DOI: 10.5061/dryad.q4432
title: Data from: Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae

description: Background: The green algae represent one of the most successful groups of
 photosynthetic eukaryotes, but compared to their land plant relatives,
 surprisingly little is known about their evolutionary history. This is in
 great part due to the difficulty of recognizing species diversity behind
 morphologically similar organisms. The Trebouxiophyceae is a species-rich
 class of the Chlorophyta that includes symbionts (e.g. lichenized algae)
 as well as free-living green algae. Members of this group display
 remarkable ecological variation, occurring in aquatic, terrestrial and
 aeroterrestrial environments. Because a reliable backbone phylogeny is
 essential to understand the evolutionary history of the Trebouxiophyceae,
 we sought to identify the relationships among the major trebouxiophycean
 lineages that have been previously recognized in nuclear-encoded 18S rRNA
 phylogenies. To this end, we used a chloroplast phylogenomic approach.
 Results: We determined the sequences of 29 chlorophyte chloroplast genomes
 and assembled amino acid and nucleotide data sets derived from 79
 chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The
 amino acid- and nucleotide-based phylogenies inferred using maximum
 likelihood and Bayesian methods and various models of sequence evolution
 revealed essentially the same relationships for the trebouxiophyceans. Two
 major groups were identified: a strongly supported clade of 29 taxa (core
 trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a
 clade comprising the Chlorellales and Pedinophyceae that represents a
 basal divergence relative to the former group. The core trebouxiophyceans
 form a grade of strongly supported clades that include a novel lineage
 represented by the desert crust alga Pleurastrosarcina brevispinosa. The
 assemblage composed of the Oocystis and Geminella clades is the deepest
 divergence of the core trebouxiophyceans. Like most of the chlorellaleans,
 early-diverging core trebouxiophyceans are predominantly planktonic
 species, whereas core trebouxiophyceans occupying more derived lineages
 are mostly terrestrial or aeroterrestrial algae. Conclusions: Our
 phylogenomic study provides a solid foundation for addressing fundamental
 questions related to the biology and ecology of the Trebouxiophyceae. The
 inferred trees reveal that this class is not monophyletic; they offer new
 insights not only into the internal structure of the class but also into
 the lifestyle of its founding members and subsequent adaptations to
 changing environments.
description: Amino acid
 datasetThis is the amino acid
 dataset used to infer the phylogeny presented in Figure 1. It contains
 15,549 positions and was assembled from 79 proteins encoded in the
 chloroplast genomes of 63 green algae. The data set is in Phylip
 format.Amino_acid_dataset.phyDegen1_nucleotide_datasetThis is the Degen1 nucleotide dataset used to infer the phylogeny presented in Figure 4. It contains 46,404 positions and was assembled from 79 chloroplast genes of 63 green algae. The data set is in Phylip format and comprises all three codon positions that were degenerated using the Degen1.pl script of Regier et al. (Nature 2010 463:1079-1083).Codon_positions_1+2_datasetThis is the nt1+2 nucleotide dataset used to infer the phylogeny presented in Figure 4. It contains 30,936 positions and was assembled from 79 chloroplast genes of 63 green algae. The data set is in Phylip format and comprises only the first two positions of the codons.