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At least 19 recordsLinked to original sources

PubMed1994

Extinction rates can be estimated from molecular phylogenies.

Molecular phylogenies can be used to reject null models of the way we think evolution occurred, including patterns of lineage extinction. They can also be used to provide maximum likelihood estimates of parameters associated with lineage birth and death rates. We illustrate: (i) how molecular phylogenies provide information about the extent to which particular clades are likely to be under threat from extinction; (ii) how cursory analyses of molecular phylogenies can lead to incorrect conclusions about the evolutionary processes that have been at work; and (iii) how different evolutionary processes leave distinctive marks on the structure of reconstructed phylogenies.

Animals↗

PubMed2006

Artificial neural networks can learn to estimate extinction rates from molecular phylogenies.

Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process, parametric functions to estimate extinction rates from phylogenies turned out to be complex and often difficult to derive. Moreover, these parametric functions are specific to a particular process (e.g. complete species level phylogeny with constant birth and death rates) and a particular type of data (e.g. times between bifurcations). Here, it is shown that artificial neural networks can substitute for parametric estimation functions once they have been sufficiently trained on simulated data. This technique can in principle be used for different processes and data types, and because it circumvents the time-consuming and difficult task of deriving parametric estimation functions, it may greatly extend the possibilities to make macro-evolutionary inferences from molecular phylogenies. This novel approach is explained, applied to estimate speciation and extinction rates from a molecular phylogeny of the reef fish genus Naso (Acanturidae), and its performance is compared to that of maximum likelihood estimation.

Animals↗

PubMed2001

The surface structure of trypanosomes in relation to their molecular phylogeny.

Molecular phylogenetic analysis using genes coding for ribosomal RNA and proteins suggests that trypanosomes are monophyletic. Salivarian trypanosomes showing antigenic variation of the variant surface glycoprotein (VSG) diverged from non-Salivarian trypanosomes some 200-300 million years ago. Representatives of the non-Salivarian group, the mammalian parasite, Trypanosoma cruzi, and the fresh-water fish trypanosome, T. carassii, are characterised by surfaces dominated by carbohydrate-rich mucin-like glycoproteins, which are not subject to antigenetic variation. It is suggested that this latter surface structure is typical for non-Salivarian trypanosomes as well as members of the other Kinetoplastid suborder, the Bodonina. This would imply that at some point in time in the evolution of the Salivaria the highly abundant and comparatively poorly immunogenetic mucin-like molecules must have been replaced for equally abundant but highly immunogenic VSG-like molecules. While the selective advantage for such a unique transition is difficult to imagine, the subsequent diversification of VSG genes/molecules may have been comparatively straightforward because even the most limited form of antigenic variation would have extended the duration of infection in the vertebrate and thus would have increased the chance for transfer to the vector.

Animals↗

PubMed1994

Application and accuracy of molecular phylogenies.

Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.

Bacteriophage T7↗

PubMed2005

Primate phylogeny: molecular evidence from retroposons.

In these postgenomic times where aspects of functional genetics and character evolution form a focal point of human-mouse comparative research, primate phylogenetic research gained a widespread interest in evolutionary biology. Nevertheless, it also remains a controversial subject. Despite the surge in available primate sequences and corresponding phylogenetic interpretations, primate origins as well as several branching events in primate divergence are far from settled. The analysis of SINEs - short interspersed elements - as molecular cladistic markers represents a particularly interesting complement to sequence data. The following summarizes and discusses potential applications of this new approach in molecular phylogeny and outlines main results obtained with SINEs in the context of primate evolutionary research. Another molecular cladistic marker linking the tarsier with the anthropoid primates is also presented. This eliminates any possibility of confounding phylogenetic interpretations through lineage sorting phenomena and makes use of a new point of view in settling the phylogenetic relationships of the primate infraorders.

Animals↗

PubMed1995

Inferring population history from molecular phylogenies.

Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.

Genetics, Population↗

PubMed1999

Ultrastructure as a Control for Protistan Molecular Phylogeny.

A variety of molecular sequences and treeing methods have been used in attempts to unravel early protistan evolution and the origins of "higher" eukaryotic taxa. How does one know which approach is closest to the real phylogenetic tree? Obviously it is the robustness of its resulting trees, the coherence with other data sets, both structural and molecular, that is the test. Simply put: it should make biological sense. It seems evident, comparing morphology, especially ultrastructure, with ribosomal DNA trees, that the major lineages have now been confirmed. In particular, the remarkably conservative mitochondrial crista type in protists is coherent with mitochondrial DNA sequences. Several amitochondrial groups, presumed to be primitive on the basis of SSU ribosomal DNA, show alarming positional volatility when other genes are used. In addition, the presence of mitochondrial genes in the nucleus of several amitochondrial flagellates raises doubts about them being primordially amitochondrial. Consequently, the root of the eukaryote tree is still in question. A disturbing question arises: can loss of features in parasitism mimic primitiveness not only in a morphological but also in a molecular way, evolving more rapidly and creating long branches that methodologically place them basal in the trees? Conflicting molecular phylogenies cannot be resolved by molecular data alone. Morpholological, especially ultrastructural, data are an essential component of phylogenetic reconstruction.

Journal Article↗

PubMed2000

Molecular phylogeny: pitfalls and progress.

Molecular phylogeny based on nucleotide or amino acid sequence comparison has become a widespread tool for general taxonomy and evolutionary analyses. It seems the only means to establish a natural classification of microorganisms, since their phenotypic traits are not always consistent with genealogy. After an optimistic period during which comprehensive microbial evolutionary pictures appeared, the discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach. In addition to biological factors, such as horizontal gene transfer, some methodological problems may produce misleading phylogenies. They are essentially (i) loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between the real evolutionary process and the assumed models of sequence evolution, and (iii) differences of evolutionary rates among species or among positions within a sequence. Here, we discuss these problems and some strategies proposed to overcome their effects.

Artifacts↗

PubMed2006

[Application of DNA-related techniques in avian molecular phylogeny].

The DNA techniques most commonly used in avian molecular phylogeny include DNA hybridization, RFLP and DNA sequence analysis, among which DNA sequence analysis is supposed to be the most effective and reliable. DNA hybridization techniques have been widely used in aves, based on which a new avian classification system was born. In avian RFLP analyses, mtDNA are widely used as target sequences. Mitochondrial DNA genes are the most frequently used in avian molecular phylogeny. Although mtDNA phylogenies are likely to be correct in many cases, use of mtDNA sequences can be problematic with such constraints as unilateral inheritance, multiple substitutions, saturations at the third-coded sites, strong bias in base composition and probable nuclear pseudogenes of mtDNA sequences. Although bias are still on the mtDNA sequences, more and more authors turn to nuclear DNA sequences and prefer to a combination of mtDNA and nuclear DNA sequences. And single-copy nuclear DNA receives the most favor. scnDNA introns can perform well in recovering relationships among intermediate to even distantly related congeneric species. scnDNA exons can be used in avian higher ranks. With the exception of molecular markers' own problems including variable rates of nucleotide site evolution, gene hybridization, gene horizontal transfer and lineage sorting, avian molecular phylogeny also faces methodological problems, such as molecular markers selection, taxon sampling and data processing. More attention should be paid to the standardization of methods, not to the new molecular markers.

Animals↗

PubMed1992

Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae).

Estimations of phylogenies from morphological and molecular data often show contrasting results. We compared morphological and molecular phylogenies in an ancient family of woody dicots, the Betulaceae (birch family). The phylogeny of the family was estimated from parsimony analysis of morphological characters in the genera Alnus, Betula, Carpinus, Corylus, Ostrya, and Ostryopsis and from parsimony and distance-matrix analyses of DNA sequences of the chloroplast gene encoding the large subunit of ribulose-1,5-biphosphate carboxylase (rbcL) in the genera Alnus, Betula, Carpinus, Corylus, and Ostrya and in two outgroups, Quercus and Liquidambar. The topologies obtained by the different methods were completely congruent, and bootstrapping strongly supported the division of the family Betulaceae into two major clades, Betuleae (Alnus and Betula) and Coryleae (other members). Only slightly more homoplasy was present in the rbcL sequence data set than in the morphological set. Relative-rate tests indicated that the Coryleae clade had a faster rate of rbcL evolution than did the Betuleae clade. Heterogeneity of rates of morphological evolution also paralleled those for rbcL.

Base Sequence↗

PubMed2003

A molecular phylogeny of enteric bacteria and implications for a bacterial species concept.

A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.

DNA, Bacterial↗

PubMedDate not supplied

[Use of the level of G+C n DNA for studying the molecular phylogeny o f methanogenic archaebacteria].

A new method for theoretical analysis of the molecular phylogeny of bacteria, successfully applied earlier to nitrifying bacteria, was used to study the molecular phylogeny of methanogenic archaebacteria. The group studied included Methanococcus igneus, Methanococcus vannielii, Methanothermus fervidus, Methanolobus tindarius, Methanobacterium formicicum, Methanosarcina barkeri, Methanobacterium thermoformicicum, Methanoplanus limicola, Methanospirillum hungatei, and Methanobacterium thermoautotrophicum. Based on the hypothesis that direct linear regression always exists between evolutionary changes in the DNA G + C content and the primary structure of rRNA, the branching order of the phylogenetic tree of methanogenic archaebacteria was determined. For this tree, the values of the evolutionary distance between 16S rRNA primary structures Ei and the values of the G + C evolutionary distance P(i) exhibited a correlation coefficient 0.78. Thus, the DNA G + C content is not only an important taxonomic characteristics but also provides information helpful for the determination of the branching order of phylogenetic trees constructed based on 16S rRNA primary structures.

Adenosine↗

PubMed2004

Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented.

Animals↗

PubMed2005

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses.

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira-Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.

Animals↗

PubMed2004

Molecular phylogeny and biogeography of the widely distributed Amanita species, A. muscaria and A. pantherina.

The molecular phylogeny and biogeography of two widely distributed Amanita species, A. muscaria and A. pantherina, were studied based on specimens from diverse localities. Analyses of both a partial sequence of the ITS region of nuclear DNA and a partial sequence of the beta-tubulin gene were able to resolve specimens of each species. Analyses revealed a greater divergence of the beta-tubulin region than the ITS region. Based on molecular phylogeny of the combination of the ITS and beta-tubulin regions, A. muscaria could be separated into at least three groups (Eurasian, Eurasian subalpine, and North American), and A. pantherina could be separated into at least two groups (North American and Eurasian). We hypothesize that the speciation of A. muscaria occurred in Eurasia with subsequent migration to North America via land bridges. However, it is impossible to determine whether A. pantherina moved from Eurasia to North America or vice versa. For both A. muscaria and A. pantherina, the intracontinental relationships of both Eurasia and North America were closer than the relationships between eastern Asia and eastern North America.

Amanita↗

PubMed1998

Escherichia coli molecular phylogeny using the incongruence length difference test.

Molecular phylogeny of the species Escherichia coli using the E. coli reference (ECOR) collection strains has been hampered by (1) the absence of rooting in the commonly used phenogram obtained from multilocus enzyme electrophoresis (MLEE) data and (2) the existence of recombination events between strains that scramble phylogenetic trees reconstructed from the nucleotide sequences of genes. We attempted to determine the phylogeny for E. coli based on the ECOR strain data by extracting from GenBank the nucleotide sequences of 11 chromosomal structural and 2 plasmid genes for which the Salmonella enterica homologous gene sequences were available. For each of the 13 DNA data sets studied, incongruence with a nonnucleotide whole-genome data set including MLEE, random amplified polymorphic DNA, and rrn restriction fragment length polymorphism data was measured using the incongruence length difference (ILD) test of Farris et al. As previously reported, the incongruence observed between the gnd and plasmid gene data and the whole-genome data was multiple, indicating numerous horizontal transfer and/or recombination events. In five cases, the incongruence detected by the ILD test was punctual, and the donor group was identified. Congruence was not rejected for the remaining data sets. The strains responsible for incongruences with the whole-genome data set were removed, leading to a "prior-agreement" approach, i.e., the determination of a phylogeny for E. coli based on several genes, excluding (1) the genes with multiple incongruences with the whole genome data, (2) the strains responsible for punctual incongruences, and (3) the genes incongruent with each other. The obtained phylogeny shows that the most basal group of E. coli strains is the B2 group rather than the A group, as generally thought. The D group then emerges as the sister group of the rest. Finally, the A and B1 groups are sister groups. Interestingly, the most primitive taxon within E. coli in terms of branching pattern, i.e., the B2 group, includes highly virulent extraintestinal strains with derived characters (extraintestinal virulence determinants) occurring on its own branch.

Enzymes↗

PubMed2003

A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean.

A molecular phylogeny is presented for the subfamily Littorininae (including representatives of all subgeneric taxa and all members of a group of southern-temperate species formerly classified as 'Nodilittorina'), based on sequence data from two nuclear (18S rRNA, 28S rRNA) and two mitochondrial (12S rRNA, CO1) genes. The phylogeny shows considerable disagreement with earlier hypotheses derived from morphological data. In particular, 'Nodilittorina' is polyphyletic and is here divided into four genera (Echinolittorina, Austrolittorina, Afrolittorina new genus, and the monotypic Nodilittorina s.s.). The phylogenetic relationships of 'Littorina' striata have been controversial and it is here transferred to the genus Tectarius, a surprising relationship for which there is little morphological support. The relationships of the enigmatic Mainwaringia remain poorly resolved, but it is not a basal member of the subfamily. The two living species of Mainwaringia are remarkable for a greatly elevated rate of evolution in all four genes examined; it is suggested that this may be connected with their protandrous hermaphroditism, which is unique in the family. The molecular phylogeny provides a new framework for the adaptive radiation of the Littorininae, showing more frequent shifts between habitats and climatic regimes than previously suspected, and striking parallelism of morphological characters. The fossil record of littorinids is poor, but ages of clades are estimated using a calibration based on a Lower Eocene age of the genus Littoraria. Using these estimates, the antitropical distribution of Littorina and Afrolittorina is an ancient pattern of possibly Cretaceous age. The five members of Austrolittorina show a Gondwanan distribution in Australia, New Zealand, and South America. Based on the morphological uniformity within this clade, relatively recent (Plio-Pleistocene) trans-Pacific dispersal events seemed a likely explanation, as proposed for numerous other congeneric marine taxa. However, molecular estimation of ages of divergence suggest an initial vicariance between Australian and South American lineages at 40-73Ma, contemporary with the later stages of fragmentation of the Gondwanan supercontinent, followed by more recent (but still mid-Cenozoic) dispersal events across the Tasman Sea and the Pacific Ocean. Afrolittorina is another Cretaceous clade, now restricted to southern Africa and southern Australia, but divergence between these lineages (29-55Ma) post-dates Gondwanan fragmentation. Within both Austrolittorina and Afrolittorina all sister-species divergences are estimated to fall in the range 10-47Ma, so that there is no evidence for speciation events in the Plio-Pleistocene.

Adaptation, Biological↗

PubMed2004

Molecular phylogeny of the hexagrammid fishes using a multi-locus approach.

Ideally, organisms are grouped into monophyletic assemblages reflecting their evolutionary histories. Single (molecular) markers can reflect the evolutionary history of the marker, rather than the species in question, therefore, phylogenetic relationships should be inferred from adequate sampling of characters. Because the use of multiple loci greatly improves the resolving power of the molecular assay, we constructed a molecular phylogeny of the family Hexagrammidae based on six loci, including two mitochondrial and four nuclear loci. The resulting molecular phylogeny, from the combined data, was significantly different from the morphological topology suggested by Shinohara [Memoirs of the Faculty of Fisheries, Hokkaido University 41 (1994) 1]. Our data support a monophyletic assemblage for the genera Hexagrammos and Pleurogrammus. However, other taxa traditionally included in the family Hexagrammidae did not form a monophyletic assemblage. The monotypic genus Ophiodon was more closely associated with cottids than with other hexagrammids. Our data concur with the morphological topology in that the genera Zaniolepis and Oxylebius formed a monophyletic clade, which was distinct and basal to the remaining hexagrammids, seven cottids and one agonid.

Alaska↗