An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks

Nikoh, Naruo; Iwabe, Naoyuki; Kuma, Kei-ichi; Ohno, Masatomi; Sugiyama, T.; Watanabe, Yoko; Yasui, Kohichiroh; Zhang, Shicui; Hori, Katsuji; Shimura, Yoichi; Miyata, Takashi

doi:10.1007/pl00006208

Cited by 75 publications

(56 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this context, the lack of resolution in metazoan phylogenies (i.e., polytomies) derived from 18S rRNA data has been interpreted as evidence for a Cambrian explosion (e.g., Erwin 1991;Phillipe et al 1994). Although this observation is consistent with the interpretations of the fossil record, it is in conflict with recent molecular analyses based on calibrated rates of sequence divergence (Runegar 1982;Doolittle et al 1996;Wray et al 1996;Nikoh et al 1997), as well as phylogenetic analyses of extant and Cambrian arthropods (Fortey et al 1997), both of which suggest deep Precambrian divergences. The recent discovery of microscopic Precambrian metazoans (Li et al 1998;Xiao et al 1998) further supports this inference.…”

Section: Introductionsupporting

confidence: 52%

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

1998

View full text Add to dashboard Cite

Abstract. We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly, excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.

show abstract

Section: Introductionsupporting

confidence: 52%

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

1998

View full text Add to dashboard Cite

show abstract

“…The duplication time, estimated as T ‫ס‬ k aa /( aa -ADH3 + aa -ADH1), was 493-500 MYA. Therefore, the ADH family would have expanded after the cephalochordate/vertebrate split [682-694 MYA for ADH3 (our estimate) ( Table 2) and 680-700 MYA for triosephosphate isomerase and 790-860 MYA for aldolase C (Nikoh et al 1997)]. …”

Section: Class 3/1 Duplicationmentioning

confidence: 99%

Ascidian and Amphioxus Adh Genes Correlate Functional and Molecular Features of the ADH Family Expansion During Vertebrate Evolution

et al. 2002

View full text Add to dashboard Cite

Abstract. The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolutionary analysis of the family was performed gathering data from protein and gene structures, exon-intron distribution, and functional features through chordate lines. Our data strongly support that the ADH family expansion occurred 500 million years ago, after the cephalochordate/vertebrate split, probably in the gnathostome subphylum line of the vertebrates. Evolutionary rates differ between the ancestral, ADH3 (glutathione-dependent formaldehyde dehydrogenase), and the emerging forms, including the classical alcohol dehydrogenase, ADH1, which has an evolutionary rate 3.6-fold that of the ADH3 form. Phylogenetic analysis and chromosomal mapping of the vertebrate Adh gene cluster suggest that family expansion took place by tandem duplications, probably concurrent with the extensive isoform burst observed before the fish/tetrapode split, rather than through the large-scale genome duplications also postulated in early vertebrate evolution. The absence of multifunctionality in lower chordate ADHs and the structures compared argue in favor of the acquisition of new functions in vertebrate ADH classes. Finally, comparison between B. floridae and B. lanceolatum Adhs provides the first estimate for a cephalochordate speciation, 190 million years ago, probably concomitant with the beginning of the drifting of major land masses from the Pangea.

show abstract

“…These genes were chosen because they had previously been shown to support the monophyly of Ecdysozoa or did not significantly support an alternative arrangement (9,22) and͞or had shown potential clock-like behavior (23). We stress that no molecule or region of a molecule was excluded from the analysis, and the successful amplification and cloning of only these seven (of 12 tested) proved tractable from this diversity of taxa using standard techniques.…”

mentioning

confidence: 99%

Estimating metazoan divergence times with a molecular clock

Peterson

Lyons

Nowak

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

427

285

View full text Add to dashboard Cite

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...

show abstract

An Estimate of Divergence Time of Parazoa and Eumetazoa and That of Cephalochordata and Vertebrata by Aldolase and Triose Phosphate Isomerase Clocks

Cited by 75 publications

References 41 publications

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

Ascidian and Amphioxus Adh Genes Correlate Functional and Molecular Features of the ADH Family Expansion During Vertebrate Evolution

Estimating metazoan divergence times with a molecular clock

Contact Info

Product

Resources

About