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     

Seasonal pattern of filial cannibalism by Apogon doederleini mouthbrooding males

In temperate waters of southern Japan, mouthbrooding males of the cardinal fish Apogon doederleini sometimes ate their entire brood within a day of spawning. In spite of annual variation in age structure and length of the breeding season, however, the annual cannibalism rate (broods cannibalized to total broods spawned) was nearly constant, 12–16%. Fish 1 year old frequently cannibalized early broods of the season, especially the first brood, whereas the cannibalism rate by 2 year-old fish did not vary within the season. In contrast, the cannibalism by older males increased late in the season. This tendency was attributed to their different allocation patterns to growth and reproduction. For 1 year-old fish, which can enhance future reproductive success by growth and cannibalizing on early broods instead of mouthbrooding (at relatively low temperatures), this may be a tactic for investing energy in growth. For fish 3 years, which have more breeding cycles and grow little, cannibalizing late broods may be energetic compensation for their poor somatic condition. No seasonal variation of cannibalism by 2 year-old fish can be explained by their intermediate nature of growth and reproduction. Multiple mate availability is one factor facilitating the cannibalism by 2 and 3 + year-old fish whose operational sex ratio is female-biased.     

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.     

Effects of genotyping errors on parentage exclusion analysis

Genetic markers are widely used to determine the parentage of individuals in studies of mating systems, reproductive success, dispersals, quantitative genetic parameters and in the management of conservation populations. These markers are, however, imperfect for parentage analyses because of the presence of genotyping errors and undetectable alleles, which may cause incompatible genotypes (mismatches) between parents and offspring and thus result in false exclusions of true parentage. Highly polymorphic markers widely used in parentage analyses, such as microsatellites, are especially prone to genotyping errors. In this investigation, I derived the probabilities of excluding a random (related) individual from parentage and the probabilities of Mendelian-inconsistent errors (mismatches) and Mendelian-consistent errors (which do not cause mismatches) in parent-offspring dyads, when a marker having null alleles, allelic dropouts and false alleles is used in a parentage analysis. These probabilities are useful in evaluating the impact of various types of genotyping errors on the information content of a set of markers in and thus the power of a parentage analysis, in determining the threshold number of genetic mismatches that is appropriate for a parentage exclusion analysis and in estimating the rates of genotyping errors and frequencies of null alleles from observed mismatches between known parent-offspring dyads. These applications are demonstrated by numerical examples using both hypothetical and empirical data sets and discussed in the context of practical parentage exclusion analyses.     

Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica

Eight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at the HrU6 locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 × 10^-8 and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker-pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra-pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra-pair offspring.     

Confidence of paternity and paternal care by eastern bluebirds

Male birds are often faced with low confidence of paternityin their mates' offspring, raising the question of how paternalcare covaries with confidence of paternity. We tested the hypothesisthat male eastern bluebirds (Sialia sialis) reduce care of nestlingsin response to experimentally decreased confidence of paternity.Actual paternity, as assessed by DNA fingerprinting, had noeffect on male feeding rates, nor did males reduce care whenconfidence of paternity was experimentally decreased. Malesthat had been removed for 2 days while their mate was fertile(experimental group) fed nestlings at absolute rates similarto those of control males. The proportion of feeding trips providedby males was also similar for control and experimental nests.We found no difference in fledging success and nestling growthbetween experimental and control broods. Seven original residentmales were displaced by previously unbanded males. Althoughthese replacement males appeared to feed nestlings at normalrates, the nests attended by replacement males suffered reducedfledging success compared to control and experimental nests.Overall, we found no evidence that males reduce feeding effortwhen confidence of paternity is experimentally decreased. Malesmay tolerate some reduction in confidence of paternity withoutreducing care if paternal care is crucial to nestling survival.Alternatively, males may assess paternity within a brood usingcues other than their ability to guard their fertile mates.     

Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework

Inferring the parentage of a sample of individuals is often a prerequisite for many types of analysis in molecular ecology, evolutionary biology and quantitative genetics. In all but a few cases, the method of parentage assignment is divorced from the methods used to estimate the parameters of primary interest, such as mate choice or heritability. Here we present a Bayesian approach that simultaneously estimates the parentage of a sample of individuals and a wide range of population-level parameters in which we are interested. We show that joint estimation of parentage and population-level parameters increases the power of parentage assignment, reduces bias in parameter estimation, and accurately evaluates uncertainty in both. We illustrate the method by analysing a number of simulated test data sets, and through a re-analysis of parentage in the Seychelles warbler, Acrocephalus sechellensis. A combination of behavioural, spatial and genetic data are used in the analyses and, importantly, the method does not require strong prior information about the relationship between nongenetic data and parentage.     

Using blocks of linked single nucleotide polymorphisms as highly polymorphic genetic markers for parentage analysis

Single nucleotide polymorphisms (SNPs) are plentiful in most genomes and amenable to high throughput genotyping, but they are not yet popular for parentage or paternity analysis. The markers are bi-allelic, so individually they contain little information about parentage, and in nonmodel organisms the process of identifying large numbers of unlinked SNPs can be daunting. We explore the possibility of using blocks of between three and 26 linked SNPs as highly polymorphic molecular markers for reconstructing male genotypes in polyandrous organisms with moderate (five offspring) to large (25 offspring) clutches of offspring. Haplotypes are inferred for each block of linked SNPs using the programs Haplore and Phase 2.1. Each multi-SNP haplotype is then treated as a separate allele, producing a highly polymorphic, 'microsatellite-like' marker. A simulation study is performed using haplotype frequencies derived from empirical data sets from Drosophila melanogaster and Mus musculus populations. We find that the markers produced are competitive with microsatellite loci in terms of single parent exclusion probabilities, particularly when using six or more linked SNPs to form a haplotype. These markers contain only modest rates of missing data and genotyping or phasing errors and thus should be seriously considered as molecular markers for parentage analysis, particularly when the study is interested in the functional significance of polymorphisms across the genome.     

Comparing parentage inference software: reanalysis of a red deer pedigree

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

Effects of parental care on resource allocation into immune defense and buccal microbiota in mouthbrooding cichlid fishes*

Sexual dimorphism is founded upon a resource allocation trade‐off between investments in reproduction versus other life‐history traits including the immune system. In species with conventional parental care roles, theory predicts that males maximize their lifetime reproductive success by allocating resources toward sexual selection, while females achieve this through prolonging their lifespan. Here, we examine the interrelation between sexual dimorphism and parental care strategies in closely related maternal and biparental mouthbrooding cichlid fishes from East African Lake Tanganyika. We measured cellular immune parameters, examined the relative expression of 28 immune system and life history‐related candidate genes and analyzed the microbiota composition in the buccal cavity. According to our predictions, maternal mouthbrooders are more sexually dimorphic in immune parameters than biparental mouthbrooders, which has possibly arisen through a differential resource allocation into parental care versus secondary sexual traits. Biparental mouthbrooders, on the other hand, which share the costs of parental care, feature an upregulated adaptive immune response and stronger antiviral properties, while their inflammation response is reduced. Overall, our results suggest a differential resource allocation trade‐off between the two modes of parental investment.     

Development of microsatellite markers for parentage analysis in the great tinamou (Tinamus major)

Eighteen microsatellite loci were isolated from great tinamous (Tinamus major), which are large terrestrial birds found in the Neotropics. These are the first primers developed for the Order Tinamiformes. Paternity analyses are possible because the levels of heterozygosity are sufficiently high (0.29-0.90).     

The future of parentage analysis: From microsatellites to SNPs and beyond

Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next‐generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next‐generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next‐generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP‐based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100–500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next‐generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next‐generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.     

A practical guide to methods of parentage analysis

The use of molecular techniques for parentage analysis has been a booming science for over a decade. The most important technological breakthrough was the introduction of microsatellite markers to molecular ecology, an advance that was accompanied by a proliferation and refinement of statistical techniques for the analysis of parentage data. Over the last several years, we have seen steady progress in a number of areas related to parentage analysis, and the prospects for successful studies continue to improve. Here, we provide an updated guide for scientists interested in embarking on parentage analysis in natural or artificial populations of organisms, with a particular focus on computer software packages that implement various methods of analysis. Our survey of the literature shows that there are a few established methods that perform extremely well in the analysis of most types of parentage studies. However, particular experimental designs or study systems can benefit from some of the less well-known computer packages available. Overall, we find that parentage analysis is feasible and satisfying in most systems, and we try to provide a simple roadmap to help other scientists navigate the confusing topography of statistical techniques.     

Impact of candidate sire number and sire relatedness on DNA polymorphism-based measures of exclusion probability and probability of unambiguous parentage

Genetic paternity testing can provide sire identity data for offspring when females have been exposed to multiple males. However, correct paternity assignment can be influenced by factors determined in the laboratory and by size and genetic composition of breeding groups. In the present study, DNA samples from 26 commingled beef bulls and their calves from the Nebraska Reference Herd-1 (NRH1), along with previously reported Illinois Reference/Resource Families data, were used to estimate the impact of sire number and sire relatedness on microsatellite-based paternity testing. Assay performance was measured by exclusion probabilities and probabilities of unambiguous parentage (PUP) were derived. Proportion of calves with unambiguous parentage (PCUP) was also calculated to provide a readily understandable whole-herd measure of unambiguous paternity assignment. For NRH1, theoretical and observed PCUP values were in close agreement (85.3 and 85.8%, respectively) indicating good predictive value. While the qualitative effects on PUP values of altering sire number and sire relatedness were generally predictable, we demonstrate that the impacts of these variables, and their interaction effects, can be large, are non-linear, and are quantitatively distinct for different combinations of sire number and degree of sire relatedness. In view of the potentially complex dynamics and practical consequences of these relationships in both research and animal production settings, we suggest that a priori estimation of the quantitative impact of a given set of interacting breeding group-specific and assay-specific parameters on PUP may be indicated, particularly when candidate sire pools are large, sire relatedness may be high, and/or loci numbers or heterozygosity values may be limiting.     

A bayesian framework for parentage analysis: the value of genetic and other biological data

We develop fractional allocation models and confidence statistics for parentage analysis in mating systems. The models can be used, for example, to estimate the paternities of candidate males when the genetic mother is known or to calculate the parentage of candidate parent pairs when neither is known. The models do not require two implicit assumptions made by previous models, assumptions that are potentially erroneous. First, we provide formulas to calculate the expected parentage, as opposed to using a maximum likelihood algorithm to calculate the most likely parentage. The expected parentage is superior as it does not assume a symmetrical probability distribution of parentage and therefore, unlike the most likely parentage, will be unbiased. Second, we provide a mathematical framework for incorporating additional biological data to estimate the prior probability distribution of parentage. This additional biological data might include behavioral observations during mating or morphological measurements known to correlate with parentage. The value of multiple sources of information is increased accuracy of the estimates. We show that when the prior probability of parentage is known, and the expected parentage is calculated, fractional allocation provides unbiased estimates of the variance in reproductive success, thereby correcting a problem that has previously plagued parentage analyses. We also develop formulas to calculate the confidence interval in the parentage estimates, thus enabling the assessment of precision. These confidence statistics have not previously been available for fractional models. We demonstrate our models with several biological examples based on data from two fish species that we study, coho salmon (Oncorhychus kisutch) and bluegill sunfish (Lepomis macrochirus). In coho, multiple males compete to fertilize a single female's eggs. We show how behavioral observations taken during spawning can be combined with genetic data to provide an accurate calculation of each male's paternity. In bluegill, multiple males and multiple females may mate in a single nest. For a nest, we calculate the fertilization success and the 95% confidence interval of each candidate parent pair.     

Power of exclusion for parentage verification and probability of match for identity in American Kennel Club breeds using 17 canine microsatellite markers

DNA analysis of microsatellite markers has become a common tool for verifying parentage in breed registries and identifying individual animals that are linked to a database or owner. Panels of markers have been developed in canines, but their utility across and within a wide range of breeds has not been reported. The American Kennel Club (AKC) authorized a study to determine the power to exclude non-parents and identify individuals using DNA genotypes of 17 microsatellite markers in two panels. Cheek swab samples were voluntarily collected at Parent Breed Club National Specialty dog shows and 9561 samples representing 108 breeds were collected, averaging 88.5 dogs per breed. The primary panel of 10 markers exceeded 99% power of exclusion for canine parentage verification of 61% of the breeds. In combination with the secondary panel of seven markers, 100% of the tested breeds exceeded 99% power of exclusion. The minimum probability match rate of the first panel was 3.6 x 10(-5) averaged across breeds, and with the addition of the second panel, the probability match rate was 3.2 x 10(-8); thus the probability of another random, unrelated dog with the same genotype is very low. The results of this analysis indicated that, on average, the primary panel meets the AKC's needs for routine parentage testing, but that a combination of 10-15 genetic markers from the two panels could yield a universal canine panel with enhanced processing efficiency, reliability and informativeness.     

Sperm competition mechanisms,confidence of paternity,and the evolution of paternal care in the golden egg bug (Phyllomorpha laciniata)

Theoretical models predict how paternal effort should vary depending on confidence of paternity and on the trade-offs between present and future reproduction. In this study we examine patterns of sperm precedence in Phyllomorpha laciniata and how confidence of paternity influences the willingness of males to carry eggs. Female golden egg bugs show a flexible pattern of oviposition behavior, which results in some eggs being carried by adults (mainly males) and some being laid on plants, where mortality rates are very high. Adults are more vulnerable to predators when carrying eggs; thus, it has been suggested that males should only accept eggs if there are chances that at least some of the eggs will be their true genetic offspring. We determined the confidence of paternity for naturally occurring individuals and its variation with the time. Paternity of eggs fertilized by the last males to mate with females previously mated in the field has been determined using amplified fragment length polymorphisms (AFLPs). The exclusion probability was 98%, showing that AFLP markers are suitable for paternity assignment. Sperm mixing seems the most likely mechanism of sperm competition, because the last male to copulate with field females sires an average of 43% of the eggs laid during the next five days. More importantly, the proportion of eggs sired does not change significantly during that period. We argue that intermediate levels of paternity can select for paternal care in this system because: (1) benefits of care in terms of offspring survival are very high; (2) males have nothing to gain from decreasing their parental effort in a given reproductive event because sperm mixing makes it difficult for males to reach high paternity levels and males are left with no cues to assess paternity; (3) males cannot chose to care for their offspring exclusively because they can neither discriminate their own eggs, nor can they predict when their own eggs will be produced; and (4) males suffer no loss of further matings with other females when they carry eggs. Thus, our findings do not support the traditional view that paternal investment is expected to arise only in species where confidence of paternity is high. The results suggest that females maximize the chances that several males will accept eggs at different times by promoting a mechanism of sperm mixing that ensures that all males that have copulated with a female have some chance of fathering offspring, that this probability remains constant with time, and that males have no cues as to when their own offspring will be produced.     

Confidence of paternity and paternal care: covariation revealed through the experimental manipulation of the mating system in the beetle Onthophagus taurus

Theoretical models of paternal care predict that facultative reductions in male care may occur under certain conditions. One important parameter that has been shown to influence the outcome of these models is a male's confidence of paternity. In this study, we tested whether the amount of care provided by horned males in the dimorphic beetle, Onthophagus taurus, varied with his confidence of paternity. Male care results in an increased weight of dung provided in the brood masses produced by the pair. Using the sterile male technique we showed that a horned male's paternity declined with the number of sneak males in the population. The relationship was nonlinear, with paternity declining most rapidly between a frequency of one and three sneaks, and stabilizing thereafter at about 50%. A horned male's paternity was directly related to the number of copulations with the female, relative to the number of copulations achieved by sneaks. Horned males were shown to reduce their care in relation to their declining paternity. Video analysis demonstrated that reductions in male care occurred through a combination of male desertion and a trade‐off between caring and paternity assurance behaviours. The number of fights with sneak males was negatively related to the amount of care provided by a horned male. These results suggest that by gauging his expected paternity through the number of fights with sneaks, a horned male is able to assess his paternity and reduce his investment accordingly. Our data thus provide strong empirical support for the proposed link between paternity and paternal care.     

The influence of territoriality and mating system on the evolution of male care: a phylogenetic study on fish

Evolution of male care is still poorly understood. Using phylogenetically matched-pairs comparisons we tested for effects of territoriality and mating system on male care evolution in fish. All origins of male care were found in pair-spawning species (with or without additional males such as sneakers) and none were found in group-spawning species. However, excluding group spawners, male care originated equally often in pair-spawning species with additional males as in strict pair-spawning species. Evolution of male care was also significantly related to territoriality. Yet, most pair-spawning taxa with male care are also territorial, making their relative influence difficult to separate. Furthermore, territoriality also occurs in group-spawning species. Hence, territoriality is not sufficient for male care to evolve. Rather, we argue that it is the combination of territoriality and pair spawning with sequential polygyny that favours the evolution of male care, and we discuss our results in relation to paternity assurance and sexual selection.