Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Heckenhauer J

PROVIDER: S-EPMC5648112 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Heckenhauer Jacqueline J Abu Salim Kamariah K Chase Mark W MW Dexter Kyle G KG Pennington R Toby RT Tan Sylvester S Kaye Maria Ellen ME Samuel Rosabelle R

PloS one 20171019 10

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 ...[more]

PMID: 29049301

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Project description:BackgroundDespite the global increase in the prevalence of autism spectrum disorders (ASD), relevant research studies are lacking in Brunei Darussalam. Various studies have shown a significant association between a lowered 2D:4D ratio (ratio of second digit/index finger to the fourth digit/ring finger) and ASD, making it one of the potential phenotypic biomarkers for early detection of autism, which is important for early intervention and management.ObjectiveThe objective of this study is to explore the association between 2D:4D ratio and ASD in Brunei Darussalam, as a potential tool to complement early ASD diagnosis.MethodsWe conducted a case-control study comprising 28 ASD and 62 typically developing (TD) children in the case and control group, respectively (age range: 3-11 years old; median age: 6 years old). Median 2D:4D ratios were measured, compared and analysed between the two groups. Logistic regression models were used to explore potential associations between the median 2D:4D ratio and ASD in respective gender, for both left and right hands, independently.ResultsOur study shows that the median 2D:4D ratio of left hand in ASD males is significantly lower than those in TD males, after adjusting for ethnicity and age [Odds Ratio (OR) = 0.57 (95% Confidence Interval (CI): 0.31-0.96); p = 0.044]. For females, there is no association of ASD with the median left hand 2D:4D ratio [OR = 3.09 (95% CI: 0.98-19.86); p = 0.144] or the median right hand 2D:4D ratio [OR = 1.23 (95% CI: 0.42-3.88); p = 0.702]. Our study also shows a significant positive correlation and/or a reduced asymmetry between the average 2D:4D ratio of left hands and right hands in ASD males (Pearson's correlation (r) = 0.48; 95% CI: 0.076-0.75, p = 0.023).ConclusionsThere is significant association between a lowered median 2D:4D ratio of the left hand (in males only) and ASD diagnosis. Once validated in a larger sample size, a lowered median 2D:4D ratio on the left hand may be a potential tool to complement ASD diagnosis for males in our study population. There is no association between the median 2D:4D ratio (left or right hands) and ASD in females, which could be due to the small female sample size and/or the possibility of different aetiology for ASD in females. Reduced asymmetry between the average 2D:4D ratio of left and right hands observed in ASD males only (not in ASD females) also suggests the importance of considering gender-specific biomarkers for ASD diagnosis.

Project description:ObjectivesWe reported the incidence and associated factors of extrapulmonary tuberculosis (EPTB).DesignA retrospective cohort study.SettingBrunei Darussalam, an intermediate tuberculosis (TB)-burden country with stagnating annual TB rates.ParticipantsAll active TB cases identified in the country between January 2001 and December 2018 (18 years).Primary and secondary outcome measuresAnnual proportions of EPTB (overall and specific) were calculated. Multiple logistic regression was done to investigate factors associated with developing EPTB, when compared with pulmonary TB (PTB). Χ2 trend test was used to determine any trends during the 18-year study period.ResultsWe identified 3916 TB cases, among which 743 (19.0%) were EPTB cases. Lymphatic (44.8%) and pleural (19.4%) EPTB were most common. The main modes of diagnosis were tissue biopsy (73.6%) and radiological assessment (18.3%). Treatment success and mortality rate were 79.7% and 7.0%, respectively. Associations with specific EPTB types varies with age-group and gender. Younger age-group (adjusted OR (aOR)≥1.94) and women (aOR: 2.45 (95% CI: 1.94 to 3.11)) had higher adjusted odds of developing lymphatic EPTB, but had lower adjusted odds of developing pleural EPTB (younger age-group (aOR≤0.54) and women (aOR: 0.41 (95% CI: 0.17 to 0.90)). When compared to foreign residents, locals had higher adjusted odds of skeletal (aOR: 4.44 (95% CI: 2.04 to 11.69)), gastrointestinal (aOR: 3.91 (95% CI: 1.84 to 9.66)) and other types of EPTB (aOR: 3.42 (95% CI: 1.53 to 9.14)). No significant trend differences were observed for overall and specific EPTB types.ConclusionDespite being generally non-infectious and less recognised than PTB, understanding EPTB epidemiology is important as it also contributes to the overall TB burden in a country. Examining EPTB cases by their specific anatomical site would provide more information on risk factors. Raising public awareness on the EPTB symptoms and that TB affects lungs and other parts of the body could promote early health seeking behaviour and early EPTB diagnosis.

Project description:Time-series data offer a way of investigating the causes driving ecological processes as phenomena. To test for possible differences in water relations between species of different forest structural guilds at Danum (Sabah, NE Borneo), daily stem girth increments (gthi), of 18 trees across six species were regressed individually on soil moisture potential (SMP) and temperature (TEMP), accounting for temporal autocorrelation (in GLS-arima models), and compared between a wet and a dry period. The best-fitting significant variables were SMP the day before and TEMP the same day. The first resulted in a mix of positive and negative coefficients, the second largely positive ones. An adjustment for dry-period showers was applied. Interactions were stronger in dry than wet period. Negative relationships for overstorey trees can be interpreted in a reversed causal sense: fast transporting stems depleted soil water and lowered SMP. Positive relationships for understorey trees meant they took up most water at high SMP. The unexpected negative relationships for these small trees may have been due to their roots accessing deeper water supplies (if SMP was inversely related to that of the surface layer), and this was influenced by competition with larger neighbour trees. A tree-soil flux dynamics manifold may have been operating. Patterns of mean diurnal girth variation were more consistent among species, and time-series coefficients were negatively related to their maxima. Expected differences in response to SMP in the wet and dry periods did not clearly support a previous hypothesis differentiating drought and non-drought tolerant understorey guilds. Trees within species showed highly individual responses when tree size was standardized. Data on individual root systems and SMP at several depths are needed to get closer to the mechanisms that underlie the tree-soil water phenomena in these tropical forests. Neighborhood stochasticity importantly creates varying local environments experienced by individual trees.

Project description:ObjectivesThis paper examines the relationship between individuals' perceptions of environmental quality and self-rated health (SRH) after controlling for dimensions of socioeconomic, demographic and healthy lifestyle variables.DesignA cross-sectional survey.SettingThe survey was conducted in Belait, an oil-rich and gas-rich district in Brunei Darussalam, from 17 October to 11 November 2019 and focused on the most populated subdistricts (Kuala Belait, Seria and Liang), where 97% of the people reside.ParticipantsA final sample of 1000 respondents aged 18 years and older were randomly selected from the population of the chosen subdistricts, with 95% CI and ±3 margin of error. Due to variable selection, only 673 respondents were available for analysis.Outcome measuresSRH was dichotomised into 1 for good health and 0 otherwise. Perceptions of environmental quality included perceptions of the natural environment (air quality, marine quality, water supply, noise and olfactory pollution) and the social environment (crime). χ2 and logistic regression models were used to assess the relationship between individuals' perceived environmental quality and SRH.ResultsMost respondents perceived themselves with good SRH (72%). The adjusted logistic regression shows that perceptions of air quality (OR=2.20, 95% CI 1.15 to 4.22, p=0.018) and marine resources (OR=1.84, 95% CI 1.24 to 2.74, p=0.002) in their surrounding areas were significantly associated with good SRH. However, other environmental variables were insignificantly associated with SRH. Among the control variables, healthy lifestyle and employment had positive associations with good SRH (OR=3.89, 95% CI 1.96 to 7.71, p=0.000, for exercising 3-5 times a week; OR=1.72, 95% CI 1.09 to 2.71, p=0.021, for being employed). In addition, frequent physical exercise compensated for the negative health impact of environmental pollution.ConclusionsThis study suggests that environmental quality has an important role in SRH. However, a healthy lifestyle measured with frequency of physical exercise seems to compensate for the adverse environmental effects on SRH.

Dataset Information

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

Publications

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

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