Genomics and the origin of marine species

The work within this doctoral thesis introduces the Caribbean reef fish genus Hypoplectrus (hamlets) into the field of speciation genomics. The overarching theme within this thesis is the investigation of the underlying evolutionary drivers that are acting at the origin of this marine radiation and facilitate rapid speciation within the ocean. Distributed over four separate manuscripts, this work addresses several aspects impacting the dynamics of the Hypoplectrus radiation. Within the first manuscript, the temporal stability of the hamlet community in a patch of reefs in Puerto Rico is investigated. The findings indicate that the hamlet community composition is dynamic and potentially impacted by ecological factors such as turbidity or the presence of specific coral species. Within the second manuscript the hamlet reference genome is introduced and whole genome resequencing is applied to investigate the signals of speciation within three of the most common hamlet species. The results show that, against a genome wide background of very low differentiation, a small number of color pattern and vision genes are highly differentiated between species and apparently co-selected for. The third manuscript explores the demographic history of a rare endemic hamlet species. It uses a coalescent approach to show the decline in population size of this particular species since the recent evolutionary split from the remaining genus. In the last manuscript, nine different hamlet species are sequenced to provide a cross section through the hamlet radiation. The results of population- and phylogenomics indicate ongoing inter-species gene flow throughout the majority of the genome with only a small set of putative barrier genes. Phylogenetic relationships through most of the genome are diffuse, yet the signal within the few differentiated genomic intervals is discordant, pointing to introgession events or differential lineage sorting at those major effect loci.


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