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PubMed2004

Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on 16S rRNA, gyrB and ectBC gene sequences.

Halomonas variabilis and phylogenetically related organisms were isolated from various habitats such as Antarctic terrain and saline ponds, deep-sea sediment, deep-sea waters affected by hydrothermal plumes, and hydrothermal vent fluids. Ten strains were selected for physiological and phylogenetic characterization in detail. All of those strains were found to be piezotolerant and psychrotolerant, as well as euryhaline halophilic or halotolerant. Their stress tolerance may facilitate their wide occurrence, even in so-called extreme environments. The 16S rDNA-based phylogenetic relationship was complemented by analyses of the DNA gyrase subunit B gene (gyrB) and genes involved in the synthesis of the major compatible solute, ectoine: diaminobutyric acid aminotransferase gene (ectB) and ectoine synthase gene (ectC). The phylogenetic relationships of H. variabilis and related organisms were very similar in terms of 16S rDNA, gyrB, and ectB. The ectC-based tree was inconsistent with the other phylogenetic trees. For that reason, ectC was inferred to derive from horizontal transfer.

Adaptation, Biological↗

PubMed2003

The variable part of the dnaK gene as an alternative marker for phylogenetic studies of rhizobia and related alpha Proteobacteria.

DnaK is the 70 kDa chaperone that prevents protein aggregation and supports the refolding of damaged proteins. Due to sequence conservation and its ubiquity this chaperone has been widely used in phylogenetic studies. In this study, we applied the less conserved part that encodes the so-called alpha-subdomain of the substrate-binding domain of DnaK for phylogenetic analysis of rhizobia and related non-symbiotic alpha-Proteobacteria. A single 330 bp DNA fragment was routinely amplified from DNA templates isolated from the species of the genera, Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium, but also from some non-symbiotic alpha Proteobacteria such as Blastochloris, Chelatobacter and Chelatococcus. Phylogenetic analyses revealed high congruence between dnaK sequences and 16S rDNA trees, but they were not identical. In contrast, the partition homogeneity tests revealed that dnaK sequence data could be combined with other housekeeping genes such as recA, atpD or glnA. The dnaK trees exhibited good resolution in the cases of the genera Mesorhizobium, Sinorhizobium and Rhizobium, even better than usually shown by 16S rDNA phylogeny. The dnaK phylogeny supported the close phylogenetic relationship of Rhizobium galegae and Agrobacterium tumefaciens (R. radiobacter) C58, which together formed a separate branch within the fast-growing rhizobia, albeit closer to the genus Sinorhizobium. The Rhizobium and Sinorhizobium genera carried an insertion composed of two amino acids, which additionally supported the phylogenetic affinity of these two genera, as well as their distinctness from the Mesorhizobium genus. Consistently with the phylogeny shown by 16S-23S rDNA intergenic region sequences, the dnaK trees divided the genus Bradyrhizobium into three main lineages, corresponding to B. japonicum, B. elkanii, and photosynthetic Bradyrhizobium strains that infect Aeschynomene plants. Our results suggest that the 330 bp dnaK sequences could be used as an additional taxonomic marker for rhizobia and related species (alternatively to the 16S rRNA gene phylogeny).

Alphaproteobacteria↗

PubMed2002

A genomic schism in birds revealed by phylogenetic analysis of DNA strings.

The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths.

Animals↗

PubMed2004

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001).

Animals↗

PubMed2005

Phylogenetic signal in AFLP data sets.

AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative.

Classification↗

PubMed2006

Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling.

We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally linked to Mediterranean-type climatic shifts of the mid-Miocene and whether climate preferences are conservative over phylogenetic timescales. Phyloclimatic modeling combines environmental niche (bioclimatic) modeling with phylogenetics in order to study evolutionary patterns in relation to climate change. We present the largest and most complete such example to date using Drosera. The bioclimatic models of extant species demonstrate clear phylogenetic patterns; this is particularly evident for the tuberous sundews from southwestern Australia (subgenus Ergaleium). We employ a method for establishing confidence intervals of node ages on a phylogeny using replicates from a Bayesian phylogenetic analysis. This chronogram shows that many clades, including subgenus Ergaleium and section Bryastrum, diversified during the establishment of the Mediterranean-type climate. Ancestral reconstructions of bioclimatic models demonstrate a pattern of preference for this climate type within these groups. Ancestral bioclimatic models are projected into palaeo-climate reconstructions for the time periods indicated by the chronogram. We present two such examples that each generate plausible estimates of ancestral lineage distribution, which are similar to their current distributions. This is the first study to attempt bioclimatic projections on evolutionary time scales. The sundews appear to have diversified in response to local climate development. Some groups are specialized for Mediterranean climates, others show wide-ranging generalism. This demonstrates that Phyloclimatic modeling could be repeated for other plant groups and is fundamental to the understanding of evolutionary responses to climate change.

Acclimatization↗

PubMed1998

Split support and split conflict randomization tests in phylogenetic inference.

Randomization tests allow the formulation and statistical testing of null hypotheses about the quality of entire data sets or the quality of fit between the data and particular phylogenetic hypotheses. Randomization tests of phylogenetic hypotheses based on the concepts of split support and split conflict are described here, as are tests where splits, rather than the data, are randomly permuted. These tree-independent randomization tests are explored through their application to phylogenetic data for caecilian amphibians. Of these tests, split support randomization tests appear to be the most promising tools for phylogeneticists. These tests seem quite conservative, are applicable to nonpolar data and unordered multistate characters, and do not have the problems of nonindependence that affect split conflict and hierarchy tests. Unlike split conflict tests, their power does not appear to be correlated with split size. However, all tests are sensitive to taxonomic scope. Split support tests may help discern data that are likely to be affected by the problems of long-branches effects. Comparison of test results for mutually incompatible splits may help identify the presence of strong misleading signals in phylogenetic data. Significant split support could be a prerequisite for considering phylogenetic hypotheses to be well supported by the data, and split support randomization tests might be usefully applied prior to or as part of tree construction.

Amphibians↗

PubMed1998

Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods.

Intraspecific variation is abundant in all types of systematic characters but is rarely addressed in simulation studies of phylogenetic method performance. We compared the accuracy of 15 phylogenetic methods using simulations to (1) determine the most accurate method(s) for analyzing polymorphic data (under simplified conditions) and (2) test if generalizations about the performance of phylogenetic methods based on previous simulations of fixed (nonpolymorphic) characters are robust to a very different evolutionary model that explicitly includes intraspecific variation. Simulated data sets consisted of allele frequencies that evolved by genetic drift. The phylogenetic methods included eight parsimony coding methods, continuous maximum likelihood, and three distance methods (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (Nei's and the modified Cavalli-Sforza and Edwards chord distance). Two sets of simulations were performed. The first examined the effects of different branch lengths, sample sizes (individuals sampled per species), numbers of characters, and numbers of alleles per locus in the eight-taxon case. The second examined more extensively the effects of branch length in the four-taxon, two-allele case. Overall, the most accurate methods were likelihood, the additive distance methods (neighbor joining and Fitch-Margoliash), and the frequency parsimony method. Despite the use of a very different evolutionary model in the present article, many of the results are similar to those from simulations of fixed characters. Similarities include the presence of the "Felsenstein zone," where methods often fail, which suggests that long-branch attraction may occur among closely related species through genetic drift. Differences between the results of fixed and polymorphic data simulations include the following: (1) UPGMA is as accurate or more accurate than nonfrequency parsimony methods across nearly all combinations of branch lengths, and (2) likelihood and the additive distance methods are not positively misled under any combination of branch lengths tested (even when the assumptions of the methods are violated and few characters are sampled). We found that sample size is an important determinant of accuracy and affects the relative success of methods (i.e., distance and likelihood methods outperform parsimony at small sample sizes). Attempts to generalize about the behavior of phylogenetic methods should consider the extreme examples offered by fixed-mutation models of DNA sequence data and genetic-drift models of allele frequencies.

Computer Simulation↗

PubMed2000

Effect of Predator-Prey Phylogenetic Similarity on the Fitness Consequences of Predation: A Trade-off between Nutrition and Disease?

A largely neglected aspect of foraging behavior is whether the costs and benefits of predation vary as a function of phylogenetic (i.e., genetic) similarity between predator and prey. Prey of varying phylogenetic similarities to predators might differ in value because both the risk of pathogen transmission and the nutritional quality of prey typically decline with decreasing phylogenetic similarity between predator and prey. I experimentally evaluated this hypothesis by feeding omnivorous spadefoot toad tadpoles (Spea bombifrons, Spea multiplicata, and Scaphiopus couchii) either conspecific tadpoles or an equal mass of three different species of heterospecific prey, all of which contained naturally occurring bacteria. I also examined which prey species Spea tadpoles preferred. I found that all three species of tadpoles performed best on, and preferred to eat, prey that were of intermediate phylogenetic similarity to the predators. Prey of intermediate phylogenetic similarity may provide the greatest fitness benefits to predators because such prey balance the nutritional benefits of closely related prey with the cost of parasite transmission between closely related individuals.

cannibalism↗

PubMed2003

Phylogenetic origin and virulence genotype in relation to resistance to fluoroquinolones and/or extended-spectrum cephalosporins and cephamycins among Escherichia coli isolates from animals and humans.

In Escherichia coli infection, the implications of fluoroquinolone (FQ) and extended-spectrum cephalosporin plus cephamycin (AmpC) resistance for phylogenetic origin and virulence potential are undefined, as is the influence of ecological context on these associations. Accordingly, 106 E. coli isolates exhibiting FQ and/or AmpC resistance and 98 susceptible isolates were compared with regard to phylogenetic background and virulence profiles, stratified by host group (104 predominantly extraintestinal human isolates and 100 predominantly intestinal cattle and swine isolates). Although resistant isolates exhibited significant shifts in phylogenetic distribution and virulence profiles, human and animal isolates exhibited different phylogenetic shifts, and only among human isolates did resistance predict reduced virulence. Evidence for similar strains being resistant versus susceptible was scant. The O15:K52:H1 clonal group and the closely related "clonal group A" featured prominently among resistant and susceptible human isolates, respectively. Thus, in E. coli, antibiotic resistance predicts phylogenetic background and virulence potential in a complex, context-dependent fashion.

Animals↗

PubMed2006

Ecology predicts large-scale patterns of phylogenetic diversification in birds.

One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large-scale patterns in avian diversification can be explained by variation in intrinsic biology.

Animals↗

PubMed2005

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships.

MOTIVATION: The prediction of protein-protein interactions is currently an important issue in bioinformatics. The mirror tree method uses evolutionary information to predict protein-protein interactions. However, it has been recognized that predictions by the mirror tree method lead to many false positives. The incentive of our study was to solve this problem by improving the method of extracting the co-evolutionary information regarding the protein pairs. RESULTS: We developed a novel method to predict protein-protein interactions from co-evolutionary information in the framework of the mirror tree method. The originality is the use of the projection operator to exclude the information about the phylogenetic relationships among the source organisms from the distance matrix. Each distance matrix was transformed into a vector for the operation. The vector is referred to as a 'phylogenetic vector'. We have proposed three ways to extract the phylogenetic information: (1) using the 16S rRNA from the same source organisms as the proteins under consideration, (2) averaging the phylogenetic vectors and (3) analyzing the principal components of the phylogenetic vectors. We examined the performance of the proposed methods to predict interacting protein pairs from Escherichia coli, using experimentally verified data. Our method was successful, and it drastically reduced the number of false positives in the prediction. AVAILABILITY: The R script for the prediction of protein-protein interactions reported in this manuscript is available at http://timpani.genome.ad.jp/~proj/ CONTACT: sato@kuicr.kyoto-u.ac.jp SUPPLEMENTARY INFORMATION: The information is also available at the same site as the R script.

Algorithms↗

PubMed2006

Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.

A self-organizing map (SOM) was developed as a novel bioinformatics strategy for phylogenetic classification of sequence fragments obtained from pooled genome samples of uncultured microbes in environmental and clinical samples. This phylogenetic classification was possible without either orthologous sequence sets or sequence alignments. We first constructed SOMs for tetranucleotide frequencies in 210,000 5 kb sequence fragments obtained from 1502 prokaryotes for which at least 10 kb of genomic sequence has been deposited in public DNA databases. The sequences could be classified primarily according to phylogenetic groups without information regarding the species. We used the SOM method to classify sequence fragments derived from environmental samples of the Sargasso Sea and of an acidophilic biofilm growing in acid mine drainage. Phylogenetic diversity of the environmental sequences was effectively visualized on a single map. Sequences that were derived from a single genome but cloned independently could be reassociated in silico. G + C% has been used for a long period as a fundamental parameter for phylogenetic classification of microbes, but the G + C% is apparently too simple a parameter to differentiate a wide variety of known species. Oligonucleotide frequency can be used to distinguish the species because oligonucleotide frequencies vary significantly among their genomes.

Algorithms↗

PubMed2003

Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus).

To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon and intron sequences of long-wavelength rhodopsin (LW Rh), arginine kinase (ArgK), and elongation factor-1alpha (EF-1alpha) F2 copy genes. LW Rh intron had only a few uninformative gaps, ArgK intron had relatively long gaps that were easily aligned, and EF-1alpha intron had many short gaps, resulting in multiple optimal alignments. The unambiguously aligned gaps within ArgK intron sequences showed no homoplasy upon the substitution-based tree, and phylogenetic signals within ambiguously aligned regions of EF-1alpha intron were highly congruent with those of base substitutions. We further analyzed the contribution of gap characters to phylogenetic reconstruction by incorporating them in parsimony analysis. Inclusion of gap characters consistently improved support for nodes recovered by substitutions, and inclusion of ambiguously aligned regions of EF-1alpha intron resolved several additional nodes, most of which were apical on the phylogeny. We conclude that gaps are an exceptionally reliable source of phylogenetic information that can be used to corroborate and refine phylogenies hypothesized by base substitutions, at least at lower taxonomic levels. At present, full use of gaps in phylogenetic reconstruction is best achieved in parsimony analysis, pending development of well-justified and generally applicable methods for incorporating indels in explicitly model-based methods.

Animals↗

PubMed2003

Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference.

A major assumption of many molecular phylogenetic methods is the homogeneity of nucleotide frequencies among taxa, which refers to the equality of the nucleotide frequency bias among species. Changes in nucleotide frequency among different lineages in a data set are thought to lead to erroneous phylogenetic inference because unrelated clades may appear similar because of evolutionarily unrelated similarities in nucleotide frequencies. We tested the effects of the heterogeneity of nucleotide frequency bias on phylogenetic inference, along with the interaction between this heterogeneity and stratified taxon sampling, by means of computer simulations using evolutionary parameters derived from genomic databases. We found that the phylogenetic trees inferred from data sets simulated under realistic, observed levels of heterogeneity for mammalian genes were reconstructed with accuracy comparable to those simulated with homogeneous nucleotide frequencies; the results hold for Neighbor-Joining, minimum evolution, maximum parsimony, and maximum-likelihood methods. The LogDet distance method, specifically designed to deal with heterogeneous nucleotide frequencies, does not perform better than distance methods that assume substitution pattern homogeneity among sequences. In these specific simulation conditions, we did not find a significant interaction between phylogenetic accuracy and substitution pattern heterogeneity among lineages, even when the taxon sampling is increased.

Algorithms↗

PubMed2003

Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca).

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a phylogenetic framework. Here, we report the first complete nucleotide sequence (16,060 bp) of the mitochondrial (mt) genome of a North American freshwater bivalve, Lampsilis ornata (Mollusca: Paleoheterodonta: Unionidae). Gene order and mt genome content is examined in a comparative phylogenetic framework for Lampsilis and five other bivalves, representing five families. Mitochondrial genome content is shown to vary by gene duplication and loss among taxa and between male and female mitotypes within a species. Although mt gene arrangement is highly variable among bivalves, when optimized on an independently derived phylogenetic hypothesis, it allows for the reconstruction of ancestral gene order states and indicates the potential phylogenetic utility of the data. However, the interpretation of reconstructed ancestral gene order states must take in to account both the accuracy of the phylogenetic estimation and the probability of character state change across the topology, such as the presence/absence of atp8 in bivalve lineages. We discuss what role, if any, doubly uniparental inheritance (DUI) and recombination between sexual mitotypes may play in influencing gene rearrangement of the mt genome in some bivalve lineages.

Animals↗

PubMed2005

Application of phylogenetic networks in evolutionary studies.

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

Animals↗

PubMed2006

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.

Animals↗