Showing papers on "Phylogenetic tree published in 1971"

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

Abstract: Fitch, W. M. (Dept. of Physiological Chemistry, Univ. of Wisconsin, Madison, Wisconsin, 53706), 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool., 20:406-416.-A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented. The character states used as examples are the four messenger RNA nucleotides encoding the amino acid sequences of proteins, but the method is general. [Evolution; parsimonious trees.] It has been a goal of those attempting to deduce phylogenetic relationships from information on biological characteristics to find the ancestral relationship(s) that would permit one to account for the descent of those characteristics in a manner requiring a minimum number of evolutionary steps or changes. The result could be called the most parsimonious evolutionary tree and might be expected to have a high degree of correspondence to the true phylogeny (Camin and Sokal, 1965). It's justification lies in the most efficient use of the information available and does not presuppose that evolution follows a most parsimonious course. There are no known algorithms for finding the most parsimonious tree(s) apart from the brute force method of examining nearly every possible tree.' This is impractical for trees involving a dozen or more taxonomic units. Most numerical taxonomic procedures (Sokal and Sneath, 1963; Farris, 1969, 1970; Fitch and Margoliash, 1967) provide dendrograms that would be among the more parsimonious solutions; one just cannot be sure that a more parsimonious tree structure does not exist. Farris (1970) has explicitly considered the parsimony principle as a part of 'An elegant beginning to an attack on the problem has recently been published by Farris (1969) who developed a method which estimates the reliability of various characters and then weights the characters on the basis of that reliability. his method which, like the present method, has its roots in the Wagner tree (Wagner,

Molecular evolution in the descent of man.

Abstract: Three computer programs applied to data from phylogenetic trees and protein polymorphism can be used to find the rate of molecular evolution of different species. It can be shown that this is slower for higher primates than for other mammals.

Gel Electrophoresis: New Approach to the Study of Evolution

Abstract: Recent excitement in the fields of population genetics, evolutionary genetics, and systematics has centered on results obtained with several techniques borrowed from the repertoire of the biochemist and the molecular biologist. The techniques make it possible to study genetic variation and the similarities and differences among organisms at the level of their enzymes or other proteins and their DNA's. The most widely used technique is gel electrophoresis which has shown that the primary amino acid structure of most proteins varies among individuals, even those from the same population. The variation can be directly equated with genetic differences. This permits a characterization, for the first time at the molecular level, of the amounts and types of genetic variability in populations of practically any organism and an estimate of the extent of genetic divergence among closely related species. The second technique involves the determination of the amino acid sequence of proteins having the same functional activity in different organisms. The information is used to study the phylogenetic relationships of the organisms from which the sequences have been made on the assumption that the greater the time since two organisms had a common ancestor, the greater the number of differences in the amino acid sequence of their proteins. The method has also led to studies of various biochemical constraints on nucleotide changes and to studies of how protein divergence occurs. The third technique is the comparison of DNA base sequences by hybridization studies. It too is beginning to yield important data on relatedness and divergence among organisms. The present article is designed as an introduction to the use of gel electrophoresis to solve problems of evolution. The use of the other two echniques has been discussed elsewhere (Hoyer, et al., 1964; Britten and Kohne, 1968; Nolan and Margoliash, 1968; Bendich and McCarthy, 1970; Fitch and Margoliash, 1970).

Comparison of the Pectoral and Pelvic Skeletons and of some other Bones and their Phylogenetic Implications in the Aulorhynchidae and Gasterosteidae (Pisces)

Abstract: Study of the pectoral and pelvic skeletons and some other bones in recognized species of the seven genera comprising the related families Aulorhynchidae (tubesnouts) and Gasterosteidae (sticklebacks) showed that the two families differ in several respects, with no one living species appearing to be intermediate. The genera Aulorhynchus, Aulichthys, Spinachia, Apeltes, and Gasterosteus each have distinctive characteristics not found in any other genus of the two families. Gasterosteus wheatlandi is the only species of the two families that lacks both the posttemporal and the supracleithrum. The interrelations of the genera form a mosaic pattern and there is no acceptable basis in the characters examined for postulating a phylogeny within the Gasterosteidae or for selecting a living species as being a primitive form or the most closely allied to the Aulorhynchidae.

Evolution of proteins.

Abstract: The amino acid sequences of proteins from living organisms are dealt with. The structure of proteins is first discussed; the variation in this structure from one biological group to another is illustrated by the first halves of the sequences of cytochrome c, and a phylogenetic tree is derived from the cytochrome c data. The relative geological times associated with the events of this tree are discussed. Errors which occur in the duplication of cells during the evolutionary process are examined. Particular attention is given to evolution of mutant proteins, globins, ferredoxin, and transfer ribonucleic acids (tRNA's). Finally, a general outline of biological evolution is presented.

Evaluation of the Efficacy of Numerical Taxonomic Methods: An Example from the Bivalve Mollusks

Abstract: Bretsky, Sara S. (Northwestern Univ., Evanston, Ill. 60201) 1971. Evaluation of the efficacy of numerical taxonomic methods: an example from the bivalve mollusks. Syst. Zool. 20:204-222.-Phenetic and phylogenetic classifications of 42 Tertiary and Recent species of the Family Lucinidae (Mollusca, Bivalvia) correspond reasonably well only at the lower taxonomic levels. On the basis of their evolutionary relationships, these species can. be assigned to 28 subgenera and 7 genera. In the phenetic study, 45 multistate, mostly qualitative characters were used to calculate correlation and distance coefficients; both similarity measures were clustered by the weighted pair-group method. Small clusters which formed at high similarity levels in the two phenograms were usually composed of species of one subgenus or two or three closely related subgenera. Major clusters in each of the phenograms, however, differed considerably both from those of the other phenogram and from the principal phylogenetic lineages (genera). "Cophylogenetic coefficients," analogous to the cophenetic coefficients used in comparing phenograms, indicated that both phenograms poorly reflected inferred phylogeny and that they did not differ significantly with regard to their correspondence to the phylogenetic classification. Simple cluster analysis probably is adequate for finding phylogenetic groups at the subgeneric level but not for recognition of higher taxa. At the generic and higher levels, phenetic classifications are not more stable than phylogenetic ones. Phylogenetic classifications, being hypotheses about genealogy rather than static descriptions of morphological similarity, are more likely than phenetic ones to be productive of future investigations. [Numerical taxonomy; evolution; Bivalvia; Lucinidae.] "Until a case of known phyletic history can be used to explore quantitatively the correspondence of morphological with phylogenetic relationships, judgments on such issues should be suspended in favor of research upon them" (Sokal and Sneath, 1963, p. 26). This paper compares phenetic and phylogenetic classifications of the Family Lucinidae (Mollusca, Bivalvia), and from the comparison draws conclusions about the relative utility of the two approaches to classification. The lucinids are marine, primarily warm-water clams. First known from rocks of Silurian age, they have a worldwide distribution in the Cenozoic and Recent fauna. Their fossil record is particularly well documented for Cenozoic time in Europe, North America, and northern South America (Chavan, 1937, 1938, 1951, 1969; Bretsky, in prep.). The genealogy of Recent lucinids can thus be traced almost continuously for seventy million years; the life habits of the fossil forms can be interpreted by analogy with the anatomy, functional morphology, and ecology of their Recent counterparts, known especially from the work of Allen (1958) and Stanley (1970). I define a phenetic classification as one based on the simultaneous consideration of a larger number of unweighted taxonomic characters (sensu Sokal and Sneath, 1963). I prefer to use the general term "numerical taxonomy" to encompass the many applications of numerical techniques to taxonomic problems, including those schemes which aim at "objective" weighting of characters. Following Simpson (1961) and Mayr (1969), I define a phylogenetic classification as one which is consistent with the evolutionary history of the organisms being classified and thus considers both branching patterns and degree of diver-

Amino acid sequences and phylogeny

Abstract: mental and genetic mechanisms and relations, and (2) Protein structure-function relations. This outline will cover only the first of these and though most of the illustrations will be taken from eukaryotic cytochromes c, whenever the data are available it will be shown how the generalizations reached apply to other proteins. Following a definition of evolutionary analogy and homology, as applied to protein structure, a description is given of statistical methods which make it possible to decide whether a set of similar proteins are or are not ancestrally related, i.e. homologous. The elaboration of species phylogenies from such sets of proteins requires a particular kind of homologous protein set, namely, one in which in the common evolutionary ancestor of all the species considered the protein was represented by a single gene. This is termed an orthologous set, and it provides a precise one-to-one correspondence between the lineage of species and the lineage of the structural gene of the protein considered in these species. A method for obtaining statistical phylogenetic trees from such protein primary structures is described. Rapidly changing peptide chains, such as fibrinopeptides, afford satisfactory phylogenetic trees for relatively small groups of species, such as artiodactyls, while very slowly changing proteins, such as cytochromes c, make it possible to obtain such relationships over the entire taxonomic scale. Such trees lead to the development of the complete mutation pathways relating the proteins of extant species back to various intermediate ancestral forms at the different branch points of the phylogenetic trees, and thus, in turn, to the amino acid sequence of the protein in the ancestral form common to all extant species. Statistical tests on model cases indicate that the procedure which accounts for the proteins of descendents in the fewest number of nucleotide replacements does indeed give good estimates of the mutation pathways followed and of the structure of ancestral forms of the protein. If this is done for two sets of orthologous sequences, it is possible to determine whether the ancestral forms of the two sets are more alike or less alike than would be expected if the present-day sequences had been unrelated, thus distinguishing

The different phylogenetic age of antigenic determinants on human L-chains.

Abstract: A careful analysis of cross-reactions between immunoglobulin L-chains from man and 3 Old World monkeys revealed the presence of two types of determinants for man: one chain-specific and one common, the latter having a higher phylogenetic age.