GENETIC VARIATION AND EVOLUTIONARY RELATIONSHIPS WITHIN A GROUP OF THIRTEEN SPECIES OF PENAEID PRAWNS

A tree money grows on: the first inclusive molecular phylogeny of the economically important pink shrimp (Decapoda : Farfantepenaeus) reveals cryptic diversity

Species of Farfantepenaeus support economically important shrimp fisheries throughout the Western Hemisphere, necessitating proper fisheries management. To be effective, species management should be informed of the potential presence of cryptic species and of the evolutionary forces driving biodiversity. This is best accomplished through a robust phylogenetic framework and evidence-based species delimitation. This study represents the first comprehensive molecular phylogeny and species delimitation analyses of shrimps belonging to the genus Farfantepenaeus. Targeting three mitochondrial genes (12S, 16S, and COI), gene trees and a phylogeny for the genus were inferred using maximum likelihood and Bayesian approaches. In general, the phylogenetic relationships inferred here largely agree with those recovered from morphological data, including the most recent designation of F. isabelae as sister to F. subtilis. Molecular divergence was found between northern and southern populations of F. brasiliensis, suggesting the existence of unrecognised subspecies. However, previous recognition of F. duorarum and F. notialis as two distinct species was not supported by this study. The phylogeny inferred here also uncovers a phylogeographic signal of latitudinal speciation in the genus. The study presented here provides valuable insight into the evolutionary history of Farfantepenaeus, improving our ability to effectively manage these economically important species.

Genetic analysis of Black Tiger shrimp (Penaeus monodon) across its natural distribution range reveals more recent colonization of Fiji and other South Pacific islands

The Black Tiger shrimp (Penaeus monodon) has a natural distribution range from East Africa to the South Pacific Islands. Although previous studies of Indo-Pacific P. monodon have found populations from the Indian Ocean and Australasia to differ genetically, their relatedness to South Pacific shrimp remains unknown. To address this, polymorphisms at eight shared microsatellite loci and haplotypes in a 418-bp mtDNA-CR (control region) sequence were examined across 682 P. monodon from locations spread widely across its natural range, including the South Pacific islands of Fiji, Palau, and Papua New Guinea (PNG). Observed microsatellite heterozygosities of 0.82-0.91, allele richness of 6.85-9.69, and significant mtDNA-CR haplotype variation indicated high levels of genetic diversity among the South Pacific shrimp. Analysis of microsatellite genotypes using a Bayesian STRUCTURE method segregated Indo-Pacific P. monodon into eight distinct clades, with Palau and PNG shrimp clustering among others from Southeast Asia and eastern Australia, respectively, and Fiji shrimp clustering as a distinct group. Phylogenetic analyses of mtDNA-CR haplotypes delineated shrimp into three groupings, with shrimp from Fiji again being distinct by sharing no haplotypes with other populations. Depending on regional location, the genetic structures and substructures identified from the genotyping and mtDNA-CR haplotype phylogeny could be explained by Metapopulation and/or Member-Vagrant type evolutionary processes. Neutrality tests of mutation-drift equilibrium and estimation of the time since population expansion supported a hypothesis that South Pacific P. monodon were colonized from Southeast Asia and eastern Australia during the Pleistocene period over 60,000 years ago when land bridges were more expansive and linked these regions more closely.

Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn, Penaeus monodon

Surveys of mitochondrial DNA (mtDNA) variation in the giant tiger prawn, Penaeus monodon, using restriction fragment length polymorphisms have provided the first clear evidence that the Indo-West Pacific region is a site of accumulation of genetic diversity rather than a site of origin of genetic diversity. No haplotyes were found in common between a group of five southeast African populations and a group of five Australian (including Western Australia) and three southeast Asian populations. The dominant haplotype was different in the Australian and southeast Asian population groups. Genetic diversity (pi) was greatest in Indonesia (pi averaged 0.05), less in the Philippines and Australia (pi averaged 0.01), and markedly less in the southeast African and the West Australian populations (pi averaged 0.003). The high diversity of the southeast Asian populations resulted from the occurrence in those populations of a set of haplotypes found only in southeast Asia but derived from the southeast African haplotypes. These genetic variants therefore evolved in the Indian Ocean and later migrated into the Indo-West Pacific region. Low genetic variation in the geographically marginal populations in southeast Africa and Western Australia is considered to be the result of bottlenecks, but mismatch distributions suggest that large population sizes have been maintained in Indonesian populations for long periods.

Observed relationships between protein heterozygosity and protein genetic distance and comparisons with neutral expectations

Relationships between protein genetic distance (D) and protein heterozygosity (H) were studied using allele frequency data for 42 proteins derived from multilocus electrophoretic surveys of genetic variation in over 200 invertebrate and over 300 vertebrate species.D¯andH¯values for the different proteins (mostly enzymes) were calculated, and large and significant correlations betweenD¯andH¯were found in comparisons of both intraspecific and interspecific populations. Empirical relationships betweenD¯andH¯were compared with neutral expectations under the stepwise model of neutral mutation with the assumption that populations are in equilibrium with respect to the effects of mutation and genetic drift.

At low divergence levels, a linear relationship ofD¯onH¯was observed, but at high levels of divergenceDtended towards an asymptote at highH¯. The results at high divergence cannot be explained using the approximate relationshipD=2ut(whereu= mutation rate,t= time). However, computer simulations of neutral models showed that changes of this nature in the relationship betweenD¯andH¯were to be expected as divergence increases, the equationD=2utbeing a poor approximation at highDWe therefore conclude that the observed relationships betweenD¯andH¯are, in fact, compatible with equilibrium neutral theory.

Estimation and interpretation of genetic distance in empirical studies

Linear functions of Nei's genetic-distance statistic are calculated frequently in the literature of population genetics. Variance estimates for these linear functions are either not presented or incorrectly calculated. Part of the problem stems from the common assumption that distance statistics are independent random variables. This assumption is not generally correct. We describe methods for estimating the variance of linear combinations of genetic-distance statistics. We also suggest a method for constructing confidence intervals on genetic-distance statistics when these values are small (< 0·10) and their distribution deviates substantially from normal.