Population structure of Litopenaeus schmitti (Decapoda: Penaeidae) from the Brazilian coast identified using six polymorphic microsatellite loci

Species distribution models to predict the impacts of environmental disasters on shrimp species of economic interest

Here, we used distribution models to predict the size of the environmentally suitable area for shrimps of fishing interest that were impacted by the tailing plume from the collapse of the Fundão Dam, one of the largest ecological disasters ever to occur in Brazil. Species distribution models (SDMs) were generated for nine species of penaeid shrimp that occurred in the impacted region. Average temperature showed the highest percentage of contribution for SDMs. The environmental suitability of penaeids varied significantly in relation to the distance to the coast and mouth river. The area of environmental suitability of shrimps impacted by tailings plumes ranged from 27 to 47 %. Notably, three protected areas displayed suitable conditions, before the disaster, for until eight species. The results obtained by the SDMs approach provide crucial information for conservation and restoration efforts of coastal biodiversity in an impacted region with limited prior knowledge about biodiversity distribution.

Phylogeography of Colpomenia sinuosa (Ectocarpales, Phaeophyceae) along the Brazilian coast

Colpomenia sinuosa is a cosmopolitan brown macroalgal species complex and hence a great candidate for evolutionary studies in the marine environment. Since 2009, three major C. sinuosa phylogenetic lineages, subdivided into eight subgroups, have been identified based on cox3 DNA sequences from worldwide collections. However, worldwide sampling remains limited and spotty. To date molecular data from Brazilian C. sinuosa populations have been limited to 10 specimens collected in a single locality. Nonetheless, C. sinuosa populations occur along the entire ~8,000 km Brazilian coast. Consequently, knowledge on population genetic diversity and spatial genetic structuring along most of the Brazilian coastline is nonexistent. To fulfill this gap in knowledge, we performed a phylogeographic analysis of C. sinuosa populations in Brazil. The highly variable cox3 marker was sequenced for 148 individuals collected in 12 localities in Brazil. Results identified two genetically distinct population groups (north vs. south) separated at 20.5° S latitude. Genetic diversity in northern populations is 14.6 and 15.5 times greater than southern populations in terms of haplotype and nucleotide diversity, respectively. Among northern populations, the Bahia state holds the largest genetic diversity. The southern populations had lower genetic diversity and no internal genetic sub-structure suggesting past bottlenecks followed by recent colonization from northern haplotypes. Our results do not indicate recent introductions of foreign haplotypes in Brazil and reinforce the crucial importance of historical and extant allopatric, parapatric, and sympatric processes driving marine macroalgal evolution in the Southwestern Atlantic Ocean.

Genome-wide assessment elucidates connectivity and the evolutionary history of the highly dispersive marine invertebrate Littoraria flava (Littorinidae: Gastropoda)

An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava, a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling.

Dual influence of terrestrial and marine historical processes on the phylogeography of the Brazilian intertidal red alga Gracilaria caudata

In this study, we explored how past terrestrial and marine climate changes have interacted to shape the phylogeographic patterns of the intertidal red seaweed Gracilaria caudata, an economically important species exploited for agar production in the Brazilian north-east. Seven sites were sampled along the north-east tropical and south-east sub-tropical Brazilian coast. The genetic diversity and structure of G. caudata was inferred using a combination of mitochondrial (COI and cox2-3), chloroplast (rbcL) and 15 nuclear microsatellite markers. A remarkable congruence between nuclear, mitochondrial and chloroplast data revealed clear separation between the north-east (from 03° S to 08° S) and the south-east (from 20° S to 23° S) coast of Brazil. These two clades differ in their demographic histories, with signatures of recent demographic expansions in the north-east and divergent populations in the south-east, suggesting the maintenance of several refugia during the last glacial maximum due to sea-level rise and fall. The Bahia region (around 12° S) occupies an intermediate position between both clades. Microsatellites and mtDNA markers showed additional levels of genetic structure within each sampled site located south of Bahia. The separation between the two main groups in G. caudata is likely recent, probably occurring during the Quaternary glacial cycles. The genetic breaks are concordant with (i) those separating terrestrial refugia, (ii) major river outflows and (iii) frontiers between tropical and subtropical regions. Taken together with previously published eco-physiological studies that showed differences in the physiological performance of the strains from distinct locations, these results suggest that the divergent clades in G. caudata correspond to distinct ecotypes in the process of incipient speciation and thus should be considered for the management policy of this commercially important species.

Contemporary and historical oceanographic processes explain genetic connectivity in a Southwestern Atlantic coral

Understanding connectivity patterns has implications for evolutionary and ecological processes, as well as for proper conservation strategies. This study examined population genetic structure and migration patterns of the coral Mussismilia hispida, one of the main reef builders in the Southwestern Atlantic Ocean. For this, 15 sites were sampled along its entire distributional range employing 10 microsatellite loci. M. hispida was divided into five genetically differentiated populations by Structure analysis. Population structure and migration estimates are consistent with present-day oceanographic current patterns, zones of upwelling and historical sea-level changes. The Central Region and Oceanic Islands populations had the highest genetic diversity, were possibly the main sources of migrants for other populations and presented mutual migrant exchange. This mutual exchange and the high diversity of Oceanic Islands, a peripherical population, is highly interesting and unexpected, but can be explained if these sites acted as refugia in past low sea-level stance. This is the first connectivity study in the region using hyper-variable markers and a fine sampling scale along 3,500 km. These results enlighten the population dynamics of an important reef building species and shows how oceanographic processes may act as barriers to dispersal for marine species, providing valuable information for management strategies.

Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish

Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo-Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.

Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus

The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource.

Isolation and mapping of telomeric pentanucleotide (TAACC)n repeats of the Pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)n repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective 1 showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA)n, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1>P2>P3>P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy

We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa.

Temporal variation of the population structure and genetic diversity of Farfantepenaeus notialis assessed by allozyme loci

Population genetic studies carried out on penaeid shrimps have disclosed different patterns of population subdivision, revealing new aspects of shrimp biology as well as the effects of historical contingency molding those patterns. However, the stability of observed allele frequencies over time still remains untested. The objective of this article is to show the analysis of the temporal variation of allozymes in a shrimp species inhabiting Cuba which proves that the genetic structure of this species could significantly change in time. The study involves four populations of Farfantepenaeus notialis sampled in a period of 8 years. The significant statistics obtained from partitions observed in 1995 were not detected in 2003 (as suggested by AMOVA and F(ST)), whereas temporal genetic differentiation and heterozygosity became highly significant. The results strongly suggest that the effect of migrations could be the cause for the loss of F. notialis genetic structure in 2003. It is therefore imperative to call attention on the vulnerability of these populations when facing unstable environmental and habitat conditions.