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PubMed2006

Life history trade-offs in tropical trees and lianas.

It has been hypothesized that tropical trees partition forest light environments through a life history trade-off between juvenile growth and survival; however, the generality of this trade-off across life stages and functional groups has been questioned. We quantified trade-offs between growth and survival for trees and lianas on Barro Colorado Island (BCI), Panama using first-year seedlings of 22 liana and 31 tree species and saplings (10 mm < dbh < 39 mm) of 30 tree species. Lianas showed trade-offs similar to those of trees, with both groups exhibiting broadly overlapping ranges in survival and relative growth rates as seedlings. Life history strategies at the seedling stage were highly correlated with those at the sapling stage among tree species, with all species showing an increase in survival with size. Only one of 30 tree species demonstrated a statistically significant ontogenetic shift, having a relatively lower survival rate at the sapling stage than expected. Our results indicate that similar life history trade-offs apply across two functional groups (lianas and trees), and that life history strategies are largely conserved across seedling and sapling life-stages for most tropical tree species.

Adaptation, Physiological↗

PubMed1997

Cross-reactivity to olive tree pollen and orchard grass pollen in patients with pollinosis.

We studied 92 patients with allergic rhinitis in Syodoshima, Japan, during the pollen season between April and June to evaluate the cross-reactivity to different antigens, including pollen from the olive tree (Olea europaea) and orchard grass (Dactylis glomerata). Olive tree pollen was present in the atmosphere for 23 days, from May 19 to June 12, 1994. Specific IgE antibodies for olive tree pollen antigen were present in 21 (26.9%) of the 78 patients with allergic rhinitis. Nine (24.3%) of the 37 patients with allergic rhinitis exhibited positive skin reactivity to an extract of olive tree pollen. Fifteen (88.2%) of the 17 patients who had IgE reactivity in their sera to olive tree pollen antigen demonstrated allergic reactions to an extract of olive tree pollen. Specific IgE antibodies for orchard grass pollen antigen were present in 43 (48.3%) of the 89 patients with allergic rhinitis and 20 (95.2%) of the 21 patients who had IgE reactivity in their sera to olive tree pollen antigen. The inhibition test using the CAP System revealed that the reactivity of the IgE antibody specific for olive tree pollen antigen was inhibited dose-dependently by an extract of orchard grass pollen. These findings show that there is a reaction in some patients with grass (Gramineae) pollinosis that might be induced by olive tree pollen.

Hemadsorption Inhibition Tests↗

PubMed1998

The limitations of decision trees and automatic learning in real world medical decision making.

The decision tree approach is one of the most common approaches in automatic learning and decision making. It is popular for its simplicity in constructing, efficient use in decision making and for simple representation, which is easily understood by humans. The automatic learning of decision trees and their use usually show very good results in various "theoretical" environments. The training sets are usually large enough for learning algorithm to construct a hypothesis consistent with the underlying concept. But in real life it is often impossible to find the desired number of training objects for various reasons. The lack of possibilities to measure attribute values, high cost and complexity of such measurements, unavailability of all attributes at the same time are the typical representatives. There are different ways to deal with some of these problems, but in a delicate field of medical decision making, we cannot allow ourselves to make any inaccurate decisions. We have measured the values of 24 attributes before and after the 82 operations of children in age between 2 and 10 years. The aim was to find the dependencies between attribute values and a child's predisposition to acidemia--the decrease of blood's pH. Our main interest was in discovering predisposition to two forms of acidosis, the metabolic acidosis and the respiratory acidosis, which can both have serious effects on child's health. We decided to construct different decision trees from a set of training objects, which was complete (there were no missing attribute values), but on the other hand not large enough to avoid the effect of overfitting. A common approach to evaluation of a decision tree is the use of a test set. In our case we decided that instead of using a test set, we ask medical experts to take a closer look at the generated trees. They examined and evaluated the decision trees branch by branch. Their comments on the generated trees can be found in this paper. The comments show, that trees generated from available training set mainly have surprisingly good branches, but on the other hand some are very "stupid" and no medical explanation could be found. Thereafter we can conclude, that the decision tree concept and automatic learning can be successfully used in real world situations, constrained with the real world limitations, but they should be used only with the guidelines of appropriate medical experts.

Acidosis↗

PubMed2002

[Potential of purifying SO2 of main tree species and their planting quota in Shenyang area].

The total potential of purifying SO2 of main tree species was studied by using the combination of field measurement and fumigation experiment in this paper. The integrated value of purifying SO2 including total bimass, absorption intensity of SO2, and absorption-transformation periods of sulfur by trees was 4.39 x 10(6) kg, which was accounted for 3.66% of total sulfur released per year in Shenyang. It indicated that the maximum daily potential of purifying SO2 of trees might be 12.19 kg.km-2. Supposed that the average annual absorption capacity for sulfur of trees in Shenyang was 0.70 kg per tree and the average annual absorption capacity for sulfur of broad-leaved trees was 1.35 kg.tree-1, 88.88 million broad-leaved trees would be required to purify the annual released SO2 thoroughly. This number was equivalent to 12.9 times of existing trees. On the conditions of strengthening environmental protection and decreasing 20% of annual released sulfur, if the broad-leaved trees was double of the present number, SO2 content in air might be below 0.06 mg.m-3 and Shenyang would become a standardizing city with clear air.

Air Pollution↗

PubMed2004

[Potential ecological risks of transgenic trees].

A new approach to genetic improvement of trees has been introduced with the birth of gene engineering technique. Compared to that in crops, gene introduction in trees has bigger potential ecological risk in environmental release and extension, because trees, most of which are wind-dispersed, grow on various habitats, have longer life span, and subject to relatively more extensive management. Extensive plantation of transgenic trees may reduce the genetic diversity of the trees concerned. Co-evolution of pests and pathogens is likely to be caused under the pressure of long-term and continuous selection of the trees derived from gene transferring. Escaping of exogenous gene may have a certain kind of influence on fitness of plants naturally generated, and as a result, have influence on species diversity in the natural world. It is not reasonable for China, a developing country, to reject gene introduction as an approach to promote forestry development. It is also important, on the other hand, to take future ecological safety into consideration because it is unwise to get present profit at the cost of future profit. To strengthen basic study on gene transferring, adopting safe management of varieties generated from gene transferring and increasing funds on research and management of transgenic trees are believed to be measures to decrease, to the greatest extent, ecological risks brought about by gene transferring of trees, and to quicken transformation of products of trees derived from gene-transferring into merchandises.

Ecosystem↗

PubMed1995

ROSE: decision trees, automatic learning and their applications in cardiac medicine.

Computerized information systems, especially decision support systems, have acquired an increasingly important role in medical applications, particularly in those where important decisions must be made effectively and reliably. But the possibility of using computers in medical decision making is limited by many difficulties, including the complexity of conventional computer languages, methodologies, and tools. Thus a conceptual simple decision making model with the possibility of automating learning should be used. In this paper, we introduce a cardiological knowledge-based system based on the decision tree approach supporting the mitral valve prolapse determination. Prolapse is defined as the displacement of a bodily part from its normal position. The term mitral valve prolapse (PMV), therefore, implies that the mitral leaflets are displaced relative to some structure, generally taken to be the mitral annulus. The implications of the PMV are: disturbed normal laminar blood flow, turbulence of the blood flow, injury of the chordae tendinae, the possibility of thrombus's composition, bacterial endocarditis, and, finally, hemodynamic changes defined as mitral insufficiency and mitral regurgitation. Uncertainty persists about how it should be diagnosed and about its clinical importance. It is our deep belief that the echocardiography enables properly trained expert armed with proper criteria to evaluate PMV almost 100%. But, unfortunately, there are some problems concerned with the use of echocardiography. With this in mind, we have decided to start a research project aimed at finding new criteria and enabling the general practitioner to evaluate the PMV using conventional methods and to select potential patients from the general population. To empower doctors to perform needed activities, we have developed a computer tool called ROSE (computeRized prOlaps Syndrome dEtermination) based on algorithms of automatic learning. This tool supports the definition of new criteria and the selection of potential PMV-patients. The ROSE is based on concepts of decision trees and automatic learning. The decisions and learning process can be presented with an easily visualized two dimensional model; thus decision trees are straightforward to build and interpret. Decision trees use different object attributes to classify different subsets of objects. (Their great advantage is that they don't use a fixed number of predetermined attributes.) In the decision tree approach, the members of a set of objects are classified as either positive or negative instances (in our case patients with PMV Syndrome or without it). Candidate attributes that may possibly describe the concept are then outlined. A decision tree construction tool uses outlined attributes to formulate the appropriate decision tree that identifies all positive instances of the underlying concept according to objects with known classification. (In our case the classification is done with the echo examination). The first set of objects used for the tree generation is usually called the training set. This decision tree characterization next becomes a basis: 1) forecasting whether an object previously unseen is a positive or negative instance of the concept being modeled, and 2) the hierarchical representation of the most important attributes of the concept being investigated. Our main interest and idea is to discover symptoms, syndromes, and illnesses related to PMV that can be distinguished by general practitioners in their everyday job and which should help them to identify possible PMV candidate patients. To this end, we constructed a computerized tool called ROSE. According to the principles presented above, we first taught ROSE using the sample of 400 examined volunteers. ROSE, considering that the clinical PMV diagnosis is practically not researched, is relatively successful. (abstract truncated)

Algorithms↗

PubMed1996

The importance of the pecan tree pollen in allergic manifestations.

BACKGROUND: Pecan tree pollen is considered to be highly allergenic. However, no specific scientific data about its role in causing allergic diseases are available. OBJECTIVE: To study the role of pecan tree pollen in the development of allergy. METHODS: The presence of pecan tree pollen was determined by weekly and monthly counting of airborne grains. The incidence of pecan tree pollen atopy and clinical manifestations were studied in 395 participants, aged 4-70 years, who comprised 78.2% of the whole eligible population of a rural community. The participants were skin tested for different extracts of allergens, completed detailed questionnaires, and their medical files were evaluated. RESULTS: During May, pecan tree pollen grains comprised 70% of the total airborne grains. A positive skin-prick test (SPT) to pecan was shown by 46 (11.6%) participants, constituting 25.4% of the atopic population. Of those who were found atopic to one or more allergens 50.3% had symptoms, whereas the parallel figure for those atopic to pecan pollen was 76.1% (P < 0.005); 58.7% of the pecan atopic participants had hay fever, 43.5% had asthma, and 31.5% had both hay fever and asthma. Among pecan atopic participants the incidence of hay fever increased with age (P = 0.05), while the incidence of bronchial asthma, as a sole manifestation of allergy, decreased in the > 17-year-old age group (P < 0.01). Of the pecan atopics 65.2% had clinical symptoms coinciding only with the pecan pollen season and an additional 10.9% had perennial symptoms. CONCLUSION: Pecan tree releases highly allergenic pollen grains, which are correlated to the incidence of hay fever in the exposed population. The contribution of pecan tree pollen to the symptoms was highly significant after discounting olive and cypress trees that also pollinate in the spring. In children, the pecan tree constitutes a possible etiologic agent for the development of asthma.

Adolescent↗

PubMed1989

Topological Link-Vertex Analysis of the growth of Purkinje cell dendritic trees in normal, reeler, and weaver mice.

The growth of Purkinje cell dendritic trees in normal, reeler, and weaver mice has been defined by using Link-Vertex Analysis. Growth probably occurs in three phases in normal and cortically located reeler trees. Phase I, completed by 7 days postnatum (dpn), establishes a rudimentary tree of 100 segments by random terminal branching. Phase II lasts from 7 to 20 dpn when some 690 and 450 segments are generated in normal and cortical reeler trees respectively. Phase II is initiated by an inductive stimulus mediated by a finite number of parallel fibres. Thereafter, dendritic trees develop a similar topology in normal and cortical reeler Purkinje cells through random interactions between parallel fibres and dendritic growth cones. We have defined this process with the aid of computer simulation techniques. Interactions appear to be restricted to a narrow growth front occupied by the highest centrifugally ordered terminals behind which adhesions occur at a greatly reduced frequency. The cortical reeler tree thus has fewer segments than normal because fewer parallel fibres are available, but it is surprisingly normal in most other respects. Phase III is a period of remodelling and extends from 20 dpn into adulthood when high-ordered terminals are eroded and middle-ordered terminals are added, with no change in total segment number in both normal and cortical reeler trees. Weaver and deeply placed reeler Purkinje cell dendritic trees are not influenced by parallel fibres. Accordingly, their growth is arrested at the end of Phase I, when both types of mutant tree have generated 100 segments by unrestrained random terminal branching. In the absence of parallel fibres, Phase II is not induced and remodelling, characteristic of Phase III, does not occur.

Aging↗

PubMed1999

The hydraulic system of trees: theoretical framework and numerical simulation

Empirical studies pose the problem of the physiological integration of the tree organism, which is also important on the scale of ecosystems. Recently, spatially distributed models emerged, which approach this problem by reflecting the close linkage between physiological processes and the structures of trees and tree stands. In the case of water flow, the tree organism can be regarded as hydraulic system and the branched tree architecture as hydraulic network. Previous models of the hydraulic system either did not take into account the network structure, or they had shortcomings regarding the translation of the underlying physiological assumptions by the discrete computation method. We have developed a theoretical framework which takes the form of a numerical simulation model of tree water flow. A discrete initial boundary value problem (IBVP) combines the phenomena of Darcy flow, water storage and conductivity losses in the hydraulic network. The software HYDRA computes the solution of the IBVP. The theoretical derivation and model tests corroborate the consistent translation of the physiological assumptions by the computational method. Simulation studies enabled us to formulate hypotheses on the following points: (1) differences in the hydraulic segmentation between Picea abies and Thuja occidentalis, (2) responses of the hydraulic system to rapid transpiration changes and to a scenario of drought stress, and (3) how these responses depend on architectural quantities of the trees. The simulation studies demonstrated our possibilities of deriving theoretically well-founded hypotheses about the functioning of the hydraulic system and its relation to system structure. The numerical simulation model is designed as a tool for structure-function studies, which is able to treat tree architecture as independent variable. The model supports the integration of data on tree level, and it can be used for computer experiments which quantify the dynamics of the hydraulic system according to the concepts of system theory. Copyright 1999 Academic Press.

Journal Article↗

PubMed2000

Direct calculation of a tree length using a distance matrix.

Comparative studies of tree-building methods have shown minimum evolution to be in general an accurate criterion for selecting a true tree. To improve the use of this criterion, this paper proposes a method for rapidly and directly calculating a length of a dichotomous tree without having to resort to branch length calculations. This direct calculation (DC) method applies to the complete final topology, giving equal importance to each branch after a dichotomy. According to this method, the tree length S(DC) is S(DC) = sigma(i) sigma(j)(D(ij)/2(B(ij))) = (sigma(i<j) sigma D(ij)2(Bmax-B(ij)))/2(Bmax)(-1) where D(ij) is the observed distance between taxa i and j, B(ij) is the number of branches connecting i and j, Bmax is the greatest B(ij) in the tree, and the powers of two are due to the dichotomy of the tree. This tree length expression may be used as a rapid method for selecting the shortest tree from a set of hypothetical or subobtimal trees.

Algorithms↗

PubMed1993

Glutathione status and glutathione reductase activity in spruce needles of healthy and damaged trees at two mountain sites.

Levels of glutathione, in both reduced and oxidized form, and glutathione reductase activity were monitored in needles of healthy and damaged spruce trees (Picea abies (L.) Karst.) during the course of four vegetation periods at two natural sites. The glutathione content and glutathione reductase activity showed a pronounced annual rhythm in undamaged trees, whereas damaged spruce trees deviated significantly from this course. In comparison with undamaged trees, damaged trees showed markedly increased levels of glutathione during the test period of 1989-1991. However, glutathione reductase activity differed in damaged and undamaged trees, only in 1989-1990. The ratio of reduced to oxidized glutathione (GSH/GSSG ratio) was slightly higher in damaged trees, and the highest levels were found during the winter months. In the case of damaged trees, a correlation between GSH/GSSG ratio and current ozone levels at the sites could be clearly established. The present results indicate that damaged trees suffer from increased oxidative stress, especially in the period from June to October.

Journal Article↗

PubMed1995

Physiology, morphology, and ozone uptake of leaves of black cherry seedlings, saplings, and canopy trees.

Patterns of ozone uptake were related to physiological, morphological, and phenological characteristics of different-sized black cherry trees (Prunus serotina Ehrh.) at a site in central Pennsylvania. Calculated ozone uptake differed among open-grown seedlings, forest gap saplings, and canopy trees and between leaves in the upper and lower crown of saplings and canopy trees. On an instantaneous basis, seedling leaves had the greatest ozone uptake rates of all tree size classes due to greater stomatal conductance and higher concentrations of ozone in their local environment. A pattern of higher stomatal conductance of seedlings was consistent with higher incident photosynthetically-active radiation, stomatal density, and predawn xylem water potentials for seedlings relative to larger trees. However, seedlings displayed an indeterminate pattern of shoot growth, with the majority of their leaves produced after shoot growth had ceased for canopy and sapling trees. Full leaf expansion occurred by mid-June for sapling and canopy trees. Because many of their leaves were exposed to ozone for only part of the growing season, seedlings had a lower relative exposure over the course of the growing season, and subsequently lower cumulative uptake, of ozone than canopy trees and a level of uptake similar to upper canopy leaves of saplings. Visible injury symptoms were not always correlated with patterns in ozone uptake. Visible symptoms were more apparent on seedling leaves in concurrence with their high instantaneous uptake rates. However, visible injury was more prevalent on leaves in the lower versus upper crown of canopy trees and saplings, even though lower crown leaves had less ozone uptake. Lower crown leaves may be more sensitive to ozone per unit uptake than upper crown leaves because of their morphology. In addition, the lower net carbon uptake of lower crown leaves may limit repair and anti-oxidant defense processes.

Journal Article↗

PubMed2006

A stable lead isotopic investigation of the use of sycamore tree rings as a historical biomonitor of environmental lead contamination.

The validity of the use of sycamore (Acer pseudoplatanus) tree-rings for the reconstruction of atmospheric lead pollution histories was investigated. Tree cores spanning 1892-2003 were collected from several sycamores from the eastern shore of Loch Lomond, Scotland, an area with no local point sources of lead emission. The lead concentration and 206Pb/207Pb profiles of the Loch Lomond region cores were compared with corresponding data for the 210Pb-dated loch sediment, and also with data for moss of known age from a Scottish herbarium collection. Two of the seven sycamore cores showed the same lead concentration trend as the lead flux to the loch, the rest having no similarity to either each other or the loch sediment record. Two further sycamore cores showed some similarity in their temporal 206Pb/207Pb trends to those seen in the sediment and moss records, but only in part of their profiles, whilst the 206Pb/207Pb ratios of the other sycamore cores remained relatively unchanged for the majority of the time covered, or exhibited an opposite trend. The 206Pb/207Pb ratios of the tree cores were also mostly higher than those of the previously established records for any given time period. Tree cores covering 1878-2002 were also collected along transects from Wanlockhead and Tyndrum, two areas of former lead mining and smelting associated with distinct 206Pb/207Pb ratios of 1.170 and 1.144, respectively. The Wanlockhead tree cores exhibited a generally decreasing trend in lead concentration with both time and distance from the lead mine. The characteristic 206Pb/207Pb ratio of 1.170 was observed in samples close to the mine but a decrease in the influence of the mine-derived lead was observed in more distant samples. The tree sampled at Tyndrum showed elevated lead concentrations, which decreased with time, and a fairly constant 206Pb/207Pb ratio of 1.15 reflecting input from the mine, features not observed in any other trees along the transect. Overall the data suggest that sycamore tree-ring analysis is an unsuitable method for obtaining records of historical lead deposition in areas with no large local lead input, although it can reveal some information about the temporal and spatial influence of point source emitters. The unsuitability probably arises from the number of active annual rings in a single year, the post-uptake radial translocation of elements, the relative importance of the different routes of uptake, and the soil depth(s) from which trees draw nutrients.

Acer↗

PubMed2003

The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi, Fungi.

A data set with 1551 fungal sequences of the small subunit ribosomal RNA has been analysed phylogenetically. Four animal sequences were used to root the tree. The parsimony ratchet algorithm in combination with tree fusion was used to find most parsimonious trees and the parsimony jackknifing method was used to establish support frequencies. The full-length consensus tree, of the most parsimonious trees, is published and jackknife frequencies above 50% are plotted on the consensus tree at supported nodes. Until recently attempts to find the most parsimonious trees for large data sets were impractical, given current computational limitations. The parsimony ratchet in combination with tree fusion was found to be a very efficient method of rapid parsimony analysis of this large data set. Parsimony jackknifing is a very fast and efficient method for establishing group support. The results show that the Glomeromycota are the sister group to a monophyletic Dikaryomycota. The majority of the species in the Glomeromycota/Dikaryomycota group have a symbiotic lifestyle--a possible synapomorphy for a group 'Symbiomycota'. This would suggest that symbiosis between fungi and green plants evolved prior to the colonization of land by plants and not as a result of the colonization process. The Basidiomycotina and the Ascomycotina are both supported as monophyletic. The Urediniomycetes is the sister group to the rest of the Basidiomycotina successively followed in a grade by Ustilaginomycetes, Tremellomycetes, Dacrymycetales, Ceratobasidiales and Homobasidiomycetes each supported as monophyletic except the Homobasidiomycetes which are left unsupported. The ascomycete node begins with a polytomy consisting of the Pneumocystidomycetes, Schizosaccharomycetes, unsupported group with the Taphrinomycetes and Neolectales, and finally an unnamed, monophyletic and supported group including the Saccharomycetes and Euascomycetes. Within the Euascomycetes the inoperculate euascomycetes (Inoperculata) are supported as monophyletic excluding the Orbiliomycetes which are included in an unsupported operculate, pezizalean sister group together with Helvellaceae, Morchellaceae, Tuberaceae and others. Geoglossum is the sister group to the rest of the inoperculate euascomycetes. The Sordariomycetes, Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes are each highly supported as monophyletic. The Leotiomycetes and the Lecanoromycetes both appear in the consensus of the most parsimonious trees but neither taxon receives any jackknife support.

DNA, Fungal↗

PubMed1980

Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences.

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127--150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151--166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

Amino Acid Sequence↗

PubMed2003

The combinatorics of tandem duplication trees.

We developed a recurrence relation that counts the number of tandem duplication trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the standard unequal recombination (or crossover) model of tandem duplications. The number of rooted duplication trees is exactly twice the number of unrooted trees, which means that on average only two positions for a root on a duplication tree are possible. Using the recurrence, we tabulated these numbers for small values of n. We also developed an asymptotic formula that for large n provides estimates for these numbers. These numbers give a priori probabilities for phylogenies of the repeated sequences to be duplication trees. This work extends earlier studies where exhaustive counts of the numbers for small n were obtained. One application showed the significance of finding that most maximum-parsimony trees constructed from repeat sequences from human immunoglobins and T-cell receptors were tandem duplication trees. Those findings provided strong support to the proposed mechanisms of tandem gene duplication. The recurrence relation also suggests efficient algorithms to recognize duplication trees and to generate random duplication trees for simulation. We present a linear-time recognition algorithm.

Algorithms↗

PubMed2003

Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: the phylogeny of Rodentia (Mammalia).

Homoplasy among morphological characters has hindered inference of higher level rodent phylogeny for over 100 years. Initial molecular studies, based primarily on single genes, likewise produced little resolution of the deep relationships among rodent families. Two recent molecular studies (Huchon et al., 2002, Mol. Biol. Evol. 19:1053-1065; Adkins et al., 2003, Mol. Phylogenet. Evol. 26:409-420), using larger samples from the nuclear genome, have produced phylogenies that are generally concordant with each other, but many of the deep superfamilial nodes were still lacking substantial statistical support. Data are presented here for a total of approximately 3,600 base pairs from portions of three different nuclear protein-coding genes, CB1, IRBP, and RAG2, from 19 rodents and three outgroups. Separate analyses, with data partitioned according to both genes and codon position, produced conflicting results. Trees obtained from all partitions of CB1 and RAG2 and those obtained from the first- plus second-position sites of IRBP were generally concordant with each other and the trees from the two recent studies, whereas trees obtained from the third-position sites of IRBP were not. Although the IRBP third-position sites represent only 1/9 of the total data set, combined analyses using either parsimony or likelihood resulted in trees in agreement with the IRBP third-position sites and in disagreement with the remaining 8/9 of the sites from this data set and the two recent multigene studies. In contrast, maximum-likelihood analysis using a site-specific rates model did recover a tree that is highly congruent with the trees in the two recent studies. If the IRBP third-position sites are removed from the current data set, then combined likelihood analyses obtain a tree that is highly congruent with those of the two recent studies. This analysis also provides, for the first time in a study of rodent phylogeny, robust statistical support for every bipartition, with just one exception. This tree divides rodents into two major clades. The first contains Myodonta (Muroidea plus Dipodidae) and the only unresolved trichotomy, from which descend Geomyoidea, Pedetidae, and Castoridae. On the other side of the root is a clade containing Sciuroidea plus Gliridae, and Hystricognathi. Some uncertainty remains on the placement of the root. Trees on which the Hystricognathi are the basal sister group to Myodonta, Geomyoidea, Pedetidae, and Castoridae are also found within a Bayesian 95% credible set, as estimated by Metropolis-coupled Markov chain Monte Carlo sampling.

Animals↗

PubMed2005

Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods.

Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in large collections of trees should be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We present a method that extends the notion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. We demonstrate the utility of this method in highlighting differences amongst maximum likelihood bootstrap values and Bayesian posterior probabilities in the placental mammal phylogeny, and also in comparing the phylogenetic signal contained in amino acid versus nucleotide characters for hexapod monophyly.

Algorithms↗