Phylogeny and molecular evolution of green algae - Phycology ...

10 CHAPTER 1
Green algal phylogenies
The estimated divergence time between Streptophyta and Chlorophyta varies considerably among
studies. The split between these lineages is generally situated in the Neoproterozoic to late
Mesoproterozoic (Fig. 7) (between 1200 and 700 million years ago: Douzery et al. 2004, Hedges et al.
2004, Yoon et al. 2004, Berney and Pawlowski 2006, Roger and Hug 2006, Zimmer et al. 2007, Herron
et al. 2009). The ancient age in combination with the short time span over which the major lineages
of green algae diverged likely caused the unstable relationships among these classes. Determining
relationships among the different orders of the Ulvophyceae poses a similar problem. Up to now,
green algal phylogenies using a broad taxon sampling were always based on SSU nrDNA (Zechman et
al. 1990), while studies using whole plastid genome sequences contend with a small taxon sampling
(Pombert et al. 2004, Pombert et al. 2005). It is well-known that phylogenetic information contained
in a single gene is often insufficient to obtain firm statistical support for deep nodes (Philippe et al.
2005). Hence, improved character sampling by the inclusion of a larger number genes often leads to
more accurate estimates of phylogenetic relationships. Unfortunately there is a limited availability of
genomic data for green algae. Whole genome sequences were only available for the chlorophycean
Chlamydomonas reinhardtii and the prasinophycean Ostreococcus tauri at the start of this project.
Some other whole genome sequences have been recently released or are on the way for the
chlorophyceae Volvox and the prasinophytes Micromonas and Bathycoccus. However, up till present
no genome has been sequenced for a representative of the Ulvophyceae or Trebouxiophyceae. In
addition to whole genome sequences, there are small to moderately sized EST libraries and complete
organelle genomes available for some green algae (table 2). However, the ulvophycean seaweed
orders remain underrepresented: no sequenced plastid genome and only 2 smaller EST libraries are
available.
This limited availability of genomic information for the Chlorophyta inevitably poses a restriction on
taxon sampling. Most studies which have addressed deep relationships of Chlorophyta are seriously
constrained in taxon sampling (e.g., Pombert et al. 2005, Rodriguez-Ezpeleta et al. 2007).
Furthermore, sparse and uneven taxon sampling, with most species belonging to either the
prasinophytes or Chlorophyceae, increases the risk of systematic error due to long branch attraction
and other biases (Verbruggen and Theriot 2008).
Resolving deep green algal relationships will inevitably request the combined analysis of many
markers. Since genomic data are rare, it will be necessary to design primers for new markers. Lowcopy
nuclear markers proved to be good candidates due to a higher evolutionary rate than organellar
genes, the potential to analyze multiple unlinked genes and the bi-parentally inheritance (Small et al.
2004). However, the greater difficulty of isolating and characterizing low-copy nuclear markers in
comparison with SSU nrDNA and chloroplast genes which can be amplified with universal primers
and the difficulty of assessing orthology are the major challenge when using low-copy nuclear
markers (Small et al. 2004).