New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data

Karolina FuäÃ­Kovã¡,Pavel Å Kaloud,Carlos F D Gurgel,Frederik Leliaert,Charles F Delwiche,Sofie D'Hondt,Endymion D Cooper,Juan M Lopez-Bautista,Paul O Lewis,Louise A Lewis,Olivier De Clerck,Heroen Verbruggen

doi:10.3389/fevo.2014.00063

Abstract

Phylogenetic relationships in the green algal phylum Chlorophyta have long been subject to debate, especially at higher taxonomic ranks (order, class). The relationships among three traditionally defined and well-studied classes, Chlorophyceae, Trebouxiophyceae, and Ulvophyceae are of particular interest, as these groups are species-rich and ecologically important worldwide. Different phylogenetic hypotheses have been proposed over the past two decades and the monophyly of the individual classes has been disputed on occasion. Our study seeks to test these hypotheses by combining high throughput sequencing data from the chloroplast genome with increased taxon sampling. Our results suggest that while many of the deep relationships are still problematic to resolve, the classes Trebouxiophyceae and Ulvophyceae are likely not monophyletic as currently defined. Our results also support relationships among several trebouxiophycean taxa that were previously unresolved. Finally, we propose that the common term for the grouping of the three classes, “UTC clade,” be replaced with the term “core Chlorophyta” for the well-supported clade containing Chlorophyceae, taxa belonging to Ulvophyceae and Trebouxiophyceae, and the classes Chlorodendrophyceae and Pedinophyceae.

Highlights

New lineages of green algae are discovered every year as unusual habitats are surveyed and cryptic diversity unveiled
We propose that the common term for the grouping of the three classes, “UTC clade,” be replaced with the term “core Chlorophyta” for the well-supported clade containing Chlorophyceae, taxa belonging to Ulvophyceae and Trebouxiophyceae, and the classes Chlorodendrophyceae and Pedinophyceae
The UTC classes plus the Chlorodendrophyceae are characterized by a novel mode of cell division, mediated by a phycoplast, which is absent in the prasinophytes and Pedinophyceae, and secondarily lost in the Ulvophyceae (Figure 1; reviewed in Leliaert et al, 2012; Marin, 2012)

Summary

Introduction

New lineages of green algae are discovered every year as unusual habitats are surveyed and cryptic diversity unveiled. Ancestors of the extant prasinophytes gave rise to the morphologically and ecologically diverse core Chlorophyta, which include three major classes: Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC). Two smaller, early diverging lineages of core Chlorophyta have been identified: the Chlorodendrophyceae and Pedinophyceae (Moestrup, 1991; Massjuk, 2006; Leliaert et al, 2012; Marin, 2012) (Figure 1). The UTC classes plus the Chlorodendrophyceae are characterized by a novel mode of cell division, mediated by a phycoplast, which is absent in the prasinophytes and Pedinophyceae, and secondarily lost in the Ulvophyceae (Figure 1; reviewed in Leliaert et al, 2012; Marin, 2012)

Methods

Results

Conclusion