Eeva Jansson

and 11 more

The architecture underpinning genomic divergence is still a largely uncharted territory and likely case-dependent. Here, we investigated genome-wide variation in Ballan wrasse, a northeastern Atlantic fish species that displays two sympatric color morphs, spotty and plain, that have been suggested to represent subspecies. We produced a chromosome-level reference genome, and thereafter investigated genomic divergence among 152 individuals including both morphs, from two localities in Spain and Norway each, and one in France. Differences between morphs dominated in Spain in accordance with sympatric divergence, whereas in Norway geographic divergence was highest supporting allopatric differentiation. Chromosomes had very large low-recombining areas that were shared across populations and have accumulated further divergence. Within the Spanish morphs, large islands of divergence covered ~11% of the genome, showed high morph-specificity, and strong selection. The same regions showed frequent admixture in the French morphs and no differentiation in Norway. In contrast, divergent regions observed between sampling localities in Norway were scattered, shorter and found throughout the genome. High inbreeding and lower diversity were observed in the Norwegian samples, consistent with the proposed recolonization bottleneck and subsequent drift. Several genomic regions were significantly associated with morphs and contained tens of genes of diverse functions, suggesting that coloration is unlikely to be the sole driver of divergence. Our results suggest that large, polygenic divergence islands were initially formed and preserved in the south but were gradually lost and uncoupled from the phenotype of the fish further north when these areas were repopulated after the last glacial maximum.

Sushma Jossey

and 12 more

Knowledge of genetic diversity and structure is essential for developing conservation strategies for endangered species. The advances in museum genomics can assist in better understanding the effects of over-hunting on the genome by comparing historical to present-day samples. Blue whales were hunted to the point of near extinction in the mid-twentieth century. Herein, we use whole genome sequencing to elucidate the poorly understood population structure of North Atlantic (NA) blue whales (Balaenoptera musculus musculus). We generated a de novo genome assembly of 2.49 Mbp for a NA blue whale (N50 of 1.46 Mb) to analyze 19 whole genomic sequences and 28 complete mitochondrial genomes. We included present-day and historical samples (earliest from 1900) from the Atlantic and Antarctica to understand the impact of whaling on the genetic diversity. We found low population structuring, but high genetic diversity, suggesting a single, panmictic population in the NA. We identified gene flow from fin whale to blue whales, accounting for ~3.5% of the genome. Introgression between blue and fin whales was observed in all the present-day samples but were lacking in some whales sampled early in the 20th century, which suggests increasing disruption in mate choice concomitant with decline in blue whale population. We also assembled and analyzed the transcriptome and revealed positive selection of oncogenes, which may be involved in reduced cancer rates in this largest of mammals ever known. Our sequencing and population structuring studies provide a genomic framework to guide ongoing conservation strategies for this iconic species.