Joint effects of climate, tree size, and year on annual tree growth derived from tree-ring records of ten globally distributed forests.

Tree rings provide an invaluable long-term record for understanding how climate and other drivers shape tree growth and forest productivity. However, conventional tree-ring analysis methods were not designed to simultaneously test effects of climate, tree size, and other drivers on individual growth. This has limited the potential to test ecologically relevant hypotheses on tree growth sensitivity to environmental drivers and their interactions with tree size. Here, we develop and apply a new method to simultaneously model nonlinear effects of primary climate drivers, reconstructed tree diameter at breast height (DBH), and calendar year in generalized least squares models that account for the temporal autocorrelation inherent to each individual tree's growth. We analyze data from 3811 trees representing 40 species at 10 globally distributed sites, showing that precipitation, temperature, DBH, and calendar year have additively, and often interactively, influenced annual growth over the past 120 years. Growth responses were predominantly positive to precipitation (usually over ≥3-month seasonal windows) and negative to temperature (usually maximum temperature, over ≤3-month seasonal windows), with concave-down responses in 63% of relationships. Climate sensitivity commonly varied with DBH (45% of cases tested), with larger trees usually more sensitive. Trends in ring width at small DBH were linked to the light environment under which trees established, but basal area or biomass increments consistently reached maxima at intermediate DBH. Accounting for climate and DBH, growth rate declined over time for 92% of species in secondary or disturbed stands, whereas growth trends were mixed in older forests. These trends were largely attributable to stand dynamics as cohorts and stands age, which remain challenging to disentangle from global change drivers. By providing a parsimonious approach for characterizing multiple interacting drivers of tree growth, our method reveals a more complete picture of the factors influencing growth than has previously been possible.

Tropical tree size-frequency distributions from airborne lidar.

In tropical rainforests, tree size and number density are influenced by disturbance history, soil, topography, climate, and biological factors that are difficult to predict without detailed and widespread forest inventory data. Here, we quantify tree size-frequency distributions over an old-growth wet tropical forest at the La Selva Biological Station in Costa Rica by using an individual tree crown (ITC) algorithm on airborne lidar measurements. The ITC provided tree height, crown area, the number of trees >10 m height and, predicted tree diameter, and aboveground biomass from field allometry. The number density showed strong agreement with field observations at the plot- (97.4%; 3% bias) and tree-height-classes level (97.4%; 3% bias). The lidar trees size spectra of tree diameter and height closely follow the distributions measured on the ground but showed less agreement with crown area observations. The model to convert lidar-derived tree height and crown area to tree diameter produced unbiased (0.8%) estimates of plot-level basal area and with low uncertainty (6%). Predictions on basal area for tree height classes were also unbiased (1.3%) but with larger uncertainties (22%). The biomass estimates had no significant bias at the plot- and tree-height-classes level (-5.2% and 2.1%). Our ITC method provides a powerful tool for tree- to landscape-level tropical forest inventory and biomass estimation by overcoming the limitations of lidar area-based approaches that require local calibration using a large number of inventory plots.

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.

BACKGROUND: Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny. RESULTS: We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled. CONCLUSIONS: TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .

Will forest size structure follow the -2 power-law distribution under ideal demographic equilibrium state?

Scaling relations formed in forest development processes are fairly important for understanding and predicting forest dynamics. During self-thinning of a relatively even-sized forest, tree abundance will decrease with an increase in average tree size, forming the size-abundance relation (SAR); while for a size-structured forest under the demographic equilibrium state, the frequency of trees also varies with size classes in a similar, decreasing pattern, manifesting as the size-frequency distribution (SFD). In the metabolic scaling theory (MST), the two scaling relations are considered to be consistent. However, in this paper, we proved that SFD can never be equivalent to SAR unless the growth rate of tree diameters is a constant. The reason derives from the time differences of transition between different size classes, which are influenced in SFD maintenance but not in SAR formation. Demographic equilibrium of a size structured forest requires a different resource allocation among different size classes at the same time, which contradicts the resource conservation during SAR formation in the self-thinning process. Consequently, if the rate of resource use per individual scales as a +2 power with its diameter according to MST, which led to the -2 power SAR, SFD can never be a -2 power-law distribution. The previous confusion between SFD of a size-structured forest and SAR formed during self-thinning processes may lead to many misunderstandings and unreliable predictions on forest structure and dynamics.

Long-term tree inventory data from mountain forest plots in France.

We present repeated tree measurement data from 63 permanent plots in mountain forests in France. Plot elevations range from 800 (lower limit of the montane belt) to 1942 m above sea level (subalpine belt). Forests mainly consist of pure or mixed stands dominated by European beech (Fagus sylvatica), Silver fir (Abies alba), and Norway spruce (Picea abies), in association with various broadleaved species at low elevation and with Arolla pine (Pinus cembra) at high elevation. The plot network includes 23 plots in stands that have not been managed for the last 40 years (at least) and 40 plots in plots managed according to an uneven-aged system with single-tree or small-group selection cutting. Plot sizes range from 0.2 to 1.9 ha. Plots were installed from 1994 to 2004 and remeasured two to five times during the 1994-2015 period. During the first census (installation), living trees more than 7.5 cm in dbh were identified, their diameter at breast height (dbh) was measured and their social status (strata) noted. Trees were spatially located, either with x, y, and z coordinates (40 plots) or within 0.25-ha square subplots (23 plots). In addition, in a subset of plots (58 plots), tree heights and tree crown dimensions were measured on a subset of trees and dead standing trees and stumps were included in the census. Remeasurements after installation include live tree diameters (including recruited trees), tree status (living, damaged, dead, stump), and for a subset of trees, height. At the time of establishment of the plots, plot densities range from 181 to 1328 stems/ha and plot basal areas range from 13.6 to 81.3 m2 /ha.

Measurements of stem diameter: implications for individual- and stand-level errors.

Stem diameter is one of the most common measurements made to assess the growth of woody vegetation, and the commercial and environmental benefits that it provides (e.g. wood or biomass products, carbon sequestration, landscape remediation). Yet inconsistency in its measurement is a continuing source of error in estimates of stand-scale measures such as basal area, biomass, and volume. Here we assessed errors in stem diameter measurement through repeated measurements of individual trees and shrubs of varying size and form (i.e. single- and multi-stemmed) across a range of contrasting stands, from complex mixed-species plantings to commercial single-species plantations. We compared a standard diameter tape with a Stepped Diameter Gauge (SDG) for time efficiency and measurement error. Measurement errors in diameter were slightly (but significantly) influenced by size and form of the tree or shrub, and stem height at which the measurement was made. Compared to standard tape measurement, the mean systematic error with SDG measurement was only -0.17 cm, but varied between -0.10 and -0.52 cm. Similarly, random error was relatively large, with standard deviations (and percentage coefficients of variation) averaging only 0.36 cm (and 3.8%), but varying between 0.14 and 0.61 cm (and 1.9 and 7.1%). However, at the stand scale, sampling errors (i.e. how well individual trees or shrubs selected for measurement of diameter represented the true stand population in terms of the average and distribution of diameter) generally had at least a tenfold greater influence on random errors in basal area estimates than errors in diameter measurements. This supports the use of diameter measurement tools that have high efficiency, such as the SDG. Use of the SDG almost halved the time required for measurements compared to the diameter tape. Based on these findings, recommendations include the following: (i) use of a tape to maximise accuracy when developing allometric models, or when monitoring relatively small changes in permanent sample plots (e.g. National Forest Inventories), noting that care is required in irregular-shaped, large-single-stemmed individuals, and (ii) use of a SDG to maximise efficiency when using inventory methods to assess basal area, and hence biomass or wood volume, at the stand scale (i.e. in studies of impacts of management or site quality) where there are budgetary constraints, noting the importance of sufficient sample sizes to ensure that the population sampled represents the true population.

Tree inventory data from permanent plots in French forest reserves.

We present a data set resulting from the first round of a national monitoring program of forest reserves. It contains 9538 permanent plots, distributed across 111 study sites in mainland France (including Corsica). Notably focusing on dead wood measurement, this protocol has primarily been applied in strict forest reserves and special nature reserves (sensu Bollmann & Braunisch 2013), with 68% (6494) of the plots being currently located in strict forest reserves (unmanaged) and 24.7% (2363 plots) in forests unmanaged for at least 50 years. Sites cover a large variety of ecological conditions, from lowland to subalpine forests, but with an underrepresentation of Mediterranean forests (Table 1). The protocol assesses all the stages of a tree's life cycle, from seedling to decomposed lying dead wood. On each plot, a combination of three sampling techniques was used: (1) fixed-area inventory for regeneration, standing dead trees, living trees, and coarse woody debris (CWD) with diameter over 30 cm; (2) transect lines for CWD with diameter <30 cm; and (3) fixed-angle plot method for living trees with diameter at breast height (DBH) >30 cm (using a relascopic angle of 3%). Measurements include exact tree location (azimuth, distance), species, diameter(s), tree-related microhabitats, decay stage and bark cover, and seedling cover. With ongoing climate change, the program network can also provide important information to monitor changes in forest ecosystems. It can also be used as forest management monitoring or conservation status assessment. These data are freely available for noncommercial scientific use (Creative Commons Attribution 4.0 CC BY SA 4.0) with attribution, and this paper must be cited if this material is reused.

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Based on the 212 re-measured permanent plots for natural Betula platyphylla fore-sts in Daxing'an Mountains and Xiaoxing'an Mountains and 30 meteorological stations data, an individual tree growth model based on meteorological factors was constructed. The differences of stand and meteorological factors between Daxing'an Mountains and Xiaoxing'an Mountains were analyzed and the diameter increment model including the regional effects was developed by dummy variable approach. The results showed that the minimum temperature (Tg min) and mean precipitation (Pg m) in growing season were the main meteorological factors which affected the diameter increment in the two study areas. Tg min and Pg m were positively correlated with the diameter increment, but the influence strength of Tg min was obviously different between the two research areas. The adjusted coefficient of determination (Ra2) of the diameter increment model with meteorological factors was 0.56 and had an 11% increase compared to the one without meteorological factors. It was concluded that meteorological factors could well explain the diameter increment of B. platyphylla. Ra2 of the model with regional effects was 0.59, and increased by 18% compared to the one without regional effects, and effectively solved the incompatible problem of parameters between the two research areas. The validation results showed that the individual tree diameter growth model with regional effect had the best prediction accuracy in estimating the diameter increment of B. platyphylla. The mean error, mean absolute error, mean error percent and mean prediction error percent were 0.0086, 0.4476, 5.8% and 20.0%, respectively. Overall, dummy variable model of individual tree diameter increment based on meteorological factors could well describe the diameter increment process of natural B. platyphylla in Daxing'an Mountains and Xiaoxing'an Mountains.

Crecimiento de Ocotea cernua (Lauraceae) en bosques aluviales inundables de la Amazonía peruana / Growth of Ocotea cernua (Lauraceae) in Peruvian Amazon floodplain forests

Ocotea cernua (Nees) Mez, "moena negra", es una especie comercial que se desarrolla en los bosques del llano aluvial inundable de la Amazonía peruana. Este estudio, proporciona información sobre su crecimiento, y que puede utilizarse en el manejo de la especie. Se analizó la abundancia y estructura de O. cernua en nueve parcelas permanentes (100 m x 100 m) y 24 transectos (40 m x 100 m). El análisis de los registros sobre crecimiento en diámetro, mostró que el incremento anual medio y el incremento anual máximo, alcanzan un valor máximo de 9.5 y 17.4 mm/año, ambos en la clase diamétrica de 25 a 30 cm. Tomando como base ambos incrementos, el tiempo necesario para que un árbol alcance diámetros >30 cm DAP, sería de 60 y 34 años, respectivamente. Basado en factores de competencia entre árboles, el modelo de crecimiento ajustado estima que la tasa máxima de crecimiento en diámetro anual es 2.10, 1.28 y 0.50 cm para árboles con baja, media y alta competencia. Esta tasa máxima de crecimiento ocurre cuando los árboles cuentan con DAP que oscilan entre 21.10, 20.28 y 20.50 cm, para baja, media y alta competencia, respectivamente; sin embargo, el tiempo que requiere un árbol para obtener dichos diámetros varía enormemente, con valores de 12.31 cm para baja competencia, 20.35 para media competencia y 54.51 años para alta competencia.

Ocotea cernua (Nees) Mez "moena negra" is a commercial species that thrives in alluvial floodplain forests in the Peruvian Amazon. This study presents information about diameter growth of O. cernua and provides useful information for its forest management. The stand density and structure was analysed in nine permanent sample plots (100 m x 100 m) and 24 transects (40 m x 100 m). Analysis of tree diameters at different time indicates maximum values of 9.5 and 17.4 mm/year for the average annual diameter increment and the maximum annual diameter increment respectively; both into 25 ‒ 30 cm diameter classes. Considering this increments, a tree will reach a diameter higher than 30 cm DAP, in 60 to 34 years respectively. Estimations of the adjusted model showed the maximum annual growth increment estimated in 2.10, 1.28 and 0.50 cm for trees with low, medium and high competition, corresponding to trees with DBHs of 21.10, 20.28 and 20.50 cm for trees with low, medium and high competition, respectively. However, the time required to reach such diameters is highly variable with values of 12.31, 20.35 and 54.51 years, respectively.