The bottleneck effect (or extended period of reduced population size) is known to increase genetic distance (D) substantially, and this can be a serious factor that disturbs the phylogenetic relationships of populations inferred from genetic distance estimates. The bottleneck effect is also known to be a factor that disturbs the hierarchial relationships of the fixation indices (FST) or the coefficients of gene differentiation (GST) in subdivided populations. To examine the extent of the bottleneck effect on D and GST in human populations, the D and GST values were computed for various groups of populations from around the world, and their relationships with within-population heterozygosities were examined by using gene frequency data for protein and immunological loci. The results obtained indicate that the D value between a pair of populations is negatively correlated with the average within-population heterozygosity. This suggests that genetic distance estimates for small populations are seriously affected by the bottleneck effect, and that phylogenetic trees should be studied by taking into account this factor. The bottleneck effect on GST was also revealed from examination of the total gene diversity HT and its components, interpopulational genetic variation (DST) and intrapopulational genetic variation (HS). That is, a large value of GST in small populations was sometimes associated with the decrease of HS rather than the increase of DST. Generally speaking, however, GST was larger when geographically distant populations were considered than when closely located populations were considered. When there is any trace of bottleneck effects, phylogenetic trees should be constructed by a method in which the rate of evoluationary change is allowed to vary from branch to branch.

Ethnicity↗

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Origins and divergence times of mammalian class II MHC gene clusters.

The class I and II major histocompatibility complex (MHC) genes are apparently subject to evolution by a birth-and-death process. The rate of gene turnover is much slower in the latter genes than in the former. In placental mammals, the class II region can be subdivided into different orthologous subregions or gene clusters (DR, DQ, DO, and DN), but the origins and evolutionary relationships of these gene clusters are not well established. Here we report the results of our study of the times of origin and evolutionary relationships of these gene clusters in mammals. Our analysis suggests that both class II alpha-chain and beta-chain gene clusters are shared by placental mammals and marsupials, but the gene clusters from nonmammalian species are paralogous to mammalian gene clusters. We estimated the times of divergence between gene clusters in placental mammals using the linearized tree and distance regression methods. Our results indicate that most gene clusters originated 170-200 million years (MY) ago, but that DO beta-chain genes diverged from the other beta-chain gene clusters approximately 210-260 MY ago. The phylogenetic trees for the alpha- and beta-chain genes were not congruent, suggesting that the evolutionary history of the class II gene clusters is more complex than previously thought.

Animals↗