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.     

The prokaryotic tree of life: past, present... and future?

No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.     

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.     

Dendrometer and intra-annual tree growth: What kind of information can be inferred?

Dendrometer measurements provide time series composed of the rhythm of water storage fluctuations over the year and seasonal tree growth. For slow-growing trees, however, difficulties have been found in the identification of crucial events such as growth onset, stem growth period and cessation, rendering it necessary to define what can be measured and at which time scale. Time scale means the time interval (from one day to one month) at which stem radius variation is extracted. In this study, two conifer species were monitored by an automatic band dendrometer to assess several time scales and analysis approaches. Data were collected from 8 trees of Picea abies (L.) Karst and Larix decidua L., growing at 1020 and 2080 m a.s.l. in the eastern Italian Alps, from 2000 to 2003. Time series of stem radius variation were extracted with different approaches, such as the stem cycle, daily mean and daily maximum. Several approaches can be used, as very similar time series of stem radius variations were produced with high coefficients of correlation among the series. At lower altitude, the approximate onset was identified at the beginning of May with a 10-day time scale, when the distribution of stem radius variation differed from zero. The main growth period, from May to June–July, corresponded mainly with earlywood cell formation. At higher altitude, a time scale of at least 15 days facilitated identification of the main period of stem growth only, corresponding with earlywood cell formation. Even if latewood cells were produced in August at both altitudes, the variability in stem radius changes was higher than the amount of growth in terms of cell-wood production. For a slow-growing species in a cold environment, an understanding of the growth period, assessed with several time scales, is necessary when using time series of stem radius variation to assess growth and climate relationships. The period used for growth and climate analysis should correspond only with the main period of stem growth.     

Leaf defoliation of tropical dry forest tree seedlings – implications for survival and growth

 The effect of herbivory on survival and growth of seedlings of four species, Cedrela odorata, Hymenaea courbaril, Manilkara chicle and Swietenia macrophylla, was studied in secondary dry forests in Guanacaste, Costa Rica. Potted seedlings were planted at two sites in a 2×2 factorial design, combining thinning to increase light levels at the forest floor, and trenching to reduce root competition around the planted seedlings. C. odorata and S. macrophylla were repeatedly severely defoliated by insects, while H. courbaril became less affected. M. chicle did not show any significant signs of defoliation and was not further analysed. Defoliation levels were generally higher in both thinned and trenched treatments, and also positively correlated with larger initial seedlings sizes. Decreased growth rates caused by defoliation were seen in S. macrophylla and C. odorata in the growing season. Defoliation of more than 50% in combination with abiotic factors, particularly drought, were sufficient to contribute to retarded seedling development and increased seedling mortality of C. odorata and S. macrophylla. Received: 10 April 1997 / Accepted: 26 June 1998     

Large-scale synchrony of gap dynamics and the distribution of understory tree species in maple–beech forests

Large-scale synchronous variations in community dynamics are well documented for a vast array of organisms, but are considerably less understood for forest trees. Because of temporal variations in canopy gap dynamics, forest communities—even old-growth ones—are never at equilibrium at the stand scale. This paucity of equilibrium may also be true at the regional scale. Our objectives were to determine (1) if nonequilibrium dynamics caused by temporal variations in the formation of canopy gaps are regionally synchronized, and (2) if spatiotemporal variations in canopy gap formation affect the relative abundance of tree species in the understory. We examined these questions by analyzing variations in the suppression and release history of Acer saccharum Marsh. and Fagus grandifolia Ehrh. from 481 growth series of understory saplings taken from 34 mature stands. We observed that (1) the proportion of stems in release as a function of time exhibited a U-shaped pattern over the last 35 years, with the lowest levels occurring during 1975–1985, and that (2) the response to this in terms of species composition was that A. saccharum became more abundant at sites that had the highest proportion of stems in release during 1975–1985. We concluded that the understory dynamics, typically thought of as a stand-scale process, may be regionally synchronized.     

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.     

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.     

The tree of life and the rock of ages: Are we getting better at estimating phylogeny?

In a recent paper,(1) palaeontologist Mike Benton claimed that our ability to reconstruct accurately the tree of Life may not have improved significantly over the last 100 years. This implies that the cladistic and molecular revolutions may have promulgated as much bad "black box" science as rigorous investigation. Benton's assessment was based on the extent to which cladograms (typically constructed with reference only to distributions of character states) convey the same narrative as the geochronological ages of fossil taxa (an independent data set). Fossil record quality varies greatly between major clades, and the palaeontological dating "yardstick" may be more appropriate for some groups than others.     

Somatic embryogenesis and organogenesis in callus cultures of a tree legume — Albizia richardiana King

Hypocotyl explants of 1 and 10 mm lengths were excised from 12-day-old in vitro-grown seedlings of Albizia richardiana. The larger pieces, after 40 days of culture, developed shoots along with green calli on B₅ + BAP (10^–7–10^–5M), while the smaller segments produced only green calli on B₅+BAP (10^–7–10^–4M) medium. Some of the green calli turned morphogenic and started producing somatic embryos with the 2nd sub-culture and shoots from 7th sub-culture onwards. Calli retained the morphogenic potential even after repeated sub-culturing for over two years. The number of embryos in an embryogenic culture varied from 2 to 20 per callus mass of 5–6.5 cm³. Sucrose at the 2% level in MS medium was optimal for embryogenesis while 4% was optimal for shoot bud differentiation. Higher levels of sucrose (6–10%) caused browning of green calli and also inhibited differentiation into embryos and shoot buds. By selective sub-culturing of 0.1 cm³ pieces of embryogenic calli on MS+10^–5M BAP, 46% of the cultures produced somatic embryos. The latter germinated into plantlets on Knop's medium.Abbreviations BAP 6-benzylaminopurine - B₅ Gamborg et al., 1968 medium - IAA Indole-3-acetic acid - MS Murashige and Skoog's (1962) medium     

Isolation and characterization of fourteen microsatellites from a tree peony (Paeonia suffruticosa)

Tree peonies are well known garden flowers and very important medicinal plants with some 1,000 cultivars. Most of the cultivars are believed to be of hybrid origin and their wild parents are suffering from severe depopulation. To rejuvenate the traditional cultivars and assess the genetic diversity of the critically endangered wild species for conservation purpose, it is crucial to use suitable molecular markers. In this study, we isolated 14 polymorphic microsatellite loci from an enriched genomic library. These loci were verified by re-cloning and re-sequencing and their characteristics were tested with 20 individuals. On average there are 5.5 alleles per locus, and mean values of observed heterozygosity and expected heterozygosity are 0.41 and 0.67, respectively.     

Isolation and characterization of ten polymorphic microsatellite in the endangered tree Erythrophleum fordii oliv

Erythrophleum fordii oliv is a famous hardwood tree distributed in South China and Vietnam. It is now endangered due to heavy exploitation and deforestation. Ten polymorphic microsatellite loci were isolated and characterized from it. The number of alleles per locus varied from two to six. The expected and observed heterozygosities ranged from 0.3802 to 0.6903, and 0.2083 to 0.7719, respectively. These microsatellite markers will provide genetic information upon which strategies for effective conservation and management could be based.     

Anatomical characteristics of xylem in tree rings and its relationship with environments北大核心CSCD

The anatomical traits of xylem are the characteristics of tree rings at the cellular and subcellular scales, and are often reflection of environmental signals. Studying the relationships between anatomical traits of xylem and environmental change not only provide physiological explanations to the statistics in dendroclimatology, but can also provide a new vision for studying the adaptation process and response strategies of tree growth to climate change. In this paper, with the relationships between the anatomical characteristics of xylem in tree-rings (cell chronology) and climate change as a main thread, we first outline the basic principles and mechanisms of wood anatomical features to record environmental signals, and expounded the basic methods involved in the process of xylem anatomy. Secondly, we discuss the relationship between the anatomical features of xylem and climate factors. We then propose the following as possible directions of future research based on the existing knowledge gap in the topical area: (1) to explore the temporal and spatial variations in the anatomical characteristics of xylem in tree-rings along radial and tangential directions and the relationships with environmental changes; (2) to explore the threshold of tree growth response to environmental plasticity and adaptation processes; (3) to assess the synergistic and antagonistic effects as well as the formation mechanisms of climate response among different tree-ring proxies, and to determine the specific roles and contributions of major climatic factors during different periods of tree-ring formation.     

Where is the root of the universal tree of life?

The currently accepted universal tree of life based on molecular phylogenies is characterised by a prokaryotic root and the sisterhood of archaea and eukaryotes. The recent discovery that each domain (bacteria, archaea, and eucarya) represents a mosaic of the two others in terms of its gene content has suggested various alternatives in which eukaryotes were derived from the merging of bacteria and archaea. In all these scenarios, life evolved from simple prokaryotes to complex eukaryotes. We argue here that these models are biased by overconfidence in molecular phylogenies and prejudices regarding the primitive nature of prokaryotes. We propose instead a universal tree of life with the root in the eukaryotic branch and suggest that many prokaryotic features of the information processing mechanisms originated by simplification through gene loss and non-orthologous displacement.     

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.     

Purification and enzymatic properties of a peroxidase from leaves of Phytolacca dioica L. (Ombú tree)

A peroxidase (PD-cP; 0.47 mg/100 g leaves) was purified from autumn leaves of Phytolacca dioica L. and characterized. PD-cP was obtained by acid precipitation followed by gel-filtration and cation exchange chromatography. Amino acid composition and N-terminal sequence of PD-cP up to residue 15 were similar to that of Spinacia oleracea (N-terminal pairwise comparison showing four amino acid differences). PD-cP showed a molecular mass of approx. 36 kDa by SDS-PAGE, pH and temperature optima at 3.0 and 50.0°C, respectively and seasonal variation. The Michaelis-Menten constant (K(M)) for H(2)O(2) was 5.27 mM, and the velocity maximum (V(max)) 1.31 nmol min(-1), while the enzyme turnover was 0.148 s(-1). Finally, the presence of Ca(2+) and Mg(2+) enhanced the PD-cP activity, with Mg(2+) 1.4-fold more effective than Ca(2+)     

Common and specific responses to iron and phosphorus deficiencies in roots of apple tree (Malus × domestica)

Plant Molecular Biology - Iron and phosphorus are abundant elements in soils but poorly available for plant nutrition. The availability of these two nutrients represents a major constraint for...