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PubMed2005

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.

Chloroplasts↗

PubMed1996

Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data

Abstract. Models of nucleotide substitution were constructed for combined analyses of heterogeneous sequence data (such as those of multiple genes) from the same set of species. The models account for different aspects of the heterogeneity in the evolutionary process of different genes, such as differences in nucleotide frequencies, in substitution rate bias (for example, the transition/transversion rate bias), and in the extent of rate variation across sites. Model parameters were estimated by maximum likelihood and the likelihood ratio test was used to test hypotheses concerning sequence evolution, such as rate constancy among lineages (the assumption of a molecular clock) and proportionality of branch lengths for different genes. The example data from a segment of the mitochondrial genome of six hominoid species (human, common and pygmy chimpanzees, gorilla, orangutan, and siamang) were analyzed. Nucleotides at the three codon positions in the protein-coding regions and from the tRNA-coding regions were considered heterogeneous data sets. Statistical tests showed that the amount of evolution in the sequence data reflected in the estimated branch lengths can be explained by the codon-position effect and lineage effect of substitution rates. The assumption of a molecular clock could not be rejected when the data were analyzed separately or when the rate variation among sites was ignored. However, significant differences in substitution rate among lineages were found when the data sets were combined and when the rate variation among sites was accounted for in the models. Under the assumption that the orangutan and African apes diverged 13 million years ago, the combined analysis of the sequence data estimated the times for the human-chimpanzee separation and for the separation of the gorilla as 4.3 and 6.8 million years ago, respectively.

Journal Article↗

PubMed1996

A comparison of isozyme and quantitative genetic variation in Pinus contorta ssp. latifolia by FST.

We employed F-statistics to analyze quantitative and isozyme variation among five populations of Pinus contorta ssp. latifolia, a wind-pollinated outcrossing conifer with wide and continuous distribution in west North America. Estimates of population differentiation (FST) for six quantitative traits were compared with the overall estimate of the differentiation (F*ST) from 19 isozymes that tested neutral to examine whether similar evolutionary processes were involved in morphological and isozyme differentiation. While the FST estimates for specific gravity, stem diameter, stem height and branch length were significantly greater than the F*ST estimate, as judged from the 95% confidence intervals by bootstrapping, the FST estimates for branch angle and branch diameter were indistinguishable from the F*ST estimate. Differentiation in stem height and stem diameter might reflect the inherent adaptation of the populations for rapid growth to escape suppression by neighboring plants during establishment and to regional differences in photoperiod, precipitation and temperature. In contrast, divergences in wood specific gravity and branch length might be correlated responses to population differentiation in stem growth. Possible bias in the estimation of FST due to Hardy-Weinberg disequilibrium (FIS not equal to 0), linkage disequilibrium, maternal effects and nonadditive genetic effects was discussed with special reference to P. contorta ssp. latifolia.

Genetic Variation↗

PubMed2006

The ancestral distance test: what relatedness can reveal about correlated evolution in large lineages with missing character data and incomplete phylogenies.

The ancestral distance test is introduced to detect correlated evolution between two binary traits in large phylogenies that may lack resolved subclades, branch lengths, and/or comparative data. We define the ancestral distance as the time separating a randomly sampled taxon from its most recent ancestor (MRA) with extant descendants that have an independent trait. The sampled taxon either has (target sample) or lacks (nontarget sample) a dependent trait. Modeled as a Markov process, we show that the distribution of ancestral distances for the target sample is identical to that of the nontarget sample when characters are uncorrelated, whereas ancestral distances are smaller on average for the target sample when characters are correlated. Simulations suggest that the ancestral distance can be estimated using the time, total branch length, taxonomic rank, or number of speciation events between a sampled taxon and the MRA. These results are shown to be robust to deviations from Markov assumptions. A Monte Carlo technique estimates P-values when fully resolved phylogenies with branch lengths are available, and we evaluate the Monte Carlo approach using a data set with known correlation. Measures of relatedness were found to provide a robust means to test hypotheses of correlated character evolution.

Classification↗

PubMed2003

Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae).

We constructed a phylogenetic hypothesis for western Indian Ocean sunbirds (Nectarinia) and used this to investigate the geographic pattern of their diversification among the islands of the Indian Ocean. A total of 1309 bp of mitochondrial sequence data was collected from the island sunbird taxa of the western Indian Ocean region, combined with sequence data from a selection of continental (African and Asian) sunbirds. Topological and branch length information combined with estimated divergence times are used to present hypotheses for the direction and sequence of colonization events in relation to the geological history of the Indian Ocean region. Indian Ocean sunbirds fall into two well-supported clades, consistent with two independent colonizations from Africa within the last 3.9 million years. The first clade contains island populations representing the species Nectarinia notata, while the second includes Nectarinia souimanga, Nectarinia humbloti, Nectarinia dussumieri, and Nectarinia coquereli. With respect to the latter clade, application of Bremer's [Syst. Biol. 41 (1992) 436] ancestral areas method permits us to posit the Comoros archipelago as the point of initial colonization in the Indian Ocean. The subsequent expansion of the souimanga clade across its Indian Ocean range occurred rapidly, with descendants of this early expansion remaining on the Comoros and granitic Seychelles. The data suggest that a more recent expansion from Anjouan in the Comoros group led to the colonization of Madagascar by sunbirds representing the souimanga clade. In concordance with the very young geological age of the Aldabra group, the sunbirds of this archipelago have diverged little from the Madagascar population; this is attributed to colonization of the Aldabra archipelago in recent times, in one or possibly two or more waves originating from Madagascar. The overall pattern of sunbird radiation across Indian Ocean islands indicates that these birds disperse across ocean barriers with relative ease, but that their subsequent evolutionary success probably depends on a variety of factors including prior island occupation by competing species.

Animals↗

PubMedDate not supplied

A likelihood approach to estimating phylogeny from discrete morphological character data.

Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores the possibility of using standard, well-behaved Markov models for estimating morphological phylogenies (including branch lengths) under the likelihood criterion. An important modification of standard Markov models involves making the likelihood conditional on characters being variable, because constant characters are absent in morphological data sets. Without this modification, branch lengths are often overestimated, resulting in potentially serious biases in tree topology selection. Several new avenues of research are opened by an explicitly model-based approach to phylogenetic analysis of discrete morphological data, including combined-data likelihood analyses (morphology + sequence data), likelihood ratio tests, and Bayesian analyses.

Biometry↗

PubMed1995

Gene for cytochrome c oxidase subunit II in the mitochondrial DNA of Culex quinquefasciatus and Aedes aegypti (Diptera: Culicidae).

The cytochrome c oxidase subunit II (COII) gene between transfer RNA for Leu and Lys in the mitochondrial DNA of Culex quinquefasciatus Say and Aedes aegypti (L.) was amplified by the polymerase chain reaction (PCR) technique. Both the gene order and direction of transcription were identical to Anopheles and Drosophila. Nucleotide sequences of the PCR-amplified COII genes in these two mosquitoes exhibited 88% homology, and the frequency of transition was very close to that of transversion. The homology of deduced amino acid sequences of COII between these two mosquitoes was 95%. Two highly conserved segments of COII proteins were found in mosquitoes, fruit flies, locust, and honeybee. These segments contain the major amino acid residues of cytochrome c oxidase involved in electron transport and ligand binding. The amino acid residues are located at the positions similar to those of the mammalian enzymes. Two sets of the phylogenetic trees of a similar pattern were generated by comparing the divergences of nucleotide and amino acid sequences of COII. The branch lengths of the trees estimated by amino acid and nucleotide sequences showed different evolution rates of Aedes and Culex from their common ancestor.

Aedes↗

PubMed2000

Coronary artery flow velocity is related to lumen area and regional left ventricular mass.

BACKGROUND: Coronary flow velocity varies widely between individuals, even at rest. Because of this variation, indices with less apparent deviation, such as the ratio of hyperemic to resting velocity (coronary flow reserve), have been more commonly studied. We tested the hypothesis that the flow continuity principle could be used to model resting coronary flow, and we examined the resulting velocity relationship. METHODS AND RESULTS: We studied coronary velocity in 59 patients using a Doppler wire to measure resting and hyperemic average peak velocities in the left anterior descending artery. Quantitative techniques were used to calculate lumen cross-sectional area and the lengths of all distal coronary branches. Branch lengths were used to estimate regional left ventricular mass. We then calculated the ratio of lumen area to regional mass (A/m). Regional perfusion was estimated from the double product of heart rate and systolic blood pressure. Resting velocity (V) varied inversely with A/m ratio [V=46.5/(A/m); r=0.68, P<0.001]. Disease in the left anterior descending artery was categorized as none or luminal irregularities only (n=22), mild (n=15), or moderate (n=22). The A/m ratio declined across these groups (8.7+/-4.0, 8.5+/-6.2, and 5. 6+/-3.0 mm(2)/100 g, respectively; P<0.04), and the resting average peak velocity increased (27+/-16, 33+/-11, and 37+/-20 cm/s, respectively; P=0.06). CONCLUSIONS: Resting coronary artery flow velocity is inversely related to the ratio of lumen area to regional left ventricular mass. Higher resting velocities are found when insufficient lumen size exists for the distal myocardial bed, as occurs with diffuse mild or moderate coronary atherosclerosis.

Adult↗

PubMed2000

Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A.

Algorithmic details to obtain maximum likelihood estimates of parameters on a large phylogeny are discussed. On a large tree, an efficient approach is to optimize branch lengths one at a time while updating parameters in the substitution model simultaneously. Codon substitution models that allow for variable nonsynonymous/synonymous rate ratios (omega = d(N)/d(S)) among sites are used to analyze a data set of human influenza virus type A hemagglutinin (HA) genes. The data set has 349 sequences. Methods for obtaining approximate estimates of branch lengths for codon models are explored, and the estimates are used to test for positive selection and to identify sites under selection. Compared with results obtained from the exact method estimating all parameters by maximum likelihood, the approximate methods produced reliable results. The analysis identified a number of sites in the viral gene under diversifying Darwinian selection and demonstrated the importance of including many sequences in the data in detecting positive selection at individual sites.

Algorithms↗

PubMed1998

A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences.

We have developed a rapid parsimony method for reconstructing ancestral nucleotide states that allows calculation of initial branch lengths that are good approximations to optimal maximum-likelihood estimates under several commonly used substitution models. Use of these approximate branch lengths (rather than fixed arbitrary values) as starting points significantly reduces the time required for iteration to a solution that maximizes the likelihood of a tree. These branch lengths are close enough to the optimal values that they can be used without further iteration to calculate approximate maximum-likelihood scores that are very close to the "exact" scores found by iteration. Several strategies are described for using these approximate scores to substantially reduce times needed for maximum-likelihood tree searches.

Animals↗

PubMed2003

Identifying site-specific substitution rates.

A maximum likelihood framework for estimating site-specific substitution rates is presented that does not require any prior assumptions about the rate distribution. We show that, when the branching pattern of the underlying tree is known, the analysis of pairs of positions is sufficient to estimate site-specific rates. In the abscense of a known topology, we introduce an iterative procedure to estimate simultaneously the branching pattern, the branch lengths, and site-specific substitution rates. Simulations show that the evolutionary rate of fast-evolving sites can be reliably inferred and that the accuracy of rate estimates depends mainly on the number of sequences in the data set. Thus, large sets of aligned sequences are necessary for reliable site-specific rate estimates. The method is applied to the complete mitochondrial DNA sequence of 53 humans, providing a complete picture of the site-specific substitution rates in human mitochondrial DNA.

Algorithms↗

PubMed2005

Using models of nucleotide evolution to build phylogenetic trees.

Molecular phylogenetics and its applications are popular and useful tools for making comparative investigations in genetics; however, estimating phylogenetic trees is not always straightforward. Some phylogenetic estimators use an explicit model of nucleotide evolution to estimate evolutionary parameters such as branch lengths and tree topology. There are many models to choose from, and use of the optimal model for a particular data set is important to avoid a loss of power and accuracy in phylogenetic estimations. Here, we review some molecular evolutionary forces and the parameters included in some common models of evolution used to interpret resulting patterns of molecular variation. We present some statistical methods of selecting a particular model of nucleotide evolution, and provide an empirical example of model selection. Statistical model selection strikes a balance between the bias introduced by some models and the increased variance of parameter estimates that results from using other models.

Animals↗

PubMed2003

Global patterns in peatmoss biodiversity.

DNA sequence data from the nuclear ribosomal internal transcribed spacers (ITS) and the trnL-trnF chloroplast DNA regions were used to quantify geographical partitioning of global biodiversity in peatmosses (Sphagnum), and to compare patterns of molecular diversity with patterns of species richness. Molecular diversity was estimated for boreal, tropical, Neotropical, nonboreal (tropical plus Southern Hemisphere), Old World and New World partitions, based on a total of 436 accessions. Diversity was partitioned among geographical regions in terms of combined nuclear and chloroplast sequence data and separately for the ITS and trnL-trnF data sets. Levels of variation were estimated using phylogenetic diversity (PD), which incorporates branch lengths from a phylogenetic tree, and the number of polymorphic nucleotide sites. Estimates of species richness suggest that peatmoss diversity is higher in New World than Old World regions, and that the Neotropics constitute a "hotspot" of diversity. Molecular estimates, in contrast, indicate that peatmoss biodiversity is almost evenly divided between New and Old World regions, and that the Neotropics account for only 20-35% of global peatmoss diversity. In general, levels of tropical and boreal peatmoss molecular diversity were comparable. Two species, S. sericeum from the Old World tropics and S. lapazense from Bolivia, are remarkably divergent in nucleotide sequences from all other Sphagna and together account for almost 20% of all peatmoss diversity, although they are represented by only three of the 436 accessions (0.7%). These species clearly demonstrate the nonequivalence of species biodiversity value.

Base Sequence↗

PubMed2004

Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences.

A biologically realistic method was used to simulate evolutionary trees. The method uses a real DNA coding sequence as the starting point, simulates mutation according to the mutational spectrum of Escherichia coli-including base substitutions, insertions, and deletions-and separates the processes of mutation and selection. Trees of 8, 16, 32, and 64 taxa were simulated with average branch lengths of 50, 100, 150, 200, and 250 changes per branch. The resulting sequences were aligned with ClustalX, and trees were estimated by Neighbor Joining, Parsimony, Maximum Likelihood, and Bayesian methods from both DNA sequences and the corresponding protein sequences. The estimated trees were compared with the true trees, and both topological and branch length accuracies were scored. Over the variety of conditions tested, Bayesian trees estimated from DNA sequences that had been aligned according to the alignment of the corresponding protein sequences were the most accurate, followed by Maximum Likelihood trees estimated from DNA sequences and Parsimony trees estimated from protein sequences.

Amino Acid Sequence↗

PubMed2002

Quantitative analysis of shoot development and branching patterns in Actinidia.

We developed a framework for the quantitative description of Actinidia vine architecture, classifying shoots into three types (short, medium and long) corresponding to the modes of node number distribution and the presence/ absence of neoformed nodes. Short and medium shoots were self-terminated and had only preformed nodes. Based on the cut-off point between their two modes of node number distribution, short shoots were defined as having nine or less nodes, and medium shoots as having more than nine nodes. Long shoots were non-terminated and had a number of neoformed nodes; the total number of nodes per shoot was up to 90. Branching patterns for each parent shoot type were represented by a succession of branching zones. Probabilities of different types of axillary production (latent bud, short, medium or long shoot) and the distributions of length for each branching zone were estimated from experimental data using hidden semi-Markov chain stochastic models. Branching was acrotonic on short and medium parent shoots, with most axillary shoots being located near the shoot tip. For long parent shoots, branching was mesotonic, with most long axillary shoots being located in the transition zone between the preformed and neoformed part of the parent shoot. Although the shoot classification is based on node number distribution there was a marked difference in average (per shoot) internode length between the shoot types, with mean values of 9, 27 and 47 mm for short, medium and long shoots, respectively. Bud and shoot development is discussed in terms of environmental controls.

Actinidia↗

PubMed2026

IQ-NET: fast and accurate quartet phylogenetic inference using deep learning trained on empirical DNA alignments.

Phylogenetic inference is fundamental to modern biology, with many applications including evolutionary biology, epidemiology, and comparative genomics. While maximum likelihood and Bayesian methods remain the gold standard for phylogenetic analysis, they rely on simplifying assumptions and are computationally intensive. Recent machine learning approaches for phylogenetics offer speed advantages, but have several limitations: exclusive reliance on simulated data for training, inadequate handling of gaps, and sensitivity to input sequence order. Here, we introduce IQ-NET (Intelligent Quartet NETwork), a deep learning framework that solves these limitations to infer four-taxon trees. IQ-NET estimates both tree topology and branch lengths directly from gapped alignments. IQ-NET outperforms existing machine learning methods in terms of accuracy, and obtained a 24-fold speedup compared with the widely used maximum likelihood software, IQ-TREE. We finally introduce a pipeline using IQ-NET and the ASTRAL software to reconstruct a larger species tree, i.e., with more than four taxa.

Empirical data training↗

PubMed2006

Rapid and reversible changes in intrahippocampal connectivity during the course of hibernation in European hamsters.

The hippocampal formation is a highly plastic brain structure that undergoes structural remodeling in response to internal and external challenges such as metabolic imbalance and repeated stress. We investigated whether the extreme alterations in metabolic status that occur during the course of hibernation in European hamsters cause structural changes in the dendritic arborizations of the CA3 pyramidal neurons and their main excitatory afferents, the mossy fiber terminals (MFT), that originate in the dentate gyrus. We report that apical, but not basal, dendritic trees of Golgi-impregnated CA3 principal neurons are significantly shorter, less branched, and less spiny in hypothermic hamsters compared with active animals. After the induction of arousal from torpor, within 2 h, the apical dendritic lengths, branching patterns, and spine density estimations returned to levels found in active, euthermic hamsters. The ultrastructure of MFT in hibernating hamsters showed a significant reduction in synaptic vesicle density and in the percentage of MFT area covered by spine profiles. Awakened hamsters showed restoration of MFT morphology to that seen in active animals. MFT of torpid animals also showed a significant increase in the percentage area of mitochondrial profiles that remained higher 3 h after induced arousal from hibernation compared with euthermic controls. Thus, the torpid/awakening cycle of the hibernating European hamster causes a rapid and reversible morphological reorganization of intrahippocampal subregions involved in information processing. The reported reductions in morphological connectivity between the dentate gyrus and the CA3 subregions could underlie the cessation of exploratory activity and spatial navigation skills during hibernation.

Animals↗

PubMed2005

Detecting coevolving amino acid sites using Bayesian mutational mapping.

MOTIVATION: The evolution of protein sequences is constrained by complex interactions between amino acid residues. Because harmful substitutions may be compensated for by other substitutions at neighboring sites, residues can coevolve. We describe a Bayesian phylogenetic approach to the detection of coevolving residues in protein families. This method, Bayesian mutational mapping (BMM), assigns mutations to the branches of the evolutionary tree stochastically, and then test statistics are calculated to determine whether a coevolutionary signal exists in the mapping. Posterior predictive P-values provide an estimate of significance, and specificity is maintained by integrating over uncertainty in the estimation of the tree topology, branch lengths and substitution rates. A coevolutionary Markov model for codon substitution is also described, and this model is used as the basis of several test statistics. RESULTS: Results on simulated coevolutionary data indicate that the BMM method can successfully detect nearly all coevolving sites when the model has been correctly specified, and that non-parametric statistics such as mutual information are generally less powerful than parametric statistics. On a dataset of eukaryotic proteins from the phosphoglycerate kinase (PGK) family, interdomain site contacts yield a significantly greater coevolutionary signal than interdomain non-contacts, an indication that the method provides information about interacting sites. Failure to account for the heterogeneity in rates across sites in PGK resulted in a less discriminating test, yielding a marked increase in the number of reported positives at both contact and non-contact sites. SUPPLEMENTARY INFORMATION: http://www.dimmic.net/supplement/

Amino Acids↗