Rates and patterns of genome evolution in Lepidoptera

The evolutionary consequences of genome restructuring and chromosomal rearrangements can be significant, but the underlying mechanisms are poorly understood. This thesis explores the relationships between genome restructuring, recombination, and maintenance of genetic diversity in different butterfly species. I also investigate the genetic underpinnings of different types of adaptations in two butterfly species with distinct life-history characteristics and adaptations. In Chapter I, whole genome alignments and linkage maps were used to characterize inter- and intra-specific chromosomal rearrangements in wood white butterflies (Leptidea spp.), revealing extensive reorganization of the chromosomes predominantly driven by fusions and fissions. Several fusion-fission polymorphisms were found segregating within populations, confirming the dynamic and ongoing process of karyotype evolution. In Chapter II, I used the linkage map information to show that chromosomal rearrangements have had considerable effects on the recombination landscape and maintenance of genetic diversity. Chapter III presents a detailed annotation of the genome of a long-distance migrant, the painted lady butterfly (Vanessa cardui). The annotation was used to identify expanded gene families, providing insight into the genetic underpinnings of this unique life-history. Here, I also developed linkage maps confirming a well-preserved karyotype in this species and showed that chromosome size is a major determinant of the recombination landscape. In Chapter IV, I explored the relationship between nucleotide composition, codon usage, and substitution rates across multiple Lepidoptera species, in an attempt to disentangle the relative effects of natural selection and neutral evolutionary forces on gene sequence evolution. The final two chapters focus on understanding the genetic basis of key adaptive traits in butterflies. Specifically, in Chapter V, I investigated potential local adaption in Leptidea sinapis by studying how host plant switch is associated with oviposition rates, larval growth and development, gene expression, and microbiome composition in populations experiencing different environmental conditions. In Chapter VI, I assessed the differential activation of regulatory elements in V. cardui females in response to host plant availability, which together with the gene family analysis in Chapter III, resulted in a set of candidate genes potentially associated with a migratory lifestyle. In conclusion, I have explored the complex interplay between proximate mechanisms and evolutionary forces shaping the genome structure and levels of genetic variation. I also investigated the genetic and regulatory underpinnings of adaptive traits in different butterfly species. In addition, I provided resources including chromosome-level genome assemblies, recombination maps, and annotations that will contribute to our understanding of evolutionary processes in general.

Quality of life after end colostomy without mesh and with prophylactic synthetic mesh in sublay position : one-year results of the STOMAMESH trial

Purpose: To determine whether prophylactic mesh in a sublay position has an impact on the quality-of-life (QoL) of patients receiving an end colostomy. Methods: One-year follow-up of patients from the STOMAMESH trial, a randomized controlled double-blinded multicenter study. Patients were randomized to either prophylactic synthetic mesh with a cruciform incision in the center, placed in sublay position, or no prophylactic mesh. Patients attended a 1-year visit and responded to the questionnaires EORTC QLQ C-30 and CR-38. The impact of having a mesh on QoL was determined by comparing a group of patients receiving a mesh with a group without. A subgroup analysis was made depending on whether a PSH was clinically present or not. Results: Of the 232 randomized patients, 211 patients reached the 1-year clinical follow-up. The response rate of these 211 patients was 70%. No differences were seen in global QoL between the groups. Mesh patients reported significantly less stoma-related problems (p = 0.014) but more sexual problems in males (p = 0.022). When excluding patients with a clinical diagnosis of PSH, the difference in stoma-related problems remained while no significant difference was seen regarding sexual problems in males. Conclusions: When forming an end colostomy, prophylactic synthetic mesh in a sublay position did not affect global QoL at 1-year follow-up, but stoma-related problems were fewer even in the presence of a clinically diagnosed PSH

Base composition, codon usage and patterns of gene sequence evolution in butterflies.

Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species and there was a negative association between the magnitude of codon usage bias and GC-content in third codon positions. In contrast, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC and selection on codon usage

Evolution of migratory behavior in butterflies: phylogenetic-wide heterozygosity patterns and signatures of selection in the highly- mobile Vanessa genus

Póster presentado en el Congreso Evolution in Sweden 2023, celebrado en Uppsala, suecia del 10 al 12 de enero de 202

No reduction in parastomal hernia rate 3 years after stoma construction with prophylactic mesh : Three-year follow-up results from stomamesh-a multicenter double-blind randomized controlled trial

OBJECTIVE: The primary objective was to compare rates of parastomal hernia (PSH) 3 years after stoma construction with prophylactic mesh or no mesh. A secondary objective was to compare complications requiring reintervention within 3 years. BACKGROUND: Recent studies have shown that a prophylactic mesh does not reduce the rate of PSH contrary to older studies. Long-term data on efficacy and safety is however scarce. METHODS: A randomized controlled double-blind multicenter trial. Patients planned for permanent end colostomy were randomized to either prophylactic mesh in the retromuscular position around the stoma site or no mesh. They were evaluated for PSH clinically and with computed tomography (CT) 3 years after stoma construction. Medical records of all patients included were also reviewed at 3 years to detect any abdominal or abdominal wall surgery during that period. RESULTS: A total of 232 patients were randomized. At 3 years, 154 patients were available for clinical evaluation and 137 underwent a CT scan. No significant difference in PSH rates was seen between the treatment allocation arms (clinical: P=0.829 and CT: P=0.761, respectively), nor was there a significant difference in the number of reinterventions, but 2 patients had their mesh removed at emergency surgery. CONCLUSIONS: Prophylactic mesh does not reduce the rate of PSH and cannot be recommended for routine use

Parastomal hernia repair with intraperitoneal mesh

Purpose. Parastomal hernia is a common complication following a stoma and may cause leakage or incarceration. No optimal treatment has been established, and existing methods using mesh repair are associated with high recurrence rates and a considerable risk for short- and long-term complications including death. A double-layer intraperitoneal on-lay mesh (IPOM), the Parastomal Hernia Patch (BARD™), consisting of ePTFE and polypropylene, has been developed and tailored to avoid recurrence. To evaluate the safety of and recurrence rate using this mesh, a nonrandomised prospective multicentre study was performed. Method. Fifty patients requiring surgery for parastomal hernia were enrolled. Clinical examination and CT scan prior to surgery were performed. All patients were operated on using the Parastomal Hernia Patch (BARD). Postoperative follow-up at one month and one year was scheduled to detect complications and hernia recurrence. Results. The postoperative complication rate at one month was 15/50 (30%). The parastomal hernia recurrence rate at one year was 11/50 (22%). The reoperation rate at one month was 7/50 (14%), and further 5/50 (10%) patients were reoperated on during the following eleven months.Originally included in thesis in manuscript form.</p

Evolution of migratory behavior in butterflies: phylogenetic-wide heterozygosity patterns and signatures of selection in the highly- mobile Vanessa genus

Póster presentado en el Congreso Evolution in Sweden 2023, celebrado en Uppsala, suecia del 10 al 12 de enero de 202

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling

Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly

Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.Financial support for this project was provided by FORMAS (Research grant 2019-00670 to N.B.) and The Swedish Collegium for Advanced Science (Natural Sciences Programme, Knut and Alice Wallenberg Foundation, Postdoc funding for D.S.). R.V. was supported by the grant PID2019-107078GB-I00 funded by MCIN/AEI/10.13039/501100011033. G.T. was supported by the grant PID2020-117739GA-I00 funded by MCIN/AEI/10.13039/501100011033 and by “La Caixa” Foundation (ID 100010434) through the grant LCF/BQ/PR19/11700004.1. Introduction 2. Results 2.1. Linkage map and genome annotation 2.2. Synteny 2.3. Gene family evolution 2.4. Patterns of recombination rate variation 2.4.1. Global and chromosome specific recombination rates 2.4.2. Intra-chromosomal variation in recombination rate and associations with genomic elements 3. Discussion 3.1. The genome of the painted lady butterfly 3.2. Sex chromosomes 3.3. Gene family analysis 3.4. Patterns of recombination rate variation 4. Conclusions 5. Methods 5.1. Linkage map 5.1.1. Sampling and DNA-extraction 5.1.2. Building the linkage map 5.2. Genome annotation and whole genome statistics 5.2.1. Genome assembly statistics 5.2.2. Gene and repeat annotation 5.3. Manual curation 5.4. Gene family evolution 5.5. Gene ontology enrichment 5.6. Recombination rate analysis 5.6.1. Chromosome level analysis 5.6.2. Window-based analysis Data access CRediT authorship contribution statement Declaration of Competing Interest Acknowledgements Appendix A. Supplementary data Data availability Reference