A molecular timescale of eukaryote evolution and the rise of complex multicellular life

Abstract

Background: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time.

Results: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma.

Conclusions: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.

Figure 1

Phylogenetic relationships of selected eukaryotes. For each data set (column), all taxa are represented in all proteins. Support values are listed for the three methods (maximum likelihood, minimum evolution, Bayesian inference) and correspond to the node indicated by the arrow (and bolded group) for each tree.

Figure 2

A timescale of eukaryote evolution. The times for each node are taken from the summary times in Table 1, except for nodes 1 (310 Ma), 2 (360 Ma), 3 (450 Ma), and 4 (520 Ma), which are from the fossil record [25]; nodes 8 (1450 Ma) and 16 (1587 Ma) are phylogenetically constrained and are the midpoints between adjacent nodes. Nodes 12–14 were similar in time and therefore shown as a multifurcation at 1000 Ma; likewise, nodes 21–22 are shown as a multifurcation at 1967 Ma. The star indicates the occurrence of red algae in the fossil record at 1200 Ma, the oldest taxonomically identifiable eukaryote [12].

Figure 3

Increase in the maximum number of cell types throughout the history of life. Data points at time zero are from living taxa [1-3,50]; earlier data points were estimated with squared-change parsimony (solid circles) and linear parsimony (hollow circles) [51] using the molecular timetree (Fig. 2). The origin of life and divergence of archaebacteria and eubacteria were set at 4000 Ma and the origin of eukaryotes at 2700 Ma [27,28], although earlier values for those events would not affect the overall trend. We follow McShea [4] in using maximum values at any given time and assuming that decreases do not occur. Dashed line shows an alternate (conservative) interpretation based on uncertainty as to the level of complexity of ancestors of early branching eukaryotes.