Phylogenetic study of the Grimmia Hedw. (Grimmiales, Bryopsida) based on a combination of morphological and molecular characters

Résumé Les mousses sont la plus ancienne lignée de plantes terrestres et leur longue évolution a été accompagnée par des tendances à la simplification des caractères morphologiques. Ce phénomène a quelque peu compliqué les reconstructions phylogénétiques basées sur la morphologie. Les analyses génétiques ont permis de donner de nouvelles informations dans le cadre des analyses phylogénétiques et une réévaluation de certains caractères morphologiques. La plupart des études combinant les données morphologiques et moléculaires ne concernent que des niveaux systématiques élevés comme l'ordre ou la famille et très peu considèrent le niveau du genre. La présente étude tend à tester les relations phylogénétiques du genre Grimmia à l'aide d'une combinaison de caractères morphologiques et moléculaires. Les 40 espèces de Grimmia utilisées dans la première partie de cette étude représentent la majorité des espèces trouvées en Eurasie, un des centres de diversification du genre. Lors de l'analyse morphologique, 52 caractères morphologiques/anatomiques (33 du gamétophyte et 19 du sporophyte) ont été numérisés. Malgré le peu de support statistique des arbres, la topologie des arbres est stable. Les Grimmia, comme décrit précédemment, sont paraphylétiques. Trois clades, correspondant respectivement aux sous-genres Rhabdogrimmia Limpr, Litoneuron I.Hagen et Gasterogrimmia Schimp. sont présents, tandis que le restant des taxons appartenant aux Grimmia forment un groupe non-résolu et indistinct des autres Grimmiaceae. Les séquences chloroplastiques trnL-trnF et rps4 combinés à la morphologie ont été ensuite utilisés pour reconstruire la phylogénie des Grimmia. Les arbres obtenus soutiennent la monophylie des Grimmiaceae tandis que les Grimmia, sont paraphylétiques. Deux clades principaux correspondant aux "Rhabdogrimmia" et aux "Grimmia" se détachent. Seules les espèces de "Rhabdogrimmia" produisent des gemmules foliaires (reproduction asexuée). Dans une étude considèrant 91 séquences trrIL-trnF les espèces appartenant aux "Rhabdogrimrnia" (reproduction asexuée essentiellement) ont des variabilités intraspécifique très faible et interspécifique relativement élevée tandis que les "Grimmia" possèdent la tendance inverse (plus de reproduction sexuée). Summary The mosses are a very old land plant lineage and their long evolutionary history has been accompanied by a trend of morphological character simplifications. This phenomenon has somewhat complicated morphological based phylogenetic reconstructions. Genetic analyses have provided new insights for phylogenetic studies, and have allowed morphological data to be re¬evaluated. Most of the studies combining morphological and molecular data have concerned the higher systematic levels of order and family and only have few considered the genus. The present study aims to test the phylogenetic relationships of the genus Grimmia using a combination of morphological and molecular characters. The 40 chosen Grimmia species represent the majority of those found in Eurasia, one diversification centers of the genus. For the morphological analysis, 52 morphological/anatomical characters (33 gametophyte and 19 sporophyte characters) were numerized. Although the internal statistical support was relatively low, the tree topologies were stable. Grimmia as currently defined was found to be paraphyletic. Three subclades, corresponding to the subgenera Rhabdogrimmia Limpr., Litoneuron I.Hagen, and Gasterogrimmia Schimp. were observed in the trees, while the reminder of the Grimmia species formed an unresolved group indistinct from other Grimmiaceae. Chloroplast (trnL-trnF and rps4) DNA sequences combined with morphology were used to reconstruct the phylogeny of Grimmia. The resulting trees supported the monophyly of Grimmiaceae and that the genus Grimmia, as currently defined, as paraphyletic. Two main clades were resolved corresponding to "Rhabdogrimmia" and "Grimmia". The species belonging to "Rhabdogrimmia" produce foliar-gemmae (asexual reproduction). In a study using 91 sequences of trnL-trnF,"Rhabdogrimmia" species (mainly asexual reproduction) have very low intraspecific variability and high interspecific variability whereas the "Grimmia" species possess the inverse tendency.

Global Diversity Lines-A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains.

Reference collections of multiple Drosophila lines with accumulating collections of "omics" data have proven especially valuable for the study of population genetics and complex trait genetics. Here we present a description of a resource collection of 84 strains of Drosophila melanogaster whose genome sequences were obtained after 12 generations of full-sib inbreeding. The initial rationale for this resource was to foster development of a systems biology platform for modeling metabolic regulation by the use of natural polymorphisms as perturbations. As reference lines, they are amenable to repeated phenotypic measurements, and already a large collection of metabolic traits have been assayed. Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe. After obtaining 12.5× coverage of paired-end Illumina sequence reads, SNP and indel calls were made with the GATK platform. Thorough quality control was enabled by deep sequencing one line to >100×, and single-nucleotide polymorphisms and indels were validated using ddRAD-sequencing as an orthogonal platform. In addition, a series of preliminary population genetic tests were performed with these single-nucleotide polymorphism data for assessment of data quality. We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample. We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

Prevalence and diversity of Chlamydiales in Swiss ruminant farms.

Chlamydia and Chlamydia-related bacteria are known to infect various organisms and may cause a wide range of diseases, especially in ruminants. To gain insight into the prevalence of these bacteria in the ruminant environment, we applied a pan-Chlamydiales PCR followed by sequencing to 72 ruminant environmental samples from water, feed bunks and floors. Chlamydiales from four family-level lineages were detected indicating a high biodiversity of Chlamydiales in ruminant farms. Parachlamydiaceae were detected in all three types of environmental samples and was the most abundant family-level taxon (60%). In contrast, only one bacterium from each of the following family-level lineages was identified: Chlamydiaceae, Criblamydiaceae and Simkaniaceae. The observed high prevalence of Parachlamydiaceae in water samples may suggest water as the main source of contamination for ruminants as well as their environment due to spoilage. The absence of reported infections in the investigated ruminant farms might indicate that either detected Chlamydiales are of reduced pathogenicity or infective doses have not been reached.

Effect of cattle on Salmonella carriage, diversity and antimicrobial resistance in free-ranging wild boar (Sus scrofa) in northeastern Spain

Salmonella is distributed worldwide and is a pathogen of economic and public health importance. As a multi-host pathogen with a long environmental persistence, it is a suitable model for the study of wildlife-livestock interactions. In this work, we aim to explore the spill-over of Salmonella between free-ranging wild boar and livestock in a protected natural area in NE Spain and the presence of antimicrobial resistance. Salmonella prevalence, serotypes and diversity were compared between wild boars, sympatric cattle and wild boars from cattle-free areas. The effect of age, sex, cattle presence and cattle herd size on Salmonella probability of infection in wild boars was explored by means of Generalized Linear Models and a model selection based on the Akaike’s Information Criterion. Prevalence was higher in wild boars co-habiting with cattle (35.67%, CI 95% 28.19–43.70) than in wild boar from cattle-free areas (17.54%, CI 95% 8.74–29.91). Probability of a wild boar being a Salmonella carrier increased with cattle herd size but decreased with the host age. Serotypes Meleagridis, Anatum and Othmarschen were isolated concurrently from cattle and sympatric wild boars. Apart from serotypes shared with cattle, wild boars appear to have their own serotypes, which are also found in wild boars from cattle-free areas (Enteritidis, Mikawasima, 4:b:- and 35:r:z35). Serotype richness (diversity) was higher in wild boars co-habiting with cattle, but evenness was not altered by the introduction of serotypes from cattle. The finding of a S. Mbandaka strain resistant to sulfamethoxazole, streptomycin and chloramphenicol and a S. Enteritidis strain resistant to ciprofloxacin and nalidixic acid in wild boars is cause for public health concern.

Diversity and genetic struture in cajá tree (spondias mombin l.) populations in northeastern Brazil

Spondias mombin L. is a fruit tree from the American continent from the Anacardiaceae family. In Brazil it is common in different vegetation types but is more frequent in the Atlantic and Amazonian rainforests. It is economically important because of its fruits, which are widely consumed raw or processed as fruit jellies, juices and ice creams. The leaves have great importance in the pharmaceutical industry because of their antibacterial properties. In the state of Pernambuco, cajá tree is widely distributed in the Zona da Mata region and less frequently in the Agreste and Sertão areas. In this work diversity and genetic structure were studied in four populations of cajá tree from Pernambuco's Zona da Mata, Northeast Brazil, using isozymes polymorphism analyses from electrophoreses. The result showed 100% of polymorphism (P) for nine alleles and the average of alleles per locus s was 2.4. The expected heterozygosity ranged from 0.530 to 0.574 and the observed heterozygosity , from 0.572 to 0.735. It was not observed inbreeding and the average F IT was -0.175, whereas within population inbreeding (f) varied from -0.08 to- 0.37. The genetic divergence among the populations (F ST) ranged from 0.006 to 0.028 and the average was 0.026. The average of estimated gene flow (Nm) was high (5.27). The CG-IPA population, corresponding to the germplasm collection of IPA, showed more than 96% of genetic similarity with other populations; therefore, it is a good representative of the existent genetic diversity in the Zona da Mata region.

Genetic diversity of a brazilian wine grape germplasm collection based on morphoagronomic traits

The objectives of this study were to evaluate the performance of cultivars, to quantify the variability and to estimate the genetic distances of 66 wine grape accessions in the Grape Germplasm Bank of the EMBRAPA Semi-Arid, in Juazeiro, BA, Brazil, through the characterization of discrete and continuous phenotypic variables. Multivariate statistics, such as, principal components, Tocher's optimization procedure, and the graphic of the distance, were efficient in grouping more similar genotypes, according to their phenotypic characteristics. There was no agreement in the formation of groups between continuous and discrete morpho-agronomic traits, when Tocher's optimization procedure was used. Discrete variables allowed the separation of Vitis vinifera and hybrids in different groups. Significant positive correlations were observed between weight, length and width of bunches, and a negative correlation between titratable acidity and TSS/TTA. The major part (84.12%) of the total variation present in the original data was explained by the four principal components. The results revealed little variability between wine grape accessions in the Grape Germplasm Bank of Embrapa Semi-Arid.

On diversity effects of alternative agricultural policy reforms in Finland : an agricultural sector modelling approach

Selostus: Maatalouspolitiikkauudistusten vaikutuksista pellonkäytön diversiteettiin

First survey of fruit fly (Diptera: Tephritidae) and parasitoid diversity among myrtaceae fruit across the state of Bahia, Brazil

The objective of this study was to evaluate the diversity of fruit fly (Diptera: Tephritidae) species that use myrtaceous fruit, particularly guava, as hosts in several localities in the state of Bahia and to determine the infestation rates, pupal viability rates, and fruit fly-parasitoid associations. Sampling of myrtaceous fruit was carried out in 24 municipalities in different regions in the state of Bahia. Four fruit fly species, Anastrepha fraterculus, Anastrepha zenildae, Anastrepha sororcula, and Ceratitis capitata were obtained from the collected fruit. Three parasitoid species (Hymenoptera: Braconidae) emerged from Anastrepha larvae/pupae, Doryctobracon areolatus, Utetes anastrephae, and Asobara anastrephae. Doryctobracon areolatus emerged from A. fraterculus, A. sororcula and A. zenildae; Utetes anastrephae emerged from A. fraterculus and A. zenildae; and Asobara anastrephae emerged from A. fraterculus. Fruit fly and myrtaceous fruit associations are reported for the first time in several municipalities in the state of Bahia. A. zenildae was found infesting Syzygium malaccense for the first time in Brazil.

Patterns of nucleotide diversity at the regions encompassing the Drosophila insulin-like peptide (dilp) genes: demography vs positive selection in Drosophila melanogaster.

In Drosophila, the insulin-signaling pathway controls some life history traits, such as fertility and lifespan, and it is considered to be the main metabolic pathway involved in establishing adult body size. Several observations concerning variation in body size in the Drosophila genus are suggestive of its adaptive character. Genes encoding proteins in this pathway are, therefore, good candidates to have experienced adaptive changes and to reveal the footprint of positive selection. The Drosophila insulin-like peptides (DILPs) are the ligands that trigger the insulin-signaling cascade. In Drosophila melanogaster, there are several peptides that are structurally similar to the single mammalian insulin peptide. The footprint of recent adaptive changes on nucleotide variation can be unveiled through the analysis of polymorphism and divergence. With this aim, we have surveyed nucleotide sequence variation at the dilp1-7 genes in a natural population of D. melanogaster. The comparison of polymorphism in D. melanogaster and divergence from D. simulans at different functional classes of the dilp genes provided no evidence of adaptive protein evolution after the split of the D. melanogaster and D. simulans lineages. However, our survey of polymorphism at the dilp gene regions of D. melanogaster has provided some evidence for the action of positive selection at or near these genes. The regions encompassing the dilp1-4 genes and the dilp6 gene stand out as likely affected by recent adaptive events.

Diversity and genetic structure in natural populations of Hancornia speciosa var. speciosa Gomes in northeastern Brazil

Hancornia speciosa Gomes is a fruit tree native from Brazil that belongs to Apocinaceae family, and is popularly known as Mangabeira. Its fruits are widely consumed raw or processed as fruit jam, juices and ice creams, which have made it a target of intense exploitation. The extractive activities and intense human activity on the environment of natural occurrence of H. speciosa has caused genetic erosion in the species and little is known about the ecology or genetic structure of natural populations. The objective of this research was the evaluation of the genetic diversity and genetic structure of H. speciosa var. speciosa. The genetic variability was assessed using 11 allozyme loci with a sample of 164 individuals distributed in six natural populations located in the States of Pernambuco and Alagoas, Northeastern Brazil. The results showed a high level of genetic diversity within the species (e= 0.36) seeing that the most of the genetic variability of H. speciosa var. speciosa is within its natural populations with low difference among populations ( or = 0.081). The inbreeding values within ( = -0.555) and among populations ( =-0.428) were low showing lacking of endogamy and a surplus of heterozygotes. The estimated gene flow ( m ) was high, ranging from 2.20 to 13.18, indicating to be enough to prevent the effects of genetic drift and genetic differentiation among populations. The multivariate analyses indicated that there is a relationship between genetic and geographical distances, which was confirmed by a spatial pattern analysis using Mantel test (r = 0.3598; p = 0.0920) with 1000 random permutations. The high genetic diversity index in these populations indicates potential for in situ genetic conservation.

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi.

Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling-although crucial for crop improvement-is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.

Diversity and genetic relatedness among genotypes of Vitis spp. using microsatellite molecular markers

The purpose of this research was to study the genetic diversity and genetic relatedness of 60 genotypes of grapevines derived from the Germplasm Bank of Embrapa Semiárido, Juazeiro, BA, Brazil. Seven previously characterized microsatellite markers were used: VVS2, VVMD5, VVMD7, VVMD27, VVMD3, ssrVrZAG79 and ssrVrZAG62. The expected heterozygosity (He) and polymorphic information content (PIC) were calculated, and the cluster analysis were processed to generate a dendrogram using the algorithm UPGMA. The He ranged from 81.8% to 88.1%, with a mean of 84.8%. The loci VrZAG79 and VVMD7 were the most informative, with a PIC of 87 and 86%, respectively, while VrZAG62 was the least informative, with a PIC value of 80%. Cluster analysis by UPGMA method allowed separation of the genotypes according to their genealogy and identification of possible parentage for the cultivars 'Dominga', 'Isaura', 'CG 26916', 'CG28467' and 'Roni Redi'.