Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.

Molecular techniques have enabled behavioural ecologists to reassess mating systems from a genetic perspective. Studies of paternity frequently reveal that mating behaviour does not always reflect parentage, and may bring to light alternative mating tactics. Here we present a comparison of behavioural and genetic measures of male reproductive success in a mammalian mating system in which both sexes are highly promiscuous. Rather than having a stable harem social structure, Soay rams (Ovis aries) on the island of Hirta, St Kilda, UK usually consort with individual oestrous ewes sequentially. Not all matings occur between consort pairs, however, and ewes have been seen to mate with up to 10 different rams on the same day. Using locus-specific polymorphism at five protein and 10 microsatellite DNA loci, we determined paternity for 236 lambs born into three cohorts, and compared paternity with estimates of mating success derived from more than one census of rutting behaviour. The correlation between the number of ewes with which each ram was witnessed in consort and the number of paternities assigned was positive and statistically significant, and rams that were observed in consort with a ewe were 18 times more likely to have sired her offspring than other candidate rams. However, most lambs (73%) were not sired by a ram seen in consort with the oestrous mother. Many juveniles, yearlings and some adult rams were rarely seen in consort with ewes, yet were assigned a significant number of paternities. These results suggest that mating tactics differ between age groups, and that alternative mating strategies among adults that do not involve forming consorts with many females also confer mating success. For these reasons, census-based observations of consort associations between individuals cannot be used to accurately estimate individual male reproductive success in this population.

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We tested 174 bovine microsatellite primer pairs for use in a primitive breed of sheep and two species of deer. Of 173 markers, 127 (73.4%) gave a product in Soay sheep (Ovis aries) of which 54 (42.5%) were polymorphic. One hundred and twenty-nine of 174 (74.1%) markers gave a product in red deer (Cervus elaphus) of which 72 (55.8%) were polymorphic. In sika deer (Cervus nippon) 126 of 171 (73.7%) microsatellite primers gave a product with 47 (37.3%) polymorphic. The proportion of bovine microsatellite loci conserved across artiodactyl species was significantly greater in this study than previously reported. Reasons for this high degree of microsatellite conservation are discussed. We suggest that a high resolution comparative map of the artiodactyls can be constructed using microsatellites.

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In most animal species, males are predicted to compete for reproductive opportunities, while females are expected to choose between potential mates. However, when males' rate of reproduction is constrained, or females vary widely in 'quality', male mate choice is also predicted to occur. Such conditions exist in the promiscuous mating system of feral Soay sheep on St Kilda, Scotland, where a highly synchronized mating season, intense sperm competition and limitations on sperm production constrain males' potential reproductive rate, and females vary substantially in their ability to produce successful offspring. We show that, consistent with predictions, competitive rams focus their mating activity and siring success towards heavier females with higher inclusive fitness. To our knowledge, this is the first time that male mate choice has been identified and shown to lead to assortative patterns of parentage in a natural mammalian system, and occurs despite fierce male-male competition for mates. An additional consequence of assortative mating in this population is that lighter females experience a series of unstable consorts with less adept rams, and hence are mated by a greater number of males during their oestrus. We have thus also identified a novel male-driven mechanism that generates variation in female promiscuity, which suggests that the high levels of female promiscuity in this system are not part of an adaptive female tactic to intensify post-copulatory competition between males.

In this study we investigate some applications of genetic markers in animal conservation, using the Arabian oryx (Oryx leucoryx) as an example. Out of 66 sets of microsatellite primers from other ruminants, 58% were found to amplify microsatellites in Arabian oryx. Polymorphism (50% of loci amplified) and allelic diversity (mean 2.1 alleles/locus amplified) were within the range found in other ruminants. Arabian oryx (n = 343) representing most of the major groups world-wide were typed at six loci. Low but significant population differentiation was found between most oryx groups, suggesting that management of Arabian oryx has led to substantial genetic mixing between populations. Forty percent of the alleles in one additional Arabian oryx sample from the pre-extinction population in Oman were not found in any contemporary Arabian oryx, and two out of four contemporary populations were deficient in rare alleles, suggesting that the species has lost some neutral genetic variation. The microsatellite loci were sufficiently polymorphic for identification of an Arabian oryx sample in a forensic context, but were not sufficiently polymorphic for large-scale parentage inference. We suggest that it is important to evaluate whether genetic markers are likely to have sufficient power to answer particular conservation questions prior to committing conservation resources to genetic typing. Key: , lineage well represented; , lineage poorly represented (e.g. via single reproducing individual); ✘, lineage absent. Sheikh Zayed and Sheikh Hamdan lineages are private collections in the United Arab Emirates.