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

Genetic connectivity and hybridization with its siter species challenge the current management paradigm of white anglerfish (Lophius piscatorius)

Understanding the inter and intraspecific dynamics of fish populations is essential to promote effective management and conservation actions and to predict adaptation to changing conditions. This is possible through the analysis of thousands of genetic markers, which has proven useful to resolve connectivity among populations. Here, we have tackled this issue in the white anglerfish (Lophius piscatorius), which inhabits the Northeast Atlantic and Mediterranean Sea and coexists with its morphologically almost identical sister species, the black anglerfish (L. budegassa). Our genetic analyses based on 16,000 SNP markers and 700 samples reveal that i) the white anglerfish from the Mediterranean Sea and the Atlantic Ocean are genetically isolated, but that no differentiation can be observed within the later, and that ii) black and white anglerfish naturally hybridize, resulting in a population of about 20% of, most likely sterile, hybrids in some areas. These findings challenge the current paradigm of white anglerfish management, which considers three independent management units within the North East Atlantic and assumes that all mature fish have reproductive potential. Additionally, the northwards distribution of both species, likely due to temperature raises, calls for further monitoring of the abundance and distribution of hybrids to anticipate the effects of climate change in the interactions between both species and their potential resilience

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

Although free living, members of the successful SAR11 group of marine alpha-proteobacteria contain a very small and A+T rich genome, two features that are typical of mitochondria and related obligate intracellular parasites such as the Rickettsiales. Previous phylogenetic analyses have suggested that Candidatus Pelagibacter ubique, the first cultured member of this group, is related to the Rickettsiales+mitochondria clade whereas others disagree with this conclusion. In order to determine the evolutionary position of the SAR11 group and its relationship to the origin of mitochondria, we have performed phylogenetic analyses on the concatenation of 24 proteins from 5 mitochondria and 71 proteobacteria. Our results support that SAR11 group is not the sistergroup of the Rickettsiales+mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias. As a consequence, genome reduction and bias toward a high A+T content may have evolved independently in the SAR11 species, which points to a different direction in the quest for the closest relatives to mitochondria and Rickettsiales. In addition, our analyses raise doubts about the monophyly of the newly proposed Pelagibacteraceae family

Experimental study of differentially rotating supersonic plasma flows produced by aluminium wire array Z-pinches

A novel approach to cylindrical wire array z-pinches has been developed in order to create a rotating plasma flow analogous to astrophysical accretion discs. The method involves subjecting the wire array to a cusp magnetic field (B_r) to create converging off axis ablation streams to form a rotating flow. The rotation is sustained by the ram pressure of the ablation streams in a quasi-equilibrium state for approximately 150 ns. This corresponds to one full rotation of the plasma about the axis. The rotating plasma is supersonic with Mach number ~2 and a radially constant rotation velocity between 60 and 75 km/s; the angular velocity therefore has an r^-1 dependence and the flow is differential. A Thomson scattering diagnostic is used to measure the electron and ion temperatures as Te ~30 eV and Ti >55 eV and the ionisation of the plasma (Z) between 6 and 8. These parameters are used to calculate the Reynolds number (10^5 to 10^6) and magnetic Reynolds numbers (20 to 100) which are large enough for viscous and resistive effects to be negligible on the large scale of the flow. These are of sufficient magnitude for the experiment to be scalable to astrophysical accretion discs. Further more the Reynolds number for the experiment is large enough for shear instabilities to manifest in the plasma. Some evidence for this can be seen in XUV images and Thomson spectra which indicate the development of perturbations and vorticity within the flow. Predictions for the growth rate of the Kelvin Helmholtz instability, 12 to 40 ns, agree reasonably well with the observed perturbation growth of ~30 ns. It is also possible that shear instabilities are driving hydrodynamic turbulence. Turbulent heating of the plasma could explain the approximately 500 eV increase in the ion temperature observed from some Thomson spectra. Further work is required however to prove the existence of shear flows and turbulence within the experiments.Open Acces

Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI).

Marine ecosystem protection and conservation initiatives rely on the assessment of ecological integrity and health status of marine environments. The AZTI's Marine Biotic Index (AMBI), which consists on using macroinvertebrate diversity as indicator of ecosystem health, is used worldwide for this purpose. Yet, this index requires taxonomic assignment of specimens, which typically involves a time and resource consuming visual identification of each sample. DNA barcoding or metabarcoding are potential harmonized, faster and cheaper alternatives for species identification, although the suitability of these methods for easing the implementation of the AMBI is yet to be evaluated. Here, we analyze the requirements for the implementation of a genetics based AMBI (gAMBI), and show, using available sequence data, that information about presence/absence of the most frequently occurring species provides accurate AMBI values. Our results set the basics for the implementation of the gAMBI, which has direct implications for a faster and cheaper marine monitoring and health status assessment