Evolutionary Tree Analysis Research Articles

The application of microsatellites in molecular pathology.

Present within the genome are large numbers of seemingly unimportant DNA segments arranged in repetitive units. Furthermore, these stretches of DNA contain variations or polymorphisms that are characteristic for an individual and results in a unique DNA fingerprint. Approximately 30% of the DNA repeat sequences are arranged as short tandem repeat sequences, which are called microsatellites. Microsatellites may consist of 1, 2 or 3 nucleotides; dinucleotides being the commonest. Microsatellites are characterised by being: stably inherited and hence highly conserved from one generation to the next, and unique to an individual and the same in different cells from the same individual. As a result of the above features, microsatellites can be used for personal identification, population genetic analysis and construction of evolutionary trees. In addition, they are located in several important gene loci and this allows microsatellites to be used as markers of disease and to provide information about individual gene status, especially in tumors. This can be accomplished by assessing allelic imbalance or loss of heterozygosity of a particular gene by analysing microsatellites located at specific loci in the gene. Recently, mutations within microsatellites have been described as a result of defective DNA repair mechanisms, resulting in the phenomenon of microsatellite instability. This has been implicated in the aetiopathogenesis of several hereditary and non-hereditary conditions. There are several ways of analysing microsatellites, the popular using radioactively-labelled primers and autoradiography. This method has several drawbacks, especially the use of radioactivity and interpretative/technical problems. The use of fluorescently-labelled primers, automated DNA sequencing coupled with a computer software package obviates these problems. This technique has the added advantage of analysing several microsatellites in large numbers of cases, simultaneously. Thus, microsatellite analysis has become an important investigative tool for the molecular biologist and has provided new information in many diseases.

Genetic Variation and Phylogeography of Central Asian and Other House Mice, Including a Major New Mitochondrial Lineage in Yemen

The mitochondrial DNA (mtDNA) control region and flanking tRNAs were sequenced from 76 mice collected at 60 localities extending from Egypt through Turkey, Yemen, Iran, Afghanistan, Pakistan, and Nepal to eastern Asia. Segments of the Y chromosome and of a processed p53 pseudogene (Psip53) were amplified from many of these mice and from others collected elsewhere in Eurasia and North Africa. The 251 mtDNA types, including 54 new ones reported here, now identified from commensal house mice (Mus musculus group) by sequencing this segment can be organized into four major lineages-domesticus, musculus, castaneus, and a new lineage found in Yemen. Evolutionary tree analysis suggested the domesticus mtDNAs as the sister group to the other three commensal mtDNA lineages and the Yemeni mtDNAs as the next oldest lineage. Using this tree and the phylogeographic approach, we derived a new model for the origin and radiation of commensal house mice whose main features are an origin in west-central Asia (within the present-day range of M. domesticus) and the sequential spreading of mice first to the southern Arabian Peninsula, thence eastward and northward into south-central Asia, and later from south-central Asia to north-central Asia (and thence into most of northern Eurasia) and to southeastern Asia. Y chromosomes with and without an 18-bp deletion in the Zfy-2 gene were detected among mice from Iran and Afghanistan, while only undeleted Ys were found in Turkey, Yemen, Pakistan, and Nepal. Polymorphism for the presence of a Psip53 was observed in Georgia, Iran, Turkmenistan, Afghanistan, and Pakistan. Sequencing of a 128-bp Psip53 segment from 79 commensal mice revealed 12 variable sites and implicated >/=14 alleles. The allele that appeared to be phylogenetically ancestral was widespread, and the greatest diversity was observed in Turkey, Afghanistan, Pakistan, and Nepal. Two mice provided evidence for a second Psip53 locus in some commensal populations.

A general method for tree-comparison based on subtree similarity and its use in a taxonomic database

A number of metrics for comparing the branching structure of trees have been used as important tools in the quantitative analysis of evolutionary trees. Less attention has been paid to developing a general comparison methodology for different leaf-labeled N-trees such as classification trees and various types of dendrograms. In this paper a method for measuring overall similarity based on subtree similarity is proposed. Association coefficients can be used to measure the similarity between each pair of subtrees in two trees, and an algorithm called the `webbing matrix method' is outlined in order to calculate the overall similarity in this method. In addition, the use of this method for tree searching and tree comparison in a taxonomic database is introduced.

Distributions of Tree Comparison Metrics--Some New Results

Measures of dissimilarity (metrics) for comparing trees are important tools in the quantitative analysis of evolutionary trees, but many of their properties are incompletely known. The present paper reports formulae for the distributions of three classes of tree comparison metrics: the partition (or symmetric difference) metric, the quartet metric (which compares subsets of four taxa), and a metric based on path-length differences between pairs of taxa. The properties studied include the mean and variance for several underlying distributions of trees, the range, the effect of the number of taxa, and methods of calculation. Three basic theorems and their proofs are reported, one for each class of tree comparison metric. The partition metric generates an asymptotic Poisson distribution for most distributions of trees (its mean is given for three tree distributions). Exact expressions are derived for the variance of the quartet metric and the mean square value of a metric based on path differences. Factors that affect the choice of a metric for a particular study include the degree of similarity of the trees being compared and the type of hypothesis being tested (e.g., whether the trees estimate the same underlying phylogeny or are simply related in some, perhaps unknown, way).

Cloning and characterization of the novel gene for mast cell carboxypeptidase A.

No gene for a hematopoietic cell carboxypeptidase has previously been characterized. Mast cell carboxypeptidase A (MC-CPA) is a prominent secretory granule marker of mast cell differentiation and phenotype. The 32-kb human MC-CPA gene was isolated, localized to chromosome 3, and found to contain 11 exons. No significant homology was found between the 5' flanking region of the MC-CPA gene and those of three rat pancreatic carboxypeptidase genes (carboxypeptidase A1 and A2, and carboxypeptidase B [CPB]). In contrast, the intron/exon organization of the MC-CPA gene was conserved, most closely resembling the CPB gene. MC-CPA is unique among carboxypeptidases in having a CPA-like substrate-binding pocket and enzymatic activity despite overall protein and gene structures more similar to CPB. Evolutionary tree analysis of the carboxypeptidase gene family showed that, before the mammalian species radiation, a common MC-CPA/CPB ancestor diverged by gene duplication from the lineage leading to CPA, and then underwent another gene duplication to form separate but similar gene structures for MC-CPA and CPB. MC-CPA mRNA was prominent in dispersed lung cells enriched for mast cells but was undetectable in other nontransformed populations of several lineages, demonstrating that transcription of MC-CPA, a novel carboxypeptidase gene, provides a specific molecular marker for mast cells among normal hematopoietic cell populations.

Sequence and diversity of rhesus monkey T-cell receptor beta chain genes.

We have sequenced 23 rearranged T-cell receptor beta chain (Tcrb) cDNA clones derived from peripheral blood lymphocytes (PBL) of a rhesus monkey. All of the clones have a variable-diversity-joining-constant (V-D-J-C) rearrangement similar to that of humans. Two rhesus constant (C) region genes were found, each closely resembling human Cb 1 and 2. All of the rhesus J region sequences align well with ten of the 13 reported human J regions. 17 of the 23 rhesus V region sequences could be assigned to families homologous with eight different human families (Vb 1, 2, 6, 7, 8, 9, 13, and 14). The remaining six V region sequences are more distantly related to human Vb 1 and 13. Thus, the organization and sequences of studied rhesus Tcrb chains resemble human homologs. An evolutionary tree analysis revealed paralogous relationships between specific members of the rhesus and human V region families. Analysis of synonymous and nonsynonymous nucleotide sequence differences indicated that the evolution of the presumed major histocompatibility complex (MHC)-contact regions of the Tcrb chains is less constrained than that of the framework regions.

Nucleotide Sequence Analysis of Isolates of Human T-Lymphotropic Virus Type 1 of Diverse Geographical Origins

Nucleotide sequences for long terminal repeat (LTR), gag, the protease gene, and pol of a human T-lymphotropic virus type 1 (HTLV-1) isolate of probable Caribbean origin (HTLV-1CH) and a Zairian isolate (HTLV-1EL) were determined providing complete proviral sequences for these isolates. These sequences were compared with those available from previously analyzed isolates. Nucleotide sequence differences of 1.2-3.3% were identified among isolates for which complete genetic information was available. Nucleotide sequence diversity was distributed relatively evenly over the genome with 1.3-5.2% differences in the LTR, 1.1-2.9% differences in gag, 0.7-2.1% differences in the protease gene, 0.9-2.5% differences in pol, 0.9-2.4% differences in env, 0.0-1.4% differences in rex, and 0.1-2.6% differences in tax. There were 1.2-2.3% amino acid differences overall, with 0.8-1.6% nonconservative amino acid alterations. Nucleotide differences were not found in regions of the LTR which are important for transcriptional activity or Tax response. Within the Rex-response element, nucleotide differences were found predominantly in loop rather than stem structures, thus, maintaining the overall secondary structure necessary for Rex activity. Evolutionary tree analysis of the sequence differences suggests a predominant clustering of different HTLV1 strains according to geographical origin. An open reading frame was also identified on the minus DNA strand situated between the env and rex/tax genes which exhibits 0.1-6.9% nucleotide sequence variation among HTLV1 strains. The limited sequence variation among HTLV-1 strains is in striking contrast to the extensive heterogeneity seen among human immunodeficiency virus (HIV) strains.

Genomic divergence of an HIV-2 from a German AIDS patient probably infected in Mali

The complete nucleotide sequence of an HIV-2 isolate derived from a German AIDS patient with predominantly neurological symptoms is reported. The HIV-2BEN sequence is highly divergent from those of previously described HIV-2 and SIV strains. Evolutionary tree analysis of eight HIV-2 sequences reveals the existence of three HIV-2 groups. HIV-2BEN belongs to a group with two isolates from Ghana and The Gambia. Based on a comparison of HIV-2BEN with six HIV-2 isolates, SIVsmm and SIVmac, the variability of the structural env and gag proteins is similar within the HIV-2/SIVsmm/mac and HIV-1 groups. In contrast, the regulatory HIV-1 proteins are more highly conserved than those from HIV-2 strains. Multiple sequence alignments reveal that some domains of the envelope and regulatory proteins are well conserved among HIV-1, HIV-2/SIVsmm/mac, SIVagm and SIVmnd. The identification of conserved domains within the external glycoprotein could help to develop broadly active vaccines.

Episodic evolution in the stomach lysozymes of ruminants

By sequencing lysozymes c from deer and pig stomachs and comparing them to the known amino acid sequences of other lysozymes c, it was possible to examine the rate of sequence change during and after the period in which this enzyme acquired a new function. Evolutionary tree analysis suggests that the rate went up while lysozyme was being recruited to function as a digestive enzyme in the stomach of early ruminants. Later, presumably after lysozyme was well adapted for functioning in the new environment, which contains acid, pepsin, and fermentation products, the rate of amino acid replacement became subnormal.

A NUMERICAL–TAXONOMIC STUDY OF THE GENUS BULNESIA (ZYGOPHYLLACEAE): CLUSTER ANALYSIS, ORDINATION AND SIMULATION OF EVOLUTIONARY TREES

Cluster analysis by four methods, ordination by principal component analysis (PCA) and simulation of evolutionary trees (Wagner Trees) were performed on morphological data from 43 characters of eight species of the South American genus Bulnesia (Zygophyllaceae). The results of cluster analysis and principal component analysis in general agree and show that there are three pairs of taxa that appear, or obviously are, closely related. These are the pairs B. arborea–B. carrapo, B. foliosa–B. schickendantzii and B. retama–B. chilensis. These methods also indicate that the southern species B. bonariensis occupies an intermediate position between the pair of northern tropical species (B. arborea, B. carrapo) and the remaining southern species. From the beginning it was assumed that these three multifoliolate species with large flowers may be rather primitive. The Prim network indicates that these three species are closely related among themselves. Also in two of the three Wagner Trees they are placed in a group. In all cases B. sarmientoi is shown as the more remote and isolated of all species. It is regarded as a unique, specialized arboreal species showing extreme reduction in number of leaflets and carpels, leaf and flower size, etc. All graphic representations (Fig. 1–3) show the phenetic similarity or the close phylogenetic relationships of the pairs B. foliosa–B. schickendantzii and B. retama–B. chilensis to each other. These four species would represent a rather advanced group. The most xerophytic species B. retama and B. chilensis are regarded as the most advanced taxa and the most specialized histophysiologically. These occupy extreme and distant positions in PCA diagrams and Prim network, and top positions in the Wagner Trees.

A Numerical-Taxonomic Study of the Genus Bulnesia (Zygophyllaceae): Cluster Analysis, Ordination and Simulation of Evolutionary Trees

Cluster analysis by four methods, ordination by principal component analysis (PCA) and simulation of evolutionary trees (Wagner Trees) were performed on morphological data from 43 characters of eight species of the South American genus Bulnesia (Zygophyllaceae). The results of cluster analysis and principal component analysis in general agree and show that there are three pairs of taxa that appear, or obviously are, closely related. These are the pairs B. arborea–B. carrapo, B. foliosa–B. schickendantzii and B. retama–B. chilensis. These methods also indicate that the southern species B. bonariensis occupies an intermediate position between the pair of northern tropical species (B. arborea, B. carrapo) and the remaining southern species. From the beginning it was assumed that these three multifoliolate species with large flowers may be rather primitive. The Prim network indicates that these three species are closely related among themselves. Also in two of the three Wagner Trees they are placed in a group. In all cases B. sarmientoi is shown as the more remote and isolated of all species. It is regarded as a unique, specialized arboreal species showing extreme reduction in number of leaflets and carpels, leaf and flower size, etc. All graphic representations (Fig. 1–3) show the phenetic similarity or the close phylogenetic relationships of the pairs B. foliosa–B. schickendantzii and B. retama–B. chilensis to each other. These four species would represent a rather advanced group. The most xerophytic species B. retama and B. chilensis are regarded as the most advanced taxa and the most specialized histophysiologically. These occupy extreme and distant positions in PCA diagrams and Prim network, and top positions in the Wagner Trees.