@article {Hedges:2004vz,
	title = {A molecular timescale of eukaryote evolution and the rise of complex multicellular life},
	journal = {Bmc Evolutionary Biology},
	volume = {4},
	year = {2004},
	publisher = {BIOMED CENTRAL LTD},
	address = {MIDDLESEX HOUSE, 34-42 CLEVELAND ST, LONDON W1T 4LB, ENGLAND},
	abstract = {Background: The pattern and timing of the rise in complex multicellular life during Earth{\textquoteright}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 similar to10 types at 1500 Ma and 50 cell types at similar to1000 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.},
	doi = {ARTN 2},
	author = {Hedges, SB and Blair, JE and Venturi, ML and Shoe, JL}
}
@booklet {BlairAndHedges2004,
	title = {Molecular clocks do not support the Cambrian explosion},
	volume = {22},
	year = {2004},
	note = {Molecular Biology and Evolution},
	pages = {387-390},
	publisher = {OXFORD UNIV PRESS},
	address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
	abstract = {The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (similar to800 to 1,200 MYA), with and without the assumption of a global molecular clock. Recently, two studies have instead reported time estimates apparently consistent with the fossil record. Here, we demonstrate that methodological problems in these studies cast doubt on the accuracy and interpretations of the results obtained. In the study by Peterson et al., young time estimates were obtained because fossil calibrations were used as maximum limits rather than as minimum limits, and not because invertebrate calibrations were used. In the study by Aris-Brosou and Yang, young time estimates were obtained because of problems with rate models and other methods specific to the study, and not because Bayesian methods were used. This also led to many anomalous findings in their study, including a primate-rodent divergence at 320 MYA. With these results aside, molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils.},
	keywords = {animals, evolution, fossil record, Metazoa, time estimation},
	author = {Blair, JE and Hedges, SB}
}
