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Following the extinction of dinosaurs, the great adaptive radiation of mammals occurred, giving rise to an astonishing ecological and phenotypic diversity of mammalian species. Even closely related species often inhabit vastly different habitats, where they encounter diverse environmental challenges and are exposed to different evolutionary pressures. As a response, mammals evolved various adaptive phenotypes over time, such as morphological, physiological and behavioural ones. Mammalian genomes vary in their content and structure and this variation represents the molecular mechanism for the long-term evolution of phenotypic variation. However, understanding this molecular basis of adaptive phenotypic variation is usually not straightforward.
The recent development of sequencing technologies and bioinformatics tools has enabled a better insight into mammalian genomes. Through these advances, it was acknowledged that mammalian genomes differ more, both within and between species, as a consequence of structural variation compared to single-nucleotide differences. Structural variant types investigated in this thesis - such as deletion, duplication, inversion and insertion, represent a change in the structure of the genome, impacting the size, copy number, orientation and content of DNA sequences. Unlike short variants, structural variants can span multiple genes. They can alter gene dosage, and cause notable gene expression differences and subsequently phenotypic differences. Thus, they can lead to a more dramatic effect on the fitness (reproductive success) of individuals, local adaptation of populations and speciation.
In this thesis, I investigated and evaluated the potential functional effect of structural variations on the genomes of mustelid species. To detect the genomic regions associated with phenotypic variation I assembled the first reference genome of the tayra (Eira barbara) relying on linked-read sequencing technology to achieve a high level of genome completeness important for reliable structural variant discovery. I then set up a bioinformatics pipeline to conduct a comparative genomic analysis and explore variation between mustelid species living in different environments. I found numerous genes associated with species-specific phenotypes related to diet, body condition and reproduction among others, to be impacted by structural variants.
Furthermore, I investigated the effects of artificial selection on structural variants in mice selected for high fertility, increased body mass and high endurance. Through selective breeding of each mouse line, the desired phenotypes have spread within these populations, while maintaining structural variants specific to each line. In comparison to the control line, the litter size has doubled in the fertility lines, individuals in the high body mass lines have become considerably larger, and mice selected for treadmill performance covered substantially more distance. Structural variants were found in higher numbers in these trait-selected lines than in the control line when compared to the mouse reference genome. Moreover, we have found twice as many structural variants spanning protein-coding genes (specific to each line) in trait-selected lines. Several of these variants affect genes associated with selected phenotypic traits. These results imply that structural variation does indeed contribute to the evolution of the selected phenotypes and is heritable.
Finally, I suggest a set of critical metrics of genomic data that should be considered for a stringent structural variation analysis as comparative genomic studies strongly rely on the contiguity and completeness of genome assemblies. Because most of the available data used to represent reference genomes of mammalian species is generated using short-read sequencing technologies, we may have incomplete knowledge of genomic features. Therefore, a cautious structural variation analysis is required to minimize the effect of technical constraints.
The impact of structural variants on the adaptive evolution of mammalian genomes is slowly gaining more focus but it is still incorporated in only a small number of population studies. In my thesis, I advocate the inclusion of structural variants in studies of genomic diversity for a more comprehensive insight into genomic variation within and between species, and its effect on adaptive evolution.
Reciprocal selection between aphids, their protective endosymbionts, and the parasitoid wasps that prey upon them offers an opportunity to study the basis of their coevolution. We investigated adaptation to symbiont‐conferred defense by rearing the parasitoid wasp Lysiphlebus fabarum on aphids (Aphis fabae) possessing different defensive symbiont strains (Hamiltonella defensa). After ten generations of experimental evolution, wasps showed increased abilities to parasitize aphids possessing the H. defensa strain they evolved with, but not aphids possessing the other strain. We show that the two symbiont strains encode different toxins, potentially creating different targets for counter‐adaptation. Phenotypic and behavioral comparisons suggest that neither life‐history traits nor oviposition behavior differed among evolved parasitoid lineages. In contrast, comparative transcriptomics of adult female wasps identified a suite of differentially expressed genes among lineages, even when reared in a common, symbiont‐free, aphid host. In concurrence with the specificity of each parasitoid lineages’ infectivity, most differentially expressed parasitoid transcripts were also lineage‐specific. These transcripts are enriched with putative venom toxins and contain highly expressed, potentially defensive viral particles. Together, these results suggest that wild populations of L. fabarum employ a complicated offensive arsenal with sufficient genetic variation for wasps to adapt rapidly and specifically to their hosts’ microbial defenses.
Objectives: Although expected, tendon adaptations in adolescent elite athletes have been underreported. Morphologically, adaptations may occur by an increase in collagen fiber density and/or organization. These characteristics can be captured using spatial frequency parameters extracted from ultrasound images. This study aims to compare Achilles tendon (AT) morphology among sports-specific cohorts of elite adolescent athletes and to compare these findings to recreationally active controls by use of spatial frequency analysis. Design: Cross-sectional observational study. Method: In total, 334 healthy adolescent athletes from four sport categories (ball, combat, endurance, explosive strength) and 35 healthy controls were included. Longitudinal ultrasound scans were performed at the AT insertion and midportion. Intra-tendinous-morphology was quantified by performing spatial frequency analysis assessing eight parameters at standardized ROls. Increased values in five parameters suggest a higher structural organization, and in two parameters higher fiber density. One parameter represents a quotient combining both organization and fiber density. Results: Among athletes, only ball sport athletes exhibited an increase in one summative parameter at pre-insertion site compared to athletes from other sport categories. When compared to athletes, controls had significantly higher values of four parameters at pre-insertion and three parameters at midportion site reflecting differences in both, fiber organization and density. Conclusions: Intra-tendinous-morphology was similar in all groups of adolescent athletes. Higher values found in non-athletes might suggest higher AT fiber density and organization. It is yet unclear whether the lesser structural organization in young athletes represents initial AT pathology, or a physiological adaptive response at the fiber cross-linking level. (C) 2019 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.
The number of people exposed to natural hazards has grown steadily over recent decades, mainly due to increasing exposure in hazard-prone areas. In the future, climate change could further enhance this trend. Still, empirical and comprehensive insights into individual recovery from natural hazards are largely lacking, hampering efforts to increase societal resilience. Drawing from a sample of 710 residents affected by flooding across Germany in June 2013, we empirically explore a wide range of variables possibly influencing self-reported recovery, including flood-event characteristics, the circumstances of the recovery process, socio-economic characteristics, and psychological factors, using multivariate statistics. We found that the amount of damage and other flood-event characteristics such as inundation depth are less important than socio-economic characteristics (e.g., sex or health status) and psychological factors (e.g., risk aversion and emotions). Our results indicate that uniform recovery efforts focusing on areas that were the most affected in terms of physical damage are insufficient to account for the heterogeneity in individual recovery results. To increase societal resilience, aid and recovery efforts should better address the long-term psychological effects of floods.
The literature on the costing of mitigation measures for reducing impacts of natural hazards is rather fragmented. This paper provides a concise overview of the current state of knowledge in Europe on the costing of mitigation measures for the reduction of natural hazard risks (droughts, floods, storms and induced coastal hazards as well as alpine hazards) and identifies knowledge gaps and related research recommendations. Furthermore, it provides a taxonomy of related mitigation options, classifying them into nine categories: (1) management plans, land-use planning, and climate adaptation; (2) hazard modification; (3) infrastructure; (4) mitigation measures (stricto sensu); (5) communication in advance of events; (6) monitoring and early warning systems; (7) emergency response and evacuation; (8) financial incentives; and (9) risk transfer (including insurance). It is found that the costing of mitigation measures in European and in other countries has almost exclusively focused on estimating direct costs. A cost assessment framework that addresses a range of costs, possibly informed by multiple stakeholders, would provide more accurate estimates and could provide better guidance to decision makers. (C) 2014 American Society of Civil Engineers.