Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Pawłowski, Jan; Bolívar, Ignacio; Fahrni, José; Vargas, Colomban de; Gouy, Manolo; Zaninetti, Louisette

doi:10.1093/oxfordjournals.molbev.a025786

Cited by 127 publications

(65 citation statements)

References 33 publications

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“…If this is confirmed, Gromia will serve as a reliable outgroup necessary to establish higher-level relationships among Foraminifera. Up to now, comparative taxonomic studies were mostly based on rDNA genes and severely restricted by different substitution rates at higher taxonomic levels (Pawlowski et al, 1997). According to the results of our preliminary study, the RPB1 gene seems to evolve at relatively stable rates in Foraminifera.…”

Section: Maximum-likelihood (mentioning

confidence: 69%

Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies

Longet

Archibald

Keeling

et al. 2003

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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Section: Maximum-likelihood (mentioning

confidence: 69%

Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies

Longet

Archibald

Keeling

et al. 2003

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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“…The precise dating of the divergence of the Foraminifera from their cercozoan ancestor is difficult because of the accelerated rates of SSU rRNA gene evolution in the foraminiferal stem lineage (33). Therefore, we estimate the beginning of foraminiferan radiation based on local molecular clocks.…”

Section: Resultsmentioning

confidence: 99%

The evolution of early Foraminifera

Pawłowski

Holzmann

Berney

et al. 2003

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

245

168

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Fossil Foraminifera appear in the Early Cambrian, at about the same time as the first skeletonized metazoans. However, due to the inadequate preservation of early unilocular (single-chambered) foraminiferal tests and difficulties in their identification, the evolution of early foraminifers is poorly understood. By using molecular data from a wide range of extant naked and testate unilocular species, we demonstrate that a large radiation of nonfossilized unilocular Foraminifera preceded the diversification of multilocular lineages during the Carboniferous. Within this radiation, similar test morphologies and wall types developed several times independently. Our findings indicate that the early Foraminifera were an important component of Neoproterozoic protistan community, whose ecological complexity was probably much higher than has been generally accepted.

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“…However, the index of dispersion, R ϭ V͞M, is often significantly greater than 1 (5,32). Rate heterogeneity occurs between lineages, but also at different times along a given lineage, both factors having significant effects (5,30,(32)(33)(34)(35)(36)(37)(38)(39).…”

Section: Discussionmentioning

confidence: 99%

Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH

Rodrı́guez-Trelles

Tarrı́o

Ayala

2001

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

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The neutrality theory predicts that the rate of neutral molecular evolution is constant over time, and thus that there is a molecular clock for timing evolutionary events. It has been observed that the variance of the rate of evolution is generally larger than expected according to the neutrality theory, which has raised the question of how reliable the molecular clock is or, indeed, whether there is a molecular clock at all. We have carried out an extensive investigation of three proteins, glycerol-3-phosphate dehydrogenase (GPDH), superoxide dismutase (SOD), and xanthine dehydrogenase (XDH). We have observed that (i) the three proteins evolve erratically through time and across lineages and (ii) the erratic patterns of acceleration and deceleration differ from locus to locus, so that one locus may evolve faster in one than another lineage, whereas the opposite may be the case for another locus. The observations are inconsistent with the predictions made by various subsidiary hypotheses proposed to account for the overdispersion of the molecular clock.T he hypothesis of the molecular clock of evolution emerged from early observations that the number of amino acid replacements in a given protein appeared to change linearly with time (1). Indeed, if proteins (and genes) evolve at constant rates they could serve as molecular clocks for timing evolutionary events and reconstructing the evolutionary history of extant species; and for delimiting the choices among mechanistic descriptions of the amino acid (and nucleotide) substitution process. A notable feature of the hypothesis of the molecular evolutionary clock is empirical multiplicity: every one of the thousands of proteins or genes of an organism would be an independent clock, each ticking at a different rate but all measuring the same events. Kimura's neutrality theory of molecular evolution provides a mathematical foundation for the clock (2, 3). The theory states that the rate of substitution, k, of adaptively neutral alleles is precisely the rate of mutation, u, of neutral alleles, k ϭ u. The neutrality theory predicts that molecular evolution behaves like a stochastic clock, such as radioactive decay, with the properties of a Poisson process; therefore, the variance of the number of substitutions, V, should be equal to the mean, M, so that the ''index of dispersion'' R ϭ V͞M ϭ 1. A common observation, however, is that genes and proteins evolve more erratically than allowed by the neutral theory (the so-called overdispersed molecular clock; refs. 4 and 5), which casts doubts on the validity of the molecular clock model (5, 6). Several subsidiary hypotheses have been proposed that modify the predictions of the neutrality theory, allowing for greater variance in evolutionary rates (6).Here we present an analysis of the rates of evolution of three genes: glycerol-3-phosphate dehydrogenase (GPDH; EC 1.1.1.8), Cu,Zn superoxide dismutase (SOD; EC 1.15.1.1), and xanthine dehydrogenase (XDH; 1.1.1.204). We have previously analyzed the evolutionary rates of GPDH and...

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Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Cited by 127 publications

References 33 publications

Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies

Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies

The evolution of early Foraminifera

Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH

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