siblings, with half-siblings and unrelated nestlings present in some broods. These findings suggest that extra-pair paternity is common in Yellow-breasted Chats, similar to other avian species, and present the first evidence of conspecific brood parasitism in warblers. Our findings add to a growing body of research informing the need to establish a national park in the south Okanagan to preserve critical habitat and connect populations of species at risk.

High degree of multiple paternity in the viviparous Shiner Perch, Cymatogaster aggregata, a fish with long-term female sperm storage

The Shiner Perch (Cymatogaster aggregata Gibbons) exhibits a viviparous reproductive mode and long-term female sperm storage, two biological features that may predispose this fish species for both intense sperm competition and frequent multiple paternity within broods. To test these hypotheses, we used polymorphic microsatellite markers to identify sires and quantify paternal contributions to the progeny arrays of 27 pregnant females from a natural population of C. aggregata. The number of sires per brood ranged from one to eight (mean 4.6), typically with skewed distributions of fertilization success by the fathers but no correlation between sire number and brood size. The extraordinarily high incidences of multiple paternity in this species probably are due in part to high rates of mate encounter, but selection pressures related to the avoidance of maternal-fetal incompatibility may further have promoted the evolution of polyandrous mating behaviors in this female-pregnant species. Our genetic data are consistent with the hypothesis that viviparity, long-term sperm storage, and extreme polyandry are interrelated reproductive phenomena that should promote the evolution of post-copulatory sperm competition and/or cryptic female choice in these fishes.

Parentage in natural populations: novel methods to detect parent-offspring pairs in large data sets

Parentage analysis in natural populations presents a valuable yet unique challenge because of large numbers of pairwise comparisons, marker set limitations and few sampled true parent-offspring pairs. These limitations can result in the incorrect assignment of false parent-offspring pairs that share alleles across multi-locus genotypes by chance alone. I first define a probability, Pr(δ), to estimate the expected number of false parent-offspring pairs within a data set. This probability can be used to determine whether one can accept all putative parent-offspring pairs with strict exclusion. I next define the probability Pr(φ|λ), which employs Bayes' theorem to determine the probability of a putative parent-offspring pair being false given the frequencies of shared alleles. This probability can be used to separate true parent-offspring pairs from false pairs that occur by chance when a data set lacks sufficient numbers of loci to accept all putative parent-offspring pairs. Finally, I propose a method to quantitatively determine how many loci to let mismatch for study-specific error rates and demonstrate that few data sets should need to allow more than two loci to mismatch. I test all theoretical predictions with simulated data and find that, first, Pr(δ) and Pr(φ|λ) have very low bias, and second, that power increases with lower sample sizes, uniform allele frequency distributions, and higher numbers of loci and alleles per locus. Comparisons of Pr(φ|λ) to strict exclusion and CERVUS demonstrate that this method may be most appropriate for large natural populations when supplemental data (e.g. genealogies, candidate parents) are absent.

Parentage identification using single nucleotide polymorphism genotypes: application to product tracing

Identification of relatives using SNP markers has many possible applications. One is as a route to tracing a food product such as a cut of meat back to its source of origin by identifying the parents of the animal from which the product was derived. We develop methods for using SNP markers with maximum likelihood, allowing for the possibility of genotyping errors that would cause false exclusions by simpler methods. We use expectations of likelihood ratios to consider how gene frequencies in the parental populations, numbers of loci, and error rates affect accuracy. This is further quantified as the risk, the probability that an incorrect sire is identified from a panel that contains many other putative sires including its relatives, using a breeding structure relevant to pig breeding. This appears to be a straightforward and potentially effective means of product tracing.

Parentage and sibship exclusions: higher statistical power with more family members

Parentage exclusion probabilities are now routinely calculated in genetic marker-assisted parentage analyses to indicate the statistical power of the analyses achievable for a given set of markers, and to measure the informativeness of a set of markers for parentage inference. Previous formulas invariably assume that parentage is to be sought for a single offspring, while in practice multiple full siblings might be sampled (for example, seeds, eggs or young from a pair of monogamous parents) and their father, mother or both are to be assigned among a number of candidates. In this study, I derive formulas for parentage exclusion probabilities for an arbitrary number (n) of fullsibs, which reduce to previous equations for the special case of n=1. I also derive sibship exclusion probabilities, and investigate the power of differentiating half-sib, avuncular and grandparent-grandoffspring relationships using unlinked autosomal markers among different numbers of tested individuals. Applications of the formulas are demonstrated using both theoretical and empirical data sets of allele frequencies. The results from the study highlight the conclusion that the power of genealogical relationship inferences can be enhanced enormously by analysing multiple individuals for a given set of markers. The equations derived in this study allow more accurate determination of marker information and of the power of a parentage/sibship analysis. In addition, they can be used to guide experimental designs of parentage analyses in selecting markers and determining the number of offspring to be sampled and genotyped.

Genetic polyandry and sexual conflict in the sandbar shark, Carcharhinus plumbeus, in the western North Atlantic and Gulf of Mexico

To investigate patterns of polyandry in the sandbar shark (Carcharhinus plumbeus), 20 pregnant females were sampled from the western North Atlantic and Gulf of Mexico. Five species-specific microsatellite markers were used to genotype each shark and its litter. Of 20 litters, 17 (85%) were shown to have multiple sires. In multiply sired litters, the estimated minimum number of sires ranged from two to five with an average of 2.3 males per litter. Regression analysis did not demonstrate a significant relationship between female reproductive success and female body size or sire number and female body size. There was a high incidence of reproductive skew noted in litters, and two groups of males with significantly different mean reproductive success were observed. Analyses using Bateman's principles suggest that there is less direct benefit for females that acquire multiple mates than for males who bias paternity within litters. In light of past morphological and behavioural studies, these data suggest that patterns of polyandry in elasmobranchs may be determined by coercive mating, and that breeding behaviour has likely evolved in the context of sexual conflict.

Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree

The confirmation of the segregation of experimentally populations is required before their commercial design of such confirmation experiments has the the pedigree while maintaining the power to detect chromosomes of a complex pedigree of 570 Charollais contained a moderately sized half-sib family which was wide level were detected in the half-sib analysis and analysis of the complex pedigree using identity-by-estimation of QTL effects was achieved by fitting all observed in the single QTL models. Both methods of different regions, and the variance components method demonstrates the viability of applying a variance inbreeding.

Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population

In the present study, molecular genetic markers were used to help estimate the degree of wrong sire information in the German Angeln dairy cattle population. Sixteen polymorphic microsatellite markers were genotyped on 5 different paternal half-sib families with a total of 805 daughters. For the genotyping process, blood samples of the daughters and semen samples of the sires were used. Allelic frequencies and exclusion probabilities were estimated. The simultaneous effect of wrong (WSI) and missing sire information (MSI) on the reliability of estimated breeding values and on the genetic gain was investigated using deterministic simulations. For these simulations, different values for the number of daughters per sire, heritability, WSI, and MSI were chosen. The estimated proportion of the WSI was 7% in the German Angeln dairy cattle population. The combined impact of WSI and MSI on the genetic gain was relatively large, especially in the case of small progeny size per sire and low heritability. The impact of WSI was more harmful than MSI on response to selection.

Informativeness of genetic markers for pairwise relationship and relatedness inference

Measuring the information content of markers in relationship/relatedness inferences is important in selecting highly informative markers to attain a given statistical power with the minimal genotyping effort. Using information-theoretic principles, I introduce the informativeness for relationship (I(R)) and the informativeness for relatedness (I(r)) to measure the amount of information provided by markers in inferring pairwise relationships (R) and relatedness (r), respectively. I also propose a fast and accurate algorithm to calculate the power (PW(R)) of a set of markers in differentiating two candidate relationships, and the reciprocal of the mean squared deviations of relatedness estimates (RMSD) to measure the amount of information of markers actually used by an estimator in estimating relatedness. All of the four measurements (I(R), I(r), PW(R), RMSD) apply to dominant and codominant markers, haploid and diploid individuals, and take into account of mutations and typing errors in data. The statistical properties of the four measurements and their relationships are investigated analytically and are examined by applying these methods to simulated and empirical data.

Genetic evaluation using parentage information from genetic markers1

Genetic evaluation relies on pedigree information to account for the trait information on individuals and their relatives. Recording pedigrees may place unfavorable restrictions on the management of breeding populations, such as the use of single-sire mating groups and the observation of parturition. The use of DNA marker information is an alternative method to identify parents, but it is difficult to assign the parents unambiguously for all progeny in extensively farmed livestock without the use of very many markers. We present methods that use DNA information on parentage within a genetic evaluation system that allow for genotyping errors and for the parentage information to be incomplete, with probabilities assigned to possible parent pairs (i.e., fractional parentage assignment). Two of these methods use a computing strategy that circumvents the high memory requirements associated with the application of previous methods designed for use with fractional parentage assignment. This strategy has an additional advantage of allowing the same statistical models to be used in the evaluation as with recorded pedigrees. The use of DNA marker-based parentage for genetic evaluation is associated with lower genetic gain (at the same survival levels) than by using the true pedigree. This decrease in gain depends on a number of factors, including trait heritability and the DNA markers used. The methods we have described show how DNA marker information could be used to replace traditional pedigree recording.

Use of microsatellites for parentage and kinship analyses in animals

Microsatellite markers are quickly becoming the molecular marker of choice for studies of parentage and kinship in animals. In this chapter, we review methods and give protocols for screening potential microsatellite markers, as well as protocols for genotyping individuals with useful markers once they have been identified. In addition, we explain how microsatellites can be used to assess parentage and kinship, give basic analytical methods, and briefly review more sophisticated approaches that can be used to circumvent many of the problems that arise in any real empirical study.

Polyandry in a marine turtle: females make the best of a bad job

The female perspective on reproductive strategies remains one of the most active areas of debate in biology. Even though a single mating is often sufficient to satisfy the fertilization needs of most females and the act of further mating incurs costs, multiple paternity within broods or clutches is a common observation in nature. Direct or indirect advantage to females is the most popular explanation. However, the ubiquity of this explanation is being challenged by an increasing number of cases for which benefits are not evident. For the first time, we test possible fitness correlates of multiple paternity in a marine turtle, an organism that has long attracted attention in this area of research. Contrary to the wide-spread assumption that multiple mating by female marine turtles confers fitness benefits, none were apparent. In this study, the environment played a far stronger role in determining the success of clutches than whether paternity had been single or multiple. A more likely explanation for observations of multiply sired clutches in marine turtles is that these are successful outcomes of male coercion, where females have conceded to superfluous matings as a compromise. Thus, multiple matings by female marine turtles may be a form of damage control as females attempt to make the best of a bad job in response to male harassment.

Methods of parentage analysis in natural populations

The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.

Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection

The proportion of cows in the UK dairy herd whose sires were misidentified was estimated using DNA markers. Genetic marker genotypes were determined on 568 cows (from 168 milk samples and 400 hair samples) and 96 putative sires (from semen samples). The estimated pedigree error rate from the hair samples was 8.8%, and from the milk samples, 13.1%, giving an overall estimate of the error rate of 10%. This level of pedigree errors will have a relatively large impact on the efficiency of progeny testing and the accuracy of cow predicted breeding values. We predict a loss of response to selection of approximately 2 to 3% given this error rate.

Parental assignment in fish using microsatellite genetic markers with finite numbers of parents and offspring

Deterministic predictions for the proportion of offspring assigned to different numbers of parent-pairs are developed in order to investigate the power of microsatellite loci for parental assignment in fish species. Comparisons with stochastic simulation results show that predictions based on exclusion probabilities are accurate, provided that the number of parents involved in the crosses is large. Accounting for sampling of parents gave very accurate predictions for a small number of parents and a single biallelic locus. For large numbers of loci or large numbers of alleles per locus stochastic simulations are, however, the only available method to predict the power of assignment of a particular set of loci when the number of parents is small. Nine 5-allele loci or six 10-allele loci with equifrequent alleles, are sufficient for assigning, with certainty, parents to 99% of the fish resulting from either 100 or 400 crosses. Results simulating a set of highly polymorphic microsatellites developed for Atlantic salmon show that the four most informative loci are sufficient to assign at least 99% of the offspring to the correct pair with 100 crosses involving 100 males and 100 females. An additional locus is required for correctly assigning 99% of the offspring when the 100 crosses are produced with 10 males and 10 females.

How cuckoldry can decrease the opportunity for sexual selection: data and theory from a genetic parentage analysis of the sand goby, Pomatoschistus minutus

Alternative mating strategies are common in nature and are generally thought to increase the intensity of sexual selection. However, cuckoldry can theoretically decrease the opportunity for sexual selection, particularly in highly polygamous species. We address here the influence of sneaking (fertilization thievery) on the opportunity for sexual selection in the sand goby Pomatoschistus minutus, a marine fish species in which males build and defend nests. Our microsatellite-based analysis of the mating system in a natural sand goby population shows high rates of sneaking and multiple mating by males. Sneaker males had fertilized eggs in approximately 50% of the assayed nests, and multiple sneakers sometimes fertilized eggs from a single female. Successful males had received eggs from 2 to 6 females per nest (mean = 3.4). We developed a simple mathematical model showing that sneaking in this polygynous sand goby population almost certainly decreases the opportunity for sexual selection, an outcome that contrasts with the usual effects of cuckoldry in socially monogamous animals. These results highlight a more complex and interesting relationship between cuckoldry rates and the intensity of sexual selection than previously assumed in much of the literature on animal mating systems.