Phylogeny and DNA-DNA hybridization.
Authors: M Ruvolo, T F Smith
Journal: Molecular Biology and Evolution (1986)

Resolving the phylogeny of the hominoid primates is a test case for molecular systematic methods because, by most genetic measures, humans, chimpanzees, and gorillas are very closely related.Recently, Sibley and Ahlquist (1984) applied DNA-DNA hybridization techniques to infer the hominoid phylogenetic tree with humans and chimpanzees closest.Templeton (1983Templeton ( , 1985) ) argues rather that the chimpanzee and gorilla are closest relatives and criticizes the DNA-DNA hybridization methodology in general as well as Sibley and Ahlquist's analysis in particular.As part of this criticism, Templeton introduces the delta Q-test, a nonparametric test ofphylogenetic relationships that is based on distance data.Applied to the DNA-DNA hybridization data, this test favors Sibley and Ahlquist's phylogeny over his own-but, according to Templeton ( 1985), not significantly.Not only does this test not support Templeton's favored phylogeny over Sibley and Ahlquist's, but it can be shown that, contrary to his claim, the delta Q-test lacks sufficient power to discriminate between these phylogenies.Templeton does raise the valid criticism that intraspecific variation needs to be documented.This criticism also applies to most molecular systematic studies, because, with few exceptions, only one individual per species is examined.Although not reported as such, Sibley and Ahlquist's original ( 1984) and new (personal communication) data include information on intraspecific variability.While Sibley and Ahlquist did not measure delta TsOH values among pairs of individuals within species, they did measure several individuals of a species against one individual of another.For example, averaged reciprocal delta TsoH (or one-way values where reciprocals are not available) vary between one human and three chimpanzee individuals by 0.23 degrees C (N = 64), between one human and four gorilla individuals by 0.53 degrees C (N = 69), and among two chimpanzees and three gorillas by 0.18 degrees C (N = 69).Eliminating the one-way reciprocal values reduces the delta TsOH range between the one human and three gorillas to 0.27 degrees C.These ranges are less than the smallest measurement in the data set, between species of Pan (delta TsoH + SE of 0.7 f 0.1 degrees C).Human intraspecific single-copy DNA variation has been estimated at 0. l%, approximately equivalent to 0.1 degrees C (R. J. Britten 1986).While we still need direct intraspecific delta TsOH measurements, the data already gathered suggest that variation between individuals within a species did not confound the hominoid intergenic measurements.Templeton (1985) refers to two types of error that can affect any data set.The first type, experimental error, is effectively dealt with by controlling experimental conditions and by repeating each measurement many times, both of which Sibley and Ahlquist (1984) do.The second type of error, stochastic variation, arises from the nature of the evolutionary process itself.There is little question that, over short time periods, the stochastic variations in the evolution of single genes could be significant and confound phylogenetic reconstruction.But Templeton's comments on stochasticity as applied to Sibley and Ahlquist's data do not take into account the great number of