Kamariah Abu Salim

Assessing calibration uncertainty in molecular dating : The assignment of fossils to alternative calibration points

Although recent methodological advances have allowed the incorporation of rate variation in molecular dating analyses, the calibration procedure, performed mainly through fossils, remains resistant to improvements. One source of uncertainty pertains to the assignment of fossils to specific nodes in a phylogeny, especially when alternative possibilities exist that can be equally justified on morphological grounds. Here we expand on a recently developed fossil cross-validation method to evaluate whether alternative nodal assignments of multiple fossils produce calibration sets that differ in their internal consistency. We use an enlarged Crypteroniaceae-centered phylogeny of Myrtales, six fossils, and 72 combinations of calibration points, termed calibration sets, to identify (i) the fossil assignments that produce the most internally consistent calibration sets and (ii) the mean ages, derived from these calibration sets, for the split of the Southeast Asian Crypteroniaceae from their West Gondwanan sister clade (node X). We found that a correlation exists between s values, devised to measure the consistency among the calibration points of a calibration set (Near and Sanderson, 2004), and nodal distances among calibration points. By ranking all sets according to the percent deviation of s from the regression line with nodal distance, we identified the sets with the highest level of corrected calibration-set consistency. These sets generated lower standard deviations associated with the ages of node X than sets characterized by lower corrected consistency. The three calibration sets with the highest corrected consistencies produced mean age estimates for node X of 79.70, 79.14, and 78.15 My. These timeframes are most compatible with the hypothesis that the Crypteroniaceae stem lineage dispersed from Africa to the Deccan plate as it drifted northward during the Late Cretaceous.

Tropical forest wood production: a cross-continental comparison

Summary: Tropical forest above-ground wood production (AGWP) varies substantially along environmental gradients. Some evidence suggests that AGWP may vary between regions and specifically that Asian forests have particularly high AGWP. However, comparisons across biogeographic regions using standardized methods are lacking, limiting our assessment of pan-tropical variation in AGWP and potential causes. We sampled AGWP in NW Amazon (17 long-term forest plots) and N Borneo (11 plots), both with abundant year-round precipitation. Within each region, forests growing on a broad range of edaphic conditions were sampled using standardized soil and forest measurement techniques. Plot-level AGWP was 49% greater in Borneo than in Amazonia (9.73 ± 0.56 vs. 6.53 ± 0.34 Mg dry mass ha -1 a -1 , respectively; regional mean ± 1 SE). AGWP was positively associated with soil fertility (PCA axes, sum of bases and total P). After controlling for the edaphic environment, AGWP remained significantly higher in Bornean plots. Differences in AGWP were largely attributable to differing height-diameter allometry in the two regions and the abundance of large trees in Borneo. This may be explained, in part, by the greater solar radiation in Borneo compared with NW Amazonia. Trees belonging to the dominant SE Asian family, Dipterocarpaceae, gained woody biomass faster than otherwise equivalent, neighbouring non-dipterocarps, implying that the exceptional production of Bornean forests may be driven by floristic elements. This dominant SE Asian family may partition biomass differently or be more efficient at harvesting resources and in converting them to woody biomass. Synthesis. N Bornean forests have much greater AGWP rates than those in NW Amazon when soil conditions and rainfall are controlled for. Greater resource availability and the highly productive dipterocarps may, in combination, explain why Asian forests produce wood half as fast again as comparable forests in the Amazon. Our results also suggest that taxonomic groups differ in their fundamental ability to capture carbon and that different tropical regions may therefore have different carbon uptake capacities due to biogeographic history. North Bornean forests have much greater AGWP rates than those in north-western Amazon when soil conditions and rainfall are controlled for. Greater resource availability and the highly productive dipterocarps may, in combination, explain why these Asian forests produce wood half as fast again as comparable forests in the Amazon. Our results also suggest that taxonomic groups differ in their fundamental ability to capture carbon and that different tropical regions may therefore have different carbon uptake capacities due to biogeographic history.

Evidence of foliar aluminium accumulation in local, regional and global datasets of wild plants

• High foliar concentrations of aluminium (Al) have been reported in numerous plant species, but progress on the understanding of the functional significance of this trait is constrained by the absence of a quantitative analysis of its distribution among plant lineages and across biomes. • We constructed a global dataset of foliar Al and nutrient concentrations for 1044 plant species from literature sources and new data collections in Brunei Darussalam. • Our results provide statistical support for the existence of Al accumulators and non-Al accumulators in global, regional and local floras based on foliar Al concentrations. A value of 1 mg Al g(-1) leaf dry mass is a suitable threshold to distinguish between these two groups in a sample of species that lacks any geographical reference. However, a higher threshold foliar Al concentration is required to distinguish between Al accumulators in tropical (2.3-3.9 mg Al g(-1) leaf dry mass) than in temperate (1.1 mg Al g(-1) leaf dry mass) floras. There was a phylogenetic signal in the foliar concentrations of Al, but phylogeny did not explain the difference in the mean foliar Al concentration between tropical and temperate floras in a phylogenetically controlled analysis. • Phylogeny and soil chemistry are potential factors driving Al accumulation in certain groups of plants.

Forest dynamics and tip‐up pools drive pulses of high carbon accumulation rates in a tropical peat dome in Borneo (Southeast Asia)

Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology)

Controls on foliar nutrient and aluminium concentrations in a tropical tree flora: phylogeny, soil chemistry and interactions among elements

Foliar elemental concentrations are predictors of life-history variation and contribute to spatial patterns in biogeochemical cycling. We examined the contributions of habitat association, local soil environment, and elemental interactions to variation in foliar elemental concentrations in tropical trees using methods that account for phylogeny. We sampled top-soils and leaves of 58 tropical trees in heath forest (HF) on nutrient-poor sand and mixed dipterocarp forest (MDF) on nutrient-rich clay soils. A phylogenetic generalized least squares method was used to determine how foliar nutrient and aluminium (Al) concentrations varied in response to habitat distribution, soil chemistry and other elemental concentrations. Foliar nitrogen (N) and Al concentrations were greater for specialists of MDF than for specialists of HF, while foliar calcium (Ca) concentrations showed the opposite trend. Foliar magnesium (Mg) concentrations were lower for generalists than for MDF specialists. Foliar element concentrations were correlated with fine-scale variation in soil chemistry in phylogenetically controlled analyses across species, but there was limited within-species plasticity in foliar elemental concentrations. Among Al accumulators, foliar Al concentration was positively associated with foliar Ca and Mg concentrations, and negatively associated with foliar phosphorus (P) concentrations. The Al-accumulation trait and relationships between foliar elemental and Al concentrations may contribute to species habitat partitioning and ecosystem-level differences in biogeochemical cycles.

How temporal patterns in rainfall determine the geomorphology and carbon fluxes of tropical peatlands

Significance A dataset from one of the last protected tropical peat swamps in Southeast Asia reveals how fluctuations in rainfall on yearly and shorter timescales affect the growth and subsidence of tropical peatlands over thousands of years. The pattern of rainfall and the permeability of the peat together determine a particular curvature of the peat surface that defines the amount of naturally sequestered carbon stored in the peatland over time. This principle can be used to calculate the long-term carbon dioxide emissions driven by changes in climate and tropical peatland drainage. The results suggest that greater seasonality projected by climate models could lead to carbon dioxide emissions, instead of sequestration, from otherwise undisturbed peat swamps. Tropical peatlands now emit hundreds of megatons of carbon dioxide per year because of human disruption of the feedbacks that link peat accumulation and groundwater hydrology. However, no quantitative theory has existed for how patterns of carbon storage and release accompanying growth and subsidence of tropical peatlands are affected by climate and disturbance. Using comprehensive data from a pristine peatland in Brunei Darussalam, we show how rainfall and groundwater flow determine a shape parameter (the Laplacian of the peat surface elevation) that specifies, under a given rainfall regime, the ultimate, stable morphology, and hence carbon storage, of a tropical peatland within a network of rivers or canals. We find that peatlands reach their ultimate shape first at the edges of peat domes where they are bounded by rivers, so that the rate of carbon uptake accompanying their growth is proportional to the area of the still-growing dome interior. We use this model to study how tropical peatland carbon storage and fluxes are controlled by changes in climate, sea level, and drainage networks. We find that fluctuations in net precipitation on timescales from hours to years can reduce long-term peat accumulation. Our mathematical and numerical models can be used to predict long-term effects of changes in temporal rainfall patterns and drainage networks on tropical peatland geomorphology and carbon storage.

Long-term carbon sink in Borneo's forests halted by drought and vulnerable to edge effects

Less than half of anthropogenic carbon dioxide emissions remain in the atmosphere. While carbon balance models imply large carbon uptake in tropical forests, direct on-the-ground observations are still lacking in Southeast Asia. Here, using long-term plot monitoring records of up to half a century, we find that intact forests in Borneo gained 0.43 Mg C ha−1 per year (95% CI 0.14–0.72, mean period 1988–2010) in above-ground live biomass carbon. These results closely match those from African and Amazonian plot networks, suggesting that the world’s remaining intact tropical forests are now en masse out-of-equilibrium. Although both pan-tropical and long-term, the sink in remaining intact forests appears vulnerable to climate and land use changes. Across Borneo the 1997–1998 El Niño drought temporarily halted the carbon sink by increasing tree mortality, while fragmentation persistently offset the sink and turned many edge-affected forests into a carbon source to the atmosphere.The existence of a pan-tropical forest carbon sink remains uncertain due to the lack of data from Asia. Here, using direct on-the-ground observations, the authors confirm remaining intact forests in Borneo have provided a long-term carbon sink, but carbon net gains are vulnerable to drought and edge effects.

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.

Field methods for sampling tree height for tropical forest biomass estimation

Abstract Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site‐to‐site variation in height–diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan‐tropical or regional allometric equations to estimate height. Using a pan‐tropical dataset of 73 plots where at least 150 trees had in‐field ground‐based height measurements, we examined how the number of trees sampled affects the performance of locally derived height–diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross‐validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate‐based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand‐level biomass produced using local allometries to estimate tree height show no over‐ or under‐estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height–diameter models with low height prediction error) entirely random or diameter size‐class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height–diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.

Height-diameter input data and R-code to fit and assess height-diameter models, from 'Field methods for sampling tree height for tropical forest biomass estimation' in Methods in Ecology and Evolution

1. Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. 2. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally-derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. 3. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally-derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with estimates using measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. 4. Our results indicate that even remarkably limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.