The whereabouts of an ancient wonderer: Global phylogeography of the solitary ascidian Styela plicata

Genetic tools have greatly aided in tracing the sources and colonization history of introduced species. However, recurrent introductions and repeated shuffling of populations may have blurred some of the genetic signals left by ancient introductions. Styela plicata is a solitary ascidian distributed worldwide. Although its origin remains unclear, this species is believed to have spread worldwide by travelling on ship's hulls. The goals of this study were to infer the genetic structure and global phylogeography of S. plicata and to look for present-day and historical genetic patterns. Two genetic markers were used: a fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and a fragment of the nuclear gene Adenine Nucleotide Transporter/ADP-ATP Translocase (ANT). A total of 368 individuals for COI and 315 for ANT were sequenced from 17 locations worldwide. The levels of gene diversity were moderate for COI to high for ANT. The Mediterranean populations showed the least diversity and allelic richness for both markers, while the Indian, Atlantic and Pacific Oceans had the highest gene and nucleotide diversities. Network and phylogenetic analyses with COI and ANT revealed two groups of alleles separated by 15 and 4 mutational steps, respectively. The existence of different lineages suggested an ancient population split. However, the geographic distributions of these groups did not show any consistent pattern, indicating different phylogeographic histories for each gene. Genetic divergence was significant for many population-pairs irrespective of the geographic distance among them. Stochastic introduction events are reflected in the uneven distribution of COI and ANT allele frequencies and groups among many populations. Our results confirmed that S. plicata has been present in all studied oceans for a long time, and that recurrent colonization events and occasional shuffling among populations have determined the actual genetic structure of this species.

Cyanobacterial diversity and a new Acaryochloris-like symbiont from Bahamian sea-squirts

Symbiotic interactions between ascidians (sea-squirts) and microbes are poorly understood. Here we characterized the cyanobacteria in the tissues of 8 distinct didemnid taxa from shallow-water marine habitats in the Bahamas Islands by sequencing a fragment of the cyanobacterial 16S rRNA gene and the entire 16S-23S rRNA internal transcribed spacer region (ITS) and by examining symbiont morphology with transmission electron (TEM) and confocal microscopy (CM). As described previously for other species, Trididemnum spp. mostly contained symbionts associated with the Prochloron-Synechocystis group. However, sequence analysis of the symbionts in Lissoclinum revealed two unique clades. The first contained a novel cyanobacterial clade, while the second clade was closely associated with Acaryochloris marina. CM revealed the presence of chlorophyll d (chl d) and phycobiliproteins (PBPs) within these symbiont cells, as is characteristic of Acaryochloris species. The presence of symbionts was also observed by TEM inside the tunic of both the adult and larvae of L. fragile, indicating vertical transmission to progeny. Based on molecular phylogenetic and microscopic analyses, Candidatus Acaryochloris bahamiensis nov. sp. is proposed for this symbiotic cyanobacterium. Our results support the hypothesis that photosymbiont communities in ascidians are structured by host phylogeny, but in some cases, also by sampling location.

Past climate-driven range shifts and population genetic diversity in arctic plants

AimHigh intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses. LocationThe circumpolar Arctic and northern temperate alpine ranges. MethodsWe estimated the climatic niches of 30 cold-adapted plant species using range maps coupled with species distribution models and hindcasted species suitable areas to reconstructions of the mid-Holocene and LGM climates. We computed the species-specific migration distances from the species glacial refugia to their current distribution and correlated distances to extant genetic diversity in 1295 populations. Differential responses among species were related to life-history traits. ResultsWe found a negative association between inferred migration distances from refugia and genetic diversities in 25 species, but only 11 had statistically significant negative slopes. The relationships between inferred distance and population genetic diversity were steeper for insect-pollinated species than wind-pollinated species, but the difference among pollination system was marginally independent from phylogenetic autocorrelation. Main conclusionThe relationships between inferred migration distances and genetic diversities in 11 species, independent from current isolation, indicate that past range shifts were associated with a genetic bottleneck effect with an average of 21% loss of genetic diversity per 1000km(-1). In contrast, the absence of relationship in many species also indicates that the response is species specific and may be modulated by plant pollination strategies or result from more complex historical contingencies than those modelled here.

Identification and ethnic diversity underlie support for multicultural rights : a multilevel analysis in Bulgaria

Bulgaria is historically a multicultural society, composed of the Bulgarian (ethnic) majority and a number of ethnic minorities among which Bulgarian Turks and Roma are the largest. Both minority communities are stigmatized in contemporary Bulgaria, though to different degrees and for different reasons. Ethnic minorities' rights to preserve their culture, customs, and language are a topic of contentious debate. The purpose of this study was to examine individual- and context-level antecedents of the ethnic Bulgarian majority's support for multicultural rights of ethnic minorities. Multilevel regression analyses were conducted with International Social Survey Programme ISSP 2003 data (N = 920 in 28 Bulgarian districts). At the individual-level, an ethnic conception of the nation and anti-Roma symbolic prejudice were negatively related to support for multicultural rights, whereas national identification was positively related to the support of these rights. Over and above individual-level effects, and in line with recent extensions of intergroup contact theory, thepercentage ofBulgarianTurks withindistricts was positively related to support for multicultural rights. Importantly, support for multicultural rights was particularly high in districts characterized by ethnic diversity, that is, in districts with high proportions of both Bulgarian Turks and Roma. The beneficial effects of ethnic diversity and theoretical implications of findings are discussed.

Patients' Needs for Care in Public Mental Health: Unity and Diversity of Self-Assessed Needs for Care.

PURPOSE: Needs assessment is recognized to be a key element of mental health care. Patients tend to present heterogeneous profiles of needs. However, there is no consensus in previous research about how patients' needs are organized. This study investigates both general and specific dimensions of patients' needs for care. METHODS: Patients' needs were assessed with ELADEB, an 18-domain self-report scale. The use of a self-assessment scale represents a unique way of obtaining patients' perceptions. A patient-centered psychiatric practice facilitates empowerment as it is based on the patients' personal motivations, needs, and wants. Four seventy-one patients' profiles were analyzed through exploratory factor analysis. RESULTS: A four-factor bifactor model, including one general factor and three specific factors of needs, was most adequate. Specific factors were (a) "finances" and "administrative tasks"; (b) "transports," "public places," "self-care," "housework," and "food"; and (c) "family," "children," "intimate relationships," and "friendship." CONCLUSION: As revealed by the general factor, patients expressing urgent needs in some domains are also more susceptible to report urgent needs in several other domains. This general factor relates to high versus low utilizers of public mental healthcare. Patients also present specific needs in life domains, which are organized in three dimensions: management, functional disabilities, and familial and interpersonal relationships. These dimensions relate to the different types of existing social support described in the literature.

Emotion and Linguistic Diversity

In this paper we shall try to explain why speakers experience their languages so passionately. One explanation is based on the role language plays in the construction of the community and in the fact that it is a clear mark of belonging. Furthermore, we support another reason. Speakers experience their language as something received from their ancestors and that they are obliged to transmit to their descendents, an imperative which carries an extraordinary emotional charge. In fact, fear of the death of a language is experienced as an act of irreparable non-fulfilment. Why? We believe that language is one of the most evident signs of community, much more than the sum of the individuals of which it is composed. Indeed, it is a long-lasting entity projected into both the past and the future and which, moreover, accumulates within the language the whole of the culture. In the survival of the community and the language we find a response, even though it may be illusory, to the need for transcendence: our ancestors live on in our language and we, if we meet our obligations, live on in the language of our descendents

Parallel declines in species and genetic diversity driven by anthropogenic disturbance: a multispecies approach in a French Atlantic dune system.

Numerous studies assess the correlation between genetic and species diversities, but the processes underlying the observed patterns have only received limited attention. For instance, varying levels of habitat disturbance across a region may locally reduce both diversities due to extinctions, and increased genetic drift during population bottlenecks and founder events. We investigated the regional distribution of genetic and species diversities of a coastal sand dune plant community along 240 kilometers of coastline with the aim to test for a correlation between the two diversity levels. We further quantify and tease apart the respective contributions of natural and anthropogenic disturbance factors to the observed patterns. We detected significant positive correlation between both variables. We further revealed a negative impact of urbanization: Sites with a high amount of recreational infrastructure within 10 km coastline had significantly lowered genetic and species diversities. On the other hand, a measure of natural habitat disturbance had no effect. This study shows that parallel variation of genetic and species diversities across a region can be traced back to human landscape alteration, provides arguments for a more resolute dune protection, and may help to design priority conservation areas.

A nonparametric method for the measurement of size diversity with emphasis on data standardization

The most suitable method for estimation of size diversity is investigated. Size diversity is computed on the basis of the Shannon diversity expression adapted for continuous variables, such as size. It takes the form of an integral involving the probability density function (pdf) of the size of the individuals. Different approaches for the estimation of pdf are compared: parametric methods, assuming that data come from a determinate family of pdfs, and nonparametric methods, where pdf is estimated using some kind of local evaluation. Exponential, generalized Pareto, normal, and log-normal distributions have been used to generate simulated samples using estimated parameters from real samples. Nonparametric methods include discrete computation of data histograms based on size intervals and continuous kernel estimation of pdf. Kernel approach gives accurate estimation of size diversity, whilst parametric methods are only useful when the reference distribution have similar shape to the real one. Special attention is given for data standardization. The division of data by the sample geometric mean is proposedas the most suitable standardization method, which shows additional advantages: the same size diversity value is obtained when using original size or log-transformed data, and size measurements with different dimensionality (longitudes, areas, volumes or biomasses) may be immediately compared with the simple addition of ln k where kis the dimensionality (1, 2, or 3, respectively). Thus, the kernel estimation, after data standardization by division of sample geometric mean, arises as the most reliable and generalizable method of size diversity evaluation

Ecological change predicts population dynamics and genetic diversity over 120 000 years.

While ecological effects on short-term population dynamics are well understood, their effects over millennia are difficult to demonstrate and convincing evidence is scant. Using coalescent methods, we analysed past population dynamics of three lizard species (Psammodromus hispanicus, P. edwardsianus, P. occidentalis) and linked the results with climate change data covering the same temporal horizon (120 000 years). An increase in population size over time was observed in two species, and in P. occidentalis, no change was observed. Temporal changes in temperature seasonality and the maximum temperature of the warmest month were congruent with changes in population dynamics observed for the three species and both variables affected population density, either directly or indirectly (via a life-history trait). These results constitute the first solid link between ecological change and long-term population dynamics. The results moreover suggest that ecological change leaves genetic signatures that can be retrospectively traced, providing evidence that ecological change is a crucial driver of genetic diversity and speciation.

Population connectivity buffers genetic diversity loss in a seabird

Background Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems" threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory"s shearwater (Calonectris borealis). Findings We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Conclusions Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

Functional diversity of macrophyte communities within and between Pyrenean lakes

Submersed vegetation is a common feature in about 70% Pyrene an high mountain (>1500 m a.s.l.) lakes. Isoetids and soft-water elodeids are common elements of this underw ater flora and can form distinct vegetation units (i.e. patches of vegetation dominated by different species) within complex mosaics of vegetation in shallow waters (<7 m). Since is oetids exert a strong influence on sediment biogeochemistry due to high radial oxygen loss, we examined the small scale characteristics of the lake environment (water and sediment) associated to vegetation patches in order to ascertain potential functional differences among them. To do so, we characterised the species composition and biomass of the main vegetation units from 11 lakes, defined plant communities based on biomass data, and then related each community with sediment properties (redox and dissolved nutrient concentration in the pore water) and water nutrient concentration within plant canopy. We also characterised lake water and sediment in areas without vegetation as a reference. A total of twenty-one vegetation units were identified, ranging from one to five per lake. A cluster analysis on biomass species composition suggested seven different macrophyte communities that were named after the most dominant species:Nitella sp.,Potamogeton praelongus, Myriophyllum alterniflorum, Sparganium angustifolium , Isoetes echinospora,Isoetes lacustris and Carex rostrata . Coupling between macrophyte communities and their immediate environment (overlying water and sediment) was manifested mainly as variation in sediment redox conditions and the dominant form of inorganic nitrogen in pore-water. These effects depended on the specific compositi on of the community, and on the allocation between above- and belowground biomass, and could be predicted with a model relating the average and standard deviation of sediment redox potential from 0 down to -20 cm, across macrophyte communities. Differences in pore-water total dissolved phosphorus were related to the trophic state of the lakes. There was no correlation between sediment and water column dissolved nutrients. However, nitrate concentrations tended to be lower in the water overlaying isoetid communities, in apparent contradiction to the patterns of dissolved nitrates in the pore-water. These tendencies were robust even when comparing the water over laying communities within the same lake, thus pointing towards a potential effect of isoetids in reducing dissolved nitrogen in the lakes.