DOI: 10.5061/dryad.ffbg79czw
title: Genomic diversity gradients and functional differentiation put Northeast Pacific ribbon kelp lineages in the speciation grey zone

description: 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 &gt;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.
 Lineages also display reproductive isolation, evidenced by a lack of
 recent admixture across genomes. Genetic distances between A. marginata
 lineages exceed levels expected of population-level divergence but fall
 short of distances between species of Alaria. Moreover, we provide
 evidence of functional genomic differences between the A. marginata
 lineages, exceeding differences expected between populations, but falling
 short of larger differences among species. Our results place A. marginata
 lineages in an evolutionary grey zone, where lineages display substantial
 differentiation, but not to the level expected of Alaria species. This
 information shifts taxonomic conversations towards a genome-scale
 framework that provides a more comprehensive picture of divergence,
 connectivity, and functional innovation for defining lineages.
description: The following datasets represent tab delimited tables of exon
 coverage calculated for various populations and species of ribbon kelp
 (genus <em>Alaria</em>). 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,
 &lt;1=less than expected level of coverage, 0=no coverage,
 &gt;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
 <em>Alaria</em> <em>esculenta</em> genome, onto
 which reads from all datasets were mapped. Three
 datasets are presented, one each for populations of
 <em>Alaria</em> <em>esculenta</em>, one for
 lineages of <em>Alaria</em> <em>marginata</em>,
 and one for all species/populations analysed. Only exons (i.e. rows) with
 differential coverage are presented (standardized coverage values of 0 or
 &gt;4). Links to other publicly accessible
 locations of the data: https://doi.org/10.6084/m9.figshare.21757691.v2. Link to <em>Alaria</em> <em>esculenta</em> genome: https://doi.org/10.6084/m9.figshare.16712797.v2 Workflow information: https://github.com/tbringloe/WGS-NOVAC
description: Any program that can open tab delimited text documents. Can also
 be imported into Excel.