Understanding evolution by genome duplication: don’t throw the baby out with the bathwater

Morten Limborg 
Natural History Museum of Denmark, Copenhague morten.limborg@gmail.com

(Seminar in English)

An outstanding topic in evolutionary biology relates to the evolutionary role of gene and genome duplications. Indeed, many polyploid-origin plants and animals are currently enjoying a genomics revolution enabled by modern sequencing and genotyping technologies. However, routine filtering of duplicated loci (so called paralogs) in most genomic studies introduces an unacceptable, but often overlooked bias when searching for genes under selection. Retained duplicates from recent Whole Genome Duplications (WGD) are concentrated at distal ends of some chromosome arms. Evidence shows that these duplications catalyze adaptation through one of two pathways: neo-functionalization or increased gene-expression due to increased copy number. Filtering paralogs may therefore completely remove distal ends of some chromosomes and impoverish interpretation of genomic data, as signals from many duplicated genes will be lost. I will present a case study from Pacific salmon where we genotype and map duplicated loci by using the overlooked strategy of creating gynogenetic haploids. I continue by presenting ongoing efforts to further screen natural populations to detect Darwinian selection in these, hitherto ignored, duplicated genes. With our new analytical pipeline, we expect to shed light on the importance of a recent WGD on the successful radiation of salmon and other polyploid-origin species.

Recent publications:

Limborg et al. (2016) Sorting duplicated loci disentangles complexities of polyploid genomes masked by geno-        typing by sequencing. Molecular Ecology 25: 2117-2129.

Limborg et al. (2015) Linkage mapping reveals strong chiasma interference in sockeye salmon: Implications for       interpreting genomic data. G3 5: 2463-2473.

Allendorf FW,…, Limborg et al. (2015) Effects of crossovers between homeologs on inheritance and population        genomics in polyploid-derived salmonid fishes. Journal of Heredity 106: 217–227.