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PubMed1979

Calculation of evolutionary trees from sequence data.

Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular for the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences.

Amino Acid Sequence↗
PubMed1982

Overlapping evolutionary affinities revealed by comparison of amino acid compositions.

Comparison of the amino acid compositions of purified proteins indicates the presence of overlapping evolutionary affinities among enzymes of the beta-ketoadipate pathway. Isofunctional enzymes from different bacterial genera share a common evolutionary origin. Moreover, enzymes that mediate isofunctional or chemically analogous reactions within an organism appear to be evolutionarily homologous. Most remarkably, closely similar amino acid compositions are found in enzymes that mediate the following consecutive metabolic steps: lactonization, decarboxylation, hydrolysis, and transfer of a thioester bond.

Adipates↗
PubMed1983

Unusual evolutionary conservation and frequent DNA segment exchange in class I genes of the major histocompatibility complex.

From comparisons of homologous DNA sequences for many different genes, it was shown that the silent positions of protein-encoding regions and introns evolve at high and remarkably similar rates for different genes. In addition, both silent positions and introns behave like clocks; they accumulated base substitutions at approximately constant rates with respect to geological time. The rates of evolution were estimated to be 5.5 X 10(-9), 3.7 X 10(-9), and 5.3 X 10(-9) per site per year for silent positions, short introns (less than approximately equal to 300 base pairs), and long introns (more than approximately equal to 500 base pairs), respectively. Contrary to expectation from the evolutionary clocks, DNA sequence comparison between pHLA 12.4 (a cloned HLA sequence) of man and Ld together with other H-2 genes of mouse, the class I genes of the major histocompatibility complex, revealed a surprisingly small amount of base substitution for both the introns and the silent positions; the degree of divergence is only about 60% of that of standard genes in the same species comparison. Furthermore, several segmental homologies have been observed between the class I genes of mouse, suggesting the frequent occurrence of gene conversion or double unequal crossing-over in evolution. Interrelations between the extreme polymorphism of the class I genes, the low evolutionary drift of the introns and the silent positions, and the frequent gene conversion or unequal crossing-over within the mouse genes are discussed.

Animals↗
PubMed1985

Intron sequences reveal evolutionary relationships among major histocompatibility complex class I genes.

The multigene family of the class I histocompatibility antigens is unusual in that allelic and intergenic differences often are of equal magnitude. It has been suggested that this is due to gene conversion events, which would produce allelic variation but at the same time reduce intergenic differences. We compared the sequences of 11 class I genes in an attempt to elucidate the evolutionary history of this gene family. Our analysis shows that the intron sequences can be used to establish the order of divergence of various class I genes from each other. The results obtained agree with the order of divergence deduced from major insertion and deletion events. It appears that certain genes in the murine TL antigen-encoding region diverged very early from the H-2 and Qa-2,3 genes. The latter can be subgrouped as H-2 and Qa-2,3 genes by both sequence homology and insertion patterns. In contrast to the introns, exon sequences provide less information on evolutionary relationships. Thus, these analyses are consistent with the view that concerted evolution due to gene conversion occurs preferentially in exons.

Animals↗
PubMed1987

The lens protein alpha A-crystallin of the blind mole rat, Spalax ehrenbergi: evolutionary change and functional constraints.

The complete structure of the single-copy alpha A-crystallin gene of the blind mole rat (Spalax ehrenbergi) has been determined in order to elucidate the evolutionary effects of the loss of vision on a lens-specific protein and its gene. The alpha A-crystallin gene appears to have all the necessary transcriptional and translational signal sequences to be expressed in the rudimentary lens of the mole rat and gives rise to probably two protein products by means of alternative splicing, as in rodents with normal vision. Comparisons of the blind mole rat alpha A-crystallin sequence with alpha A sequences from other rodents reveal a considerable acceleration of the substitution rate at nonsynonymous positions in the mole rate lineage, which reflects a relaxation of selective constraints, but the acceleration is not to the extent that might be expected if the gene were now without any function. The remaining evolutionary constraints still imposed upon the mole rat alpha A-crystallin gene may possibly reflect the need for alpha-crystallin expression as an indispensable component in the developmental program of the atrophied eye.

Amino Acids↗
PubMed1987

Evolutionary changes in the developmental expression of silkmoth chorion genes and their morphological consequences.

Discrete changes in silkmoth choriogenesis have occurred during evolution, as exemplified in the present report in Antheraea polyphemus and Hyalophora cecropia. At the level of morphology, the chorion of A. polyphemus has surface structures, called aeropyle crowns, that are absent from H. cecropia. Aeropyle crowns form during the very late period of choriogenesis and consist of two substructures--lamellae and filler. Filler is present in H. cecropia in greatly reduced amounts. At the level of protein synthesis, overall similarities in the two species are maintained until the very late period of choriogenesis, when synthesis of aeropyle crown components is maximal. In H. cecropia, very late period-specific proteins are reduced in number and abundance. Several of these minor proteins are candidates for E1 and E2, the components of filler. E1 and E2 RNAs are about 35 times more abundant in A. polyphemus, despite very similar gene copy numbers and times of expression in the two species. These results support the hypothesis that evolutionary changes in chorion morphology have resulted from regulatory changes in the expression of chorion genes, either at the level of transcription or mRNA decay. The hypothesis that evolutionary changes in chorion morphology are based on terminal addition onto a preexisting developmental program is discussed.

Animals↗
PubMed1987

Evolutionary relationship between the natural anti-Gal antibody and the Gal alpha 1----3Gal epitope in primates.

Anti-Gal is a natural antibody, which constitutes as much as 1% of circulating IgG in humans and displays a distinct specificity for the structure Gal alpha 1----3Gal. This glycosidic structure has been found on various tissues of many nonprimate mammals. A comparative study of the occurrence of anti-Gal versus the expression of the Gal alpha 1----3Gal epitope was performed in primates, and a distinct evolutionary pattern was observed. Whereas anti-Gal was found to be present in Old World monkeys and apes in titers comparable to those in humans, its corresponding antigenic epitope is abundantly expressed on erythrocytes of New World monkeys. Immunostaining with anti-Gal of glycolipids from New World monkey erythrocytes indicated that the molecules to which anti-Gal binds are similar to those found in rabbit and bovine erythrocytes. These findings indicate that there is an evolutionary reciprocity between New World and Old World primates in the production of the Gal alpha 1----3Gal structure and the antibody that recognizes it. The expression of the Gal alpha 1----3Gal epitope was evolutionarily conserved in New World monkeys, but it was suppressed in ancestral lineages of Old World primates. The suppression of this epitope was accompanied by the production of anti-Gal. The observed in vivo binding of anti-Gal to human normal senescent and some pathologic erythrocytes implies that the Gal alpha 1----3Gal epitope is present in man in a cryptic form.

Animals↗
PubMed1989

On the evolutionary origin of the plant mitochondrion and its genome.

Higher plants occupy very different positions in the mitochondrial and nuclear lineages of global phylogenetic trees based on conserved regions of small subunit (SSU) and large subunit (LSU) rRNA sequences. In the nuclear subtree, plants branch off late, at a position reflecting a massive radiation of the major multicellular (and some unicellular) groups; in the mitochondrial subtree, in contrast, plants branch off early, near the point of connection between the mitochondrial and eubacterial lineages. Moreover, in the nuclear lineage, plants branch together with the unicellular green alga Chlamydomonas reinhardtii, whereas in the mitochondrial lineage (in both SSU and LSU trees), metaphytes and chlorophyte branch separately. Statistical evaluation indicates that the anomalous branching position of higher plants in the mitochondrial lineage is not a treeing artifact attributable to the relatively rapid rate of sequence divergence of non-plant mitochondrial rRNA sequences. In considering alternative biological explanations for these results, we are led to propose that the rRNA genes in plant mitochondria may be of more recent evolutionary origin than the rRNA genes in other mitochondria. This proposal has implications for monophyletic vs. polyphyletic scenarios of mitochondrial origin and is consistent with other evidence indicating that plant mtDNA is an evolutionary mosaic.

Journal Article↗
PubMed1994

rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.

Pteriodophytes have a longer evolutionary history than any other vascular land plant and, therefore, have endured greater loss of phylogenetically informative information. This factor has resulted in substantial disagreements in evaluating characters and, thus, controversy in establishing a stable classification. To compare competing classifications, we obtained DNA sequences of a chloroplast gene. The sequence of 1206 nt of the large subunit of the ribulose-bisphosphate carboxylase gene (rbcL) was determined from 58 species, representing almost all families of leptosporangiate ferns. Phlogenetic trees were inferred by the neighbor-joining and the parsimony methods. The two methods produced almost identical phylogenetic trees that provided insights concerning major general evolutionary trends in the leptosporangiate ferns. Interesting findings were as follows: (i) two morphologically distinct heterosporous water ferns, Marsilea and Salvinia, are sister genera; (ii) the tree ferns (Cyatheaceae, Dicksoniaceae, and Metaxyaceae) are monophyletic; and (iii) polypodioids are distantly related to the gleichenioids in spite of the similarity of their exindusiate soral morphology and are close to the higher indusiate ferns. In addition, the affinities of several "problematic genera" were assessed.

Base Sequence↗
PubMed1995

An evolutionary theory of the family.

An evolutionary framework for viewing the formation, the stability, the organizational structure, and the social dynamics of biological families is developed. This framework is based upon three conceptual pillars: ecological constraints theory, inclusive fitness theory, and reproductive skew theory. I offer a set of 15 predictions pertaining to living within family groups. The logic of each is discussed, and empirical evidence from family-living vertebrates is summarized. I argue that knowledge of four basic parameters, (i) genetic relatedness, (ii) social dominance, (iii) the benefits of group living, and (iv) the probable success of independent reproduction, can explain many aspects of family life in birds and mammals. I suggest that this evolutionary perspective will provide insights into understanding human family systems as well.

Animals↗
PubMed1995

Evolutionary importance for the membrane enhancement of the production of vitamin D3 in the skin of poikilothermic animals.

The photoproduction of vitamin D in the skin was essential for the evolutionary development of terrestrial vertebrates. During exposure to sunlight, previtamin D3 formed in the skin is isomerized to vitamin D3 (calciol) by a temperature-dependent process. Since early land vertebrates were poikilothermic, the relatively slow conversion of previtamin D3 to vitamin D3 at ambient temperature put them at serious risk for developing vitamin D deficiency, thus leading to a poorly mineralized skeleton that could have ultimately halted further evolutionary development of vertebrates on land. We evaluated the rate of isomerization of previtamin D3 to vitamin D3 in the skin of iguanas and found the isomerization rate was enhanced by 1100% and 1700% at 25 degrees C and 5 degrees C, respectively. It is likely that the membrane entrapment of previtamin D3 in its s-cis,s-cis conformation is responsible for the markedly enhanced conversion of previtamin D3 to vitamin D3. The membrane-enhanced production of vitamin D3 ensures the critical supply of vitamin D3 to poikilothermic animals such as iguanas.

Animals↗
PubMed1996

Evolutionary theory predicts late-life mortality plateaus.

Most demographic data indicate a roughly exponential increase in adult mortality with age, a phenomenon that has been explained in terms of a decline in the force of natural selection acting on age-specific mortality. Scattered demographic findings suggest the existence of a late-life mortality plateau in both humans and dipteran insects, seemingly at odds with both prior data and evolutionary theory. Extensions to the evolutionary theory of aging are developed which indicate that such late-life mortality plateaus are to be expected when enough late-life data are collected. This expanded theory predicts late-life mortality plateaus, with both antagonistic pleiotropy and mutation accumulation as driving population genetic mechanisms.

Adult↗
PubMed1997

The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum.

A coenzyme B12-dependent ribonucleotide reductase was purified from the archaebacterium Thermoplasma acidophila and partially sequenced. Using probes derived from the sequence, the corresponding gene was cloned, completely sequenced, and expressed in Escherichia coli. The deduced amino acid sequence shows that the catalytic domain of the B12-dependent enzyme from T. acidophila, some 400 amino acids, is related by common ancestry to the diferric tyrosine radical iron(III)-dependent ribonucleotide reductase from E. coli, yeast, mammalian viruses, and man. The critical cysteine residues in the catalytic domain that participate in the thiyl radical-dependent reaction have been conserved even though the cofactor that generates the radical is not. Evolutionary bridges created by the T. acidophila sequence and that of a B12-dependent reductase from Mycobacterium tuberculosis establish homology between the Fe-dependent enzymes and the catalytic domain of the Lactobacillus leichmannii B12-dependent enzyme as well. These bridges are confirmed by a predicted secondary structure for the Lactobacillus enzyme. Sequence similarities show that the N-terminal domain of the T. acidophila ribonucleotide reductase is also homologous to the anaerobic ribonucleotide reductase from E. coli, which uses neither B12 nor Fe cofactors. A predicted secondary structure of the N-terminal domain suggests that it is predominantly helical, as is the domain in the aerobic E. coli enzyme depending on Fe, extending the homologous family of proteins to include anaerobic ribonucleotide reductases, B12 ribonucleotide reductases, and Fe-dependent aerobic ribonucleotide reductases. A model for the evolution of the ribonucleotide reductase family is presented; in this model, the thiyl radical-based reaction mechanism is conserved, but the cofactor is chosen to best adapt the host organism to its environment. This analysis illustrates how secondary structure predictions can assist evolutionary analyses, each important in "post-genomic" biochemistry.

Amino Acid Sequence↗
PubMed1997

The muscle of lawrence in Drosophila: a case of repeated evolutionary loss.

The muscle of Lawrence (MOL) is a bilaterally symmetrical muscle spanning the tergite of the fifth abdominal segment of adult male Drosophila melanogaster. It is not, however, a general feature of male-specific development within the subfamily Drosophilinae. Of 95 species surveyed within this subfamily, 67 exist with no MOL at all. By drawing comparisons with published cladograms of species relatedness, three conclusions regarding the evolutionary history of the MOL are made: (i) The MOL predates the major radiations of the genus Drosophila, given its presence in earlier-branching Chymomyza and Scaptodrosophila; the MOL has been subsequently excluded in at least one present species of each of these two primitive genera. (ii) Within the genus Drosophila the MOL is present sporadically in the radiation of the subgenus Sophophora, showing repetitive loss even in very close evolutionary lineages. (iii) The MOL may have been entirely excluded from the prolific radiation of the subgenus Drosophila. Thus the MOL shows a uniquely incongruous pattern of presence or absence relative to accepted drosophilid phylogeny.

Animals↗
PubMed1999

Evolutionary demographic models for mortality plateaus.

Plateaus in the age pattern of hazard functions at extreme ages have been discovered in large populations of medflies, Drosophila, nematodes, and people. Mueller and Rose [(1996) Proc. Natl. Acad. Sci. USA 93, 15249-15253] have proposed several age-structured demographic models to represent effects of mutation accumulation and antagonistic pleiotropy on randomly evolving schedules of demographic rates. They assert that "evolutionary theory [as embodied in their models] predicts late-life mortality plateaus." This paper defines a class of Markovian models that includes those of Mueller and Rose and obtains a characterization of the possible limiting states. For the basic model, the result implies that schedules with late-life mortality plateaus above a minimal threshold are not limiting states. The models fail, but not for reasons previously conjectured. Transient states, visited early by the process, do display mortality plateaus. Other models from this class may have a role to play in reconciling observed plateaus with evolutionary theory.

Animals↗
PubMed1999

Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space.

Random mutations under neutral or near-neutral conditions are studied by considering plausible evolutionary trajectories on "neutral nets"-i.e., collections of sequences (genotypes) interconnected via single-point mutations encoding for the same ground-state structure (phenotype). We use simple exact lattice models for the mapping between sequence and conformational spaces. Densities of states based on model intrachain interactions are determined by exhaustive conformational enumeration. We compare results from two very different interaction schemes to ascertain robustness of the conclusions. In both models, sequences in a majority of neutral nets center around a single "prototype sequence" of maximum mutational stability, tolerating the largest number of neutral mutations. General analytical considerations show that these topologies by themselves lead to higher steady-state evolutionary populations at prototype sequences. On average, native thermodynamic stability increases toward a maximum at the prototype sequence, resulting in funnel-like arrangements of native stabilities in sequence space. These observations offer a unified perspective on sequence design, native stability, and mutational stability of proteins. These principles are generalizable from native stability to any measure of fitness provided that its variation with respect to mutations is essentially smooth.

Algorithms↗
PubMed2001

Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors.

The divergent evolution of protein sequences from genomic databases can be analyzed by the use of different mathematical models. The most common treat all sites in a protein sequence as equally variable. More sophisticated models acknowledge the fact that purifying selection generally tolerates variable amounts of amino acid replacement at different positions in a protein sequence. In their "stationary" versions, such models assume that the replacement rate at individual positions remains constant throughout evolutionary history. "Nonstationary" covarion versions, however, allow the replacement rate at a position to vary in different branches of the evolutionary tree. Recently, statistical methods have been developed that highlight this type of variation in replacement rates. Here, we show how positions that have variable rates of divergence in different regions of a tree ("covarion behavior"), coupled with analyses of experimental three-dimensional structures, can provide experimentally testable hypotheses that relate individual amino acid residues to specific functional differences in those branches. We illustrate this in the elongation factor family of proteins as a paradigm for applications of this type of analysis in functional genomics generally.

Amino Acid Sequence↗
PubMed1999

The protozoan parasite Toxoplasma gondii expresses two functional plant-like glycolytic enzymes. Implications for evolutionary origin of apicomplexans.

The recent discovery of a vestigial, nonphotosynthetic plastid ("apicoplast") in the Apicomplexa has considerably modified our perception of the evolutionary origin of these parasites. Phylogenetic analysis and the presence of four surrounding membranes of the apicoplast provide important support for the hypothesis that apicomplexans have acquired their apicoplast by secondary endosymbiosis, probably from a green alga. This suggests that genes encoding predicted homologs of proteins of green algae or related photosynthetic lineages could have entered the nucleus of apicomplexan parasites by transfer from the ancestor harboring the apicoplast. We describe here complementary DNAs encoding two Toxoplasma gondii glycolytic enzymes, glucose-6-phosphate isomerase (G6-PI) and enolase, which have considerable identities with land plant counterparts. Both cDNAs of T. gondii complement Escherichia coli mutants lacking G6-PI and enolase genes and lead to the expression of active enzymes. In the drug untreatable encysted bradyzoites of T. gondii, G6-PI and enolase genes are overexpressed or exclusively expressed at both transcriptional and protein levels. Moreover, three-dimensional models and protein phylogeny confirmed that G6-PIs and enolases of T. gondii, Plasmodium falciparum, and land plants are closely related. Because these glycolytic enzymes are plant homologs, which differ from those of animals, they will be useful to trace the evolutionary origin of Apicomplexa and might offer novel chemotherapeutic targets in diseases caused by apicomplexan parasites.

Amino Acid Sequence↗