ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast

Phylogeography of a canopy-forming kelp, Eisenia bicyclis (Laminariales, Phaeophyceae), based on a genome-wide sequencing analysis

Analyses of phylogeographic patterns and genetic diversity provide fundamental information for the management and conservation of species. However, little is published about these patterns in Japanese kelp species. In this study, we conducted phylogeographic analyses of a canopy-forming kelp, Eisenia bicyclis, based on genome-wide SNPs identified by ddRAD-seq. We obtained 1,299 SNPs for 76 samples from nine localities across the distribution. STRUCTURE, NeighborNet, and discriminant analysis of principal components consistently showed high genetic differentiation among the Eastern Pacific, Central Pacific, and Sea of Japan coastal regions. Relatively strong gene flow was detected only within populations in the Eastern Pacific and in the Sea of Japan. Genetic diversity and genetic uniqueness were high in the Central Pacific and low in the Sea of Japan. These results suggest that there were at least three independent refugia corresponding to the three regions during the Last Glacial Maximum (LGM). Furthermore, relatively larger populations in the Central Pacific and smaller populations in the Sea of Japan have been maintained in the demographic history from before the LGM to the present. These phylogeographic histories were supported by an Approximate Bayesian Computation analysis. From a conservation genetics perspective, the loss of southern populations in the Central Pacific would greatly reduce the total genetic diversity of the species. Southern populations in the Sea of Japan, which have relatively low genetic diversity, may be highly vulnerable to environmental change, such as heat waves and increased feeding. Therefore, careful monitoring and conservation are needed in the two regions.

Whole-genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

The genomic era continues to revolutionize our understanding of the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long-standing questions about the evolution of biodiversity largely unexplored. Here, we used whole-genome sequencing (WGS) datasets to survey species diversity in the kelp genus Alaria, compare phylogenetic signals across organellar and nuclear genomes, and specifically test whether phylogenies behave like trees or networks. Genomes were sequenced from across the global distribution of Alaria (including Alaria crassifolia, A. praelonga, A. crispa, A. marginata, and A. esculenta), representing over 550 GB of data and over 2.2 billion paired reads. Genomic datasets retrieved 3,814 and 4,536 single-nucleotide polymorphisms (SNPs) for mitochondrial and chloroplast genomes, respectively, and upwards of 148,542 high-quality nuclear SNPs. WGS revealed an Arctic lineage of Alaria, which we hypothesize represents the synonymized taxon A. grandifolia. The SNP datasets also revealed inconsistent topologies across genomic compartments, and hybridization (i.e., phylogenetic networks) between Pacific A. praelonga, A. crispa, and putative A. grandifolia, and between some lineages of the A. marginata complex. Our analysis demonstrates the potential for WGS data to advance our understanding of evolution and biodiversity beyond amplicon sequencing, and that hybridization is potentially an important mechanism contributing to novel lineages within Alaria. We also emphasize the importance of surveying phylogenetic signals across organellar and nuclear genomes, such that models of mixed ancestry become integrated into our evolutionary and taxonomic understanding.