Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales.
| Autor: | F Costa J; School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia. costaj@student.unimelb.edu.au., Lin SM; Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan., Macaya EC; Departamento de Oceanografıa, Universidad de Concepción, Casilla, 160-C, Chile.; Millennium Nucleus Ecology and Sustainable Management of Oceanic Island (ESMOI), Coquimbo, Chile., Fernández-García C; 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., Verbruggen H; School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia. |
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| Jazyk: | angličtina |
| Zdroj: | BMC evolutionary biology [BMC Evol Biol] 2016 Oct 10; Vol. 16 (1), pp. 205. Date of Electronic Publication: 2016 Oct 10. |
| DOI: | 10.1186/s12862-016-0772-3 |
| Abstrakt: | Background: 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. Results: 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. Conclusions: 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. |
| Databáze: | MEDLINE |
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