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Shade trees reduce building energy use and CO2 emissions from power plants.

Urban shade trees offer significant benefits in reducing building air-conditioning demand and improving urban air quality by reducing smog. The savings associated with these benefits vary by climate region and can be up to $200 per tree. The cost of planting trees and maintaining them can vary from $10 to $500 per tree. Tree-planting programs can be designed to have lower costs so that they offer potential savings to communities that plant trees. Our calculations suggest that urban trees play a major role in sequestering CO2 and thereby delay global warming. We estimate that a tree planted in Los Angeles avoids the combustion of 18 kg of carbon annually, even though it sequesters only 4.5-11 kg (as it would if growing in a forest). In this sense, one shade tree in Los Angeles is equivalent to three to five forest trees. In a recent analysis for Baton Rouge, Sacramento, and Salt Lake City, we estimated that planting an average of four shade trees per house (each with a top view cross section of 50 m2) would lead to an annual reduction in carbon emissions from power plants of 16,000, 41,000, and 9000 t, respectively (the per-tree reduction in carbon emissions is about 10-11 kg per year). These reductions only account for the direct reduction in the net cooling- and heating-energy use of buildings. Once the impact of the community cooling is included, these savings are increased by at least 25%.

Air Conditioning↗

Lack of correlation between regional pollen counts and percutaneous reactivity to tree pollen extracts in patients with seasonal allergic rhinitis.

BACKGROUND: Although seasonal patterns of tree pollination have been reported, it is unknown if aerobiologic data correlate with patterns of in vivo sensitization. OBJECTIVE: To evaluate the relationship between regional tree pollen exposure and patterns of in vivo percutaneous reactivity to specific tree pollen extracts in a local patient population with seasonal allergic rhinitis. METHODS: Patients with spring seasonal allergic rhinitis and percutaneous sensitivity to 1 or more regional tree pollens were studied. Tree pollen counts were collected at the same urban site from 1997 to 2002 and at a suburban site in 2002. Patients underwent skin prick testing with commercial extracts of 15 indigenous tree species. Serum specific IgE measurements were assayed in a subset of sensitized patients. RESULTS: Of 127 patients who reported symptoms consistent with seasonal allergic rhinitis during the spring pollen season, 93 qualified based on demonstration of at least 1 positive skin prick test result. Mean 5-year pollen counts (1997-2001) and 2002 urban counts were highly correlated (Spearman r = 0.95, P < .001), indicating that year-to-year pollen counts were consistent. No significant correlation was found between mean seasonal pollen counts (urban site, 1997-2001) and frequencies of skin prick test reactivity to specific tree pollen allergens (Spearman r = -0.03, P = .93). No significant relationship was found between 5-year mean tree pollen counts and positive serum specific IgE tests for specific tree pollens (Spearman r = -0.42, P = .30). Eight of 15 species elicited percutaneous reactions in more than 50% of patients (ie, satisfying definition of a major in vivo allergen). However, 6 of the 8 major tree allergens each represented 5% or less of 5-year mean total tree pollen counts. CONCLUSION: No correlation was found between overall frequencies of in vivo sensitization to tree pollen allergens in a local population and regional pollen exposure data.

Adolescent↗

Evaluation of a statistically derived decision tree for the cytodiagnosis of fine needle aspirates of the breast (FNAB).

A decision tree for the diagnosis of FNAB was derived from defined human observations using a rule induction method, C4.5 (a derivative of the ID3 algorithm). This algorithm is an implementation of the top-down induction method where the tree is determined iteratively by adding those nodes and branches which maximize the information gain at each step. The tree was derived from a training set of 200 FNAB with known outcome using 10 defined features (from one observer) and patient age. The tree contained a total of seven nodes (six observable features and patient age) with eight endpoints (four benign, four malignant). The tree was applied to a test set of 400 further FNAB with observations from the training observer and produced a sensitivity of 95%, specificity of 93% and a positive predictive value (PPV) of a malignant result of 89%. Four trainee pathologists were given a training session on the observable features and then used the tree to determine outcome in a further 50 FNAB. The observers were blind to clinical details apart from age and the endpoints were coded with letters and not labelled benign or malignant. The results from these observers produced ranges of sensitivity 80-96%, specificity 64-92%, PPV 73-92% and kappa statistics (with known outcome) 0.6-0.8. Reported difficulties in using the tree included estimation of nuclear size. These results were worse than the performance of the observers on a further 50 cases without using the decision tree (sensitivity 80-100%, specificity 72-100%, PPV 78-100%, kappa 0.72-0.92). The original 50 case test set was rerandomized and the four trainee observers made all 10 defined observations on each specimen without using the decision tree; these observations were then used to derive decisions from the tree. The performance from this method was similar to that using selected features from the tree, suggesting that observation of all features together does not improve the reliability of each specific observation. The poor performance of this tree suggests that this methodology may be unsuitable for producing decision support aids for diagnostic or training purposes in this domain.

Biopsy, Needle↗

Regulation of water flux through tropical forest canopy trees: do universal rules apply?

Tropical moist forests are notable for their richness in tree species. The presence of such a diverse tree flora presents potential problems for scaling up estimates of water use from individual trees to entire stands and for drawing generalizations about physiological regulation of water use in tropical trees. We measured sapwood area or sap flow, or both, in 27 co-occurring canopy species in a Panamanian forest to determine the extent to which relationships between tree size, sapwood area and sap flow were species-specific, or whether they were constrained by universal functional relationships between tree size, conducting xylem area, and water use. For the 24 species in which active xylem area was estimated over a range of size classes, diameter at breast height (DBH) accounted for 98% of the variation in sapwood area and 67% of the variation in sapwood depth when data for all species were combined. The DBH alone also accounted for > or = 90% of the variation in both maximum and total daily sap flux density in the outermost 2 cm of sapwood for all species taken together. Maximum sap flux density measured near the base of the tree occurred at about 1,400 h in the largest trees and 1,130 h in the smallest trees studied, and DBH accounted for 93% of the variation in the time of day at which maximum sap flow occurred. The shared relationship between tree size and time of maximum sap flow at the base of the tree suggests that a common relationship between diurnal stem water storage capacity and tree size existed. These results are consistent with a recent hypothesis that allometric scaling of plant vascular systems, and therefore water use, is universal.

Panama↗

Canopy and hydraulic conductance in young, mature and old Douglas-fir trees.

We tested for reductions in water transport with increasing tree size, a key component in determining whether gas exchange and growth are hydraulically limited in tall trees. During the summers of 1998 and 1999, we measured water transport with Granier-type, constant-heat sap flow probes, vapor pressure deficit, and leaf and soil water potentials in overstory Pseudotsuga menziesii (Mirb.) Franco trees in three stands differing in size and age (15, 32 and 60 m in height and about 20, 40 and 450 years in age, respectively) in a P. menziesii-dominated forest in the Pacific Northwest, USA. A total of 24 trees were equipped with sap flow sensors--six 60-m trees, nine 32-m trees and nine 15-m trees. Based on the sap flow measurements and leaf area information estimated from leaf area-sapwood area relationships, we estimated crown-averaged stomatal conductance (GS) and leaf-specific hydraulic conductance (KL). We tested the hypothesis that GS and KL vary inversely with tree height (15 > 32 > 60 m). Analysis of variance of GS ranked as 15 = 60 > 32 m during the early summer and 15 > 60 > 32 m during late season drought. Over the growing season, mean daily GS (+/- SE) was 29.2 +/- 4.4, 24.0 +/- 6.8 and 17.7 +/- 7.2 mmol m-2 s-1 for the 15-, 60- and 32-m trees, respectively. The value of K(L) differed among tree heights only during late season drought and ranked 15 > 32 = 60 m. A hydraulic mass balance suggests that greater sapwood conductivity in 60-m trees compared with 32- and 15-m trees is a likely cause for the departure of the above rankings from those predicted by height and leaf-to-sapwood area ratio.

Circadian Rhythm↗

Stem breakage of trees and energy dissipation during rockfall impacts.

The capacity of individual trees to dissipate the energy released by rockfalls has previously only been quantified based on data obtained from static tree-pulling tests or from dynamic impact tests on wood samples. We predicted that these data are not representative of the maximum amount of energy that can be dissipated by living trees during rockfall impacts. To test this prediction, we carried out rockfall experiments on a forested slope in the French Alps. To calculate the rock's energy before and after impact, rockfalls were filmed digitally. The recordings of nine impacts causing instantaneous breakage of Abies alba Mill. trees were analyzed in detail. An exponential relationship between stem diameter at breast height (DBH) and the maximum amount of energy a tree can dissipate was highly correlated for all of our experimental data. We applied this relationship to other tree species based on published fracture energies. The relationships obtained for Cedrus spp., Fagus sylvatica L. and Picea abies (L.) Karst. were significantly correlated with data from other dynamic impact tests in the field and with maximum bending moments obtained from tree-pulling experiments. Multiple linear regressions showed that impact height influences the energy that will be dissipated by an A. alba tree, particularly for trees with a DBH less than 15 cm. For trees with a DBH greater than 15 cm, the effect of impact height was minimal up to a height of 1 m. There was a strong relationship between the amount of energy dissipated by a tree and the horizontal distance between the impact center and the vertical central axis of the tree.

Ecosystem↗

[Effects of nitrogen forms on nutrient uptake and growth of trees].

Forest tree species take up both NH4(+)-N and NO3(-)-N forms of nitrogen (N) during their growth. However, the effects of N form on nutrition uptake and tree growth are different due to the different N forms. Generally, trees show preference to N source, and most conifers prefer to NH4(+)-N while the preference to N form of broadleaved trees is unclear. The preference may be correlated with the pH value of the site on which the trees grown. The trees grown on acid soil generally appear preference to NH4(+)-N while trees grown on litmusless or alkaline soil prefer to NO3(-)-N. Fungus also can alter the tree uptake characteristic to NH4(+)-N and NO3(-)-N. In some species, the NO3(-)-N uptake capacity increased remarkably while uptake capacity of NH4(+)-N keep consistent when fungus were inoculated. NH4(+)-N and NO3(-)-N have different effects on other nutrient ions uptake because of the difference charge of NH4(+)-N and NO3(-)-N. In general, NH4(+)-N accelerates the anion absorption while inhibits cation absorption. The effects of nitrogen forms on nutrition uptake are related with not only the charge of NH4(+)-N and NO3(-)-N, but also the restrain effects among other ions. Sometimes, NH4(+)-N inhibits NO3(-)-N uptake, but the mechanism is not very clear now. The form of which nitrogen is taken up by trees will induce the change of rhizospheric pH value. Uptake of NH4(+)-N results in the decrease of rhizospheric pH value. Contrary, uptake of NO3(-)-N will cause the increase of rhizospheric pH value. The change of rhizospheric pH value will affect nutrient availability and thus affect nutrition uptake and utilization by trees. Trees grow differently after NH4(+)-N and NO3(-)-N uptake. When supplied with NH4(+)-N, some confers that prefer to NH4(+)-N grow better while a few ammonium-preference conifers hardly show the better growth. Nevertheless, most plants grow better when both forms of N supplied simultaneously than either of N source supplied alone. For few similar studies were carried out with tree species, it needs to do more researches.

Nitrates↗

[Significance of senescence study on tree roots and its advances].

Root system is one of the important components of trees, and has some important physiological functions such as nutrient and water absorption, transport and storage, anchoring, and supporting. After tree root systems formed, roots often suffer from nutrient- and water-deficient stress, and thus, their absorption of nutrients and water appears more important. Soil nutrient and water have a great spatiotemporal heterogeneity. As the heterogeneity occurs, trees regulate carbon partitioning to roots, resulting in the senescence or death of some roots of the whole root system. In forestry, the senescence of tree roots is closely related to tree productivity, because there is a close relationship between the senescence of tree roots and the absorption of soil nutrient and water. At ecosystem and global scale, the senescence of tree roots influences the cycling of carbon and nutrients, because roots exhaust a great deal of carbon fixed by source leaves through photosynthesis, and there are great amounts of nutrients in tree roots. The senescence of tree roots is influenced by many environmental factors, biotic (e.g., fungi, bacteria, viruses, small edaphic animals) and abiotic (e.g., water, temperature, soil nutrients, heavy metals). These factors affect the senescence of tree roots by different mechanisms. Although we have much knowledge on the senescence of tree roots and some hypotheses have been proposed, some problems still remain to be resolved, and further experiments are needed to test these hypotheses. Interdisciplinary studies integrating cytology, biochemistry, soil science, and genetics are the prerequisite for rapid advances in understanding the essence of tree root senescence.

Biological Transport↗

Choosing among alternative trees of multigene families.

Estimation of gene trees is the first step in testing alternative hypotheses about the evolution of multigene families. The standard practice for inferring gene family history is to construct trees that meet some objective criteria based on the fit of the character state changes (nucleotide or amino acid changes) to the gene tree. Unfortunately, analysis of character state data can be misleading. In addition, this approach ignores information about the relationships of the species from which the genes have been sampled. In this paper I explore using statistics of fit between the character data and gene trees and the reconciliation of the gene and species trees for choosing among alternative evolutionary hypotheses of gene families. In particular, I advocate a two-pronged strategy for choosing among alternative gene trees. First, the character data are used to define a set of acceptable gene trees (i.e., trees that are not significantly different from the minimum length tree). Next, the set of acceptable gene trees is reconciled with a known species tree, and the gene tree requiring the fewest number of gene duplications and losses is adopted as the best estimate of evolutionary history. The approach is illustrated using three gene families: BMP, EGR, and LDH.

Animals↗

A general approach to proving the minimality of phylogenetic trees illustrated by an example with a set of 23 vertebrates.

We have recently described a method of building phylogenetic trees and have outlined an approach for proving whether a particular tree is optimal for the data used. In this paper we describe in detail the method of establishing lower bounds on the length of a minimal tree by partitioning the data set into subsets. All characters that could be involved in duplications in the data are paired with all other such characters. A matching algorithm is then used to obtain the pairing of characters that reveals the most duplications in the data. This matching may still not account for all nucleotide substitutions on the tree. The structure of the tree is then used to help select subsets of three or more characters until the lower bound found by partitioning is equal to the length of the tree. The tree must then be a minimal tree since no tree can exist with a length less than that of the lower bound. The method is demonstrated using a set of 23 vertebrate cytochrome c sequences with the criterion of minimizing the total number of nucleotide substitutions. There are 131130 7045768798 96033440625 topologically distinct trees that can be constructed from this data set. The method described in this paper does identify 144 minimal tree variants. The method is general in the sense that it can be used for other data and other criteria of length. It need not however always be possible to prove a treee minimal but the method will give an upper and lower bound on the length of minimal trees.

Amino Acid Sequence↗

Hydraulic lift in Acacia tortilis trees on an East African savanna.

Recent studies suggest that savanna trees in semi-arid areas can increase understorey plant production. We hypothesized that one of the mechanisms that explains the facilitation between trees and grasses in East African savannas is hydraulic lift (HL). HL in large Acacia tortilis trees was studied during the first 3 months of the dry season during a relatively wet year (1998) and a very dry year (2000). In 1998, we found distinct diel fluctuation in soil water potential (psi(s)), with increasing values during the night and decreasing again the following day. These fluctuations in psi(s )are consistent with other observations of HL and in A. tortilis were found up to 10 m from the tree. In 2000, during a severe drought, psi(s) measurements indicated that HL was largely absent. The finding that HL occurred in wetter years and not in drier years was supported by data obtained on the delta(18)O values in soil, rain and groundwater. The delta(18)O of water extracted from the xylem water of grasses indicated that when they grew near trees they had values similar to those of groundwater. This could be because they either (1) use water from deeper soil layers or (2) use hydraulically lifted water provided by the tree; this was not seen in the same grass species growing outside tree canopies. While our data indicate that HL indeed occurs under Acacia trees, it is also true that psi(s) was consistently lower under trees when compared to outside tree canopies. We believe that this is because tree-grass mixtures take up more water from the upper soil layers than is exuded by the tree each night. This limits the beneficial effect of HL for understorey grasses and suggests that in savannas both facilitation via HL and competition are active processes. The importance of each process may depend upon how wet or dry that particular site or year is.

Acacia↗

Immunological analysis of allergenic cross-reactivity between peanut and tree nuts.

BACKGROUND: Peanut and tree nut allergy is characterized by a high frequency of life-threatening anaphylactic reactions and typically lifelong persistence. Peanut allergy is more common than tree nut allergy, but many subjects develop hypersensitivity to both peanuts and tree nuts. Whether this is due to the presence of cross-reactive allergens remains unknown. OBJECTIVE: The aim of this study was to investigate the presence of allergenic cross-reactivity between peanut and tree nuts. METHODS: Western blotting and ELISA were performed using sera from subjects with or without peanut and tree nut allergy to assess immunoglobulin E (IgE) reactivity to peanut and tree nut extracts. Inhibition ELISA studies were conducted to assess the presence of allergenic cross-reactivity between peanut and tree nuts. RESULTS: Western blot and ELISA results showed IgE reactivity to peanut, almond, Brazil nut, hazelnut and cashew nut for peanut- and tree nut-allergic subject sera. Raw and roasted peanut and tree nut extracts showed similar IgE reactivities. Inhibition ELISA showed that pre-incubation of sera with almond, Brazil nut or hazelnut extracts resulted in a decrease in IgE binding to peanut extract, indicating allergenic cross-reactivity. Pre-incubation of sera with cashew nut extract did not cause any inhibition. CONCLUSION: These results show that multiple peanut and tree nut sensitivities observed in allergic subjects may be due to cross-reactive B cell epitopes present in different peanut and tree nut allergens. The plant taxonomic classification of peanut and tree nuts does not appear to predict allergenic cross-reactivity.

Adult↗

A general bijective algorithm for trees.

Trees are combinatorial structures that arise naturally in diverse applications. They occur in branching decision structures, taxonomy, computer languages, combinatiorial optimization, parsing of sentences, and cluster expansions of statistical mechanics. Intuitively, a tree is a collection of branches connected at nodes. Formally, it can be defined as a connected graph without cycles. Schroder trees, introduced in this paper, are a class of trees for which the set of subtrees at any vertex is endowed with the structure of ordered partitions. An ordered partition is a partition of a set in which the blocks are linearly ordered. Labeled rooted trees and labeled planed trees are both special classes of Schroder trees. The main result gives a bijection between Schroder trees and forests of small trees--namely, rooted trees of height one. Using this bijection, it is easy to encode a Schroder tree by a sequence of integers. Several classical algorithms for trees, including a combinatorial proof of the Lagrange inversion formula, are immediate consequences of this bijection.

Journal Article↗

The roots of phylogeny: how did Haeckel build his trees?

Haeckel created much of our current vocabulary in evolutionary biology, such as the term phylogeny, which is currently used to designate trees. Assuming that Haeckel gave the same meaning to this term, one often reproduces Haeckel's trees as the first illustrations of phylogenetic trees. A detailed analysis of Haeckel's own evolutionary vocabulary and theory revealed that Haeckel's trees were genealogical trees and that Haeckel's phylogeny was a morphological concept. However, phylogeny was actually the core of Haeckel's tree reconstruction, and understanding the exact meaning Haeckel gave to phylogeny is crucial to understanding the information Haeckel wanted to convey in his famous trees. Haeckel's phylogeny was a linear series of main morphological stages along the line of descent of a given species. The phylogeny of a single species would provide a trunk around which lateral branches were added as mere ornament; the phylogeny selected for drawing a tree of a given group was considered the most complete line of progress from lower to higher forms of this group, such as the phylogeny of Man for the genealogical tree of Vertebrates. Haeckel's phylogeny was mainly inspired by the idea of the scala naturae, or scale of being. Therefore, Haeckel's genealogical trees, which were only branched on the surface, mainly represented the old idea of scale of being. Even though Haeckel decided to draw genealogical trees after reading On the Origin of Species and was called the German Darwin, he did not draw Darwinian branching diagrams. Although Haeckel always saw Lamarck, Goethe, and Darwin as the three fathers of the theory of evolution, he was mainly influenced by Lamarck and Goethe in his approach to tree reconstruction.

Anatomy, Comparative↗

Is homoplasy or lineage sorting the source of incongruent mtdna and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura)?

We evaluated the potential effects of homoplasy, ancestral polymorphism, and hybridization as obstacles to resolving phylogenetic relationships within Nomonyx-Oxyura stiff-tailed ducks (Oxyurinae; subtribe Oxyurina). Mitochondrial DNA (mtDNA) control region sequences from 94 individuals supported monophyly of mtDNA haplotypes for each of the six species and provided no evidence of extant incomplete lineage sorting or inter-specific hybridization. The ruddy ducks (O. j. jamaicensis,O. j. andina, O. j. ferruginea) are each others' closest relatives, but the lack of shared haplotypes between O. j. jamaicensis and O. j. ferruginea suggests long-standing historical isolation. In contrast, O. j. andina shares haplotypes with O. j. jamaicensis and O. j. ferruginea, which supports Todd's (1979) and Fjeldså's (1986) hypothesis that O. j. andina is an intergrade or hybrid subspecies of O. j. jamaicensis and O. j. ferruginea. Control region data and a much larger data set composed of approximately 8800 base pairs of mitochondrial and nuclear sequence for each species indicate that the two New World species, O. vittata and O. jamaicensis, branch basally within Oxyura. A clade of three Old World species (O. australis, O. maccoa, O. leucocephala) is well supported, but different loci and also different characters within the mtDNA data support three different resolutions of the Old World clade, yielding an essentially unresolved trichotomy. Fundamentally different factors limited the resolution of the mtDNA and nuclear gene trees. Gene trees for most nuclear loci were unresolved due to slow rates of mutation and a lack of informative variation, whereas uncertain resolution of the mtDNA gene tree was due to homoplasy. Within the mtDNA, approximately equal numbers of characters supported each of three possible resolutions. Parametric and nonparametric bootstrap analyses suggest that resolution of the mtDNA tree based on ~4300 bp per taxon is uncertain but that complete mtDNA sequences would yield a fully resolved gene tree. A short internode separating O. leucocephala from (O. australis, O. maccoa) in the best mtDNA tree combined with long terminal branches and substantial rate variation among nucleotide sites allowed the small number of changes occurring on the internode to be obscured by homoplasy in a significant portion of simulated data sets. Although most nuclear loci were uninformative, two loci supported a resolution of the Old World clade (O. maccoa, O. leucocephala) that is incongruent with the best mtDNA tree. Thus, incongruence between nuclear and mtDNA trees may be due to random sorting of ancestral lineages during the short internode, homoplasy in the mtDNA data, or both. The Oxyura trichotomy represents a difficult though likely common problem in molecular systematics. Given a short internode, the mtDNA tree has a greater chance of being congruent with the history of speciation because its effective population size (N(e)) is one-quarter that of any nuclear locus, but its resolution is more likely to be obscured by homoplasy. In contrast, gene trees for more slowly evolving nuclear loci will be difficult to resolve due to a lack of substitutions during the internode, and when resolved are more likely to be incongruent with the species history due to the stochastic effects of lineage sorting. We suggest that researchers consider first whether independent gene trees are adequately resolved and then whether those trees are congruent with the species history. In the case of Oxyura, the answer to both questions may be no. Complete mtDNA sequences combined with data from a very large number of nuclear loci may be the only way to resolve such trichotomies.

Animals↗

Analysis and visualization of tree space.

We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring "tree islands" (sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapping and Bayesian sampling, for comparing trees obtained from the analysis of several different genes, and for comparing multiple Bayesian analyses. The technique was also useful as a teaching aid for illustrating the progress of a Bayesian analysis and as an exploratory tool for examining large sets of phylogenetic trees. We also identified some limitations to the method, including distortions of the multidimensional tree space into two dimensions through the MDS technique, and the definition of the MDS-defined space based on a limited sample of trees. Nonetheless, the technique is a useful approach for the analysis of large sets of phylogenetic trees.

Bayes Theorem↗

Designing an A* algorithm for calculating edit distance between rooted-unordered trees.

Tree structures are useful for describing and analyzing biological objects and processes. Consequently, there is a need to design metrics and algorithms to compare trees. A natural comparison metric is the "Tree Edit Distance," the number of simple edit (insert/delete) operations needed to transform one tree into the other. Rooted-ordered trees, where the order between the siblings is significant, can be compared in polynomial time. Rooted-unordered trees are used to describe processes or objects where the topology, rather than the order or the identity of each node, is important. For example, in immunology, rooted-unordered trees describe the process of immunoglobulin (antibody) gene diversification in the germinal center over time. Comparing such trees has been proven to be a difficult computational problem that belongs to the set of NP-Complete problems. Comparing two trees can be viewed as a search problem in graphs. A* is a search algorithm that explores the search space in an efficient order. Using a good lower bound estimation of the degree of difference between the two trees, A* can reduce search time dramatically. We have designed and implemented a variant of the A* search algorithm suitable for calculating tree edit distance. We show here that A* is able to perform an edit distance measurement in reasonable time for trees with dozens of nodes.

Algorithms↗

A hybrid micro-macroevolutionary approach to gene tree reconstruction.

Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do not have strong support in the sequence data to minimize the duplication/lost cost. Components of the tree with strong support are left intact. This hybrid approach incorporates both micro- and macroevolutionary considerations, yet its computational requirements are modest in practice because the two-phase approach constrains the search space. Our hybrid algorithm can also be used to resolve nonbinary nodes in a multifurcating gene tree. We have implemented these algorithms in a software tool, NOTUNG 2.0, that can be used as a unified framework for gene tree reconstruction or as an exploratory analysis tool that can be applied post hoc to any rooted tree with bootstrap values. The NOTUNG 2.0 graphical user interface can be used to visualize alternate duplication/loss histories, root trees according to duplication and loss parsimony, manipulate and annotate gene trees, and estimate gene duplication times. It also offers a command line option that enables high-throughput analysis of a large number of trees.

ATP-Binding Cassette Transporters↗