An evaluation of the AFLP fingerprinting technique for the analysis of paternity in natural populations of Persoonia mollis (Proteaceae)

The accurate assignment of paternity in natural plant populations is required to address important issues in evolutionary biology, such as the factors that affect reproductive success. Newly developed molecular fingerprinting techniques offer the potential to address these aims. Here, we evaluate the utility of a new PCR-based multi-locus fingerprinting technique called Amplified Fragment Length Polymorphism (AFLP) for paternity studies in Persoonia mollis (Proteaceae). AFLPs were initially scored for five individuals from three taxonomic levels for 64 primer pairs: between species (P. mollis and P, levis), between subspecies (P. mollis subsp. nectens and subsp. livens), between individuals within a single population of P. mollis, as well as for a naturally pollinated seed from a single P. mollis subsp. nectens plant. Overall, 1164 fragments (24.6% of all fragments) were polymorphic between species, 743 (16.5%) between subspecies, 371 (8.6%) between individuals within a single population, and 265 (6.2%) between a plant and its seed. Within a single P. mollis population of 14 plants, 42 polymorphic fragments were scored from profiles generated by a single AFLP primer pair. The mean frequency of the recessive allele (q) over these 42 loci was 0.773. Based on these observations, it will be feasible to generate well over 100 polymorphic AFLP loci with as few as three AFLP primer pairs. This level of polymorphism is sufficient to assign paternity unambiguously to more than 99% of all seed in experiments involving Small, known paternity pools. More generally, the AFLP procedure is well suited to molecular ecological studies, because it produces more polymorphism than allozymes or RAPDs but, unlike conventionally developed microsatellite loci, it requires no prior sequence knowledge and minimal development time.