Genotype data set with threat categories

Summary of genetic diversity and disturbances for each meadow

Questionnaire

Results of questionnaire on meadow statu

Discriminant analysis of principal components (DAPC).

Geographic samples are encompassed by ellipses. See Table 1 for abbreviations.</p

Characteristics of sampling sites, including geographic information and genetic diversity indices per geographic sample.

<p>N: number of individuals sampled in each site; N_pa: number of private alleles; A_r: allelic richness per geographic sample; H_e and H_o indicate expected and observed heterozygosity respectively; <i>F</i>_IS is the inbreeding coefficient calculated in each population sample. In italics values after correction for null alleles.</p

GENECLASS2 assignment test.

<p>In the pie graphs, each value indicates the percentage of individuals correctly assigned to the source sampling locality. nas indicates individuals that were not unambiguously assigned. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149496#pone.0149496.t001" target="_blank">Table 1</a> for abbreviations.</p

Description of microsatellite loci utilised in this work.

<p>Abbreviations: N_a (number of alleles per locus), A_r (allelic richness), H_e (expected heterozygosity), H_o (observed heterozygosity). In italics values corrected for null alleles. The column Multiplex refers to the combinations of loci for PCR amplification.</p

Map of sampling localities.

<p>Eight geographic samples were collected across the Mediterranean Sea and the Atlantic Ocean. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149496#pone.0149496.t001" target="_blank">Table 1</a> for geographic coordinates and other information.</p

DataSheet_1_Differential Leaf Age-Dependent Thermal Plasticity in the Keystone Seagrass Posidonia oceanica.docx

Introduction: Gene-expression patterns and their upstream regulatory mechanisms (e.g. epigenetic) are known to modulate plant acclimatability and thus tolerance to heat stress. Within species, thermal plasticity (i.e. temperature-sensitive phenotypic plasticity) and differential thermo-tolerance are recognized among different genotypes, development stages, organs or tissues. Leaf age and lifespan have been demonstrated to strongly affect photosynthetic thermo-tolerance in terrestrial species, whereas there is no information available for marine plants.Materials and Methods: Here, we investigated how an intense warming event affects molecular and photo-physiological functions in the large-sized seagrass Posidonia oceanica, at fine spatial resolution. Plants were exposed for one week at 34°C in a controlled-mesocosm system. Subsequent variations in the expression of 12 target genes and global DNA methylation level were evaluated in three leaf-age sections (i.e. basal, medium and high) established along the longitudinal axis of youngest, young and fully mature leaves of the shoot. Targeted genes were involved in photosynthesis, chlorophyll biosynthesis, energy dissipation mechanisms, stress response and programmed cell death. Molecular analyses paralleled the assessment of pigment content and photosynthetic performance of the same leaf segments, as well as of plant growth inhibition under acute warming.Results: Our data revealed, for the first time, the presence of variable leaf age-dependent stress-induced epigenetic and gene-expression changes in seagrasses, underlying photo-physiological and growth responses to heat stress. An investment in protective responses and growth arrest was observed in immature tissues; while mature leaf sections displayed a higher ability to offset gene down-regulation, possibly through the involvement of DNA methylation changes, although heat-induced damages were visible at photo-physiological level.Discussion: Overall, mature and young leaf tissues exhibited different strategies to withstand heat stress and thus a variable thermal plasticity. This should be taken in consideration when addressing seagrass response to warming and other stressors, especially in large-sized species, where sharp age differences are present within and among leaves, and other gradients of environmental factors (e.g. light) could be at play. Molecular and physiological evaluations conducted only on adult leaf tissues, as common practice in seagrass research, could give inadequate estimates of the overall plant state, and should not be considered as a proxy for the whole shoot.</p

Image2_2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation.PNG

Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.</p

<i>Octopus vulgaris</i> (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure

<div><p>The common octopus, <i>Octopus vulgaris</i> Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of <i>O</i>. <i>vulgaris</i> using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of <i>O</i>. <i>vulgaris</i> in the area of interest, which can be used as guidelines for a fisheries management perspective.</p></div