Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.Peer reviewe

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Progress in understanding disruptions triggered by massive gas injection via 3D non-linear MHD modelling with JOREK

3D non-linear MHD simulations of a D 2 massive gas injection (MGI) triggered disruption in JET with the JOREK code provide results which are qualitatively consistent with experimental observations and shed light on the physics at play. In particular, it is observed that the gas destabilizes a large m/n = 2/1 tearing mode, with the island O-point coinciding with the gas deposition region, by enhancing the plasma resistivity via cooling. When the 2/1 island gets so large that its inner side reaches the q = 3/2 surface, a 3/2 tearing mode grows. Simulations suggest that this is due to a steepening of the current profile right inside q = 3/2. Magnetic field stochastization over a large fraction of the minor radius as well as the growth of higher n modes ensue rapidly, leading to the thermal quench (TQ). The role of the 1/1 internal kink mode is discussed. An I p spike at the TQ is obtained in the simulations but with a smaller amplitude than in the experiment. Possible reasons are discussed

Advances in studying the role of genetic divergence and recombination in adaptation in non-model species

Understanding the role of genetic divergence and recombination in adaptation is crucial to understanding the evolutionary potential of species since they can directly affect the levels of genetic variation present within populations or species. Genetic variation in the functional parts of the genome such as exons or regulatory regions is the raw material for evolution, because natural selection can only operate on phenotypic variation already present in the population. When natural selection acts on a phenotype, it usually results in reduction in the levels of genetic variation at the causal loci, and the surrounding linked loci, due to recombination dynamics (i.e. linkage); the degree to which natural selection influences the genetic differentiation in the linked regions depends on the local recombination rates. Studies investigating the role of genetic divergence and recombination are common in model species such as Drosophila melanogaster. Only recently have genomic tools allowed us to start investigating their role in shaping genetic variation in non-model species. This thesis adds to the growing research in that domain. In this thesis, I have asked a diverse set of questions to understand the role of genetic divergence and recombination in adaptation in non-model species, with a focus on Lepidoptera. First, how do we identify causal genetic variation causing adaptive phenotypes? This question is fundamental to evolutionary biology and addressing it requires a well-assembled genome, the generation of which is a cost, labor, and time intensive task. In paper I, I present a tool, MESPA, that stitches together exonic sequences in fragmented assemblies to produce high-quality gene models. These high-quality gene models can be used by researchers in the downstream analyses, providing genomic insights for a fraction of cost of a high quality genome.  Second, what does the pattern of recombination rate look like in chromosomes that lack centromeres (i.e.holocentric chromosomes)? In paper II, I compare the recombination landscape and the patterns of nucleotide diversity in three Lepidotera with holocentric chromosomes, Pieris napi, Bombyx mandarina, and Bombyx mori, with a monocentric species. Our results show that on average these three Lepidoptera have high rates of recombination across the vast majority of their genome. Our results also suggest that given similar effective population sizes, these species are likely to harbor more genetic diversity compared to monocentric species, which has important evolutionary consequences for these species. Third, what is the potential for parallelism at the genetic level in convergent melanic phenotypes? In paper III, I investigated the genetic basis of the female-limited melanic phenotype in the green-veined white (Pieris napi) butterfly, and found a 20kb region, approximately 50kb from the gene cortex, associated with this trait. This gene has been implicated in melanic phenotypes in other Lepidoptera that diverged from Pieris approximately 100my, indicating very high predictability for this trait. Finally, what is the role of cis-regulatory variation in local adaptation? In paper IV, I analyzed the relationship between allele specific expression (ASE) and genetic divergence (FST) in the F1 hybrids of Pieris napi napi and Pieris napi adalwinda. I show that intersecting results from ASE with FST is a powerful approach to identify genes involved in local adaptation.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p

Advances in studying the role of genetic divergence and recombination in adaptation in non-model species

Understanding the role of genetic divergence and recombination in adaptation is crucial to understanding the evolutionary potential of species since they can directly affect the levels of genetic variation present within populations or species. Genetic variation in the functional parts of the genome such as exons or regulatory regions is the raw material for evolution, because natural selection can only operate on phenotypic variation already present in the population. When natural selection acts on a phenotype, it usually results in reduction in the levels of genetic variation at the causal loci, and the surrounding linked loci, due to recombination dynamics (i.e. linkage); the degree to which natural selection influences the genetic differentiation in the linked regions depends on the local recombination rates. Studies investigating the role of genetic divergence and recombination are common in model species such as Drosophila melanogaster. Only recently have genomic tools allowed us to start investigating their role in shaping genetic variation in non-model species. This thesis adds to the growing research in that domain. In this thesis, I have asked a diverse set of questions to understand the role of genetic divergence and recombination in adaptation in non-model species, with a focus on Lepidoptera. First, how do we identify causal genetic variation causing adaptive phenotypes? This question is fundamental to evolutionary biology and addressing it requires a well-assembled genome, the generation of which is a cost, labor, and time intensive task. In paper I, I present a tool, MESPA, that stitches together exonic sequences in fragmented assemblies to produce high-quality gene models. These high-quality gene models can be used by researchers in the downstream analyses, providing genomic insights for a fraction of cost of a high quality genome.  Second, what does the pattern of recombination rate look like in chromosomes that lack centromeres (i.e.holocentric chromosomes)? In paper II, I compare the recombination landscape and the patterns of nucleotide diversity in three Lepidotera with holocentric chromosomes, Pieris napi, Bombyx mandarina, and Bombyx mori, with a monocentric species. Our results show that on average these three Lepidoptera have high rates of recombination across the vast majority of their genome. Our results also suggest that given similar effective population sizes, these species are likely to harbor more genetic diversity compared to monocentric species, which has important evolutionary consequences for these species. Third, what is the potential for parallelism at the genetic level in convergent melanic phenotypes? In paper III, I investigated the genetic basis of the female-limited melanic phenotype in the green-veined white (Pieris napi) butterfly, and found a 20kb region, approximately 50kb from the gene cortex, associated with this trait. This gene has been implicated in melanic phenotypes in other Lepidoptera that diverged from Pieris approximately 100my, indicating very high predictability for this trait. Finally, what is the role of cis-regulatory variation in local adaptation? In paper IV, I analyzed the relationship between allele specific expression (ASE) and genetic divergence (FST) in the F1 hybrids of Pieris napi napi and Pieris napi adalwinda. I show that intersecting results from ASE with FST is a powerful approach to identify genes involved in local adaptation.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p