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  • 1
    Electronic Resource
    Electronic Resource
    Man's place in hominoidea revealed by mitochondrial DNA genealogy (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 32-43 
    Details
    ISSN: 1432-1432
    Keywords: Hominoid phylogeny ; Mitochondrial DNA ; Nucleotide substitutions ; Molecular clock ; Phylogenetic trees ; Divergence times
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Molecular biology has resurrected C. Darwin and T.H. Huxley's question about the origin of humans, but the precise branching pattern and dating remain controversial. To settle this issue, a large amount of sequence information is required. We determined mitochondrial (mt) DNA sequences for five hominoids; pygmy and common chimpanzees, gorilla, orangutan, and siamang. The common region compared with the known human sequence is 4759 by long, encompassing genes for 11 transfer RNAs and 6 proteins. Because of the high substitution rates in mammalian mtDNA and an unprecedentedly large region compared, the sequence differences clearly indicate that the closest relatives to human are chimpanzees rather than gorilla. For dating the divergences of human, chimpanzee, and gorilla, we used only unsaturated parts of sequence differences in which the mtDNA genealogy is not obscured by multiple substitutions. The result suggests that gorilla branched off 7.7 ± 0.7 million years (Myr) ago and human 4.7 ± 0.5 Myr ago; the time difference between these divergences being as long as 3 Myr.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160258
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  • 2
    Electronic Resource
    Electronic Resource
    Evolution of hominoid mitochondrial DNA with special reference to the silent substitution rate over the genome (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 517-531 
    Details
    ISSN: 1432-1432
    Keywords: Hominoid mitochondrial DNA ; Nucleotide substitution rate ; Transition bias ; Base compositions ; Functional constraints ; Multiple hit corrections ; Transfer RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Focusing on the synonymous substitution rate, we carried out detailed sequence analyses of hominoid mitochondrial (mt) DNAs of ca. 5-kb length. Owing to the outnumbered transitions and strong biases in the base compositions, synonymous substitutions in mtDNA reach rapidly a rather low saturation level. The extent of the compositional biases differs from gene to gene. Such changes in base compositions, even if small, can bring about considerable variation in observed synonymous differences and may result in the region-dependent estimate of the synonymous substitution rate. We demonstrate that such a region dependency is due to a failure to take proper account of heterogeneous compositional biases from gene to gene but that the actual synonymous substitution rate is rather uniform. The synonymous substitution rate thus estimated is 2.37 ± 0.11 × 10−8 per site per year and comparable to the overall rate for the noncoding region. On the other hand, the rate of nonsynonymous substitutions differs considerably from gene to gene, as expected under the neutral theory of molecular evolution. The lowest rate is 0.8 × 10−9 per site per year forCOI and the highest rate is 4.5 × 10−9 forATPase 8, the degree of functional constraints (measured by the ratio of the nonsynonymous to the synonymous substitution rate) being 0.03 and 0.19, respectively. Transfer RNA (tRNA) genes also show variability in the base contents and thus in the nucleotide differences. The average rate for 11 tRNAs contained in the 5-kb region is 3.9 × 10−9 per site per year. The nucleotide substitutions in the genome suggest that the transition rate is about 17 times faster than the transversion rate.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00556356
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  • 3
    Electronic Resource
    Electronic Resource
    Evolution of Mhc–DRB Introns: Implications for the Origin of Primates (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 663-674 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Major histocompatibility complex (Mhc) — Intron evolution — Primate origin — Mammalian evolution — Scandentia — Chiroptera —DRB genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006510
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  • 4
    Electronic Resource
    Electronic Resource
    Evolutionary relationship ofHLA-DRB genes inferred from intron sequences (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 648-657 
    Details
    ISSN: 1432-1432
    Keywords: Major histocompatibility complex (Mhc) ; HumanMhc (HLA) ; DRB genes ; Gene duplication ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The major histocompatibility complex (Mhc) consists of class I and class II genes. In the humanMhc (HLA) class II genes, nineDRB loci have been identified. To elucidate the origin of these duplicated loci and allelic divergences at the most polymorphicDRBI locus, introns 4 and 5 as well as the 3′ untranslated region (altogether approximately 1,000 base pairs) of sevenHLA-DRB loci, threeHLA-DRBI alleles, and nine nonhuman primateDRB genes were examined. It is shown that there were two major diversification events inHLA-DRB genes, each involving gene duplications and allelic divergences. Approximately 50 million years (my) ago,DRBI *04 and an ancestor of theDRB1 *03 cluster (DRBI *03, DRBI*15, andDRB3) diverged from each other andDRB5, DRB7, DRB8, and an ancestor of theDRB2 cluster (DRB2, DRB4, andDRB6) arose by gene duplication. Later, about 25 my ago,DRBI *15 diverged fromDRBI*03, andDRB3 was duplicated fromDRBI *03. Then, some 20 my ago, the lineage leading to theDRB2 cluster produced two new loci,DRB4 andDRB6. TheDRBI *03 andDRBI *04 allelic lineages are extraordinarily old and have persisted longer than some duplicated genes. The orthologous relationships ofDRB genes between human and Old World monkeys are apparent, but those between Catarrhini and New World monkeys are equivocal because of a rather rapid expansion and contraction of primateDRB genes by duplication and deletion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02338798
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  • 5
    Electronic Resource
    Electronic Resource
    Footprints of intragenic recombination at HLA loci (1998)
    Springer
    Immunogenetics 47 (1998), S. 430-441 
    Details
    ISSN: 1432-1211
    Keywords: Key words Linkage ; Balancing selection ; Neutral polymorphism ; Allelic lineages
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  To evaluate the effect of balancing selection and intragenic recombination (or gene conversion) at six individual HLA loci, synonymous nucleotide diversity in different exon groups is examined within (πw) and between (πb) allelic lineages that may be defined by either serological or DNA sequence differences. Both π values are high in exons which encode for the peptide binding region (PBR) and tend to decrease in other exons. The value of πw is significantly smaller than that of πb in any exon of any locus. However, even πw is much greater than nucleotide diversity at non-HLA loci. These observations provide additional strong evidence for the operation of balancing selection in PBR-encoding exons and its indirect effects on polymorphism at linked neighboring regions. It appears that allelic lineages have generally evolved in isolation but the linkage relationships within and between exons are incomplete throughout the long evolutionary history. To quantify intragenic recombination and account for the large discrepancy between the HLA and non-HLA diversity, a population genetics model is analyzed with special reference to the evolution of modern humans. The analysis suggests that the recombination rate between two sites 1000 base pairs apart is about 10–5 per generation and that the effective size of human populations (equivalent roughly to the number of breeding individuals in a randomly mating population) has dropped from 105 to 104 in most of the Quaternary. One possibility for this reduction is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050380
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  • 6
    Electronic Resource
    Electronic Resource
    Mhc class II B gene evolution in East African cichlid fishes (2000)
    Springer
    Immunogenetics 51 (2000), S. 556-575 
    Details
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex ; Haplochromines ; Convergent evolution ; Gene conversion ; Oreochromis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  A distinctive feature of essential major histocompatibility complex (Mhc) loci is their polymorphism characterized by large genetic distances between alleles and long persistence times of allelic lineages. Since the lineages often span several successive speciations, we investigated the behavior of the Mhc alleles during or close to the speciation phase. We sequenced exon 2 of the class II B locus 4 from 232 East African cichlid fishes representing 32 related species. The divergence times of the (sub)species ranged from 6000 to 8.4 million years. Two types of evolutionary analysis were used to elucidate the pattern of exon 2 sequence divergence. First, phylogenetic methods were applied to reconstruct the most likely evolutionary pathways leading from the last common ancestor of the set to the extant sequences, and to assess the probable mechanisms involved in allelic diversification. Second, pairwise comparisons of sequences were carried out to detect differences seemingly incompatible with origin by nonparallel point mutations. The analysis revealed point mutations to be the most important mechanism behind allelic divergences, with recombination playing only an auxiliary part. Comparison of sequences from related species revealed evidence of random allelic (lineage) losses apparently associated with speciation. Sharing of identical alleles could be demonstrated between species that diverged 2 million years ago. The phylogeny of the exon was incongruent with that of the flanking introns, indicating either a high degree of convergent evolution at the peptide-binding region-encoding sites, or intron homogenization.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510000181
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  • 7
    Electronic Resource
    Electronic Resource
    Some comments on calibration of molecular evolutionary rates (1992)
    Springer
    Immunogenetics 36 (1992), S. 126-129 
    Details
    ISSN: 1432-1211
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00215290
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  • 8
    Electronic Resource
    Electronic Resource
    How the ratio of nonsynonymous to synonymous pseudogene substitutions can be less than one (1993)
    Springer
    Immunogenetics 38 (1993), S. 450-454 
    Details
    ISSN: 1432-1211
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00184527
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  • 9
    Electronic Resource
    Electronic Resource
    Evolutionary history and mechanism of the Drosophila Cecropin gene family (1998)
    Springer
    Immunogenetics 47 (1998), S. 417-429 
    Details
    ISSN: 1432-1211
    Keywords: Key words Antibacterial peptides ; Gene turnover ; Introgression ; Intragenic recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Upon bacterial infection, insects secrete a set of synthesized antibacterial proteins into the hemolymph and initiate synergistic destruction of invaders. Cecropin is one such antibacterial protein which is also found in vertebrates. To study the evolutionary history and mechanism of the Cecropin gene family, we determined DNA sequences of one isogenic In(3R)C and six isofemale lines of Drosophila melanogaster as well as one line of D. simulans and of D. yakuba. The phylogenetic analysis of these sequences together with those published for D. virilis and Sarcophaga peregrina reveals frequent gene re-organization. It was also found that silent nucleotide differences within D. melanogaster are quite heterogeneous across the gene region of approximately 3 kilobases and the extent of polymorphism is unusually usually high. These data suggest that the Cecropin gene region of D. melanogaster underwent intragenic recombination as well as introgression from a closely related sibling species, D. simulans.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050379
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  • 10
    Electronic Resource
    Electronic Resource
    Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway (2006)
    [s.l.] : Nature Publishing Group
    Nature genetics 38 (2006), S. 158-167 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The mammalian Y chromosome has unique characteristics compared with the autosomes or X chromosomes. Here we report the finished sequence of the chimpanzee Y chromosome (PTRY), including 271 kb of the Y-specific pseudoautosomal region 1 and 12.7 Mb of the male-specific region of the Y chromosome. ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng1729
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