Mangrove sediments are prone to anthropogenic activities that could enrich antibiotics resistance genes (ARGs). The emergence and dissemination of ARGs are of serious concern to public health worldwide. Therefore, a comprehensive resistome analysis of global mangrove sediment is of paramount importance. In this study, we have implemented a deep machine learning approach to analyze the resistome of mangrove sediments from Brazil, China, Saudi Arabia, India, and Malaysia. Geography (RANOSIM = 39.26%; p 0.05). Several genes including multidrug efflux pumps were significantly (p ecosystem harbored the lowest ARG diversity (Chao1 = 71.12) followed by mangroves (Chao1 = 258.07) and terrestrial ecosystem (Chao1 = 294.07). ARG subtypes such as abeS and qacG were detected exclusively in ocean datasets. Likewise, rpoB2, multidrug ABC transporter, and macB, detected in mangrove and terrestrial datasets, were not detected in the ocean datasets. This study shows that the socioeconomic factors strongly determine the antibiotic resistome in the mangrove. Direct anthropogenic intervention in the mangrove environment also enriches antibiotic resistome.
The Bornean orangutan is critically endangered and monitoring its population is needed to inform effective conservation management. In this paper, we present results of 2014-17 aerial nest surveys of the major orangutan populations in Sabah and compare them with baseline data produced during surveys conducted in 2002-03 using similar methods. Our results show three important points: a) by increasing the survey effort (estimated at 15-25% cover), sparsely scattered orangutan sub-populations not recorded in the previous aerial surveys were located and the accuracy of the nest count estimates is expected to improve; b) large populations in the interior forests of Sabah, occupying sustainably managed logged and unlogged forests, have been stable over 15 years and are of vital importance for the species' conservation; c) fragmented populations located in eastern Sabah, that are surrounded by extensive oil palm plantations, have declined at varying rates.
Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.
Nest predation is the main cause of hatching failure for many turtle populations. For green turtles (Chelonia mydas) nesting at Chagar Hutang in Redang Island, Malaysia, Asian water monitors (Varanus salvator) are a potential nest predator. However, no studies have documented the space use of this species in coastal habitat adjacent to a sea turtle nesting beach to assess its potential impact on turtle nests. Here, we used Global Positioning System (GPS) data loggers to quantify space use of Asian water monitors in order to establish the extent to which they use sea turtle nesting areas. Asian water monitors had a diurnal activity pattern and spent most of their time in rain forest habitat behind the sea turtle nesting beach. The home range occupied by Asian water monitors varied between 0.015 and 0.198 km2 calculated by the Kernel Brownian Bridge method. The space use patterns of individual Asian water monitors varied between individuals. Two males had relatively small home ranges, whereas one male and the female had a relatively large home range. Because tracked Asian water monitors in this study rarely visited the sea turtle nesting areas, it is probable that only a few individuals are responsible for opening nests.
The ornamental fish trade has been considered as one of the most important routes of invasive alien fish introduction into native freshwater ecosystems. Therefore, the species composition and invasion risks of fish species from 60 freshwater fish pet stores in Klang Valley, Malaysia were studied. A checklist of taxa belonging to 18 orders, 53 families, and 251 species of alien fishes was documented. Fish Invasiveness Screening Test (FIST) showed that seven (30.43%), eight (34.78%) and eight (34.78%) species were considered to be high, medium and low invasion risks, respectively. After the calibration of the Fish Invasiveness Screening Kit (FISK) v2 using the Receiver Operating Characteristics, a threshold value of 17 for distinguishing between invasive and non-invasive fishes was identified. As a result, nine species (39.13%) were of high invasion risk. In this study, we found that non-native fishes dominated (85.66%) the freshwater ornamental trade in Klang Valley, while FISK is a more robust tool in assessing the risk of invasion, and for the most part, its outcome was commensurate with FIST. This study, for the first time, revealed the number of high-risk ornamental fish species that give an awareness of possible future invasion if unmonitored in Klang Valley, Malaysia.
The application of metabarcoding to environmental and invertebrate-derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land-use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood-feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human-modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments.
We introduce a novel framework for conceptualising, quantifying and unifying discordant patterns of species richness along geographical gradients. While not itself explicitly mechanistic, this approach offers a path towards understanding mechanisms. In this study, we focused on the diverse patterns of species richness on mountainsides. We conjectured that elevational range midpoints of species may be drawn towards a single midpoint attractor - a unimodal gradient of environmental favourability. The midpoint attractor interacts with geometric constraints imposed by sea level and the mountaintop to produce taxon-specific patterns of species richness. We developed a Bayesian simulation model to estimate the location and strength of the midpoint attractor from species occurrence data sampled along mountainsides. We also constructed midpoint predictor models to test whether environmental variables could directly account for the observed patterns of species range midpoints. We challenged these models with 16 elevational data sets, comprising 4500 species of insects, vertebrates and plants. The midpoint predictor models generally failed to predict the pattern of species midpoints. In contrast, the midpoint attractor model closely reproduced empirical spatial patterns of species richness and range midpoints. Gradients of environmental favourability, subject to geometric constraints, may parsimoniously account for elevational and other patterns of species richness.
Mosquitoes are principal vectors of major vector-borne diseases. They are widely found throughout urban and rural areas in Malaysia. They are responsible for various vector-borne diseases such as dengue, malaria, filariasis and encephalitis. A total of 158 mosquito larvae specimens were collected from the National Zoo, Malaysia, from 11 types of breeding habitats during the study period from end of May 2007 to July 2007. Aedes albopictus was the predominant species (35.4%), followed by Tripteroides aranoides (26.6%), Lutzia halifaxii (11.4%), Aedes alboscutellatus (10.1%), Aedes caecus (8.9%), Armigeres spp. (4.4%), Malaya genurostris (2.5%) and Culex vishnui (0.6%). It is important to have a mosquito free environment in a public place like the zoo. Routine larval surveillance should be implemented for an effective mosquito control program in order to reduce mosquito population.
Niche theory suggests that sympatric species reduce interspecific competition through segregation of shared resources by adopting different attack manoeuvres. However, the fact that flycatcher-like bird species exclusively use the sally manoeuvre may thus challenge this view. We studied the foraging ecology of three flycatcher-like species (i.e. Paradise-flycatcher Terpsiphone sp., Black-naped Monarch Hypothymis azurea, and Rufous-winged Philentoma Philentoma pyrhoptera) in the Krau Wildlife Reserve in central Peninsular Malaysia. We investigated foraging preferences of each bird species and the potential niche partitioning via spatial or behavioural segregation. Foraging substrate was important parameter that effectively divided paradise-flycatcher from Black-naped Monarch and Rufous-winged Philentoma, where monarch and philentoma foraged mainly on live green leaves, while paradise-flycatcher foraged on the air. They also exhibited different foraging height preferences. Paradise-flycatcher, for instance, preferred the highest studied strata, while Black-naped Monarch foraged mostly in lower strata, and Rufous-winged Philentoma made use of the lowest strata. This study indicates that niche segregation occurs among sympatric species through foraging substrate and attack manoeuvres selection.
Deforestation, climate change and invasive species constitute three global threats to biodiversity that act synergistically. However, drivers and rates of loss of freshwater biodiversity now and in the future are poorly understood. Here we focus on the potential impacts of global change on freshwater mussels (Order Unionida) in Sundaland (SE Asia), a vulnerable group facing global declines and recognized indicators of overall freshwater biodiversity. We used an ensemble of distribution models to identify habitats potentially suitable for freshwater mussels and their change under a range of climate, deforestation and invasion scenarios. Our data and models revealed that, at present, Sundaland features 47 and 32 Mha of habitat that can be considered environmentally suitable for native and invasive freshwater mussels, respectively. We anticipate that by 2050, the area suitable for palm oil cultivation may expand between 8 and 44 Mha, representing an annual increase of 2-11%. This is expected to result in a 20% decrease in suitable habitat for native mussels, a drop that reaches 30% by 2050 when considering concomitant climate change. In contrast, the habitat potentially suitable for invasive mussels may increase by 44-56% under 2050 future scenarios. Consequently, native mussels may compete for habitat, food resources and fish hosts with invasive mussels across approximately 60% of their suitable range. Our projections can be used to guide future expeditions to monitor the conservation status of freshwater biodiversity, and potentially reveal populations of endemic species on the brink of extinction. Future conservation measures-most importantly the designation of nature reserves-should take into account trends in freshwater biodiversity generally, and particularly species such as freshwater mussels, vital to safeguard fundamental ecosystem services.
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.
Human land use is continuously altering the natural environment, yet the greater ecological implications of this change for many groups that are key to healthy ecosystem functioning remains uncharacterised in the tropics. Terrestrial scavenging vertebrates are one such group, providing integral ecosystem services through the removal of carrion which is a crucial component of both nutrient cycling and disease dynamics. To explore how anthropogenic processes may affect forest scavengers, we investigated the changes in the relative occupancy of two important terrestrial scavengers along a gradient of land use intensity, ranging from protected forest to oil palm plantation in Borneo. We found the Malay civet (Viverra tangalunga) had highest, albeit variable, occupancy in areas of low land use intensity and the Southeast Asian water monitor (Varanus salvator macromaculatus) had highest occupancy in areas of high land use intensity. Land use had no effect on the combined occupancy of the two species. In high land use intensity sites, individual water monitors were larger and had better body condition, but at population level had a highly biased sex ratio with more males than females and increased signs of intraspecific conflict. We did not assess scavenging rate or efficiency as a process, but the high occupancy rates and apparent health of the scavengers in high land use intensity landscapes suggests this ecological process is robust to land use change.
A three-dimensional Regional Ocean Modeling System is used to study the seasonal water circulations and transports of the Southern South China Sea. The simulated seasonal water circulations and estimated transports show consistency with observations, e.g., satellite altimeter data set and re-analysis data of the Simple Ocean Data Assimilation. It is found that the seasonal water circulations are mainly driven by the monsoonal wind stress and influenced by the water outflow/inflow and associated currents of the entire South China Sea. The intrusion of the strong current along the East Coast of Peninsular Malaysia and the eddies at different depths in all seasons are due to the conservation of the potential vorticity as the depth increases. Results show that the water circulation patterns in the northern part of the East Coast of Peninsular Malaysia are generally dominated by the geostrophic currents while those in the southern areas are due solely to the wind stress because of negligible Coriolis force there. This study clearly shows that individual surface freshwater flux (evaporation minus precipitation) controls the sea salinity balance in the Southern South China Sea thermohaline circulations. Analysis of climatological data from a high resolution Regional Ocean Modeling System reveals that the complex bathymetry is important not only for water exchange through the Southern South China Sea but also in regulating various transports across the main passages in the Southern South China Sea, namely the Sunda Shelf and the Strait of Malacca. Apart from the above, in comparision with the dynamics of the Sunda Shelf, the Strait of Malacca reflects an equally significant role in the annual transports into the Andaman Sea.
It is generally accepted that organisms that naturally exploit an ecosystem facilitate coexistence, at least partially, through resource partitioning. Resource availability is, however, highly variable in space and time and as such the extent of resource partitioning must be somewhat dependent on availability. Here we test aspects of resource partitioning at the inter- and intra-specific level, in relation to resource availability in an atypical aquatic environment using an isotope approach. Using closely related key organisms from an ephemeral pond, we test for differences in isotopic signatures between two species of copepod and between sexes within each species, in relation to heterogeneity of basal food resources over the course of the ponds hydroperiod. We show that basal food resource heterogeneity increases over time initially, and then decreases towards the end of the hydroperiod, reflective of the expected evolution of trophic complexity for these systems. Resource partitioning also varied between species and sexes, over the hydroperiod with intra- and inter-specific specialisation relating to resource availability. Intra-specific specialisation was particularly evident in the omnivorous copepod species. Our findings imply that trophic specialisation at both the intra- and inter-specific level is partly driven by basal food resource availability.
Leptospirosis, a widespread zoonotic disease, is a public health problem, especially in major urban centres, and is mainly reported to be associated with rats. In Malaysia, focus has been primarily given to the Leptospira prevalence in rodents per se, but there is lack of information on the microhabitat structure of the outbreak areas. We aimed to determine the diversity of small mammal species, microhabitat types, and their prevalence of pathogenic Leptospira spp. in the outbreak areas, which were categorized as urban, semi-urban, and recreational forests. Sampling involved deploying 100 to 300 live traps at each study site. Kidney samples were extracted from selected individuals, for screening of pathogenic Leptospira spp. by PCR. Out of 537 individuals from 15 small mammal species captured, 4 species were recorded from urban, 13 from semi-urban, and 11 from recreational forest sites. From 389 individuals screened, 58 were tested positive for pathogenic Leptospira. Recreational forests recorded the highest prevalence with 19.4% (n = 93), followed by urban, 16.6% (n = 163) and semi-urban sites with 9.8% (n = 133). Seven rodent species were tested positive for pathogenic Leptospira from all areas. R. norvegicus was found to harbour the highest prevalence (66.7%) in urban, R. rattus (53.8%) in semi-urban, whereby M. whiteheadi (44.4%) in recreational forest sites. Microhabitat analysis revealed that rubbish quantity contributed especially strongly to a high prevalence of Leptospira. This study contributes to understanding of the host and microhabitat preferences of Leptospira, which is important in controlling the spread of this disease in human's landscapes.
Soil temperature has a vital importance in biological, physical and chemical processes of terrestrial ecosystem and its modeling at different depths is very important for land-atmosphere interactions. The study compares four machine learning techniques, extreme learning machine (ELM), artificial neural networks (ANN), classification and regression trees (CART) and group method of data handling (GMDH) in estimating monthly soil temperatures at four different depths. Various combinations of climatic variables are utilized as input to the developed models. The models' outcomes are also compared with multi-linear regression based on Nash-Sutcliffe efficiency, root mean square error, and coefficient of determination statistics. ELM is found to be generally performs better than the other four alternatives in estimating soil temperatures. A decrease in performance of the models is observed by an increase in soil depth. It is found that soil temperatures at three depths (5, 10 and 50 cm) could be mapped utilizing only air temperature data as input while solar radiation and wind speed information are also required for estimating soil temperature at the depth of 100 cm.
Elasmobranchs are key to a healthy marine ecosystem but are under threat from human activities, such as destructive fisheries and shark finning. Embryos of oviparous elasmobranchs may be further challenged during development by rising temperatures and falling dissolved oxygen concentrations in their intertidal environment. However, the impact of climate change on survival and growth of oviparous elasmobranchs is still poorly understood. Here, we investigate the effects of temperature and hypoxia on the growth and survival of small-spotted catshark (Scyliorhinus canicula) embryos by incubating eggs in normoxia 15°C, normoxia 20°C, hypoxia 15°C, or hypoxia 20°C. Incubation under the elevated temperature increased the embryonic growth rate, yolk consumption rate and Fulton's condition factor at hatching, whilst decreasing the total length and body mass of newly hatched sharks. Under low oxygen conditions (50% air saturation) the survival rate of S. canicula embryos dropped significantly and the temperature-induced increase in Fulton's condition factor was reversed. Together, these data demonstrate both the individual and compound effects of elevated temperature and hypoxia on the survival and growth during early ontogeny of a ubiquitous, coastal elasmobranch, S. canicula.
Knowledge of niche partitioning with respect to habitat is indispensable to understand the mechanism of coexistence of multiple species. Among primates, however, data are still deficient because repeated survey for a sufficiently long time, covering seasonal changes over a large area, is the only way to clarify habitat segregation within a seasonally fluctuating environment. Southeast Asia is particularly interesting because of the supra-annual, highly unpredictable seasonality in fruiting known as mast fruiting. We conducted repeated route census, habitat monitoring, and group tracking for 25 months in two study sites (ca. 10 km apart) in the largely primary lowland dipterocarp forest of the Danum Valley Conservation Area, eastern Sabah, northern Borneo, Malaysia. The five species of diurnal primates (Bornean orangutan Pongo pygmaeus, Müeller's gibbon Hylobates muelleri, red leaf monkey Presbytis rubicunda, long-tailed macaque Macaca fascicularis, and southern pig-tailed macaque M. nemestrina) did not show horizontal spatial segregation. Red leaf monkeys showed preferences for places with short tree height, but their distribution was not confined to such places. In response to the fruiting peak observed once during the study period, orangutans increased their numbers simultaneously in the two study sites. The average tree height used by the five species was different, but their range overlapped substantially. Compared with other primate communities, the lack of horizontal spatial segregation and the suggested long-distance movement of orangutans seem to be unique characteristics in Borneo, although the use of different forest strata is a widespread phenomenon among primate communities throughout the world.
Our previous study demonstrated that among different habitat sites (mangrove, estuary, river, seagrass and Open Sea) in Johor Strait, Malaysia, seagrass showed highest family diversity and abundance of larval fish. However, it is unclear whether this was due to difference in habitat complexity or water quality parameters.? To test this, larval fish were collected by using a bongo net equipped with a flow meter by subsurface horizontal towing from different habitats in Johor Strait between October 2007 and September 2008.? Various physico-chemical parameters were measured and then examined for any relationship to fish larvae diversity and abundance. Among the 24 families identified from the sites, seven families (Blenniidae, Clupeidae, Mullidae, Nemipteridae, Syngnathidae, Terapontidae and Uranoscopeidae) were significantly correlated with the tested waters quality parameters.? Salinity showed a positive and negative significant correlation with Clupeidae (p < 0.01) and Uranoscopeidae (p < 0.05), respectively. Terapontidae was significantly correlated with dissolved oxygen (p < 0.01), while both Mullidae and Syngnathidae were significantly correlated with pH (p < 0.05). However, a canonical correspondence analysis test indicated weak overall correlation (36.4%) between larval assemblage and in the seagrass-mangrove ecosystem of Johor Strait, Malaysia. This likely indicates that habitat structure was more important in determining larval abundance (highest in the seagrass habitat) as compared to water quality at the tested sites. This study emphasizes the need to conserve seagrass beds as important nursery grounds for various fish larvae to ensure adequate recruitment and ultimately sustainable fisheries management. ?