title: Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales.
abstract: Obtaining strongly supported phylogenies that permit confident taxonomic and evolutionary interpretations has been a challenge in algal biology. High-throughput sequencing has improved the capacity to generate data and yields more informative datasets. We sequenced and analysed the chloroplast genomes of 22 species of the order Nemaliales as a case study in the use of phylogenomics as an approach to achieve well-supported phylogenies of red algae.
  
  
  
  Chloroplast genomes of the order Nemaliales are highly conserved, gene-dense and completely syntenic with very few cases of gene loss. Our ML estimation based on 195 genes recovered a completely supported phylogeny, permitting re-classification of the order at various taxonomic levels. Six families are recognised and the placement of several previously contradictory clades is resolved. Two new sub-orders are described, Galaxaurineae and Nemaliineae, based on the early-branching nature and monophyly of the groups, and presence or absence of a pericarp. Analyses of subsets of the data showed that >90 % bootstrap support can be achieved with datasets as small as 2500 nt and that fast and medium evolving genes perform much better when it comes to resolving phylogenetic relationships.
  
  
  
  In this study we show that phylogenomics is an efficient and effective approach to investigate phylogenetic relationships. The six currently circumscribed Nemaliales families are clustered into two evolutionary lineages with strong statistical support based on chloroplast phylogenomic analyses. The conserved nature of red algal chloroplast genomes is a convenient and accessible source of data to resolve their ancient relationships.
authors.affiliation: School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia. costaj@student.unimelb.edu.au.
authors.forename: Joana
authors.initials: J
authors.lastname: F Costa
authors.affiliation: Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan.
authors.forename: Showe-Mei
authors.initials: SM
authors.lastname: Lin
authors.affiliation: Departamento de Oceanografıa, Universidad de Concepción, Casilla, 160-C, Chile.|Millennium Nucleus Ecology and Sustainable Management of Oceanic Island (ESMOI), Coquimbo, Chile.
authors.forename: Erasmo C
authors.initials: EC
authors.lastname: Macaya
authors.affiliation: Escuela de Biología, Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, 11501-2060, Costa Rica.
authors.forename: Cindy
authors.initials: C
authors.lastname: Fernández-García
authors.affiliation: School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia.
authors.forename: Heroen
authors.initials: H
authors.lastname: Verbruggen
mesh_terms: D002736:Chloroplasts / Q000235:genetics; D048028:DNA, Algal / Q000235:genetics; D019143:Evolution, Molecular; D054628:Genome, Chloroplast; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D000461:Rhodophyta / Q000145:classification* / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D048028:DNA, Algal
keywords: Chloroplast phylogenomics; Conserved genomes; Nemaliales; Plastid genomes; Red algae