A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly. The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence

Penny et al. have written that "The most fundamental criterion for a scientific method is that the data must, in principle, be able to reject the model. Hardly any [phylogenetic] tree-reconstruction methods meet this simple requirement." The ability to reject models is of such great importance because the results of all phylogenetic analyses depend on their underlying models--to have confidence in the inferences, it is necessary to have confidence in the models. In this paper, a test statistic suggested by Cox is employed to test the adequacy of some statistical models of DNA sequence evolution used in the phylogenetic inference method introduced by Felsenstein. Monte Carlo simulations are used to assess significance levels. The resulting statistical tests provide an objective and very general assessment of all the components of a DNA substitution model; more specific versions of the test are devised to test individual components of a model. In all cases, the new analyses have the additional advantage that values of phylogenetic parameters do not have to be assumed in order to perform the tests.

https://www.webpages.uidaho.edu/%7ejacks/Goldman.1993.pdf

Statistical tests of models of DNA substitution

This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach,Salmonella typhimurium andEscherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago.

Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes

During the first two years of human life a common neural substrate (roughly Broca's area) underlies the hierarchical organization of elements in the development of speech as well as the capacity to combine objects manually, including tool use. Subsequent ~rticd daerentiation, beginning at age two, creates distinct, relatively modularized capacities for linguistic grammar . . and more complex combination of objects. An evolutionary homologue of the neural substrate for language production and manual , . action is hypothesized to have provided afoundation for the evolution oflanguage before the divergence of the horninids and the great apes. Support comes from the discovery of a Broca's area homologue and related neural circuits in contemporary primates. In addition, chimpanzees have an identical constraint on hierarchical complexity in both tool use and symbol combination. Their . . performance matches that of the two-year-old child who has not yet developed the neural circuits for complex grammar and camplex manual combination of objects.

/pdf/language-tools-and-brain-the-ontogeny-and-phylogeny-of-1xmpkl4iu5.pdf

Language, tools and brain: The ontogeny and phylogeny of hierarchically organized sequential behavior

Molecular studies indicate that chimpanzee and gorilla are the closest relatives of man (refs 1–7 and refs therein). The small molecular distances found point to late ancestral separations2,4,7, with the most recent being between chimpanzee and man, as judged by DNA hybridization3,8. Kluge9 and Schwartz10 contest these conclusions: morphological characters group a chimpanzee–gorilla clade with the Asian ape orang-utan in Kluge's cladistic study and with an orang-utan–human clade in Schwartz's study. Clearly, extensive sequencing of nuclear DNA is needed to resolve by cladistic analysis the branching order within Hominoidea11. Towards this goal, we are sequencing orthologues of the primate ψη-globin locus12,13. Here, we compare the newly completed sequences of orang-utan and rhesus monkey with human, chimpanzee, gorilla, owl monkey, lemur and goat orthologues. Our findings substantially increase the evidence indicative of a human–chimpanzee–gorilla clade with ancestral separations around 8 to 6 Myr ago. We also verify that neutral hominoid DNA evolved at markedly retarded rates.

Keith Chan

Papers

Primate η-globin DNA sequences and man's place among the great apes