Search

Flying pigeons (Columbia livia) are extensively studied for their physical endurance and superior sense of orientation. The extreme physical endurance of which these birds are capable creates a unique opportunity to investigate the possible impact of long-distance flying on the taxonomy and metabolic function of the gut microbiota. This project was enabled by access to two groups of pigeons raised by the same breeder in the same conditions, except that one group was trained in long-distance flying and participated in multiple races covering a total distance of over 2600 km over a 9-week period. In contrast, the second group did not fly. The fecal microbiota was analyzed using 16S amplicon sequencing, and the taxonomy and metabolic function were inferred from this sequence data. Based on phylogenetic distance and metabolic function, flying and non-flying pigeons were found to harbor distinct bacterial microbiota. The microbiota taxonomy varied extensively between the birds, whereas the inferred metabolic potential was relatively stable. Age was not a significant determinant of the fecal microbiota profile. In flying birds, the metabolic pathways annotated with biosynthesis were enriched, representing 60% of the 20 metabolic pathways that were most closely associated with flying.

Patients not responding to therapy as expected is one of the most pressing healthcare concerns of today. It causes economical, medical and societal issues along with suffering for patients. This project aimed to address this problem and evaluate how to find the best suited drug treatments for individual patients to treat Covid-19. This project was carried out in collaboration with the company AB Mavatar, that have two networks, one experimental and one predicted, which produce drug treatment rankings differently. Different methods are used to connect drug targets to disease associated genes and thus evaluate what drugs are best suited for specific patients to treat Covid-19. The aim of this project is to examine how network, method and drug category affect the ranking of a drug treatment for four mapped Covid-19 patients. Which drug category a drug belongs to did not seem to significantly affect the drug ranking. Yet, certain drug subcategories were closely correlated. However, these subcategories were not those that are typically associated with Covid-19. The method used to connect drug targets to disease associated genes heavily impacts the ranking of the drug treatment. The methods should be further evaluated to see if some should be excluded or weighted less in drug ranking calculations. The two networks are similar in how they rank different drugs, especially in severely ill patients. Through this project and the evaluation of the impact of method choice, one can start to figure out what should be prioritized among disease related changes. Also, important parameters for personalized treatment can be evaluated. Patienter som inte svarar på terapi som förväntat är en av de största utmaningarna inom hälso- och sjukvård idag. Det orsakar ekonomiska, medicinska och samhälleliga problem samt lidande för patienter. Det här projektet adresserade detta problem och evaluerade hur man kan hitta det bäst lämpade läkemedlet för specifika patienter för att behandla Covid-19. Projektet gjordes tillsammans med företaget AB Mavatar, som har två interaktom, en experimentell och en datadriven, som rangordnar läkemedelsrekommendationer på olika sätt. Olika metoder används för att koppla samman läkemedelsmål med sjukdomsrelaterade gener och således evaluera vilka läkemedel som är bäst lämpade för specifika patienter för behandling av Covid-19. Syftet med projektet var att undersöka hur nätverk, metod och läkemedelskategori påverkar hur läkemedel rangordnas för fyra kartlagda Covid-19-patienter. Vilken läkemedelskategori ett läkemedel tillhör tycks inte märkbart påverka läkemedelsrangordning. Trots detta var vissa läkemedelsunderkategorier nära korrelerade. Dock var dessa underkategorier inte typiskt associerade med Covid-19. Metoden för att koppla samman läkemedelsmål med sjukdomsassocierade gener påverkade läkemedelsrangordningen väsentligt. Metoderna borde dock evalueras ytterligare för att eventuellt exkludera eller vikta vissa mindre i uträkningar av läkemedelsrang. De två nätverken är lika i hur de rangordnar olika läkemedel, särskilt för svårt sjuka patienter. Genom detta projekt och genom evaluering av metodvalets påverkan kan man börja begripa hur man borde priorita bland sjukdomsrelaterade förändringar. Dessutom kunde viktiga parametrar inom personlig behandling evalueras.

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single- nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.

The Environmental Impact Assessment (EIA) is a legal and administrative tool aimed to identify, predict, and interpret the impact of a project or activity on the environment and human health. The EIA also evaluates the accuracy of the predictions and audits the effectiveness of the established preventive measures. Regarding the sanitation sector, efficiency of wastewater treatments and sanitation networks determine the pollutant level of the discharged liquid effluents and the subsequent impact on the environment and human health. This problematic makes necessary to assess how proper the regulatory follow-ups of sanitation projects is. This paper evaluates the performance of the Chilean EIA System concerning to sanitation projects. Taking into account that the more restrictive Environmental Impact Study (EIS) and more permissive Environmental Impact Declaration (EID) are the ways for projects’ entry to the EIA System in Chile, 5336 sanitation projects submitted to EIA between 1994 and 2019 were complied. A representative sample of 76 projects (15 entered as EIS and 61 as EID) was analyzed by using a principal coordinate analysis (PCoA) through 14 selected performance indicators. Observed weaknesses have led to propose improvement opportunities of the EIA focused on the follow-ups after the environmental license is obtained, such as creation of a simplified sanctioning procedure, decentralization of decision-making, deadline establishment in each stage, and unified direct link for each project. These proposals seek to improve the effectiveness of monitoring and possible sanctions to early identify impacts of sanitation projects on the environment and human health. This paper introduces a robust methodology for evaluation criteria focused on the follow-ups analysis, which can be used in other countries that consider respectful sanitation projects have direct social and environmental benefits leading to long-term indirect cultural and economic values.

Parametric and nonparametric multivariate control charts that are proven very useful in monitoring the covariance matrix of multivariate normally or “nearly” normally distributed continuous datasets have been proposed in statistical process control (SPC) literature. However, in many recent practical applications of SPC, the underlying systems or processes are characterised by discrete or a mixture of discrete and continuous multivariate random variables. In such cases, the available multivariate control charts for monitoring the covariance matrix of continuous processes are inadequate. We propose a multivariate nonparametric Shewhart-type chart for monitoring shifts in the covariance matrix of multivariate discrete or mixture of discrete and continuous random variables. The proposed chart first projects the multivariate dataset into Euclidean space. It then uses the Alt's likelihood ratio obtained from the least absolute shrinkage and selection operator estimator that guarantees a well-conditioned estimate of the covariance matrix as the monitoring statistic. The proposed scheme does not require any parametric model assumptions and can be based on any distance measure of choice. It has the advantage of handling multivariate datasets of any type, including discrete, continuous or a mixture of discrete and continuous random variables. It uses the relationships among the process variables to build new variables that capture the dominant structure among the original variables. A bootstrap procedure is employed to obtain the control limit of the proposed chart for a suitable distance-based model through time. Simulation results show the advantage of the proposed chart in monitoring shifts in the covariance matrix. An illustrative example involving monitoring covariance structures of the lapping process in wafer semiconductor manufacturing and diagnosis single-proton emission computed tomography are provided to show the applications of the proposed chart.

The Chinese coffee consumption is growing with the domestic market mainly dominated by imported coffee beans and coffee brands. In this study, the check-all-that-apply (CATA) method was used to evaluate two groups of coffee products. One group was consisting of commercial samples containing four foreign and four domestic brands. The other group comprised lab-roasted samples using raw coffee beans grown in China, in the Yunnan province. The hedonic scores of each sample were collected to present subjects’ liking intensities. The results showed that Chinese young subjects participating in this study preferred coffee with cocoa, caramel, nutty aroma, and a distinct mouthfeel. They also prefer coffee with milder bitter and less sour taste. Over-roasting Yunnan coffee beans may cause undesired musty sensation, while mild thermal processing tend to result in lower roasted notes. This study provided an efficient way to obtain sensory profiles of coffee samples using CATA. Different from the traditional consumer survey, this method presents clues for the coffee industry to optimise their products, which resonate with Chinese consumers’ sensory preference.

The present article offers a concise theoretical conceptualization and operational analysis of the contribution of innovation to regional development. The latter concepts are closely related to geographical proximity, knowledge diffusion and filters and clustering. Institutional innovation profiles and regional patterns of innovation are two mutually linked, novel conceptual elements in this article. Next to a theoretical framing, the article employs the regional innovation systems concept as a vehicle to analyse institutional innovation profiles. Our case study addresses three Portuguese regions and their institutions, included in a web-based inventory of innovation agencies which offered the foundation for an extensive database. This data-set was analysed by means of a recently developed principal coordinates analysis followed by a Logistic Biplot approach (leading to a Voronoi mapping) to design a systemic typology of innovation structures where each institution is individually represented. There appears to be a significant difference in the regional innovation patterns resulting from the diverse institutional innovation profiles concerned. These profiles appear to be region specific. Our conclusion highlights the main advantages in the use of the method used for policy-makers and business companies.

Background & Aims Bile-acid metabolism and the intestinal microbiota are impaired in alcohol-related liver disease. Activation of the bile-acid receptor TGR5 (or GPBAR1) controls both biliary homeostasis and inflammatory processes. We examined the role of TGR5 in alcohol-induced liver injury in mice. Methods We used TGR5-deficient (TGR5-KO) and wild-type (WT) female mice, fed alcohol or not, to study the involvement of liver macrophages, the intestinal microbiota (16S sequencing), and bile-acid profiles (high-performance liquid chromatography coupled to tandem mass spectrometry). Hepatic triglyceride accumulation and inflammatory processes were assessed in parallel. Results TGR5 deficiency worsened liver injury, as shown by greater steatosis and inflammation than in WT mice. Isolation of liver macrophages from WT and TGR5-KO alcohol-fed mice showed that TGR5 deficiency did not increase the pro-inflammatory phenotype of liver macrophages but increased their recruitment to the liver. TGR5 deficiency induced dysbiosis, independently of alcohol intake, and transplantation of the TGR5-KO intestinal microbiota to WT mice was sufficient to worsen alcohol-induced liver inflammation. Secondary bile-acid levels were markedly lower in alcohol-fed TGR5-KO than normally fed WT and TGR5-KO mice. Consistent with these results, predictive analysis showed the abundance of bacterial genes involved in bile-acid transformation to be lower in alcohol-fed TGR5-KO than WT mice. This altered bile-acid profile may explain, in particular, why bile-acid synthesis was not repressed and inflammatory processes were exacerbated. Conclusions A lack of TGR5 was associated with worsening of alcohol-induced liver injury, a phenotype mainly related to intestinal microbiota dysbiosis and an altered bile-acid profile, following the consumption of alcohol. Lay summary Excessive chronic alcohol intake can induce liver disease. Bile acids are molecules produced by the liver and can modulate disease severity. We addressed the specific role of TGR5, a bile-acid receptor. We found that TGR5 deficiency worsened alcohol-induced liver injury and induced both intestinal microbiota dysbiosis and bile-acid pool remodelling. Our data suggest that both the intestinal microbiota and TGR5 may be targeted in the context of human alcohol-induced liver injury., Graphical abstract, Highlights • TGR5 deficiency (TGR5-KO) worsened alcohol-induced liver injury in mice. • This is linked to bile acid and intestinal microbiota changes. • Bacterial genes involved in bile-acid transformation are decreased in TGR5-KO mice. • Liver macrophage content increases without worsening of the inflammatory phenotype. • Transferring TGR5-KO microbiota in wild-type mice exacerbates liver inflammation.

Ulhas River Estuary and Thane Creek are two adjacent inward water bodies in the highly polluting environment of urban Thane City. These are impacted due to various anthropogenic activities which almost have subjected them to irreversible status. The hydrological conditions were highly alarming during this study which impacted the biological health of the inhabitant fish species. Nevertheless, Mystus gulio (Hamilton, 1822), Boleophthalmus dussumieri (Valenciennes, 1837) and Scylla serrata (Forskål, 1775) are commonly found species in Ulhas River Estuary and Thane Creek. These were studied for correlating their biological parameters with the deteriorated condition of the study areas. The Principal Coordinate Analysis (PCO) discerned the relationship of environmental pollution with Hepatosomatic index (I), Fulton’s Condition Factor (K), body glycogen, body fats, and allometric growth coefficient (b-value) of the ambient fish species, Published in J-BNB: A Multidisciplinary Journal, ISSN 2454-2776

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single-nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.

The method of multidimensional scaling (MDS) has long existed, but could only recently be applied to animal traits in the context of dynamic energy budget (DEB) theory. The application became possible because of the following: (i) the Add-my-Pet (AmP) collection of DEB parameters and traits (approximately 280) recently reached 3000 animal species with 45000 data sets of measurements; (ii) we found a natural distance measure for species based on their traits as a side result of our research on parameter estimation in DEB context; and (iii) we developed plotting code for visualization that allows labelling of taxonomic relationships. Traits, here defined as DEB parameters or any function of these parameters, have different dimensions, which hamper application of many popular distance measures since they (implicitly) assume that all traits have the same dimensions. The AmP collection follows the workflow that measured data determine parameters and parameters determine trait values. In this way we could fill up the species traits table completely, which we could not do by using measured values only, as data availability varies considerably between species and is typically poor. The goodness of fit of predictions for all data sets is generally excellent. This paper discusses links between the MDS method and parameter estimation and illustrates the application of MDS for the AmP collection to five taxa, three ectothermic and two endothermic, which we consider to be ‘complete’, in the sense that we expect that it will be difficult to find more species with data in the open literature. This application of MDS shows links between traits and taxonomy that supplements our efforts to find patterns in the co-variation of parameter values. Knowledge about metabolic performance is key to conservation biology, sustainable management and environmental risk assessment, which are seen as interlinked fields.

Rhizobia are soilborne bacteria that form symbiotic relations with legumes and fix atmospheric nitrogen. The nitrogen fixation potential depends on several factors such as the type of host and symbionts and on environmental factors that affect the distribution of rhizobia. We isolated bacteria nodulating common bean in Southern Ethiopia to evaluate their genetic diversity and phylogeography at nucleotide, locus (gene/haplotype) and species levels of genetic hierarchy. Phylogenetically, eight rhizobial genospecies (including previous collections) were determined that had less genetic diversity than found among reference strains. The limited genetic diversity of the Ethiopian collections was due to absence of many of the Rhizobium lineages known to nodulate beans. Rhizobium etli and Rhizobiumphaseoli were predominant strains of bean-nodulating rhizobia in Ethiopia. We found no evidence for a phylogeographic pattern in strain distribution. However, joint analysis of the current and previous collections revealed differences between the two collections at nucleotide level of genetic hierarchy. The differences were due to genospecies Rhizobium aethiopicum that was only isolated in the earlier collection., There is a substantial genetic diversity of bean rhizobia but with no local geographic structure in Ethiopia.

Dyrosauridae is a clade of neosuchian crocodyliforms that diversified in terrestrial and aquatic environments across the Cretaceous-Paleogene transition. The postcranial anatomy of dyrosaurids has long been overlooked, obscuring both their disparity and their locomotive adaptations. Here we thoroughly describe of the postcranial remains of an unusually small dyrosaurid, Cerrejonisuchus improcerus, from the middle-late Paleocene Cerrejón Formation of Colombia, and we provide a wealth of new data concerning the postcranial anatomy of the key dyrosaurids: Congosaurus bequaerti and Hyposaurus rogersii. We identify a series of postcranial autapomorphies in Cerrejonisuchus improcerus (an elliptic-shaped odontoid laterally wide, a ulna possessing a double concavity, a fibula bearing a widely flattened proximal end, a pubis showing a large non-triangular distal surface) as well as functionally-important traits such as a relatively long ulna (85% of the humerus’ length), short forelimb (83% of hindlimb’s length), or thoracic vertebra bearing comparatively large lateral process (with widened parapophysis and diapophysis) along with strongly arched thoracic ribs allowing a more sturdy and cylindrical rib cage. These indicate a more terrestrial lifestyle for Cerrejonisuchus compared to the derived members of the clade. We also built a dataset of 187 traits on 27 taxa, that extensively samples the cranial and postcranial architectures of exemplar crocodyliforms. We analyze these data in via Principal Coordinate Analysis (PCoA) to visualize the postcranial morphospace occupation of Dyrosauridae, Thalattosuchia, and Crocodylia. Our data reveal the existence of a distinctive postcranial anatomy for Dyrosauridae that is markedly distinct from that of crocodylians. As a result, modern crocodylians are probably not good functional analog for extinct crocodyliformes. Postcranial data should also be more widely used in phylogenetic and disparity analyses of Crocodyliformes.

Macadamia is an Australian native rainforest tree that has been domesticated and traded internationally for its premium nuts. Common cultivars rely upon a limited gene pool that has exploited only two of the four species. Introducing a more diverse germplasm will broaden the genetic base for future crop improvement and better adaptation for changing environments. This study investigated the genetic structure of 302 accessions of wild germplasm using 2872 SNP and 8415 silicoDArT markers. Structure analysis and principal coordinate analysis (PCoA) assigned the 302 accessions into four distinct groups: (i) Macadamia integrifolia, (ii) M. tetraphylla, and (iii) M. jansenii and M. ternifolia, and (iv) admixtures or hybrids. Assignment of the four species matched well with previous characterisations, except for one M. integrifolia and four M. tetraphylla accessions. Using SNP markers, 94 previously unidentified accessions were assigned into the four distinct groups. Finally, 287 accessions were identified as pure examples of one of the four species and 15 as hybrids of M. integrifolia and M. tetraphylla. The admixed accessions showed the highest genetic diversity followed by M. integrifolia, while M. ternifolia and M. jansenii accessions were the least diverse. Mantel test analysis showed a significant correlation between genetic and geographic distance for M. integrifolia (r = 0.51, p = 0.05) and a positive but not significant correlation for M. tetraphylla (r = 0.45, p = 0.06). This study provides a population genetics overview of macadamia germplasm as a background for a conservation strategy and provides directions for future macadamia breeding.

Background. Population genetic structure is one of the most important population genetic parameters revealing its demographic features. The aim of this study was to evaluate the homogeneity of the Lithuanian population on the basis of the genome-wide genotyping data. The comparative analysis of three methods – multidimensional scaling, principal components, and principal coordinates analysis – to visualize multidimensional genetics data was performed. The results of visualization (mapping images) are also presented. Materials and methods. The data set consisted of 425 samples from six ethnolinguistic groups of the Lithuanian population. Genomic DNA was extracted from whole venous blood using either the phenol-chloroform extraction method or the automated DNA extraction platform TECAN Freedom EVO. Genotyping was performed at the Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Lithuania, with the Illumina HumanOmniExpress-12 v1.1 and the Infinium OmniExpress-24. For the estimation of homogeneity of the Lithuanian population, PLINK data file was obtained using PLINK v1.07 program. The Past3 software was used to visualize the genotype data with multidimensional scaling and principal coordinates methods. The SmartPCA from EIGENSOFT 7.2.1 program was used in the principal component analysis to determine the population structure. Conclusions. Methods of multidimensional scaling, principal coordinate, and principal component for the genetic structure of the Lithuanian population were investigated and compared. The principal coordinate and principal component methods can be used for genotyping data visualization, since any essential differences in the results obtained were not observed and compared to multidimensional scaling. The Lithuanian population is homogenous whereas the points are strongly close when we use the principal coordinates or principal component methods.

Terrestrial orchid species are natural sources of salep and a closely related group of plant species widely distributed throughout Turkey. The phylogenetic relationship among fourteen different tuber-producing orchid species was investigated after analyzing phenotypic and genetic variation within and among the natural population through fifteen morphometric traits and ten random amplified polymorphic DNA (RAPD) primer combinations. Statistical analyses (principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster analysis) using the generated data identified taxonomic and genetic distance within the studied plant samples. The results of PCA from morphological traits show that there are no major groupings within and among different species instead somehow overlapping with few distinctly characterized species. In addition, the UPGMA-based phenogram with Euclidean distance (0-1) produces five major clusters among the studied orchid species according to their taxonomic status with few exceptions. On the other hand, PCoA and the phylogenetic dendrogram with the coefficient (0.56-0.79) from RAPD band profiles determine the true genetic diversity of those species. Although both combinations of genetic and phenotypic characteristics reveal the phylogenetic relationship of some those studied species very effectively, they are not clear for others. These results suggest that in the natural population of terrestrial orchid species significant amounts of gene flow are ongoing at intra/interspecies level. Therefore, it is recommended that conservation studies of these groups of orchid species should be done as a geographical unit rather than according to taxonomic status.

Sulfur dioxide (SO2) is an antioxidant and antimicrobial agent used in winemaking. Its effects on spoilage microorganisms has been studied extensively, but its effects on commercial Saccharomyces cerevisiae strains, the dominant yeast in winemaking, require further investigation. To our knowledge, no previous studies have investigated both the potential SO2 resistance mechanisms of commercial yeasts as well as their production of aroma-active volatile compounds in response to SO2. To study this, fermentations of two commercial yeast strains were conducted in the presence (50 mg/L) and absence (0 mg/L) of SO2. Strain QA23 was more sensitive to SO2 than Strain BRL97, resulting in delayed cell growth and slower fermentation. BRL97 exhibited a more rapid decrease in free SO2, a higher initial production of hydrogen sulfide, and a higher production of acetaldehyde, suggesting that each strain may utilize different mechanisms of sulfite resistance. SO2 addition did not affect the production of aroma-active volatile compounds in QA23, but significantly altered the volatile profiles of the wines fermented by BRL97.

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups, however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

The hydrodistilled essential oils (EOs) from flowers of five Adriatic populations of Anthemis maritima were analyzed by GC-FID and GC/MS. Anthemis maritima is a psammophilous plant living generally on coastal sand dunes but occasionally on sea cliffs and shingle beaches. A total of 163 chemical compounds were identified, accounting for 90.5% of the oils. The main classes of compounds represented in the EOs were monoterpene hydrocarbons, oxygenated monoterpenes, sesquiterpene hydrocarbons, oxygenated sesquiterpenes, and terpene esters.The multivariate chemometric techniques, in particular cluster analysis and principal coordinate analysis, used to classify the samples, highlighted three different chemotypes linked to a geographic origin. One group living in northern Italy was characterized by the highest content of β-pinene, γ-terpinene, and β-caryophyllene, a second chemotype was in central Italy with the highest amount of trans-chrysanthenyl acetate and a third group living in southern Italy with a more heterogeneous volatile profile was characterized by the highest values of cis-chrysanthenyl acetate, trans-chrysanthenyl isobutyrate, cis-carveol propionate, α-zingiberene, and cubenol. Moreover, the comparison of the Adriatic populations with the Tyrrhenian samples, analyzed in a previous research, showed that cubenol (absent in all the Tyrrhenian populations) and (E)-β-farnesene (absent in all the Adriatic samples) play a crucial role in discriminating the Italian populations.

Schneider’s dwarf caimanPaleosuchus trigonatusis one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis thatP. trigonatusis comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages withinP. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future ofP. trigonatusand these lineages.

Thiamine diphosphate‐dependent decarboxylases catalyze both cleavage and formation of C‐C‐bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP‐dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (Principle Component Analysis, PCA, and Principal Coordinate Analysis, PCoA) enabling complexity reduction. The different results obtained both locally and globally, i.e. individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP‐dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, in order to facilitate family assignments for homologous protein sequences.

The dynamics of plant communities is an important issue for sustainable forest management. In case of several parallel dynamic tendencies occurring within a group of research objects similar to each other, their demarcation may be difficult. The aim of the research was to check the applicability of numerical classification to distinguish the dynamic trends of plant communities on the example of multidirectional reaction of oligotrophic pine forest Peucedano−Pinetum W. Mat. (1962) 1973 to surface fire. The research was conducted in the post−fire site originated in spring 2015 in the Kampinoski National Park (central Poland). The set of 45 permanent plots was established. They differed in the degree of disturbance, measured as the share of the total burnout of the soil organic horizon. The phytosociological survey was carried out every year between 2015 and 2018, using the Londo scale. The use of cluster analysis for classification of vegetation changes requires an uniform unit for each of the variables. It was expressed as the ratio of the difference between the positions of the research plots (registered vegetation states) in the indirect space of the ordination analysis and the time elapsed between them. Thus the subject of the classification were the multidimensional changes (beta diversity) expressed in the unit of speed. The obtained material was arithmetically transformed and ordered using the PCoA method with the Bray−Curtis distance. The range of changes was calculated as differences in the plot position in three annual intervals separately for each of the four main gradients of the ordination. The 12 annual change values obtained for each of the plot were subjected to Ward classification. In order to verify the nature of the obtained clusters, collective covers of species belonging to higher syntaxones were calculated and their changes during the research period compared using the Kruskal−Wallis and Mann−Whitney tests. The significance of differences in the degree of initial disturbance was also checked. On the basis of the Ward classification, the division into five dynamic groups of plots was obtained. An analysis of the changes in the coverage of higher syntaxonomic groups revealed the existence of statistically significant differences between the clusters in 55 out of 110 possible cases. The presence of significant differences in the initial degree of disturbance by fire was also noted. The studied plot groups represent the regeneration process (A and B), pine forest regression combined with secondary succession (groups C and D) and the control group – not−disturbed pine forest (E). The cluster analysis method was proved to be an effective tool for classifying objects in terms of different tendencies of vegetation dynamic., Sylwan 163 (11): 924-935

Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania.

Understanding the population structure and genetic diversity in sugarcane (Saccharum officinarum L.) accessions from INTA germplasm bank (Argentina) will be of great importance for germplasm collection and breeding improvement as it will identify diverse parental combinations to create segregating progenies with maximum genetic variability for further selection. A Bayesian approach, ordination methods (PCoA, Principal Coordinate Analysis) and clustering analysis (UPGMA, Unweighted Pair Group Method with Arithmetic Mean) were applied to this purpose. Sixty three INTA sugarcane hybrids were genotyped for 107 Simple Sequence Repeat (SSR) and 136 Amplified Fragment Length Polymorphism (AFLP) loci. Given the low probability values found with AFLP for individual assignment (4.7%), microsatellites seemed to perform better (54%) for STRUCTURE analysis that revealed the germplasm to exist in five optimum groups with partly corresponding to their origin. However clusters shown high degree of admixture, F ST values confirmed the existence of differences among groups. Dissimilarity coefficients ranged from 0.079 to 0.651. PCoA separated sugarcane in groups that did not agree with those identified by STRUCTURE. The clustering including all genotypes neither showed resemblance to populations find by STRUCTURE, but clustering performed considering only individuals displaying a proportional membership > 0.6 in their primary population obtained with STRUCTURE showed close similarities. The Bayesian method indubitably brought more information on cultivar origins than classical PCoA and hierarchical clustering method.

Sunflower is one of the most important oilseed crops. Evaluation of genetic diversity and grouping of genotypes and lines are computed as important agents for plant breeding programms. In this study, the genetic diversity and classification of some advanced inbred lines of sunflower developed during different breeding programs were studied using ISSR markers. Among 21 primers, 15 ISSR primers were selected for their reproducibility. A total of 70 bands were produced through ISSR primers which 27 and 43 bands out of them were monomorphic and polymorphic, respectively. Results revealed that primer UBC 807 (0.4) had the highest polymorphism information content value and primer UBC 804 (0.15) had the lowest value. Using Dice similarity coefficient the lowest amount of genetic similarity (0.65) was observed between breeding lines SF25 with SF278 and the highest ones (0.93) was observed between lines HA336 and SF315. Cluster analysis using UPGMA algorithm was divided the studied lines into 8 separate groups. Regarding to principal coordinates analysis; each component accounts a small percentage of the total variation which emphasis on good genomic distribution of selected ISSR primers.

Analysis of genetic diversity is a major step for understanding evolution and breeding applications. Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD technique has been successfully used in a variety of taxonomic and genetic diversity studies. The genetic diversity of 18 accessions of Thymus kotschyanus collected from different districts of Iran has been reported in this study, using 30 random amplified polymorphic DNA primers. Multivariate statistical analyses including principal coordinate analysis (PCOA) and cluster analysis were used to group the accessions. From 29 primers, 385 bands were scored corresponding to an average of 13.27 bands per primer with 298 bands showing polymorphism (77.40%). A dendrogram constructed based on the UPGMA clustering method revealed three major clusters. The obtained results from grouping 18 accessions of T. kotschyanus with two studied methods indicated that in the most cases the applied methods produced similar grouping results. This study revealed nearly rich genetic diversity among T. kotschyanus accessions from different regions of Iran. The results showed RAPD marker was a useful marker for genetic diversity studies of T. kotschyanus and it was indicative of geographica variations.

Easy access to next generation sequencing has enabled the rapid analysis of complex microbial populations. To take full advantage of these technologies, animal models enabling the manipulation of human microbiomes and the study of the impact of such perturbations on the host are needed. To this aim we are developing experimentally tractable and clinically relevant pig models of the human adult and infant gastro-intestinal tract. The intestine of germ-free piglets was populated with human adult or infant fecal microbial populations, and the piglets were maintained on solid or milk diet, respectively. Amplicons of 16S rRNA V6 region were deep-sequenced to monitor to what extent the transplanted human microbiomes changed in the pig. Within 24 h of transfer of human fecal microbiome to pigs, bacterial microbiomes rich in Proteobacteria emerged. These populations evolved toward a more diverse composition rich in Bacteroidetes and Firmicutes. In the experiment where infant microbiome was used, the phylogenetic composition of the transplanted bacterial population converged toward that of the human inoculum. A majority of sequences belonged to a relatively small number of operational taxonomic units, whereas at the other end of the abundance spectrum, a large number of rare and transient OTUs were detected. Analysis of fecal and colonic microbiomes originating from the same animal indicate that feces closely replicate the colonic microbiome. We conclude that the pig intestine can be colonized with human fecal microbiomes to generate a realistic model of the human GI tract.

International audience; To enhance table olive tree authentication, relationship, and productivity, we consider the analysis of 18 worldwide table olive cultivars (Olea europaea L.) based on morphological, biological, and physicochemical markers analyzed by bioinformatic and biostatistic tools. Accordingly, we assess the relationships between the studied varieties, on the one hand, and the potential productivity-quantitative parameter links on the other hand. The bioinformatic analysis based on the graphical representation of the matrix of Euclidean distances, the principal components analysis, unweighted pair group method with arithmetic mean, and principal coordinate analysis (PCoA) revealed three major clusters which were not correlated with the geographic origin. The statistical analysis based on Kendall's and Spearman correlation coefficients suggests two highly significant associations with both fruit color and pollinization and the productivity character. These results are confirmed by the multiple linear regression prediction models. In fact, based on the coefficient of determination (R-2) value, the best model demonstrated the power of the pollinization on the tree productivity (R-2 = 0.846). Moreover, the derived directed acyclic graph showed that only two direct influences are detected: effect of tolerance on fruit and stone symmetry on side and effect of tolerance on stone form and oil content on the other side. This work provides better understanding of the diversity available in worldwide table olive cultivars and supplies an important contribution for olive breeding and authenticity.

Made available in DSpace on 2018-11-12T17:28:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2017. Added 1 bitstream(s) on 2018-11-12T17:36:01Z : No. of bitstreams: 1 S1984-46702017000100309.pdf: 3250536 bytes, checksum: 4333e8e56132d2bc2496715bb3a81790 (MD5) ABSTRACT Stretching for more than 10,000 ha in the Metropolitan Area of São Paulo, southeastern Brazil, Serra da Cantareira comprises the largest native urban rainforest in the World, harboring a rich and diverse Atlantic Forest avifauna. Despite its closeness to major urban areas, few bird surveys have been conducted there. In this article we present an updated compilation of all bird species recorded for Serra da Cantareira, including personal records from the authors. A total of 326 species have been recorded for Serra da Cantareira since 1901; of these, nine have not been sighted there for the last two decades. The number of bird species endemic to the Atlantic Forest is high (80), and seven of its species are globally threatened. According to multivariate analyses the species diversity at Serra da Cantareira is similar to other regions of the Atlantic Forest, such as Carlos Botelho and Intervales state parks, where the vegetation is also ombrophilous dense forest. We discuss local changes in the avifaunal composition over the last decades and suggest the incorporation of large forest remnants to the Cantareira State Park to mitigate the impact of the northern section of Rodoanel Mário Covas, a highway (SP-21) that will soon be operational and will negatively impact the biodiversity of Serra da Cantareira. Universidade Estadual Paulista Departamento de Ecologia Lousiana State University Museum of Natural Science Unaffiliated BirdLife SAVE Brasil Universidade de São Paulo Instituto de Biociências Departamento de Zoologia Universidade de São Paulo Museu de Zoologia Universidade Estadual Paulista Departamento de Ecologia

The Opuntia spp., most likely few individuals, were introduced in the Iberian Peninsula in the beginning of the 16th century, after the discovery of America, spreading afterwards throughout the Mediterranean basin. We analysed, for the first time, the genetic diversity in a set of 19 Portuguese Opuntia spp. populations from the species O. ficus-indica, O. elata, O. dillenii and O. robusta using nuclear microsatellite (nuSSR) markers. The Italian cultivars ‘Bianca’, ‘Gialla’ and ‘Rossa’ were included in the study for comparison purposes. The nuSSR amplifications produced from five to 16 alleles, with an average of 9.2 alleles per primer pair, and average polymorphism information content of 0.71. The estimated Dice coefficient among populations varied from 0.26 to 1.0, indicating high interspecific genetic diversity but low genetic diversity at the intraspecific level. The hierarchical clustering analysis revealed four major groups that clearly separated the four Opuntia species. Among the O. ficus-indica populations, two sub-clusters were found, one including the white pulp fruits (with cv. Bianca) and the other with the orange pulp ones and including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population. No genetic differences were found between the inermis form, O. ficus-indica f. ficus-indica, and the rewilded spiny one, O. ficus-indica f. amyclaea. The dendrogram indicated that the clustering pattern was unrelated to geographical origin. The results revealed a low level of genetic diversity among the Portuguese populations of O. ficus-indica. info:eu-repo/semantics/publishedVersion

Information about the genetic diversity and relationships among breeding lines and varieties is not only useful for germplasm conservation and inbred line identification, but also for the selection of parental lines for quantitative trait loci (QTL) mapping as well as hybrid breeding in crops, including sunflower. In order to develop mapping populations, genetic distances among twenty eight sunflower genotypes were evaluated using simple sequence repeat (SSR) markers. One hundred and two markers were generated by 38 SSR loci and the mean for the number of allele per locus was 2.32. Polymorphism information content (PIC) values ranged from 0.09 (locus ha3555) to 0.62 (locus ORS598) with an average of 0.41. Jaccard's coefficient similarity matrix for the studied sunflower genotypes varied from 0.25 to 0.9 indicating a broad genetic base. The maximum similarity (0.9) was observed between genotypes RT931 and ENSAT-R5, while the lowest similarity (0.25) was between genotypes LC1064C and LR64. Based on unweighted pair group method with arithmetic mean (UPGMA) clustering algorithm, the studied genotypes were clustered in four groups. However, some genotypes have the same specific characters that influence their clustering, and as a result, the results of the principal coordinate analysis (PCoA) largely corresponded to those obtained through cluster analysis.Key words: Cluster analysis, genetic diversity, principal coordinate analysis, sunflower, simple sequence repeat.

32 Pag., 5 Tabl., 4 Fig. The definitive version is available at: http://www.springerlink.com/content/0040-5752/, The pool of Western Mediterranean landraces has been under-utilised for barley breeding so far. The objectives of this study were to assess genetic diversity in a core collection of inbred lines derived from Spanish barley landraces to establish its relationship to barleys from other origins, and to correlate the distribution of diversity with geographical and climatic factors. To this end, 64 SSR were used to evaluate the polymorphism among 225 barley (Hordeum vulgare ssp. vulgare) genotypes, comprising two-row and six-row types. These included 159 landraces from the Spanish barley core collection (SBCC) plus 66 cultivars, mainly from European countries, as a reference set. Out of the 669 alleles generated, a large proportion of them were unique to the six-row Spanish barleys. An analysis of molecular variance revealed a clear genetic divergence between the six-row Spanish barleys and the reference cultivars, whereas this was not evident for the two-row barleys. A model-based clustering analysis identified an underlying population structure, consisting of four main populations for the whole genotype set, and suggested further possible subdivision within two of these populations. Most of the six-row Spanish landraces clustered into two groups that corresponded to geographic regions with contrasting environmental conditions. The existence of wide genetic diversity in Spanish germplasm, possibly related to adaptation to a broad range of environmental conditions, and its divergence from current European cultivars confirm its potential as a new resource for barley breeders, and make the SBCC a valuable tool for the study of adaptation in barley., This research was funded by project RTA01-088-C3, granted by the Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), of the Spanish Ministry of Science and Technology, and co-funded by the European Regional Development Fund. Samia Yahiaoui was supported by a scholarship from the Agencia Española de Cooperación Internacional (AECI), of the Spanish Ministry of Foreign Affairs.

Rao developed the DISC dissimilarity coefficient to summarize the dissimilarity between pairs of plots based on species abundances and interspecies dissimilarities. In this paper, we review the potential of the DISC coefficient for assessing plot-to-plot phylogenetic dissimilarity. First, the relationship between plot-to-plot dissimilarity and additive beta diversity is discussed. Next, we show that additive diversity decomposition can be interpreted in terms of a sum of classical Euclidean distances. Based on this geometrical interpretation of additive diversity decomposition, we then suggest an alternative way for calculating an analog of the DISC coefficient directly from the centroids of two species plots in multivariate phylogenetic space. The key to this method is that the centroids can be easily calculated by applying a principal coordinate analysis (PCoA) to the corresponding species phylogenetic distances. Finally, to show the potential of the DISC coefficient for analyzing the relationship between community structure and ecosystem functioning, we used the proposed measure by comparing phylogenetic and functional changes in plant communities along a primary succession on a glacier foreland in northern Italy. Our results show that changes in Grime's CSR functional classification of plant assemblages as competitors (C), stress-tolerators (S) and ruderals (R) along the successional gradient are also reflected in phylogenetic changes, indicating that species sorting by environmental filtering tends to favor the co-occurrence of phylogenetically related species. From a more theoretical viewpoint, the relationship between the proposed measure and the DISC coefficient helps in shedding new light on the additive decomposition of biological diversity into alpha, beta and gamma components.

A total of 90 grapevine samples collected in five countries of the Western Balkan region were evaluated for trueness-to-type and kinship relations based on comparative analysis with 1,130 grapevine genotypes held at the INRA "Domaine de Vassal" French Grape Germplasm Repository, using 14 microsatellite markers. In the context of the comparative analysis, twenty-four synonyms/counterparts and the putative parents for twelve Balkan accessions were identified. We discovered five pairs of homonyms, subsequently confirming the identity or parentage of three of them. Some of the examined accessions were identified either on the basis of the genotypes found in the literature, or through parentage relationships revealed in this study. For the remaining fifty accessions we were unable to establish either their pedigree or to identify them on the basis of SSR profiles available elsewhere. Finally, the Balkan genotypes that were not well classified by synonymy or parentage analysis were further studied with a Principal Coordinate Analysis to reveal genetic clustering within larger datasets of genotypes. The graphical display of the individual and group distances showed that about forty accessions (85 %) are structured within a group of Balkan and Eastern Europe genotypes and only a minor proportion resulted in admixed population assignment., VITIS - Journal of Grapevine Research, Vol. 54 (2015): Vitis (Special Issue)

ObjectiveTo determine the impact of 2 probiotic bifidobacteria on the fecal microbiota of premature infants fed either human milk or formula.Study designIn the first of two phase 1 clinical trials, 12 premature infants receiving formula feedings were assigned randomly to receive either Bifidobacterium longum ssp infantis or Bifidobacterium animalis ssp lactis in increasing doses during a 5-week period. In the second, 9 premature infants receiving their mother's milk received each of the two bifidobacteria for 2 weeks separated by a 1-week washout period. Serial stool specimens from each infant were analyzed by terminal restriction fragment-length polymorphism and quantitative polymerase chain reaction for bacterial composition.ResultsAmong the formula-fed infants, there was a greater increase in fecal bifidobacteria among infants receiving B infantis (Binf) than those receiving B lactis (Blac). This difference was most marked at a dose of 1.4× 10(9) colony-forming units twice daily (P < .05). Bacterial diversity improved over dose/time in those infants receiving Binf. Among the human milk-fed infants, greater increases in fecal bifidobacteria and decreases in γ-Proteobacteria followed the administration of Binf than Blac. The B longum group (which includes Binf but not Blac) was the dominant bifidobacteria among the human milk-fed infants, regardless of the probiotic administered.ConclusionsBinf was more effective at colonizing the fecal microbiota than Blac in both formula-fed and human milk-fed premature infants. The combination of human milk plus Binf resulted in the greatest fecal levels of bifidobacteria.

Objective: The aim of the present study was to determine the alterations in the handwriting characteristics of multiple sclerosis (MS) patients acquired along one year at three different time points by using statistical shape analysis. Material and Methods: The handwriting samples of multiple sclerosis patients and control subjects were taken at three different time points. Statistical shape analysis of handwriting characteristics was performed. Principal coordinate analysis was applied to tangent coordinate which derived from Procrustes analysis. Results: Analysis of the handwriting samples at different time points suggested that upper case letters, both in the same box and in separate boxes, showed more changes in MS patients. Lower case letters in the same box showed more changes in MS patients while lower case letters in separate boxes showed more changes in the control subjects. Conclusion: There are only a few studies about analysis of handwriting by statistical shape analysis. In recent years, it has been observed that there has been considerable interest in the statistical analysis of shape. This study has imaginative aspects as it analyzed the handwriting characteristics of MS patients by using statistical shape analysis for the first time. We hope that this study enables further studies using this method of application. Bu çalışmanın amacı, multipl skleroz (MS)’lu hastaların bir yıl boyunca üç farklı zamanda alınan el yazısı karakteristiklerindeki değişimi istatistiksel şekil analizi ile incelemektir. Gereç ve Yöntemler: MS’li hastaların ve kontrol grubunun el yazısı örnekleri farklı üç zaman diliminde elde edildi. Toplanan bu el yazısı karakteristiklerine istatistiksel şekil analizi uygulandı. Procrustes analiz sonucunda elde edilen tanjant koordinatlarına temel koordinat analizi uygulandı. Bulgular: Üç farklı zaman noktasında toplanan büyük harfli el yazısı örneklerinin analiz sonucunda hem aynı kutu içerisinde hem de harflerin ayrı kutu içerisinde yer aldığı durumdaki değişim MS’li hastalarda daha fazla bulunmuştur. Aynı kutu içerisinde küçük harfli el yazısı karakteristikleri MS’li hastalarda daha fazla değişim gösterirken, ayrı kutulardaki küçük harfli el yazısı karakteristikleri kontrol grubunda daha fazla değişim göstermiştir. Sonuç: İstatistiksel şekil analizi ile el yazılarının incelendiği çalışma sayısı oldukça azdır. Son yıllarda istatistiksel şekil analizi giderek artan bir ilgi görmektedir. Bu çalışmanın yaratıcı olan yönü, MS’li hastaların el yazısı karakteristiklerinin ilk kez istatistiksel şekil analiziyle incelenmesidir. Çalışmamızda kullanılan yöntemin benzer çalışmalarda uygulanabileceğini düşünmekteyiz.

Background The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to protein families, MDS provides information complementary to the information derived from tree-based methods. Moreover, MDS gives a unique opportunity to compare orthologous sequence sets because it can add supplementary elements to a reference space. Results The R package bios2mds (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. Bios2mds starts with a sequence alignment, builds a matrix of distances between the aligned sequences, and represents this matrix by MDS to visualize a sequence space. This package also offers the possibility of performing K-means clustering in the MDS derived sequence space. Most importantly, bios2mds includes a function that projects supplementary elements (a.k.a. “out of sample” elements) onto the space defined by reference or “active” elements. Orthologous sequence sets can thus be compared in a straightforward way. The data analysis and visualization tools have been specifically designed for an easy monitoring of the evolutionary drift of protein sub-families. Conclusions The bios2mds package provides the tools for a complete integrated pipeline aimed at the MDS analysis of multiple sets of orthologous sequences in the R statistical environment. In addition, as the analysis can be carried out from user provided matrices, the projection function can be widely used on any kind of data.

This study was carried out on 13 local cornelian cherry (Cornus mas L.) genotypes grown in Yusufeli (Artvin) in Northeast Anatolia in Turkey. Cornelian cherry fruits from these 13 genotypes were harvested and analyzed during the ripening period in 2010. Some physical and chemical characteristics of cultivars were determined. Fruit weight and fruit flesh ratio of these genotypes ranged from 2.72 to 4.11 g and 79.08 to 89.99%. Soluble solid content were determined the lowest as 13.7% and the highest as 18.6%. The genotypes had vitamin C between 31 to 70 mg/100 g with average of 50 mg/100 g. Total protein, cellulose, tannin and ash content of genotypes were determined between 0.75-2.18%; 0.36-1.08%; 0.57-1.28% and 0.51-1.13%. The genotypes were found to be free of pest and diseases. The present study showed that there were enough variability among cornelian cherry genotypes grown in same ecological conditions of a small area and these genotypes could be important both to improve nutritional value through germplasm enhancement programmes and to use them in organic production.

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed. Marcadores moleculares AFLP, RAPD e SSR foram usados para estudo da diversidade e estrutura genética do germoplasma de Híbrido de Timor. As análises de coordenadas principais, de agrupamento UPGMA baseado na dissimilaridade genética de Jaccard, de agrupamento baseado no modelo Bayesiano, a percentagem de locos polimórficos, o índice de Shannon e a diversidade genética de Nei foram utilizadas para acessar a diversidade genética. As análises demonstraram alta diversidade genética entre os acessos de Híbrido de Timor. A análise de agrupamento UPGMA e o modelo Bayesiano permitiram a alocação dos acessos em três grupos. A estrutura genética dos acessos de Híbrido de Timor foi descrita. A manutenção e manuseio da variabilidade do germoplasma de Híbrido de Timor e seu potencial uso nos programas de melhoramento de cafeeiro foram discutidos.

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon?s information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breedin programs are discussed.

Sequence Tagged Microsatellite Sites (STMSs) and morphological trait markers were used to evaluate 33 rhododendron germplasm for genetic diversity assessment and discrimination power. The average genetic diversity estimates were 0.724 (morphological traits) and 0.174 (STMSs) marker datasets. The Shannon index was higher for morphological traits (1.797) than STMS (0.302). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the two markers, showed that estimated values of relationships given for morphological and STMS were not significantly related (p > 0.05). The dataset from STMS, supported by the total probability of identity (1.13 × 10−9) and total paternity exclusion probability (0.9999), allowed all accessions to be uniquely identified. In summary, STMS marker proved to be an efficient tool in assessing the genetic variability among old broad leaf rhododendron genotypes. The pattern of variation appeared to be consistent, and it can be used for germplasm conservation and management for restoration of historical genetic resources.

Two new DNA-based marker methodologies, the nucleotide binding site (NBS) and myb gene profiling, were evaluated to assess their discriminating capacity and efficiency in genetic analyses of 11 Campanula populations (C. latifolia, C. rapunculoides, C. spicata and C. trachelium). Three restriction enzymes (MseI, RsaI and HaeIII) with two NBS primers (GLPL6 and NBS2) and one myb primer (MYB2) were used. Looking at the number of banding pattern, both techniques discriminated the genotypes very effectively. On an individual assay basis, NBS profiling completely distinguished all the genotypes of one population of C. latifolia and C. trachelium. To test the usefulness of the overall information provided by these markers for establishing genetic variability and distances, AMOVA and two Principal Coordinate Analyses were performed. Both NBS and myb gene profiling resulted to be remarkably effective for group discrimination and genetic diversity studies. However, some differences could be highlighted. The myb marker resulted to be more efficient to differentiating species than populations, while NBS profiling appeared to better discriminate the populations. In general, the plots reflected the geographical distributions. The use of these techniques is discussed in terms of the appropriate choice for studying different aspects of Campanula species and populations evaluation.

Biplots simultaneously provide information on both the samples and the variables of a data matrix in two- or three-dimensional representations. The BiplotGUI package provides a graphical user interface for the construction of, interaction with, and manipulation of biplots in R. The samples are represented as points, with coordinates determined either by the choice of biplot, principal coordinate analysis or multidimensional scaling. Various transformations and dissimilarity metrics are available. Information on the original variables is incorporated by linear or non-linear calibrated axes. Goodness-of-fit measures are provided. Additional descriptors can be superimposed, including convex hulls, alpha-bags, point densities and classification regions. Amongst the interactive features are dynamic variable value prediction, zooming and point and axis drag-and-drop. Output can easily be exported to the R workspace for further manipulation. Three-dimensional biplots are incorporated via the rgl package. The user requires almost no knowledge of R syntax.

Functional diversity is at the heart of current research in the field of conservation biology. Most of the indices that measure diversity depend on variables that have various statistical types (e.g. circular, fuzzy, ordinal) and that go through a matrix of distances among species. We show how to compute such distances from a generalization of Gower's distance, which is dedicated to the treatment of mixed data. We prove Gower's distance can be extended to include new types of data. The impact of this generalization is illustrated on a real data set containing 80 plant species and 13 various traits. Gower's distance allows an efficient treatment of missing data and the inclusion of variable weights. An evaluation of the real contribution of each variable to the mixed distance is proposed. We conclude that such a generalized index will be crucial for analyzing functional diversity at small and large scales.

Gower and Krzanowski (1999) described the analysis of a multivariate dataset that violated the assumptions of normality for multivariate analysis of variance. They developed a method comprising two aspects: a graphical representation of the points in a fewer number of dimensions, known as principal coordinate analysis; and a technique similar to MANOVA except that it was based on partitioning the distances between subjects, rather than sums of squares, and did not assume that the data followed any particular distribution. This article summarizes both aspects of their analysis and describes the Stata pco and aod commands, which perform principal coordinate analysis and analysis of distance.

Este artículo ofrece una panorámica generalizada de la relevancia en Estadística de ideas geométricas basadas en el concepto de distancia. Sus aplicaciones se agrupan según cuatro áreas: Estimación Puntual, Contrastes de Hipótesis, Representación de Conjuntos y Predicción basada en Distancias.

Background Lentil is a self-pollinated annual diploid (2n = 2× = 14) crop with a restricted history of genetic improvement through breeding, particularly when compared to cereal crops. This limited breeding has probably contributed to the narrow genetic base of local cultivars, and a corresponding potential to continue yield increases and stability. Therefore, knowledge of genetic variation and relationships between populations is important for understanding of available genetic variability and its potential for use in breeding programs. Single nucleotide polymorphism (SNP) markers provide a method for rapid automated genotyping and subsequent data analysis over large numbers of samples, allowing assessment of genetic relationships between genotypes. Results In order to investigate levels of genetic diversity within lentil germplasm, 505 cultivars and landraces were genotyped with 384 genome-wide distributed SNP markers, of which 266 (69.2%) obtained successful amplification and detected polymorphisms. Gene diversity and PIC values varied between 0.108-0.5 and 0.102-0.375, with averages of 0.419 and 0.328, respectively. On the basis of clarity and interest to lentil breeders, the genetic structure of the germplasm collection was analysed separately for cultivars and landraces. A neighbour-joining (NJ) dendrogram was constructed for commercial cultivars, in which lentil cultivars were sorted into three major groups (G-I, G-II and G-III). These results were further supported by principal coordinate analysis (PCoA) and STRUCTURE, from which three clear clusters were defined based on differences in geographical location. In the case of landraces, a weak correlation between geographical origin and genetic relationships was observed. The landraces from the Mediterranean region, predominantly Greece and Turkey, revealed very high levels of genetic diversity. Conclusions Lentil cultivars revealed clear clustering based on geographical origin, but much more limited correlation between geographic origin and genetic diversity was observed for landraces. These results suggest that selection of divergent parental genotypes for breeding should be made actively on the basis of systematic assessment of genetic distance between genotypes, rather than passively based on geographical distance. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0150-3) contains supplementary material, which is available to authorized users.