Estimating metazoan divergence times with a molecular clock

Abstract

Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are Ϸ555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (Drosophila) Ϸ900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla.A lthough the Cambrian explosion is of singular importance to our understanding of the history of life, it continues to defy explanation (1). This defiance stems, in part, from our inability to distinguish between two competing hypotheses: whether the Cambrian explosion reflects the rapid appearance of fossils with animals having a deep but cryptic precambrian history, or whether it reflects the true sudden appearance and diversification of animals in the Cambrian (2). Because each hypothesis makes a specific prediction of when animals arose in time, one way to distinguish between these two hypotheses is to date animal diversifications by using a molecular clock (2). A number of previous clock studies (reviewed in refs. 3 and 4) have suggested that the last common ancestor of bilaterians (LCB) lived well over one billion years ago (5, 6), whereas others suggest that LCB arose Ϸ900 million years ago (Ma) (e.g., refs. 7-10), and still others are more consistent with an origination closer to the Cambrian (11-13). These deep estimates for the origin of LCB raise the question of how hundreds of millions of years of bilaterian evolution can escape detection, given that LCB and its near relatives should have had the capability of leaving both body and trace fossils (14-16).Because molecular clocks have several inherent problems, including how the clock is calibrated, how molecular substitution rates are estimated, and how heterogeneity in these rates is detected and corrected (3, 4), as well...

Hox, ParaHox, ProtoHox: facts and guesses

“…Hox: facts and guesses J Garcia-Fernàndez peared. However, it was soon found that dipoblast Cnidarians already possessed Hox and ParaHox genes (Finnerty and Martindale, 1999) The four-gene model is supported by phylogenetic analyses of the 60 aa homeodomain alone (or the homeodomain plus five flanking aa), of proteins that diverged more than 800 million years ago (Banerjee-Basu and Baxevanis, 2001; Peterson et al, 2004). The bootstrap values for any particular grouping of Hox vs ParaHox genes range from 40 to 70% (Brooke et al, 1998;Finnerty and Martindale, 1999;Banerjee-Basu and Baxevanis, 2001;Minguillón and Garcia-Fernàndez, 2003).…”

A molecular palaeobiological hypothesis for the origin of aplacophoran molluscs and their derivation from chiton-like ancestors

“…The chosen root prior is based on the observed presence of both ecdysozoans and lophotrochozoans (protostomes) at the base of the Cambrian indicating an older divergence (earlier than 542 Ma) of this group. Previous molecular clock studies also recovered a divergence of the protostomes at this time [33,42]. The analyses were run initially under the prior in order to confirm that the distribution of ages was sufficiently uninformative for posterior sampling.…”

“…Molecular analyses so far have not been able to confirm either of the morphological hypotheses. In order to assess the relative merits of the different morphological hypotheses for the position of aplacophorans, we sequenced seven nuclear housekeeping gene mRNAs [33] from all major classes of molluscs (except monoplacophorans). These data were combined with a representative set of lophotrochozoan and ecdysozoan taxa as outgroups and analysed in a Bayesian phylogenetic framework.…”

Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives

“…Early application of a Bayesian relaxed clock method to the problem of metazoan divergence times by Aris-Brosou & Yang (2003) found phylum-level splits in the Deuterostomia at ca 520-530 Myr ago, matching Peterson et al's (2004) results. However, they used an unrealistic model of molecular evolution in their analysis (Ho et al 2005) and other analyses that apply potentially more appropriate models (Douzery et al 2004) have continued to find somewhat deeper divergence dates for the Bilateria.…”