Molecular Ecology (2001) 10, 1011–1024 © 2001 Blackwell Science Ltd Blackwell Science, Ltd Multiple paternity and mating patterns in the American alligator, Alligator mississippiensis LISA M. DAVIS,*† TRAVIS C. GLENN,*† RUTH M. ELSEY,‡ HERBERT C. DESSAUER§ and ROGER H. SAWYER* *Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA, †Savannah River Ecology Laboratory, Drawer E, Aiken SC 29802, USA, ‡Louisiana Department of Wildlife and Fisheries, Rockefeller Wildlife Refuge, Grand Chenier, LA 70643, USA, §Department of Biochemistry, Louisiana State University, New Orleans, LA 70119, USA Abstract Eggs were sampled from 22 wild American alligator nests from the Rockefeller Wildlife Refuge in south-west Louisiana, along with the females guarding the nests. Three nests were sampled in 1995 and 19 were sampled in 1997. Females and offspring from all clutches were genotyped using five polymorphic microsatellite loci and the three nests from 1995 were also genotyped using one allozyme locus. Genotypes of the hatchlings were consistent with the guarding females being the mothers of their respective clutches. Multiple paternity was found in seven of the 22 clutches with one being fathered by three males, and the remaining six clutches having genotypes consistent with two males per clutch. Paternal contributions of multiply sired clutches were skewed. Some males sired hatchlings of more than one of the 22 clutches either as one of two sires of a multiple paternity clutch, as the sole sire of two different clutches, or as the sole sire of one clutch and one of two sires of a multiply sired clutch. There was no significant difference between females that had multiple paternity clutches and those that had singly sired clutches with respect to female total length (P = 0.844) and clutch size (P = 0.861). Also, there was no significant correlation between genetic relatedness of nesting females and pairwise nest distances ( r 2 = 0.003, F 1,208 = 0.623, P = 0.431), indicating that females in this sample that nested close to one another were no more related than any two nesting females chosen at random. Eleven mutations were detected among hatchlings at the five loci over the 22 clutches. Most of these mutations (eight of 11) occurred at Amiμ-17, the only compound microsatellite locus of the five used in this study, corresponding to a mutation rate of 1.7 × 10 –3 . Finally, most of the mutations (82%) were homoplasious, i.e., mutating to an allelic state already present in this Louisiana population. Keywords: alligator, mating systems, microsatellites, multiple paternity, mutation rate, population genetics Received 29 July 2000; revision received 25 October 2000; accepted 25 October 2000 Introduction Many molecular techniques currently available allow insight into areas of reproductive dynamics and patterns of gene flow that have been unattainable previously. Recent genetic studies of mating systems have contrasted sharply with prior hypotheses regarding mating behaviour and reproductive output. For example, most bird species were thought to form monogamous pair bonds that produce singly sired clutches exclusively (Lack 1968). It is now well recognized that extra-pair copulations in ‘monogamous’ bird species often result in offspring sired by males other than the attendant male (Gowaty & Karlin 1984; Birkhead et al. 1987; Westneat et al. 1990). While traditional etho- logical studies have yielded invaluable insight into behavi- oural patterns in animal populations, molecular markers such as randomly amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), and mini- and microsatellites have advanced our ability to identify individuals in populations (Parker et al. 1998). High-resolution genetic markers can provide detailed information about mating systems such as how many and Correspondence: Travis C. Glenn. Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken SC 29802, USA. Fax: (803) 725 – 3309; E-mail: Glenn@srel.edu.