Carles Pla

Postglacial colonization of brown trout in Europe based on distribution of allozyme variants

Compatible data from 11 polymorphic allozyme loci were assembled from 14 published studies and additional unpublished information for 232 native collections of brown trout sampled over a broad geographical range. Most of the genetic variation was explained by the distribution of allelic variation at the LDH-C* and CK-A1* loci. Patterns of geographical distribution coupled with postglacial geological events supported a model of colonization from three preglacial lineages, each fixed for different sets of alleles at these two loci. During glacial retreat, recolonization is proposed to have occurred mainly into adjacent areas through (i) a north-western migration from an eastern Mediterranean–Caspian refuge, (ii) a northern expansion from a refuge in Atlantic drainages of Iberia and southern France, and (iii) a northern and eastern radiation from a refuge centred near the English Channel. Extant populations in deglaciated areas are suggested to represent mixed or pure descendants of these migrating groups. Repopulation from a fourth Mediterranean refuge distinguished by the presence of the LDH-A2*100QL allele was excluded based on the absence of this allele in repopulated areas.

Population genetic structure of European hake, Merluccius merluccius

Allozyme analysis of tissue samples of 910 European hake Merluccius merluccius from six North Atlantic Ocean and four Mediterranean Sea locations revealed polymorphism at 21 out of 34 protein-coding loci examined. A major subdivision between Atlantic and Mediterranean collections (mean Neis genetic distance within regions 0.005; between regions 0.014) was particularly evident from allelic differences at the GAPDH-1* and GR-2* loci. Further population subdivision was indicated within both regions, and gene flow from adjacent Atlantic to proximal Mediterranean populations was suggested by allele frequencies and relevant oceanographic and geological information. The data support present management based on distinct Atlantic and Mediterranean populations and indicate that the population structure within the Atlantic is more complex than the discrete northern and southern stocks proposed by ICES.

Molecular and morphologic approaches to discrimination of variability patterns in chub mackerel, Scomber japonicus

The systematic status and the evolutionary biology of chub mackerel (Scomber japonicus) in the South West Atlantic Ocean is confusing with an unknown degree of genetic differentiation and reproductive isolation between units. Simultaneous genetic and morphologic analyses were made on 227 fish collected from two areas of the South West Atlantic Ocean and one from the Mediterranean Sea. The genetic analysis was based on 36 protein-coding loci, 16 of which were variable. The morphologic analyses include six morphometric length measurements and a meristic character. Correspondence between genetic and morphologic variability patterns indicates isolated Mediterranean and Southwest Atlantic subgroups of S. japonicus and, less clearly, possible additional divergence in two regional stocks within the latter group. The most conservative approach to management is to manage the stocks independently of one another.

Enzymatic and morphometric analyses in mediterranean populations of the rose shrimp, Aristeus antennatus (Risso, 1816)

Eleven samples of rose shrimp (Aristeus antennatus) from different areas of the Mediterranean Sea and adjacent Atlantic waters were subjected to morphometric and electrophoretic analyses. The object was to characterize possible population differences that would account for previously reported differences in behavioural patterns observed in commercial fishing activity. Genetic analysis of 27 enzyme systems yielded only fifteen useful loci of which fibre had allele variants, but only two of them were polymorphic within 95%. Morphometric analysis of nine body and appendage measurements revealed significant differences between sampling sites in scaphocerite length, uropodal length, and the length of the articles on the third walking leg. The samples analysed genetically could not be differentiated, but morphological differences were compared between different hydrographic regions of the Mediterranean Basin.

A genetic assessment of the population structure of swordfish (Xiphias gladius) in the Mediterranean Sea

Nine samples of swordfish from different Mediterranean areas plus a sample obtained in Atlantic waters adjacent to the Strait of Gibraltar were examined for temporal and spatial heterogeneity using allozyme analysis. Only two out of 38 loci (IDHP-2* and LDH-3*) were polymorphic based on a frequency of less than 0.95 in one or more samples. Both polymorphism and heterozygosity revealed a low genetic variability for swordfish in comparison with other pelagic species. No heterogeneity due to differences between age groups was observed for those samples including juvenile and adult specimens. The lack of temporal or spatial heterogeneity found in this study is consistent with a single population of swordfish in the Mediterranean Sea and adjacent waters of the Atlantic Ocean.

Facts and uncertainties about the genetic population structure of Atlantic bluefin tuna (Thunnus thynnus) in the Mediterranean. Implications for fishery management

The Atlantic bluefin tuna (Thunnus thynnus) is an extraordinary fish that has amazed humanity since ancient times. However, the continuous overexploitation of this fishery, particularly in the Mediterranean Sea, could result in a total collapse of this resource. Currently, this species is managed as two stocks: Western Atlantic and Mediterranean-Eastern Atlantic, with a recognized genetic differentiation between them. On the other hand, the population structure within the Mediterranean Sea is still unclear. The biological data supports the idea of two separate populations in the eastern and western Mediterranean basins. However, nuclear microsatellite and mitochondrial DNA (mtDNA) analyses of two samples representative of these two basins result in a lack of heterogeneity. A comparison of these results with previously published studies reveals some discrepancies. We have compared 59 genetic differentiation tests that include samples within the Mediterranean. Of these, about 60% gave significant differentiation while the remaining 40% were non-significant. But, when only nuclear-based loci were considered, genetic differentiation was detected in up to 73% of the cases with an average significant FST of only 0.018, whereas the average significant FST of the mtDNA-based studies was significantly higher (0.029). However, in some cases, it is difficult to reconcile the biology of the species with the results suggesting genetic differentiation. In conclusion, although it is not yet possible to reach a definitive conclusion about the population structure, but considering all biological and genetic data, we suggest an independent management approach for each basin to avoid the impact of a type II error that could lead to the possible loss of the regional subpopulations.

Melanism in guinea fowl (Numida meleagris) is associated with a deletion of Phenylalanine‐256 in the MC1R gene

We have characterized a deletion in the MC1R gene causing the loss of one amino acid (p.Phe256del), which is perfectly associated with melanism in guinea fowl (Numida meleagris). Co-segregation of the p.Phe256del with melanism was confirmed in 25 offspring born from a cross of two heterozygote birds; therefore we suggest that this mutation is responsible for the black phenotype. Interestingly, this is the first case of recessive melanism linked to MC1R.

Using Massive Parallel Sequencing for the Development, Validation, and Application of Population Genetics Markers in the Invasive Bivalve Zebra Mussel ( Dreissena polymorpha )

The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process.

Identification of 246 microsatellites in the Asiatic clam (Corbicula fluminea)

Asiatic clam (Corbicula fluminea) is one of the most invasive freshwater bivalves. Despite the ecologic and economic impacts of this species, there are only a few polymorphic microsatellites. In this study, we screened the genome from C. fluminea in search of microsatellite markers using massive parallel sequencing. We identified 246 new microsatellites involving di-, tri-, tetra- and pentanucleotide single repeats and different compound microsatellites, and we used a validation protocol to characterize a sample of those. Nine of them presented two or more alleles indicating a low level of variability.

A sex determination protocol for the Iberian desman (Galemys pyrenaicus) based on a three primer amplification of DBX and DBY fragments with non-invasive samples

We have sequenced partial fragments of DBX and DBY genes of the endangered Iberian desman (Galemys pyrenaicus). The sequences were used to design a sex determination protocol for non-invasive samples based on a PCR reaction, using only three primers. This protocol allows the simultaneous amplification of two fragments, one corresponding to the DBX gene and the other to the DBY gene, both differing in size. To increase sensitivity on the detection of positive amplifications and on the determination of fragment size we use a fluorescently labelled primer. The protocol has been tested in DNA samples from hair and stool, revealing major difficulties in sexing faecal samples, but unambiguous sexing of hair samples.