Value and application of Genome Sequencing in Ecology and Evolution

Remarkably, gene names are currently not standardised, and, especially for non-model species, genome information is scattered across publicly available data collections and the literature. Preparatory data collection for gene and genome studies is therefore time-consuming, and there is a risk that candidates may be overlooked. Chapter 1 describes the design and implementation of a relational database to disentangle ambiguous gene names. By aggregating molecular data
of over 1,000 distinct avian immune genes spanning 363 non-model bird species, this database contributes to basic and applied research in disease ecology, comparative genomics, gene expression, functional variation, conservation genomics and molecular evolution. Infectious diseases are increasing worldwide and have a detrimental impact on wildlife, human health and the global economy. The tufted duck (Aythya fuligula) is highly susceptible to the avian influenza A virus and–as a short-distance migrant–can infect other waterfowl species. Chapter 2 provides the first long-read sequencing of the transcriptome and annotation of expressed genes in six different tissues of the tufted duck. Thereby, it contributes to research in the zoonotic ecology of avian diseases in the natural reservoir. Hybridisation is frequently observed in waterfowl and can lead to the interspecific exchange of genetic material. Whole-genome sequencing allows studying genomic regions presumably exposed to different selection pressures and evolutionary histories. Introgressed regions can be identified by inferring their ancestral sequences in a probabilistic framework. Chapter 3 aims to quantify introgression in the genome assemblies of 20 true geese. A state-of-the-art piece of software for introgression quantification running on a high-performance computing cluster did not reveal conclusive results after more than two million CPU hours. Nevertheless, this study provided valuable insights for future research in the area of introgressive hybridisation. Current developments in sequencing technology allow the generation of reference-grade genome data to facilitate research in biodiversity conservation. Chapter 4 presents a review article on the current sixth mass extinction. It proposes how high-quality reference genomes can inform conservation plans such as population health monitoring, targeted breeding and species resurrection.