Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

The evolution of massive clumps in star forming regions

In this thesis two related arguments are investigated: - The first stages of the process of massive star formation, investigating the physical conditions and -properties of massive clumps in different evolutionary stages, and their CO depletion; - The influence that high-mass stars have on the nearby material and on the activity of star formation. I characterise the gas and dust temperature, mass and density of a sample of massive clumps, and analyse the variation of these properties from quiescent clumps, without any sign of active star formation, to clumps likely hosting a zero-age main sequence star. I briefly discuss CO depletion and recent observations of several molecular species, tracers of Hot Cores and/or shocked gas, of a subsample of these clumps. The issue of CO depletion is addressed in more detail in a larger sample consisting of the brightest sources in the ATLASGAL survey: using a radiative tranfer code I investigate how the depletion changes from dark clouds to more evolved objects, and compare its evolution to what happens in the low-mass regime. Finally, I derive the physical properties of the molecular gas in the photon-dominated region adjacent to the HII region G353.2+0.9 in the vicinity of Pismis 24, a young, massive cluster, containing some of the most massive and hottest stars known in our Galaxy. I derive the IMF of the cluster and study the star formation activity in its surroundings. Much of the data analysis is done with a Bayesian approach. Therefore, a separate chapter is dedicated to the concepts of Bayesian statistics.