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  • 1
    Electronic Resource
    Electronic Resource
    Comparative Evolutionary Rates of Introns and Exons in Murine Rodents (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 125 -130 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Exons — Introns — Murine rodents — Nucleotide content — Nucleotide substitution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Analysis of DNA sequences of 132 introns and 140 exons from 42 pairs of orthologous genes of mouse and rat was used to compare patterns of evolutionary change between introns and exons. The mean of the absolute difference in length (measured in base pairs) between the two species was nearly five times as high in the case of introns as in the case of exons. The average rate of nucleotide substitution in introns was very similar to the rate of synonymous substitution in exons, and both were about three times the rate of substitution at nonsynonymous sites in exons. G+C content of introns and exons of the same gene were correlated; but mean G+C content at the third positions of exons was significantly higher than that of introns or positions 1–2 of exons from the same gene. G+C content was conserved over evolutionary time, as indicated by strong correlations between mouse and rat; but the change in G+C content was greatest at position 3 of exons, intermediate in introns, and lowest at positions 1–2 in introns.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006211
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  • 2
    Electronic Resource
    Electronic Resource
    Coordinated Amino Acid Changes in the Evolution of Mammalian Defensins (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. 675 -682 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Mammalian defensin — Amino acid — Propiece
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The mammalian defensin molecule is a short, highly cationic peptide cytotoxic to both microbial and mammalian cells which is cleaved from a precursor including a signal peptide and a highly anionic propiece. A phylogenetic analysis of 28 complete sequences from five mammalian species (mouse, rat, guinea pig, rabbit, and human) showed species-specific clusters of sequences, indicating that the genes duplicated after divergence of these species. Comparison of rates of synonymous and nonsynonymous nucleotide substitution suggested that gene duplication has often been followed by a period in which diversification of the mature defensins at the amino acid level has been selectively favored. In some comparisons, it appeared that amino acid differences in this region have appeared in a nonrandom fashion so as to change the pattern of residue charges. Because it has been hypothesized that the negative charge in the propiece serves to balance the positive charge in the mature defensin and thus to prevent cytotoxicity prior to cleavage, we used a maximum likelihood method of reconstructing ancestral states in order to test whether this balance has been maintained over evolutionary time in spite of rapid diversification of the mature defensin at the amino acid level. Reconstructed ancestral sequences always maintained a charge balance between mature defensin and propiece, and changes in the net positive charge of the mature defensin were balanced by corresponding changes in the propiece. The results support the hypothesis that, in the evolution of these proteins, amino acid changes have occurred in a coordinated fashion so as to preserve an adaptive phenotype.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006191
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  • 3
    Electronic Resource
    Electronic Resource
    Gene duplication and recombination in the evolution of mammalian Fc receptors (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 4-10 
    Details
    ISSN: 1432-1432
    Keywords: Fc receptors ; Gene duplication ; Gene recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The immunoglobulin-related chains of cell-surface receptors for the Fc region of immunoglobulins (FCERIα, FcγRI, FcγRII, and FcγRIIIα) are encoded by members of a gene family. Phylogenetic analysis of representative members of this family from mammals revealed that FcγRIIIα genes of human, mouse, and rat are not orthologous to one another in the region of the gene encoding the Immunoglobulin C2-set domains. In phylogenetic trees of this region, FcγRIIIα and FcγRII clustered together. However, in trees based on both coding and noncoding regions 5′ and 3′ to the C2 domains, FcγRIIIα genes of human, mouse, and rat clustered together. This pattern of relationship is most easily explained as a result of two independent recombinational events occurring in the mouse and rat after these two species diverged, in each of which the exons encoding the C2 domains were donated to an FcγRIIIα gene by an FcγRII gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02352293
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  • 4
    Electronic Resource
    Electronic Resource
    Adaptive evolution in the rat olfactory receptor gene family (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 249-254 
    Details
    ISSN: 1432-1432
    Keywords: Adaptive evolution ; Olfactory receptor ; Multigene families
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Comparison of DNA sequences of the rat (Rattus norvegicus) olfactory receptor gene family revealed an unusual pattern of nucleotide substitution in the gene region encoding the second extracellular domain (E2) of the protein. In this domain, nonsynonymous nucleotide differences between members of this subfamily that caused a change in amino acid residue polarity were over four times more frequent than nonsynonymous differences that did not cause a polarity change. This nonrandom pattern of nucleotide substitution is evidence of past directional selection favoring diversification of the E2 domain among members of this subfamily. This in turn suggests that E2 may play some important role in the functions unique to each member of the olfactory receptor family, and that it may perhaps be an odorant binding domain.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160480
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  • 5
    Electronic Resource
    Electronic Resource
    Phylogenies of Developmentally Important Proteins Do Not Support the Hypothesis of Two Rounds of Genome Duplication Early in Vertebrate History (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 565-576 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Gene duplication — Genome duplication — Vertebrates — Evolution of development — Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. It has been proposed that two rounds of duplication of the entire genome (polyploidization) occurred early in vertebrate history (the 2R hypothesis); and the observation that certain gene families important in regulating development have four members in vertebrates, as opposed to one in Drosophila, has been adduced as evidence in support of this hypothesis. However, such a pattern of relationship can be taken as support of the 2R hypothesis only if (1) the four vertebrate genes can be shown to have diverged after the origin of vertebrates, and (2) the phylogeny of the four vertebrate genes (A–D) exhibits a topology of the form (AB) (CD), rather than (A) (BCD). In order to test the 2R hypothesis, I constructed phylogenies for nine protein families important in development. Only one showed a topology of the form (AB) (CD), and that received weak statistical support. In contrast, four phylogenies showed topologies of the form (A) (BCD) with statistically significant support. Furthermore, in two cases there was significant support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes: in one case there was significant support for duplication of the vertebrate genes at least prior to the divergence of vertebrates and urochordates, and in one case there was weak support for duplication of the vertebrate genes prior to the divergence of deuterostomes and protostomes. Taken together with other recently published phylogenies of developmentally important genes, these results provide strong evidence against the 2R hypothesis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006499
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  • 6
    Electronic Resource
    Electronic Resource
    Evolution of the interleukin-1 gene family in mammals (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 6-12 
    Details
    ISSN: 1432-1432
    Keywords: Mammals ; Gene family ; Interleukin-1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogeny of interleukin-1 family genes shows that human interleukin-1α (IL-1α) is more closely related to IL-1α of the bovine than to IL-1α of the mouse, whereas human interleukin-1β (IL-1β) is more closely related to IL-1α of the mouse than to IL-1β of the bovine. The IL-1 receptor antagonist (IL-1α) shows homology to the C-terminal region of both IL-1α and IL-1β. In the C-terminal region, the IL-1α genes of human and mouse have diverged more from each other at nonsynonymous sites than have either IL-1β or IL-1α; because the same pattern is not seen at synonymous sites, it must be due not to a difference in mutation rate but rather to a greater degree of functional constraint on this region in the IL-1β and IL-1α proteins than in the IL-1α protein. But synonymous sites in IL-1β of mouse have evolved more rapidly than in IL-1β of human, indicating a higher rate of mutation in the former gene. In the N-terminal region of the protein, nonsynonymous sites have evolved at similar rates in IL-1α and IL-1β. The first exon of the IL-1α gene, which encodes the leader peptide, shows evidence of homology with the first exon of IL-1β, which is not translated. Thus, it seems likely that IL-1α evolved by duplication of an IL-1β gene and loss of expression of exons 2–4.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178244
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  • 7
    Electronic Resource
    Electronic Resource
    Evolution of the src-Related Protein Tyrosine Kinases (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 247-256 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Tyrosine kinases — Protein — Phylogenetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A phylogenetic analysis of src-related protein tyrosine kinases (PTKs) showed that one group of these genes is quite ancient in the animals, its divergence predating the divergence of the diploblast and triploblast phyla. Three other major groupings of genes were found to predate the divergence of protostome and deuterostome phyla. Most known src-related PTKs of mammals were found to belong to five well-differentiated families: srcA, srcB, abl, csk, and tec. One srcA gene (fyn) has an alternatively spliced seventh exon which shows a different pattern of relationship from the remainder of the gene; this suggests that this exon may have been derived by a recombinational event with another gene, perhaps one related to fgr. The recently published claim that mammalian members of this family expressed in the nervous system evolve more slowly at nonsynonymous nucleotide sites than do those expressed in the immune system was not supported by an analysis of 13 pairs of human and mouse orthologues. Rather, T-cell-specific src-related PTKs were found to have higher rates of nonsynonymous substitution than were those having broader expression. This effect was particularly marked in the peptide binding site of the SH2 domain. While the SH2 binding site was highly conserved among paralogous mammalian members of the srcA and srcB subfamilies, no such effect was seen in the comparison of paralogous members of the csk and tec subfamilies. This suggests that, while the peptide binding function of SH2 is conserved within both srcA and srcB subfamilies, paralogous members of the csk and tec subfamilies have diverged functionally with respect to peptide recognition by SH2.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198851
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  • 8
    Electronic Resource
    Electronic Resource
    A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 117-123 
    Details
    ISSN: 1432-1432
    Keywords: Alu sequence ; Retrotransposon ; SINES ; Repetitive DNA ; Collagen gene ; Polymorphism ; Population studies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Alu elements are a class of repetitive DNA sequences found throughout the human genome that are thought to be duplicated via an RNA intermediate in a process termed retroposition. Recently inserted Alu elements are closely related, suggesting that they are derived from a single source gene or closely related source genes. Analysis of the type III collagen gene (COL3A1) revealed a polymorphic Alu insertion in intron 8 of the gene. The Alu insertion in the COL3A1 gene had a high degree of nucleotide identity to the Sb family of Alu elements, a family of older Alu elements. The Alu sequence was less similar to the consensus sequence for the PV or Sb2 subfamilies, subfamilies of recently inserted Alu elements. These data support the observations that at least three source genes are active in the human genome, one of which is distinct from the PV and Sb2 subfamilies and predates either of these two subfamilies. Appearance of the Alu insertion in different ethnic populations suggests that the insertion may have occurred in the last 100,000 years. This Alu insert should be a useful marker for population studies and for marking COL3A1 alleles.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198836
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  • 9
    Electronic Resource
    Electronic Resource
    Evolution of thesrc-related protein tyrosine kinases (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 247-256 
    Details
    ISSN: 1432-1432
    Keywords: Tyrosine kinases ; Protein ; Phylogenetic analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A phylogenetic analysis ofsrc-related protein tyrosine kinases (PTKs) showed that one group of these genes is quite ancient in the animals, its divergence predating the divergence of the diploblast and triploblast phyla. Three other major groupings of genes were found to predate the divergence of protostome and deuterostome phyla. Most knownsrc-related PTKs of mammals were found to belong to five well-differentiated families: srcA, srcB, abl, csk, and tec. One srcA gene (fyn) has an alternatively spliced seventh exon which shows a different pattern of relationship from the remainder of the gene; this suggests that this exon may have been derived by a recombinational event with another gene, perhaps one related tofgr. The recently published claim that mammalian members of this family expressed in the nervous system evolve more slowly at nonsynonymous nucleotide sites than do those expressed in the immune system was not supported by an analysis of 13 pairs of human and mouse orthologues. Rather, T-cell-specificsrc-related PTKs were found to have higher rates of nonsynonymous substitution than were those having broader expression. This effect was particularly marked in the peptide binding site of the SH2 domain. While the SH2 binding site was highly conserved among paralogous mammalian members of the srcA and srcB subfamilies, no such effect was seen in the comparison of paralogous members of the csk and tec subfamilies. This suggests that, while the peptide binding function of SH2 is conserved within both srcA and srcB subfamilies, paralogous members of the csk and tec subfamilies have diverged functionally with respect to peptide recognition by SH2.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198851
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  • 10
    Electronic Resource
    Electronic Resource
    Comparative Evolutionary Rates of Introns and Exons in Murine Rodents (1998)
    Springer
    Journal of molecular evolution 46 (1998), S. 497-497 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006330
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