Dugesia sicula (Platyhelminthes, Tricladida): the colonizing success of an asexual Planarian

Background Dugesia sicula is the only species of its genus not presenting an endemic or restricted distribution within the Mediterranean area. It mostly comprises fissiparous populations (asexual reproduction by body division and regeneration), most likely sexually sterile, and characterized by an extremely low genetic diversity interpreted as the consequence of a recent anthropic expansion. However, its fissiparous reproduction can result in an apparent lack of diversity within the species, since genetic variation within individuals can be as large as between them because most individuals within a population are clones. We have estimated haplotype and nucleotide diversity of cytochrome oxidase I within and among individuals along the species distribution of a broad sample of D. sicula, including asexual and the two only sexual populations known today; and predicted its potential distribution based on climatic variables. Our aim was to determine the centre of colonisation origin, whether the populations are recent, and whether the species is expanding. Results The species presents 3 most frequent haplotypes, differing in a maximum of 11 base pairs. As expected from their fissiparous mode of reproduction, in half of all the analysed localities many individuals have multiple heteroplasmic haplotypes. The distribution of haplotypes is not geographically structured; however, the distribution of haplotypes and heteroplasmic populations shows higher diversity in the central Mediterranean region. The potential distribution predicted by climatic variables based modelling shows a preference for coastal areas and fits well with the observed data. Conclusions The distribution and frequency of the most frequent haplotypes and the presence of heteroplasmic individuals allow us to gain an understanding of the recent history of the species, together with previous knowledge on its phylogenetic relationships and age: The species most probably originated in Africa and dispersed through the central Mediterranean. After one or multiple populations became triploid and fissiparous, the species colonized the Mediterranean basin, likely both by its own means and helped by human activities. Its present distribution practically fulfils its potential distribution as modelled with climatic variables. Its prevalence in coastal regions with higher water temperatures predicts a likely future expansion to northern and more interior areas following the increase in temperatures due to climate change.

Influence of biocontrol strain Pseudomonas fluorescens CHA0 and its antibiotic overproducing derivative on the diversity of root colonizing pseudomonads

Non-target effects of biocontrol strains of Pseudomonas on the population of resident pseudomonads should be assessed prior to their large scale application in the environment. The rifampicin resistant bacterium P. fluorescens CHA0-Rif and its antibiotic overproducing derivative CHA0-Rif/pME3424 were introduced into soil microcosms and the population of resident pseudomonads colonizing cucumber roots was investigated after 10 and 52 days. Both CHA0-Rif and CHA0-Rif/pME3424 displaced a part of the resident pseudomonad population after 10 days. To investigate the population structure, utilization of 10 carbon sources and production of two exoenzymes was assessed for 5600 individual pseudomonad isolates and 1700 isolates were subjected to amplified ribosomal DNA restriction analysis of the spacer region (spacer-ARDRA). After 10 days, only the proportion of pseudomonads able to degrade -tryptophan was reduced in treatments inoculated with either biocontrol strain. In parallel the phenotypic diversity was reduced. These effects were only observed 10 days after inoculation, and they were similar for inoculation with CHA0-Rif and CHA0-Rif/pME3424. Changes in the population structure of resident pseudomonads on cucumber roots during plant growth were more pronounced than changes due to the inoculants. The inoculants did not affect the genotypic diversity detected with spacer-ARDRA, but the genotypic fingerprints corresponded only partially to the phenotypic profiles. Overall CHA0-Rif had a small and transient impact on the population of resident pseudomonads and the effect was essentially the same for the genetically engineered derivative CHA0-

Hot spots for diversity of Magnaporthe oryzae physiological races in irrigated rice fields in Brazil

The objective of this work was to evaluate the Magnaporthe oryzae pathotype diversity in new commercial irrigated rice fields in the Araguaia River Valley, state of Tocantins, Brazil. The causal agent of rice blast has heavily affected rice production in the region. Despite the efforts of breeding programs, blast resistance breakdown has been recorded shortly after the release of new resistant cultivars developed for the region. Among the causes of resistance breakage is the capacity of the fungus to rapidly develop new pathotypes. A sample of 479 M. oryzae monosporic isolates was obtained and tested using the international rice blast differential set. Isolate collections were made in small areas designed as trap nurseries and in scattered sites in their vicinity. Analysis of 250 M. oryzae isolates from three trap nurseries indicated the presence of 45 international M. oryzae races belonging to seven pathotype groups (IA-IG). In the isolates tested, 61 M. oryzae pathotypes belonging to all but the IH group were detected. The new areas of irrigated rice in the Araguaia River Valley have the highest diversity of M. oryzae pathotypes reported so far in Brazil.

Genetic diversity in soybean germplasm identified by SSR and EST-SSR markers

The objectives of this work were to investigate the genetic variation in 79 soybean (Glycine max) accessions from different regions of the world, to cluster the accessions based on their similarity, and to test the correlation between the two types of markers used. Simple sequence repeat markers present in genomic (SSR) and in expressed regions (EST-SSR) were used. Thirty SSR primer-pairs were selected (20 genomic and 10 EST-SSR) based on their distribution on the 20 genetic linkage groups of soybean, on their trinucleotide repetition unit and on their polymorphism information content. All analyzed loci were polymorphic, and 259 alleles were found. The number of alleles per locus varied from 2-21, with an average of 8.63. The accessions exhibit a significant number of rare alleles, with genotypes 19, 35, 63 and 65 carrying the greater number of exclusive alleles. Accessions 75 and 79 were the most similar and accessions 31 and 35, and 40 and 78, were the most divergent ones. A low correlation between SSR and EST-SSR data was observed, thus genomic and expressed microsatellite markers are required for an appropriate analysis of genetic diversity in soybean. The genetic diversity observed was high and allowed the formation of five groups and several subgroups. A moderate relationship between genetic divergence and geographic origin of accessions was observed.

Mating type, mefenoxam sensitivity, and pathotype diversity in Phytophthora infestans isolates from tomato in Brazil

The objective of this work was to characterize 79 Phytophthora infestans isolates collected in tomato (Solanum lycopersicum) fields, as to mating type, mefenoxam sensitivity, and pathotype composition. The isolates were sampled in 2006 and 2007 in seven Brazilian states as well as in the Distrito Federal. They were characterised as to mating type (n=79), sensitivity to fungicide mefenoxam (n=79), and virulence to three major resistance genes Ph-1, Ph-2, and Ph-3/Ph-4 (n=62). All isolates were of the mating type A1. Resistant isolates were detected in all sampled states, and its average frequency was superior to 50%. No difference was detected in pathotype diversity, neither between subpopulations collected in 2006 and 2007 nor between isolates grouped as resistant or intermediately sensitive to mefenoxam. All major resistance genes were overcome at different frequencies: Ph-1, 88.7%; Ph-2, 64.5%; and Ph-3/Ph-4, 25.8%. Isolates with virulence genes able to overcome all major resistance genes were detected at low frequencies. Tomato breeding programs in Brazil must avoid the development of cultivars with resistance based exclusively on major genes.

Fiscal Year 2015 Report on the Condition of Affirmative Action, Diversity, and Multi-cultural Programs in State Government and Fiscal Year 2016 Plan, September 30, 2015

Each agency is invited and encouraged to send a representative to a quarterly Department of Administrative Services State Recruitment Coordinating Committee “Committee” meeting. This Committee conducts strategic planning sessions to identify top goals and initiatives for the next 2-3 years.

Quantification of the diversity among common bean accessions using Ward-MLM strategy

The present work aimed at evaluating the divergence among common bean accessions by their agronomic, morphological and molecular traits, based on the Ward-MLM procedure. A collection of 57 accessions from the gene bank of Universidade Federal do Espírito Santo was used in this study, from which: 31 were landraces belonging to the community Fortaleza, in the municipality of Muqui, ES, Brazil; 20 accessions were provided by Embrapa Trigo; and 6 were commercial cultivars. Five agronomic traits (plant cycle, number of seeds per pod, number of pods per plant, weight of 100 seeds, and grain yield), five morphological traits (growth habit, plant size, seed shape, seed color, and commercial group) and 16 microsatellite primers were evaluated. High genetic variability was detected considering morphological, agronomic and molecular traits in the 57 common bean accessions studied. The Ward-MLM procedure showed that the ideal number of groups was five, according to the pseudo F and pseudo t² criteria. The accessions from Andean origin had heavier seeds than others and formed a cluster. The Ward-MLM statistical procedure is a useful technique to detect genetic divergence and to cluster genotypes by simultaneously using morphological, agronomic and molecular data.

Genetic diversity for gliadin patterns of durum wheat landraces in the Northwest of Iran and Azerbaijan

The objective of this study was to identify gliadin band patterns and the extent of genetic diversity in durum wheat genotypes from Northwestern Iran and the Republic of Azerbaijan. Gliadins from 46 landraces and four cultivars were evaluated through acid PAGE analyses. Sixty-six polymorphic bands and 81 patterns were identified. Twenty-four different motility bands and 22 patterns were found in the ω gliadin region with 14 polymorph bands and 20 patterns for α and γ gliadins, and 14 bands and 19 different patterns for β gliadins. The combination of these patterns generated 38 and 39 combinations for Gli-1 and Gli-2 loci, respectively. The genetic diversity index (H) was higher for α gliadins (0.924), followed by ω and γ gliadins (0.899 and 0.878, respectively), and for β gliadin patterns (0.866). Extensive polymorphism (H = 0.875) was observed in four gliadin pattern regions, with higher genetic diversity in the Iranian landraces than in the Azerbaijani ones. Each genotype had special identifying patterns in the gliadin acid PAGE analysis, and cluster analysis based on Jaccard's similarity coefficients formed six groups. Gliadin has a simple, repeatable and economic analysis, and can be used in genetic studies

Genetic diversity in table grapes based on RAPD and microsatellite markers

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: selectome@unil.ch or nicolas.salamin@unil.ch.

Genetic diversity of cultivated accessions and wild species of rubber tree using EST‑SSR markers

The objective of this work was to evaluate the efficiency of EST‑SSR markers in the assessment of the genetic diversity of rubber tree genotypes (Hevea brasiliensis) and to verify the transferability of these markers for wild species of Hevea. Forty‑five rubber tree accessions from the Instituto Agronômico (Campinas, SP, Brazil) and six wild species were used. Information provided by modified Roger's genetic distance were used to analyze EST‑SSR data. UPGMA clustering divided the samples into two major groups with high genetic differentiation, while the software Structure distributed the 51 clones into eight groups. A parallel could be established between both clustering analyses. The 30 polymorphic EST‑SSRs showed from two to ten alleles and were efficient in amplifying the six wild species. Functional EST‑SSR microsatellites are efficient in evaluating the genetic diversity among rubber tree clones and can be used to translate the genetic differences among cultivars and to fingerprint closely related materials. The accessions from the Instituto Agronômico show high genetic diversity. The EST‑SSR markers, developed from Hevea brasiliensis, show transferability and are able to amplify other species of Hevea.

Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers revealed robust amplification profiles and were able to differentiate the 41 genotypes of sweet sorghum evaluated. Analysis of the frequency and distribution of polymorphic fragments allowed for the detection of unique (AFLP) and rare (SSR) alleles in several genotypes (RBSS‑8, RBSS‑9, RBSS‑25, RBSS‑32, and RBSS‑37), indicating that these markers may be associated with a feature that has not yet been determined or may be useful for the identification of these genotypes. The genetic relationships indicated the presence of at least two types of sweet sorghum: a group of modern genotypes used for sugar and biofuel production, and another group consisting of historic and modern genotypes used for the production of syrups. Sweet sorghum genotypes may be used to develop new varieties with higher sugar and juice contents.

Genetic diversity between improved banana diploids using canonical variables and the Ward-MLM method

The objective of this work was to estimate the genetic diversity of improved banana diploids using data from quantitative analysis and from simple sequence repeats (SSR) marker, simultaneously. The experiment was carried out with 33 diploids, in an augmented block design with 30 regular treatments and three common ones. Eighteen agronomic characteristics and 20 SSR primers were used. The agronomic characteristics and the SSR were analyzed simultaneously by the Ward-MLM, cluster, and IML procedures. The Ward clustering method considered the combined matrix obtained by the Gower algorithm. The Ward-MLM procedure identified three ideal groups (G1, G2, and G3) based on pseudo-F and pseudo-t² statistics. The dendrogram showed relative similarity between the G1 genotypes, justified by genealogy. In G2, 'Calcutta 4' appears in 62% of the genealogies. Similar behavior was observed in G3, in which the 028003-01 diploid is the male parent of the 086079-10 and 042079-06 genotypes. The method with canonical variables had greater discriminatory power than Ward-MLM. Although reduced, the genetic variability available is sufficient to be used in the development of new hybrids.

Multilocus phylogeography of the common lizard Zootoca vivipara at the Ibero-Pyrenean suture zone reveals lowland barriers and high-elevation introgression.

BACKGROUND: The geographic distribution of evolutionary lineages and the patterns of gene flow upon secondary contact provide insight into the process of divergence and speciation. We explore the evolutionary history of the common lizard Zootoca vivipara (= Lacerta vivipara) in the Iberian Peninsula and test the role of the Pyrenees and the Cantabrian Mountains in restricting gene flow and driving lineage isolation and divergence. We also assess patterns of introgression among lineages upon secondary contact, and test for the role of high-elevation trans-mountain colonisations in explaining spatial patterns of genetic diversity. We use mtDNA sequence data and genome-wide AFLP loci to reconstruct phylogenetic relationships among lineages, and measure genetic structure RESULTS: The main genetic split in mtDNA corresponds generally to the French and Spanish sides of the Pyrenees as previously reported, in contrast to genome-wide AFLP data, which show a major division between NW Spain and the rest. Both types of markers support the existence of four distinct and geographically congruent genetic groups, which are consistent with major topographic barriers. Both datasets reveal the presence of three independent contact zones between lineages in the Pyrenean region, one in the Basque lowlands, one in the low-elevation mountains of the western Pyrenees, and one in the French side of the central Pyrenees. The latter shows genetic evidence of a recent, high-altitude trans-Pyrenean incursion from Spain into France. CONCLUSIONS: The distribution and age of major lineages is consistent with a Pleistocene origin and a role for both the Pyrenees and the Cantabrian Mountains in driving isolation and differentiation of Z. vivipara lineages at large geographic scales. However, mountain ranges are not always effective barriers to dispersal, and have not prevented a recent high-elevation trans-Pyrenean incursion that has led to asymmetrical introgression among divergent lineages. Cytonuclear discordance in patterns of genetic structure and introgression at contact zones suggests selection may be involved at various scales. Suture zones are important areas for the study of lineage formation and speciation, and our results show that biogeographic barriers can yield markedly different phylogeographic patterns in different vertebrate and invertebrate taxa.