What genes make a tree a tree?

Woody growth is evolutionarily ancient, yet has been gained and lost multiple times in plant evolution and is readily enhanced or minimized in eudicot speciation. New molecular genetic and genomic studies in Populus and Arabidopsis that are defining the genes responsible for cambium function and woody growth suggest that the genes regulating woody growth are not unique to woody plants. Surprisingly, key genetic mechanisms originally characterized as regulating the meristematic cells of the shoot apical meristem are also expressed in the vascular cambium during woody growth. This has important implications for the development of Populus as a model species and illustrates why forest trees constitute a contrived group of plants that have more in common with herbaceous relatives than we foresters like to admit.     

A spatial model of tree α-diversity and tree density for the Amazon

Large-scale patterns of Amazonian biodiversity have until now been obscured by a sparse and scattered inventory record. Here we present the first comprehensive spatial model of tree -diversity and tree density in Amazonian rainforests, based on the largest-yet compilation of forest inventories and bolstered by a spatial interpolation technique that allows us to estimate diversity and density in areas that have never been inventoried. These data were then compared to continent-wide patterns of rainfall seasonality. We find that dry season length, while only weakly correlated with average tree -diversity, is a strong predictor of tree density and of maximum tree -diversity. The most diverse forests for any given DSL are concentrated in a narrow latitudinal band just south of the equator, while the least diverse forests for any given DSL are found in the Guayana Shield and Amazonian Bolivia. Denser forests are more diverse than sparser forests, even when we used a measure of diversity that corrects for sample size. We propose that rainfall seasonality regulates tree -diversity and tree density by affecting shade tolerance and subsequently the number of different functional types of trees that can persist in an area.     

Drought limitation on tree growth at the Northern Hemisphere’s highest tree line

The alpine tree line is generally assumed to be controlled by low temperatures, and thus to be experiencing an upward shift under global warming. As global temperatures rise, tree growth at the tree line could either increase if temperature is the limiting factor or decrease if a warming-induced loss of moisture limits growth. Here, we use dendrochronological techniques to understand the abiotic drivers of the Northern Hemisphere’s highest tree line ecotones on the southern Tibetan Plateau (TP). Ring-width measurements from three juniper sites between 4680 and 4900 m asl were significantly and negatively correlated with May-June-July evapotranspiration (ET₀), and positively correlated with relative humidity and other moisture-related meteorological variables. At the same time, ring widths were negatively correlated with temperature means and sunshine rates. Our results highlight the common sensitivity of tree growth to moisture variations despite the differential growth trends occurring since 1850 (end of the Industrial Revolution) at the three tree line ecotones. These findings indicate that low temperatures may not be the sole driving force behind tree growth and the range dynamics of alpine tree lines. Tree lines in the dry parts of the TP and possibly also beyond are likely to retreat rather than to advance in a warmer world due to water limitations.     

Is there a star tree paradox?

Concerns have been raised that posterior probabilities on phylogenetic trees can be unreliable when the true tree is unresolved or has very short internal branches, because existing methods for Bayesian phylogenetic analysis do not explicitly evaluate unresolved trees. Two recent papers have proposed that evaluating only resolved trees results in a "star tree paradox": when the true tree is unresolved or close to it, posterior probabilities were predicted to become increasingly unpredictable as sequence length grows, resulting in inflated confidence in one resolved tree or another and an increasing risk of false-positive inferences. Here we show that this is not the case; existing Bayesian methods do not lead to an inflation of statistical confidence, provided the evolutionary model is correct and uninformative priors are assumed. Posterior probabilities do not become increasingly unpredictable with increasing sequence length, and they exhibit conservative type I error rates, leading to a low rate of false-positive inferences. With infinite data, posterior probabilities give equal support for all resolved trees, and the rate of false inferences falls to zero. We conclude that there is no star tree paradox caused by not sampling unresolved trees.     

Does predation contribute to tree diversity?

Seed and seedling predation may differentially affect competitively superior tree species to increase the relative recruitment success of poor competitors and contribute to the coexistence of tree species. We examined the effect of seed and seedling predation on the seedling recruitment of three tree species, Acer rubrum (red maple), Liriodendron tulipifera (yellow poplar), and Quercus rubra (northern red oak), over three years by manipulating seed and seedling exposure to predators under contrasting microsite conditions of shrub cover, leaf litter, and overstory canopy. Species rankings of seedling emergence were constant across microsites, regardless of exposure to seed predators, but varied across years. A. rubrum had the highest emergence probabilities across microsites in 1997, but Q. rubra had the highest emergence probabilities in 1999. Predators decreased seedling survival uniformly across species, but did not affect relative growth rates (RGRs). Q. rubra had the highest seedling survivorship across microsites, while L. tulipifera had the highest RGRs. Our results suggest that annual variability in recruitment success contributes more to seedling diversity than differential predation across microsites. We synthesized our results from separate seedling emergence and survival experiments to project seedling bank composition. With equal fecundity assumed across species, Q. rubra dominated the seedling bank, capturing 90% of the regeneration sites on average, followed by A. rubrum (8% of sites) and L. tulipifera (2% of sites). When seed abundance was weighted by species-specific fecundity, seedling bank composition was more diverse; L. tulipifera captured 62% of the regeneration sites, followed by A. rubrum (21% of sites) and Q. rubra (17% of sites). Tradeoffs between seedling performance and fecundity may promote the diversity of seedling regeneration by increasing the probability of inferior competitors capturing regeneration sites.     

Is the microbial tree of life verificationist?

The field of microbial phylogenetics has questioned the feasibility of using a tree‐like structure to the describe microbial evolution. This debate centres on two main points. First, because microorganisms are able to transfer genes from one to another in zero generations (horizontal gene transfer, or HGT), the use of molecular characters to perform phylogenetic analyses will yield an erroneous topology and HGT clearly makes the evolution of microorganisms non tree‐like. Second, the use of concatenated gene sequences in a total evidence approach to phylogenetic systematics is a verificationist endeavour, the aim of which is to bolster support. However, the goal of the total evidence approach to phylogenetic research is based in the idea of increasing explanatory power over background knowledge through test and corroboration, rather than to bolster support for nodes in a tree. In this context, the testing of phylogenetic data is a falsificationist endeavour that includes the possibility of not rejecting the null hypothesis that there is no tree‐like structure in molecular phylogenetic data. We discuss several tests that aim to test rigorously the hypothesis that a tree of life exists for microorganisms. We also discuss the philosophical ramifications of background knowledge and corroboration in microbial studies that need to be considered when suggesting that HGT confounds the tree of life. © The Willi Hennig Society 2009.     

How the biliary tree maintains immune tolerance?

The liver is a vital organ with distinctive anatomy, histology and heterogeneous cell populations. These characteristics are of particular importance in maintaining immune homeostasis within the liver microenvironments, notably the biliary tree. Cholangiocytes are the first line of defense of the biliary tree against foreign substances, and are equipped to participate through various immunological pathways. Indeed, cholangiocytes protect against pathogens by TLRs-related signaling; maintain tolerance by expression of IRAK-M and PPARγ; limit immune response by inducing apoptosis of leukocytes; present antigen by expressing human leukocyte antigen molecules and costimulatory molecules; recruit leukocytes to the target site by expressing cytokines and chemokines. However, breach of tolerance in the biliary tree results in various cholangiopathies, exemplified by primary biliary cholangitis, primary sclerosing cholangitis and biliary atresia. Lessons learned from immune tolerance of the biliary tree will provide the basis for the development of effective therapeutic approaches against autoimmune biliary tract diseases. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.     

Cutting the forest to see a single tree?

The development of single-molecule tools has significantly impacted the way we think about biochemical processes. Watching a single protein in action allows us to observe kinetic details and rare subpopulations that are hidden in ensemble-averaging techniques. I will discuss here the pros and cons of the single-molecule approach in studying ligand binding in macromolecular systems and how these techniques can be applied to characterize the behavior of large multicomponent biochemical systems.     

��13C signature of tree rings and radial increment of Fagus sylvatica trees as dependent on tree neighborhood and climate

We conducted dendroecological analyses in 80-year-long tree ring chronologies to detect neighborhood effects (competition intensity, species identity) on the δ¹³C signature of tree rings and radial stem increment of Fagus sylvatica trees growing either in monospecific or mixed patches of a temperate forest. We hypothesized that tree ring δ¹³C is a more sensitive indicator of neighborhood effects and the impact of climate variability on growth than is ring width. We found a closer correlation of summer precipitation to δ¹³C than to ring width. While the ring width showed a decline over the test period (1926–2005), the mean curve of δ¹³C increased until the mid of the 1970s, remained high until about 1990, and markedly decreased thereafter. Possible explanations related to ontogeny and environmental change (‘age effect’ due to canopy closure; elevated atmospheric SO₂ concentrations in the 1960s–1980s) are discussed. Beech target trees surrounded by many allospecific trees had a significantly lower mean δ¹³C in the period 1926–1975 than beech with predominantly or exclusively conspecific neighborhood, possibly indicating a more favorable water supply of beech in diverse stands. Contrary to expectation, trees subject to more intense competition by neighboring trees (measured by Hegyi’s competition index) had lower δ¹³C values in their tree rings, which is thought to reflect denser canopies being linked to increased shading. We conclude that tree ring δ¹³C time series represent combined archives of climate variability, stand history and neighborhood effects on tree physiology and growth that may add valuable information to that obtained from conventional tree ring analysis.     

Is tree diversity different in the Southern Hemisphere?

Questions: Is tree diversity higher in the southern hemisphere? Are latitudinal asymmetries in diversity sensitive to sampling effects? Location: 198 forested locales worldwide. Methods: I re‐analysed the Gentry database, which I augmented with an additional survey from New Zealand. Data were used to test whether latitudinal declines in tree diversity differ between the northern and southern hemispheres. Data were also used to test whether hemispheric asymmetries in diversity are sensitive to sampling effects, or geographic variation in tree densities. Results: Area‐based measurements of species diversity are higher in the southern hemisphere. However, southern forests house denser plant populations. After controlling for geographic variation in tree densities, diversity patterns reverse, indicating tree diversity is higher in the northern hemisphere. Conclusions: Latitudinal changes in tree diversity differ between hemispheres. However, the nature of hemispherical asymmetries in species diversity hinges on how diversity is defined, illustrating how different definitions of diversity can yield strikingly different solutions to common ecological problems.     

Biodiversity Realism: Preserving the tree of life

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’.     

The Cajeput tree—A boon and an affliction

The cajeput tree, native from Australia through Burma, is planted in forestry projects, for reclamation of swamps, and as an ornamental in warm climates; often escapes and invades vast areas of low land. The hard wood is durable underground and under water; checks and warps unless slowly seasoned, but is handsome when finished and prized for cabinetwork. The bark, chemically similar to cork, has many uses. Cajeput oil, obtained from the leaves, is in limited pharmaceutical demand, being more costly than oil of eucalyptus. Formerly acclaimed as an “antiseptic” tree, “subduing malarial vapors,” the cajeput has become in Florida a prime respiratory irritant. Since the pollen is not airborne, the irritant factor is apparently the volatile properly. Florida beekeepers, previously in opposition to the spread of the nectar-rich cajeput because of the unpleasant odor and taste of the honey, now have found it valuable for brood-rearing and salable after standing and blending.     

Understanding causes of tree growth response to gap formation: ∆13C-values in tree rings reveal a predominant effect of light

Key message

Carbon isotope ratios in growth rings of a tropical tree species show that treefall gaps stimulate diameter growth mainly through changes in the availability of light and not water. The formation of treefall gaps in closed canopy forests usually entails considerable increases in light and nutrient availability for remaining trees, as well as altered plant water availability, and is considered to play a key role in tree demography. The effects of gaps on tree growth are highly variable and while usually stimulatory they may also include growth reductions. In most studies, the causes of changes in tree growth rates after gap formation remain unknown. We used changes in carbon isotope ¹³C discrimination (Δ¹³C) in annual growth rings to understand growth responses after gap formation of Peltogyne cf. heterophylla, in a moist forest of Northern Bolivia. We compared growth and Δ¹³C of the 7 years before and after gap formation. Forty-two trees of different sizes were studied, half of which grew close (<10 m) to single treefall gaps (gap trees), the other half more than 40 m away from gaps (controls). We found variable responses among gap trees in growth and Δ¹³C. Increased growth was mainly associated with decreased Δ¹³C, suggesting that the growth response was driven by increased light availability, possibly in combination with improved nutrient availability. Most trees showing zero or negative growth change after gap formation had increased Δ¹³C, suggesting that increased water stress did not play a role, but rather that light conditions had not changed much or nutrient availability was insufficient to support increased growth. Combining growth rates with Δ¹³C proved to be a valuable tool to identify the causes of temporal variation in tree growth.     

Do tree species characteristics influence soil respiration in tropical forests? A test based on 16 tree species planted in monospecific plots

The high spatial variability of soil respiration in tropical rainforests is well evaluated, but influences of biotic factors are not clearly understood. This study underlines the influence of tree species characteristics on soil respiration across a 16-monospecific plot design in a tropical plantation of French Guiana. A large variability of soil CO₂ fluxes was observed among plots (i.e. 2.8 to 6.8 μmol m^?2 s^?1) with the ranking being constant across seasons. There were no significant relationships between soil respiration and soil moisture or soil temperature, neither spatially, nor seasonally. The variability of soil respiration was mainly explained by quantitative factors such as leaf litterfall and basal area. Surprisingly, no significant relationship was observed between soil respiration and root biomass. However, the influence of substrate quality was revealed by a strong relationship between soil respiration and litterfall P (and litterfall N, to a lesser extent).     

Patch dynamics integrate mechanisms for savanna tree–grass coexistence

Many mechanisms have been suggested to explain the coexistence of woody species and grasses in savannas. However, evidence from field studies and simulation models has been mixed. Patch dynamics is a potentially unifying mechanism explaining tree–grass coexistence and the natural occurrence of shrub encroachment in arid and semi-arid savannas. A patch-dynamic savanna consists of a spatial mosaic of patches. Each patch maintains a cyclical succession between dominance of woody species and grasses, and the succession of neighbouring patches is temporally asynchronous. Evidence from empirical field studies supports the patch dynamics view of savannas. As a basis for future tests of patch dynamics in savannas, several hypotheses are presented and one is exemplarily examined: at the patch scale, realistically parameterized simulation models have generated cyclical succession between woody and grass dominance. In semi-arid savannas, cyclical successions are driven by precipitation conditions that lead to mass recruitment of shrubs in favourable years and to simultaneous collapse of shrub cohorts in drought years. The spatiotemporal pattern of precipitation events determines the scale of the savanna vegetation mosaic in space and time. In a patch-dynamic savanna, shrub encroachment is a natural, transient phase corresponding to the shrub-dominated phase during the successional cycle. Hence, the most promising management strategy for encroached areas is a large-scale rotation system of rangelands. In conclusion, patch dynamics is a possible scale-explicit mechanism for the explanation of tree–grass coexistence in savannas that integrates most of the coexistence mechanisms proposed thus far for savannas.     

Does tree diversity increase wood production in pine forests?

Recent experimental advances on the positive effect of species richness on ecosystem productivity highlight the need to explore this relationship in communities other than grasslands and using non-synthetic experiments. We investigated whether wood production in forests dominated by Aleppo pine (Pinus halepensis) and Pyrenean Scots pine (Pinus sylvestris) differed between monospecific and mixed forests (2-5 species) using the Ecological and Forest Inventory of Catalonia (IEFC) database which contains biotic and environmental characteristics for 10,644 field plots distributed within a 31,944 km(2) area in Catalonia (NE Spain). We found that in Pyrenean Scots pine forests wood production was not significantly different between monospecific and mixed plots. In contrast, in Aleppo pine forests wood production was greater in mixed plots than in monospecific plots. However, when climate, bedrock types, radiation and successional stage per plot were included in the analysis, species richness was no longer a significant factor. Aleppo pine forests had the highest productivity in plots located in humid climates and on marls and sandstone bedrocks. Climate did not influence wood production in Pyrenean Scots pine forests, but it was highest on sandstone and consolidated alluvial materials. For both pine forests wood production was negatively correlated with successional stage. Radiation did not influence wood production. Our analysis emphasizes the influence of macroenvironmental factors and temporal variation on tree productivity at the regional scale. Well-conducted forest surveys are an excellent source of data to test for the association between diversity and productivity driven by large-scale environmental factors.     

Does Donglan lacquer tree belong to Rhus vernicifera species?

The lacquer trees in Donglan of Guangxi Province, China, were identified totally as the species Rhus succedanea found in Vietnam and Taiwan region, based on the results of pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), an easy and effective method to identify species of trees among those with similar properties. Analyses by IR and NMR, the drying properties, and conventional morphology also confirmed that the Donglan lacquer trees do not belong to Rhus vernicifera, like most trees of the China mainland. Some differences, however, such as the enzymatic activity and the components of the lacquer, were found between the Donglan lacquer and the Vietnam lacquer. The Donglan lacquer has a shorter drying time than the latter.