Extensive nuclear datasets resolve the phylogeny of siphonous green algae and identify genome duplications as a contributing factor to evolutionary adaptations

The Bryopsidales, a group of siphonous green algae, are of particular evolutionary interest due to their unusual cellular organization and striking morphological and ecological diversity. There are indications of genome duplication, but low taxon sampling has limited our insights into these processes and how they may contribute to these traits. The relationships among certain bryopsidalean lineages remain unresolved, even with plastid genome-scale datasets. Nuclear genomes offer promise for resolving phylogenetic uncertainties and pinpointing duplication events, but progress has been hindered by the limited availability of such datasets. Here, we present new nuclear genome data for 44 taxa sampled across the phylogenetic breadth of Bryopsidales, and conduct phylogenomic analyses of 708 nuclear genes with coalescent and concatenation approaches. Our results significantly advance the resolution of Bryopsidales relationships, including confident placement of previously hard-to-resolve lineages like Pseudobryopsis, Ostreobineae, and the Halimedineae tribes. We identified many ancient gene duplications across the Bryopsidales tree, including potential whole-genome duplications in the Ostreobiaceae and Caulerpaceae. Our work presents the most highly resolved phylogeny of Bryopsidales to date and offers an extensive framework for the exploration of the potential roles of genome duplications that may have facilitated niche adaptations and invasive trait development.