Response : Dating the Cenancester of Organisms

Abstract

zontal gene transfer or lineage fusion (4) is reflected in the dating and not the age of the last common ancestor.2) As Doolittle et al. recognize (1), proteins are conserved over billions of years because natural selection eliminates amino acid substitutions that significantly reduce functionality. Sites involved in catalysis or substrate binding often do not vary at all, while others may vary considerably without affecting protein functionality, leading to variation among sites in substitution rates. Doolittle et al. consider the influence of among-site rate variation on their molecular clock calibration, but significantly underestimate its effect. Rate variation among sites appears to be much greater than can be accounted for by irreplaceable residues alone and much greater than the "extreme distribution of probabilities" that Doolittle et al. assumed in their simulations.The gamma distribution has been widely used in analyses of nucleotide sequence data to examine the effects of among-site rate variation on phylogenetic analysis and molecular distance estimates. The shape parameter, ot, is inversely related to the amount of rate variation among sites. Low values of a correspond to large differences among sites in underlying rates of substitution, while high values correspond to small differences. Estimates of the shape parameter obtained from aligned amino acid sequences for the 70-kD heat shock protein family, the triose phosphate isomerases, and V-ATPase catalytic subunits range from 0.57 to 1.21 (7). A model assuming an invariant class of sites and a gamma distribution of rates among remaining sites provides a significantly better fit to the data and gives estimates of the shape parameter ranging from 2.42 to 3.29 with between 18 and 21% of the sites invariant ( Fig. 1).At low levels of difference, where

The tufB-secE-nusG-rplKAJL-rpoB gene cluster of the liberibacters: sequence comparisons, phylogeny and speciation

“…To estimate the time of divergence between liberibacters, the molecular clock was calibrated using the time of divergence between the genera Escherichia and Salmonella. This time was estimated as 102 million years (Myr) by Battistuzzi et al (2004), in agreement with previous work by others (Ochman & Wilson, 1987;Doolittle et al, 1996).…”

“…The value of 102 Myr was chosen according to Battistuzzi et al (2004). This estimation was in accordance with other evaluations proposing that the two lineages had diverged 100-160 Myr ago (Ochman & Wilson, 1987;Doolittle et al, 1996;Fig. 8).…”

The Role of the 3-Hydroxy 3-Methylglutaryl Coenzyme A Reductase Cytosolic Domain in Karmellae Biogenesis

“…In plants, the membrane domain contains two transmembrane helices (Denbow et al, 1996;Re et al, 1997), whereas in animals and fungi, it contains of a series of seven or eight transmembrane helices (Liscum et al, 1985;Basson et al, 1988;Sengstag et al, 1990;Olender and Simon, 1992;Roitelman et al, 1992). Although there is little obvious primary sequence conservation, the structural conservation of this complex membrane domain over the 1 billion years of evolution since divergence of fungi and animals (Doolittle et al, 1996;Lum et al, 1996;Feng et al, 1997) suggests that the structure has an important functional role. However, the molecular logic of tethering the catalytic activity to a membrane appears enigmatic, because prokaryotic HMG-CoA reductase proteins are soluble (Beach and Rodwell, 1989;Bischoff and Rodwell, 1996;Baltscheffsky et al, 1997;Bochar et al, 1997;Takahashi et al, 1999), and the catalytic domain of eukaryotic HMG-CoA reductase can support apparently normal growth of cells when it is freed from the membrane domain (Gil et al, 1985;Donald et al, 1997).…”

Potassium- or sodium-efflux ATPase, a key enzyme in the evolution of fungi The GenBank accession numbers for the sequences reported in this paper are: Pleurotus ostreatus ENA1, AJ420741; Phycomyces blakesleeanus ENA1, AJ420742; Ph. blakesleeanus PCA1, AJ420743; Blakeslea trispora ENA1, AJ420744; B. trispora BCA1, AJ420745; B. trispora BCA2, AJ420746.

“…This is not the case for fungi and plants, which left the sea probably during the Precambrian era. They last shared a common ancestor about a billion years ago (Doolittle et al, 1996 ;Lee, 1999), but later evolved together in an oligotrophic medium with a low Na + content (Retallack & Germa! n-Heins, 1994 ;Retallack, 1997).…”