Une approche phylogénomique pour inférer l'évolution des eucaryotes

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?

Restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely used tool in molecular ecology studies as it allows to cost-effectively recover thousands of polymorphic sites across individuals of non-model organisms. However, its successful implementation in population genetics relies on correct data processing that would minimize potential loci-assembly biases and consequent genotyping error rates. RAD-seq data processing when no reference genome is available involves the assembly of hundreds of thousands high-throughput sequencing reads into orthologous loci, for which various key parameter values need to be selected by the researcher. Previous studies exploring the effect of these parameter values found or assumed that a larger number of recovered polymorphic loci is associated with a better assembly. Here, using three RAD-seq datasets from different species, we explore the effect of read filtering, loci assembly and polymorphic site selection on number of markers obtained and genetic differentiation inferred using the Stacks software. We find (i) that recovery of higher numbers of polymorphic loci is not necessarily associated with higher genetic differentiation, (ii) that the presence of PCR duplicates, selected loci assembly parameters and selected SNP filtering parameters affect the number of recovered polymorphic loci and degree of genetic differentiation, and (iii) that this effect is different in each dataset, meaning that defining a systematic universal protocol for RAD-seq data analysis may lead to missing relevant information about population differentiation

Geografías Imaginarias. Experiencias de escritura colectiva en el aula virtual de secundaria

La finalidad de este Trabajo de Fin de Máster es plantear nuevas formas de abordar el desarrollo de la competencia en comunicación escrita en el alumnado de Educación Secundaria Obligatoria; y para ello se presenta una propuesta didáctica que, partiendo de la motivación personal, se centra en fomentar un cambio de mentalidad entre el alumnado a partir del trabajo desde nuevos enfoques metodológicos, relacionados con la literatura comparada, las humanidades digitales y las narrativas transmedia.<br /

Tratamiento odontológico rehabilitador en el paciente adulto: a propósito de dos casos

Existen diferentes patologías de tejidos duros y blandos que conllevan a la pérdida dental, situación que se puede ver agravada por posibles parafunciones y enfermedades sistémicas. Los pacientes afectados acudirán al odontólogo, demandando un tratamiento rehabilitador que les devuelva la función y estética perdidas, de la manera más fisiológica posible. Con el presente trabajo, se pretende realizar un estudio completo de dos pacientes que acuden al Servicio de Prácticas Odontológicas de la Universidad de Zaragoza, con el fin de poder realizar un correcto diagnóstico y plan de tratamiento rehabilitador, teniendo en cuenta las necesidades y demandas del paciente, realizando para este fin las exploraciones y pruebas que se estimen oportunas. Por último, se realizará una discusión de las diferentes opciones de tratamiento en base a la literatura más actualizada.<br /

Identification of a broad lipid repertoire associated to the endothelial cell protein C receptor (EPCR)

Evidence is mounting that the nature of the lipid bound to the endothelial cell protein C receptor (EPCR) has an impact on its biological roles, as observed in anticoagulation and more recently, in autoimmune disease. Phosphatidylethanolamine and phosphatidylcholine species dominate the EPCR lipid cargo, yet, the extent of diversity in the EPCR-associated lipid repertoire is still unknown and remains to be uncovered. We undertook mass spectrometry analyses to decipher the EPCR lipidome, and identified species not yet described as EPCR ligands, such as phosphatidylinositols and phosphatidylserines. Remarkably, we found further, more structurally divergent lipids classes, represented by ceramides and sphingomyelins, both in less abundant quantities. In support of our mass spectrometry results and previous studies, high-resolution crystal structures of EPCR in three different space groups point to a prevalent diacyl phospholipid moiety in EPCR¿s pocket but a mobile and ambiguous lipid polar head group. In sum, these studies indicate that EPCR can associate with varied lipid classes, which might impact its properties in anticoagulation and the onset of autoimmune disease.Ramón y Cajal, Grant RYC‐2017‐21683, Ministry of Science and Innovation, Government of Spain (JLS). Generación de Conocimiento, Ministry of Science and Innovation, Government of Spain, Grant PGC2018-094894-B-I00 (JLS and EEA). Ministry of Science, Innovation and Universities of Spain (MICINN) and The European Regional Development Fund (FEDER) funding Grant RTI2018-095166-B-I00 (Antonia García y Francisco Javier Rupérez). Predoctoral Fellowship, Ministry of Universities, Government of Spain, Grant FPU19/06206 (MMG). Alejandro Urdiciain is a recipient of a Margarita Salas contract funded by UPNA and the Ministry of Universities of Spain within the Plan of Recovery, Transformation and Resilience and the European Recovery Instrument Next Generation EU

Allele Frequencies of 15 STR Loci (Identifiler™ Kit) in Basque-Americans

Individuals with Basque ancestry form a historically and culturally important minority of the population of the western United States. Allele frequencies for the 15 autosomal STRs in the AmpFlSTR® Identifiler® PCR Amplification Kit (Applied Biosystems) from 156 unrelated self-identified Basque individuals born in the United States are presented. Allele frequencies were used to calculate parameters commonly used in genetics and forensics including power of discrimination (PD), power of exclusion (PE), polymorphic information content (PIC), and expected heterozygosity (He). The sample population was also compared with the European Basque population and the major American ethnicities

Visualization of Misuse-Based Intrusion Detection: Application to Honeynet Data

This study presents a novel soft computing system that provides network managers with a synthetic and intuitive representation of the situation of the monitored network, in order to reduce the widely known high false-positive rate associated to misuse-based Intrusion Detection Systems (IDSs). The proposed system is based on the use of different projection methods for the visual inspection of honeypot data, and may be seen as a complementary network security tool that sheds light on internal data structures through visual inspection. Furthermore, it is intended to understand the performance of Snort (a well-known misuse-based IDS) through the visualization of attack patterns. Empirical verification and comparison of the proposed projection methods are performed in a real domain where real-life data are defined and analyzed

Organellar inheritance in the green lineage: insights from Ostreococcus tauri

Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Systematic Biology 59 (2010): 518-533, doi:10.1093/sysbio/syq037.An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ‘Chromalveolata’ is rejected. Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxonrich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data