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Needle anatomy changes with increasing tree age in Douglas-fir.

Morphological differences between old-growth trees and saplings of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) may extend to differences in needle anatomy. We used microscopy with image analysis to compare and quantify anatomical parameters in cross sections of previous-year needles of old-growth Douglas-fir trees and saplings at the Wind River Canopy Crane site in Washington and at three sites in the Cascade Mountains of Oregon. We also compared needle anatomy across a chronosequence of 10-, 20-, 40- and 450-year-old Douglas-fir trees from the Wind River site. Anatomy differed significantly between needles of old-growth trees and saplings at all sites, suggesting a developmental change in needle anatomy with increasing tree age. Compared with needles of old-growth trees, needles of saplings were longer and had proportionately smaller vascular cylinders, larger resin canals and few hypodermal cells. Astrosclereids, which sequester lignin in their secondary cell walls and occupy space otherwise filled by photosynthetic cells, were scarce in needles of saplings but abundant in needles of old-growth trees. Needles of old-growth trees had an average of 11% less photosynthetic mesophyll area than needles of saplings. The percentage of non-photosynthetic area in needles increased significantly with increasing tree age from the chronosequence of 10-, 20-, 40- and 450-year-old trees at the Wind River site. This reduction in photosynthetic area may contribute to decreased growth rates in old trees.

Microscopy, Electron, Scanning↗

Response of photosynthesis in second-generation Pinus radiata trees to long-term exposure to elevated carbon dioxide partial pressure.

Second-generation Pinus radiata D. Don trees, propagated from cuttings of 4-year-old trees previously grown at ambient (36 Pa) and elevated (65 Pa) CO2 partial pressure (Ca) were grown under the same conditions in open-top chambers for a further year. As cuttings of the original trees, these second-generation trees were physiologically the same age as the first-generation trees with the only difference between the two being size. This allowed us to test the effects of tree size independently of age or duration of exposure. Total non-structural carbohydrate concentration, area-based nitrogen concentration, leaf mass per unit area and chlorophyll concentration measured in three foliage age cohorts were unaffected by either age or Ca. There were no signs of photosynthetic down-regulation in trees grown at elevated Ca. When measured at the growth Ca, photosynthetic rate in young needles during summer, autumn and spring was 34, 43 and 38% higher, respectively, in trees grown at elevated Ca than in trees grown at ambient Ca. In older needles, the corresponding photosythetic rate increases were 26, 47 and 49%. Water-use efficiency, determined by stable carbon isotope analysis, was 49% higher in foliage in the elevated Ca treatment than in foliage in the ambient Ca treatment. This increase was entirely due to photosynthetic enhancement, because stomatal conductance did not differ between treatments. We conclude that down-regulation of photosynthesis at elevated Ca is related to tree size rather than tree age or duration of exposure, and that enhanced photosynthetic rates can be maintained while sink strength is high enough to use the excess photosynthates.elevated CO2, needle age, photosynthetic down-regulation, photosynthetic enhancement, sink strength, water-use efficiency.

Carbon Dioxide↗

Time series diagnosis of tree hydraulic characteristics.

An in vivo method for diagnosing hydraulic characteristics of branches and whole trees is described. The method imposes short-lived perturbations of transpiration and traces the propagation of the hydraulic response through trees. The water uptake response contains the integrated signature of hydraulic resistance and capacitance within trees. The method produces large signal to noise ratios for analysis, but does not cause damage or destruction to tree stems or branches. Based on results with two conifer tree species, we show that the method allows for the simple parameterization of bulk hydraulic resistance and capacitance of trees. Bulk tree parameterization of resistance and capacitance predicted the overall diel shape of water uptake, but did not predict the overshoot water uptake response in trees to shorter-term variations in transpiration, created by step changes in transpiration rate. Stomatal dynamics likely complicated the use of simple resistance-capacitance models of tree water transport on these short time scales. The results provide insight into dominant hydraulic and physiological factors controlling tree water flux on varying time scales, and allow for the practical assessment of necessary tree hydraulic model complexity in relation to the time step of soil- vegetation-atmosphere transport models.

Models, Biological↗

Stomatal conductance, transpiration and sap flow of tropical montane rain forest trees in the southern Ecuadorian Andes.

We investigated tree water relations in a lower tropical montane rain forest at 1950-1975 m a.s.l. in southern Ecuador. During two field campaigns, sap flow measurements (Granier-type) were carried out on 16 trees (14 species) differing in size and position within the forest stand. Stomatal conductance (g(s)) and leaf transpiration (E(l)) were measured on five canopy trees and 10 understory plants. Atmospheric coupling of stomatal transpiration was good (decoupling coefficient Omega = 0.25-0.43), but the response of g(s) and E(l) to the atmospheric environment appeared to be weak as a result of the offsetting effects of vapor pressure deficit (VPD) and photosynthetic photon flux (PPF) on g(s). In contrast, sap flow (F) followed these atmospheric parameters more precisely. Daily F depended chiefly on PPF sums, whereas on short time scales, VPD impeded transpiration when it exceeded a value of 1-1.2 kPa. This indicates an upper limit to transpiration in the investigated trees, even when soil water supply was not limiting. Mean g(s) was 165 mmol m(-2) s(-1) for the canopy trees and about 90 mmol m(-2) s(-1) for the understory species, but leaf-to-leaf as well as tree-to-tree variation was large. Considering whole-plant water use, variation in the daily course of F was more pronounced among trees differing in size and crown status than among species. Daily F increased sharply with stem diameter and tree height, and ranged between 80 and 120 kg day(-1) for dominant canopy trees, but was typically well below 10 kg day(-1) for intermediate and suppressed trees of the forest interior.

Ecuador↗

Tree species and mycorrhizal associations influence the magnitude of rhizosphere effects.

Previous research on the effects of tree species on soil processes has focused primarily on the role of leaf litter inputs. We quantified the extent to which arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree species influence soil microbial activity and nutrient availability through rhizosphere effects. Rhizosphere soil, bulk soil, and fine roots were collected from 12 monospecifc plots (six AM and six ECM tree species) planted on a common soil at the Turkey Hill Plantations in Dryden, New York. Rhizosphere effects were estimated by the percentage difference between rhizosphere and bulk soil samples for several assays. Rhizosphere effects on soil microbes and their activities were significant for ECM species but in only a few cases for AM species. In AM tree species, microbial biomass, net N mineralization, and phosphatase enzyme activity in the rhizosphere were 10-12% greater than in bulk soil. In ECM tree species, rhizosphere effects for microbial biomass, C mineralization rates, net N mineralization, and phosphatase activity were 25-30% greater than bulk soil, and significantly greater than AM rhizosphere effects. The magnitude of rhizosphere effects was negatively correlated with the degree of mycorrhizal colonization in AM tree species (r = -0.83) and with fine root biomass (r = -0.88) in ECM tree species, suggesting that different factors influence rhizosphere effects in tree species forming different mycorrhizal associations. Rhizosphere effects on net N mineralization and phosphatase activity were also much greater in soils with pH < 4.3 for both AM and ECM tree species, suggesting that soil pH and its relation to nutrient availability may also influence the magnitude of rhizosphere effects. Our results support the idea that tree roots stimulate nutrient availability in the rhizosphere, and that systematic differences between AM and ECM may result in distinctive rhizosphere effects for C, N, and P cycling between AM and ECM tree species.

Biomass↗

Patterns of animal diversity in different forms of tree cover in agricultural landscapes.

As tropical regions are converted to agriculture, conservation of biodiversity will depend not only on the maintenance of protected forest areas, but also on the scope for conservation within the agricultural matrix in which they are embedded. Tree cover typically retained in agricultural landscapes in the neotropics may provide resources and habitats for animals, but little is known about the extent to which it contributes to conservation of animal species. Here, we explore the animal diversity associated with different forms of tree cover for birds, bats, butterflies, and dung beetles in a pastoral landscape in Nicaragua. We measured species richness and abundance of these four animal taxa in riparian and secondary forest, forest fallows, live fences, and pastures with high and low tree cover. We recorded over 20,000 individuals of 189 species including 14 endangered bird species. Mean abundance and species richness of birds and bats, but not dung beetles or butterflies, were significantly different among forms of tree cover. Species richness of bats and birds was positively correlated with tree species richness. While the greatest numbers of bird species were associated with riparian and secondary forest, forest fallows, and pastures with >15% tree cover, the greatest numbers of bat species were found in live fences and riparian forest. Species assemblages of all animal taxa were different among tree cover types, so that maintaining a diversity of forms of tree cover led to conservation of more animal species in the landscape as a whole. Overall, the findings indicate that retaining tree cover within agricultural landscapes can help conserve animal diversity, but that conservation efforts need to target forms of tree cover that conserve the taxa that are of interest locally. Preventing the degradation of remaining forest fragments is a priority, but encouraging farmers to maintain tree cover in pastures and along boundaries may also make an important contribution to animal conservation.

Agriculture↗

Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life.

The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotes in distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree.

Algorithms↗

Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.

Algorithms↗

Towards building the tree of life: a simulation study for all angiosperm genera.

Comprehensive phylogenetic trees are essential tools to better understand evolutionary processes. For many groups of organisms or projects aiming to build the Tree of Life, comprehensive phylogenetic analysis implies sampling hundreds to thousands of taxa. For the tree of all life this task rises to a highly conservative 13 million. Here, we assessed the performances of methods to reconstruct large trees using Monte Carlo simulations with parameters inferred from four large angiosperm DNA matrices, containing between 141 and 567 taxa. For each data set, parameters of the HKY85+G model were estimated and used to simulate 20 new matrices for sequence lengths from 100 to 10,000 base pairs. Maximum parsimony and neighbor joining were used to analyze each simulated matrix. In our simulations, accuracy was measured by counting the number of nodes in the model tree that were correctly inferred. The accuracy of the two methods increased very quickly with the addition of characters before reaching a plateau around 1000 nucleotides for any sizes of trees simulated. An increase in the number of taxa from 141 to 567 did not significantly decrease the accuracy of the methods used, despite the increase in the complexity of tree space. Moreover, the distribution of branch lengths rather than the rate of evolution was found to be the most important factor for accurately inferring these large trees. Finally, a tree containing 13,000 taxa was created to represent a hypothetical tree of all angiosperm genera and the efficiency of phylogenetic reconstructions was tested with simulated matrices containing an increasing number of nucleotides up to a maximum of 30,000. Even with such a large tree, our simulations suggested that simple heuristic searches were able to infer up to 80% of the nodes correctly.

Base Sequence↗

Comparison of additive trees using circular orders.

It has been postulated that existing species have been linked in the past in a way that can be described using an additive tree structure. Any such tree structure reflecting species relationships is associated with a matrix of distances between the species considered which is called a distance matrix or a tree metric matrix. A circular order of elements of X corresponds to a circular (clockwise) scanning of the subset X of vertices of a tree drawn on a plane. This paper describes an optimal algorithm using circular orders to compare the topology of two trees given by their distance matrices. This algorithm allows us to compute the Robinson and Foulds topologic distance between two trees. It employs circular order tree reconstruction to compute an ordered bipartition table of the tree edges for both given distance matrices. These bipartition tables are then compared to determine the Robinson and Foulds topologic distance, known to be an important criterion of tree similarity. The described algorithm has optimal time complexity, requiring O(n(2)) time when performed on two n x n distance matrices. It can be generalized to get another optimal algorithm, which enables the strict consensus tree of k unrooted trees, given their distance matrices, to be constructed in O(kn(2)) time.

Algorithms↗

Size distribution, growth and inter-year variation in sex expression of Bischofia javanica, an invasive tree.

Flowering activity and sex expression of Bischofia javanica Blume were investigated for 3 years. B. javanica is an invasive dioecious tree of subtropical forests on the Bonin Islands in the western Pacific of Japan. The sex ratio showed a significant male bias (1.25-2.33). Smaller trees were significantly male biased, whereas larger trees showed no significant difference in sex expression, suggesting that males tend to be more precocious in sexual reproduction. We found evidence for sex changes in B. javanica; these have not been reported previously. Most of the 1,653 census trees remained non-flowering (58.1 %); 3.7 % of them showed sex changes, and the percentage of trees repeatedly flowering as males and females was 10.5 and 3.4 %, respectively. Sex changes were observed in both directions but a larger percentage of male trees became female. Flowering frequency and sex expression were significantly related to tree size (i.e. diameter at breast height). Over the 3 years, trees that were consistent females were the largest; inconsistent trees (switching sex between years) were intermediate in size, whereas consistent males were the smallest. There were no significant differences in relative growth rate (RGR) among trees of different sex or flowering frequencies. These results suggest that the maintenance of female reproduction is not related to changes in RGR of diameter but to flowering frequency or the reversal to the male form, dependent upon the internal resource status of individual trees.

Euphorbiaceae↗

When, how and how much: Gender-specific resource-use strategies in the dioecious tree Juniperus thurifera.

BACKGROUND AND AIMS: In dioecious species male and female plants experience different selective pressures and often incur different reproductive costs. An increase in reproductive investment habitually results in a reduction of the resources available to other demands, such as vegetative growth. Tree-ring growth is an integrative measure that tracks vegetative investment through the plant's entire life span. This allows the study of gender-specific vegetative allocation strategies in dioecious tree species thoughout their life stages. METHODS: Standard dendrochronological procedures were used to measure tree-ring width. Analyses of time-series were made by means of General Mixed Models with correction of autocorrelated values by the use of an autoregressive covariance structure of order one. Bootstrapped correlation functions were used to study the relationship between climate and tree-ring width. KEY RESULTS: Male and female trees invest a similar amount of resources to ring growth during the early life stages of Juniperus thurifera. However, after reaching sexual maturity, tree-ring growth is reduced for both sexes. Furthermore, females experience a significantly stronger reduction in growth than males, which indicates a lower vegetative allocation in females. In addition, growth was positively correlated with precipitation from the current winter and spring in male trees but only to current spring precipitation in females. CONCLUSIONS: Once sexual maturity is achieved, tree rings grow proportionally more in males than in females. Differences in tree-ring growth between the genders could be a strategy to respond to different reproductive demands. Therefore, and responding to the questions of when, how and how much asked in the title, it is shown that male trees invest more resources to growth than female trees only after reaching sexual maturity, and they use these resources in a different temporal way.

Climate↗

Upper bounds on maximum likelihood for phylogenetic trees.

We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple 'partition' bound is introduced for general models. Tighter bounds are developed for the simplest model of evolution, the two state symmetric model of nucleotide substitution under the molecular clock. This follows earlier theoretical work which has been restricted to this model by analytic complexity. A weakness of current numerical computation is that reported 'maximum likelihood' results cannot be guaranteed, both for a specified tree (because of the possibility of multiple maxima) or over the full tree space (as the computation is intractable for large sets of trees). The bounds we develop here can be used to conclusively eliminate large proportions of tree space in the search for the maximum likelihood tree. This is vital in the development of a branch and bound search strategy for identifying the maximum likelihood tree. We report the results from a simulation study of approximately 10(6) data sets generated on clock-like trees of five leaves. In each trial a likelihood value of one specific instance of a parameterised tree is compared to the bound determined for each of the 105 possible rooted binary trees. The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed-up factor of between 12 and 44.

Algorithms↗

IQPNNI: moving fast through tree space and stopping in time.

An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n(2)) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm. These steps are repeated several times and the best tree, with respect to the likelihood criterion, is considered as the inferred phylogenetic tree. Moreover, we suggest a rule which indicates when to stop the search. Simulations show that IQPNNI gives a slightly better accuracy than other programs tested. Moreover, we applied the approach to 218 small subunit rRNA sequences and 500 rbcL sequences. We found trees with higher likelihood compared to the results by others. A program to reconstruct DNA or amino acid based phylogenetic trees is available online (http://www.bi.uni-duesseldorf.de/software/iqpnni).

Algorithms↗

An error-correcting map for quartets can improve the signals for phylogenetic trees.

From the DNA sequences for N taxa, the (generally unknown) phylogenetic tree T that gave rise to them is to be reconstructed. Various methods give rise, for each quartet J consisting of exactly four taxa, to a predicted tree L(J) based only on the sequences in J, and these are then used to reconstruct T. The author defines an "error-correcting map" (Ec), which replaces each L(J) with a new tree, Ec(L)(J), which has been corrected using other trees, L(K), in the list L. The "quartet distance" between two trees is defined as the number of quartets J on which the two trees differ, and two distinct trees are shown to always have quartet distance of at least N - 3. If L has quartet distance at most (N - 4)/2 from T, then Ec(L) will coincide with the correct list for T; and this result cannot be improved. In general, Ec can correct many more errors in L. Iteration of the map Ec may produce still more accurate lists. Simulations are reported which often show improvement even when the quartet distance considerably exceeds (N - 4)/2. Moreover, the Buneman tree for Ec(L) is shown to refine the Buneman tree for L, so that strongly supported edges for L remain strongly supported for Ec(L). Simulations show that if methods such as the C-tree or hypercleaning are applied to Ec(L), the resulting trees often have more resolution than when the methods are applied only to L.

Likelihood Functions↗

Assessment of nitrogen, phosphorus, and potassium uptake capacity and root growth in mature alternate-bearing pistachio (Pistacia vera) trees.

We examined interrelationships between crop load, nitrogen (N), phosphorus (P), and potassium (K) uptake, and root growth in mature, alternate-bearing pistachio (Pistacia vera L.) trees. Pistachio trees bear heavy (on-year) and light (off-year) fruit crops in alternate years. Uptake and partitioning of N, P, and K among tree parts were determined during (a) spring flush (mid-March to late May), (b) nut fill (late May to early September), and (c) postharvest-leaf senescence (late September to early December). Nutrient uptake occurred primarily during nut fill in both on-year and off-year trees. In on-year trees, N and K uptake increased by 35 and 112%, respectively, during nut fill compared with off-year trees. During this period, nutrients were allocated largely to embryo development in on-year trees and to storage in perennial tissues in off-year trees. Nutrient uptake was negligible between harvest and leaf senescence. Although root growth was reduced during nut fill in on-year trees compared with off-year trees, there was no relationship between root growth and the uptake of N, P or K from the soil. Our data support the hypothesis that sink demand regulates the uptake and distribution of N, P, and K in pistachio trees.

Journal Article↗

Using max cut to enhance rooted trees consistency.

Supertree methods are used to construct a large tree over a large set of taxa from a set of small trees over overlapping subsets of the complete taxa set. Since accurate reconstruction methods are currently limited to a maximum of a few dozen taxa, the use of a supertree method in order to construct the tree of life is inevitable. Supertree methods are broadly divided according to the input trees: When the input trees are unrooted, the basic reconstruction unit is a quartet tree. In this case, the basic decision problem of whether there exists a tree that agrees with all quartets is NP-complete. On the other hand, when the input trees are rooted, the basic reconstruction unit is a rooted triplet and the above decision problem has a polynomial time algorithm. However, when there is no tree which agrees with all triplets, it would be desirable to find the tree that agrees with the maximum number of triplets. However, this optimization problem was shown to be NP-hard. Current heuristic approaches perform min cut on a graph representing the triplets inconsistency and return a tree that is guaranteed to satisfy some required properties. In this work, we present a different heuristic approach that guarantees the properties provided by the current methods and give experimental evidence that it significantly outperforms currently used methods. This method is based on a divide and conquer approach, where the min cut in the divide step is replaced by a max cut in a variant of the same graph. The latter is achieved by a lightweight semidefinite programming-like heuristic that leads to very fast running times.

Algorithms↗

Simplifying gene trees for easier comprehension.

BACKGROUND: In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important. RESULTS: We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tree to a "cartoon tree" created manually, we note that both agree to a high degree. CONCLUSION: Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families. The software is available at http://www.uni-muenster.de/Bioinformatics/services/treesim/.

Algorithms↗