Population structures, evolutionary relationships and genetic effects of domestication in American Penaeid shrimp

Abstract

Starch-gel electrophoresis of enzymatic proteins, restriction fragment length polymorphisms and random amplified polymorphic DNA w ere used to evaluate population structures of three species of Penaeid shrimp: Penaeus vannamei, P. stylirostris, and P. duorarum. The effects of domestication on two aquaculture populations of P. vannamei were also examined with these markers. Allozymes and the mitochondrial Cytochrome Oxidase I gene were used to establish the evolutionary relationships between species in the genus. A species-specific identification system using allozyme allele profiles was also developed. P. vannamei was polymorphic at three of 14 allozyme loci, while P. stylirostris and P. duorarum were polymorphic at five of 10 loci and four of eight loci, respectively. The frequency of the most common mitochondrial haplotype was <95% in all natural populations. Restriction site variation in the nuclear 28s ribosomal genes was not detected in any species, but the frequency of ribosomal DNA length variants in P. stylirostris was different (p<0.005) between Mexico and Ecuador. Eight of ten random amplified polymorphic DNA markers were variable in P. stylirostris, the only species tested. Allele and haplotype F[ST] values of 0.163 to 0.892 for P. stylirostris indicate more population subdivision than in P. duorarum and P. vannamei with F[ST] values of 0.004 to 0.017 and 0.007 to 0.049, respectively. The effective size of a closed aquaculture population managed to avoid inbreeding was estimated to be 8.3 to 12 individuals using mitochondrial markers and 203 to 282 individuals using allozymes. In a second aquaculture population founded by 20 shrimp, the estimates of effective size were 5.8 to 12 (mitochondrial) and 31 to 41 (allozymes.) Phylogenetic groupings based on allozymes and DNA sequences were consistent with current taxonomic classification into subgenera, but disputed the traditional designation of the subgenus Litopeneaus as primitive. A species identification system was developed using allozyme allele profiles. As few as three loci were sufficient to differentiate shrimp of American origin from indigenous Australian and Asian species. Every American species had a unique allele profile across the thirteen loci used.