title: Multigene phylogeny of the red algal subclass Nemaliophycidae.
abstract: The red algae (Rhodophyta) are a lineage of primary endosymbionts whose ancestors represent some of the first photosynthetic eukaryotes on the planet. They primarily inhabit marine ecosystems, with only ∼5% of species found in freshwater systems. The subclass Nemaliophycidae is very diverse in ecological and life history features and therefore a useful model to study these traits, but the phylogenetic relationships among the orders are, for the most part, poorly resolved. To elucidate the phylogeny of the Nemaliophycidae, we constructed a nine-gene dataset comprised of nuclear, plastid, and mitochondrial markers for 67 red algal specimens. The resulting maximum likelihood (ML) phylogeny confirmed the monophyly of all orders. The sister relationship of the Acrochaetiales and Palmariales received high support and the relationship of the Balliales with Balbianiales and Entwisleiales with Colaconematales was moderately supported. The Nemaliales, Entwisleiales, Colaconematales, Palmariales and Acrochaetiales formed a highly supported clade. Unfortunately, all other relationships among the orders had low bootstrap support. Although the ML analysis did not resolve many of the relationships, further analyses suggested that a resolution is possible. A Phycas analysis supported a dichotomously branching tree and Bayesian analysis showed a similar topology with all relationships highly supported. Simulations extrapolating the number of nucleotide characters beyond the current size of the dataset suggested that most nodes in the phylogeny would be resolved if more data become available. Phylogenomic approaches will be necessary to provide a well-supported phylogeny of this subclass with all relationships resolved such that the evolution of freshwater species from marine ancestors as well as reproductive traits can be explored.
authors.affiliation: Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, United States. Electronic address: daryl.w.lam@gmail.com.
authors.forename: Daryl W
authors.initials: DW
authors.lastname: Lam
authors.affiliation: School of BioSciences, University of Melbourne, Victoria 3010, Australia. Electronic address: heroen.verbruggen@gmail.com.
authors.forename: Heroen
authors.initials: H
authors.lastname: Verbruggen
authors.affiliation: Centre for Environmental & Molecular Algal Research, Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada. Electronic address: gws@unb.ca.
authors.forename: Gary W
authors.initials: GW
authors.lastname: Saunders
authors.affiliation: Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, United States. Electronic address: vis-chia@ohio.edu.
authors.forename: Morgan L
authors.initials: ML
authors.lastname: Vis
mesh_terms: D001499:Bayes Theorem; D017343:Genes, Plant; D005819:Genetic Markers; D008928:Mitochondria / Q000235:genetics; D058889:Molecular Typing; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D000461:Rhodophyta / Q000145:classification*
chemical_list: D005819:Genetic Markers
keywords: Freshwater macrophytes; Hard polytomy; Red algae; Seaweeds; Simulation analysis; Tree of life