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

Abstract

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.

Sea Ice and Substratum Shape Extensive Kelp Forests in the Canadian Arctic

“…We classified Alaria species as A. esculenta in this study. However, genetic analyses on Alaria collected from Pond Inlet during this sampling campaign subsequently revealed this species to be a unique Arctic lineage of Alaria (Bringloe et al, 2021), which was also difficult to distinguish using morphology, so this A. esculenta grouping may be two species (A. esculenta and possibly a distinct species of Alaria).…”

An NGS-Based Phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) With the Proposal of the New Genus Rehubryum From Zealandia

“…On the other hand, there is a need to obtain additional molecular data that could help to discern the evolutionary history of the group. As an example, the conflicting solutions suggested by this study (based on nuclear loci) and those previously published (which include data from organellar genomes) could reflect a complex evolutionary history with ancient hybridization events, as it has been observed in other groups such as algae (e.g., Bringloe et al, 2021 ), angiosperms (e.g., Bogdanova et al, 2021 ), or other bryophytes ( Meleshko et al, 2021 ).…”

Arctic marine forest distribution models showcase potentially severe habitat losses for cryophilic species under climate change

“…clathratum were conflated with congeners from this diverse region with limited survey information. The reliability of the occurrence records as a single, cohesive species with consistent niche preferences should always be scrutinized if considering the individual species models, and updated in light of genomic level information (e.g., Bringloe et al, 2021). Besides confirming the true extent of species, such data would add further insight on the adaptive capacity of species under climate change.…”

“…fully selected on the basis of confident taxonomic IDs, it is possible Northwest Pacific records for E. cristata and A. clathratum were conflated with congeners from this diverse region with limited survey information. The reliability of the occurrence records as a single, cohesive species with consistent niche preferences should always be scrutinized if considering the individual species models, and updated in light of genomic level information (e.g.,Bringloe et al, 2021).…”

“…fully selected on the basis of confident taxonomic IDs, it is possible Northwest Pacific records for E. cristata and A. clathratum were conflated with congeners from this diverse region with limited survey information. The reliability of the occurrence records as a single, cohesive species with consistent niche preferences should always be scrutinized if considering the individual species models, and updated in light of genomic level information (e.g.,Bringloe et al, 2021).amount of Arctic habitat available to marine forests. The northern shorelines of Alaska, which were mostly excluded from our models, are known to host patches of marine forests interspersed among sediment-laden bays(Wilce & Dunton, 2014), and substrate requirements may be less strict in some species (i.e.,Lee (1973) reports on seemingly healthy unattached communities in calm bays, whilst Filbee-…”