Molecular Ecology (1999) 8, 1417–1429 © 1999 Blackwell Science Ltd Blackwell Science, Ltd Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal (Halichoerus grypus) J. WORTHINGTON WILMER,* P. J. ALLEN,† P. P. POMEROY,‡ S. D. TWISS§ and W. AMOS* *Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK, †BBC Natural History Unit, Broadcasting House, Whiteladies Road, Bristol BS8 2LR, UK, ‡Sea Mammal Research Unit, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife KY16 8LB, UK, §Department of Biological Sciences, Durham University, Durham, DH1 3LE, UK Abstract Microsatellites were used to conduct an extensive analysis of paternity of grey seals from two Scottish breeding colonies at North Rona (n = 1189) and the Isle of May (n = 694), spanning more than a decade. A maximum of 46% of pups at North Rona and 29% of pups at the Isle of May could be allocated a father, even though the majority of candidate males for specific study sites within each colony were believed to have been sampled. Based on the paternities which could be assigned, both colonies showed evidence of reproductive skew, apparently due to the presence of approximately five males who were exceptionally successful. Some males were assigned paternities at least 10 years before, and colleagues 10 years after, being sampled, implying a reproductive lifespan of at least 10 years, and there are indications that the real maximum lies in the range 15–20 years. Male grey seals appear to have at least two breeding strategies they can adopt. On land, some males benefit from a traditionally polygynous system. However, between 50 and 70% of grey seal pups born at a particular colony are not fathered by males who are likely to be sampled by us, implying that these males seldom venture ashore here. We conclude that aquatic mating may play a much larger role in the grey seal than has previously been thought. Keywords: grey seal, microsatellites, paternity analysis, Pinniped, reproductive success Received 6 February 1999; revision received 1 April 1999; accepted 16 April 1999 Introduction Theoretical discussions on the evolution of pinniped polygyny (Bartholomew 1970; Stirling 1975) and sexual dimorphism (reviewed in Ralls (1976)) predict that a species such as the grey seal (Halichoerus grypus), which breeds colonially on land and displays marked sexual dimorphism, should have a mating system characterized by a strong degree of polygyny. In such species, male reproductive success is expected to correlate strongly with male competitive ability, which in turn is often cor- related with body mass (e.g. Clutton-Brock 1989). Domin- ant males are able to maximize the duration of tenure on territories or among female aggregations and hence have more opportunities to mate. Although little is known about the intraspecific plasticity of mating systems, we might also expect that the degree of polygyny will be influenced by the degree of aggregation shown by females, and by the local operational sex ratios (OSR) (Emlen & Oring 1977). Both these characteristics may be influenced by environmental conditions and breeding site topographies (Stirling 1975; Emlen & Oring 1977; Alexander et al. 1979; Boness & James 1979; Anderson & Fedak 1985; Boness 1991; Twiss et al. 1998). Numerous behavioural studies of grey seals lend support to these predictions, showing a polygynous breeding system. Although the relationship between body mass and male competitive ability is ambiguous in grey seals (Anderson & Fedak 1985; Godsell 1991; Twiss 1991; Tinker et al. 1995) and males form only an approximation to a linear dominance hierarchy (Twiss et al. 1998), variance Correspondence: J. Worthington Wilmer. Fax: + 44 (0)1223-336676; E-mail: jmw60@cam.ac.uk