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PubMed2003

Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing.

A multilocus sequence typing (MLST) scheme has been developed for the unambiguous characterization of encapsulated and noncapsulated Haemophilus influenzae isolates. The sequences of internal fragments of seven housekeeping genes were determined for 131 isolates, comprising a diverse set of 104 serotype a, b, c, d, e, and f isolates and 27 noncapsulated isolates. Many of the encapsulated isolates had previously been characterized by multilocus enzyme electrophoresis (MLEE), and the validity of the MLST scheme was established by the very similar clustering of isolates obtained by these methods. Isolates of serotypes c, d, e, and f formed monophyletic groups on a dendrogram constructed from the differences in the allelic profiles of the isolates, whereas there were highly divergent lineages of both serotype a and b isolates. Noncapsulated isolates were distinct from encapsulated isolates and, with one exception, were within two highly divergent clusters. The relationships between the major lineages of encapsulated H. influenzae inferred from MLEE data could not be discerned on a dendrogram constructed from differences in the allelic profiles, but were apparent on a tree reconstructed from the concatenated nucleotide sequences. Recombination has not therefore completely eliminated phylogenetic signal, and in support of this, for encapsulated isolates, there was significant congruence between many of the trees reconstructed from the sequences of the seven individual loci. Congruence was less apparent for noncapsulated isolates, suggesting that the impact of recombination is greater among noncapsulated than encapsulated isolates. The H. influenzae MLST scheme is available at www.mlst.net, it allows any isolate to be compared with those in the MLST database, and (for encapsulated isolates) it assigns isolates to their phylogenetic lineage, via the Internet.

Bacterial Capsules↗

PubMed1994

Molecular evolutionary processes and conflicting gene trees: the hominoid case.

Molecular evolutionary processes modify DNA over time, creating both newly derived substitutions shared by related descendant lineages (phylogenetic signal) and "false" similarities which confound phylogenetic reconstruction (homoplasy). However, some types of DNA regions, for example those containing tandem duplicate repeats, are preferentially subject to homoplasy-inducing processes such as sporadically occurring concerted evolution and DNA insertion/deletion. This added level of homoplasic "noise" can make DNA regions with repeats less reliable in phylogenetic reconstruction than those without repeats. Most molecular datasets which distinguish among African hominoids support a human-chimpanzee clade; the most notable exception is from the involucrin gene. However, phylogenetic resolution supporting a chimpanzee-gorilla clade is based entirely on involucrin DNA repeat regions. This is problematic because (1) involucrin repeats are difficult to align, and published alignments are contradictory; (2) involucrin repeats are subject to DNA insertion/deletion; (3) gorillas are polymorphic in that some do not have repeats reported to be synapomorphies linking chimpanzees and gorillas. Gene tree/species tree conflicts can occur due to the sorting of ancestrally polymorphic alleles during speciation. Because hominoid females transfer between groups, mitochondrial and nuclear gene flow occur to the same extent, and the probability of conflict between mitochondrial and nuclear gene trees is theoretically low. When hominoid intraspecific mitochondrial variability is taken into account [based on cytochrome oxidase subunit II (COII) gene sequences], humans and chimpanzees are most closely related, showing the same relative degree of separation from gorillas as when single individuals representing species are analyzed. Conflicting molecular phylogenies can be explained in terms of molecular evolutionary processes and sorting of ancient polymorphisms. This perspective can enhance our understanding of hominoid molecular phylogenies.

Alleles↗

PubMed2005

Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates.

Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model--the nucleotide composition--is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the "common ancestor" of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.

Animals↗

PubMed1998

Evolution of histone H4 and H3 genes in different ciliate lineages.

The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4 genes including the intergenic region. The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences. The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones. The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates.

Amino Acid Sequence↗

PubMed2005

Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences.

Mitochondrial DNA (mtDNA) sequences are comonly used for inferring phylogenetic relationships. However, the strand-specific bias in the nucleotide composition of the mtDNA, which is thought to reflect assymetric mutational constraints, combined with the important compositional heterogeneity among taxa, are known to be highly problematic for phylogenetic analyses. Here, nucleotide composition was compared across 49 species of Metazoa (34 arthropods, 2 annelids, 2 molluscs, and 11 deuterosomes), and analyzed for a mtDNA fragment including six protein-coding genes, i.e., atp6, atp8, cox1, cox2, cox3, and nad2. The analyses show that most metazoan species present a clear strand assymetry, where one strand is biased in favor of A and C, whereas the other strand has reverse bias, i.e. in favor of T and G. the origin of this strand bias can be related to assymetric mutational constraints involving deaminations of A and C nucleotides during the replication and/or transcription processes. The analyses reveal that six unrelated genera are characterized by a reversal of the usual strand bias, i.e., Argiope (Araneae), Euscorpius (Scorpiones), Tigrioupus (Maxillopoda), Branchiostoma (Cephalochordata) Florometra (Echinodermata), and Katharina (Mollusca). It is proposed that assymetric mutational constraints have been independantly reversed in these six genera, through an inversion of the control region, i.e., the region that contains most regulatory elements for replication and transcription of the mtDNA. We show that reversals of assymetric mutational constraints have dramatic consequences on the phylogenetic analyses, as taxa characterized by reverse strand bias tend to group together due to long-branch attraction artifacts. We propose a new method for limiting this specific problem in tree reconstruction under the Bayesian approach. We apply our method to deal with the question of phylogenetic relationships of the major lineages of Arthropoda, This new approach provides a better congruence with nuclear analyses based on mtDNA sequences, our data suggest that Chelicerata, Crustacea, Myriapoda, Pancrustacea, and Paradoxopoda are monophyletic.

Animals↗

PubMed2004

Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data.

A phylogeny of Iberian Aphodiini dung beetles was reconstructed based on morphological and molecular data. The data set included a total of 84 variable characters from wing venation, mouthparts, genitalia, and external morphology, as well as mitochondrial partial cytochrome c oxidase I (COI), complete tRNA-Leu (UUR), and partial cytochrome c oxidase II (COII) gene nucleotide sequences (1210 positions). Phylogenetic trees based on molecular data were relatively more resolved than those based on morphological characters. The Bayesian analysis of combined molecular and morphological data provided resolution not achieved by each data set separately. Ammoecius and Aphodius are the first lineages that branch off from the tree, followed by Acrossus, Nimbus, and Heptaulacus. The remaining studied taxa are recovered in a more derived clade that lacks internal resolution. Reconstructed trees based on molecular data showed relatively short internal nodes that were weakly supported. Such pattern may reflect a rapid radiation at the origin of the tribe Aphodiini, but also saturation of mutational changes. Several tests were conducted to discern between both competing hypotheses, as well as to assess the effect of incomplete taxon sampling.

Animals↗

PubMed1999

The Tangled Web: Gene Genealogies and the Origin of Eukaryotes.

Accessing data from the genomes of organisms (individual genes) and analyzing these data using sophisticated alignment and phylogenetic methods led to the expectation that we would be able to paint a clear picture of the evolution of eukaryotes. Previous analyses based on morphology and ultrastructure failed to pinpoint both the sister taxon to eukaryotes and the branching order of eukaryotic lineages. However, the expectation that molecular data would provide resolution has not been met since a growing number of gene genealogies present conflicting hypotheses for the origin and diversification of eukaryotes. Instead of reconstructing a simple bifurcating tree of life, these gene genealogies have generated a complex picture of eukaryotic genomes whereby ancient lateral transfers (of individual genes or perhaps even entire genomes) has tangled the evolutionary history of eukaryotes. Resolution of these conflicting genealogies comes in recognizing that eukaryotes are chimeric, containing genetic information from multiple ancestral lineages.

Journal Article↗

PubMed1997

A proposal to revive the genus Kitasatospora (Omura, Takahashi, Iwai, and Tanaka 1982).

We determined almost complete 16S ribosomal DNA sequences for 12 actinomycete strains which were either previously classified as Kitasatospora strains or defined as Streptomyces strains but shown to contain major amounts of meso-diaminopimelic acid in their whole-cell hydrolysates. These sequences were subjected to phylogenetic analyses together with the sequences of 34 Streptomyces species. Phylogenetic trees were reconstructed by using both neighbor-joining and maximum-parsimony methods. The Kitasatospora species always formed a stable monophyletic clade. However, the genus Kitasatospora appeared to be either a sister taxon of the genus Streptomyces or a lineage that originated from within Streptomyces species, depending on the outgroup used. Phylogenetic trees were also constructed by using the sequences of the 16S-23S rRNA gene spacers. Streptomyces and Kitasatospora species were consistently recovered as two distinct clades independent of the outgroup used. On the basis of phylogenetic, chemotaxonomic, and phenotypic evidence, we propose that the genus Kitasatospora Omura et al. 1982 should be revived.

Actinomycetaceae↗

PubMed2000

Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA.

Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new method called the serial-sample unweighted pair grouping method with arithmetic means (sUPGMA) is presented that reconstructs a genealogy or phylogeny of sequences sampled serially in time using a matrix of pairwise distances. The resulting tree depicts the terminal lineages of each sample ending at a different level consistent with the sample's temporal order. Since sUPGMA is a variant of UPGMA, it will perform best when sequences have evolved at a constant rate (i.e., according to a molecular clock). On simulated data, this new method performs better than standard cluster analysis under a variety of longitudinal sampling strategies. Serial-sample UPGMA is particularly useful for analysis of longitudinal samples of viruses and bacteria, as well as ancient DNA samples, with the minimal requirement that samples of sequences be ordered in time.

DNA, Viral↗

PubMed2004

Reconstructing evolutionary relationships from functional data: a consistent classification of organisms based on translation inhibition response.

The last two decades have witnessed an unsurpassed effort aimed at reconstructing the history of life from the genetic information contained in extant organisms. The availability of many sequenced genomes has allowed the reconstruction of phylogenies from gene families and its comparison with traditional single-gene trees. However, the appearance of major discrepancies between both approaches questions whether horizontal gene transfer (HGT) has played a prominent role in shaping the topology of the Tree of Life. Recent attempts at solving this controversy and reaching a consensus tree combine molecular data with additional phylogenetic markers. Translation is a universal cellular function that involves a meaningful, highly conserved set of genes: both rRNA and r-protein operons have an undisputed phylogenetic value and rarely undergo HGT. Ribosomal function reflects the concerted expression of that genetic network and consequently yields information about the evolutionary paths followed by the organisms. Here we report on tree reconstruction using a measure of the performance of the ribosome: antibiotic sensitivity of protein synthesis. A large database has been used where 33 ribosomal systems belonging to the three major cellular lineages were probed against 38 protein synthesis inhibitors. Different definitions of distance between pairs of organisms have been explored, and the classical algorithm of bootstrap evaluation has been adapted to quantify the reliability of the reconstructions obtained. Our analysis returns a consistent phylogeny, where archaea are systematically affiliated to eukarya, in agreement with recent reconstructions which used information-processing systems. The integration of the information derived from relevant functional markers into current phylogenetic reconstructions might facilitate achieving a consensus Tree of Life.

Archaea↗

PubMed2005

Mitochondrial phylogeny of pine cone beetles (Scolytinae, Conophthorus) and their affiliation with geographic area and host.

Pine cone beetles (Conophthorus spp.) feed and kill immature cones of Pinus species, thereby reducing seed production and seriously impairing reforestation of forest ecosystems. Population variation of Conophthorus reproductive behavior has hampered the development of semiochemical control of these pests. This difficulty is compounded by a lack of taxonomic knowledge and species diagnostic characters. Researchers and managers rely, in part, on host associations and geographic locality for species identifications and these have arguable taxonomic utility. However, host use and/or geographic separation may influence Conophthorus lineage diversification. To improve Conophthorus taxonomy and understand the association of host and geography with lineage diversification, a phylogeny of 43 individuals, including all valid species and a robust sample of C. ponderosae from different hosts, is reconstructed using 785 nucleotides of the 3'-end of the mitochondrial cytochrome oxidase I gene. Thirty trees were recovered in a parsimony analysis and the strict consensus was well resolved and supported by branch support measures. Conophthorus was monophyletic but mitochondrial polyphyly was uncovered for several species. The data also suggested an underestimation of species diversity. Phylogenetically related Conophthorus lineages were significantly associated with geographic proximity but not with host, as indicated by comparisons of character optimized geographic distributions and host associations against randomized distributions of these attributes on the parsimony tree. These results suggest that geographic separation better explains the mode of Conophthorus lineage diversification than does host specialization. Based on these results, researchers and managers of Conophthorus should consider populations as potentially different evolutionary entities until species boundaries are delineated via a robust phylogenetic revision of Conophthorus.

Amino Acids↗

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↗

PubMed2006

Genome histories clarify evolution of the expansin superfamily: new insights from the poplar genome and pine ESTs.

Expansins comprise a superfamily of plant cell wall-loosening proteins that has been divided into four distinct families, EXPA, EXPB, EXLA and EXLB. In a recent analysis of Arabidopsis thaliana and Oryza sativa expansins, we proposed a further subdivision of the families into 17 clades, representing independent lineages in the last common ancestor of monocots and eudicots. This division was based on both traditional sequence-based phylogenetic trees and on position-based trees, in which genomic locations and dated segmental duplications were used to reconstruct gene phylogeny. In this article we review recent work concerning the patterns of expansin evolution in angiosperms and include additional insights gained from the genome of a second eudicot species, Populus trichocarpa, which includes at least 36 expansin genes. All of the previously proposed monocot-eudicot orthologous groups, but no additional ones, are represented in this species. The results also confirm that all of these clades are truly independent lineages. Furthermore, we have used position-based phylogeny to clarify the history of clades EXPA-II and EXPA-IV. Most of the growth of the expansin superfamily in the poplar lineage is likely due to a recent polyploidy event. Finally, some monocot-eudicot clades are shown to have diverged before the separation of the angiosperm and gymnosperm lineages.

Arabidopsis↗

PubMed1993

Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.).

Copia-like retrotransposable elements were identified in allotetraploid cotton, Gossypium hirsutum, and two species representing its diploid progenitors, G. herbaceum and G. raimondii. These elements are present in high copy number in all three species. Because the two diploid genomic groups have been isolated on opposite sides of the world for 6-11 million years, horizontal transfer of elements between these species is highly unlikely. Elements were intensively sampled to generate a model of copia-like retrotransposable element evolution in systems where vertical transmission is the sole probable means of descent. Copia-like retrotransposon diversity is equally great in all three Gossypium species. Despite this high heterogeneity, analysis of 89 partial reverse transcriptase sequences resulted in the recognition of nine sharply differentiated retrotransposon lineages, each containing elements that share high sequence similarity. No evidence of horizontal transfer from other taxa was obtained. Phylogenetic analyses demonstrate that element topologies are incongruent with Gossypium phylogeny. Consideration of processes that obscure phylogenetic reconstruction of multigene families (including sampling error, variable degrees of orthology and paralogy, differential lineage age and lineage loss and/or proliferation) demonstrates that incongruence between organismal and retrotransposon trees is expected under conditions in which vertical processes are the sole means of transmission. Identification of closely related elements between species allowed rates of copia-like retrotransposon sequence evolution to be estimated as approximately 10(-9) nucleotide substitutions/site/year. These rates are consistent with the interpretation that these retrotransposons have been evolving under functional constraints for most of the time frame bracketed by the species studied. Extrapolation of these results to previous studies that sampled from more highly divergent taxa indicates that horizontal transfer need not be invoked to explain observed phylogenetic patterns.

Amino Acid Sequence↗

PubMed2004

Widespread vertical transmission and associated host sex-ratio distortion within the eukaryotic phylum Microspora.

Vertical transmission (VT) and associated manipulation of host reproduction are widely reported among prokaryotic endosymbionts. Here, we present evidence for widespread use of VT and associated sex-ratio distortion in a eukaryotic phylum. The Microspora are an unusual and diverse group of eukaryotic parasites that infect all animal phyla. Following our initial description of a microsporidian that feminizes its crustacean host, we survey the diversity and distribution of VT within the Microspora. We find that vertically transmitted microsporidia are ubiquitous in the amphipod hosts sampled and that they are also diverse, with 11 species of microsporidia detected within 16 host species. We found that infections were more common in females than males, suggesting that host sex-ratio distortion occurs in five out of eight parasite species tested. Phylogenetic reconstruction demonstrates that VT occurs in all major lineages of the phylum Microspora and that sex-ratio distorters are found on multiple branches of the phylogenetic tree. We propose that VT is either an ancestral trait or evolves with peculiar frequency in this phylum. If the association observed here between VT and host sex-ratio distortion holds true across other host taxa, these eukaryotic parasites may join the bacterial endosymbionts in their importance as sex-ratio distorters.

Amphipoda↗

PubMed2004

Reticulate sympatric speciation in Cameroonian crater lake cichlids.

BACKGROUND: Traditionally the rapid origin of megadiverse species flocks of extremely closely related species is explained by the combinatory action of three factors: Disruptive natural selection, disruptive sexual selection and partial isolation by distance. However, recent empirical data and theoretical advances suggest that the diversity of complex species assemblages is based at least partially on the hybridization of numerous ancestral allopatric lineages that formed hybrids upon invasion of new environments. That reticulate speciation within species flocks may occur under sympatric conditions after the primary formation of species has been proposed but not been tested critically. RESULTS: We reconstructed the phylogeny of a complex cichlid species flock confined to the tiny Cameroonian crater lake Barombi Mbo using both mitochondrial and nuclear (AFLP) data. The nuclear phylogeny confirms previous findings which suggested the monophyly and sympatric origin of the flock. However, discordant intra-flock phylogenies reconstructed from mitochondrial and nuclear data suggest strongly that secondary hybridization among lineages that primarily diverged under sympatric conditions had occurred. Using canonical phylogenetic ordination and tree-based tests we infer that hybridization of two ancient lineages resulted in the formation of a new and ecologically highly distinct species, Pungu maclareni. CONCLUSIONS: Our findings show that sympatric hybrid speciation is able to contribute significantly to the evolution of complex species assemblages even without the prior formation of hybrids derived from allopatrically differentiated lineages.

Journal Article↗

PubMed1999

Phylogeny, host-parasite relationship and zoogeography.

Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates.

Animals↗

PubMed1999

The effect of gene duplication on homology.

Genes related by gene duplication within an organism's evolutionary lineage are termed paralogues; genes related by speciation are orthologues. It is generally agreed that orthologous genes must be compared when using DNA sequences to reconstruct the evolutionary history of organisms. There is an important exception: information from paralogous genes can reveal the root position of a phylogenetic tree. The duplicated rDNA genes of arrow worms provide an example. Gene duplication is also relevant when comparing gene expression between taxa; for example, when trying to identify homologous roles of genes. When gene duplication occurred after lineage divergence, single orthologues no longer exist, and comparison is complicated. This is a particular problem when comparing roles of vertebrate and invertebrate genes. Amphioxus and ascidian genes can be useful in such situations, since they diverged before extensive gene duplication in the vertebrate lineage. Using Otx and Pax as examples, I show how examination of amphioxus or ascidian genes reveals patterns of gene divergence after duplication, assisting the identification of homologous gene functions. Given the problems of comparing duplicated genes between species, the time is ripe for the introduction of additional terminology to elaborate on the concepts of paralogy and orthology.

Animals↗