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PubMed2006

Evolutionary paths underlying flower color variation in Antirrhinum.

To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.

Adaptation, Biological↗
PubMed2006

Large punctuational contribution of speciation to evolutionary divergence at the molecular level.

A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.

Animals↗
PubMed2006

Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient.

The evolutionary dynamics underlying the latitudinal gradient in biodiversity have been controversial for over a century. Using a spatially explicit approach that incorporates not only origination and extinction but immigration, a global analysis of genera and subgenera of marine bivalves over the past 11 million years supports an "out of the tropics" model, in which taxa preferentially originate in the tropics and expand toward the poles without losing their tropical presence. The tropics are thus both a cradle and a museum of biodiversity, contrary to the conceptual dichotomy dominant since 1974; a tropical diversity crisis would thus have profound evolutionary effects at all latitudes.

Animals↗
PubMed1967

Hormones and endocrine glands of fishes. Studies of fish endocrinology reveal major physiologic and evolutionary problems.

The structures discussed above illustrate some of the evolutionary knowledge to be obtained from studies of the comparative biology of the endocrine system among the fishes (see also 17, 78). The interrenal (adrenocortical) gland is an example of an endocrine structure which shows great morphologic variation in the vertebrate series, and among the fishes themselves. The structural variability implies little selective value for any particular pattern, and, in fact, biochemically the interrenal tissue would seem to be involved in much the same kind of steroidogenesis in the vertebrates generally. However, the hormone aldosterone may be a tetrapod novelty. The caudal neurosecretory system is a good example of a ubiquitous endocrine apparatus, among at least teleostean and elasmo-branch fishes, for which a function has yet to be elucidated and which continues to challenge the comparative physiologist. This system, along with the Stannius corpuscles, is lacking in the tetrapods. The existence of these structures makes it clear that the endocrine biology of fishes cannot be tacitly summarized as being essentially similar to that of the tetrapods, only less well developed. The prolactin situation illustrates the existence of a gland-the pituitary-present among fishes as among tetrapods, which secretes a product only partly related to the tetrapod hormone and having a very different functional significance. In this case it is clear that "the hormone and the uses to which it is put" have undergone evolutionary change during vertebrate phylogeny.

Adrenal Glands↗
PubMed1969

Hemoglobins A and A2 in New World primates: comparative variation and its evolutionary implications.

Hemoglobin A(2) (alpha(2)delta(2)) in New World primates represents about 1/160 to 1/16 of total hemoglobin and, by virtue of this low proportion, is presumed to be functionally unimportant. Nonetheless, A(2) exhibits genetic polymorphism by electrophoresis in three out of five genera, whereas the major component, hemoglobin A (alpha(2)beta(2)), is electrophoretically invariant. Moreover, in four genera, including man, the evolutionary accumulation of mutations has been greater in delta than in beta Such findings suggest that both polymorphism and evolutionary changes can accrue to an effectively functionless and thus selectively nearly netutral gene.

Amino Acid Sequence↗
PubMed1972

Evolutionary clock: nonconstancy of rate in different species.

By using various methods for comparing polypeptide sequences we find that the evolutionary divergence of rattlesnake cytochrome c from cytochromes c of species in other classes has been more rapid than that of cytochrome c of another reptile, the snapping turtle. This suggests that the evolutionary rate of change of cytochromes c is species-dependent as well as time-dependent.

Amino Acid Sequence↗
PubMed2000

Nonrandom extinction and the loss of evolutionary history.

The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature of threat for the loss of biodiversity. An additional 120 avian and mammalian genera are at risk compared with the number predicted under random extinction. We estimate that the prospective extra loss of mammalian evolutionary history alone would be equivalent to losing a monotypic phylum.

Animals↗
PubMed2000

Evolutionary biology. In search of biological weirdness.

The late William D. Hamilton (1936-2000) was drawn to the unusual and paradoxical. His observations led to a new understanding of social interactions and shaped a generation of evolutionary biologists. At a symposium here in October honoring this giant of evolutionary biology, who died of malaria in March at age 63, about 70 researchers discussed where Hamilton's ideas have taken them.

Animals↗
PubMed1988

Evolutionary social psychology and family homicide.

Homicide is an extreme manifestation of interpersonal conflict with minimal reporting bias and can thus be used as a conflict "assay." Evolutionary models of social motives predict that genetic relationship will be associated with mitigation of conflict, and various analyses of homicide data support this prediction. Most "family" homicides are spousal homicides, fueled by male sexual proprietariness. In the case of parent-offspring conflict, an evolutionary model predicts variations in the risk of violence as a function of the ages, sexes, and other characteristics of protagonists, and these predictions are upheld in tests with data on infanticides, parricides, and filicides.

Age Factors↗
PubMed1993

Monophyletic origins of the metazoa: an evolutionary link with fungi.

A phylogenetic framework inferred from comparisons of small subunit ribosomal RNA sequences describes the evolutionary origin and early branching patterns of the kingdom Animalia. Maximum likelihood analyses show the animal lineage is monophyletic and includes choanoflagellates. Within the metazoan assemblage, the divergence of sponges is followed by the Ctenophora, the Cnidaria plus the placozoan Trichoplax adhaerens, and finally by an unresolved polychotomy of bilateral animal phyla. From these data, it was inferred that animals and fungi share a unique evolutionary history and that their last common ancestor was a flagellated protist similar to extant choanoflagellates.

Animals↗
PubMed2002

Predicting evolution by in vitro evolution requires determining evolutionary pathways.

In an early example of DNA shuffling, Stemmer (W. P. C. Stemmer, Nature 370:389-390, 1994) demonstrated a dramatic improvement in the activity of the TEM-1 beta-lactamase toward cefotaxime as the consequence of six amino acid substitutions. It has been pointed out (B. G. Hall, FEMS Microbiol. Lett. 178:1-6, 1999; M. C. Orencia, J. S. Yoon, J. E. Ness, W. P. Stemmer, and R. C. Stevens, Nat. Struct. Biol. 8:238-242, 2001) that the power of DNA shuffling might be applied to the problem of predicting evolution in nature from in vitro evolution in the laboratory. As a predictor of natural evolutionary processes, that power may be misleading because in nature mutations almost always arise one at a time, and each advantageous mutation must be fixed into the population by an evolutionary pathway that leads from the wild type to the fully evolved sequence. Site-directed mutagenesis was used to introduce each of Stemmer's six substitutions into TEM-1, the best single mutant was chosen, and each of the remaining five substitutions was introduced. Repeated rounds of site-directed mutagenesis and selection of the best mutant were used in an attempt to construct a pathway between the wild-type TEM-1 and Stemmer's mutant with six mutations. In the present study it is shown (i) that no such pathway exists between the wild-type TEM-1 and the supereffective cefotaxime-hydrolyzing mutant that was generated by six amino acid substitutions via DNA shuffling (Stemmer, Nature 370:389-390, 1994) but that a pathway to a fourfold more efficient enzyme resulting from four of the same substitutions does exist, and (ii) that the more efficient enzyme is likely to arise in nature as the result of a single mutation in the naturally occurring TEM-52 allele.

Alleles↗
PubMed2000

Simultaneous enhancement of thermostability and catalytic activity of phospholipase A(1) by evolutionary molecular engineering.

The thermal stability and catalytic activity of phospholipase A(1) from Serratia sp. strain MK1 were improved by evolutionary molecular engineering. Two thermostable mutants were isolated after sequential rounds of error-prone PCR performed to introduce random mutations and filter-based screening of the resultant mutant library; we determined that these mutants had six (mutant TA3) and seven (mutant TA13) amino acid substitutions. Different types of substitutions were found in the two mutants, and these substitutions resulted in an increase in nonpolar residues (mutant TA3) or in differences between side chains for polar or charged residues (mutant TA13). The wild-type and mutant enzymes were purified, and the effect of temperature on the stability and catalytic activity of the enzymes was investigated. The melting temperatures of the TA3 and TA13 enzymes were increased by 7 and 11 degrees C, respectively, compared with the melting temperature of the wild-type enzyme. Thus, we found that evolutionary molecular engineering was an effective and efficient approach for increasing thermostability without compromising enzyme activity.

Catalysis↗
PubMed2001

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiological research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made.

Bacteria↗
PubMed2005

Biological transmission of arboviruses: reexamination of and new insights into components, mechanisms, and unique traits as well as their evolutionary trends.

Among animal viruses, arboviruses are unique in that they depend on arthropod vectors for transmission. Field research and laboratory investigations related to the three components of this unique mode of transmission, virus, vector, and vertebrate host, have produced an enormous amount of valuable information that may be found in numerous publications. However, despite many reviews on specific viruses, diseases, or interests, a systematic approach to organizing the available information on all facets of biological transmission and then to interpret it in the context of the evolutionary process has not been attempted before. Such an attempt in this review clearly demonstrates tremendous progress made worldwide to characterize the viruses, to comprehend disease transmission and pathogenesis, and to understand the biology of vectors and their role in transmission. The rapid progress in molecular biologic techniques also helped resolve many virologic puzzles and yielded highly valuable data hitherto unavailable, such as characterization of virus receptors, the genetic basis of vertebrate resistance to viral infection, and phylogenetic evidence of the history of host range shifts in arboviruses. However, glaring gaps in knowledge of many critical subjects, such as the mechanism of viral persistence and the existence of vertebrate reservoirs, are still evident. Furthermore, with the accumulated data, new questions were raised, such as evolutionary directions of virus virulence and of host range. Although many fundamental questions on the evolution of this unique mode of transmission remained unresolved in the absence of a fossil record, available observations for arboviruses and the information derived from studies in other fields of the biological sciences suggested convergent evolution as a plausible process. Overall, discussion of the diverse range of theories proposed and observations made by many investigators was found to be highly valuable for sorting out the possible mechanism(s) of the emergence of arboviral diseases.

Animals↗
PubMed2004

Evolutionary and functional relationships of colonization factor antigen i and other class 5 adhesive fimbriae of enterotoxigenic Escherichia coli.

Colonization factor antigen I (CFA/I) is the archetype of eight genetically related fimbriae of enterotoxigenic Escherichia coli (ETEC) designated class 5 fimbriae. Assembled by the alternate chaperone pathway, these organelles comprise a rigid stalk of polymerized major subunits and an apparently tip-localized minor adhesive subunit. We examined the evolutionary relationships of class 5-specific structural proteins and correlated these with functional properties. We sequenced the gene clusters encoding coli surface antigen 4 (CS4), CS14, CS17, CS19, and putative colonization factor antigen O71 (PCFO71) and analyzed the deduced proteins and the published homologs of CFA/I, CS1, and CS2. Multiple alignment and phylogenetic analysis of the proteins encoded by each operon define three subclasses, 5a (CFA/I, CS4, and CS14), 5b (CS1, CS17, CS19, and PCFO71), and 5c (CS2). These share distant evolutionary relatedness to fimbrial systems of three other genera. Subclass divisions generally correlate with distinguishing in vitro adherence phenotypes of strains bearing the ETEC fimbriae. Phylogenetic comparisons of the individual structural proteins demonstrated greater intrasubclass conservation among the minor subunits than the major subunits. To correlate this with functional attributes, we made antibodies against CFA/I and CS17 whole fimbriae and maltose-binding protein fusions with the amino-terminal half of the corresponding minor subunits. Anti-minor subunit Fab preparations showed hemagglutination inhibition (HAI) of ETEC expressing homologous and intrasubclass heterologous colonization factors while anti-fimbrial Fab fractions showed HAI activity limited to colonization factor-homologous ETEC. These results were corroborated with similar results from the Caco-2 cell adherence assay. Our findings suggest that the minor subunits of class 5 fimbriae may be superior to whole fimbriae in inducing antiadhesive immunity.

Bacterial Adhesion↗
PubMed1976

Methyl galactosidase activity: an alternative evolutionary destination for the ebgA0 gene.

Previous studies (Campbell et al., 1973; Hall and Hartl, 1974; Hall and Hartl, 1975) have shown that the ebgA0 gene, whose product does not hydrolyze lactose may evolve so that its product does hydrolyze lactose; i.e., lactase activity is one evolutionary destination of the ebgA0 gene. Beginning with a strain that synthesizes ebgA0 gene product constitutively and grows extremely slowly (doubling time, 30 to 50 h) on methyl-beta-D-galactopyranoside (MG), a derivative was selected capable of growth on MG at a moderate rate (doubling time, 5.9 h). Genetic evidence is presented showing that the gene that permits growth on MG is an allele of ebgA. A comparison among strains bearing several alleles of ebgA shows that the new allele, termed ebgAmg, synthesizes a product specific for MG and thus represents a true alternative evolutionary destination for the ebgA0 gene.

Alleles↗
PubMed1988

Evolutionary relationships among cyanobacteria and green chloroplasts.

The 16S rRNAs from 29 cyanobacteria and the cyanelle of the phytoflagellate Cyanophora paradoxa were partially sequenced by a dideoxynucleotide-terminated, primer extension method. A least-squares distance matrix analysis was used to infer phylogenetic trees that include green chloroplasts (those of euglenoids, green algae, and higher plants). The results indicate that many diverse forms of cyanobacteria diverged within a short span of evolutionary distance. Evolutionary depth within the surveyed cyanobacteria is substantially less than that separating the major eubacterial taxa, as though cyanobacterial diversification occurred significantly after the appearance of the major eubacterial groups. Three of the five taxonomic sections defined by Rippka et al. (R. Rippka, J. Deruelles, J. B. Waterbury, M. Herdman, and R. Y. Stanier, J. Gen. Microbiol. 111:1-61, 1979) (sections II [pleurocapsalean], IV [heterocystous, filamentous, nonbranching], and V [heterocystous, filamentous, branching]) are phylogenetically coherent. However, the other two sections (I [unicellular] and III [nonheterocystous, filamentous]) are intermixed and hence are not natural groupings. Our results not only support the conclusion of previous workers that the cyanobacteria and green chloroplasts form a coherent phylogenetic group but also suggest that the chloroplast lineage, which includes the cyanelle of C. paradoxa, is not just a sister group to the free-living forms but rather is contained within the cyanobacterial radiation.

Base Sequence↗
PubMed1989

Evolutionary trees for the genus Bordetella.

Recent data on enzyme electrophoretic mobility and DNA sequences for pertussis toxin allow the construction of evolutionary trees for various strains belonging to the genus Bordetella. In contrast to previous analyses, these data can be seen to support the separate clustering of Bordetella pertussis strains, in agreement with the traditional classification based on other phenotypic characteristics. An earlier argument placing the divergence of B. pertussis and B. parapertussis before 1912 does not follow from the evolutionary trees proposed here, which also have different implications for several other claims concerning the evolution of these strains.

Biological Evolution↗