Man's place in Hominoidea as inferred from molecular clocks of DNA

Abstract

Divergence dates among primates were estimated by molecular clock analysis of DNA sequence data. A molecular clock of eta-globin pseudogene was calibrated by setting the date of divergence between Catarrhini and Platyrrhini at 38 million years (Myr) ago. The clock gave dates of 25.3 +/- 2.4, 11.9 +/- 1.7, 5.9 +/- 1.2, and 4.9 +/- 1.2 Myr ago ( +/- refers to standard error) for the separation of rhesus monkey, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. In placing confidence intervals of the estimates in a robust way, a bootstrap method was used. The 95% confidence intervals are 20.5-29.5, 9.0-14.8, 4.1-7.8, and 3.1-7.0 Myr ago for the separation of rhesus monkey, orangutan, gorilla, and chimpanzee, respectively. By a molecular clock dating of the Prosimii-Anthropoidea splitting, it was suggested that the evolutionary rate of the eta-globin gene was high early in primate evolution and subsequently decreased in the line of Anthropoidea. And, by a relative rate test using bootstrap sampling, the possibility of further decrease of the rate (more than 10%) in the line of Hominoidea compared with that of Cercopithecoidea was suggested. Therefore, the above dating of the splittings within Hominoidea may be biased slightly toward younger dates. On the other hand, mitochondrial DNA (mtDNA) seems to have evolved in mammals with a more uniform rate than the eta-globin gene. The ratio of the dates of orangutan splitting to chimpanzee splitting is larger for the mtDNA clock than that for the eta-globin clock, suggesting the possibilities of mtDNA introgression among the early hominids and the early African apes, and/or of mtDNA polymorphism within the common ancestral species of orangutan and the African apes that obscures the date of the true species separation of orangutans.

In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

“…Our analyses of the AL 53 and AL 292 data sets generated estimates for τ HC-G of 5.9 and 6.1 Mya, respectively, regardless of the priors. Our larger data set estimate of a 6.1-Mya gorilla divergence time agrees with the majority of previous molecular studies: 5.9 Mya (Hasegawa et al 1987 (Schrago 2014). In contrast, both of our AE data sets suggest a far more recent gorilla divergence (3.0-3.4 Mya).…”

“…Our AL 292 data set yielded estimates of τ HC ranging from 3.8-4.1 Mya, indicating the priors exerted little influence over the larger data set. Our estimates of τ HC based on AL 292 are comparable with the majority of previous molecular studies: 4.9 Mya (Hasegawa et al 1987), 4.6 Mya (based on diffuse prior) (Yang 2002) (Hobolth et al 2011), and 3.6-4.1 Mya (Schrago 2014). Interestingly, our two AE data set yielded substantially more recent N HC divergence times of 2.1-2.6 Mya, which, in light of the other estimates, must represent underestimates of the true divergence date.…”

“…We followed the method of Burgess and Yang (2008), who used α = 4 for a diffuse speciation time prior. Previous studies have produced a wide array of estimates for τ HCG-O : 9-13 Mya (Hobolth et al 2011), 10-13 Mya (Schrago 2014), 12 Mya (Hasegawa et al 1987), 14-15 Mya (Goodman et al 1998;Burgess and Yang 2008), and 18 Mya (Satta et al 2004;Steiper and Young 2006). Given this range, we specified two priors for τ HCG-O , which cover this 10-to 18-Mya range and therefore allowed us to assess the sensitivity of our results to the priors.…”

Humanity from African Naissance to Coming Millennia

“…Pioneering work was done by Morris Goodman (1963) using immunological methods which grouped the humans in the same clade as the African apes. This was confirmed by other studies using different loci and different analytical methods Ferris et al, 1981;Brown et al, 1982;Goodman et al, 1983;Hasegawa et al, 1987: Kishino & Hasegawa, 1989Koop et al, 1989). Goodman (1963) was the first to suggest taxonomic revision, when he proposed that the great apes be classified in the same family as humans.…”

Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes

“…For likelihood-based analyses of the mtDNA multigene fragment, the general time reversible model (Tavaré, 1986) was found by the AIC to be the best fit model of sequence evolution, with the distribution of rates of evolution among sites described by the gamma density shape parameter, a (Yang, 1994), and a proportion of invariable sites, I (Hasegawa et al, 1987), aka, the GTR + C + I model. A limited case of the preceding model was selected by the AIC for the c-myc data, i.e., equal base frequencies and equal transition rates (aka, TVMef + C + I).…”