Delaware Bay and Chesapeake Bay populations of the horseshoe crab limulus polyphemus are genetically distinct

The Delaware Bay contains the world's largest population of horseshoe crabs , which constitute an ecologically significant component of this estuarine ecosystem. The North Atlantic species Limulus polyphemus has an extensive g eographical distribution, ranging from New England to the Gulf of Mexico. R ecent assessments of the Delaware Bay population based on beach spawning an d trawling data have suggested a considerable decrease in the number of adu lt animals since 1990. Considerable debate has centered on the accuracy of these estimates and their impact on marine fisheries management planning. C ompounding this problem is the lack of information concerning the genetic s tructure of Atlantic horseshoe crab populations. This study assessed patter ns of genetic variation within and between the horseshoe crab populations o f Delaware Bay and Chesapeake Bay, using both Random Amplification of Polym orphic DNA (RAPD) and DNA sequence analysis of the mitochondrial cytochrome oxidase I gene (COI). We examined 41 animals from Delaware Bay and 14 anim als from the eastern shore of Chesapeake Bay. To provide high quality, unco ntaminated genomic DNA for RAPD analysis, DNA was isolated from hemocytes b y direct cardiac puncture, purified by spin column chromatography, and quan tified by agarose gel electrophoresis. RAPD fingerprints revealed a relativ e paucity of polymorphic fragments, with generally homogeneous banding patt erns both within and between populations. DNA sequence analysis of 515 base s of the 5' portion of the mitochondrial COI gene showed haplotype diversit y in the Chesapeake Bay sample to be significantly higher than in the Delaw are Bay sample, despite the larger size of the latter. Haplotype analysis i ndicates minimal contemporary gene flow between Delaware Bay and Chesapeake Bay crab populations, and further suggests that the Delaware Bay populatio n is recovering from a recent population decline.