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Carl-Johan Rubin

On-site nanopore sequencing of Darwin's finch genomes in the Galapagos

About Carl-Johan Rubin

Carl-Johan Rubin received his PhD in Molecular Medicine at Uppsala University in 2008. As a postdoc in the Leif Andersson lab in Uppsala, he used short-read sequencing methods to explore the genetics of chicken, porcine and rabbit domestication. Current research interests include quantitative genetics and genomics studies in Equidae, Atlantic salmon and Atlantic halibut, as well as evolutionary genetics of natural populations such as Darwin’s finches, rabbits and Atlantic herring.

Recent publications

Lamichhaney, S. et al. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518, 371–375 (2015).

Abstract

The Galapagos Islands are situated in geologically young archipelago about 900 km west of continental Ecuador. Owing to their recent origin, their isolated location and strong conservation efforts, the islands boast a rich repertoire of endemic species of both plants and animals. Perhaps most famous among endemic species are the Darwin's finch, 18 species of passerine birds that evolved from a common ancestor in the last 1.5-2.0 million years in a remarkable adaptive radiation affecting body size and beak morphology. During his travels around the world, Charles Darwin visited the Galapagos and collected these finches that so beautifully illustrate his theory of evolution of phenotypic diversity due to natural selection. For a two week expedition in March/April 2018, we went to San Cristóbal island in the Galapagos to sequence birds representing all the major phylogenetic groups of Darwin’s finches. From each bird we collected a small amount of blood then isolated DNA, made sequencing libraries and sequenced birds representing seven species of Darwin's finches using GridION/MinION and 48 flow cells, for a combined yield of around 200 Gb. In this presentation I will present our de novo Darwin's finch genome assembly, inter-species contrasts for structural variants (SV), as well as our inference regarding the importance of such SV’s on the adaptive radiation.

Carl-Johan Rubin

Carl-Johan Rubin

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