Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis

Biologia (Impact Factor: 0.83). 08/2010; 65(4):688-696. DOI: 10.2478/s11756-010-0069-8


Surveys of allozyme polymorphisms in the carpet shell clam Ruditapes decussatus have revealed sharp genetic differentiation of populations. Analysis of population structure in this species has now been
extended to include nuclear and mitochondrial genes. A partial sequence of a mitochondrial COI gene and of the internal transcribed
spacer region (ITS-1) were used to study haplotype distribution, the pattern of gene flow, and population genetic structure
of R. decussatus. The samples were collected from twelve populations from the eastern and western Mediterranean coasts of Tunisia, one from
Concarneau and one from Thau. A total of twenty and twenty-one haplotypes were detected in the examined COI and ITS1 regions
respectively. The study revealed higher levels of genetic diversity for ITS1 compared to COI. The analysis of haplotype frequency
distribution and molecular variation indicated that the majority of the genetic variation was distributed within populations
(93% and 86% for COI and ITS1 respectively). No significant differentiation was found among eastern and western groups on
either side of the Siculo-Tunisian strait. However, distinct and significant clinal changes in haplotypes frequencies between
eastern and western samples were found at the most frequent COI haplotype and at three out of five major ITS1 haplotypes.
These results suggest the relative importance of historical processes and contemporary hydrodynamic features on the observed
patterns of genetic structure.

Key wordsRuditapes decussates-COI-ITS1-Tunisia

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    • "Despite the importance of the analysis of genetic variability and population structure in managing exploited populations, the genetic status of R. decussatus populations in Spain is poorly studied. Available genetic markers to perform genetic studies in R. decussatus include some allozymes (e.g., Borsa et al., 1994), RAPDs (Pereira et al., 2011), introns (Cordero et al., 2008; Gharbi et al., 2010), and mitochondrial loci (Gharbi et al., 2010), which are often characterised by a moderate level of polymorphism and/or low reproducibility. This work reports the identification of the first panel of microsatellite markers in R. decussatus, the development of multiplex PCR for quick and cheap genetic analyses within the species and a first evaluation of their utility for population analyses and parentage studies that could help improve supplementation strategies used in R. decussatus stock enhancement programmes. "
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    ABSTRACT: Supplementation aquaculture is intended to reinforce harvestable abundances of viable, naturally reproducing populations. The grooved carpet shell Ruditapes decussatus is one of the most important shellfish species in northern Spain (Asturias and Galicia), and their wild populations are annually supplemented using seeds produced in hatcheries. The current genetic status of these populations and a genetic evaluation of the consequences of the supplementation campaigns are lacking due to the absence of useful genetic markers that allow these kinds of studies. In this work, twelve variable microsatellite markers (mean HE = 0.663) and two useful multiplex PCRs are reported for R. decussatus. Different genetic characteristics were found between wild clams from Asturias and Galicia. Moreover, the seeds obtained in hatcheries for supplementation campaigns did not represent the wild gene pools well. Reductions of effective breeding numbers relative to the actual number of breeders were as large as 65%, due to unequal parental contributions and family variances. Finally, in an experimental supplementation programme conducted in a Galician population (Cambados), we report that the genetic status of the studied population changed significantly from one year to the next (FST = 0.011 P < 0.05) and we found what could be hatchery-produced seed (15%) in the wild restocked population. The accuracy of this estimate was evaluated using simulation procedures and we found less than 3% of type I error and values of 8–11% of type II error for three situations under analysis (32%, 10% and 1% of sampled true parent–offspring pairs) when using 95% as the threshold limit for parentage assignations. This work demonstrates the importance of temporal evaluations of the genetic status of supplemented and unsupplemented wild populations and indicates the need for changes in the protocols used for hatchery seed production for restocking purposes. A successful supplementation campaign can decrease genetic variance, and thus probably damage, the genetic status of wild populations.
    Aquaculture 04/2014; s 426–427:49–59. DOI:10.1016/j.aquaculture.2014.01.010 · 1.88 Impact Factor
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    ABSTRACT: The population genetic structure of the Peruvian scallop Argopecten purpuratus from three different wild populations along the Peruvian coast was analyzed using nine microsatellite loci and a partial region (530bp) of the mitochondrial 16S rRNA gene. A total of 19 polymorphic sites in the 16S rRNA gene defined 18 unique haplotypes. High genetic diversity was presented in all populations. Statistical analysis of mitochondrial DNA revealed no significant genetic structure (ΦST=0.00511, P=0.32149) among the three localities. However, microsatellite analysis showed low (2.86%) but highly significant (P=0.0001) genetic differentiation among populations, most of the variation was found in Independencia Bay population, which is located in the Peruvian National Reserve of Paracas. Neutrality tests based on mitochondrial haplotypes were performed to assess signatures of recent historical demographic events. Overall results from Tajima's D and Fu's FS tests indicated significant deviations from neutrality. To our knowledge, this study constitutes the first investigation based on mitochondrial and microsatellite markers on the genetic structure of A. purpuratus.
    Marine Genomics 03/2013; 9:1-8. DOI:10.1016/j.margen.2012.04.007 · 1.79 Impact Factor
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