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A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus.

The WNT: gene family is large, and new members are still being discovered. We constructed a parsimony tree for the WNT: family based on all 82 of the full-length sequences currently available. The inclusion of sequences from the cephalochordate amphioxus is especially useful in comprehensive gene trees, because the amphioxus genes in each subfamily often mark the base of the vertebrate diversification. We thus isolated full-length cDNAs of five amphioxus WNT: genes (AmphiWnt1, AmphiWnt4, AmphiWnt7, AmphiWnt8, and AmphiWnt11) for addition to the overall WNT: family tree. The analysis combined amino acid and nucleotide sequences (excluding third codon positions), taking into account 97% of the available data for each sequence. This combinatorial method had the advantage of generating a single most-parsimonious tree that was trichotomy-free. The reliability of the nodes was assessed by both jackknifing and Bremer support (decay index). A regression analysis revealed that branch length was strongly correlated with branch support, and possible reasons for this pattern are discussed. The tree topology suggested that in amphioxus, at least an AmphiWnt5 and an AmphiWnt10 have yet to be discovered.

Animals↗

On the use of nucleic acid sequences to infer early branchings in the tree of life.

Simplifying assumptions made in various tree reconstruction methods--notably rate constancy among nucleotide sites, homogeneity, and stationarity of the substitutional processes--are clearly violated when nucleotide sequences are used to infer distant relationships. Use of tree reconstruction methods based on such oversimplified assumptions can lead to misleading results, as pointed out by previous authors. In this paper, we made use of a (discretized) gamma distribution to account for variable rates of substitution among sites and built models that allowed for unequal base frequencies in different sequences. The models were nonhomogeneous Markov-process models, assuming different patterns of substitution in different parts of the tree. Data of the small-subunit rRNAs from four species were analyzed, where base frequencies were quite different among sequences and rates of substitution were highly variable at sites. Parameters in the models were estimated by maximum likelihood, and models were compared by the likelihood-ratio test. The nonhomogeneous models provided significantly better fit to the data than homogeneous models despite their involvement of many parameters. They also appeared to produce reasonable estimation of the phylogenetic tree; in particular, they seemed able to identify the root of the tree.

Base Sequence↗

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

Animals↗

A growth model of a single sugi (Cryptomeria japonica) tree based on the dry matter budget of its aboveground parts.

Growth of a single sugi (Cryptomeria japonica (L.f.) D. Don.) tree was analyzed on the basis of a dry matter budget. The aboveground net production rate and death rate were defined as the anabolic rate and catabolic rate, respectively. Growth rate of aboveground tree weight, v(w) (kg(dw) year(-1)), was defined as follows: v(w) = v(p) - v(d) (1) where v(p) (kg(dw) year(-1)) is the aboveground net production rate and v(d) (kg(dw) year(-1)) is the aboveground death rate. The value of v(d) is obtained by measuring the monthly clippings of new dead leaves and branches attached to a sample tree. The value of v(w) was calculated as the annual difference in the estimated aboveground tree weight, w(T) (kg(dw)). Finally, the value of v(p) was estimated as the sum of the values of v(d) and v(w). The following allometric relationships were found between v(p) and w(T) and between v(d) and w(T): v(p) = aw(T) (alpha), v(d) = bw(T) (beta) (2). Combining Equations 1 and 2 gives a growth equation, Bertalanffy's equation, of the sample tree. dw(T)/dt = v(w) = aw(T) (alpha) - bw(T) (beta) (3). Because the growth curve of w(T) was derived from Equation 3, the analysis of the growth of w(T) is based on direct measurement of the dry matter budget.

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Shape of tree stems-a re-examination of the uniform stress hypothesis.

The transfer matrix method of structural analysis was used to examine the hypothesis that tree stems grow to a shape that tends to equalize the average bending plus axial stresses to which they are subjected along their length. The method and computational procedures were checked by comparing computed height-diameter profiles with those calculated using elementary stress theory for trees with simple force distributions in the crown. Measured height-diameter profiles for trees were then taken from the literature and shown to be well-fitted by profiles calculated to give uniform stress along the stems, using the most realistic average forces and force distributions within the crowns. At high wind speeds, the height-diameter profile giving uniform stress was more tapered than the profile giving uniform stress at low wind speeds. The profile giving uniform stress was similar over the normal range of average wind speeds of 2.5 to 10.0 m s(-1) (at the top of the canopy). But a tree that had grown to give uniform stress along its stem in an average wind of 5 m s(-1) showed markedly decreased stress with height at wind speeds of about 15 m s(-1) or more, and increased stress with height (to the crown base) at wind speeds of about 1.25 m s(-1) or less. The fact that tree stems develop shapes in response to average conditions, but show varying stress distribution in extreme conditions, may help to explain some of the apparent evidence for non-uniform stress distribution in the literature. In general, our analysis supports the above hypothesis for the stem region above the butt swell.

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14C Allocation in tree-soil systems.

We studied whole-tree C allocation with special emphasis on the quantification of C allocation to roots and root respiration. To document seasonal patterns of C allocation, 2-year-old hybrid poplar trees greater than 3 m tall were labeled with (14)CO(2) in a large Plexiglas chamber in the field, in July and September. Climate and CO(2) concentration were controlled to track ambient conditions during labeling. Individual tree canopy CO(2) assimilation averaged 3.8 micromol CO(2) m(-2) s(-1) (12.9 g C day(-1) tree(-1)) in July and 6.2 micromol CO(2) m(-2) s(-1) (9.8 g C day(-1) tree(-1)) in September. Aboveground dark respiration was 12% of net daytime C fixation in July and 15% in September. Specific activity of root-soil respiration peaked 2 days after labeling and stabilized to less than 5% of maximum 2 weeks later. Low specific activity of root-soil respiration and a labeled pool of root C demonstrated that current photosynthate was the primary source of C for root growth and maintenance during the growing season. Root respiration averaged 20% of total soil respiration in both July and September based on the proportion of labeled C respired to labeled C fixed. In July, 80% of the recovered (14)C was found above ground and closely resembled the weight distribution of the growing shoot. By September, 51% of the recovered (14)C was in the root system and closely resembled the weight distribution of different size classes of roots. The finding that the distribution of biomass and (14)C were similar verified that the C introduced during labeling followed normal seasonal translocation pathways. Results are compared to smaller scale labeling studies and the suitability of the approach for studying long-term C fluxes is discussed.

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Response of Eucalyptus grandis trees to soil water deficits.

The use of potential transpiration models to simulate transpiration rates in areas prone to soil water deficits leads to overestimates of water use as the soil dries. Therefore, I carried out studies on Eucalyptus grandis W. Hill ex Maiden trees subjected to soil drying at two field sites in the Mpumalanga province of South Africa to determine the relation between transpiration rate and soil water availability. I hypothesized that, with this relationship defined, simple modeling of the soil water balance could be used to predict what fraction of potential transpiration was taking place at a given time. Site 1 supported a stand of 3-year-old E. grandis trees, whereas 9-year-old trees were growing on Site 2, situated 2 km away. At each site, plastic sheeting was laid over the ground to prevent soil water recharge and thereby allow the roots in the soil to induce a continuous progressive depletion of soil water. Measurements of predawn xylem pressure potential, leaf area index, growth and sap flow rates revealed that prevention of soil water recharge resulted in only moderate drought stress. At Site 1, the trees abstracted water down to 8 m below the surface, whereas trees at Site 2 obtained most of their water from depths below 8 m. I found that modeling the water balance of deep rooting zones is impractical for the purpose of simulating nonpotential transpiration rates because of uncertainties about the depth of the root system, the soil water recharge mechanism and the water retention characteristics of the deep subsoil strata. I conclude that predicting the occurrence and severity of soil water deficits from the soil water balance is not feasible at these sites.

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Sap flow measurements of lateral tree roots in agroforestry systems.

Successful extension of agroforestry to areas of the semi-arid tropics where deep reserves of water exist requires that the tree species be complementary to the associated crops in their use of water within the crop rooting zone. However, it is difficult to identify trees suitable for dryland agroforestry because most existing techniques for determining water uptake by roots cannot distinguish between absorption by tree and crop roots. We describe a method for measuring sap flow through lateral roots using constant temperature heat balance gauges, and the application of this method in a study of complementarity of water use in agroforestry systems containing Grevillea robusta A. Cunn. Sap flow gauges were attached to the trunks and roots of Grevillea with minimum disturbance to the soil. Thermal energy emanating from the soil adversely affected the accuracy of sap flow gauges attached to the roots, with the result that the uncorrected values were up to eightfold greater than the true water uptake determined gravimetrically. This overestimation was eliminated by using a calibration method in which nonconducting excised root segments, with sap flow gauges attached, were placed adjacent to the live roots. The power consumption and temperature differentials of the excised roots were used to correct for external sources and internal losses of heat within the paired live root. The fraction of the total sap flow through individual trees supplied by the lateral roots varied greatly between trees of similar canopy size. Excision of all lateral roots, except for one to which a heat balance gauge was attached, did not significantly increase sap flow through the intact root, suggesting that it was functioning at near maximum capacity.

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Microculture of western white pine (Pinus monticola) by induction of shoots on bud explants from 1- to 7-year-old trees.

We developed a protocol for the production of shoots from bud explants from 1- to 7-year-old trees of western white pine (Pinus monticola Dougl.). The best explant was a 2-mm-thick cross-sectional slice of the early winter bud. Genotype of the donor tree was a significant factor affecting shoot production, but more than 80% of the genotypes tested produced shoots. Of the media tested, bud slices from 1- to 3-year-old trees grew best in Litvay's medium containing N(6)-benzyladenine in the range of 1 to 30 micro M, whereas bud slices from older trees grew best in Gupta and Durzan's DCR medium with zeatin riboside. Up to 400 shoots more than 3 mm in height were obtained from 100 bud-slice explants taken from 7-year-old western white pine trees.

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Field measurements of isoprene emission from trees in response to temperature and light.

The atmospheric hydrocarbon budget is important for predicting ozone episodes and the effects of pollution mitigation strategies. Isoprene emission from plants is an important part of the atmospheric hydrocarbon budget. We measured isoprene emission capacity at the bottom, middle, and top of the canopies of a white oak (Quercus alba L.) tree and a red oak (Quercus rubra L.) tree growing adjacent to a tower in the Duke University Forest. Leaves at the top of the white oak tree canopy had a three- to fivefold greater capacity for emitting isoprene than leaves at the bottom of the tree canopy. Isoprene emission rate increased with increasing temperature up to about 42 degrees C. We conclude that leaves at the top of the white oak tree canopy had higher isoprene emission rates because they were exposed to more sunlight, reduced water availability, and higher temperature than leaves at the bottom of the canopy. Between 35 and 40 degrees C, white oak photosynthesis and stomatal conductance declined, whereas red oak (Quercus rubra) photosynthesis and stomatal conductance increased over this range. Red oak had lower rates of isoprene emission than white oak, perhaps reflecting the higher stomatal conductance that would keep leaves cool. The concentration of isoprene inside the leaf was estimated with a simplified form of the equation used to estimate CO(2) inside leaves.

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Leaf distribution in large trees and stands of the floodplain forest in southern Moravia.

Vertical distributions of leaf dry mass (M(d)) and leaf area (A(f)) were related to relative irradiance (I(r); I(r) above the stand = 1) in closed-canopy, old-growth stands of the floodplain forest in southern Moravia composed largely of Quercus, Fraxinus and Tilia species. Foliage area and mass at any given canopy height were converted to solar equivalent leaf area (A(s)) and mass (M(s)) by multiplying actual values at a given level in the canopy by the relative irradiance at that position. Stand leaf area index (LAI) was 5 (7 including shrub and herb layer), and solar equivalent parameters reached about 25% of that amount. In all species, vertical profiles of both relative irradiance and leaf dry mass to area ratio (LMA) were sigmoidal and the two variables were linearly related. The dominant, upper canopy species had a larger proportion of solar equivalent foliage than suppressed understory species. For individual trees of all species, the upper canopy had a larger proportion of solar equivalent foliage than the lower canopy. Light compensation points at both the leaf and whole-tree level were defined according to leaf or tree position, size and structure. I conclude that optimization of A(s) for forest stands may be used as a basis for determining thinning schedules and evaluating tree survival after damage to tree crowns by various factors.

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Effects of elevated CO(2) concentration and nutrition on net photosynthesis, stomatal conductance and needle respiration of field-grown Norway spruce trees.

To study the effects of elevated CO(2) on gas exchange, nonstructural carbohydrate and nutrient concentrations in current-year foliage of 30-year-old Norway spruce (Picea abies (L.) Karst.) trees, branches were enclosed in ventilated, transparent plastic bags and flushed with ambient air (mean 370 &mgr;mol CO(2) mol(-1); control) or ambient air + 340 &mgr;mol CO(2) mol(-1) (elevated CO(2)) during two growing seasons. One branch bag was installed on each of 24 selected trees from control and fertilized plots. To reduce the effect of variation among trees, results from each treated branch were compared with those from a control branch on the same whorl of the same tree. Elevated CO(2) increased rates of light-saturated photosynthesis on average by 55% when measured at the treatment CO(2) concentration. The increase was larger in shoots with high needle nitrogen concentrations than in shoots with low needle nitrogen concentrations. However, shoots grown in elevated CO(2) showed a decrease in photosynthetic capacity compared with shoots grown in ambient CO(2). When measured at the internal CO(2) concentration of 200 &mgr;mol CO(2) mol(-1), photosynthetic rates of branches in the elevated CO(2) treatments were reduced by 8 to 32%. The elevated CO(2) treatment caused a 9 to 20% reduction in carboxylation efficiency and an 18% increase in respiration rates. In response to elevated CO(2), starch, fructose and glucose concentrations in the needles increased on average 33%, whereas concentrations of potassium, nitrogen, phosphorus, magnesium and boron decreased. Needle nitrogen concentrations explained 50-60% of the variation in photosynthesis and CO(2) acclimation was greater at low nitrogen concentrations than at high nitrogen concentrations. We conclude that the enhanced photosynthetic rates found in shoots exposed to elevated CO(2) increased carbohydrate concentrations, which may have a negative feedback on the photosynthetic apparatus and stimulate cyanide-resistant respiration. We also infer that the decrease in nutrient concentrations of needles exposed to elevated CO(2) was the result of retranslocation of nutrients to other parts of the branch or tree.

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Long-term photosynthetic acclimation to increased atmospheric CO(2) concentration in young birch (Betula pendula) trees.

To study the long-term response of photosynthesis to elevated atmospheric CO(2) concentration in silver birch (Betula pendula Roth.), 18 trees were grown in the field in open-top chambers supplied with 350 or 700 &mgr;mol mol(-1) CO(2) for four consecutive growing seasons. Maximum photosynthetic rates, stomatal conductance and CO(2) response curves were measured over the fourth growing season with a portable photosynthesis system. The photosynthesis model developed by Farquhar et al. (1980) was fitted to the CO(2) response curves. Chlorophyll, soluble proteins, total nonstructural carbohydrates, nitrogen and Rubisco activity were determined monthly. Elevated CO(2) concentration stimulated photosynthesis by 33% on average over the fourth growing season. However, comparison of maximum photosynthetic rates at the same CO(2) concentration (350 or 700 &mgr;mol mol(-1)) revealed that the photosynthetic capacity of trees grown in an elevated CO(2) concentration was reduced. Analysis of the response curves showed that acclimation to elevated CO(2) concentration involved decreases in carboxylation efficiency and RuBP regeneration capacity. No clear evidence for a redistribution of nitrogen within the leaf was observed. Down-regulation of photosynthesis increased as the growing season progressed and appeared to be related to the source-sink balance of the trees. Analysis of the main leaf components revealed that the reduction in photosynthetic capacity was accompanied by an accumulation of starch in leaves (100%), which was probably responsible for the reduction in Rubisco activity (27%) and to a lesser extent for reductions in other photosynthetic components: chlorophyll (10%), soluble protein (9%), and N concentrations (12%) expressed on an area basis. Despite a 21% reduction in stomatal conductance in response to the elevated CO(2) treatment, stomatal limitation was significantly less in the elevated, than in the ambient, CO(2) treatment. Thus, after four growing seasons exposed to an elevated CO(2) concentration in the field, the trees maintained increased photosynthetic rates, although their photosynthetic capacity was reduced compared with trees grown in ambient CO(2).

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Photosynthetic adjustment in field-grown ponderosa pine trees after six years of exposure to elevated CO(2).

Photosynthesis of tree seedlings is generally enhanced during short-term exposure to elevated atmospheric CO(2), but longer-term photosynthetic responses are often more variable because they are affected by morphological, biochemical and physiological feedback mechanisms that regulate carbon assimilation to meet sink demand. To examine biochemical and morphological factors that might regulate the long-term photosynthetic response of field-grown trees to elevated CO(2), we grew ponderosa pine (Pinus ponderosa Dougl. ex Laws.) trees in open-top chambers for six years in native soil at ambient CO(2) (35 Pa) and elevated CO(2) (70 Pa) at a site near Placerville, CA. Trees were well watered and exposed to natural light and ambient temperature. At the end of the sixth growing season at elevated CO(2), net photosynthesis was enhanced 53%, despite reductions in photosynthetic capacity. The positive net photosynthetic response to elevated CO(2) reflected greater relative increases in Rubisco sensitivity compared with the decreases resulting from biochemical adjustments. Analyses of net photosynthetic rate versus internal CO(2) partial pressure curves indicated that reductions in photosynthetic capacity in response to elevated CO(2) were the result of significant reductions in maximum photosynthetic rate (20%), Rubisco carboxylation capacity (36%), and electron transport capacity (21%). Decreased photosynthetic capacity was accompanied by reductions in various photosynthetic components, including total chlorophyll (24%), Rubisco protein content (38%), and mass-based leaf nitrogen concentration (14%). Net photosynthesis was unaffected by morphological adjustments because there was no change in leaf mass per unit area at elevated CO(2). An apparent positive response of photosynthetic adjustment in the elevated CO(2) treatment was the redistribution of N within the photosynthetic system to balance Rubisco carboxylation and electron transport capacities. We conclude that trees, without apparent limitations to root growth, may exhibit photosynthetic adjustment responses in the field after long-term exposure to elevated CO(2).

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Parameterization and testing of a biochemically based photosynthesis model for walnut (Juglans regia) trees and seedlings.

The biochemically based leaf photosynthesis model proposed by Farquhar et al. (1980) and the stomatal conductance model proposed by Jarvis (1976) were parameterized for walnut. Responses of photosynthesis to CO(2) and irradiance were used to determine the key parameters of the photosynthesis model. Concurrently, stomatal conductance responses to leaf irradiance (Q), leaf temperature (T(l)), water vapor pressure deficit at the leaf surface (D), and air CO(2) concentration at the leaf surface (C(s)) were used to parameterize the stomatal conductance model. To test the generality of the model parameters, measurements were made on leaves from a 20-year-old tree growing in the field, and from sunlit and shaded greenhouse-grown seedlings. The three key parameters of the photosynthesis model (maximum carboxylation rate V(cmax), electron transport capacity J(max), and dark respiration rate R(d)) and the key parameter of the conductance model (reference stomatal conductance, g(sref)) were linearly correlated with the amount of leaf nitrogen per unit leaf area. Unique relationships could be used to describe nitrogen effects on these parameters for leaves from both the tree and the seedlings. Our data allowed separation of the effects of increasing total photosynthetic apparatus per unit leaf area from the effects of partitioning nitrogen among different pools of this apparatus for foliage acclimation to leaf irradiance. Strong correlations were found between stomatal conductance g(s) and Q, D and C(s), whereas the relationship between g(s) and T(l) was weak. Based on these parameterizations, the model adequately predicted leaf photosynthesis and stomatal conductance when tested with an independent set of data obtained for the tree and seedlings. Total light-driven electron flows derived from chlorophyll fluorescence data obtained at different leaf temperatures were consistent with values computed by the model. The model was also tested with branch bag data acquired from a three-year-old potted walnut tree. Despite a relatively large variance between observed and simulated values, the model predicted stomatal conductance and photosynthesis reasonably well at the branch scale. The results indicate that the photosynthesis-conductance model developed here is robust and can be applied to walnut trees and seedlings under various environmental conditions where water is non-limiting.

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Transpiration and water relations of poplar trees growing close to the water table.

Sap flow was measured on five branches of two poplar (Populus trichocarpa Torr. & A. Gray x P. tacamahaca L.) trees from June to September 1994 in the south of England with stem-surface, heat balance gauges, and was scaled up to estimate transpiration from single trees on the basis of leaf area. On six days, stomatal conductance and plant water potential were measured simultaneously with a porometer and pressure chamber, respectively. The effects of solar radiation (S), vapor pressure deficit (D) and stomatal conductance on transpiration were evaluated. Sap flow per unit leaf area (F(a)) was closely related to the time course of demand attributable to S and D throughout the season, and only slightly affected by the water content of the top 120 cm of soil. Although F(a) increased linearly at low values of D, it showed a plateau with increases in D above 1.2 kPa. The canopy coupling coefficient (1 - Omega) ranged from 0.48 to 0.78 with a mean of 0.65 +/- 0.01, indicating that transpiration was controlled more by stomatal conductance than by incident radiation. The seasonal pattern of tree water loss followed potential evaporation with a peak in late June or early July. On bright days, daily transpiration over the projected crown area was 3.6 mm early in the season, 3.8 mm in mid-season, and 2.7 mm late in the season. The water balance of the system indicated that poplar trees took 15-60% of water transpired from groundwater, with the proportion increasing as the soil in the unsaturated zone dried out. Access to the water table resulted in high predawn water potentials throughout the season. Estimated hydraulic resistance to water flow in the soil-tree system was in the range of 1.5 to 1.93 x 10(6) MPa s m(-3).

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Physiographic, stand, and environmental effects on individual tree growth and growth efficiency in subalpine forests.

Annual volume growth of subalpine trees in the central Rocky Mountains was studied in relation to site and stand conditions. Growth of individual trees was most strongly influenced by estimated potential absorbed radiation, which varied with physiographic conditions and tree leaf area. Growth efficiency was estimated by the ratio of annual volume growth to potential radiation absorption by the crown. Growth efficiency was higher in young lodgepole pine (Pinus contorta var. latifolia Engelm.) than in Engelmann spruce (Picea engelmannii Parry ex Engelm.) or subalpine fir (Abies lasiocarpa (Hook.) Nutt.). In all species, growth efficiency declined sharply with age, and suppressed and overtopped trees had growth efficiencies equal to the highest efficiencies observed for dominant/codominant or intermediate trees. Lodgepole pine growth was most responsive to site and stand variables, Engelmann spruce was intermediate, and subalpine fir was rather unresponsive.

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Spatial variations in xylem sap flux density in the trunk of orchard-grown, mature mango trees under changing soil water conditions.

Circumferential and radial variations in xylem sap flux density in trunks of 13-year-old mango (Mangifera indica L.) trees were investigated with Granier sap flow sensor probes under limiting and non-limiting soil water conditions. Under non-limiting soil water conditions, circumferential variation was substantial, but there was no apparent relationship between sap flux density and aspect (i.e., the radial position of the sensor probes on the trunk relative to the compass). Hourly sap flux densities over 24 hours at different aspects were highly pair-wise correlated. The relationships between different aspects were constant during well-watered periods but highly variable under changing soil water conditions. Sap flux density showed marked radial variation within the trunk and a substantial flux was observed at the center of the trunk. For each selected aspect on each tree, changes in sap flux densities over time at different depths were closely correlated, so flux at a particular depth could be extrapolated as a multiple of flux from 0 to 2 cm beneath the cambium. However, depth profiles of sap flux density differed between trees and even between aspects within a tree, and also varied in an unpredictable manner as soil water conditions changed. Nevertheless, over a period of non-limiting soil water conditions, depth profiles remained relatively constant. Based on the depth profiles obtained during these periods, a method is described for calculating total sap flow in a mango tree from sap flux density at 0-2 cm beneath the cambium. Total daily sap flows obtained were consistent with water use estimated from soil water balance.

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