Calibrating Evolutionary Rates at Major Histocompatibility Complex Loci

Satta, Yoko; Takahata, Naoyuki; Schönbach, Christian; Gutknecht, Jutta; Klein, Jan

doi:10.1007/978-3-642-84622-9_4

Cited by 30 publications

(16 citation statements)

References 29 publications

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“…The estimated average nonsynonymous substitution rate for the peptidebinding region (PBR) of the Mhc loci is 5.9 × 10 -9 substitutions per nonsynonymous site per year (Satta et al 1991). The average synonymous substitution rate of the Mhc class II loci is 1.18 × 10 -9 substitutions per synonymous site per year.…”

Section: Jan Kleinmentioning

confidence: 99%

Trans-species polymorphism of class IIMhc loci in danio fishes

et al. 1996

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Section: Jan Kleinmentioning

confidence: 99%

Trans-species polymorphism of class IIMhc loci in danio fishes

et al. 1996

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“…3 is a phylogenetic reconstruction of the 58 alleles. The time scale has been determined by the "minimumminimum" method (39,40), which is based on the comparison between pairs of species that share the same divergence node, such as the three pairs orangutan-human, orangutangorilla, and orangutan-chimpanzee. The minimum distance observed in such a set of comparisons will correspond to alleles that diverge at, or close to, the time of the species divergence.…”

Section: The Mhcmentioning

confidence: 99%

Molecular genetics of speciation and human origins.

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Ó'hUigín

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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The major histocompatibility complex (MHC) plays a cardinal role in the defense of vertebrates against parasites and other pathogens. In some genes there are extensive and ancient polymorphisms that have passed from ancestral to descendant species and are shared among contemporary species. The polymorphism at the DRBI locus, represented by 58 known alleles in humans, has existed for at least 30 million years and is shared by humans, apes, and other primates. The coalescence theory of population genetics leads to the conclusion that the DRBI polymorphism requires that the population ancestral to modern humans has maintained a mean effective size of 100,000 individuals over the 30-millionyear persistence of this polymorphism. We explore the possibility of occasional population bottlenecks and conclude that the ancestral population could not have at any time consisted of fewer than several thousand individuals. The MHC polymorphisms exclude the theory claiming, on the basis of mitochondrial DNA polymorphisms, that a constriction down to one or few women occurred in Africa, at the transition from archaic to anatomically modern hans, some 200,000 years ago. The data are consistent with, but do not provide specific support for, the claim that human populations throughout the World were at that time replaced by populations migrating from Africa. The MHC and other molecular polymorphisms are consistent with a "muIlIregionalI theory of Pleistocene human evolution that proposes regional continuity of human populations since the time of migrations of Homo erectus to the present, with distinctive regional selective pressures and occasional migrations between populations.

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“…5). Where there were several pairs of sequences in a given species combination, we chose the one giving the lowest divergence under the assumption that it is closest to the species divergence (Satta et al 1991). The observed linear correlation between the divergences indicates that the DRB introns evolve at a rate similar to that of the EG synonymous sites.…”

Section: Tempo and Mode Of Mhc Intron Evolutionmentioning

confidence: 99%

“…The reason for the transition could be an error in estimating the species divergence time from the fossil record or a change in the nucleotide substitution rate during primate evolution. Under the assumption that the minimum rate is closest to the true rate (Satta et al 1991), the initial substitution rate is estimated to have been 1.3 × 10 −9 per site per year.…”

Section: Tempo and Mode Of Mhc Intron Evolutionmentioning

confidence: 99%

Evolution of Mhc–DRB Introns: Implications for the Origin of Primates

et al. 1999

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Introns are generally believed to evolve too rapidly and too erratically to be of much use in phylogenetic reconstructions. Few phylogenetically informative intron sequences are available, however, to ascertain the validity of this supposition. In the present study the supposition was tested on the example of the mammalian class II major histocompatibility complex (Mhc) genes of the DRB family. Since the Mhc genes evolve under balancing selection and are believed to recombine or rearrange frequently, the evolution of their introns could be expected to be particularly rapid and subject to scrambling. Sequences of intron 4 and 5 DRB genes were obtained from polymerase chain reaction-amplified fragments of genomic DNA from representatives of six eutherian orders-Primates, Scandentia, Chiroptera, Dermoptera, Lagomorpha, and Insectivora. Although short stretches of the introns have indeed proved to be unalignable, the bulk of the intron sequences from all six orders, spanning >85 million years (my) of evolution, could be aligned and used in a study of the tempo and mode of intron evolution. The analysis has revealed the Mhc introns to evolve at a rate similar to that of other genes and of synonymous sites of non-Mhc genes. No evidence of homogenization or large-scale scrambling of the intron sequences could be found. The Mhc introns apparently evolve largely by point mutations and insertions/deletions. The phylogenetic signals contained in the intron sequences could be used to identify Scandentia as the sister group of Primates, to support the existence of the Archonta superorder, and to confirm the monophyly of the Chiroptera.

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Calibrating Evolutionary Rates at Major Histocompatibility Complex Loci

Cited by 30 publications

References 29 publications

Trans-species polymorphism of class IIMhc loci in danio fishes

Trans-species polymorphism of class IIMhc loci in danio fishes

Molecular genetics of speciation and human origins.

Evolution of Mhc–DRB Introns: Implications for the Origin of Primates

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