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  • 1
    Electronic Resource
    Electronic Resource
    Protein Tyrosine Phosphatases from Amphioxus, Hagfish, and Ray: Divergence of Tissue-Specific Isoform Genes in the Early Evolution of Vertebrates (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 302-311 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Protein tyrosine phosphatase — Amphioxus — Hagfish — Ray — Tissue-specific isoform — Gene duplication — Phylogenetic tree — Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Since separation from fungi and plants, multicellular animals evolved a variety of gene families involved in cell–cell communication from a limited number of ancestral precursors by gene duplications in two separate periods of animal evolution. In the very early evolution of animals before the separation of parazoans and eumetazoans, animals underwent extensive gene duplications by which different subtypes (subfamilies) with distinct functions diverged. The multiplicity of members (isoforms) in the same subtype increased by further gene duplications (isoform duplications) in the first half of chordate evolution before the fish–tetrapod split; different isoforms are virtually identical in structure and function but differ in tissue distribution. From cloning and phylogenetic analyses of four subfamilies of the protein tyrosine kinase (PTK) family, we recently showed extensive isoform duplications in a limited period around or just before the cyclostome–gnathostome split. To obtain a reliable estimate for the divergence time of vertebrate isoforms, we have conducted isolation of cDNAs encoding the protein tyrosine phosphatases (PTPs) from Branchiostoma belcheri, an amphioxus, Eptatretus burgeri, a hagfish, and Potamotrygon motoro, a ray. We obtained 33 different cDNAs in total, most of which belong to known PTP subfamilies. The phylogenetic analyses of five subfamilies based on the maximum likelihood method revealed frequent isoform duplications in a period around or just before the gnathostome–cyclostome split. An evolutionary implication was discussed in relation to the Cambrian explosion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910035
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  • 2
    Electronic Resource
    Electronic Resource
    Maximum likelihood inference of protein phylogeny and the origin of chloroplasts (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 151-160 
    Details
    ISSN: 1432-1432
    Keywords: Evolutionary tree ; Amino acid sequence ; Insertion/deletion ; Bootstrap probability ; psbA ; Prochlorothrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but also insertion/deletion events during evolution were incorporated into the Markov model. A simple method for estimating a bootstrap probability for the maximum likelihood tree among alternatives without performing a maximum likelihood estimation for each resampled data set was developed. These methods were applied to amino acid sequence data of a photosynthetic membrane protein,psbA, from photosystem II, and the phylogeny of this protein was discussed in relation to the origin of chloroplasts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109483
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  • 3
    Electronic Resource
    Electronic Resource
    Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 380-388 
    Details
    ISSN: 1432-1432
    Keywords: Entamoeba histolytica ; Protozoa lacking mitochondria ; Eukaryotic kingdoms ; Elongation factor-1α ; Maximum likelihood ; Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading—especially when G+C content differs widely among lineages—and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1α by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182185
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  • 4
    Electronic Resource
    Electronic Resource
    Compartmentalized isozyme genes and the origin of introns (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 205-210 
    Details
    ISSN: 1432-1432
    Keywords: Isozyme ; Intron ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (=1.3×10−3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109497
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  • 5
    Electronic Resource
    Electronic Resource
    Interchromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 181-183 
    Details
    ISSN: 1432-1432
    Keywords: ZFY ; Sex chromosome ; Evolutionary rate ; Gene conversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The divergence pattern of mammalian ZFY-related genes from human (ZFY and ZFX) and mouse (Zfy-1 and Zfx) was reexamined on the basis of nucleotide substitutions at the synonymous codon-alternating positions. It is possible to explain the unusual divergence pattern of the mammalian Y-linked ZF genes by interchromosomal gene conversion by X-linked ZF genes. Furthermore, the rates of evolution of mammalian X- and Y-linked ZF genes were shown to agree well with those expected from our model.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00183228
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  • 6
    Electronic Resource
    Electronic Resource
    Multiple Protein Tyrosine Phosphatases in Sponges and Explosive Gene Duplication in the Early Evolution of Animals Before the Parazoan–Eumetazoan Split (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 654-662 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Protein tyrosine phosphatase — Classification — Sponge — Gene duplication — Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Protein tyrosine phosphatases (PTPs) regulate various physiological events in animal cells. They comprise a diverse family which are classified into two categories, receptor type and nonreceptor type. From the domain organization and phylogenetic tree, we have classified known PTPs into 17 subtypes (9 receptor-type and 8 nonreceptor-type PTPs) which are characterized by different organization of functional domain and independent cluster in tree. The receptor type PTPs are thought to be implicated in cell–cell adhesion by association of cell adhesion molecules. Since sponges are the most primitive multicellular animals and are thought to be lacking cell cohesiveness and coordination typical of eumetazoans, cloning and sequencing of PTP cDNAs of Ephydatia fluviatilis (freshwater sponge) have been conducted by RT-PCR to determine whether or not sponges have PTP genes in their genomes. We have isolated nine PTPs, of which five are possibly receptor type. A phylogenetic tree including the sponge PTPs revealed that most of the gene duplications that gave rise to the 17 subtypes had been completed in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among extant animal phyla. The family tree also revealed the rapid evolutionary rate of PTP subtypes in the early stage of animal evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006509
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  • 7
    Electronic Resource
    Electronic Resource
    Extensive Gene Duplication in the Early Evolution of Animals Before the Parazoan–Eumetazoan Split Demonstrated by G Proteins and Protein Tyrosine Kinases from Sponge and Hydra (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 646-653 
    Details
    ISSN: 1432-1432
    Keywords: Key words: G protein — Tyrosine kinase — Sponge — Gene duplication — Cambrian explosion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. To know whether genes involved in cell–cell communication typical of multicellular animals dramatically increased in concert with the Cambrian explosion, the rapid evolutionary burst in the major groups of animals, and whether these genes exist in the sponge lacking cell cohesiveness and coordination typical of eumetazoans, we have carried out cloning of the G-protein α subunit (Gα) and the protein tyrosine kinase (PTK) cDNAs from Ephydatia fluviatilis (freshwater sponge) and Hydra magnipapillata strain 105 (hydra). We obtained 13 Gα and 20 PTK cDNAs. Generally animal gene families diverged first by gene duplication (subtype duplication) that gave rise to diverse subtypes with different primary functions, followed by further gene duplication in the same subtype (isoform duplication) that gave rise to isoform genes with virtually identical function. Phylogenetic trees of Gα and PTK families including cDNAs from sponge and hydra revealed that most of the present-day subtypes had been established in the very early evolution of animals before the parazoan–eumetazoan split, the earliest branching among the extant animal phyla, by extensive subtype duplication: for PTK and Gα families, 23 and 9 subtype duplications were observed in the early stage before the parazoan–eumetazoan split, respectively, and after that split, only 2 and 1 subtype duplications were found, respectively. After the separation from arthropods, vertebrates underwent frequent isoform duplications before the fish–tetrapod split. Furthermore, rapid amino acid changes appear to have occurred in concert with the extensive subtype duplication and isoform duplication. Thus the pattern of gene diversification during animal evolution might be characterized by bursts of gene duplication interrupted by considerably long periods of silence, instead of proceeding gradually, and there might be no direct link between the Cambrian explosion and the extensive gene duplication that generated diverse functions (subtypes) of these families.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006508
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  • 8
    Electronic Resource
    Electronic Resource
    Two types of amino acid substitutions in protein evolution (1979)
    Springer
    Journal of molecular evolution 12 (1979), S. 219-236 
    Details
    ISSN: 1432-1432
    Keywords: Amino acid substitution ; Physico-chemical difference ; Conservative ; Low-constraint ; Protein evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The frequency of amino acid substitutions, relative to the frequency expected by chance, decreases linearly with the increase in physico-chemical differences between amino acid pairs involved in a substitution. This correlation does not apply to abnormal human hemoglobins. Since abnormal hemoglobins mostly reflect the process of mutation rather than selection, the correlation manifest during protein evolution between substitution frequency and physico-chemical difference in amino acids can be attributed to natural selection. Outside of ‘abnormal’ proteins, the correlation also does not apply to certain regions of proteins characterized by rapid rates of substitution. In these cases again, except for the largest physico-chemical differences between amino acid pairs, the substitution frequencies seem to be independent of the physico-chemical parameters. The limination of the substituents involving the largest physicochemical differences can once more be attributed to natural selection. For smaller physico-chemical differences, natural selection, if it is operating in the polypeptide regions, must be based on parameters other than those examined.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732340
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular clock of silent substitution: At least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 28-35 
    Details
    ISSN: 1432-1432
    Keywords: Synonymous substitution ; Uniform Rate of Evolution ; Rapid Evolution of mtDNA ; Ck Gene of b4 Rabbit
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary For each of eleven different types of nuclear genes, comparisons of the protein coding sequences were made between human, mouse and rat pairwisely, and the evolutionary rate of silent substitution, v S nucl. , was estimated. It is shown that the v S nucl. is not only very high (=5.37×10−9/site/yr), but also approximately uniform for different genes regardless of the types, which confirms our previous results (Miyata et al. 1980b). This is in sharp contrast to the rate of protein evolution which differes greatly from protein to protein. Furthermore the v S nucl. is shown to be approximately constant with respect to different divergence times, at least within a short time period (≤75 Myr). Based on these observations, we propose a new molecular clock which has several advantages over a protein clock. Using this clock, we show that the rate of amino acid replacement in the immunoglobulin Ck gene of b4 rabbit is unexpectedly high, almost comparable to the rate of silent changes. This rate may be the highest one for protein evolution that we know so far. We further examine the rate of silent substitutions in mitochondrial genes comparing mouse and rat. Surprisingly the rate is extremely high (≥35×10−9/site/yr), at least 6-times as high as the corresponding rate of nuclear genes. Based on the estimate, we discuss a possible origin of the rapid rate found in mitochondrial DNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100221
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  • 10
    Electronic Resource
    Electronic Resource
    Evolutionary changes of nucleotide sequences of papova viruses BKV and SV40: They are possibly hybrids (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 72-79 
    Details
    ISSN: 1432-1432
    Keywords: Sequence Difference ; Recombination ; Overlapping genes ; Functional constraint
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Complete nucleotide sequences were compared between papova viruses BKV and SV40 and the degrees of sequence divergences were compared between structurally and/or functionally different segments or genes in details. It was shown that the rate of synonymous substitution is not only very high but also approximately uniform among different genes in these viruses as in eukaryotic genes examined to date. While all the non-coding regions including the intron showed marked sequence preservation which is in sharp contrasted with the case of eukaryotic genes where the large bulk of non-coding regions evolve at a rate as rapidly as that of synonymous substitution. It is remarkable that a long continuous stretch of sequence including the putative VPX gene and a 5′ half of VP2 gene showed strong homology between BKV and SV40. A close examination of the pattern of base substitutions revealed that this unusual homology was derived by recombination between the two viruses during their evolution. On the basis of the pattern of base substitutions and the bias in code word utilization, we also showed that the putative VPX gene actually could code for a functional polypeptide. In papova viruses, the 3′ terminal sequence of VP2/3 gene overlaps with the 5′ terminal sequence of VPI gene. The pattern of base substitutions in the overlapping segment was examined in detail in comparison with those in the non-overlapping portions of VP2/3 and VP1 genes. It was shown that the evolutionary mode of the overlapping genes is in good agreement with our previous prediction.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100225
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