A note on positive identification of paternity by using genetic markers

To see the efficiency of the statistical methods for positive identification of fathers using genetic markers, the statistical properties of the paternity index are studied algebraically and numerically. It is found that the currently used statistical methods are not powerful enough to discriminate between true fathers and non-excluded non-fathers, and, more often than not, may lead to false attributions of paternity. It is, therefore, suggested that exclusion of paternity is the only conclusive evidence that can be accepted by courts of law until better methods are devised.     

Do marker‐based paternity assignments favour heterozygous and unrelated males?

Genetic marker‐based parentage analyses are widely applied to studies of natural populations in the fields of evolutionary biology, conservation biology and ecology. When the same markers used in a parentage analysis are used together with the inferred parentage in a downstream analysis, such as the analysis of mate choice in terms of heterozygosity or relatedness, a bias may be incurred because a subset of the genotypes are favoured in parentage assignments or non‐exclusions. A previous simulation study shows that exclusion‐based paternity analyses are biased in favour of heterozygous males, and males less related to the mothers than expected under random mating. In this study, I investigated the biases of genetic paternity analyses achieved by both exclusion‐ and likelihood‐based methods, using both analytical and simulation approaches. It is concluded that while both exclusion‐ and likelihood‐based methods can lead to biased paternity assignments or non‐exclusions in favour of a subset of genotypes, the bias is not consistently towards heterozygous males or males apparently less related to mothers. Both the direction and extent of the bias depend heavily on the allele frequency distribution and the number of markers, the methods used for paternity assignments, and the estimators of relatedness. There exist important differences in the patterns of the biases between exclusion‐ and likelihood‐based paternity analysis methods. It is concluded that the markers, except when they are highly informative to yield accurate paternity assignments or exclusions, should be split into two subsets which are used separately in the paternity and downstream analyses.     

Do male paternity guards ensure female fidelity in a duetting fairy-wren?

Most socially monogamous bird species engage in extra-pair mating,and consequently males may adopt various behavioral strategiesto guard paternity. However, the relationship between mate guardingand extra-pair paternity is unclear: low levels of extra-pairpaternity can be associated either with no mate guarding orwith intense mate guarding. We investigate paternity guardsin the purple-crowned fairy-wren (Malurus coronatus), a duettingspecies where extra-pair paternity is rare. This species isunusual in a genus known for extremely high levels of extra-pairmating. We examine the behavioral interactions between the sexesunderlying these low rates of extra-pair paternity and showthat male purple-crowned fairy-wrens do not use frequent copulationor courtship feeding to assure paternity or guard females acousticallyby duetting. Males maintain close proximity to females bothwhen they are fertile and when they are not breeding and donot invest in courtship displays to extra-pair females. Consistentwith predictions of theoretical models, low extra-pair paternityin this species may be related to female fidelity rather thanmale paternity assurance strategies, but short-term removalof males would be necessary to test this experimentally.     

Relative fitness components measured with competitive PCR

In mating systems with sperm competition, paternity is frequently established with modern DNA techniques. These methods are often expensive and cumbersome, and can be especially difficult for highly fecund species. An additional objective of many paternity studies is to discover the relationship between sperm number and paternity. We present here a competitive polymerase chain reaction (PCR) protocol, coupled with the use of an automated sequencer, that has two functions: (i) to measure directly relative sperm output of males in sperm competition; and (ii) to estimate paternity distributions of large numbers of offspring simultaneously. Our technique was calibrated using a microsatellite locus of the bluehead wrasse, Thalassoma bifasciatum, with the result that product ratio after competitive PCR accurately reflected the initial template proportions of known mixtures of DNA. When we applied our technique to multiple larvae of separate mating events we found that paternity distributions estimated with the competitive PCR technique closely matched the estimates derived from the traditional method of pooling paternity data from individual larvae. Finally, we compared paternity of these spawns with relative sperm contribution estimates. This comparison suggests that ejaculate size alone does not predict a male's proportion of paternity within the group.     

Genetic Patterns of Paternity and Testes Size in Mammals

Background

Testes size is used as a proxy of male intrasexual competition, with larger testes indicative of greater competition. It has been shown that in some taxa, social mating systems reflect variance in testes size, but results are not consistent, and instead it has been suggested that genetic patterns of mating may reflect testes size. However, there are different measures of genetic patterns of mating. Multiple paternity rates are the most widely used measure but are limited to species that produce multi-offspring litters, so, at least for group living species, other measures such as loss of paternity to males outside the social group (extra group paternity) or the proportion of offspring sired by the dominant male (alpha paternity) might be appropriate. This study examines the relationship between testes size and three genetic patterns of mating: multiple paternity, extragroup paternity and alpha paternity.

Methodology/Principal Findings

Using data from mammals, phylogenetically corrected general linear models demonstrate that both multiple paternity and alpha paternity, but not extra group paternity, relate to testes size. Testes size is greater in species with high multiple paternity rates, whereas the converse is found for alpha paternity. Additionally, length of mating season, ovulation mode and litter size significantly influenced testes size in one model.

Conclusions/Significance

These results demonstrate that patterns of mating (multiple paternity and alpha paternity rates) determined by genetic analysis can provide reliable indicators of male postcopulatory intrasexual competition (testes size), and that other variables (length of mating season, ovulation mode, litter size) may also be important.     

A retrospective assessment of the accuracy of the paternity inference program CERVUS

CERVUS is a Windows-based software package written to infer paternity in natural populations. It offers advantages over exclusionary-based methods of paternity inference in that multiple nonexcluded males can be statistically distinguished, laboratory typing error is considered and statistical confidence is determined for assigned paternities through simulation. In this study we use a panel of 84 microsatellite markers to retrospectively determine the accuracy of statistical confidence when CERVUS was used to infer paternity in a population of red deer (Cervus elaphus). The actual confidence of CERVUS-assigned paternities was not significantly different from that predicted by simulation.     

Certainty of paternity and paternal effort in the collared flycatcher

Models of optimal parental investment predict that variationin certainty of paternity can affect the optimal level of paternalinvestment when a male's expected paternity in different nestingattempts is not fixed throughout his lifetime. Several attemptsto test this prediction experimentally in monogamous birds havefailed to induce a reduction in care by males. This may be becausethe method used, detaining males, is a poor model for what happenswhen a male's certainly of paternity is naturally reduced. Wecaught and detained female collared flycatchers Ficedula albicollisfor 1 h immediately after laying on one or two occasions inan attempt to induce variation in certainty of paternity forthe males they were mated to. By capturing females immediatelyafter laying we hoped to exploit the existence of an "inseminationwindow" since males should be very sensitive to female absenceduring this period. The general effect of the experimental manipulationwas consistent with reduced certainty of paternity: males respondedby reducing their level of paternal care to nestlings, and malesmated to females that had been caught on one morning fed nestlingssignificantly less often and made a smaller share of feedingvisits than males mated to control females. The effects of theexperiment were generally weak, however, and we argue that certaintyof paternity may be fixed well before egg laying, in which caseexperimental manipulations are unlikely to have large effects.It is difficult to predict die effects of natural variationin certainty of paternity on levels of male paternal care becausedifferential allocation by females mated to attractive malesmay act in the opposite direction     

Direct visualization of sperm competition and sperm storage in Drosophila.

Drosophila females engage in multiple matings [1] [2] [3] [4] even though they can store sperm in specialized organs for most of their life [5]. The existence of sperm competition in Drosophila has been inferred from the proportion of progeny sired by the second male in double-mating experiments [6] [7] [8]. Investigators have used this approach to quantify genetic variation underlying sperm competition [8] [9] [10], to elucidate its genetic basis [11], to identify the dependence of different male competitive ability on the genotype of the females with which they mate [12] and to discern the potential role of sperm competition in species isolation [13] [14]. This approach assumes that the sperm from two males stored in a female compete to fertilize the eggs. The mechanism by which sperm competition is accomplished is still unknown, however. Here, fluorescence microscopy, cytometry, and differently labeled sperm were used to analyze the fate of sperm inside the female's sperm storage organs, to quantify sperm competition, and to assess how closely paternity success corresponds to the appearance and location of the sperm. The results show that the first male's sperm is retained for a shortened period if the female remates, and that the second males that sire more progeny either induce females to store and use more of their sperm or strongly displace resident sperm.     

Exclusion probabilities for pedigree testing farm animals

Pedigree testing, using genetic markers, may be undertaken for a variety of situations, of which the classical paternity testing is only one. This has not always been made clear in the literature. Exclusion probabilities associated with various testing situations, including the use of autosomal or X-linked codominant marker systems with any number of alleles, are presented. These formulae can be used to determine the appropriate exclusion probability for the situation being investigated. One such situation is where sire groups of progeny are to be verified without knowledge of the dams' genotypes, in which case the classical paternity exclusion probability is too high, and if used may result in an optimistic declaration about the progeny that have not been excluded. On the other hand, if mating pairs are known then incorrect progeny can be excluded at a higher rate than suggested by paternity exclusion calculations. The formulae also assist in determining the usefulness of X-linked markers, particularly if the pedigree checks involve progeny of only one sex. A system of notation that is useful for the algebraic manipulation of genetic probabilities, including exclusion probabilities as presented here, is also given.     

Paternity and the evolution of male parental care

It is generally believed that level of paternity (the proportion of zygotes in a brood that were fertilized by the male providing parental care) has an important role in the evolution of parental care. We have used population genetics models to investigate this role. The models indicate that only in mating systems where a parental male “sacrifices” promiscous matings can paternity influence the evolution of male parental care. This is because level of paternity can reflect the number of opportunities for these promiscuous fertilizations. For example, high paternity can mean few opportunities and therefore a low cost for paternal care.Certain behaviors may preadapt a species for the evolution of male parental care because they decrease the costs of providing care. For example, in fish species where male care has evolved from spawning territories, the very establishment of territories may have precluded males from gaining promiscuous matings, thereby eliminating the promiscuity costs and facilitating the evolution of care. Without a promiscuity cost, level of paternity will not have influenced the evolution of male care in fishes.Because paternity has limited influence in the evolution of male care, differences in reliability of parentage between males and females are unlikely to explain the prevalence of female care. Our analysis suggests that paternity differences between species cannot serve as a general explanation for the observed patterns of parental care behavior.     

Effects of ovarian fluid and genetic differences on sperm performance and fertilization success of alternative reproductive tactics in Chinook salmon

In many species, sperm velocity affects variation in the outcome of male competitive fertilization success. In fishes, ovarian fluid (OF) released with the eggs can increase male sperm velocity and potentially facilitate cryptic female choice for males of specific phenotypes and/or genotypes. Therefore, to investigate the effect of OF on fertilization success, we measured sperm velocity and conducted in vitro competitive fertilizations with paired Chinook salmon (Oncorhynchus tshawytscha) males representing two alternative reproductive tactics, jacks (small sneaker males) and hooknoses (large guarding males), in the presence of river water alone and OF mixed with river water. To determine the effect of genetic differences on fertilization success, we genotyped fish at neutral (microsatellites) and functional [major histocompatibility complex (MHC) II ß1] markers. We found that when sperm were competed in river water, jacks sired significantly more offspring than hooknoses; however, in OF, there was no difference in paternity between the tactics. Sperm velocity was significantly correlated with paternity success in river water, but not in ovarian fluid. Paternity success in OF, but not in river water alone, was correlated with genetic relatedness between male and female, where males that were less related to the female attained greater paternity. We found no relationship between MHC II ß1 divergence between mates and paternity success in water or OF. Our results indicate that OF can influence the outcome of sperm competition in Chinook salmon, where OF provides both male tactics with fertilization opportunities, which may in part explain what maintains both tactics in nature.     

基于微单体型分子标记的草鱼亲子鉴定方法

研究选择一种新型分子标记——微单体型用于亲子鉴定, 构建了高效的标记筛选和亲子鉴定流程, 并以草鱼(Ctenopharyngodon idellus) 为例评估了该亲子鉴定方法的效果。结果表明, 利用基因组重测序数据能够准确完成微单体型标记的分型, 效果和适应性明显优于传统的基于群体遗传学推断的分型; 通过信息熵的大小能够高效筛选微单体型标记组合, 3个和5个微单体型标记的亲子鉴定结果与微卫星序列(SSR)鉴定结果的一致性分别达到97.08%和99.42%。研究表明使用微单体型分子标记可以快速而准确地完成鱼类的亲子鉴定工作。     

Fractional paternity assignment: theoretical development and comparison to other methods

Summary There has recently been a burgeoning interest in the analysis of paternity patterns for natural populations because of its relevance to population genetic phenomena such as the distance between successful mates, relative male reproductive success and gene flow. In this paper we develop a method of analyzing populational patterns of paternity, the fractional paternity method, and compare its performance to two other commonly used methods of paternity analysis (simple exclusion and the most-likely methods). We show that the fractional method is the most accurate method for determining populational patterns of paternity because it assigns paternity to all progeny examined, and because it avoids biases inherent in the other paternity analysis methods when model assumptions are met. In particular, it avoids a systematic bias of the most-likely paternity assignment method, which has a tendency to over-assign paternity of progeny to certain male parents with a greater than average number of homozygous marker loci. We also demonstrate the effect of linkage of some of the marker loci on paternity assignment, showing how the knowledge of the linkage phase of male and female parents in the population can significantly improve the accuracy of the estimates of populational patterns of paternity. Knowledge of the linkage phase of individuals in a population is usually unknown and difficult to assess without progeny testing, which involves considerable labor. However, we show how the linkage phase of hermaphroditic individuals in a population can be obtained in conjunction with the paternity analysis if progeny can be obtained from each hermaphroditic individual in the population, thereby avoiding the problem of traditional progeny testing. Applications of the fractional paternity approach developed herein should contribute significantly to our understanding of the mating patterns in, and hence the evolution of, natural populations.     

Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale

We present a new method for paternity analysis in natural populations that is based on genotypic data that can take the sampling fraction of putative parents into account. The method allows paternity assignment to be performed in a decision theoretic framework. Simulations are performed to evaluate the utility and robustness of the method and to assess how many loci are necessary for reliable paternity inference. In addition we present a method for testing hypotheses regarding relative reproductive success of different ecologically or behaviorally defined groups as well as a new method for estimating the current population size of males from genotypic data. This method is an extension of the fractional paternity method to the case where only a proportion of all putative fathers have been sampled. It can also be applied to provide abundance estimates of the number of breeding males from genetic data. Throughout, the methods were applied to genotypic data collected from North Atlantic humpback whales (Megaptera novaeangliae) to test if the males that appear dominant during the mating season have a higher reproductive success than the subdominant males.     

Genetic conflicts,multiple paternity and the evolution of genomic imprinting.

We present nine diallelic models of genetic conflict in which one allele is imprintable and the other is not to examine how genomic imprinting may have evolved. Imprinting is presumed to be either maternal (i.e., the maternally derived gene is inactivated) or paternal. Females are assumed to be either completely monogamous or always bigamous, so that we may see any effect of multiple paternity. In contrast to previous verbal and quantitative genetic models, we find that genetic conflicts need not lead to paternal imprinting of growth inhibitors and maternal imprinting of growth enhancers. Indeed, in some of our models--those with strict monogamy--the dynamics of maternal and paternal imprinting are identical. Multiple paternity is not necessary for the evolution of imprinting, and in our models of maternal imprinting, multiple paternity has no effect at all. Nevertheless, multiple paternity favors the evolution of paternal imprinting of growth inhibitors and hinders that of growth enhancers. Hence, any degree of multiple paternity means that growth inhibitors are more likely to be paternally imprinted, and growth enhancers maternally so. In all of our models, stable polymorphism of imprinting status is possible and mean fitness can decrease over time. Neither of these behaviors have been predicted by previous models.     

Identification of visual paternity cues in humans

Understanding how individuals identify their relatives has implications for the evolution of social behaviour. Kinship cues might be based on familiarity, but in the face of paternity uncertainty and costly paternal investment, other mechanisms such as phenotypic matching may have evolved. In humans, paternal recognition of offspring and subsequent discriminative paternal investment have been linked to father–offspring facial phenotypic similarities. However, the extent to which paternity detection is impaired by environmentally induced facial information is unclear. We used 27 portraits of fathers and their adult sons to quantify the level of paternity detection according to experimental treatments that manipulate the location, type and quantity of visible facial information. We found that (i) the lower part of the face, that changes most with development, does not contain paternity cues, (ii) paternity can be detected even if relational information within the face is disrupted and (iii) the signal depends on the presence of specific information rather than their number. Taken together, the results support the view that environmental effects have little influence on the detection of paternity using facial similarities. This suggests that the cognitive dispositions enabling the facial detection of kinship relationships ignore genetic irrelevant facial information.     

CPI distribution and cutoff values for duo kinship testing

DNA-based tests commonly use 13 STR (short tandem repeat) loci in human identification and paternity testing--the Combined DNA Index System or CODIS. Its average degree of accuracy of paternity identification is greater than 0.9999 under the circumstance of a mother, a child and a putative father. However, the possibility of false inclusions increases under circumstances such as [1] only two members of a family group are available--a duo case during determination of paternity or [2] identification of human remains while only one living relative is present. In Taiwan, the National Unidentified Human Remains Database uses the CODIS 13 STR for the identification of family members. Two or more reference samples in the DNA database have been found to share one allele at all loci tested. Then the Combined Paternity Index (CPI) is used to determine and provide an estimate of kinship in such cases. Combining 499,500 sets of DNA data for the 13 STR CODIS loci, totally 431 (0.086%) cases are false inclusions where all 13 loci shared at least one allele. Simulated partial DNA profiles (not all 13 loci yielded results) were created to mimic the mutation and degradation process. All 431 real duo cases were analyzed to evaluate sensitivity and specificity. This report provided four kinship-matching situations with CPI cutoff values when the number of allele-sharing loci exceeded 11. CPI values greater or lesser than the suggested cutoff point will provide a greater degree of confidence in determining whether two samples are derived from first-degree relatives.     

Restrictive mating by females on black grouse leks

In bird species with pair bonds, extra-pair matings could allow females to choose genetically superior males. This is not needed in lekking species because female choice is not constrained by pairing opportunities. However, polyandry has been reported in most lekking species studied so far. Using 12 microsatellite loci, we determined the paternity of 135 broods of black grouse sampled between 2001 and 2005 (970 hatchlings and 811 adult birds genotyped). The paternity assignments were combined to lek observations to investigate the mating behaviour of black grouse females. About 10% of the matings seemed to take place with males displaying solitarily. Forty per cent of the copulations between males displaying on the studied leks and radio-tagged females were not recorded. This was due to difficulties in identifying the females and because our observations did not cover all the possible time for matings. However, females of the undetected copulations had chosen males that were already known to be successful on the leks. There was a strong consistency between the observations and true paternity, even when the copulation was disturbed by a neighbouring male. Multiple mating and multiple paternities were rare. We can now confidently ascertain that most females mate only once with one male for the whole clutch. This mating behaviour requires that a single insemination is sufficient to fertilize a clutch and that females can determine whether the sperm has been successfully transferred. Grouse Tetraoninae with many lekking species may be the only bird taxon that has evolved these traits.     

Infant mortality following male takeovers in wild geladas

Since Sugiyama's [1965] first observations of infanticide, empirical evidence from a multitude of primate species has supported the sexual selection hypothesis-the idea that males enhance their reproductive success by killing nonrelated, unweaned infants to hasten the mothers' return to fertility. Like other primates that live in social groups where paternity certainty is high, the social structure of geladas [Theropithecus gelada] suggests that infanticide by males could enhance their reproductive success. Nevertheless, empirical evidence for infanticide in this species is limited to anecdotal accounts. Using the timing of infant mortality and female reproductive and behavioral data collected across 26 months from a population of geladas living in the Simien Mountains National Park, Ethiopia, we test whether sexually selected infanticide occurs in this species. We also examine two additional hypotheses [noninfanticide hypothesis and generalized aggression hypothesis] for this population. Results suggest that sexually selected infanticide in geladas may, indeed, be a threat to females with dependent infants. First, male takeovers-the most likely time for infanticide-were associated with subsequently elevated rates of infant death [a 32-fold increase] comprising nearly 60% of all infant mortality. Second, females who lost infants during this period returned to fertility more quickly than if infants had lived [IBIs were 50% shorter], and third, all of these females were observed to mate with the new male. We found little to no support for other hypotheses. Finally, these results raise the possibility that anecdotal reports [from previous studies and this study] of pregnancy termination, accelerated weaning, and deceptive sexual swellings may represent female counterstrategies to male infanticide in geladas.     

Mating system, multiple paternity and effective population size in the endemic flatback turtle (Natator depressus) in Australia

In recent years, genetic studies have been used to investigate mating systems of marine turtles, but to date no such research has been conducted on the flatback turtle (Natator depressus). This study investigates paternity of flatback turtle clutches at two rookeries in Queensland, Australia; Peak Island (Keppel Bay), and Mon Repos (Bundaberg). In the 2004–2005 nesting season, tissue samples were taken from either single or multiple clutches (n = 16) of nesting females (n = 8) representing a sampling effort ranging from 25% to 50% offspring per nest. Determination of the extent of multiple paternity was done using a comparative approach that included initial inferences based on observed alleles, Chi-square tests for deviations from Mendelian expectations, and three software programs (PARENTAGE1.0, GERUD2.0 and MER3.0). Results varied depending on the approach, but by calculating a consensus value of the output from these different methods, the null hypothesis of single paternity could be rejected in at least 11 of the 16 clutches (69%). Multiple paternity was thus observed in the clutches of six of nine females (67%), with two or three fathers being the most likely outcome. Analyses of successive clutches illustrated that paternal contribution to clutch fertilization can vary through time, as observed for two females. This first evidence regarding the mating system of flatback turtles indicates that multiple paternity is common in this species and that the observed frequency of multiple paternity is among the higher values reported in marine turtle species. Application of these results to estimates of effective population size (N _e) suggests that population size may have been relatively stable over long periods. Continued monitoring of population dynamics is recommended to ensure that future changes in the east coast can be detected.