New insights into the genetic diversity of zooxanthellae in Mediterranean anthozoans

Symbiotic dinoflagellates of the genus Symbiodinium, also called zooxanthellae, are found in association with a wide diversity of shallow-water anthozoans. The Symbiodinium genus includes numerous lineages, also referred to as clades or phylotypes, as well as a wide diversity of genetic sub-clades and sub-phylotypes. There are few studies characterizing the genetic diversity of zooxanthellae in Mediterranean anthozoans. In this study, we included anthozoans from the Western Mediterranean Sea and by means of internal transcriber (ITS) and large sub-unit (LSU) rRNA markers we corroborate what has been previously identified, demonstrating that phylotype “Temperate A” is very common among host Cnidaria in this basin. Our finding of fixed differences in ITS and LSU markers that correspond to different host taxa, indicate that this clade may comprise several closely-related species. Previous studies have reported the occurrence of Symbiodinium psygmophilum (formerly sub-clade B2) associated with Oculina patagonica and Cladocora caespitosa in the Eastern Mediterranean. Here, we identify this association in O. patagonica from the Western Mediterranean but not in C. caespitosa, suggesting some differences in symbiotic combinations between the Western and Eastern Mediterranean Basins.     

Wheat genetic diversity trends during domestication and breeding

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheats genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.     

Glacial refugia influence plant diversity patterns in the Mediterranean Basin

Aim The aims of this study were to assess the distribution of putative Mediterranean refugia of plants, to compare the locations of refugia and those of regional hotspots of plant biodiversity, and to provide a critical analysis of the Mediterranean refugium paradigm. Furthermore, we consider how biogeographical and genetic results can be combined to guide global conservation strategies. Location The Mediterranean region. Methods We started from a detailed analysis of the scientific literature (1993–2007) in order to identify refugia in the Mediterranean region, based on intra‐specific phylogeographical studies of plant species. We used population locations together with gene‐pool identity to establish the database, comparing patterns of phylogeographical concordance with the locations of Mediterranean refugia. We then tested the biogeographical congruence between two biodiversity components, namely phylogeographical refugia and regional hotspots. Results We identified 52 refugia in the Mediterranean bioclimatic region and confirmed the role played by the three major peninsulas, with a shared total of 25 refugia. We emphasize the importance of areas that have previously been attributed a lesser role (large Mediterranean islands, North Africa, Turkey, Catalonia). Of the 52 refugia identified, 33 are situated in the western Mediterranean Basin and 19 in the eastern part. The locations of the phylogeographically defined refugia are significantly associated with the 10 regional hotspots of plant biodiversity, with 26 of these refugia (i.e. 50%) occurring within the hotspots. Main conclusions The locations of refugia are determined by complex historical and environmental factors, the cumulative effects of which need to be considered because they have occurred since the Tertiary, rather than solely during the last glacial period. Refugia represent climatically stable areas and constitute a high conservation priority as key areas for the long‐term persistence of species and genetic diversity, especially given the threat posed by the extensive environmental change processes operating in the Mediterranean region. The refugia defined here represent ‘phylogeographical hotspots’; that is, significant reservoirs of unique genetic diversity favourable to the evolutionary processes of Mediterranean plant species.     

Patterns of genetic diversity in the Andean gene pool of common bean reveal a candidate domestication gene

Most studies on the genetic diversity of common bean (Phaseolus vulgaris L.) have focussed on accessions from the Mesoamerican gene pool compared to the Andean gene pool. A deeper knowledge of the genetic structure of Argentinian germplasm would enable researchers to determine how the Andean domestication event affected patterns of genetic diversity in domesticated beans and to identify candidates for genes targeted by selection during the evolution of the cultivated common bean. A collection of 116 wild and domesticated accessions representing the diversity of the Andean bean in Argentina was genotyped by means of 114 simple sequence repeat (SSR) markers. Forty-seven Mesoamerican bean accessions and 16 Andean bean accessions representing the diversity of Andean landraces and wild accessions were also included. Using the Bayesian algorithm implemented in the software STRUCTURE we identified five major groups that correspond to Mesoamerican and Argentinian wild accessions and landraces and a group that corresponds to accessions from different Andean and Mesoamerican countries. The neighbour-joining algorithm and principal coordinate clustering analysis confirmed the genetic relationships among accessions observed with the STRUCTURE analysis. Argentinian accessions showed a substantial genetic variation with a considerable number of unique haplotypes and private alleles, suggesting that they may have played an important role in the evolution of the species. The results of statistical analyses aimed at identifying genomic regions with consistent patterns of variation were significant for 35 loci (~20 % of the SSRs used in the Argentinian accessions). One of these loci mapped in or near the genomic region of the glutamate decarboxylase gene. Our data characterize the population structure of the Argentinian germplasm. This information on its diversity will be very valuable for use in introgressing Argentinian genes into commercial varieties because the majority of present-day common bean varieties are of Andean origin.     

Loss of genetic diversity from heterogeneous self-pollinating genebank accessions

Genebank seed accessions of predominantly self-pollinating species may be stored either as bulked (mixed) seed lines or as pure line cultivars. If seed lines are bulked in storage then when considered over several regeneration cycles, loss of genetic diversity within heterogeneous self pollinating genebank accessions is shown to be severe. This within-accession loss of diversity represents opportunities foregone through the random loss of individual genotypes. Amongst working collections, the utility and repeatability of genebank accessions is paramount in the justification of the germ plasm resource. Therefore, the only practical solution to the management of predominantly self-pollinating species is to preserve individual accessions as pure lines.     

Centennial olive trees as a reservoir of genetic diversity

Background and Aims

Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin.

Methods

The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars.

Key Results

Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives.

Conclusions

This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.     

Development of phoH as a novel signature gene for assessing marine phage diversity

Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified, phoH was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage phoH sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the phoH gene were used to determine the diversity of phage phoH sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide. phoH was present at all sites examined, and a high diversity of phoH sequences was recovered. Most phoH sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct phoH composition, although most phoH clusters were recovered from multiple sites. Overall, phoH is an effective signature gene for examining phage diversity in the marine environment.     

Molecular diversity, structure and domestication of grasses

Map-based cloning has been considered problematic for isolating quantitative trait loci (QTLs) due to the confounding phenotypic effects of environment and other QTLs. However, five recent studies, all in plants, have succeeded in cloning QTLs using map-based methods. We review the important features of these studies and evaluate the prospects for broader application of the techniques. Successful map-based cloning requires that QTLs represent single genes that can be isolated in near-isogenic lines, and that genotypes can be unambiguously inferred by progeny testing. In plants or animals for which map-based cloning of genes with discrete phenotypes is feasible, the modified procedures required for QTLs should not be limiting in most cases. The choice between map-based cloning and alternative methods will depend on details of the species and traits being studied.     

Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Concerns over the reductionist nature of the domestication of forest-tree species focus on the possibility of potential genetic erosion during this process. To address these concerns, genetic diversity assessments in a breeding zone the Province of British Columbia “interior” spruce (Picea glauca×engelmanni) program was conducted using allozyme markers. Genetic-variation comparisons were made between natural and production (seed orchard) populations as well as seed and seedling crops produced from the same breeding zone’s seed orchard. The natural population sample consisted of a total of 360 trees representing three stands within each of three watersheds present in the Shuswap-Adams low-elevation zone of interior British Columbia. Small amounts of genetic differentiation were observed among the nine natural populations (4%) and this was attributable to extensive gene flow Consequently, the sum of these nine populations was considered as a baseline for the genetic variation present in the breeding zone. The comparisons between the seed orchard and the breeding zone produced a similar percentage of polymorphic loci while the expected hetrozygosity (0.207 vs 0.210) and the average number of alleles per locus (2.7 vs 2.4) were slightly lower in the seed orchard. A total of seven natural populations’ rare alleles were not present in the orchard population, while one allele was unique to the orchard. The %P increased to 70.6% in the seedlot, but dropped to the natural populations level (64.7%) in the plantation. The observed increase in %P was a result of pollen contamination in the orchard. It is suspected that the reduction in the plantation was caused by an unintentional selection in the nursery. Simulated roguing in the orchard did not drastically reduce even if up to 50% of the orchard’s clones were rogued. However, roguing was associated with a reduction in the average number of alleles per locus (i.e., sampling effect). Received: 2 January 1996 / Accepted: 24 May 1996     

Aedes albopictus in Italy and possible diffusion of the species into the Mediterranean area

Aedes albopictus (Skuse), the important Asian vector mosquito recently introduced in United States and Brazil, is reported from Genoa, North Italy. The infestation was discovered in a kindergarten pre-school center in September 1990 just after the summer holidays. Many discarded tires, well known to provide excellent breeding places for Ae albopictus, had been left in the school playground to be used as toys by the children. After sampling a few biting mosquito specimens for identification, the local health service carried out on September 18 an extensive indoor/outdoor treatment with pyrethroid insecticide. The extent of the infestation in the city of Genoa and in other areas of the Ligurian region has not been evaluated since the identification of the species was available in October, at the end of Ae albopictus reproductive period. A general survey in various Italian regions is being planned for the 1991 spring-summer period. The present record, together with the previous report of Ae albopictus in Albania, clearly supports the hypothesis of a spreading of the species in the Mediterranean area.     

Conservation genetics of an endemic from the Mediterranean Basin: high genetic differentiation but no genetic diversity loss from the last populations of the Sicilian Grape Hyacinth Leopoldia gussonei

The Mediterranean Basin is a biodiversity hotspot, housing >11.000 narrowly endemic plant species, many of which are declining due to mass tourism and agricultural intensification. To investigate the genetic resource impacts of ongoing habitat loss and degradation, we characterized the genetic variation in the last known populations of Leopoldia gussonei, a self-compatible endangered Sicilian Grape Hyacinth numbering less than 3,000 remaining individuals, using AFLP. Results demonstrated significant genome-wide genetic differentiation among all extant populations (Φ_ST = 0.05–0.56), and genetic clustering according to geographic location. Gene diversity was fairly constant across population (mean H_E = 0.13) and was neither affected by current population size nor by spatial isolation. Vegetation analysis showed the presence of known invasive weeds in a quarter of the populations, but we found no relation between genetic diversity and plant community composition. The marked genetic differences among populations and the profusion of rare and private alleles indicate that any further population loss will lead to significant losses of genetic diversity. Conservation efforts should therefore focus on the preservation of all sites where L. gussonei still occurs, yet the deliberate introduction of diverse material into the smallest populations seems unneeded as clonality likely mitigated genetic drift effects thus far. More generally, our findings support the view that endemic plant species with a narrow ecological amplitude, as many specialists in Mediterranean coastal ecosystems, are highly genetically differentiated and that conservation of their genetic diversity requires preservation of most, if not all of their extant populations.     

Tetraploid wheat landraces in the Mediterranean basin: taxonomy, evolution and genetic diversity

The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields.     

Eddy diffusion as a possible determinant of vertical nitrate and chlorophyll distributions in the Mediterranean Sea

Using coupled biological and physical submodels, simulated distributionsof nitrate and chlorophyll agree well with summer observations,but are very sensitive to vertical velocity profiles and calculatedrates of eddy diffusion.     

Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality

The endemic New Zealand Hector's dolphin is considered the rarest species of marine dolphin with a total abundance of less than 4000. The species is listed as vulnerable because of fisheries-related mortality due to entanglement in set nets. The vulnerability of this species is further increased by its fidelity to local natal ranges and the genetic isolation of regional populations. Here we present evidence, based on 108 contemporary samples and 55 historical samples dating back to 1870, of a significant loss of mitochondrial DNA (mtDNA) diversity in two regional populations of Hector's dolphin. The haplotype diversity (h) was calculated from sequences of a 206 bp fragment in the mtDNA control region, designed to identify 13 out of the 14 known maternal lineages. Over the last 20 years, the North Island population has been reduced from at least three lineages (h = 0.41) to a single lineage (h = 0; p < 0.05). Given its small size, reproductive isolation and reduced genetic diversity, this population is likely to become extinct. The diversity of the East Coast South Island population has declined significantly from h = 0.65 to h = 0.35 (p < 0.05). Based on trend analysis of the mtDNA diversity, we predict that the East Coast population will lose all mtDNA diversity within the next 20 years. This time-series of reduction in genetic variation provides independent evidence of the severity of population decline and habitat contraction resulting from fisheries and perhaps other human activities.     

Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT^® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r ² of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT^® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley.     

Hybridization and genetic control of esterase in apricot

Inheritance of esterase was studied in nine segregating progenies. It was established that fast migrating components are controlled by two loci, Est-1 (monomeric alpha-esterase) and Est-2 (dimeric beta-esterase). Their polymorphism is determined by three active alleles, a, a', b for Est-1 and a, b, c for Est-2, respectively. Allelic frequencies and heterozygosity of loci in ecological-geographical groups and Central Asian subgroups were estimated. Genetic control of esterase in stone fruits was proposed for the first time.