The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Abstract

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes.Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

Multiple secondary origins of the anaerobic lifestyle in eukaryotes

“…However, most methods of phylogenetic analysis assume a homogeneous process, i.e. that all sequences evolve in the same way, so the aberrant behaviour of Archezoan sequences can make their phylogenetic position difficult to infer reliably (see Roger & Hug 2006). The difficulty experienced when trying to resolve the origins of the Trichomonas hydrogenosomal NADH dehydrogenase provides just one example of the kind of problems that can be encountered (Dyall et al 2004b;Hrdy et al 2004;Gray 2005).…”

“…Phylogenetic analyses previously taken to support the deep branching positions of archezoans have also come under increasing scrutiny with the result that they are no longer viewed as reliable (Stiller & Hall 1999;Hirt et al 1999;Philippe et al 2000;Inagaki et al 2004;Thomarat et al 2004;Roger & Hug 2006). The molecular sequences of the former Archezoa often evolve differently to those of other eukaryotes to which they are being compared.…”

“…It thus seems possible that all eukaryotes might contain an organelle of mitochondrial ancestry, emphasizing the pivotal role that the mitochondrial endosymbiosis has played in eukaryotic evolution. Although we still need a reliable root for the eukaryotic tree (see Cavalier-Smith 2006;Roger & Hug 2006), it is evident that anaerobic eukaryotes have repeatedly arisen from within ancestrally aerobic groups with mitochondria. Anaerobic eukaryotes are neither rare nor primitive as once thought.…”

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

“…We implemented different evolutionary models, data partitioning strategies, tree reconstruction and clock estimation methods to assess their effects on tree topology, branch lengths and rates since they are prone to several error sources that aggravate at deep phylogenetic levels (Roger and Hug, 2006;Philips, 2009 and references therein). We explored five different partitioning strategies: (1) a single partition with the 13 MPCGs concatenated; (2) two partitions, sites of first and second codons versus positions of third codon; (3) three partitions, by codon (first, second and third); (4) codon-based models that explicitly incorporate information on the genetic code (i.e., AA replacement rates) but have codons rather than nucleotides as states (Goldman and Yang, 1994); and finally (5) we applied 13 partitions, one for each protein-coding gene.…”

Prospects for elucidating the phylogeny of the Apicomplexa

“…a parsimony analysis and a maximum-likelihood analysis) will not successfully deal with either of these two problems, as all of the analyses will be affected in the same way. Other potential problems are reviewed by Roger & Hug (2006). This does not mean that the results of basic and more sophisticated analyses must necessarily disagree.…”