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PubMed2000

The complete external transcribed spacer of 18S-26S rDNA: amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied families.

For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is needed that evolves more rapidly than the internal transcribed spacer (ITS) of the 18S-26S nuclear ribosomal DNA (nrDNA) repeat. If the region identified is nuclear, it would also be desirable for it to undergo rapid concerted evolution to eliminate problems with coalescence. The external transcribed spacer (ETS) of the nrDNA repeat has shown promise for intrageneric phylogenetic reconstruction, but only the 3' end of the region has been utilized for phylogenetic reconstruction and "universal" primers for PCR amplification have been elusive. We present a method for reliably amplifying and sequencing the entire ETS throughout Asteraceae and some closely allied families. We also show that the ETS is more variable and phylogenetically informative than the ITS in three disparate genera of Asteraceae-Argyranthemum (tribe Anthemideae), Asteriscus (tribe Inuleae), and Helianthus (tribe Heliantheae). The full ETS was amplified using a primer (ETS1f) within the intergenic spacer in combination with a primer (18S-2L) in the 5' end of the highly conserved 18S gene. ETS1f was designed to correspond to a highly conserved region found in Helianthus and Crepis, which are in separate subfamilies of Asteraceae. ETS1f/18S-2L primed in all of the tribes of Asteraceae as well as exemplar taxa from Campanulaceae, Goodeniaceae, and Calyceraceae. For both Argyranthemum and Asteriscus, we were able to directly sequence the ETS PCR products when a single band was produced. When multiple bands were produced, we gel-purified and occasionally cloned the band of interest before sequencing. Although PCR produced single bands for Helianthus species, it was necessary to clone Helianthus amplifications prior to sequencing due to multiple intragenomic ETS repeat types. Alignment of ETS sequences for Argyranthemum and Asteriscus was straightforward and unambiguous despite some subrepeat structure in the 5' end. For Helianthus, different numbers of large tandem subrepeats in different species required analysis of the orthology of the subrepeats prior to alignment. In all three genera, the ETS provided more informative variation for phylogenetic reconstruction and allowed better resolution of relationships than the ITS. Although cloned sequences from Helianthus differed, intragenomic clones consistently formed clades. This result indicated that concerted evolution was proceeding rapidly enough in ETS that species-specific phylogenetic signal was retained. It should be now be possible to use the entire ETS for phylogenetic reconstruction of recently diverged lineages in Asteraceae and at least three other families (approximately 26,000 species or about 8% of all angiosperms).

Asteraceae↗

PubMed1999

Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions.

It is now well-established that compositional bias in DNA sequences can adversely affect phylogenetic analysis based on those sequences. Phylogenetic analyses based on protein sequences are generally considered to be more reliable than those derived from the corresponding DNA sequences because it is believed that the use of encoded protein sequences circumvents the problems caused by nucleotide compositional biases in the DNA sequences. There exists, however, a correlation between AT/GC bias at the nucleotide level and content of AT- and GC-rich codons and their corresponding amino acids. Consequently, protein sequences can also be affected secondarily by nucleotide compositional bias. Here, we report that DNA bias not only may affect phylogenetic analysis based on DNA sequences, but also drives a protein bias which may affect analyses based on protein sequences. We present a striking example where common phylogenetic tools fail to recover the correct tree from complete animal mitochondrial protein-coding sequences. The data set is very extensive, containing several thousand sites per sequence, and the incorrect phylogenetic trees are statistically very well supported. Additionally, neither the use of the LogDet/paralinear transform nor removal of positions in the protein alignment with AT- or GC-rich codons allowed recovery of the correct tree. Two taxa with a large compositional bias continually group together in these analyses, despite a lack of close biological relatedness. We conclude that even protein-based phylogenetic trees may be misleading, and we advise caution in phylogenetic reconstruction using protein sequences, especially those that are compositionally biased.

Animals↗

PubMed2003

The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids.

Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (alpha- and beta-tubulin) from mitochondria-containing organisms robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated nuclear genes (actin, elongation factor-1alpha, alpha-tubulin, and beta-tubulin) reliably resolved the phylogeny only in the maximum parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance, quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated 4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The primary plastid endosymbiosis likely occurred once in the common ancestor of this large clade, and the primary plastids were subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta, and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of "Plantae" is proposed for phototrophic and nonphototrophic organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis. The Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial origin acquired in the primary endosymbiosis.

Cell Nucleus↗

PubMed2005

Entanglement invariants and phylogenetic branching.

It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous continuous time Markov chain model of phylogenetics with branching events generated by dynamical operations. Standard results from phylogenetics are shown to be derivable from the tensor framework. We summarize a powerful approach to entanglement measures in quantum physics and present its relevance to phylogenetic analysis. Entanglement measures are found to give distance measures that are equivalent to, and expand upon, those already known in phylogenetics. In particular we make the connection between the group invariant functions of phylogenetic data and phylogenetic distance functions. We introduce a new distance measure valid for three taxa based on the group invariant function known in physics as the "tangle". All work is presented for the homogeneous continuous time Markov chain model with arbitrary rate matrices.

Evolution, Molecular↗

PubMed2005

Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases.

Phylogenetics is a powerful tool for microbial epidemiology, but it is a tool that is often misused and misinterpreted by the field. Microbial epidemiologists are cautioned that in order to draw any inferences about the order of descent from a common ancestor it is necessary to correctly root a phylogenetic tree. Epidemiological samples of microbial populations typically include both ancestors and their descendants. In order to illustrate the relationships of those isolates, the phylogenetic method used must be able to detect zero-length branches. Unweighted Pair-Group Method (UPGMA) is the phylogenetic method that is most widely used in microbial epidemiology. Because UPGMA cannot detect zero length branches, and because it places the root of the tree based on a usually-false assumption, UPGMA is the worst possible choice among the several phylogenetic methods available. Because microbial epidemiology deals with relationships among strains within a species, rather than with relationships among species, recombination within those species can render phylogenetic trees meaningless and positively misleading. When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates.

Base Sequence↗

PubMedDate not supplied

Discrimination of Klebsiella pneumoniae and Klebsiella oxytoca phylogenetic groups and other Klebsiella species by use of amplified fragment length polymorphism.

Bacteria of the genus Klebsiella are opportunistic pathogens responsible for an increasing number of multiresistant infections in hospitals. The two clinically and epidemiologically most important species, Klebsiella pneumoniae and K. oxytoca, have recently been shown to be subdivided into three and two phylogenetic groups, respectively. The aim of this study was an in depth evaluation of the amplified fragment length polymorphism (AFLP) genetic characterization method for epidemiological and phylogenic analyzes of Klebsiella isolates. First, we investigated the variability of AFLP patterns for Klebsiella strains within and between different outbreaks. Second, by use of carefully characterized phylogenetically representative strains, we examined whether different Klebsiella species and phylogenetic groups can be discriminated using AFLP. Twenty-four strains originating from seven presumed outbreaks and 31 non-associated strains were investigated. The AFLP fingerprints of all epidemiologically associated strains showed three or fewer fragment differences, whereas unrelated strains differed by at least four fragments. Cluster analysis of the AFLP data revealed a very high concordance with the phylogenetic assignation of strains based on the gyrA sequence and ribotyping data. The species K. pneumoniae, K. oxytoca, K. terrigena and the possibly synonymous pair K. planticola/K. ornithinolytica each formed a separate cluster. Similarly, strains of the phylogenetic groups of K. pneumoniae and K. oxytoca fell into their corresponding clusters, with only two exceptions. This study provides a preliminary cut-off value for distinguishing epidemiologically non-related Klebsiella isolates based on AFLP data; it confirms the sharp delineation of the recently identified phylogenetic groups, and demonstrates that AFLP is suitable for identification of Klebsiella species and phylogenetic groups.

Bacterial Proteins↗

PubMed2005

Magic bullets and golden rules: data sampling in molecular phylogenetics.

Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no 'magic bullet' that will fit all phylogenetic problems, and no specific 'golden rules' have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6-10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study.

Classification↗

PubMed2002

Utility of low-copy nuclear gene sequences in plant phylogenetics.

Low-copy nuclear genes in plants are a rich source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstruction at all taxonomic levels, especially where universal markers such as cpDNA and nrDNA are unable to generate strong phylogenetic hypotheses. Low-copy nuclear genes, however, remain underused in plant phylogenetic studies due to practical and theoretical complications in unraveling the evolutionary dynamics of nuclear gene families. The lack of the universal markers or universal PCR primers of low-copy nuclear genes has also hampered their phylogenetic utility. It has recently become clear that low-copy nuclear genes are particularly helpful in resolving close interspecific relationships and in reconstructing allopolyploidization in plants. Gene markers that are widely, if not universally, useful have begun to emerge. Although utilizing low-copy nuclear genes usually requires extra lab work such as designing PCR primers, PCR-cloning, and/or Southern blotting, rapid accumulation of gene sequences in the databases and advances in cloning techniques have continued to make such studies more feasible. With the growing number of theoretical studies devoted to the gene tree and species tree problem, a solid foundation for reconstructing complex plant phylogenies based on multiple gene trees began to build. It is also realized increasingly that fast evolving introns of the low-copy nuclear genes will provide much needed phylogenetic information around the species boundary and allow us to address fundamental questions concerning processes of plant speciation. Phylogenetic and molecular evolutionary analyses of developmentally important genes will add a new dimension to systematic and evolutionary studies of plant diversity.

Cell Nucleus↗

PubMed2005

Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data.

Phylogenetic relationships among salamander families illustrate analytical challenges inherent to inferring phylogenies in which terminal branches are temporally very long relative to internal branches. We present new mitochondrial DNA sequences, approximately 2,100 base pairs from the genes encoding ND1, ND2, COI, and the intervening tRNA genes for 34 species representing all 10 salamander families, to examine these relationships. Parsimony analysis of these mtDNA sequences supports monophyly of all families except Proteidae, but yields a tree largely unresolved with respect to interfamilial relationships and the phylogenetic positions of the proteid genera Necturus and Proteus. In contrast, Bayesian and maximum-likelihood analyses of the mtDNA data produce a topology concordant with phylogenetic results from nuclear-encoded rRNA sequences, and they statistically reject monophyly of the internally fertilizing salamanders, suborder Salamandroidea. Phylogenetic simulations based on our mitochondrial DNA sequences reveal that Bayesian analyses outperform parsimony in reconstructing short branches located deep in the phylogenetic history of a taxon. However, phylogenetic conflicts between our results and a recent analysis of nuclear RAG-1 gene sequences suggest that statistical rejection of a monophyletic Salamandroidea by Bayesian analyses of our mitochondrial genomic data is probably erroneous. Bayesian and likelihood-based analyses may overestimate phylogenetic precision when estimating short branches located deep in a phylogeny from data showing substitutional saturation; an analysis of nucleotide substitutions indicates that these methods may be overly sensitive to a relatively small number of sites that show substitutions judged uncommon by the favored evolutionary model.

Animals↗

PubMed2005

The logical basis of phylogenetic taxonomy.

Phylogenetic taxonomy, like modern Linnean taxonomy, was modeled on a phylogenetic tree rather than a cladogram and, like its predecessor, perpetuates the use of morphology as a means of recognizing clades. Both practices have generated confusion in graphical representation, operational terminology, and definitional rationale in phylogenetic taxonomy, the history of which is traced. The following points are made: (1) cladograms, rather than trees or hybrid cladogram-trees, provide the framework for the simplest graphical depiction of phylogenetic definitions; (2) a complete notational scheme for phylogenetic definitions is presented that distinguishes symbolic notation from shorthand and longhand versions; (3) phylogenetic definitions are composed of three components (paradigm, specifier, qualifier) arranged in two fundamental patterns-node and stem; (4) apomorphies do not constitute a fundamental definitional pattern but rather serve to qualify a stem-based definition (as do time and geographic range); (5) formulation of phylogenetic definitions involves three heuristic criteria (stability, simplicity, prior use); (6) reasoned definitional revision is encouraged and better defined (textual substitution, first-and second-order revision); and (7) a database, TaxonSearch, allows rapid recall of taxonomic and definitional information.

Classification↗

PubMed1998

Measuring the phylogenetic randomness of biological data sets.

Two qualitative taxonomic characters are potentially compatible if the states of each can be ordered into a character state tree in such a way that the two resulting character state trees are compatible. The number of potentially compatible pairs (NPCP) of qualitative characters from a data set may be considered to be a measure of its phylogenetic randomness. The value of NPCP depends on the number of evolutionary units (EUs), the number of characters, the number of states in the characters, the distributions of EUs among these states, and the amount and distribution of missing information and so does not directly indicate degree of phylogenetic randomness. Thus, for an observed data set, we used Monte Carlo methods to estimate the probability that a data set chosen equiprobably from among those identical (with respect to all the other above determining features) to the observed data set would have as high (or low) an NPCP as the observed data set. This probability, the realized significance of the observed NPCP, is attractive as an indication of phylogenetic randomness because it does not require the assumptions made by other such methods: No character state trees are assumed and consequently, only potential compatibility can be determined; no particular method of phylogenetic estimation is assumed; and no phylogenetic trees are constructed. We determined the values and significances of NPCP for analyses of 57 data sets taken from 53 published sources. All data sets from 37 of those sources exhibited realized significances of < 0.01, indicating high levels of phylogenetic nonrandomness. From each of the remaining 16 sources, at least one data set was more phylogenetically random. Inclusion of outgroups changed significance in some cases, but not always in the same direction. Data sets with significantly low NPCP may be consistent with an ancient hybrid origin (or other ancient polyphyletic gene exchange, crossing over, viral transfer, etc.) of the study group.

Monte Carlo Method↗

PubMed1999

Species names in phylogenetic nomenclature.

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.

Phylogeny↗

PubMed2026

Bit-reproducible parallel phylogenetic tree inference.

MOTIVATION: Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between different genomic sites, parallel computation is commonly deployed. This is followed by a parallel summation over the per-site scores to obtain the overall likelihood score of the tree. However, basic arithmetic operations on IEEE 754 floating-point numbers, such as addition and multiplication, inherently introduce rounding errors. Consequently, the order by which floating-point operations are executed affects the exact resulting likelihood value since these operations are not associative. Moreover, parallel reduction algorithms in numerical codes re-associate operations as a function of the core count and cluster network topology, inducing different round-off errors. These low-level deviations can cause heuristic searches to diverge and induce high-level result discrepancies (e.g. yield topologically distinct phylogenies). This effect has also been observed in multiple scientific fields beyond phylogenetics. RESULTS: We observe that varying the degree of parallelism results in diverging phylogenetic tree searches (high-level results) for over 31% out of 10 179 empirical datasets. More importantly, 8% of these diverging datasets yield trees that are statistically significantly worse than the best-known ML tree for the dataset (AU-test, P < .05). To alleviate this, we develop a variant of the widely used phylogenetic inference tool RAxML-NG, which does yield bit-reproducible results under varying core-counts, with a slowdown of only 0%-12.7% (median 0.8%) on up to 768 cores. For this, we introduce the ReproRed reduction algorithm, which yields bit-identical results under varying core-counts, by maintaining a fixed operation order that is independent of the communication pattern. ReproRed is thus applicable to all associative reduction operations-in contrast to competitors, which are confined to summation. Our ReproRed reduction algorithm only exchanges the theoretical minimum number of messages, overlaps communication with computation, and utilizes fast base-cases for local reductions. ReproRed is able to all-reduce (via a subsequent broadcast) 4.1×106 operands across 48-768 cores in 19.7-48.61 μs, thereby exhibiting a slowdown of 13%-93% over a non-reproducible all-reduce algorithm. ReproRed outperforms the state-of-the-art reproducible all-reduction algorithm ReproBLAS (offers summation only) beyond 10 000 elements per core. In summary, we re-assess non-reproducibility in parallel phylogenetic inference, present the first bit-reproducible parallel phylogenetic inference tool, as well as introduce a general algorithm and open-source code for conducting reproducible associative parallel reduction operations. AVAILABILITY AND IMPLEMENTATION: ReproRed: https://doi.org/10.5281/zenodo.15004918 (LGPL)-Reproducible RAxML-NG version https://doi.org/10.5281/zenodo.15017407 (GPL).

Phylogeny↗

PubMed1996

Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates.

A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes to recover two expected phylogenies of tetrapods and mammals. According to these tests, mitochondrial protein-coding genes can be roughly classified into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COII, COIII, ND1, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L) phylogenetic performers in recovering these expected trees among phylogenetically distant relatives. How general our findings are is unclear. Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance. The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny such as the density of lineage creation events in time, the phylogenetic "depth" of the question, lineage-specific rate heterogeneity, and the completeness of taxa representation.

Adenosine Triphosphatases↗

PubMed2006

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

Eukaryotic Cells↗

PubMed1997

A phylogenetic analysis of the genus Saccharomyces based on 18S rRNA gene sequences: description of Saccharomyces kunashirensis sp. nov. and Saccharomyces martiniae sp. nov.

A phylogenetic investigation of the ascomycetous yeast genus Saccharomyces was performed by using 18S rRNA gene sequence analysis. Comparative sequence analysis showed that the genus is phylogenetically very heterogeneous. Saccharomyces species were found to be phylogenetically interdispersed with members of other ascomycetous genera (e.g., the genera Kluyveromyces, Torulaspora, and Zygosaccharomyces). The four species of the Saccharomyces sensu stricto complex (viz., Saccharomyces bayanus, Saccharomyces cerevisiae, Saccharomyces paradoxus, and Saccharomyces pastorianus) were found to be phylogenetically closely related to one another, displaying exceptionally high levels of sequence similarity (> or = 99.9%). These four species formed a natural group that was quite separate from the other Saccharomyces and non-Saccharomyces species examined. Saccharomyces exiguus and its anamorph, Candida holmii, were found to be genealogically almost identical and, along with Saccharomyces barnettii, formed a stable group closely related to, but nevertheless distinct from, Kluyveromyces africanus, Kluyveromyces lodderae, Saccharomyces rosinii, Saccharomyces spencerorum, and Saccharomyces sp. strain CBS 7662T (T = type strain). Saccharomyces spencerorum and Kluyveromyces lodderae displayed a particularly close genealogical affinity with each other, as did Saccharomyces castellii and Saccharomyces dairensis. Similarly, Saccharomyces servazzii, Saccharomyces unisporus, and Saccharomyces sp. strain CBS 6904 were found to be genotypically highly related and to form a phylogenetically distinct lineage. The recently reinstated species Saccharomyces transvaalensis was found to form a distinct lineage and displayed no specific association with any other Saccharomyces or non-Saccharomyces species. Saccharomyces kluyveri formed a very loose association with a group which included Kluyveromyces thermotolerans, Kluyveromyces waltii, Zygosaccharomyces cidri, and Zygosaccharomyces fermentati. Saccharomyces spp. strain CBS 6334T, on the other hand, displayed no specific association with any of the other Saccharomyces spp. studied, although a neighbor-joining analysis did reveal that this strain exhibited a loose phylogenetic affinity with Kluyveromyces polysporus and Kluyveromyces yarrowii. On the basis of the phylogenetic findings, two new Saccharomyces species, Saccharomyces kunashirensis (with type strain CBS 7662) and Saccharomyces martiniae (with type strain CBS 6334), are described.

DNA, Fungal↗

PubMed2005

Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group.

Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

Animals↗

PubMed2005

Improved prediction of critical residues for protein function based on network and phylogenetic analyses.

BACKGROUND: Phylogenetic approaches are commonly used to predict which amino acid residues are critical to the function of a given protein. However, such approaches display inherent limitations, such as the requirement for identification of multiple homologues of the protein under consideration. Therefore, complementary or alternative approaches for the prediction of critical residues would be desirable. Network analyses have been used in the modelling of many complex biological systems, but only very recently have they been used to predict critical residues from a protein's three-dimensional structure. Here we compare a couple of phylogenetic approaches to several different network-based methods for the prediction of critical residues, and show that a combination of one phylogenetic method and one network-based method is superior to other methods previously employed. RESULTS: We associate a network with each member of a set of proteins for which the three-dimensional structure is known and the critical residues have been previously determined experimentally. We show that several network-based centrality measurements (connectivity, 2-connectivity, closeness centrality, betweenness and cluster coefficient) accurately detect residues critical for the protein's function. Phylogenetic approaches render predictions as reliable as the network-based measurements, although, interestingly, the two general approaches tend to predict different sets of critical residues. Hence we propose a hybrid method that is composed of one network-based calculation--the closeness centrality--and one phylogenetic approach--the Conseq server. This hybrid approach predicts critical residues more accurately than the other methods tested here. CONCLUSION: We show that network analysis can be used to improve the prediction of amino acids critical for protein function, when utilized in combination with phylogenetic approaches. It is proposed that such improvement is due to the complementary nature of these approaches: network-based methods tend to predict as critical those residues that are highly connected and internal (i.e., non-surface), although some surface residues are indeed identified as critical by network analyses; whereas residues chosen by phylogenetic approaches display a lower overall probability of being surface inaccessible.

Computational Biology↗