Unveiling African rainforest composition and vulnerability to global change.

Africa is forecasted to experience large and rapid climate change1 and population growth2 during the twenty-first century, which threatens the world's second largest rainforest. Protecting and sustainably managing these African forests requires an increased understanding of their compositional heterogeneity, the environmental drivers of forest composition and their vulnerability to ongoing changes. Here, using a very large dataset of 6 million trees in more than 180,000 field plots, we jointly model the distribution in abundance of the most dominant tree taxa in central Africa, and produce continuous maps of the floristic and functional composition of central African forests. Our results show that the uncertainty in taxon-specific distributions averages out at the community level, and reveal highly deterministic assemblages. We uncover contrasting floristic and functional compositions across climates, soil types and anthropogenic gradients, with functional convergence among types of forest that are floristically dissimilar. Combining these spatial predictions with scenarios of climatic and anthropogenic global change suggests a high vulnerability of the northern and southern forest margins, the Atlantic forests and most forests in the Democratic Republic of the Congo, where both climate and anthropogenic threats are expected to increase sharply by 2085. These results constitute key quantitative benchmarks for scientists and policymakers to shape transnational conservation and management strategies that aim to provide a sustainable future for central African forests.

Integrative models for joint analysis of shoot growth and branching patterns.

Plants exhibit dependences between shoot growth and branching that generate highly structured patterns. The characterization of the patterning mechanism is still an open issue because of the developmental processes involved with both succession of events (e.g. internode elongation, axillary shoot initiation and elongation) and complex dependences among neighbouring positions along the parent shoot. Statistical models called semi-Markov switching partitioned conditional generalized linear models were built on the basis of apple and pear tree datasets. In these models, the semi-Markov chain represents both the succession and lengths of branching zones, whereas the partitioned conditional generalized linear models represent the influence of parent shoot growth variables on axillary productions within each branching zone. Parent shoot growth variables were shown to influence specific developmental events. On this basis, the growth and branching patterns of two apple tree (Malus domestica) cultivars, as well as of pear trees (Pyrus spinosa) between two successive growing cycles, were compared. The proposed integrative statistical models were able to decipher the roles of successive developmental events in the growth and branching patterning mechanisms. These models could incorporate other parent shoot explanatory variables, such as the local curvature or the maximum growth rate of the leaf.

New insights for estimating the genetic value of segregating apple progenies for irregular bearing during the first years of tree production.

Because irregular bearing generates major agronomic issues in fruit-tree species, particularly in apple, the selection of regular cultivars is desirable. Here, we aimed to define methods and descriptors allowing a diagnostic for bearing behaviour during the first years of tree maturity, when tree production is increasing. Flowering occurrences were collected at whole-tree and (annual) shoot scales on a segregating apple population. At both scales, the number of inflorescences over the years was modelled. Two descriptors were derived from model residuals: a new biennial bearing index, based on deviation around yield trend over years and an autoregressive coefficient, which represents dependency between consecutive yields. At the shoot scale, entropy was also considered to represent the within-tree flowering synchronicity. Clusters of genotypes with similar bearing behaviours were built. Both descriptors at the whole-tree and shoot scales were consistent for most genotypes and were used to discriminate regular from biennial and irregular genotypes. Quantitative trait loci were detected for the new biennial bearing index at both scales. Combining descriptors at a local scale with entropy showed that regular bearing at the tree scale may result from different strategies of synchronization in flowering at the local scale. The proposed methods and indices open an avenue to quantify bearing behaviour during the first years of tree maturity and to capture genetic variations. Their extension to other progenies and species, possible variants of descriptors, and their use in breeding programmes considering a limited number of years or fruit yields are discussed.

Acoustic, aerodynamic, and perceptual analyses of the voice of cochlear-implanted children.

OBJECTIVES: The purposes of this study were to compare, from an acoustic approach, the voice of cochlear-implanted children and the one of deaf children using conventional hearing aids (HA) to a control group; to characterize, from an aerodynamic approach, the voice of congenital/prelingual profound deaf children wearing cochlear implants for at least 3 years and implanted before 3 years old; and to classify, from a perceptual approach, the voice of implanted children, of fitted children with conventional HA, and of normal hearing (NH) children as "normal or dysphonic voices." METHODS: We analyzed 78 voices of children aged 5-13 years using EVA 2 workstation: 38 children with NH, 40 deaf children wearing HA and cochlear implants for at least 3 years and being implanted before 3 years old. Acoustic parameters were measured from a sustained vowel /a/ and speech production and aerodynamic parameters from a set of 10 syllables /pa/. Perceptive assessment was performed by a jury of experienced listeners using G component of Hirano's GRBAS (Grade, Rough, Breathy, Asthenic, Strained) scale. RESULTS: Some acoustic parameters differ significantly between NH children and deaf children's groups with HA and cochlear implants, whereas other parameters are similar between control and cochlear-implanted groups. Analysis of aerodynamic parameters indicates that the phonatory physiological behavior of the implanted group is following an evolution within the norm. Finally, results of perceptual analysis reveal that the implanted group's voice samples can be classified in the first two grades (G0=9, G1=11, n=20) according to the G component (overall dysphonia) of the GRBAS scale. CONCLUSION: Cochlear implants may improve the majority of acoustic parameters of the voice better than HA for deaf children. Glottal and laryngeal efficiencies were significantly increased with the chronological age and the time of wearing an implant. Results suggest that voices of implanted children in our study do not reveal vocal characteristics traditionally used to determine the dysphonic voice.

Deciphering structural and temporal interplays during the architectural development of mango trees.

Plant architecture is commonly defined by the adjacency of organs within the structure and their properties. Few studies consider the effect of endogenous temporal factors, namely phenological factors, on the establishment of plant architecture. This study hypothesized that, in addition to the effect of environmental factors, the observed plant architecture results from both endogenous structural and temporal components, and their interplays. Mango tree, which is characterized by strong phenological asynchronisms within and between trees and by repeated vegetative and reproductive flushes during a growing cycle, was chosen as a plant model. During two consecutive growing cycles, this study described vegetative and reproductive development of 20 trees submitted to the same environmental conditions. Four mango cultivars were considered to assess possible cultivar-specific patterns. Integrative vegetative and reproductive development models incorporating generalized linear models as components were built. These models described the occurrence, intensity, and timing of vegetative and reproductive development at the growth unit scale. This study showed significant interplays between structural and temporal components of plant architectural development at two temporal scales. Within a growing cycle, earliness of bud burst was highly and positively related to earliness of vegetative development and flowering. Between growing cycles, flowering growth units delayed vegetative development compared to growth units that did not flower. These interplays explained how vegetative and reproductive phenological asynchronisms within and between trees were generated and maintained. It is suggested that causation networks involving structural and temporal components may give rise to contrasted tree architectures.

Genetic determinism of anatomical and hydraulic traits within an apple progeny.

The apple tree is known to have an isohydric behaviour, maintaining rather constant leaf water potential in soil with low water status and/or under high evaporative demand. However, little is known on the xylem water transport from roots to leaves from the two perspectives of efficiency and safety, and on its genetic variability. We analysed 16 traits related to hydraulic efficiency and safety, and anatomical traits in apple stems, and the relationships between them. Most variables were found heritable, and we investigated the determinism underlying their genetic control through a quantitative trait loci (QTL) analysis on 90 genotypes from the same progeny. Principal component analysis (PCA) revealed that all traits related to efficiency, whether hydraulic conductivity, vessel number and area or wood area, were included in the first PC, whereas the second PC included the safety variables, thus confirming the absence of trade-off between these two sets of traits. Our results demonstrated that clustered variables were characterized by common genomic regions. Together with previous results on the same progeny, our study substantiated that hydraulic efficiency traits co-localized with traits identified for tree growth and fruit production.

Markov and semi-Markov switching linear mixed models used to identify forest tree growth components.

Tree growth is assumed to be mainly the result of three components: (i) an endogenous component assumed to be structured as a succession of roughly stationary phases separated by marked change points that are asynchronous among individuals, (ii) a time-varying environmental component assumed to take the form of synchronous fluctuations among individuals, and (iii) an individual component corresponding mainly to the local environment of each tree. To identify and characterize these three components, we propose to use semi-Markov switching linear mixed models, i.e., models that combine linear mixed models in a semi-Markovian manner. The underlying semi-Markov chain represents the succession of growth phases and their lengths (endogenous component) whereas the linear mixed models attached to each state of the underlying semi-Markov chain represent-in the corresponding growth phase-both the influence of time-varying climatic covariates (environmental component) as fixed effects, and interindividual heterogeneity (individual component) as random effects. In this article, we address the estimation of Markov and semi-Markov switching linear mixed models in a general framework. We propose a Monte Carlo expectation-maximization like algorithm whose iterations decompose into three steps: (i) sampling of state sequences given random effects, (ii) prediction of random effects given state sequences, and (iii) maximization. The proposed statistical modeling approach is illustrated by the analysis of successive annual shoots along Corsican pine trunks influenced by climatic covariates.

Is axis position within tree architecture a determinant of axis morphology, branching, flowering and fruiting? An essay in mango.

BACKGROUND AND AIMS: Growth and reproductive strategies of plants are often related to particular, although usually poorly characterized, spatial distributions of shoots within the plant's architecture. In this study it is therefore hypothesized that a close relationship exists between architectural position, axis morphology (length, diameter, leaf area), and functional behaviour (branching, flowering and fruiting). The study focused on the architectural position of mango growth units, defined here as being the relative position, apical or lateral, on the parent growth unit, i.e. growing from the apical or a lateral meristem, respectively. METHODS: Stem length and leaf characteristics (area, dry weight) were measured on apical and lateral growth units of four mango cultivars over two years. Branching, flowering and fruiting were assessed for both growth unit types using an exhaustive description of tree vegetative and reproductive growth over two years. The relationships between growth unit diameter and flowering and fruiting were assessed for one of the four cultivars. KEY RESULTS: A pronounced morphological dimorphism was observed for the four cultivars. Across cultivars, stem length was significantly 1.31-1.34 times longer and total leaf area was 2.54-3.47 times larger in apical compared to lateral growth units. Apical growth units tended to branch, flower and fruit more than lateral growth units. The relationship between growth unit diameter and flowering rate was quadratic and dependent on growth unit position. The relationship between growth unit diameter and fruiting rate was linear and independent of growth unit position. CONCLUSIONS: Morphological traits of mango growth units were clearly involved in the determinism of flowering and fruiting, although in different ways. The results, however, showed that current hypotheses of flowering, such as carbohydrate availability and florigenic promoters, are not sufficient in themselves if they neglect the hierarchical relationships between axes, i.e. their relative position, apical or lateral.

Apple shoot architecture: evidence for strong variability of bud size and composition and hydraulics within a branching zone.

* In the apple tree (Malus domestica), shoot architecture - the distribution of lateral bud types and growth along the parent shoot - has been extensively investigated. The distal zone of a shoot is characterized by a high proportion of vegetative or floral axillary branches mixed with latent buds and aborted laterals. The hypothesis tested here was that bud development was related to hydraulic conductance of the sap pathway to the bud, independently of an acrotonic (proximal vs distal) effect. * The distal zone of 1-yr-old shoots was studied on five cultivars for bud size and composition (number of appendages) and hydraulic conductance before bud burst. * Bud size, composition and hydraulic conductance were highly variable for all cultivars. A positive correlation was demonstrated between both the number of cataphylls and green-leaf primordia, and hydraulic conductance. Cultivar and bud size affected the intercept of these relationships more than the slope, suggesting similar scaling between these variables, but different hydraulic efficiencies. A great proportion of small buds were also characterized by null values of hydraulic conductance. * This study suggests that hydraulically mediated competition exists between adjacent buds within the same branching zone, prefiguring the variability of lateral types in the following growing season. It is hypothesized that this developmental patterning is driven by hydraulic characteristics of the whole metamer, including the subtending leaf, during bud development.

Effects of shoot bending on lateral fate and hydraulics: invariant and changing traits across five apple genotypes.

The aim of this work was to study the variability of physiological responses to bending and the relationship with hydraulic conductance of the sap pathway to the laterals for five apple genotypes. The study focuses on the fate of the laterals. The genetic variability of bending can have two sources: a genetic variability of stem geometry which can lead to differences in mechanical state; and a genetic variability of sensitivity to bending. Since the aim was to check if some genetic variability of sensitivity to bending exists, the genetic variability of shoot geometry was taken into account. To do so, bending was controlled by imposing different bending intensities using guides of different curvature conferring a similar level of deformation to the five genotypes. Bending was done either in the proximal zone or in the distal zone of shoots, in June and in the following winter, respectively. A Principal Component Analysis comparing upright and bent shoots revealed that bending in the proximal zone stimulated vegetative growth of buds which would otherwise stay latent. A second Principal Component Analysis restricted to bent shoots revealed that bending increased the abortion of laterals in the lower face of the shoots. The abortion phenomenon was to the detriment of sylleptic laterals or of inflorescence, depending on the genotype. There was a strong effect of position around the shoot on within-shoot hydraulics. Hydraulic conductance was significantly decreased in the lower face of the shoot bent in winter. This result suggested a causal relationship between this phenomenon and lateral abortion.

Architecture and size relations: an essay on the apple (Malus x domestica, Rosaceae) tree.

The influence of tree size independent of age on some architectural features (annual shoot length, lateral branching, flowering) was investigated on 4-yr-old apple (Malus × domestica) trees either own-rooted or grafted on the dwarfing rootstock M.9, giving rise to large and small trees, respectively. Tree size significantly affected the length of the first annual shoot of bottom branches with a lesser effect on the subsequent annual shoots of the same branches and on branches situated higher in the tree canopy. The linear regression parameters, i.e., slopes and intercepts, between annual shoot length and number of growing laterals were affected by the genotype and, depending on genotype, by tree size. Flowering was generally lower, delayed, and more irregular on large trees compared to small trees, with on average similar ranking of genotypes regardless of tree size. This study provides evidence for a specific effect of tree size, as affected by the root system, on architectural development of the apple tree regardless of the genotype. From an architectural viewpoint, the dwarfing mechanism could be interpreted as a faster physiological aging essentially related to the reduction in length of the first annual shoot of bottom branches and the high flowering on this shoot.

Patterns of size and fate relationships of contiguous organs in the apple (Malus domestica) crown.

• In apple (Malus domestica), the size of a shoot and the vegetative or reproductive fate of the terminal bud on that shoot are considered to be related phenomena but with contrasted results depending on studies. Our hypothesis was that these relationships would be partly cultivar-dependent. • Over a 3-yr period, the size relationships between shoots and fruit on two architecturally contrasted apple cultivars were assessed. For shoots, flowering frequency (dependent variable) was related to subtending shoot size (independent variable). • Linear correlations were adjusted for size relationships between contiguous shoots in the same year (inflorescence vs bourse-shoot), and between years with differences in slopes and intercepts between the two cultivars. The relationships between the size of a shoot and flowering frequency differed between the two cultivars, with high flowering whatever shoot size vs parabolic relationships between the two variables, respectively. • It is concluded that the relationships between shoot size and fate are cultivar-dependent. It is speculated that the flowering pattern not only depends on the property of the shoot alone, but also on the structural proportions of the parent branch and branching density.