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.     

Prey–predator mutualism in a tritrophic system on a camphor tree

We report the discovery of a mutualistic system encompassing prey–predator interactions. A domatium is a small space in a vein axil on the underside of leaves of woody angiosperms. Cinnamomum camphora Linn. has domatia that harbor a microphytophagous eriophyid mite (sp. 1). We previously reported that a predatory mite, Euseius sojaensis (Ehara), depends on this eriophyid mite as food. We revealed that E. sojaensis also preyed upon another eriophyid mite (sp. 2) that induces galls on leaves, and that the mean area of C. camphora leaves with galls was usually less than half that of leaves without galls. We experimentally tested the effect of E. sojaensis on galls, and confirmed that the presence of E. sojaensis reduced gall induction. Therefore, C. camphora, eriophyid mite sp. 1, and E. sojaensis comprise a mutualistic system, in spite of the prey–predator interactions among them. The conventional concept of mutualism does not apply to such prey–predator interactions, so we defined them as systematic mutualism. Here, the system consists of three trophic levels, and individuals that constitute this system benefit from the other species that constitute this system.     

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.     

Masting in a temperate tree: Evidence for environmental prediction?

Many plant species produce large fruit crops in some years and then produce few or no fruits in others. Synchronous, inter‐annual variation in plant reproduction is known as ‘masting’ and its adaptive significance has yet to be fully resolved. For 8 consecutive years, I quantified every fruit produced by 22 females of a New Zealand tree species (Dysoxylum spectabile), which has an unusual habit of taking a full calendar year to mature fruits after flowering. Fruit production varied strongly among years and was tightly synchronized among trees. Annual variability in fruit production declined with total reproductive output, indicating trees with lower fecundity exhibited a stronger tendency to mast. Although unrelated to temperature, annual fruit production was positively related to precipitation during annual periods of fruit development, and negatively related to fruit production in the previous year. Seedlings had higher rates of survivorship in a wet, high‐seed year than in a dry, low‐seed year, suggesting that seedlings might be drought sensitive. Therefore, D. spectabile produced large fruit crops during periods of high rainfall prior to fruit maturation, which may enhance survivorship of drought‐intolerant seeds. Results were inconsistent with several hypotheses that are widely believed to be the most likely explanations for masting. Instead, results were consistent with the environmental prediction hypothesis, suggesting that this hypothesis may be more important than previously appreciated.     

Foliar chemistry and tree ring δ13C of Pinus densiflora in relation to tree growth along a soil pH gradient

Background and aims

Soil acidification is known to be one of the constraints of tree growth; however, it is unclear how it affects tree growth at photosynthesis level (i.e., through affecting stomatal conductance vs. carboxylation rate) during the growth of trees. This paper studied the effects of soil acidification on Pinus densiflora foliar chemistry and tree ring C isotope ratio (¹³C/¹²C, expressed as δ¹³C) and their relationship with tree growth.

Methods

Tree growth (diameter, annual growth ring area, and root biomass), soil chemistry (pH, mineral N, and exchangeable Ca and Al), foliage chemistry (N, Ca/Al, and δ¹³C), and tree ring δ¹³C in P. densiflora stands along a soil pH gradient (from 4.38 to 4.83, n?=?9) in southern Korea were investigated.

Results

Overall, trees with relatively poor growth under more acidic soil conditions (low pH and Ca/Al) had lower values of foliar N concentration and δ¹³C and tree ring δ¹³C, suggesting that restricted N uptake under more acidic soil conditions caused N limitation for photosynthesis, leading to poor tree growth. In addition, relationships between mean annual area increment and carbon isotope discrimination of tree rings at five-yr intervals from 1968 to 2007 revealed that the impact of soil acidification on tree growth became severer during the last 15 yrs as negative correlations between them became significant after 1993.

Conclusions

Reduced N uptake under acidic soil conditions resulted in lower radial growth of P. densiflora via non-stomatal limitation of photosynthesis.     

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.     

Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

Background

Specialised leaf-eating is almost universally regarded as the ancestral state of all ruminants, yet little evidence can be cited in support of this assumption, apart from the fact that all early ruminants had low crowned cheek teeth. Instead, recent years have seen the emergence evidence contradicting the conventional view that low tooth crowns always indicate leaf-eating and high tooth crowns grass-eating.

Results

Here we report the results of two independent palaeodietary reconstructions for one of the earliest deer, Procervulus ginsburgi from the Early Miocene of Spain, suggesting that despite having lower tooth crowns than any living ruminant, this species included a significant proportion of grass in its diet.

Conclusion

The phylogenetic distribution of feeding styles strongly supports that leaf-grass mixed feeding was the original feeding style of deer, and that later dietary specialization on leaves or grass occurred independently in several lineages. Evidence for other ruminant clades suggests that facultative mixed feeding may in fact have been the primitive dietary state of the Ruminantia, which would have been morphologically expressed only under specific environmental factors.     

Populus: arabidopsis for forestry. Do we need a model tree?

Trees are used to produce a variety of wood-based products including timber, pulp and paper. More recently, their use as a source of renewable energy has also been highlighted, as has their value for carbon mitigation within the Kyoto Protocol. Relative to food crops, the domestication of trees has only just begun; the long generation time and complex nature of juvenile and mature growth forms are contributory factors. To accelerate domestication, and to understand further some of the unique processes that occur in woody plants such as dormancy and secondary wood formation, a 'model' tree is needed. Here it is argued that Populus is rapidly becoming accepted as the 'model' woody plant and that such a 'model' tree is necessary to complement the genetic resource being developed in arabidopsis. The genus Populus (poplars, cottonwoods and aspens) contains approx. 30 species of woody plant, all found in the Northern hemisphere and exhibiting some of the fastest growth rates observed in temperate trees. Populus is fulfilling the 'model' role for a number of reasons. First, and most important, is the very recent commitment to sequence the Populus genome, a project initiated in February 2002. This will be the first woody plant to be sequenced. Other reasons include the relatively small genome size (450-550 Mbp) of Populus, the large number of molecular genetic maps and the ease of genetic transformation. Populus may also be propagated vegetatively, making mapping populations immortal and facilitating the production of large amounts of clonal material for experimentation. Hybridization occurs routinely and, in these respects, Populus has many similarities to arabidopsis. However, Populus also differs from arabidopsis in many respects, including being dioecious, which makes selfing and back-cross manipulations impossible. The long time-to-flower is also a limitation, whilst physiological and biochemical experiments are more readily conducted in Populus compared with the small-statured arabidopsis. Recent advances in the development of large expressed sequence tagged collections, microarray analysis and the free distribution of mapping pedigrees for quantitative trait loci analysis secure Populus as the ideal subject for further exploitation by a wide range of scientists including breeders, physiologists, biochemists and molecular biologists. In addition, and in contrast to other model plants, the genus Populus also has genuine commercial value as a tree for timber, plywood, pulp and paper.     

How do deer affect tree seedlings on a dwarf bamboo-dominated forest floor?

A field experiment was conducted in Mt. Ôdaigahara, west-central Japan, to reveal the effects of two herbivores, Sika deer (Cervus nippon) and mice (Apodemus spp.), on the seedlings of five cohorts of three tree species, Abies homolepis, Fraxinus lanuginosa f. serrata and Fagus crenata. The forest floor of the study site was covered with dwarf bamboo, Sasa nipponica, which would also affect the seedlings. Eight combinations of three treatments were set: exclusion of deer, exclusion of mice and removal of dwarf bamboo. Deer were expected to affect the seedlings not only negatively by foraging but also positively by browsing dwarf bamboo that overshadows seedlings. The survival of these cohorts was analyzed by survival analysis and the differences in their survival between the treatments were investigated. The results of the experiment showed that: (1) exclusion of deer increased the aboveground biomass of dwarf bamboo and made it more difficult for seedlings to survive under the regenerated dwarf bamboo stand, and (2) deer negatively affected the seedlings, but they had positive, indirect effects in some cohorts by decreasing the aboveground biomass of dwarf bamboo. However, such effects were not detected in some cohorts which were affected excessively by deer or dwarf bamboo. No clear results on the effect of mice on seedlings were obtained. We conclude that a positive, indirect effect of deer on seedling survivorship would be observable when the magnitude of a positive, indirect effect caused by decreasing dwarf bamboo is larger than that of a negative, direct effect of deer.     

Can germination explain the distribution of tree species in a savanna wetland?

The relationship between seed germination and ecological niche is determined by matching germination characteristics with environmental features. In this study, we selected tree species occurring in the largest savanna wetland in South America – the Pantanal. Very few species are endemic or exclusively found in savanna wetlands, and the majority of tree species occurring in the Pantanal are also found in the neighbouring Brazilian Cerrado, a drier vegetation type that does not flood. We investigated the relationship between germination characteristics and occurrence of savanna trees in wetlands testing the hypothesis that such seeds are tolerant to flooding. We also addressed the question of whether seed tolerance to flood, assessed by survival analysis, explains tree distribution along a gradient of flooding intensity. In this flooding gradient, widely distributed species are those that occur in areas subjected to low as well as to high flooding intensity whereas restricted distributed species are those that occur only in areas subjected to a low level of flood. Seeds from tree species occurring in areas subjected to different flooding intensities were collected. Seed tolerance and germination during and after both one and two months of simulated flood were evaluated. Our results show that seeds of most of the studied savanna species tolerated submergence, which helps to explain their occurrence and wide distribution in wetlands. Nevertheless, germination behaviour checked by survival functions (i.e. how germination is distributed over time) partially explained tree species distribution along a flooding gradient. We conclude that seed tolerance to flooding is one of the components of the regeneration niche that determines tree occurrence and distribution at the regional scale, from savanna to wetland, but not at a local scale along a flooding gradient.     

In vitro somatic embryogenesis ofDalbergia sissoo Roxb. —a multipurpose timber-yielding tree

Somatic embryogenesis was achieved in callus cultures dervied from 40-day-old semimature zygotic embryos ofDalbergia sissoo on semi-solid Murashige and Skoog (MS) salts and vitamins supplemented with 0.46–1.16 M kinetin, 6.78–9.04 M 2,4-dichlorophenoxy acetic acid (2,4-D) and 30 g/1 sucrose. Somatic embryos proliferated rapidly by secondary somatic embryogenesis after transfer to half-strength basal MS medium supplemented with 0.46-1.16 M kinetin and 6.78–9.04 M 2,4-D with 2% (w/v) sucrose. The light-green somatic embryos germinated on half-strength MS salts and vitamins supplemented with 0.5 mg/1 abscisic acid and 2% (w/v) sucrose. The developmental stages of somatic embryogenesis were studied by light and scanning electron microscopy.Abbreviations ABA Abscisic acid - BA 6-benzyladenine - Kn kinetin - 2,4-D 2,4-dichlorophenoxyacetic acid - NAA 1-naphthaleneacetic acid - MS Murashige and Skoog (1962) basal medium     

Phylogenetic information complexity: Is testing a tree easier than finding it?

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following question: Is the amount of sequence data required to accurately reconstruct a tree significantly more than the amount required to test whether or not a candidate tree was the ‘true’ tree? By ‘significantly’, we mean that the two quantities do not behave the same way as a function of the number of species being considered. We prove that, for a certain type of model, the amount of information required is not significantly different; while for another type of model, the information required to test a tree is independent of the number of leaves, while that required to reconstruct it grows with this number. Our results combine probabilistic and combinatorial arguments.     

How many species of host-specific insects feed on a species of tropical tree?

The assumptions on the host specificity of beetles that led Terry Erwin to suggest that there may be over 30 million arthropod species were tested for 10 species of trees and their insect associates at a rainforest site in Papua New Guinea. The data included 391 species and 4696 individuals of herbivorous beetles collected during a one year period using hand collecting, beating, branch clipping, intercept flight traps and pyrethrum knockdown. Insect host specificity was assessed by feeding trials in captivity. The data suggest that between 23 and 37 monophagous leaf-feeding species are most likely to be present in this system, whereas Erwin's method yields an estimate of 138 monophagous species. The major factors responsible for the discrepancy between our observations and Erwin's assumptions appears to be (a) the importance of transient species; (b) the insect fauna that is shared among tree species; (c) some generalist wood-eating species may inflate the apparent species richness of leaf-feeding beetles; and (d) the proportion of specialist species varies significantly among tree species. We conclude that studies reporting the proportion of specialist insect herbivores associated with particular tropical tree species will yield only a portion of the information needed to estimate global arthropod species richness, but may be useful for elucidating certain aspects of food-web ecology in tropical rain forests.     

Soil moisture redistribution as a mechanism of facilitation in savanna tree–shrub clusters

Plant–soil water relations were examined in the context of a selective removal study conducted in tree–shrub communities occupying different but contiguous soil types (small discrete clusters on shallow, duplex soils versus larger, extensive groves on deep, sandy soils) in a subtropical savanna parkland. We (1) tested for the occurrence of soil moisture redistribution by hydraulic lift (HL), (2) determined the influence of edaphic factors on HL, and (3) evaluated the significance of HL for overstory tree–understory shrub interactions. Diel cycling and nocturnal increases in soil water potential (Ψ_soil), characteristic signatures of HL, occurred intermittently throughout an annual growth cycle in both communities over a range of moisture levels (Ψ_soil=−0.5 to −6.0 MPa) but only when soils were distinctly stratified with depth (dry surface/wet deep soil layers). The magnitude of mean (±SE) diel fluctuations in Ψ_soil (0.19±0.01 MPa) did not differ on the two community types, though HL occurred more frequently in groves (deep soils) than clusters (shallow soils). Selective removal of either Prosopis glandulosa overstory or mixed-species shrub understory reduced the frequency of HL, indicating that Prosopis and at least one other woody species was conducting HL. For Zanthoxylum fagara, a shallow-rooted understory shrub, Prosopis removal from clusters decreased leaf water potential (Ψ_leaf) and net CO₂ exchange (A) during periods of HL. In contrast, overstory removal had neutral to positive effects on more deeply-rooted shrub species (Berberis trifoliolata and Condalia hookeri). Removal of the shrub understory in groves increased A in the overstory Prosopis. Results indicate the following: (a) HL is common but temporally dynamic in these savanna tree–shrub communities; (b) edaphic factors influencing the degree of overstory/understory development, rooting patterns and soil moisture distribution influence HL; (c) net interactions between overstory and understory elements in these woody patches can be positive, negative and neutral over an annual cycle, and (d) Prosopis-mediated HL is an important mechanism of faciliation for some, but not all, understory shrubs.     

Carbon uptake and respiration in above-ground parts of a Larix decidua × leptolepis tree

Summary Shade needles of hybrid larch (Larix decidua × leptolepis) had the same rates of photosynthesis as sun needles per dry weight and nitrogen, and a similar leaf conductance under conditions of light saturation at ambient CO₂ (A_max). However, on an area basis, A_max and specific leaf weight were lower in shade than in sun needles. Stomata of sun needles limited CO₂ uptake at light saturation by about 20%, but under natural conditions of light in the shade crown, shade needles operated in a range of saturating internal CO₂ without stomatal limitation of CO₂ uptake. In both needle types, stomata responded similarly to changes in light, but shade needles were more sensitive to changes in vapor pressure deficit than sun needles. Despite a high photosynthetic capacity, the ambient light conditions reduced the mean daily (in summer) and annual carbon gain of shade needles to less than 50% of that in sun needles. In sun needles, the transpiration per carbon gain was about 220 mol mol^–1 on an annual basis. The carbon budget of branches was determined from the photosynthetic rate, the needle biomass and respiration, the latter of which was (per growth and on a carbon basis) 1.6 mol mol^–1 year^–1 in branch and stem wood. In shade branches carbon gains exceeded carbon costs (growth + respiration) by only a factor of 1.6 compared with 3.5 in sun branches. The carbon balance of sun branches was 5 times higher per needle biomass of a branch or 9 times higher on a branch length basis than shade branches. The shade foliage (including the shaded near-stem sun foliage) only contributed approximately 23% to the total annual carbon gain of the tree.     

In vitro regeneration of plantlets in Fagraea fragrans Roxb. — a tropical tree

Different vegetative parts of Fagraea fragrans Roxb., a valuable timber tree of South East Asia, were used as explants in in vitro studies.Nodal segments showed the best growth response as numerous adventitious shoots were regenerated in MS medium supplemented with Benzyl adenine (BA, 8.8 um) and 2,4-dichlorophenoxyacetic acid (2,4-D, 0.5 um). Shoot buds also developed from the leaf and root segments that were subcultured. The detailed process of callus growth and differentiation leading to the formation of whole plantlets is described. Uniform plantlets obtained could be transplanted successfully in soil.     

How does forest landscape structure explain tree species richness in a Mediterranean context?

Although the strong relationship between vegetation and climatic factors is widely accepted, other landscape composition and configuration characteristics could be significantly related with vegetation diversity patterns at different scales. Variation partitioning was conducted in order to analyse to what degree forest landscape structure, compared to other spatial and environmental factors, explained forest tree species richness in 278 UTM 10 × 10 km cells in the Mediterranean region of Catalonia (NE Spain). Tree species richness variation was decomposed through linear regression into three groups of explanatory variables: forest landscape (composition and configuration), environmental (topography and climate) and spatial variables. Additionally, the forest landscape characteristics which significantly contributed to explain richness variation were identified through a multiple regression model. About 60% of tree species richness variation was explained by the whole set of variables, while their joint effects explained nearly 28%. Forest landscape variables were those with a greater pure explanatory power for tree species richness (about 15% of total variation), much larger than the pure effect of environmental or spatial variables (about 2% each). Forest canopy cover, forest area and land cover diversity were the most significant composition variables in the regression model. Landscape configuration metrics had a minor effect on forest tree species richness, with the exception of some shape complexity indices, as indicators of land use intensity and edge effects. Our results highlight the importance of considering the forest landscape structure in order to understand the distribution of vegetation diversity in strongly human-modified regions like the Mediterranean.     

Birds girdling activity on exotic tree species as a form of adaptive behavior?

Four tree species in the Kostelec n. ?. l. arboretum (Czech Republic) have been repeatedly damaged by Dendrocopos medius. The unique aspect of this otherwise common behavior called girdling consists in regularly visiting the same trees every spring, although there are more than 1.200 tree species within the arboretum. We monitored transpiration, leaf phenology and the chemical composition of the xylem sap of girdled and nongirdled trees. Spectral analysis revealed slightly higher amounts of sugars, especially saccharose, in Cladrastis Raf. as the most regularly girdled tree among other conditions, comparing girdled to non-girdled trees. Higher transpiration rates were not confirmed in connection with girdling—quite the opposite—Cladrastis Raf. as the most highly favored tree for girdling showed the lowest transpiration rates (in average 6 kg water per day within spring months) compared to other non-girdled trees. We presume that the birds do not choose a particular tree on the basis of any visible or chemical traits but they examine many trees within their territory. Afterwards they probably remember the position of trees whose xylem sap starts to flow early in the spring compared to other trees, as their transpiration stream is enriched with sweet organic substances that represent an advantage for the forthcoming nesting period.     

Do understorey or overstorey traits drive tree encroachment on a drained raised bog?

• One of the most important threats to peatland ecosystems is drainage, resulting in encroachment of woody species. Our main aim was to check which features – overstorey or understorey vegetation – are more important for shaping the seedling bank of pioneer trees colonising peatlands (Pinus sylvestris and Betula pubescens). We hypothesised that tree stand parameters will be more important predictors of natural regeneration density than understorey vegetation parameters, and the former will be negatively correlated with species diversity and richness and also with functional richness and functional dispersion, which indicate a high level of habitat filtering.
• The study was conducted in the ‘Zielone Bagna’ nature reserve (NW Poland). We assessed the structure of tree stands and natural regeneration (of B. pubescens and P. sylvestris) and vegetation species composition. Random forest and DCA were applied to assess relationships between variables studied.
• Understorey vegetation traits affected tree seedling density (up to 0.5‐m height) more than tree stand traits. Density of older seedlings depended more on tree stand traits. We did not find statistically significant relationships between natural regeneration densities and functional diversity components, except for functional richness, which was positively correlated with density of the youngest tree seedlings.
• Seedling densities were higher in plots with lower functional dispersion and functional divergence, which indicated that habitat filtering is more important than competition. Presence of an abundant seedling bank is crucial for the process of woody species encroachment on drained peatlands, thus its dynamics should be monitored in protected areas.