Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences.
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Animals↗
Biomedical subjects
J Czelusniak
Publications and source records attributed to J Czelusniak.
Molecular phylogeny of the family of apes and humans.
The morphological picture of primate phylogeny has not unambiguously identified the nearest outgroup of Anthropoidea and has not resolved the branching pattern within Hominoidea. The molecular picture provides more resolution and clarifies the systematics of Hominoidea. Protein and DNA evidence divides Hominoidea into Hylobatidae (gibbons) and Hominidae, family Hominidae into Ponginae (orangutan) and Homininae, and subfamily Homininae into two tribes, one for Gorilla, and the other for Pan (chimpanzee) and Homo. Parsimony and maximum likelihood analyses, carried out on orthologous noncoding nucleotide sequences from primate beta-globin gene clusters, provide significant evidence for the human-chimpanzee tribe and overwhelming evidence for the human-chimpanzee-gorilla clade. These analyses also indicate that the rate of molecular evolution became slower in hominoids than in other primates and mammals.
Animals↗
An evolutionary tree for invertebrate globin sequences.
A phylogenetic tree was constructed from 245 globin amino acid sequences. Of the six plant globins, five represented the Leguminosae and one the Ulmaceae. Among the invertebrate sequences, 7 represented the phylum Annelida, 13 represented Insecta and Crustacea of the phylum Arthropoda, and 6 represented the phylum Mollusca. Of the vertebrate globins, 4 represented the Agnatha and 209 represented the Gnathostomata. A common alignment was achieved for the 245 sequences using the parsimony principle, and a matrix of minimum mutational distances was constructed. The most parsimonious phylogenetic tree, i.e., the one having the lowest number of nucleotide substitutions that cause amino acid replacements, was obtained employing clustering and branch-swapping algorithms. Based on the available fossil record, the earliest split in the ancestral metazoan lineage was placed at 680 million years before present (Myr BP), the origin of vertebrates was placed at 510 Myr BP, and the separation of the Chondrichthyes and the Osteichthyes was placed at 425 Myr BP. Local "molecular clock" calculations were used to date the branch points on the descending branches of the various lineages within the plant and invertebrate portions of the tree. The tree divided the 245 sequences into five distinct clades that corresponded exactly to the five groups plants, annelids, arthropods, molluscs, and vertebrates. Furthermore, the maximum parsimony tree, in contrast to the unweighted pair group and distance Wagner trees, was consistent with the available fossil record and supported the hypotheses that the primitive hemoglobin of metazoans was monomeric and that the multisubunit extracellular hemoglobins found among the Annelida and the Arthropoda represent independently derived states.
Amino Acid Sequence↗
Globins: a case study in molecular phylogeny.
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Animals↗
Nucleotide sequence and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats.
We have mapped and sequenced the epsilon globin gene and seven surrounding Alu repeat sequences in the orangutan beta globin gene cluster and have compared these and other orangutan sequences to orthologously related human sequences. Noncoding flanking and intron sequences, synonymous sites of alpha, gamma, and epsilon globin coding regions, and Alu sequences in human and orangutan diverge by 3.2%, 2.7%, and 3.7%, respectively. These values compare to 3.6% from DNA hybridizations and 3.4% from the psi eta globin gene region. If as suggested by fossil evidence and "molecular clock" calculations, human and orangutan lineages diverged about 10-15 MYA, the rate of noncoding DNA evolution in the two species is 1.0-1.5 X 10(-9) substitutions per site per year. We found no evidence for either the addition or deletion of Alu sequences from the beta globin gene cluster nor is there any evidence for recent concerted evolution among the Alu sequences examined. Both phylogenetic and phenetic distance analyses suggest that Alu sequences within the alpha and beta globin gene clusters arose close to the time of simian and prosimian primate divergence (about 50-60 MYA). We conclude that Alu sequences have been evolving at the rate typical of noncoding DNA for the majority of primate history.
Amino Acid Sequence↗
Paenungulata: a comparison of the hemoglobin sequences from elephant, hyrax, and manatee.
Inspection of the amino acid differences among hemoglobin sequences of a wide range of mammalian species suggested that at alpha 19, alpha 110, alpha 111, beta 23, beta 44, and beta 56, synapomorphies group manatee (Trichechus inungius, Sirenia), Indian and African elephant (Elephas maximus and Loxodonta africana, Proboscidea), and rock hyrax (Procavia habessinica, Hyracoidea) into a monophyletic clade. Results obtained by parsimony analysis provide evidence for this grouping--and thus support for the genealogical validity of Simpson's superorder Paenungulata, which contains as the extant orders Proboscidea, Sirenia, and Hyracoidea. All of the 39 most, or nearly most, parsimonious of 10,395 trees constructed from a tandemly combined alpha- and beta-hemoglobin sequence for 103 vertebrate species (of which 79 were mammals from 16 extant orders), depicted Paenungulata as one of the most anciently separated branches of Eutheria. It was found on examining thousands of alternative trees that to not group Proboscidea, Hyracoidea, and Sirenia in a monophyletic clade required at least four additional substitutions.
Amino Acid Sequence↗
Codon usage in the vertebrate hemoglobins and its implications.
A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.
Animals↗
The eta-globin gene. Its long evolutionary history in the beta-globin gene family of mammals.
In phylogenetic reconstructions by the parsimony method, utilizing 62 sequenced globin genes and pseudogenes (including 34 of the beta-globin gene family from eutherian orders Primates, Lagomorpha, Artiodactyla and Rodentia), the branch of primate psi beta pseudogenes and the goat embryonically expressed epsilon II gene group monophyletically together as orthologues of a common ancestral gene (labelled eta) distinct from orthologues of epsilon, gamma, delta and beta. This primate psi eta-goat eta branch is cladistically closer to epsilon and gamma than to delta and beta branches. In each eutherian order gene conversions replaced portions of delta by beta sequences, whereas in descent of Primates epsilon, gamma and eta mostly retained their separate ancient identities predating the radiation of Eutheria in all their exons and non-coding regions. The loci of the ancestral beta-globin gene cluster in basal eutherians and proto-primates, as deduced from beta-clusters representing the four eutherian orders, were linked 5'-epsilon-gamma-eta-delta-beta-3' with epsilon, gamma and eta being embryonically expressed genes, and delta and beta ontogenetically later expressed genes. Through deletions gamma was lost in artiodactyl evolution, eta in lagomorph and rodent evolution, and all DNA between exon 2 3' boundaries of eta and delta in prosimian lemuriform evolution (lemur having the hybrid pseudogene psi eta delta). Simian primates retained intact the five loci of the ancestral cluster. Not only did eta, after it became a pseudogene in the basal primates, persist intact in descent to present-day simians but in the line to hominoids it evolved during the last 40 million years at the decelerated rate of 1 X 10(-9) substitutions/site per year which is one-fifth the expected neutral rate. The possibility is suggested that the psi eta locus situated between fetal and adult chromosomal domains of the simian beta-globin gene cluster might play some role in a mechanism for ontogenetic switches of globin gene expression. However, not enough sequence data on genes and intergenic regions in DNA of species of primates and other mammals as yet exist to know if the slow rate of 1 X 10(-9) reflects the rate of a conserved functional gene or primarily reflects a decelerated neutral rate of hominoid DNA evolution, conceivably from enhanced DNA repair and longer generation times in hominoids. The further possibility is raised that gene correction (repair of damaged DNA that prevents emergence of new alleles) and gene conversion both more often involve strand copying of conserved than of rapidly evolving DNA.
Animals↗
The sequence of the gorilla fetal globin genes: evidence for multiple gene conversions in human evolution.
Two fetal globin genes (G gamma and A gamma) from one chromosome of a lowland gorilla (Gorilla gorilla gorilla) have been sequenced and compared to three human loci (a G gamma-gene and two A gamma-alleles). A comparison of regions of local homology among these five sequences indicates that long after the duplication that produced the two nonallelic gamma-globin loci of catarrhine primates, about 35 million years (Myr) ago, at least one gene conversion event occurred between these loci. This conversion occurred not long before the ancestral divergence (about 6 Myr ago) of Homo and Gorilla. After this ancestral divergence, a minimum of three more gene conversion events occurred in the human lineage. Each human A gamma-allele shares specific sequence features with the gorilla A gamma-gene; one such distinctive allelic feature involves the simple repeated sequence in IVS 2. This suggests that early in the human lineage the A gamma-genes may have undergone a crossing-over event mediated by this simple repeated sequence. The DNA sequences from coding regions of both G gamma- and A gamma-loci, a comparison of 292 codons in the corresponding gorilla and human genes, show an unusually low evolutionary rate, with only two nonsilent differences and, surprisingly, not even one silent substitution. The two nonsynonymous substitutions observed predict a glycine at codon 73 and an arginine at codon 104 in the gorilla A gamma-sequence rather than aspartic acid and lysine, respectively, in human A gamma. Because only arginine has been found at position 104 in gamma-chains of Old World monkeys, it may represent the ancestral residue lost in gorilla and human G gamma-chains and in the human A gamma-chain. Possibly the arginine codon (AGG) was replaced by the lysine codon (AAG) in the G gamma-gene of a common ancestor of Homo and Gorilla and then was transferred to the A gamma-gene by subsequent conversions in the human lineage. DNA sequence conversions, similar to that attributed to the fetal gamma-globin genes, appear to be relatively frequent phenomena and, if widespread throughout the genome, may have profound evolutionary consequences.
Alleles↗
Origins and molecular evolution of the carbonic anhydrase isozymes.
Work on membrane-bound and subcellular forms of CA at the protein level, and the possibility of multiple forms of the mouse CA II gene at the DNA level, indicate that CA may represent an extensive multigene family. A method for classifying newly sequenced CA molecules, or genes encoding them, is discussed. Phylogenetic trees based on the existing sequence data are presented and discussed in terms of gene evolution. The active-site residues of CA II have been more conserved in evolution than those of CA I or CA III. After the gene duplications, CA III and CA I initially evolved more rapidly than CA II. Since the mammalian radiation, the CA II molecule as a whole has been accepting substitutions more frequently than CA I, which in turn is evolving more rapidly than CA III. These findings can be explained if external regions of CA I and CA III have been conserved in evolution owing to interactions with other molecules. Two such regions appear to be residues 18-37 in CA I and 231-250 in CA III. Spinach CA was purified and a small amount of sequence data collected. The difficulty in aligning it with animal CAs suggests that a plant CA may not be suitable to shed light on the active site and character of the ancestral eukaryote CA.
Amino Acid Sequence↗
The spatial distribution of fixed mutations within genes coding for proteins.
We have examined the extensive amino acid sequence data now available for five protein families - the alpha crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromes c - with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10(-44). Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.
Amino Acid Sequence↗
Phylogenetic origins and adaptive evolution of avian and mammalian haemoglobin genes.
Recent years have seen rapid growth in amino acid sequence data on globins and nucleotide sequence data on haemoglobin genes and pseudogenes, and cladistic analysis of these data continues to reveal new facets of globin evolution. Our present findings demonstrate: (1) avian and mammalian embryonic alpha genes (pi and xi, respectively) had a monophyletic origin involving an alpha locus duplication about 400 Myr ago soon after the duplication which separated alpha and beta genes; (2) much later in phylogeny, independent beta-gene duplications produced the embryonic rho locus of birds and embryonic epsilon and fetal gamma loci of mammals. This parallels the earlier finding that myoglobins evolved more than once from generalized globin ancestors. Here we support the view that such globin evolution resulted from natural selection acting on mutations in duplicated genes. Thus, our evidence contradicts the neutralist view in which almost all amino acid substitutions in descent to extant globins evaded positive selection.
Amino Acid Sequence↗
Evolution of cytochrome C investigated by the maximum parsimony method.
Rates of evolution for cytochrome c over the past one billion years were calculated from a maximum parsimony dendrogram which approximates the phylogeny of 87 lineages. Two periods of evolutionary acceleration and deceleration apparently occurred for the cytochrome c molecule. The tempo of evolutionary change indicated by this analysis was compared to the patterns of acceleration and deceleration in the ancestry of several other proteins. The synchrony of these tempos of molecular change supports the notion that rapid genetic evolution accompanied periods of major adaptive radiations. Rates of change at different time in several structural-functional areas of cytochrome c were also investigated in order to test the Darwinian hypothesis that during periods of rapid evolution, functional sites accumulate proportionately more substitutions than areas with no known functions. Rates of change in four proposed functional groupings of sites were therefore compared to rates in areas of unknown function for several different time periods. This analysis revealed a significant increase in the rate of evolution for sites associated with the regions of cytochrome c oxidase and reductase interaction during the period between the emergence of the eutherian ancestor to the emergence of the anthropoid ancestor.
Animals↗
The evolutionary relationship of the enzymes involved in blood coagulation and hemostasis.
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Animals↗
On investigating the statistical properties of the populous path algorithm by computer simulation. Counterconclusions to those of Tateno and Nei.
Goodman et al.'s (1974) populous path algorithm for estimating hidden mutational change in protein evolution is designed to be used as an adjunct to the maximum parsimony method. When the algorithm is so used, the augmented maximum parsimony distances, far from being overestimates, are underestimates of the actual number of nucleotide substitutions which occur in Tateno and Nei's (1978) computer simulation by the Poisson process model, even when the simulation is carried out at two and a half times the sequence density. Although underestimates, our evidence shows that they are nevertheless more accurate than estimates obtained by a Poisson correction. In the maximum parsimony reconstruction, there is a bias towards overrepresenting the number of shared nucleotide identities between adjacent ancestral and descendant nodal sequences with the bias being stronger in those portions of the evolutionary tree sparser in sequence data. Because of this particular property of maximum parsimony reconstructed sequences, the conclusions of Tateno and Nei concerning the statistical properties of the populous path algorithm are invalid. We conclude that estimates of protein evolutionary rates by the maximum parsimony--populous path approach will become more accurate rather than less as larger numbers of closely related species are included in the analysis.
Biological Evolution↗