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 Cretaceou

Changes in the Contribution of Termites to Mass Loss of Dead Wood among Three Tree Species during 23 Months in a Lowland Tropical Rainforest

This study investigated the contribution of termites to mass loss of dead wood (Macaranga bancana, Elateriospermum tapos, and Dillenia beccariana) in a lowland tropical rainforest, Brunei Darussalam. Mesh bag method was used to exclude termites, and the mass remaining was monitored after 3, 7, 13, and 23 months. C/N ratio of the samples was analyzed after 13 and 23 months. Initial wood density was 0.63, 0.92, and 1.02 g/cm3 for M. bancana, E. tapos, and D. beccariana, respectively, and the termite contribution to mass loss was an average (range) of 13.05±5.68 (4.17-29.59%), 3.48±1.13 (2.20-6.49), and 3.40±1.92% (0.74-10.78), respectively. Until 7 months, termites contributed highly to mass loss, given the low initial wood density, and interaction effect of species and treatment was significant. After 7 months, the contribution decreased in M. bancana and E. tapos, whereas it increased consistently in D. beccariana. The interaction effect was not significant, whereas differences in C/N ratio among the species were significant, with a lower C/N ratio in M. bancana and E. tapos than in D. beccariana. After 23 months, the differences in C/N ratio were not significant, and ants were present at 40% of control samples in M. bancana and E. tapos. Our results suggest that the contribution of termites to mass loss varies by dead wood species and is temporally variable. Initial wood traits could affect the termite feeding in the beginning, however, termites thereafter could forage in response to the varying C/N ratio among species and predators

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

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

Persepsi pelajar berisiko terhadap iklim pembelajaran

Learning is a process which occurs in a social context. The streaming of students into academically weak classrooms creates a negative learning context or climate for teaching and learning. Therefore, the risk of failure increases among these students in their learning process. As such, it is important to understand the learning climate in these classrooms in order to overcome the problems of at-risk students. This paper attempts to highlight the findings of a study pertaining to perceptions of students toward their classroom learning climate, involving 1,689 form two students from 28 schools in Kuala Lumpur and Selangor. Data were gathered by utilizing the questionnaire and analyzed descriptively. The findings reveal that in general, students in the various streams perceive their classroom learning climate as moderate. However there is a significant difference in perceptions of students from the three streams studied, with regards to their teachers in terms of their treatment of students, their teaching approaches and their expectations of their students. High achievers have more positive perception towards their teachers, as compared to the low and extremely low achievers. Implications of the findings and some suggestions are also discussed

At-Risk Students' Response to Learning Mathematics and Science in a Second Language

The Malaysian government recently reverted to the English language as the medium of instruction in its education system for important content subjects such as Mathematics and the Sciences. This policy decision was made in the midst of widespread concern over the perceived falling standards of English language proficiency after the country had used Malay, the native language of the majority Malays, as the medium of instruction for almost two decades. This year marks the first year high school students will sit for the national standardized examinations in English. Dissenters to this policy shift in the language of instruction fear that many will suffer as a result of this change. In this study, the self reports of academically high and low performing students are compared in terms of their ability to perform language related tasks in Malay and the English language. Using the Chi-square statistic, the results of the yes-no responses given by the students indicate that while high performing students report no major difficulties in either language, responses from the low performing students indicate otherwise. Additionally open-ended responses to learning Science and Mathematics in a second language are also qualitatively analysed in order to obtain a more comprehensive view of the challenges these students may face. Several implications based on these results are also discussed

Tropical forest wood production: a cross-continental comparison

1. 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. 2. 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. 3. 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. 4. 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. 5. 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

Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses

Long-term thermal sensitivity of Earth’s tropical forests

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (−9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth’s climate

Height-diameter allometry of tropical forest trees

Tropical tree height-diameter (H:D) relationships may vary by forest type and region making large-scale estimates of above-ground biomass subject to bias if they ignore these differences in stem allometry. We have therefore developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries. Utilising this database, our objectives were: 1. to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap). 2. to ascertain if the H:D relationship is modulated by climate and/or forest structural characteristics (e.g. stand-level basal area, A). 3. to develop H:D allometric equations and evaluate biases to reduce error in future local-to-global estimates of tropical forest biomass. Annual precipitation coefficient of variation (PV), dry season length (SD), and mean annual air temperature (TA) emerged as key drivers of variation in H:D relationships at the pantropical and region scales. Vegetation structure also played a role with trees in forests of a high A being, on average, taller at any given D. After the effects of environment and forest structure are taken into account, two main regional groups can be identified. Forests in Asia, Africa and the Guyana Shield all have, on average, similar H:D relationships, but with trees in the forests of much of the Amazon Basin and tropical Australia typically being shorter at any given D than their counterparts elsewhere. The region-environment-structure model with the lowest Akaike's information criterion and lowest deviation estimated stand-level H across all plots to within amedian −2.7 to 0.9% of the true value. Some of the plot-to-plot variability in H:D relationships not accounted for by this model could be attributed to variations in soil physical conditions. Other things being equal, trees tend to be more slender in the absence of soil physical constraints, especially at smaller D. Pantropical and continental-level models provided less robust estimates of H, especially when the roles of climate and stand structure in modulating H:D allometry were not simultaneously taken into account. © 2011 Author(s)