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PubMed2002

Evolutionary relationships among Astroviridae.

To study the evolutionary relationships among astroviruses, all available sequences for members of the family Astroviridae were collected. Phylogenetic analysis distinguished two deep-rooted groups: one comprising mammalian astroviruses, with ovine astrovirus being an outlier, and the other comprising avian astroviruses. All virus species as well as serotypes of human astroviruses represented individual lineages within the tree. All human viruses clustered together and separately from non-human viruses, which argue for their common evolutionary origin and against ongoing animal-to-human transmissions. The branching order of mammalian astroviruses was exactly the opposite of that of their host species, suggesting at least two cross-species transmissions involving pigs, cats and humans, possibly through intermediate hosts. Analysis of synonymous (Ds) versus non-synonymous (Da) distances revealed that negative selection is dominating in the evolution of astroviruses, with the Ds:Da ratios being up to 46 for the comparisons of the most closely related viruses. Phylogenetic analyses of all open reading frames (ORFs) based on Ds resulted in the loss of tree structures, with virus species--and in ORF2, even serotypes of human astroviruses--branching out from virtually a single node, suggesting their ancient separation. The strong selection against non-synonymous substitutions, the low number of which is, therefore, not proof of a recent separation between lineages, together with the position of the oldest available human astrovirus strain (1971) far from the common node of its serotype 4, suggest that intraserotype diversification originates from an earlier date.

Animals↗
PubMed1999

Estimating cell lineage from distributions of randomly introduced markers.

Cell lineage of a multicellular organism has been analysed by introducing a genetic or chemical marker that is inherited from a cell to its daughter cells and is detectable even after several cell divisions. To construct a complete cell lineage, all the cells at different developmental stages need to be identified, and then the intracellular marker must be introduced to each cell. In this paper, I study a new method of estimating cell lineage based on distributions of intercellular markers observed at a single stage, which are introduced randomly at earlier stages. Assumptions are: (1) cell lineage is invariant between embryos; (2) a small number of cells are marked in each experiment; and (3) the total number of replicate experiments is sufficiently large. Then we identify the most likely cell lineage pattern (or tree topology) as the one that requires the least marker insertions to be compatible with the observed distributions of cell markers. This method is essentially the same as the principle of persimony widely used for ancestral phylogeny reconstruction in evolutionary biology. When the total number of cells is small, we can generate all the possible cell lineages and calculate the minimum number of marker insertions for each candidate, and then choose the cell lineage that requires the least marker insertions. If the number of cells is large, we can use clustering method in which a pair of cells with the highest correlation in marker labelling are merged sequentially. The efficiency of the clustering method in estimating the correct cell lineage is confirmed by computer simulations. Finally, the clustering method is applied to reconstruct the cell lineage of ascidian from experimental data.

Animals↗
PubMed1989

On the evolutionary origin of the plant mitochondrion and its genome.

Higher plants occupy very different positions in the mitochondrial and nuclear lineages of global phylogenetic trees based on conserved regions of small subunit (SSU) and large subunit (LSU) rRNA sequences. In the nuclear subtree, plants branch off late, at a position reflecting a massive radiation of the major multicellular (and some unicellular) groups; in the mitochondrial subtree, in contrast, plants branch off early, near the point of connection between the mitochondrial and eubacterial lineages. Moreover, in the nuclear lineage, plants branch together with the unicellular green alga Chlamydomonas reinhardtii, whereas in the mitochondrial lineage (in both SSU and LSU trees), metaphytes and chlorophyte branch separately. Statistical evaluation indicates that the anomalous branching position of higher plants in the mitochondrial lineage is not a treeing artifact attributable to the relatively rapid rate of sequence divergence of non-plant mitochondrial rRNA sequences. In considering alternative biological explanations for these results, we are led to propose that the rRNA genes in plant mitochondria may be of more recent evolutionary origin than the rRNA genes in other mitochondria. This proposal has implications for monophyletic vs. polyphyletic scenarios of mitochondrial origin and is consistent with other evidence indicating that plant mtDNA is an evolutionary mosaic.

Journal Article↗
PubMed2000

Origin and relationships of the tarweed-silversword lineage (Compositae-Madiinae).

Based on results from phylogenetic analyses of nuclear 18S-26S rDNA internal transcribed spacer (ITS) region sequences, we suggest that the monophyletic tarweed and silversword subtribe (Madiinae) is phylogenetically nested among epaleate, x = 19 species of helenioid Heliantheae. Strong bootstrap support (100%) was obtained for a sister-group relationship between Madiinae and Arnica (including Mallotopus and Whitneya) in an analysis including representatives of recognized genera in a principally Californian clade (Madieae sensu Baldwin) identified from a phylogenetic investigation of Heliantheae s.l. (sensu lato) and Eupatorieae. In all minimum-length trees, the robust lineage comprising Madiinae and Arnica (x = 19) is part of a larger clade that also comprises Eatonella s.s. (sensu stricto), Hulsea, and Venegasia, all with x = 19. The phylogenetic position of Madiinae within a group of genera based uniformly on x = 19 leads us to conclude that the modal numbers of n = 7 and n = 8 (and other numbers, as low as n = 4) in Madiinae are the results of extreme dysploidy. Among the x = 19 "arnicoid" taxa, the near-universal characteristics of perenniality (except in the monotypic Eatonella s.s. and a minority of hulseas) and montane or high-latitudinal occurrence (except in the monotypic Venegasia) lead us to suggest that the most recent common ancestor of the tarweeds (a principally annual group of seasonally dry, low-elevation habitats) was probably a montane, herbaceous perennial resembling the unusual subalpine and alpine tarweeds constituting Raillardella s.s. (x = 17), an arnica-like genus. In Madiinae, Raillardella s.s. may be plesiomorphic in habit, capitular and ecological characteristics, and high base chromosome number. Shifts to an annual habit and to low chromosome numbers in Madiinae have been followed by subsequent episodes of polyploidy and descending dysploidy. We conclude that genome evolution in Madiinae has been marked by wide swings in chromosome number that confuse identification of diploids and polyploids.

Journal Article↗
PubMed1992

Statistical method for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages.

A statistical method is developed for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitution among different lineages. This method can be easily used for testing whether the length of an interior branch in a reconstructed tree is positive, i.e., whether the topology of the tree is correct. Computer simulations indicate that this method is appropriate for a statistical test. As an example, this method is applied to phylogenetic trees reconstructed for the four hominoid species: human, chimpanzee, gorilla, and orangutan. The results obtained show that the present method provides a powerful statistical test.

Animals↗
PubMed2025

Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae).

Allopolyploidization, resulting from hybridization and subsequent whole-genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS-Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of incomplete lineage sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himalayas from the Middle to Late Miocene was a key driver in the rapid diversification of the Maddenia clade, an endemic group in East Asia. This geological event facilitated extensive hybridization and allopolyploidization, particularly the introgression between the Himalayas-Hengduan and Central-Eastern China clades. This case study demonstrates the robustness and efficacy of our analytical approach in precisely identifying WGD events and elucidating the evolutionary mechanisms underlying allopolyploidization in polyploid Prunus.

Polyploidy↗
PubMed1998

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.

Animals↗
PubMed2004

Population structure of the Bacillus cereus group as determined by sequence analysis of six housekeeping genes and the plcR Gene.

The population structure of the Bacillus cereus group (52 strains of B. anthracis, B. cereus, and B. thuringiensis) was investigated by sequencing seven gene fragments (rpoB, gyrB, pycA, mdh, mbl, mutS, and plcR). Most of the strains were classifiable into two large subgroups in six housekeeping gene trees but not in the plcR tree. In addition, several consistent clusters were identified, which were unrelated to species distinction. Moreover, interrelationships among these clusters were incongruent in each gene tree. The incongruence length difference test and split decomposition analyses also showed incongruences between genes, suggesting horizontal gene transfer. The plcR gene was observed to have characteristics that differed from those of the other genes in terms of phylogenetic topology and pattern of sequence diversity. Thus, we suggest that the evolutionary history of the PlcR regulon differs from those of the other chromosomal genes and that recombination of the plcR gene may be frequent. The homogeneity of B. anthracis, which is depicted as an independent lineage in phylogenetic trees, is suggested to be of recent origin or to be due to the narrow taxonomic definition of species.

Animals↗
PubMed2006

A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in the reconstruction of phylogenetic relationships.

Partial genome sequencing (PGS) and restriction fragment analysis (RFA) are used frequently in molecular epidemiologic investigations. The relative accuracy of PGS and RFA in phylogenetic reconstruction has not been assessed. In this study, 32 model phylogenetic trees with 16 extant lineages were generated, for which DNA sequences were simulated under varying conditions of genome length, nucleotide substitution rate, and between-site substitution rate variation. Genotyping using PGS and RFA was simulated. The effect of tree structure (stemminess, imbalance, lineage variation) on the accuracy of phylogenetic reconstruction (topological and branch length similarity) was evaluated. Overall, PGS was more accurate than RFA. The accuracy of PGS increased with increasing sequence length. The accuracy of RFA increased with the number of restriction enzymes used. In fragment size comparison, the Dice and Nei-Li algorithms differed little, with both more accurate than the Fragment Size Distribution algorithm. For RFA, higher tree stemminess and longer genome length were associated with higher topological accuracy, whereas lower tree stemminess and lower substitution rates were associated with higher branch length accuracy. For PGS, lower tree imbalance was associated with higher topological accuracy, whereas lower tree stemminess, higher substitution rate, and lower between-site substitution rate variation were associated with higher branch length accuracy. RFA had higher topological accuracy than PGS only for the shortest sequence length (200 bps) at a low substitution rate, high tree stemminess, and long genome length. PGS had equal or higher accuracy in branch length reconstruction than RFA under all conditions investigated. Thus, partial genome sequencing is recommended over restriction fragment analysis for conditions within the parameter space examined.

Computational Biology↗
PubMed1991

Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens.

Analysis of its 16S rRNA sequence shows that the newly discovered hyperthermophilic methanogen, Methanopryus kandleri, is phylogenetically unrelated to any other known methanogen. The organism represents a separate lineage originating near the root of the archaeal tree. Although the 16S rRNA sequence of Mp. kandleri resembles euryarchaeal 16S rRNAs more than it does crenarchaeal, it shows more crenarchaeal signature features than any known euryarchaeal rRNA. Attempts to place it in relation to the root of the archaeal tree show that the Mp. kandleri lineage likely arises from the euryarchaeal branch of the tree. While the existence of so deeply branching a methanogenic lineage brings into question the thesis that methanogenesis evolved from an earlier metabolism similar to that seen in Thermococcus, it at the same time reinforces the notion that the aboriginal [correction of aborginal] archaeon was a thermophile.

Archaea↗
PubMed1994

Molecular phylogenetics of cupped oysters based on partial 28S rRNA gene sequences.

Partial sequences of 28S-like rDNA were amplified using PCR and sequenced for eight species of oyster and one species of mussel. Phylogenetic relationships among seven species of Crassostreinid oyster were inferred from aligned sequences by parsimony and maximum-likelihood methods. Of the 315 sites that varied, 90 were phylogenetically informative in parsimony analysis. Inference by maximum parsimony (MP) is consistent with maximum-likelihood (ML) analysis for the major lineages, yielding a tree with the topology (Mytilus edulis (Ostrea edulis ((Crassostrea rivularis (C. belcheri, C. gigas))(C. virginica, C. rhizophorae, Saccostrea cuccullata, S. commercialis)))). MP and ML analyses resolved the systematic relationships of the Saccostrea and Atlantic Crassostrea differently such that a polytomy linking these four taxa is preferred with the data available. Molecular data support a later divergence of the tropical Pacific Saccostrea from a common ancestor of the Atlantic Crassostrea species. Molecular data from domains D1, D2, and partial D3 of the 28S rDNA supply sufficient phylogenetic information to determine systematic relationships among the extant oyster taxa, from the major species groups to the family level, thus providing valuable characters that are able to supplement the paucity of morphological characters so far recognized.

Animals↗
PubMedDate not supplied

Clues from Xanthomonas campestris about the evolution of aromatic biosynthesis and its regulation.

The recent placement of major Gram-negative prokaryotes (Superfamily B) on a phylogenetic tree (including, e.g., lineages leading to Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter calcoaceticus) has allowed initial insights into the evolution of the biochemical pathway for aromatic amino acid biosynthesis and its regulation to be obtained. Within this prokaryote grouping, Xanthomonas campestris ATCC 12612 (a representative of the Group V pseudomonads) has played a key role in facilitating deductions about the major evolutionary events that shaped the character of aromatic biosynthesis within this grouping. X. campestris is like P. aeruginosa (and unlike E. coli) in its possession of dual flow routes to both L-phenylalanine and L-tyrosine from prephenate. Like all other members of Superfamily B, X. campestris possesses a bifunctional P-protein bearing the activities of both chorismate mutase and prephenate dehydratase. We have found an unregulated arogenate dehydratase similar to that of P. aeruginosa in X. campestris. We separated the two tyrosine-branch dehydrogenase activities (prephenate dehydrogenase and arogenate dehydrogenase); this marks the first time this has been accomplished in an organism in which these two activities coexist. Superfamily B organisms possess 3-deoxy-D-arabino-heptulosonate 7-P (DAHP) synthase as three isozymes (e.g., in E. coli), as two isozymes (e.g., in P. aeruginosa), or as one enzyme (in X. campestris). The two-isozyme system has been deduced to correspond to the ancestral state of Superfamily B. Thus, E. coli has gained an isozyme, whereas X. campestris has lost one. We conclude that the single, chorismate-sensitive DAHP synthase enzyme of X. campestris is evolutionarily related to the tryptophan-sensitive DAHP synthase present throughout the rest of Superfamily B. In X. campestris, arogenate dehydrogenase, prephenate dehydrogenase, the P-protein, chorismate mutase-F, anthranilate synthase, and DAHP synthase are all allosteric proteins; we compared their regulatory properties with those of enzymes of other Superfamily B members with respect to the evolution of regulatory properties. The network of sequentially operating circuits of allosteric control that exists for feedback regulation of overall carbon flow through the aromatic pathway in X. campestris is thus far unique in nature.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed1996

Molecular evolution of nitrate reductase genes.

To understand the evolutionary mechanisms and relationships of nitrate reductases (NRs), the nucleotide sequences encoding 19 nitrate reductase (NR) genes from 16 species of fungi, algae, and higher plants were analyzed. The NR genes examined show substantial sequence similarity, particularly within functional domains, and large variations in GC content at the third codon position and intron number. The intron positions were different between the fungi and plants, but conserved within these groups. The overall and nonsynonymous substitution rates among fungi, algae, and higher plants were estimated to be 4.33 x 10(-10) and 3.29 x 10(-10) substitutions per site per year. The three functional domains of NR genes evolved at about one-third of the rate of the N-terminal and the two hinge regions connecting the functional domains. Relative rate tests suggested that the nonsynonymous substitution rates were constant among different lineages, while the overall nucleotide substitution rates varied between some lineages. The phylogenetic trees based on NR genes correspond well with the phylogeny of the organisms determined from systematics and other molecular studies. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated to be about 340 Myr when the fungi-plant or algae-higher plant divergence times were used as reference points and 191 Myr when the rice-barley divergence time was used as a reference point. These two estimates are consistent with other estimates of divergence times based on these reference points. The lack of consistency between these two values appears to be due to the uncertainty of the reference times.

Base Composition↗
PubMed1997

Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards.

A phylogenetic tree for major lineages of iguanian lizards is estimated from 1,488 aligned base positions (858 informative) of newly reported mitochondrial DNA sequences representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Two well-supported groups are defined, the Acrodonta and the Iguanidae (sensu lato). This phylogenetic hypothesis is used to investigate evolutionary shifts in mitochondrial gene order, origin for light-strand replication, and secondary structure of tRNACys. These three characters shift together on the branch leading to acrodont lizards. Plate tectonics and the fossil record indicate that these characters changed in the Jurassic. We propose that changes to the secondary structure of tRNACys may destroy function of the origin for light-strand replication which, in turn, may facilitate shifts in gene order.

Animals↗
PubMed2002

Evidence of gene conversion events between paralogous sequences produced by tetraploidization in Salmoninae fish.

We investigated the occurrence of gene conversions between paralogous sequences of Salmoninae derived from ancestral tetraploidization and their effect on the evolutionary history of DNA sequences. A microsatellite with long flanking regions (750 bp) including both coding and noncoding sequences was analyzed. Microsatellite size polymorphism was used to detect the alleles of both paralogous counterparts and infer linkage arrangement between loci. DNA sequencing of seven Salmoninae species revealed that paralogous sequences were highly differentiated within species, especially for noncoding regions. Ten gene conversion events between paralogous sequences were inferred. While these events appears to have homogenized regions of otherwise highly differential paralogous sequences, they amplified the differentiation among orthologous sequences. Their effects were larger on coding than on noncoding regions. As a consequence, noncoding sequences grouped by orthologous lineages in phylogenetic trees, whereas coding regions grouped by taxa. Based upon these results, we present a model showing how gene conversion events may also result in the PCR amplification of nonorthologous sequences in different taxa, with obvious complications for phylogenetic inferences, comparative mapping, and population genetic studies.

Animals↗
PubMed2006

Efficient methods for estimating amino acid replacement rates.

Replacement rate matrices describe the process of evolution at one position in a protein and are used in many applications where proteins are studied with an evolutionary perspective. Several general matrices have been suggested and have proved to be good approximations of the real process. However, there are data for which general matrices are inappropriate, for example, special protein families, certain lineages in the tree of life, or particular parts of proteins. Analysis of such data could benefit from adaption of a data-specific rate matrix. This paper suggests two new methods for estimating replacement rate matrices from independent pairwise protein sequence alignments and also carefully studies Müller-Vingron's resolvent method. Comprehensive tests on synthetic datasets show that both new methods perform better than the resolvent method in a variety of settings. The best method is furthermore demonstrated to be robust on small datasets as well as practical on very large datasets of real data. Neither short nor divergent sequence pairs have to be discarded, making the method economical with data. A generalization to multialignment data is suggested and used in a test on protein-domain family phylogenies, where it is shown that the method offers family-specific rate matrices that often have a significantly better likelihood than a general matrix.

Amino Acid Substitution↗
PubMed1996

Cloning and characterization of the gene encoding Halobacterium halobium adenylate kinase.

The gene (AK) encoding adenylate kinase (AK) of Halobacterium halobium was cloned. AK consisted of 648 bp and coded for 216 amino acids (aa). S1 mapping and primer extension experiments indicated that the transcription start point (tsp) was located immediately upstream from the start codon. The TAT-like promoter sequence was found at a position 20-24 bp upstream from tsp. The most striking property of the enzyme was a putative Zn finger-like structure with four cysteines. It might contribute to the structural stability of the molecule in high-salt conditions. Phylogenetic analysis indicated two lineages of the AK family, the short and long types which diverged a long time ago, possibly before the separation of prokaryotes and eukaryotes. Although the H. halobium AK belongs to the long-type AK lineage, it is located in an intermediary position between the two lineages of the phylogenetic tree, indicating early divergence of the gene along the long-type lineage.

Adenylate Kinase↗
PubMed2005

Evolutionary history of the genus Listeria and its virulence genes.

The genus Listeria contains the two pathogenic species Listeria monocytogenes and Listeria ivanovii and the four apparently apathogenic species Listeria innocua, Listeria seeligeri, Listeria welshimeri, and Listeria grayi. Pathogenicity of the former two species is enabled by an approximately 9 kb virulence gene cluster which is also present in a modified form in L. seeligeri. For all Listeria species, the sequence of the virulence gene cluster locus and its flanking regions was either determined in this study or assembled from public databases. Furthermore, some virulence-associated internalin loci were compared among the six species. Phylogenetic analyses were performed on a data set containing the sequences of prs, ldh, vclA, and vclB (all directly flanking the virulence gene cluster), as well as the iap gene and the 16S and 23S-rRNA coding genes which are located at different sites in the listerial chromosomes. L. grayi represents the deepest branch within the genus. The remaining five species form two groupings which have a high bootstrap support and which are consistently found by using different treeing methods. One lineage represents L. monocytogenes and L. innocua, while the other contains L. welshimeri, L. ivanovii and L. seeligeri, with L. welshimeri forming the deepest branch. Based on this perception, we tried to reconstruct the evolution of the virulence gene cluster. Since no traces of lateral gene transfer events could be detected the most parsimonious scenario is that the virulence gene cluster was present in the common ancestor of L. monocytogenes, L. innocua, L. ivanovii, L. seeligeri and L. welshimeri and that the pathogenic capability has been lost in two separate events represented by L. innocua and L. welshimeri. This hypothesis is also supported by the location of the putative deletion breakpoints of the virulence gene cluster within L. innocua and L. welshimeri.

Bacterial Proteins↗