Allozyme and microsatellite loci provide discordant estimates of population differentiation in the endangered dusky grouper (Epinephelus marginatus) within the Mediterranean Sea

Abstract

The dusky grouper, Epinephelus marginatus, inhabits coastal reefs in the Mediterranean Sea and Atlantic Ocean. A decline in the abundance of this long-lived protogynous hermaphrodite has led to its listing as an endangered species in the Mediterranean, and heightened management concerns regarding its genetic variability and population substructure. To address these concerns, we analysed genetic variation at seven microsatellite and 28 allozyme loci in dusky groupers sampled from seven areas (for microsatellites) and three areas (for allozymes) in the west-central Mediterranean. Levels of genetic variability were higher for microsatellites than for allozymes (mean H(E) = 0.78 and 0.07, respectively), but similar to those observed in other marine fishes with comparable markers. Both microsatellites and allozymes revealed significant genetic differentiation among all areas analysed with each class of marker, but the magnitude of differentiation revealed by allozymes over three locales (F(ST) = 0.214) was greater than that detected with microsatellites over seven areas, or over the three areas shared with the allozyme analysis (F(ST) = 0.018 and approximately 0, respectively). A large proportion of the allozyme differentiation was due to a single locus (ADA*) possibly influenced by selection, but allozyme differentiation over the three areas was still highly significant (F(ST) = 0.06, P < 0.0001), and the 95% confidence intervals for allozyme and microsatellite F(ST) did not overlap when this locus was excluded. There was no evidence of isolation by distance with either class of markers. Our results lead us to conclude that dusky groupers are not panmictic in the Mediterranean Sea and suggest that they should be managed on a local basis. However, more work is needed to elucidate genetic relationships among populations.

Evidence for fine-scale genetic structure and estuarine colonisation in a potential high gene flow marine goby (Pomatoschistus minutus)

“…This pattern is not unusual in populations of marine organisms, as has been shown elsewhere (Smith, 1987;García de Leó n et al, 1997;De Innocentiis et al, 2001), and might find its origin in the Wahlund effect (Wahlund, 1928), cryptic species, inbreeding, groupings of relatives, scoring errors, the occurrence of null alleles or selection against heterozygotes.…”

“…Stefanni et al (2003) compared the scoring of this locus also using starch gel electrophoresis (SGE) as cellulose acetate gel electrophoresis (CAGE), and concluded that the observed difference could be due to the weak staining of LDH-C* on SGE, resulting in the observed differences between the studies. The genetic diversity of the microsatellite loci, assessed as the expected level of heterozygosity H E , exhibited a wide range (0.157-0.976) and was generally comparable to other marine fish species (García de Leó n et al, 1997; Ruzzante et al, 1998;De Innocentiis et al, 2001), except for loci Pmin-07 and Pmin-11. The level of polymorphism of the loci Pmin-01 (86 alleles), Pmin-05 (88 alleles) and Pmin-10 (45 alleles) were striking in that they were much higher than in any other species studied (DeWoody and Avise, 2000).…”

“…Moreover, a discrepancy between allozyme and microsatellite markers has been described in several marine species (Lemaire et al, 2000;De Innocentiis et al, 2001). It is indicative of either differentiation in one or both markers (Lemaire et al, 2000;De Innocentiis et al, 2001), suggesting that the observed differentiation was either due to selection or stochastic events (drift-gene flow) (De Innocentiis et al, 2001;McLean and Taylor, 2001). In our data set, microsatellite loci exhibited higher F ST values than allozyme loci, suggesting that the higher mutation rate in microsatellites has increased the allele frequency divergence among populations (Allendorf and Seeb, 2000).…”

Mito-nuclear discordance in the degree of population differentiation in a marine goby

“…It has been suggested that balancing selection may significantly influence the distribution of allozyme diversity (De Innocentiis et al, 2001). Loci experiencing balancing selection will have allele frequencies more similar than expected under neutrality, reducing the F ST estimates.…”

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

“…In fact, evidence of genetic differentiation across large and small spatial scales has been reported in a great number of marine fishes using microsatellites Larsson et al 2007;Bradbury et al 2009;Earl et al 2010;González-Wangüemert et al 2010Larmuseau et al 2010a;Horne et al 2011;. These nuclear markers are especially useful to study the fine geographical variation of marine populations because they tend to be highly variable and can discern even subtle genetic differences (Waples 1998;Hedgecock et al 2007), resolving population structures that are not detected by mitochondrial DNA and allozyme markers (De Innocentiis et al 2001;Pampoulie et al 2004;Bisol et al 2007;Canino et al 2010). In this sense, several studies based on microsatellite markers have suggested that estuaries and coastal lagoons may offer special opportunities (because of their environmental features) to find local genetic structuring of fish populations (Beheregaray and Sunnucks, 2001;Bisol et al 2007;Roberts et al 2010;McCraney et al 2010;.…”