Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences.

A common assumption in comparative sequence analysis is that the sequences have evolved with the same pattern of nucleotide substitution (homogeneity of the evolutionary process). Violation of this assumption is known to adversely impact the accuracy of phylogenetic inference and tests of evolutionary hypotheses. Here we propose a disparity index, ID, which measures the observed difference in evolutionary patterns for a pair of sequences. On the basis of this index, we have developed a Monte Carlo procedure to test the homogeneity of the observed patterns. This test does not require a priori knowledge of the pattern of substitutions, extent of rate heterogeneity among sites, or the evolutionary relationship among sequences. Computer simulations show that the ID-test is more powerful than the commonly used chi2-test under a variety of biologically realistic models of sequence evolution. An application of this test in an analysis of 3789 pairs of orthologous human and mouse protein-coding genes reveals that the observed evolutionary patterns in neutral sites are not homogeneous in 41% of the genes, apparently due to shifts in G + C content. Thus, the proposed test can be used as a diagnostic tool to identify genes and lineages that have evolved with substantially different evolutionary processes as reflected in the observed patterns of change. Identification of such genes and lineages is an important early step in comparative genomics and molecular phylogenetic studies to discover evolutionary processes that have shaped organismal genomes.     

Ecology in relation to speciation rates: some case histories of Miocene-Recent mammal clades

Summary Some African mammal clades are used to analyse evolutionary processes. The clades chosen are especially suitable for this purpose because they include both extant species, for which there is an abundant literature, and fossil records from various Miocene-Recent strata mainly in Eastern and Southern Africa. The monophyletic groups in this sample differ considerably in speciation rates and in the magnitudes of long-term trends. I take a number of rival hypotheses as to why such disparate macroevolutionary patterns should have evolved (the Birth Rate, Gene Flow, Resource-Use, Extrinsic and Random Hypotheses) and test their predictions. The tests involve comparisons of phylogenetic patterns with biological variation (in life histories, population structure, mobility and habitat-specificity) among the extant species. The results accord best with the Resource-Use Hypothesis.     

PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya

SUMMARY: With increasing numbers of eukaryotic genome sequences, phylogenetic profiles of eukaryotic genes are becoming increasingly informative. Here, we introduce a new web-tool Phylopro (http://compsysbio.org/phylopro/), which uses the 120 available eukaryotic genome sequences to visualize the evolutionary trajectories of user-defined subsets of model organism genes. Applied to pathways or complexes, PhyloPro allows the user to rapidly identify core conserved elements of biological processes together with those that may represent lineage-specific innovations. PhyloPro thus provides a valuable resource for the evolutionary and comparative studies of biological systems.     

The phylogeny of polar fishes and the structure,function and molecular evolution of hemoglobin

Fishes thriving in polar habitats offer many opportunities for comparative approaches to understanding protein thermal adaptations. Investigations on the remarkable evolutionary adaptations to these environments of basic proteins such as hemoglobin, the oxygen carrier, can provide new insights into the mechanisms studied in temperate organisms and can shed light on convergent processes evolved in response to thermal adaptations. At the molecular level, hemoglobins are one of the most intriguing systems for studying the relationships between environmental conditions and adaptations. This review summarizes the current knowledge on molecular structure, biological function and phylogeny of hemoglobins of fish species living in both polar habitats but having different evolutionary histories. In benthic, non-migratory, cold-adapted fishes, the stability of thermal conditions may have generated no or few variations in selective pressures on globin sequences through evolutionary time, so that sequences retain the species phylogenetic “signal”. In pelagic, migratory, cold-adapted or temperate fishes, variations in selective pressures on globin sequences caused by variations in temperature accompanying the dynamic life style may have disrupted the phylogenetic “signal” in phenetic trees.     

Tests of applicability of several substitution models for DNA sequence data

Using linear invariants for various models of nucleotide substitution, we developed test statistics for examining the applicability of a specific model to a given dataset in phylogenetic inference. The models examined are those developed by Jukes and Cantor (1969), Kimura (1980), Tajima and Nei (1984), Hasegawa et al. (1985), Tamura (1992), Tamura and Nei (1993), and a new model called the eight-parameter model. The first six models are special cases of the last model. The test statistics developed are independent of evolutionary time and phylogeny, although the variances of the statistics contain phylogenetic information. Therefore, these statistics can be used before a phylogenetic tree is estimated. Our objective is to find the simplest model that is applicable to a given dataset, keeping in mind that a simple model usually gives an estimate of evolutionary distance (number of nucleotide substitutions per site) with a smaller variance than a complicated model when the simple model is correct. We have also developed a statistical test of the homogeneity of nucleotide frequencies of a sample of several sequences that takes into account possible phylogenetic correlations. This test is used to examine the stationarity in time of the base frequencies in the sample. For Hasegawa et al.'s and the eight-parameter models, analytical formulas for estimating evolutionary distances are presented. Application of the above tests to several sets of real data has shown that the assumption of stationarity of base composition is usually acceptable when the sequences studied are closely related but otherwise it is rejected. Similarly, the simple models of nucleotide substitution are almost always rejected when actual genes are distantly related and/or the total number of nucleotides examined is large.      

Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes

Evolutionary processes such as adaptation, ecological filtering, and niche conservatism involve the interaction of organisms with their environment and are thus commonly studied along environmental gradients. Elevational gradients have become among the most studied environmental gradients to understand large-scale patterns of species richness and composition because they are highly replicated with different combinations of geographical, environmental and historical factors. We here review the literature on using elevational gradients to understand evolutionary processes in ferns. Some phylogenetic studies of individual fern clades have considered elevation in the analysis or interpretation and postulated that fern diversification is linked to the colonization of mountain habitats. Other studies that have linked elevational community composition and hence ecological filtering with phylogenetic community composition and morphological traits, usually only found limited phylogenetic signal. However, these studies are ultimately only correlational, and there are few actual tests of the evolutionary mechanisms leading to these patterns. We identify a number of challenges for improving our understanding of how evolutionary and ecological processes are linked to elevational richness patterns in ferns: i) limited information on traits and their ecological relevance, ii) uncertainties on the dispersal kernels of ferns and hence the delimitation of regional species pools from which local assemblages are recruited, iii) limited genomic data to identify candidate genes under selection and hence actually document adaptation and selection, and iv) conceptual challenges in developing clear and testable hypotheses to how specific evolutionary processes can be linked to patterns in community composition and species richness.     

Evolutionary Models and Phylogenetic Signal Assessment via Mantel Test

Phylogenetically closely related species tend to be more similar to each other than to more distantly related ones, a pattern called phylogenetic signal. Appropriate tests to evaluate the association between phylogenetic relatedness and trait variation among species are employed in a myriad of eco-evolutionary studies. However, most tests available to date are only suitable for datasets describing continuous traits, and are most often applicable only for single trait analysis. The Mantel test is a useful method to measure phylogenetic signal for multiple (continuous, binary and/or categorical) traits. However, the classical Mantel test does not incorporate any evolutionary model (EM) in the analysis. Here, we describe a new analytical procedure, which incorporates explicitly an evolutionary model in the standard Mantel test (EM-Mantel). We run numerical simulations to evaluate its statistical properties, under different combinations of species pool size, trait type and number. Our results showed that EM-Mantel test has appropriate type I error and acceptable power, which increases with the strength of phylogenetic signal and with species pool size but depended on trait type. EM-Mantel test is a good alternative for measuring phylogenetic signal in binary and categorical traits and for datasets with multiple traits.     

Reconstructing the Clavariaceae using nuclear large subunit rDNA sequences and a new genus segregated from Clavaria

Fungi that produce clavarioid fruit bodies have evolved independently many times in the Basidiomycota. The evolutionary significance of this morphology is difficult to interpret because the phylogenetic positions of many clavarioid fungi are still unknown. In this study we examined the phylogenetic diversity of the Clavariaceae sensu lato among Homobasidiomycetidae by adding partial nuclear large subunit ribosomal DNA sequences from clavarioid and corticioid fungi to a large euagaric dataset and analyzing them both together and separately. Our results indicate that the clavarioid morphology has evolved at least five times in the euagarics while the inclusion of type species enabled us to evaluate the taxonomic consequences of this polyphyletic distribution. Although the sampling available at present is incomplete, a qualitative assessment of our phylogenetic hypotheses indicates that the clavarioid habit might not be as evolutionary labile as previously reported. We propose the new genus Alloclavaria to accommodate Clavaria purpurea, which is not related to Clavaria but is derived within the hymenochaetoid clade. The Physalacriaceae and Clavariaceae are redefined to reflect monophyletic groups, and the limits of Clavaria, Clavulinopsis and Ramariopsis should be reconsidered when additional data are available.     

NETGEN: generating phylogenetic networks with diploid hybrids

SUMMARY: NetGen is an event-driven simulator that creates phylogenetic networks by extending the birth-death model to include diploid hybridizations. DNA sequences are evolved in conjunction with the topology, enabling hybridization decisions to be based on contemporary evolutionary distances. NetGen supports variable rate lineages, root sequence specification, outgroup generation and many other options. This note describes the NetGen application and proposes an extension of the Newick format to accommodate phylogenetic networks. AVAILABILITY: NetGen is written in C and is available in source form at http://www.phylo.unm.edu/~morin/.     

Studies in cave life evolution: a rationale for future theoretical developments using phylogenetic inference

As in every field of comparative biology, phylogeny provides an independent reference system in studies on cave life evolution to test current theoretical proposals. Using phylogeny, sound hypotheses on the ancestral states of characters and their subsequent changes can be made by polarizing the characters between related taxa. Hypotheses on evolutionary processes can also be tested by comparing the patterns they imply with independently inferred phylogenetic patterns. The power of the tests relies upon the independence of phylogenetic patterns (built with cladistics using Wagner parsimony) and the theoretical proposals under study. Classical assumptions on the evolution of troglobitic life are analysed with this methodology. The following points are discussed: what is a troglobitic taxon? Are there features characteristic of troglobitic taxa? Is troglobitic life an evolutionary dead end? What circumstances favour troglobitic evolution? Using phylogenetic analysis, the presence or absence of so-called troglomorphic features were inferred in troglobitic taxa. In fact these taxa can be characterized only by their behavioural ecology. Pre-adaptations (exaptations) can also be precisely defined. Cave living does not appear to be an evolutionary dead end. Two patterns subsequent to cave life appearance have been documented: speciation of troglobitic taxa in the subterranean environment, and reversal to an epigean habitat. Troglobitic life thus turns out to be one step in the diversification of clades. Troglobitic life is usually explained as an evolution under the pressure of unfavourable environmental conditions, or the conquest of a new resource, or the result of biological interactions (competition, predation). Phylogenetic analyses show that none of these hypotheses propose clear alternatives on cave life evolution. Moreover most of their a priori statements cannot easily be falsified. As such they have only limited explanatory power.     

Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.     

THE EVOLUTION OF THERMOTOLERANCE IN HOT SPRING CYANOBACTERIA OF THE GENUS SYNECHOCOCCUS

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the twenty laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S ribosomal RNA gene sequences were identified. Phylogenies constructed using these sequence data indicated that the clones were polyphyletic but also that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in thermal niche breadth, which may have implications for the geographic distributions of these organisms. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.     

SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides

Most phylogenetic methods assume that the sequences evolved under homogeneous, stationary and reversible conditions. Compositional heterogeneity in data intended for studies of phylogeny suggests that the data did not evolve under these conditions. SeqVis, a Java application for analysis of nucleotide content, reads sequence alignments in several formats and plots the nucleotide content in a tetrahedron. Once plotted, outliers can be identified, thus allowing for decisions on the applicability of the data for phylogenetic analysis. AVAILABILITY: http://www.bio.usyd.edu.au/jermiin/programs.htm.     

Biological and molecular characterisation of Prunus necrotic ringspot virus isolates and possible approaches to their phylogenetic typing

Seven isolates of Prunus necrotic ringspot virus (PNRSV) originating from Slovakia were subjected to biological tests under glasshouse conditions. Mainly mild symptoms were observed on chip‐budded test cherry rootstocks. The complete sequence for the capsid protein (CP) gene of four isolates was determined. All sequences were 675 nucleotides long and clustered in the largest of four groups delineated by phylogenetic analyses of all so far known PNRSV CP sequences. A set of restriction endonucleases was suggested to differentiate four isolate clusters by restriction enzyme digestion of CP sequences.     

Evolution of Thermotolerance in Hot Spring Cyanobacteria of the Genus Synechococcus

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.     

Dead-end evolution of the Cnidaria as deduced from 5S ribosomal RNA sequences

Using nucleotide sequences of 5S ribosomal RNAs from 2 hydrozoan jellyfishes, 3 scyphozoan jellyfishes and 2 sea anemones, a phylogenetic tree of Cnidaria has been constructed to elucidate the evolutionary relationships of radial and bilateral symmetries. The 3 classes of Cnidaria examined herein belong to one branch, which does not include other metazoan phyla such as the Platyhelminthes. The Hydrozoa (having radial symmetry without septa) and the Scyphozoa (having radial symmetry with septa) are more closely related to each other than to the Anthozoa (having bilateral symmetry with septa). In classical taxonomy, multicellular animals are considered to have evolved through organisms with radial symmetry (e.g., Cnidaria) to bilateral symmetry. Our results, however, indicate that the emergence of the Bilateria was earlier than that of the Radiata, suggesting (in opposition to Haeckel's view) that the radial symmetry of Cnidaria is an evolutionary dead end.     

Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals

Relationships among families and suborders of scleractinian corals are poorly understood because of difficulties 1) in making inferences about the evolution of the morphological characters used in coral taxonomy and 2) in interpreting their 240-million-year fossil record. Here we describe patterns of molecular evolution in a segment of the mitochondrial (mt) 16S ribosomal gene from taxa of 14 families of corals and the use of this gene segment in a phylogenetic analysis of relationships within the order. We show that sequences obtained from scleractinians are homologous to other metazoan 16S ribosomal sequences and fall into two distinct clades defined by size of the amplified gene product. Comparisons of sequences from the two clades demonstrate that both sets of sequences are evolving under similar evolutionary constraints: they do not differ in nucleotide composition, numbers of transition and transversion substitutions, spatial patterns of substitutions, or in rates of divergence. The characteristics and patterns observed in these sequences as well as the secondary structures, are similar to those observed in mt 16S ribosomal DNA sequences from other taxa. Phylogenetic analysis of these sequences shows that they are useful for evaluating relationships within the order. The hypothesis generated from this analysis differs from traditional hypotheses for evolutionary relationships among the Scleractinia and suggests that a reevaluation of evolutionary affinities in the order is needed. Received: 4 September 1996 / Accepted: 7 April 1997     

Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences

Myriapods play a pivotal position in the arthropod phylogenetic tree. The monophyly of Myriapoda and its internal relationships have been difficult to resolve. This study combined nearly complete 28S and 18S ribosomal RNA gene sequences (3,826 nt in total) to estimate the phylogenetic position of Myriapoda and phylogenetic relationships among four myriapod classes. Our data set consists of six new myriapod sequences and homologous sequences for 18 additional species available in GenBank. Among the six new myriapod sequences, those of the one pauropod and two symphylans are very important additions because they were such difficult taxa to classify in past molecular-phylogenetic studies. Phylogenetic trees were constructed with maximum parsimony, maximum likelihood, and Bayesian analyses. All methods yielded moderate to strong support for the monophyly of Myriapoda. Symphyla grouped strongly with Pauropoda under all analytical conditions. The KH test rejected the traditional view of Dignatha and Progoneata, and the topology obtained here, though not significantly supported, was Diplopoda versus ((Symphyla + Pauropoda) + Chilopoda).