Genomic diversity gradients and functional differentiation put Northeast Pacific ribbon kelp lineages in the speciation grey zone

The transition from reproductively isolated populations to species is not well understood. Genotyping entire genomes holds promise to enhance insights into the process of speciation and the evolutionary relationships among related taxa. Gulf of Alaska ribbon kelp was once recognized as four species before they were folded into Alaria marginata on the basis of DNA barcode markers, though several lineages have continued to be recognized. Here, we used whole genome sequencing datasets to test the hypothesis that these lineages represent incipient species. Whole genomes of 69 individuals from five genetically distinctive lineages in the Gulf of Alaska (USA) and Salish Sea (Canada) were analyzed, along with 63 genomes from three other species of Alaria. Our analysis of >3.4 million Single Nucleotide Polymorphisms reaffirms that organellar and nuclear phylogenetic signals are incongruent in Alaria, producing different topologies among five organellar and six nuclear A. marginata lineages. ..., The following datasets represent tab delimited tables of exon coverage calculated for various populations and species of ribbon kelp (genus Alaria). The tables include gene names and functional annotations (UniProt IDs). The values for coverage are 1) standardized using mean coverage for confirmed single copy exons within each specimen analysed, then 2) averaged for each populations/lineage/species of interest. 1=expected coverage, <1=less than expected level of coverage, 0=no coverage, >1=more than expected coverage. Values of 0 could be interpreted as exon loss, while high values could be interpreted as duplications/expansions, though caveats to these interpretations are explored in our manuscript. The exons represent annotations for the Alaria esculenta genome, onto which reads from all datasets were mapped.
Three datasets are presented, one each for populations of Alaria esculenta, one for lineages of Alaria marginata, and one for all species/populations analysed. Only exons (..., Any program that can open tab delimited text documents. Can also be imported into Excel.