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Suppose that we seek a tree T giving the phylogenetic relationships among the species in a set S. A common method selects for such a tree a maximum parsimony tree using the genome of the species in S. Suppose that K is a proper subset of S. Then T induces a tree U which gives the same relationships among the species in K but omits the species of S which are not in K. Unfortunately, when T is a maximum parsimony tree for the species in S, then U need not be a maximum parsimony tree for the species in K. This phenomenon exhibits an inconsistency in the criterion of maximum parsimony-maximum parsimony trees for different groups of species may be "inconsistent". It implies that the addition of a new species scan change relationships already "established" for prior species if the trees are obtained by the criterion of maximum parsimony. The phenomenon occurs both in artificial examples and with real data. An alternative method for generating phylogenetic trees seeks to minimize such inconsistencies. For each group J consisting of four of the species, we find a tree T(J) describing the relationship only among the four species in J, for example by the use of maximum parsimony on those four species alone. In favorable cases one may combine all the trees T(J) into a single tree T that is consistent with all the trees T(J). If such a tree T exists, then it is unique, and there is a computationally efficient algorithm for finding the tree T. In unfavorable bases such a tree T does not exist, but there may still be a tree containing only "mild" inconsistencies with the trees T(J). A numerical measure is given for the inconsistency I(T) of a tree T in terms of the treelengths of the various trees with set J of leaves in comparison with the tree T. We may then seek a "minimally inconsistent tree T" that minimizes the inconsistency I(T). We describe procedures which find a tree T with low inconsistency I(T). Examples are provided using both artificial strings and data from the complete mitochondrial DNA sequences for 16 species. In particular, minimally inconsistent trees are identified for the 16 species. The definition permits a proof that the trees are in fact minimally inconsistent. The criterion can be applied in both a relative and an absolute sense.
We examined manganese uptake and translocation in 30-year-old silver fir trees (Abies alba Mill.) showing severe symptoms of needle chlorosis by analyzing both xylem and phloem sap of shoots and an extract of root sap originating from both xylem and phloem elements. Manganese concentrations in shoot xylem and phloem sap were significantly lower in chlorotic trees than in neighboring healthy trees. The Mn concentration of root sap was also lower in these Mn-deficient trees than in healthy trees, indicating reduced Mn uptake by Mn-deficient trees. Although Mn deficiency had no effect on the Mn concentration of whole roots, separation of root tissue into root cortex and stele (wood) suggested impaired translocation of Mn from the cortex to the stele in Mn-deficient trees. Triphenyltetrazolium chloride (TTC) tests indicated that there was no decrease in reducing capacity of the fine roots (< 1 mm in diameter) of Mn-deficient trees. Fine roots of Mn-deficient trees contained significantly more organic acids than fine roots of healthy trees, including increased concentrations of malic, quinic, trans-acontic and formic acid; however, concentrations of pyruvic and acetic acid were lower than in fine roots of healthy trees. The total amounts of organic acids in the rhizospheric soil were similar for healthy and Mn-deficient trees. Pyruvic acid concentration was significantly increased in the rhizospheric soil of Mn-deficient trees, and concentrations of simple aliphatic acids like formic and acetic acid also tended to be higher in the rhizospheric soil of Mn-deficient trees. Both pH and water content were higher in bulk soil and rhizospheric soil around Mn-deficient trees compared with soil around healthy trees. Although lower concentrations of exchangeable Mn were found in the soil around Mn-deficient trees, the active Mn concentration (sum of exchangeable and reducible Mn) did not differ between healthy and Mn-deficient trees. A considerable proportion of manganese was in an oxidized form in the soil around Mn-deficient trees.
Sap flow rates were measured simultaneously by the heat pulse and deuterium tracing techniques in nine Eucalyptus grandis W. Hill ex Maiden. trees at two sites (1) to compare results from the two techniques and (2) to assess the impact of the assumptions underlying the deuterium tracing method on the calculation of sap flow for a range of tree sizes. The trees ranged in height from 4 to 14 m with leaf areas of 5 to 35 m(2). In all trees, sap flow estimated by the deuterium tracing technique was higher than sap flow estimated by the heat pulse method, with differences of 11 to 43% in eight of the trees and 113% in one tree. The largest difference was attributed to errors in the heat pulse method, as indicated by aberrant relationships between sap flow measured by the heat pulse method and tree size characteristics (i.e., diameter, sap wood area, leaf area) for that tree compared with the other experimental trees. Drilling holes in the trees to allow injection of deuterium had no significant effect on sap flow, even when 32 holes were drilled. Sap flow measured by the heat pulse method was only lower after drilling than before drilling in three trees, and the difference only persisted for about 1 h. Deuterium concentrations of water collected from the tree canopies had not returned to background values 17 days after injection. Twenty-one days after injection, sapwood and heartwood samples taken from trunks near the injection sites contained considerable concentrations of deuterium, indicating that some of the deuterium injected into the trees was still present. An experiment performed on two trees showed that deuterium was stored in the heartwood and sapwood throughout the trees, and its distribution within the trees four days after injection was similar whether it was injected into only the sapwood (where it should mix with sap and be transported from the tree most readily) or into both the sapwood and heartwood, indicating that there was considerable movement of deuterium between the heartwood and sapwood. Deuterium storage was accounted for by an approximate means in the sap flow calculations, and may have resulted in an error of about 10% in sap flow estimated by this method. We conclude that the heat pulse and deuterium tracing techniques can be used simultaneously to increase the number of sap flow measurements obtained from a forest, thereby increasing the precision of forest water use estimates. Their combination would be most effective in stands with a wide range of tree sizes and sap flow rates, where the relative differences in sap flux estimates between the methods is small compared with differences in sap flow between trees.
Testing for tree pollen hypersensitivity typically requires the use of several tree pollens. Identifying patterns of cross-sensitivity to tree pollens could reduce the number of trees used for testing. The goal of this study was to relate reported tree pollen levels to hypersensitivity patterns. Three hundred seventy-one allergy patients were tested serologically for hypersensitivity toward prevalent tree pollens in the surrounding New York area over the years 1993-2000. Specific tree pollens that were examined included oak (Quercus alba), birch (Betula verrucosa), beech (Fagus grandifolia), poplar (Populus deltoides), maple (Acer negundo), ash (Fraxinus americana), hickory (Carya pecan), and elm (Ulmus americana). Statistical analysis of the levels of hypersensitivity was performed to identify correlations and grouping factors. Pollen levels, obtained from published annual pollen and spore reports, were characterized and related to the prevalence of hypersensitivity for the various trees. The highest prevalence of hypersensitivity (score > or = class 1) was for oak (34.3%), birch (32.9%), and maple (32.8%) tree pollens. Lower prevalences were observed for beech (29.6%), hickory (27.1%), ash (26%), elm (24.6%), and poplar (20.6%) trees. Significant correlations were observed between oak, birch, and beech radioallergosorbent test scores. Factor analysis identified two independent pollen groups with oak, birch, and beech consisting of one group and the other five tree pollens constituting the other group. Peak pollen counts clearly were highest for oak, birch, and maple trees. The peak pollen counts corresponded roughly to seropositivity prevalences for the tree pollens. When elm, poplar, and beech test scores were not used to identify patients who were allergic to tree pollens, only 1 of 106 patients with any positive tree radioallergosorbent test score was missed. It is concluded that in the New York City area, hypersensitivity to tree pollens most often is manifested with allergy to oak, birch, and maple tree pollens. Identifying beech, poplar, and elm hypersensitivity adds little toward identifying patients who are allergic to tree pollens. This may relate in part to cross-reactive epitopes. These data suggest that these three trees can be eliminated from testing with only a < 1% loss of sensitivity.
We studied correlation between crown conditions and tree-ring widths in 260 trees of pedunculate oak (Quercus robur L.) growing on 33 sites in southern Sweden. The tree-ring increment over 1998-2002 was highest in trees with healthy crowns, intermediate in trees with moderately declined crowns, and lowest in trees with heavily declining crowns. The time period with significant correlation between crown status and tree-ring increment varied between 10 years (given autocorrelation in tree-ring chronologies preserved) and 4 years (autocorrelation removed). In pairwise comparisons of three crown classes, differences in tree-ring increment between trees with healthy crowns and trees with heavily declining crowns were the most pronounced, Fisher LSD P value staying below 0.05 over 13 years (autocorrelation preserved ) or 4 years (autocorrelation removed). Over two 5-year periods (1993-1997 vs. 1998-2002) the cumulative increment increased significantly for trees with healthy crowns, did not change in trees with moderately declining crowns, and significantly decreased in trees with heavily declining crowns. For trees with healthy crowns, this dynamics may represent growth recovery after 1992 drought. Instead, oaks with defoliation above 60% appear to reach a threshold in their ability to recover growth. At sites on nutrient-poor soils cumulative increments over 1998-2002 differed significantly among trees with different crown condition and no differences were observed at sites on nutrient-rich soils. Analyses and interpretation of the oak growth trends as recovered from tree-ring chronologies may be improved by controlling for the crown status of the trees sampled, e.g., by using sampling strategy that would represent the average crown and growth conditions of the sites.
Numerous researchers have used the isotopic signatures of C, H, and O in tree rings to provide a long-term record of changes in the physiological status, climate, or water-source use of trees. The frequently limiting element N is also found in tree rings, and variation in its isotopic signature may provide insight into long-term changes in soil N availability of a site. However, research has suggested that N is readily translocated among tree ring of different years; such infidelity between the isotopic compositions of the N taken up from the soil and the N contained in the ring of that growth year would obscure the long-term N isotopic record. We used a 15-year 15N-tracer study to assess the degree of N translocation among tree rings in ponderosa pine (Pinus ponderosa) trees growing in a young, mixed-conifer plantation. We also measured delta13C and delta15N values in unlabeled trees to assess the degree of their covariance in wood tissue, and to explore the potential for a biological linkage between them. We found that the maximum delta15N values in rings from the labeled trees occurred in the ring formed one-year after the 15N was applied to the roots. The delta15N value of rings from labeled trees declined exponentially and bidirectionally from this maximum peak, toward younger and older rings. The unlabeled trees showed considerable interannual variation in the delta15N values of their rings (up to 3 and 5 per thousand), but these values correlated poorly between trees over time and differed by as much as 6 per thousand. Removal of extractives from the wood reduced their delta15N value, but the change was fairly small and consistent among unlabeled trees. The delta13C and delta15N values of tree rings were correlated over time in only one of the unlabeled trees. Across all trees, both delta13C values of tree rings and annual stem wood production were well correlated with annual precipitation, suggesting that soil water balance is an important environmental factor controlling both net C gain and transpirational water loss at this site. Our results suggest that interannual translocation of N among tree rings is substantial, but may be predictable enough to remove this source of variation from the tree-ring record, potentially allowing the assessment of long-term changes in soil N availability of a site.
In this study I investigated the effects of the extreme, 1997/98 El Niño related drought on tree mortality and understorey light conditions of logged and unlogged tropical rain forest in the Indonesian province of East Kalimantan (Borneo). My objectives were to test (1) whether drought had a significant effect on tree mortality and understorey light conditions, (2) whether this effect was greater in logged than in undisturbed forest, (3) if the expected change in tree mortality and light conditions had an effect on Macaranga pioneer seedling and sapling densities, and (4) which (a)biotic factors influenced tree mortality during the drought. The 1997/1998 drought led to an additional tree mortality of 11.2, 18.1, and 22.7% in undisturbed, old logged and recently logged forest, respectively. Mortality was highest in logged forests, due to extremely high mortality of pioneer Macaranga trees (65.4%). Canopy openness was significantly higher during the drought than during the non-drought year (6.0, 8.6 and 10.4 vs 3.7, 3.8 and 3.7 in undisturbed, old logged and recently logged forest, respectively) and was positively correlated with the number of dead standing trees. The increase in light in the understorey was accompanied by a 30 to 300-fold increase in pioneer Macaranga seedling densities. Factors affecting tree mortality during drought were (1) tree species successional status, (2) tree size, and (3) tree location with respect to soil moisture. Tree density and basal area per surface unit had no influence on tree mortality during drought. The results of this study show that extreme droughts, such as those associated with El Niño events, can affect the tree species composition and diversity of tropical forests in two ways: (1) by disproportionate mortality of certain tree species groups and tree size classes, and (2) by changing the light environment in the forest understorey, thereby affecting the recruitment and growth conditions of small and immature trees.
Environmentally sound management of N in apple orchards requires that N supply meets demand. In 1997, newly planted apple trees (Malus domestica Borkh. var. Golden Delicious on M.9 rootstock) received daily applications of N for six weeks as Ca(15NO3)(2) through a drip irrigation system at a concentration of 112 mg l(-1) at 2-8, 5-11 or 8-14 weeks after planting. Irrigation water was applied either to meet estimated evaporative demand or at a fixed rate. In 1997, trees were harvested at 5, 8, 11 and 14 weeks after planting; and in 1998 at 3 weeks after full bloom. The amount of fertilizer N recovered was similar in trees in both irrigation treatments, but efficiency of fertilizer use was greater for trees receiving demand-controlled irrigation than fixed-rate irrigation. This was attributed to lower N inputs, greater retention time in the root zone and less N leaching in the demand-controlled irrigation treatments compared with fixed-rate irrigation treatments. Less fertilizer N was recovered by trees receiving an early application of N than a later application of N and this was related to the timing of N supply with respect to tree demand. Demand for root-supplied N was low until 11 weeks after planting, because early shoot and root growth was supported by N remobilized from woody tissue, which involved 55% of the total tree N content at planting. Rapid development of roots > 1 mm in diameter occurred between 11 and 14 weeks after planting, after remobilization ended, and was greater for trees receiving an early application of N than for trees receiving a later application of N. Late-season tree N demand was supplied by native soil N, and uptake and background soil solution N concentrations were higher for trees receiving demand-supplied irrigation compared with fixed-rate irrigation. Total annual N uptake by roots was unaffected by treatments and averaged 6-8 g tree(-1). Nitrogen applications in 1997 affected growth and N partitioning in 1998. Trees receiving early applications of N had more flowers, spur leaves and bourse shoots than trees receiving later applications of N. Consequently, more N was remobilized into fruits in trees receiving early applications of N compared with fruits in trees receiving later applications of N. Demand for N in the young apple trees was low. Early season demand was met by remobilization from woody tissues and the timing of demand for root-supplied N probably depends on whether flowering occurs. Method of N delivery affected the efficiency of N use. We conclude that N demand can be met at soil solution N concentrations of around 20 mg l(-1).
Bench-grafted Fuji/M.26 apple (Malus domestica Borkh.) trees were fertilized with a nutrient solution (fertigation) containing 0, 2.5, 5, 7.5, 10, 15 or 20 mM nitrogen (N) in a modified Hoagland's solution from June 30 to September 1. In mid-October, half of the trees in each N treatment were sprayed twice with 3% urea, 1 week apart. The remaining trees served as controls. All trees were harvested after leaf fall and stored at 2 degrees C over winter. One group of trees from each treatment was destructively sampled before bud break to determine amounts of reserve N and total nonstructural carbohydrates (TNC); the remaining trees were transplanted to N-free medium in the spring. These trees were supplied with Hoagland's solution with or without 10 mM N (from 15N-depleted NH4NO3) for 60 days, starting from bud break. With increasing N supply from fertigation, tree N concentration increased, whereas TNC concentration decreased. Foliar urea applications increased tree N concentration and decreased TNC concentration in each N fertigation treatment. There was a negative linear relationship between tree N concentration and TNC concentration. Irrespective of whether N was provided the following spring, trees with high N reserves but low carbohydrate reserves produced a larger total leaf area at the end of the regrowth period than trees with low N reserves but high carbohydrate reserves. The pooled data on reserve N used for new growth showed that, regardless of the spring N supply, there was a linear relationship between total N accumulated in the tree during the previous season and the amount of reserve N remobilized for new shoot and leaf growth. About 50% of tree N content was remobilized to support new shoot and leaf growth over the range of tree N status examined. We conclude that the initial growth of young apple trees in the spring is determined mainly by reserve N, not reserve carbohydrates. The amount of reserve N remobilized for new growth in spring was proportional to tree N status and was unaffected by current N supply.
Ontogenetic changes in gas exchange parameters provide both insight into mechanisms underlying tree growth patterns, and data necessary to scale environmental impacts on young trees to predict responses of older trees. We present a quantitative review and meta-analysis of field measurements of gas exchange parameters in saplings and mature trees of 35 tree species (seven conifers, seven temperate deciduous trees, and 21 tropical evergreen trees). Data for saplings were obtained in both understory environments and open areas or large gaps. We also present data on ontogenetic changes in photosynthesis for Pseudotsuga menziesii (Mirb.) Franco and Tsuga heterophylla (Raf.) Sarg., species of particular interest because of their large maximal heights and long life-spans. Among tree species, there is evidence for both ontogenetic increases and ontogenetic decreases in photosynthetic capacity on a leaf area basis (A(area)). Overall, A(area) is generally higher for upper-canopy leaves of adult trees than for saplings, especially in temperate deciduous trees. However, the pattern for photosynthetic capacity on a leaf mass basis (A(mass)) is the reverse of that observed for A(area). Saplings of both conifers and broad-leaved trees, even when acclimated to low-light conditions, characteristically have a higher A(mass) than adult trees. This pattern is driven largely by an ontogenetic increase in leaf mass per unit area (LMA), as found in 100% of studies reviewed. Data for Pacific Northwest conifers, although including measurements on some of the tallest trees studied, did not differ greatly from patterns found in other tree species. We conclude that ontogenetic changes in LMA are the single most consistent difference between saplings and adult trees, and that changes in LMA and related aspects of leaf morphology may be critical to understanding both variation in gas exchange during tree growth, and stage-dependent responses of trees to environmental change.
BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.
BACKGROUND: The investigation was conducted in a savanna area covered by what was considered an undesirably dense stand of Colophospermum mopane trees, mainly because such a dense stand of trees often results in the suppression of herbaceous plants. The objectives of this study were to determine the influence of intensity of tree thinning on the dry matter yield of herbaceous plants (notably grasses) and to investigate differences in herbaceous species composition between defined subhabitats (under tree canopies, between tree canopies and where trees have been removed). Seven plots (65 x 180 m) were subjected to different intensities of tree thinning, ranging from a totally cleared plot (0%) to plots thinned to the equivalent of 10%, 20%, 35%, 50% and 75% of the leaf biomass of a control plot (100%) with a tree density of 2711 plants ha(-1). The establishment of herbaceous plants (grasses and forbs) in response to reduced competition from the woody plants was measured during three full growing seasons following the thinning treatments. RESULTS: The grass component reacted positively to the tree thinning in terms of total dry matter (DM) yield, but forbs were negatively influenced. Rainfall interacted with tree density and the differences between grass DM yields in thinned plots during years of below average rainfall were substantially higher than those of the control. At high tree densities, yields differed little between seasons of varying rainfall. The relation between grass DM yield and tree biomass was curvilinear, best described by the exponential regression equation. Subhabitat differentiation by C. mopane trees did provide some qualitative benefits, with certain desirable grass species showing a preference for the subhabitat under tree canopies. CONCLUSION: While it can be concluded from this study that high tree densities suppress herbaceous production, the decision to clear/thin the C. mopane trees should include additional considerations. Thinning of C. mopane with the exclusive objective of increasing productivity of the grass layer would thus invariably involve a compromise situation where some trees should be left for the sake of the qualitative benefits on the herbaceous layer, soil enrichment, provision of browse and stability of the ecosystem.
The effects of habitat fragmentation on diverse tropical tree communities are poorly understood. Over a 20-year period we monitored the density of 52 tree species in nine predominantly successional genera (Annona, Bellucia, Cecropia, Croton, Goupia, Jacaranda, Miconia, Pourouma, Vismia) in fragmented and continuous Amazonian forests. We also evaluated the relative importance of soil, topographic, forest dynamic, and landscape variables in explaining the abundance and species composition of successional trees. Data were collected within 66 permanent 1-ha plots within a large (approximately 1000 km2) experimental landscape, with forest fragments ranging from 1 to 100 ha in area. Prior to forest fragmentation, successional trees were uncommon, typically comprising 2-3% of all trees (> or =10 cm diameter at breast height [1.3 m above the ground surface]) in each plot. Following fragmentation, the density and basal area of successional trees increased rapidly. By 13-17 years after fragmentation, successional trees had tripled in abundance in fragment and edge plots and constituted more than a quarter of all trees in some plots. Fragment age had strong, positive effects on the density and basal area of successional trees, with no indication of a plateau in these variables, suggesting that successional species could become even more abundant in fragments over time. Nonetheless, the 52 species differed greatly in their responses to fragmentation and forest edges. Some disturbance-favoring pioneers (e.g., Cecropia sciadophylla, Vismia guianensis, V. amazonica, V. bemerguii, Miconia cf. crassinervia) increased by >1000% in density on edge plots, whereas over a third (19 of 52) of all species remained constant or declined in numbers. Species responses to fragmentation were effectively predicted by their median growth rate in nearby intact forest, suggesting that faster-growing species have a strong advantage in forest fragments. An ordination analysis revealed three main gradients in successional-species composition across our study area. Species gradients were most strongly influenced by the standlevel rate of tree mortality on each plot and by the number of nearby forest edges. Species-composition also varied significantly among different cattle ranches, which differed in their surrounding matrices and disturbance histories. These same variables were also the best predictors of total successional-tree abundance and species richness. Successional-tree assemblages in fragment interior plots (>150 m from edge), which are subjected to fragment area effects but not edge effects, did not differ significantly from those in intact forest, indicating that area effects per se had little influence on successional trees. Soils and topography also had little discernable effect on these species. Collectively, our results indicate that successional-tree species proliferate rapidly in fragmented Amazonian forests, largely as a result of chronically elevated tree mortality near forest edges and possibly an increased seed rain from successional plants growing in nearby degraded habitats. The proliferation of fast-growing successional trees and correlated decline of old-growth trees will have important effects on species composition, forest dynamics, carbon storage, and nutrient cycling in fragmented forests.
Applying the tree bisection and reconnection (TBR) algorithm, we have developed a heuristic method (maximum likelihood (ML)-TBR) for inferring the ML tree based on tree topology search. For initial trees from which iterative processes start in ML-TBR, two cases were considered: one is 100 neighbor-joining (NJ) trees based on the bootstrap resampling and the other is 100 randomly generated trees. The same ML tree was obtained in both cases. All different iterative processes started from 100 independent initial trees ultimately converged on one optimum tree with the largest log-likelihood value, suggesting that a limited number of initial trees will be quite enough in ML-TBR. This also suggests that the optimum tree corresponds to the global optimum in tree topology space and thus probably coincides with the ML tree inferred by intact ML analysis. This method has been applied to the inference of phylogenetic tree of the SOX family members. The mammalian testis-determining gene SRY is believed to have evolved from SOX-3, a member of the SOX family, based on several lines of evidence, including their sequence similarity, the location of SOX-3 on the X chromosome and some aspects of their expression. This model should be supported directly from the phylogenetic tree of the SOX family, but no evidence has been provided to date. A recently published NJ tree shows implausibly remote origin of SRY, suggesting that a more sophisticated method is required for understanding this problem. The ML tree inferred by the present method showed that the SRYs of marsupial and placental mammals form a monophyletic cluster which had diverged from the mammalian SOX-3 in the early evolution of mammals.