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PubMed1990

A maximum likelihood approach to the detection of selection from a phylogeny.

A large amount of information is contained within the phylogenetic relationships between species. In addition to their branching patterns it is also possible to examine other aspects of the biology of the species. The influence that deleterious selection might have is determined here. The likelihood of different phylogenies in the presence of selection is explored to determine the properties of such a likelihood surface. The calculation of likelihoods for a phylogeny in the presence and absence of selection, permits the application of a likelihood ratio test to search for selection. It is shown that even a single selected site can have a strong effect on the likelihood. The method is illustrated with an example from Drosophila melanogaster and suggests that deleterious selection may be acting on transposable elements.

Animals↗

PubMed1991

Molecular evolution and phylogeny of the Drosophila virilis species group as inferred by two-dimensional electrophoresis.

Systematic relationship among the 12 species of the Drosophila virilis species group, and Drosophila robusta, were investigated by the use of two-dimensional electrophoresis (2-DE). A total of 389 protein characters (about 200 loci) were scored and analyzed both phylogenetically and phenetically. The resulting phylogeny was found to be largely concordant with the current views of evolution among these species based on other independent morphological, chromosomal, electrophoretic, and immunological data sets, although some notable differences were observed. The 2-DE data also appeared to be useful for constructing a molecular clock to date the absolute times of divergence among the species. It appears from this analysis that the evolution of the major clades within the species group occurred about 20 million years ago. Previous suggestions that the rate of molecular evolution was different between the virilis and montana phylads was not confirmed. The technique of 2-DE seems to be an excellent tool for reconstructing phylogenies and should be particularly valuable for examining relatively closely related species.

Animals↗

PubMed1989

Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing microorganisms.

The complete nucleotide sequence of a nitrogenase (nifH) gene was determined from a second strain (HRN18a) of Frankia, an aerobic soil bacterium. The open reading frame is 870 bp long and encodes a polypeptide of 290 amino acids. The amino acid and nucleotide sequences were compared with 21 other published sequences. The two Frankia strains were 96% similar at the amino acid level and 93% similar at the nucleotide level. A number of methods were used to infer phylogenies of these nitrogen fixers, based on nifH amino acid and nucleotide sequences. The results obtained do not agree completely with other phylogenies for these bacteria and thus make probable occurrences of lateral transfer of the nif genes. The time of divergence of the two Frankia strains could be estimated at about 100 million years. The vanadium-dependent (Type 2) nitrogenase present in Azotobacter spp. appears to be a recent derivation from the conventional molybdenum-dependent (Type 1) enzyme, whereas the iron-dependent (Type 3) alternative nitrogenase would have a much older origin.

Actinomyces↗

PubMed1975

Nuclear characteristics and phylogeny in the protistan phylum Ciliophora.

Ciliates possess a number of nuclear characteristics which, in combination, are unique among the Protista. Nevertheless, attempts to understand the origin - presumably from a flagellate ancestry - of the Ciliophora as a phylum must be made, as well as efforts to elucidate phylogenetic pathways within the large and diverse assemblage represented by its present-day forms. The macronucleus may provide an important clue to early ciliate phylogeny, since we still have, among extant species, groups of distinct "karyological relicts" exhibiting the very features expected in hypothetical forms corresponding to postulated stages in macronuclear origin and evolution. The relationship of the groups of "relict" species to the predominant polyploid-macronucleate forms, with a direct impact on the classification system as well as ciliate evolution and phylogeny in general, is discussed in some detail. Arguments are presented for taxonomic separation of the relatively primitive homokaryotic and diploid-macronucleate forms, which also share other features in common related to their being members of the interstitial fauna, from the more advanced ciliates. The problem is complicated by the non-nuclear structural complexities of these sand-dwelling forms, apparently secondarily-derived specializations which, by convergence, have come to resemble certain non-homologous features of the allegedly more highly evolved groups.

Biological Evolution↗

PubMed1988

The importance of protistan phylogeny for macroevolution.

Explicit estimates of protist phylogeny should play a key role in the development of macroevolutionary theory. Nearly half the evolutionary history of living systems involved only protists, and many trends and traits of macroevolutionary significance originated in protist groups. Special areas of research that can make use of protist phylogenies include: (1) origin of life studies, (2) biotic aspects of the evolution of the environment, (3) developmental biology and evolution, and (4) macroevolutionary trends in the diversification of life.

Animals↗

PubMed1988

Molecular evolution of the 5'-terminal domain of large-subunit rRNA from lower eukaryotes. A broad phylogeny covering photosynthetic and non-photosynthetic protists.

This paper summarizes the present status of an analysis of protist phylogeny using rapid partial sequencing of 28S rRNA. Data from 12 protistan phyla are now available and have been used to construct a tentative dendrogram based on a distance matrix method. The tree is robust and has considerable internal consistency. The following salient points are observed: a number of flagellate groups (particularly Euglenozoa) emerge very early among eukaryotes, whereas ciliates and dinoflagellates emerge late, suggesting that some characteristics that had been considered as primitive may in fact be derived. Both chlorophytic and chromophytic photosynthetic protists emerge very late in the tree, close to the Metazoa-Metaphyta-Fungi radiation, suggesting relatively late occurrence of the photosynthetic symbiosis. Taxonomic and phylogenetic information is also obtained within a phylum where rRNA of enough species are sequenced. A deep trichotomy is thus observed within the ciliates. The data are discussed with respect to classical protist phylogenies.

Animals↗

PubMed1992

Molecular phylogeny of the prickly shark, Echinorhinus cookei, based on a nuclear (18S rRNA) and a mitochondrial (cytochrome b) gene.

The classification of the sharks is unclear. This is particularly true for the superorder Squalomorphii. The relationships between the squalomorphs and other superorders of sharks and the relationships between the different orders within the squalomorphs are a matter of debate. Here, we report a molecular phylogeny for a little known member of this superorder, the genus Echinorhinus. Echinorhinus is most commonly classified in either the family Echinorhinidae (Squaliformes) or the family Squalidae (Squaliformes). However, some authors have suggested a closer relationship to the order Hexanchiformes. In an attempt to shed light on this controversy, we have cloned, sequenced, and compared two genes widely used in molecular phylogeny studies, the cytochrome b and the 18S rRNA from the rare prickly shark, Echinorhinus cookei, and two potential relatives, the spiny dogfish Squalus acanthias (Squaliformes), and the sevengill shark, Notorynchus cepedianus (Hexanchiformes). The sequences of these genes for the prickly shark, the dogfish, and the sevengill shark were found to be equally divergent, suggesting that the prickly shark is no closer to the order Squaliformes than to the order Hexanchiformes.

Animals↗

PubMed1987

Computational complexity of inferring phylogenies from chromosome inversion data.

In systematics, parsimony methods construct phylogenies, or evolutionary trees, in which characters evolve with the least evolutionary change. The chromosome inversion, or polymorphism, parsimony criterion is used when each character of a population may exhibit homozygous or heterozygous states, but when the heterozygous state must evolve uniquely. Variations of the criterion concern whether or not the ancestral states of characters are specified. We establish that problems of inferring phylogenies by these criteria are NP-complete and thus are so difficult computationally that efficient optimal algorithms for them are unlikely to exist.

Algorithms↗

PubMed1989

Phylogeny congruence analysis and isozyme classification: the pyruvate kinase system.

As the isozymes of pyruvate kinase (PK) are best known in rats, the characteristics of the rat isozymes are generally used to classify the PK isozymes in other species. Given the discrepancies generated by this classification by analogy, we evaluated a classification using a phylogeny congruence analysis of the compositional relatedness of vertebrate PK's. While our phylogenetic analysis confirmed the well established separation of the L and R isozymes from the K and M isozymes, its power became most evident in the identification of non-orthologous (or variant) forms of PK. Our analysis emphasized the uniqueness of chicken liver PK which cannot be classified either as a K or an L isozyme, confirmed that tumors express a variety of forms of PK, and indicated that lungs systematically express PK's which are not orthologous with PK's from other tissues. The determination of orthology by the phylogeny congruence analysis assumes that the structural data from different sources are subject to similar methodological error. However, we cannot reject the possibility that an apparent lack of orthology be due to artifacts during purification and analysis.

Amino Acids↗

PubMed1986

Mammalian phylogeny: comparison of morphological and molecular results.

In an attempt to resolve the "bushy" part at the root of the eutherian tree, 182 nondental morphological characters from 100 species (79 extant and 21 extinct; 98 mammalian and 2 nonmammalian) were analyzed using two maximum-parsimony tree-building algorithms. Parallel analyses of 2,258 pairwise immunodiffusion comparisons with chicken antisera on 101 mammalian species and of amino acid sequence data of alpha and beta hemoglobins and other published protein sequences were also carried out. The morphological and molecular phylogenies agree in depicting the infraclass Eutheria as consisting of five major clades (thus resolving part of the "bush"). Rates of evolution were also found to be similar in the two types of phylogenies.

Amino Acid Sequence↗

PubMed1992

The consistency of several phylogeny-inference methods under varying evolutionary rates.

A phylogenetic method is a consistent estimator of phylogeny if and only if it is guaranteed to give the correct tree, given that sufficient (possibly infinite) independent data are examined. The following methods are examined for consistency: UPGMA (unweighted pair-group method, averages), NJ (neighbor joining), MF (modified Farris), and P (parsimony). A two-parameter model of nucleotide sequence substitution is used, and the expected distribution of character states is calculated. Without perfect correction for superimposed substitutions, all four methods may be inconsistent if there is but one branch evolving at a faster rate than the other branches. Partial correction of observed distances improves the robustness of the NJ method to rate variation, and perfect correction makes the NJ method a consistent estimator for all combinations of rates that were examined. The sensitivity of all the methods to unequal rates varies over a wide range, so relative-rate tests are unlikely to be a reliable guide for accepting or rejecting phylogenies based on parsimony analysis.

Biological Evolution↗

PubMed1992

Experimental phylogenetics: generation of a known phylogeny.

Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

Biological Evolution↗

PubMed1975

[Ethology and phylogeny of the family Belontiidae (Anabantoidei, pisces)].

1. The behavioural patterns of the following species of the family Belontiidae were qualitatively examined and compared with each other: Colisa lalia, C. fasciata, C. chuna, Trichogaster trichopterus, T. leeri, T. microlepis, Macropodu, opercularis, Pseudosphromenus (Macropodus) cupanus cupanus, Betta splendens, Trichopsis pumilus, T. vittatus vittatus, T. vittatus schalleri, Belontia signata and the hybrids Colisa fasciata X lalia. 2. Among other points the paper puts some emphasis on the description of the reproductive behaviour of the various species (nest building, mating, parental behaviour). In addition aspects of feeding and fighting behaviour are described. 3. The subfamilies established by Liem (1963) on the basis of osteological characteristics can also be substantiated ethologically. 4. Liem's conception of the phylogeny of Belontiidae is criticized. His system conceiving phylogeny as a process of branching off successively is contrasted with a phylogenetic fan. The subfamilies Belontiinae, Trichogasterinae and Macropodinae differentiated almost at the same time. 5. The genus of Macropodus has a very isolated position within the sub-family of Macropodinae. The remaining genera are on a higher level of development regarding their reproductive behaviour. As a result of the paper Pseudosphromenus (Macropodus) cupanus has to be eliminated from the genus of Macropodus.

Aggression↗

PubMed1992

Nucleotide sequence of the 18S ribosomal ribonucleic acid gene from two teleosts and two sharks and their molecular phylogeny.

The 18S rRNA sequence was determined for two teleostean fish species, Fundulus heteroclitus and Sebastolobus altivelis, and two sharks, Squalus acanthias and Echinorhinus cookei. To study the molecular phylogeny of these taxa, the sequences were compared with 18S rRNA sequences of the Coelacanth Latimeria chalumnae, the frog Xenopus laevis, and humans. Maximum parsimony analysis of the sequences resulted in a single most parsimonious tree that is in agreement with the expected phylogeny. The correct phylogenetic tree was also found when using S. altivelis alone as the teleost representative. In contrast, the most parsimonious tree found by using F. heteroclitus as the teleost representative presented anomalous groupings (the teleost branch being grouped with humans), matching results previously obtained. However, a bootstrap analysis showed that some branches containing anomalous relationships were not significantly supported. An explanation for this peculiarity, the differences between our tree and previously identified ones, and their phylogenetic implications are discussed.

Animals↗

PubMed1986

Genetic brain malformations recapitulate phylogeny.

It is generally difficult to establish whether a congenital brain malformation has a genetic basis or is due to other factors. A thesis has been developed, that brain malformations with a genetic basis recapitulate phylogeny. In order to validate this thesis a retrospective CT investigation of brain dysmorphology was carried out in 50 cases of dysgenesis of the corpus callosum, 20 cases of the holoprosencephaly complex, 25 cases of Dandy-Walker malformation, and 50 cases of miscellaneous brain anomalies. This group was compared with 100 neonates with brain damage from acquired causes. The results strongly suggest that a brain malformation that recapitulates phylogeny is very likely to be based on genetic aberration.

Animals↗

PubMed1985

[Ontogeny and phylogeny: a quantitative theory of heterochrony].

Developmental variability in organisms underlies the relationship between ontogeny and phylogeny. The concept entropy permits a quantitative characterization of this variability and provides a basis for interpreting the phylogeny of heterochrony in evolution.

Animals↗

PubMed2025

Backtracking Cell Phylogenies in the Human Brain with Somatic Mosaic Variants.

Somatic mosaic variants, and especially somatic single nucleotide variants (sSNVs), occur in progenitor cells in the developing human brain frequently enough to provide permanent, unique, and cumulative markers of cell divisions and clones. Here, we describe an experimental workflow to perform lineage studies in the human brain using somatic variants. The workflow consists in two major steps: (1) sSNV calling through whole-genome sequencing (WGS) of bulk (non-single-cell) DNA extracted from human fresh-frozen tissue biopsies, and (2) sSNV validation and cell phylogeny deciphering through single nuclei whole-genome amplification (WGA) followed by targeted sequencing of sSNV loci.

Humans↗

PubMed2025

Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.

Recent theoretical and algorithmic advances in introgression detection, coupled with the growing availability of genome-scale data, have highlighted the widespread occurrence of interspecific gene flow across the tree of life. However, current methods largely depend on the molecular clock assumption-a questionable premise given empirical evidence of substitution rate variation across lineages. While such rate heterogeneity is known to compromise gene flow detection among divergent lineages, its impact on closely related taxa at shallow evolutionary timescales remains poorly understood, likely because these taxa are often assumed to adhere to a molecular clock. To address this gap, we combine theoretical analyses and simulations to evaluate the robustness of widely used site pattern methods (D-statistic and HyDe) to rate variation across phylogenetic timescales. Our results demonstrate that both methods exhibit high sensitivity to even minor deviations from the molecular clock at shallow timescales, complementing previous findings at deeper scales. Specifically, in young phylogenies (with an age of 3 × 105 generations) with small population sizes, weak (17% difference) and moderate (33% difference) rate variation can inflate false-positive rates up to 35% and 100%, respectively, using site pattern counts from a 500 Mb genome. Employing a more distant outgroup intensifies these spurious signals. Our study demonstrates that summary tests for introgression are pervasively vulnerable to minor rate variations and underscores the critical need for advanced methodologies to disentangle genuine introgression from false signals generated by rate heterogeneity.

Phylogeny↗