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 reaffirm 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.

The datasets presented here pertain to values of exon coverage for the various species of Alaria and lineages of A. marginata. These include gene name/product, uniprot IDs, and GO terms. Tables are for Alaria esculenta populations, Alaria species, and A. marginata lineages.

从生殖隔离种群到物种的演化过渡机制目前尚未被充分阐明。全基因组基因分型技术有望加深我们对物种形成过程以及近缘类群间演化关系的理解。阿拉斯加湾带形昆布曾被归类为4个独立物种，后基于DNA条形码标记被归入边翅藻（Alaria marginata），不过目前仍有多个演化支得到学界认可。本研究利用全基因组测序数据集，验证了“这些演化支代表处于物种形成初期的类群”这一假说。我们对采自美国阿拉斯加湾与加拿大萨利希海的5个遗传分化显著的演化支的69份个体全基因组，以及另外3个翅藻属（Alaria）物种的63份基因组进行了分析。通过对超过340万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的分析，本研究再次证实翅藻属中细胞器与细胞核的系统发育信号存在冲突，导致边翅藻的5个细胞器演化支与6个细胞核演化支呈现出不同的拓扑结构。各演化支间还表现出生殖隔离特征，基因组中未检测到近期的基因交流混合信号即可为佐证。边翅藻各演化支间的遗传距离超出了种群水平分化的预期范围，但仍低于翅藻属不同物种间的遗传距离。此外，本研究还证实边翅藻各演化支间存在功能基因组层面的差异，该差异程度高于种群间的预期差异，但仍未达到翅藻属不同物种间的差异水平。本研究结果表明，边翅藻的各演化支处于演化灰色地带：它们已出现显著分化，但尚未达到翅藻属物种间的分化水平。该研究成果推动分类学研究转向基因组尺度的分析框架，该框架可为界定演化支提供关于分化水平、基因交流程度与功能创新的更全面视角。

本研究提供的数据集涵盖翅藻属各物种与边翅藻各演化支的外显子覆盖度数值，相关信息包含基因名称/产物、通用蛋白质知识库（Universal Protein Resource, UniProt）编号以及基因本体（Gene Ontology, GO）术语。相关表格涉及食用翅藻（Alaria esculenta）种群、翅藻属物种以及边翅藻演化支的相关数据。