Emerging infectious diseases continue to pose a significant burden on global public health, and there is a critical need to better understand transmission dynamics arising at the interface of human activity and wildlife habitats. Passive acoustic monitoring (PAM), more typically applied to questions of biodiversity and conservation, provides an opportunity to collect and analyse audio data in relative real time and at low cost. Acoustic methods are increasingly accessible, with the expansion of cloud-based computing, low-cost hardware, and machine learning approaches. Paired with purposeful experimental design, acoustic data can complement existing surveillance methods and provide a novel toolkit to investigate the key biological parameters and ecological interactions that underpin infectious disease epidemiology.
Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts.
In recent years, Malaysia has experienced quite a few number of chronic air pollution problems and it has become a
major contributor to the deterioration of human health and ecosystems. This study aimed to assess the air quality data
and identify the pattern of air pollution sources using chemometric analysis through hierarchical cluster analysis (HCA),
discriminant analysis (DA), principal component analysis (PCA) and multiple linear regression analysis (MLR). The air
quality data from January 2016 until December 2016 was obtained from the Department of Environment Malaysia. Air
quality data from eight sampling stations in Selangor include the selected variables of nitrogen dioxide (NO2
), ozone (O3
),
sulfur dioxide (SO2
), carbon monoxide (CO) and particulate matter (PM10). The HCA resulted in three clusters, namely low
pollution source (LPS), moderate pollution source (MPS) and slightly high pollution source (SHPS). Meanwhile, DA resulted
in two and four variables for the forward stepwise mode and the backward stepwise mode, respectively. Through PCA,
it was identified that the main pollutants of LPS, MPS and SHPS came from industrial and vehicle emissions, agricultural
systems, residential factors and natural emission sources. Among the three models yielded from the MLR analysis, it was
found that SHPS is the most suitable model to be used for the prediction of Air Pollution Index. This study concluded that
a clearer review and practical design of air quality monitoring network would be beneficial for better management of
air pollution. The study also suggested that chemometric techniques have the ability to show significant information on
spatial variability for large and complex air quality data.
A series of check dams (or small dams in shallow streams) have been placed on many streams throughout Thailand and
the number of them continue to increase. Check dam construction activities have been emphasized by the government
and private sector entities over the last decade to prevent severe flood or drought due to changes in rainfall patterns. This
study evaluated distribution of functional feeding groups (FFG) in a stream with a high density of check dams. Twelve
sampling sites at three altitudes (500, 900 and 1500 m asl) included undammed and nearby dammed sections (above
and below check dams) were used. Aquatic insects were collected monthly at each site for a year and categorized into
FFG. Aquatic insect composition of undammed and above dam sites was different. Abundance within each FFG at above
dam sites significantly differed from undammed sites. Taxonomic richness at 1500 and 900 m altitudes was decreased
at above dam sites compared with the corresponding undammed sites, whereas above dam sites of 500 m altitude had
higher richness than undammed site. High abundance of predators and collector-gatherers associated with reservoirs
and fine sediment accumulation above dams, where filter-feeders were scarce. Shredder abundance varied among sites
and was highest where leaf packs were most abundant. Scrapers were least abundant group and inconsistent with the
dams. Distribution of FFG was similar to changes in other regulated streams. The composition of FFG reflected the
stream ecosystem conditions through adaptation of communities to stream habitat and food resources, including those
associated with check dam construction.
Citizen science-based research has been used effectively to estimate animal abundance and breeding patterns, to monitor animal movement, and for biodiversity conservation and education. Here, we evaluate the feasibility of using social media observations to assess the distribution of small apes in Peninsular Malaysia. We searched for reports of small ape observations in Peninsular Malaysia on social media (e.g., blogs, Facebook, Instagram, Twitter, YouTube, iNaturalist, etc.), and also used online, radio, print messaging, and word of mouth to invite citizen scientists such as birders, amateur naturalists, hikers, and other members of the public to provide information about small ape observations made during their activities. These reports provided new information about the occurrence of all three species of small apes (Hylobates agilis, Hylobates lar, and Symphalangus syndactylus) in Peninsular Malaysia. Social media users reported observations of small apes in almost every state. Despite the fact that small apes are believed to occur primarily in the interior of large forested areas, most observations were from fairly small (<100 km2 ) forests near areas of high traffic and high human population (roads and urban areas). This suggests that most outdoor enthusiasts primarily visit well-traveled and easily accessible areas, which results in biased sampling if only incidental observations reported on social media are used. A more targeted approach specifically soliciting reports from citizen scientists visiting large, less-accessible forests may result in better sampling in these habitats. Social media reports indicated the presence of small apes in at least six habitats where they had not been previously reported. We verified the reported data based on whether reports included a date, location, and uploaded photographs, videos and/or audio recordings. Well-publicized citizen science programs may also build awareness and enthusiasm about the conservation of vulnerable wildlife species.
This paper illustrates the role of plants to assist the treatment of water pollution in man-made wetlands in tropical and temperate climates. It also considers the potential for environmental education of these wetland systems. The management and natural treatment of pollution is described in the Mai Po Marshes, Hong Kong and a wetland in London which is also an important site for birds. The design of the Putrajaya Lake and Wetland system in Malaysia is compared with a constructed wetland and lake for the treatment of urban surface runoff in a new residential development in the United Kingdom. The benefits of these natural systems are discussed in the context of the global trend for introducing sustainable methods of environmental management and low cost pollution treatment systems.
Biodiversity surveys are crucial for monitoring the status of threatened aquatic ecosystems, such as tropical estuaries and mangroves. Conventional monitoring methods are intrusive, time-consuming, substantially expensive, and often provide only rough estimates in complex habitats. An advanced monitoring approach, environmental DNA (eDNA) metabarcoding, is promising, although only few applications in tropical mangrove estuaries have been reported. In this study, we explore the advantages and limitations of an eDNA metabarcoding survey on the fish community of the Merbok Estuary (Peninsular Malaysia). COI and 12S eDNA metabarcoding assays collectively detected 178 species from 127 genera, 68 families, and 25 orders. Using this approach, significantly more species have been detected in the Merbok Estuary over the past decade (2010-2019) than in conventional surveys, including several species of conservation importance. However, we highlight three limitations: (1) in the absence of a comprehensive reference database the identities of several species are unresolved; (2) some of the previously documented specimen-based diversity was not captured by the current method, perhaps as a consequence of PCR primer specificity, and (3) the detection of non-resident species-stenohaline freshwater taxa (e.g., cyprinids, channids, osphronemids) and marine coral reef taxa (e.g., holocentrids, some syngnathids and sharks), not known to frequent estuaries, leading to the supposition that their DNA have drifted into the estuary through water movements. The community analysis revealed that fish diversity along the Merbok Estuary is not homogenous, with the upstream more diverse than further downstream. This could be due to the different landscapes or degree of anthropogenic influences along the estuary. In summary, we demonstrated the practicality of eDNA metabarcoding in assessing fish community and structure within a complex and rich tropical environment within a short sampling period. However, some limitations need to be considered and addressed to fully exploit the efficacy of this approach.
Coastal ecosystems are facing heightened risks due to human-induced climate change, including rising water levels and intensified storm events. Accurate bathymetry data is crucial for assessing the impacts of these threats. Traditional data collection methods can be cost-prohibitive. This study investigates the feasibility of using freely accessible Landsat and Sentinel satellite imagery to estimate bathymetry and its correlation with hydrographic chart soundings in Port Klang, Malaysia. Through analysis of the blue and green spectral bands from the Landsat 8 and Sentinel 2 datasets, a bathymetry map of Port Klang's seabed is generated. The precision of this derived bathymetry is evaluated using statistical metrics like Root Mean Square Error (RMSE) and the coefficient of determination. The results reveal a strong statistical connection (R2 = 0.9411) and correlation (R2 = 0.7958) between bathymetry data derived from hydrographic chart soundings and satellite imagery. This research not only advances our understanding of employing Landsat imagery for bathymetry assessment but also underscores the significance of such assessments in the context of climate change's impact on coastal ecosystems. The primary goal of this research is to contribute to the comprehension of Landsat imagery's utility in bathymetry evaluation, with the potential to enhance safety protocols in seaport terminals and provide valuable insights for decision-making concerning the management of coastal ecosystems amidst climate-related challenges. The findings of this research have practical implications for a wide range of stakeholders involved in coastal management, environmental protection, climate adaptation and disaster preparedness.
Dietary study provides understanding in predator-prey relationships, yet diet of tropical forest birds is poorly understood.
In this study, a non-invasive method, next-generation sequencing (Illumina MiSeq platform) was used to identify prey in
the faecal samples of the Rufous-winged Philentoma (Philentoma pyrhoptera). Dietary samples were collected in lowland
tropical forest of central Peninsular Malaysia. A general invertebrate primer pair was used for the first time to assess
diet of tropical birds. The USEARCH was used to cluster the COI mtDNA sequences into Operational Taxonomic Unit (OTU).
OTU sequences were aligned and queried through the GenBank or Biodiversity of Life Database (BOLD). We identified
26 distinct arthropod taxa from 31 OTUs. Of all OTUs, there was three that could be identified up to species level, 20 to
genus level, three to family level and five could not assigned to any taxa (the BLAST hits were poor). All sequences were
identified to class Insecta belonging to 18 families from four orders, where Lepidoptera representing major insect order
consumed by study bird species. This non-invasive molecular approach provides a practical and rapid technique to
understand of how energy flows across ecosystems. This technique could be very useful to screen for possible particular
pest insects consumed by insectivores (e.g. birds and bats) in crop plantation. A comprehensive arthropod studies and
local reference sequences need to be added to the database to improve the proportion of sequences that can be identified.
Understanding the drivers of community structure is fundamental for adequately managing ecosystems under global change. Here we used a large dataset of eighty-four headwater stream sites in three catchments in the Eastern Highlands of Zimbabwe, which represent a variety of abiotic conditions and levels of impairment, to examine the drivers of benthic macroinvertebrate community structure. We focused our assessment on macroinvertebrate family level community composition and functional feeding group classifications. Taxonomic richness was weakly positively correlated with ammonium, phosphates and pH, and weakly negatively correlated with detrital cover and dissolved oxygen. Measured abiotic variables, however, had limited influence on both macroinvertebrate diversity and functional feeding group structure, with the exception of ammonium, channel width and phosphates. This reflected the fact that many macroinvertebrate families and functional feeding guilds were well represented across a broad range of habitats. Predatory macroinvertebrates were relatively abundant, with collector-filterers having the lowest relative abundances. The findings of the study suggest that for certain ecological questions, a more detailed taxonomic resolution may be required to adequately understand the ecology of aquatic macroinvertebrates within river systems. We further recommend management and conservation initiatives on the Save River system, which showed significant impact from catchment developmental pressures, such as urbanisation, agriculture and illegal mining.
In Amazonian tropical forests, recent studies have reported increases in aboveground biomass and in primary productivity, as well as shifts in plant species composition favouring fast-growing species over slow-growing ones. This pervasive alteration of mature tropical forests was attributed to global environmental change, such as an increase in atmospheric CO2 concentration, nutrient deposition, temperature, drought frequency, and/or irradiance. We used standardized, repeated measurements of over 2 million trees in ten large (16-52 ha each) forest plots on three continents to evaluate the generality of these findings across tropical forests. Aboveground biomass increased at seven of our ten plots, significantly so at four plots, and showed a large decrease at a single plot. Carbon accumulation pooled across sites was significant (+0.24 MgC ha(-1) y(-1), 95% confidence intervals [0.07, 0.39] MgC ha(-1) y(-1)), but lower than reported previously for Amazonia. At three sites for which we had data for multiple census intervals, we found no concerted increase in biomass gain, in conflict with the increased productivity hypothesis. Over all ten plots, the fastest-growing quartile of species gained biomass (+0.33 [0.09, 0.55] % y(-1)) compared with the tree community as a whole (+0.15 % y(-1)); however, this significant trend was due to a single plot. Biomass of slow-growing species increased significantly when calculated over all plots (+0.21 [0.02, 0.37] % y(-1)), and in half of our plots when calculated individually. Our results do not support the hypothesis that fast-growing species are consistently increasing in dominance in tropical tree communities. Instead, they suggest that our plots may be simultaneously recovering from past disturbances and affected by changes in resource availability. More long-term studies are necessary to clarify the contribution of global change to the functioning of tropical forests.
Co-management is now established as a mainstream approach to small-scale fisheries management across the developing world. A comprehensive review of 204 potential cases reveals a lack of impact assessments of fisheries co-management. This study reports on a meta-analysis of the impact of fisheries co-management in developing countries in 90 sites across 29 case-studies. The top five most frequently measured process indicators are participation, influence, rule compliance, control over resources, and conflict. The top five most frequently measured outcome indicators are access to resources, resource well-being, fishery yield, household well-being, and household income. To deal with the diversity of the 52 indicators measured and the different ways these data are collected and analysed, we apply a coding system to capture change over time. The results of the meta-analysis suggest that, overall fisheries co-management delivers benefits to end-users through improvements in key process and outcome indicators. However, the dataset as a whole is constituted primarily of data from the Philippines. When we exclude this body of work, few generalisations can be made about the impact of fisheries co-management. The lack of comparative data suitable for impact assessment and the difficulties in comparing data and generalising across countries and regions reiterates calls in other fields for more systematic approaches to understanding and evaluating governance frameworks.
Sweet cherries, Prunus avium (L.) L., grown in the western United States are exported to many countries around the world. Some of these countries have enforced strict quarantine rules and trade restrictions owing to concerns about the potential establishment and subsequent spread of western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), a major quarantine pest of sweet cherry. We used 1) niche models (CLIMEX and MaxEnt) to map the climatic suitability, 2) North Carolina State University-Animal and Plant Health Inspection Service Plant Pest Forecasting System to examine chilling requirement, and 3) host distribution and availability to assess the potential for establishment of R. indifferens in areas of western North America where it currently does not exist and eight current or potential fresh sweet cherry markets: Colombia, India, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam. Results from niche models conformed well to the current distribution of R. indifferens in western North America. MaxEnt and CLIMEX models had high performance and predicted climatic suitability in some of the countries (e.g., Andean range in Colombia and Venezuela, northern and northeastern India, central Taiwan, and parts of Vietnam). However, our results showed no potential for establishment of R. indifferens in Colombia, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam when the optimal chilling requirement to break diapause (minimum temperature < or = 3 degree C for at least 15 wk) was used as the criterion for whether establishment can occur. Furthermore, these countries have no host plant species available for R. indifferens. Our results can be used to make scientifically informed international trade decisions and negotiations by policy makers.
The proliferation of camera-trapping studies has led to a spate of extensions in the known distributions of many wild cat species, not least in Borneo. However, we still do not have a clear picture of the spatial patterns of felid abundance in Southeast Asia, particularly with respect to the large areas of highly-disturbed habitat. An important obstacle to increasing the usefulness of camera trap data is the widespread practice of setting cameras at non-random locations. Non-random deployment interacts with non-random space-use by animals, causing biases in our inferences about relative abundance from detection frequencies alone. This may be a particular problem if surveys do not adequately sample the full range of habitat features present in a study region. Using camera-trapping records and incidental sightings from the Kalabakan Forest Reserve, Sabah, Malaysian Borneo, we aimed to assess the relative abundance of felid species in highly-disturbed forest, as well as investigate felid space-use and the potential for biases resulting from non-random sampling. Although the area has been intensively logged over three decades, it was found to still retain the full complement of Bornean felids, including the bay cat Pardofelis badia, a poorly known Bornean endemic. Camera-trapping using strictly random locations detected four of the five Bornean felid species and revealed inter- and intra-specific differences in space-use. We compare our results with an extensive dataset of >1,200 felid records from previous camera-trapping studies and show that the relative abundance of the bay cat, in particular, may have previously been underestimated due to the use of non-random survey locations. Further surveys for this species using random locations will be crucial in determining its conservation status. We advocate the more wide-spread use of random survey locations in future camera-trapping surveys in order to increase the robustness and generality of inferences that can be made.
Surface water is one of the essential resources for supporting sustainable development. The suitability of such water for a given use depends both on the available quantity and tolerable quality. Temporary status for a surface water quality has been identified extensively. Still the suitability of the water for different purposes needs to be verified. This study proposes a water quality evaluation system to assess the aptitude of the Selangor River water for aquatic biota, drinking water production, leisure and aquatic sport, irrigation use, livestock watering, and aquaculture use. Aptitude of the water has been classified in many parts of the river segment as unsuitable for aquatic biota, drinking water production, leisure and aquatic sport as well as aquaculture use. The water quality aptitude classes of the stream water for nine locations along the river are evaluated to contribute to decision support system. The suitability of the water for five different uses and its aquatic ecosystem are verified.
The usage of cladocerans as non-model organisms in ecotoxicological and risk assessment studies has intensified in recent years due to their ecological importance in aquatic ecosystems. The molecular assessment such as gene expression analysis has been introduced in ecotoxicological and risk assessment to link the expression of specific genes to a biological process in the cladocerans. The validity and accuracy of gene expression analysis depends on the quantity, quality and integrity of extracted ribonucleic acid (RNA) of the sample. However, the standard methods of RNA extraction from the cladocerans are still lacking. This study evaluates the extraction of RNA from tropical freshwater cladocerans Moina micrura using two methods: the phenol-chloroform extraction method (QIAzol) and a column-based kit (Qiagen Micro Kit). Glycogen was introduced in both approaches to enhance the recovery of extracted RNA and the extracted RNA was characterised using spectrophotometric analysis (NanoDrop), capillary electrophoresis (Bioanalyzer). Then, the extracted RNA was analysed with reverse transcription polymerase chain reaction (RT-PCR) to validate the RNA extraction method towards downstream gene expression analysis. The results indicate that the column-based kit is most suitable for the extraction of RNA from M. micrura, with the quantity (RNA concentration = 26.90 ± 6.89 ng/μl), quality (A260:230 = 1.95 ± 0.15, A280:230 = 1.85 ± 0.09) and integrity (RNA integrity number, RIN = 7.20 ± 0.16). The RT-PCR analysis shows that the method successfully amplified both alpha tubulin and actin gene at 33-35 cycles (i.e. Ct = 32.64 to 33.48). The results demonstrate that the addition of glycogen is only suitable for the phenol-chloroform extraction method. RNA extraction with high and comprehensive quality control assessment will increase the accuracy and reliability of downstream gene expression, thus providing more ecotoxicological data at the molecular biological level on other freshwater zooplankton species.
Most investigations on heavy metals content in fish were either conducted on single markets, ports, seaside markets or direct sampling from natural habitat, and there were very few studies done on fish samples from both wet markets and supermarkets. This paper presents the assessment outcome of Cd and Pb levels in commercial fish sold between wet markets and supermarkets in Klang Valley, Malaysia. In this study, the organs of four commercial fish species (Rastrellinger kanagurta, Epinephelus sexfasciatus, Lates calcarifer, and Decapterus maruadsi) sampled from different markets within the sampling area were assessed using dry ashing-acid digestion method and Flame AAS. Results obtained concluded that Cd and Pb in fishes sampled from supermarkets are generally higher compared to wet markets, while both metals content in the edible organs fall well within the permissible limits for human consumption when compared to the Fourteenth Schedule of the Malaysian Food Regulations 1985.
A study on the quality of water abstracted for potable use was conducted in the Selangor River basin from November 2008 to July 2009. Seven sampling sites representing the intake points of water treatment plants in the basin were selected to determine the occurrence and level of 15 organochlorine pesticides (OCPs), six phthalate esters (PAEs) and bisphenol A (BPA). Results indicated OCPs were still detected regularly in 66.1 % of the samples with the Σ(15)OCPs ranging from 0.6-25.2 ng/L. The first data on PAEs contamination in the basin revealed Σ(6)PAEs concentrations were between 39.0 and 1,096.6 ng/L with a median concentration of 186.0 ng/L while BPA concentration ranged from <1.2 to 120.0 ng/L. Although di-n-butyl phthalate was detected in all the samples, concentrations of di-ethyl(hexyl)phthalate were higher. Sampling sites located downstream recorded the highest concentrations, together with samples collected during the dry season. Comparison of the detected contaminants with the Department of Environment Water Quality Index (DOE-WQI) showed some agreement between the concentration and the current classification of stream water. While the results suggest that the sites were only slightly polluted and suitable to be used as drinking water source, its presence is cause for concern especially to the fragile firefly "Pteroptyx tener" ecosystem located further downstream.
This study assesses four predictive ecological models; Fuzzy Logic (FL), Recurrent Artificial Neural Network (RANN), Hybrid Evolutionary Algorithm (HEA) and multiple linear regressions (MLR) to forecast chlorophyll- a concentration using limnological data from 2001 through 2004 of unstratified shallow, oligotrophic to mesotrophic tropical Putrajaya Lake (Malaysia). Performances of the models are assessed using Root Mean Square Error (RMSE), correlation coefficient (r), and Area under the Receiving Operating Characteristic (ROC) curve (AUC). Chlorophyll-a have been used to estimate algal biomass in aquatic ecosystem as it is common in most algae. Algal biomass indicates of the trophic status of a water body. Chlorophyll- a therefore, is an effective indicator for monitoring eutrophication which is a common problem of lakes and reservoirs all over the world. Assessments of these predictive models are necessary towards developing a reliable algorithm to estimate chlorophyll- a concentration for eutrophication management of tropical lakes.
In the current context of rapid development and urbanization, land use and land cover (LULC) types have undergone unprecedented changes, globally and nationally, leading to significant effects on the surrounding ecological environment quality (EEQ). The urban agglomeration in North Slope of Tianshan (UANST) is in the core area of the Silk Road Economic Belt of China. This area has experienced rapid development and urbanization with equally rapid LULC changes which affect the EEQ. Hence, this study quantified and assessed the spatial-temporal changes of LULC on the UANST from 2001 to 2018 based on remote sensing analysis. Combining five remote sensing ecological factors (WET, NDVI, IBI, TVDI, LST) that met the pressure-state-response(PSR) framework, the spatial-temporal distribution characteristics of EEQ were evaluated by synthesizing a new Remote Sensing Ecological Index (RSEI), with the interaction between land use change and EEQ subsequently analyzed. The results showed that LULC change dominated EEQ change on the UANST: (1) From 2001 to 2018, the temporal and spatial pattern of the landscape on the UANST has undergone tremendous changes. The main types of LULC in the UANST are Barren land and Grassland. (2) During the study period, RSEI values in the study area were all lower than 0.5 and were at the [good] levels, reaching 0.31, 0.213, 0.362, and 0346, respectively. In terms of time and space, the overall EEQ on the UANST experienced three stages of decline-rise-decrease. (3) The estimated changes in RSEI were highly related to the changes of LULC. During the period 2001 to 2018, the RSEI value of cropland showed a trend of gradual increase. However, the rest of the LULC type's RSEI values behave differently at different times. As the UANST is the core area of Xinjiang's urbanization and economic development, understanding and balancing the relationship between LULC and EEQ in the context of urbanization is of practical application in the planning and realization of sustainable ecological, environmental, urban, and social development in the UANST.