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.     

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.     

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.     

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.     

��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.     

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’.     

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.     

Quantifying the risk of mis-estimating correlation significance of climate–tree growth relationships

In dendroecology, sampling effort has a strong influence of both regional chronology properties and climate–tree growth relationships assessment. Recent studies evidenced that decreasing sample size leads to a weakening of the bootstrapped correlation coefficients ( ${\text{BCC}}$ BCC ). The present analysis focused on the risk of mis-estimating the significance of population ${\text{BCC}}\,\left( {{\text{BCC}}_{\text{POP}} } \right)$ BCC ( BCC POP ) from a sample of N trees, and then proposed an approach to detect and correct mis-estimations using the properties of the sample. The sample size effect and the limits of the correction were illustrated from 840 individual growth chronologies of Corsican pine (Pinus nigra Arnold ssp. laricio Poiret var. Corsicana) sampled in Western France. The 840 trees were used to assess the population characteristics, and the effect of sampling effort was investigated through a simulation approach based on a resampling procedure of N trees amongst 840 (N ? [5; 50]). Our results evidenced that the risk strongly varied amongst the climatic regressors. The highest risks were evidenced for significant ${\text{BCC}}_{\text{POP}}$ BCC POP , with a percentage of mis-estimation ranging from 25 to 80. On the contrary, small samples allowed providing an reliable estimation of the significance of non-significant ${\text{BCC}}_{\text{POP}}$ BCC POP . To a lesser extent, the risk slightly decreased with increasing N, according to a negative exponential trend. The detection and correction method was found relevant to detect mis-estimation only for significant ${\text{BCC}}_{\text{POP}}$ BCC POP ; otherwise, the ${\text{BCC}}_{\text{POP}}$ BCC POP significance was generally overestimated.     

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.     

Morphogenetic responses of cultured cells of cambial origin of a mature tree — Dalbergia sissoo Roxb

Regeneration of plantlets was achieved from cell suspension derived calli of cambial origin from mature elite trees of Dalbergia sissoo. Callus proliferation occurred on the cambial tissue pieces cultured on MS medium supplemented with 2, 4-dichlorophenoxyacetic acid (2.0 mg/1) and benzylaminopurine (0.1 mg/l). Suspension cultures were obtained by transferring and agitating callus lumps in liquid medium composed as above. Aggregates of about 30 cells were plated on semi solid medium, which developed into calli. Shoot bud differentiation was observed in the calli transferred to medium devoid of auxin but containing 0.5–2.0 mg/1 benzylaminopurine. The isolated microshoots were rooted on modified MS medium containing low organic salts and auxins.Abbreviations BAP 6-benzylaminopurine - 2,4-D 2,4-dichlorophenoxyacetic acid - IAA indole-3-acetic acid - IPA indole-3-propionic acid - KN kinetin - MS Murashige and Skoog (1962) - NAA 1-naphthaleneacetic acid - IBA indole-3-butyric acid     

Robustness of Taylor’s law under spatial hierarchical groupings of forest tree samples

Testing how well Taylor's law (TL) describes spatial variation of the population density of a species requires grouping sampling areas (patches of habitat) into blocks so that a mean and a variance of the population density can be calculated over the patches in each block. The relationship between specific groupings and TL remains largely unknown. Here, using tree counts from a deciduous forest, we studied the effect of four biological methods of grouping sampling areas into blocks on the form and parameters of TL. Regardless of the method of grouping, the species-specific basal area densities obeyed TL, and the estimated slopes were not significantly different from one grouping method to another. Surprisingly, TL remained valid when four kinds of randomizations were performed to the biological groupings and tree census. These randomizations randomly assigned sampling areas to blocks, and/or randomized the species composition within or across sampling areas. We found that the form of TL was robust to different grouping methods and species randomizations, but its parameter values depended significantly on species compositions at sampling areas.     

Micropropagation of Sterculia urens Roxb. — an endangered tree species

An in vitro procedure for large scale multiplication of Sterculia urens Roxb. (Gum Kadaya Tree) has been developed using cotyledonary node segments. An average of 4.0 shoots per node were obtained on Murashige and Skoog's (MS) medium containing 2.0 mgl^–1 6-benzyl amino-purine (BAP) within 21 days of initial culture. Upon subsequent subculture 16 shoots/node could be harvested every three weeks and upto three times. Sixty per cent of the shoots were successfully rooted. Rooted plantlets were transferred to plastic pots containing soil under mist house conditions before they were finally exposed to an external environment. Fifty seven per cent of the plantlets survived in nursery sheds.     

Where does fission yeast sit on the tree of life?

The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe are as different from each other as either is from animals: their ancestors separated about 420 to 330 million years ago. Now that S. pombe is poised to join the post-genome era, its evolutionary position should become much clearer.     

The composting of tree bark in small reactors— self-heating experiments

The effects of aeration, moisture content and temperature on the rate of decomposition of tree bark were studied in small reactors (26 litres) in the laboratory. Aeration was found to be essential in the rapid self-heating phase; thereafter vigorous aeration only served to cool the reactor. Decomposition was optimal at a moisture content of 60% with constant rates of aeration. When aeration was reduced to prevent cooling, decomposition was not appreciably different in bark with moisture contents of 60 or 70%, although higher temperatures were achieved at 60%. It was postulated that the lower thermal capacity of bark at a moisture content of 60% was partly responsible for this latter difference.     

Coefficient of variation of lifespan across the tree of life: Is it a signature of programmed aging?

Measurements of variation are of great importance for studying the stability of pathological phenomena and processes. For the biology of aging, it is very important not only to determine average mortality, but also to study its stability in time and the size of fluctuations that are indicated by the variation coefficient of lifespan (CV_LS). It is believed that a relatively small (～20%) value of CV_LS in humans, comparable to the coefficients of variation of other events programmed in ontogenesis (for example, menarche and menopause), indicates a relatively rigid determinism (N. S. Gavrilova et al. (2012) Biochemistry (Moscow), 77, 754-760). To assess the prevalence of this phenomenon, we studied the magnitude of CV_LS, as well as the coefficients of skewness and kurtosis in diverse representatives of the animal kingdom using data provided by the Institute for Demographic Research (O. R. Jones et al. (2014) Nature, 505, 169-173). We found that, unlike humans and laboratory animals, in most examined species the values of CV_LS are rather high, indicating heterogeneity of the lifespan in the cohorts studied. This is probably due to the large influence of background mortality, as well as the non-monotonicity of total mortality in the wild, especially at the earliest ages. One way to account for this influence is to “truncate” the data (removing the earliest and latest ages from consideration). To reveal the effect of this procedure, we proposed a new indicator, the stability coefficient of mortality dynamics, which indicates how quickly CV_LS is reduced to values that characterize a relatively homogeneous population (33%) when the data are “truncated”. Such indicators facilitate the use of the parameters of survival curves for analysis of the effects of geroprotectors, lifestyle, and other factors on lifespan, and for the quantification of relative contributions of genetic and environmental factors to the dynamics of aging in human and animal populations, including those living in the wild.     

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.     

The phylogenetic system of primates—character evolution in the light of a consolidated tree

Molecular analyses of the last decades helped solving the major open questions on the external and internal phylogenetic relationships of primates. The present review uses these data for the inference of character evolution along the branches of the primate tree. Altogether, more than 200 evolutionary changes in hard and soft tissue anatomy/morphology, behavior, physiology, and protein constitution are presented in the context of their functional relevance and adaptive value. The compilation focuses on primates as a whole and on the higher-ranked primate subtaxa with living representatives: Strepsirhini: Lorisiformes, Galagidae, Lorisidae, Lemuriformes; Haplorhini: Tarsioidea, Anthropoidea, Platyrrhini, Atelidae + Cebidae, Atelidae, Cebidae, Aotinae, Callithrichinae, Cebinae, Pitheciidae, Pithecinae, Catarrhini, Cercopithecoidea, Cercopithecinae, Colobinae, Colobini, and Hominoidea. Within Hominoidea character evolution is traced down to more peripheral branches: Hylobatidae, Hominidae, Pongo, Homininae, Gorilla, Pan + Homo, Pan, and modern humans. Character states in extinct representatives of Plesiadapiformes, Omomyoidea, Propliopithecidae, Hominini, etc. are always taken into account; they are presented in detail whenever character-state distribution in living species is ambiguous or misleading. The taxonomic sample and the characters included combine to a phylogenetic system that illustrates primate evolution and diversity. The data presented additionally provide a detailed picture of the evolutionary steps and trends involved in hominization. Reflections on the frequently underestimated role of polymorphisms in phylogenetic analyses complete the survey.     

Micropropagation of Capparis decidua (Forsk.) Edgew. — a tree of arid horticulture

A method for micropropagation of mature trees of Capparis decidua was developed. Multiple shoots were obtained from nodal explants on Murashige and Skoog's (1962) medium+0.1mgl^–1 NAA+5.0mgl^–1BAP+additives (50mgl^–1 ascorbic acid and25 mgl^–1 each of adenine sulphate, L-arginine and citric acid) at 28 ± 2°C, 12 h/dphotoperiod and 35–40 mol m^-2s^–1 photon flux density. The shoots were multiplied by (i) subculture of nodal shoot segments onto MS +0.1 mgl^-–1 IAA+1.0mgl^–1 BAPH+additives, and (ii) repeated transfer of original explant onto MS+ 0.1mgl^–1 IAA+mg l^–1 BAP+additives, at intervals of 3 weeks. Sixty to 70% of the shoots rooted when pulse treated with 100 mg l^–1 IBA in half strength MS liquid medium for 4h, and then transferred onto hormone-free half-strength agar-gelled MS basal saltmedium. Incubation in dark at 33 ± 2°C for 6d favoured root induction. In vitro hardened plants were transferred to pots.Abbreviations IAA Indole-3-aceticacid - IBA Indole-3-butyric acid - NAA -naphthaleneacetic acid - BAP 6-benzylaminopurine - Kn 6-furfurylaminopurine - 2-ip Isopentenyl adenine - B₅ Gamborg et al. (1968) medium - MS Murashige and Skoog's (1962) medium - WP Woody plant medium (Lloyd and McCown 1981)     

In vitro development of plantlets from axillary buds of Acacia auriculiformis — a leguminous tree

Multiple shoots have developed from axillary buds excised from in vitro grown seedlings of Acacia auriculiformis on Gamborg's (B5) basal medium supplemented with coconut milk (5 or 10%) and benzylaminopurine (10^-6M). These shoots, if transferred individually to indole-3-acetic acid (10^-7M) or naphthaleneacetic acid (10^-6 or 10^-7M) augmented B5 medium, produced roots at their base.Abbreviations B5 Gamborg's basal medium (BM) - CM coconut milk - BA 6-benzylaminopurine - Kn kinetin - IAA indole-3-acetic acid - NAA -naphthaleneacetic acid