Two new species of diminutive, sympatric, lowland, leaf-litter skinks of the genus Tytthoscincus Linkem, Diesmos Brown from the Sekayu region of Hulu Terengganu, Terengganu State in northeastern Peninsular Malaysia are described on the basis genetic and morphological data. One of the new species, T. monticolus sp. nov., was collected in a hilly riparian area along Sungai (=river) Bubu and is most closely related to an undescribed species from the Tembak Reservoir area. The other, T. keciktuek sp. nov. collected along Sungai Peres, is most closely related to T. perhentianensis Grismer, Wood, Grismer from Pulau (=island) Perhentian Besar. Sympatry and syntopy of multiple, specialized, unrelated, leaf-litter species of Tytthoscincus was previously only known from upland areas and these new species represent the first example of lowland of sympatry. More importantly, however, these endemic species add to a growing body of research and discoveries that continue to underscore the unrealized biodiversity of the riparian systems of Hulu Terengganu and the Sekayu region and their need for protection and continued study.
The marine pelagic tunicates of Family Salpidae Lahille, 1888 presence in the coastal waters of Terengganu was studied for the first time. Samples were collected from April to July 2016 using 200µm Bongo net; hauled vertically from a stationary vessel; and preserved in 5% buffered formaldehyde. A total of 4 species under this family were found, observed and identified: Thalia rhomboides (Quoy and Gaimard 1824); Thalia sibogae (van Soest 1973); Weelia cylindrica (Cuvier 1804) and Brooksia rostrata (Traustedt 1893). All species were identified as new records in Malaysian waters. The description on morphological characteristics and a key to the solitary and aggregate of the recorded species is added. The distribution was analyzed from the 18 sampling stations in theTerengganu waters including Pulau Bidong, Pulau Yu and Pulau Kapas. The collected data was then compiled with previous available global literature on the distribution and occurrence of these four species, consequently updating the biodiversity of Malaysian fauna and its worldwide biogeography distribution.
Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.
Field studies integrating pollination investigations with an assessment of floral scent composition and thermogenesis in tropical aroids are rather few. Thus, this study aimed to investigate the pollination biology of nine species belonging to Schismatoglottis Calyptrata Complex Clade. The flowering mechanism, visiting insect activities, reproductive system, thermogenesis and floral scent composition were examined. Anthesis for all species started at dawn and lasted 25-29 h. Colocasiomyia (Diptera, Drosophilidae) are considered the main pollinators for all the investigated species. Cycreon (Coleoptera, Hydrophilidae) are considered secondary pollinators as they are only present in seven of the nine host plants, despite the fact that they are the most effective pollen carrier, carrying up to 15 times more pollen grains than Colocasiomyia flies. However, the number of Colocasiomyia individuals was six times higher than Cycreon beetles. Chaloenus (Chrysomelidae, Galeuricinae) appeared to be an inadvertent pollinator. Atheta (Coleoptera, Staphylinidae) is considered a floral visitor in most investigated species of the Calyptrata Complex Clade in Sarawak, but a possible pollinator in S. muluensis. Chironomidae midges and pteromalid wasps are considered visitors in S. calyptrata. Thermogenesis in a biphasic pattern was observed in inflorescences of S. adducta, S. calyptrata, S. giamensis, S. pseudoniahensis and S. roh. The first peak occurred during pistillate anthesis; the second peak during staminate anthesis. Inflorescences of all investigated species of Calyptrata Complex Clade emitted four types of ester compound, with methyl ester-3-methyl-3-butenoic acid as a single major VOC (volatile organic compound). The appendix, pistillate zone, staminate zone and spathe emitted all these compounds. A mixed fly-beetle pollination system is considered an ancestral trait in the Calyptrata Complex Clade, persisting in Sarawak taxa, whereas the marked reduction of interpistillar staminodes in taxa from Peninsular Malaysia and especially, Ambon, Indonesia, is probably linked to a shift in these taxa to a fly-pollinated system.
Tioman Island is one of many sources for underexplored actinobacterial diversity in Malaysia. Selective isolation, molecular profiling, 16S rRNA gene sequencing and phylogenetic analyses were carried out to highlight the diversity of the marine actinobacterial community in a sediment collected off Tioman Island. A high number of diverse actinobacteria were recovered using skim milk/HEPES pre-treatment on a mannitol-based medium. A total of 123 actinobacterial strains were isolated, including thirty obligate marine actinobacteria putatively identified as Salinispora spp. Molecular fingerprinting profiles obtained with a double digestion approach grouped the remaining non-Salinispora-like strains into 24 different clusters, with Streptomyces and Blastococcus as the major clusters. A total of 17 strains were identified as novel actinobacterial species within the genera Streptomyces (n = 6), Blastococcus (n = 5), Marinactinospora (n = 3), Nocardiopsis (n = 1), Agromyces (n = 1) and Nonomuraea (n = 1) based on 16S rRNA gene sequence analyses. Polyphasic data from three putative Marinactinospora spp. showed that the strains represent a new genus in the Nocardiopsaceae family. Crude extracts from the strains were also found to inhibit the growth of Gram-positive (Staphylococcus aureus, Bacillus subtilis) and Gram-negative (Providencia alcalifaciens) pathogens. Hierarchical clustering of the bioactivities of an active fraction revealed a unique profile, which is closely related that of fosfomycin.
Understanding how anthropogenic disturbance influences patterns of community composition and the reinforcing interactive processes that structure communities is important to mitigate threats to biodiversity. Competition is considered a primary reinforcing process, yet little is known concerning disturbance effects on competitive interaction networks. We examined how differences in ant community composition between undisturbed and disturbed Bornean rainforest, is potentially reflected by changes in competitive interactions over a food resource. Comparing 10 primary forest sites to 10 in selectively-logged forest, we found higher genus richness and diversity in the primary forest, with 18.5% and 13.0% of genera endemic to primary and logged respectively. From 180 hours of filming bait cards, we assessed ant-ant interactions, finding that despite considered aggression over food sources, the majority of ant interactions were neutral. Proportion of competitive interactions at bait cards did not differ between forest type, however, the rate and per capita number of competitive interactions was significantly lower in logged forest. Furthermore, the majority of genera showed large changes in aggression-score with often inverse relationships to their occupancy rank. This provides evidence of a shuffled competitive network, and these unexpected changes in aggressive relationships could be considered a type of competitive network re-wiring after disturbance.
Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales. Genomic sequence analyses revealed phage YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content. Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome, using bioinformatics annotation software; Rapid Annotation using Subsystem Technology (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are classified as hypothetical proteins and there are two unidentified proteins. Even though majority of the coded putative proteins have high amino acids similarities to phages from the genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its' own distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.
The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×107 and 1.50×107, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.
Tropical rainforests are subject to extensive degradation by commercial selective logging. Despite pervasive changes to forest structure, selectively logged forests represent vital refugia for global biodiversity. The ability of these forests to buffer temperature-sensitive species from climate warming will be an important determinant of their future conservation value, although this topic remains largely unexplored. Thermal buffering potential is broadly determined by: (i) the difference between the "macroclimate" (climate at a local scale, m to ha) and the "microclimate" (climate at a fine-scale, mm to m, that is distinct from the macroclimate); (ii) thermal stability of microclimates (e.g. variation in daily temperatures); and (iii) the availability of microclimates to organisms. We compared these metrics in undisturbed primary forest and intensively logged forest on Borneo, using thermal images to capture cool microclimates on the surface of the forest floor, and information from dataloggers placed inside deadwood, tree holes and leaf litter. Although major differences in forest structure remained 9-12 years after repeated selective logging, we found that logging activity had very little effect on thermal buffering, in terms of macroclimate and microclimate temperatures, and the overall availability of microclimates. For 1°C warming in the macroclimate, temperature inside deadwood, tree holes and leaf litter warmed slightly more in primary forest than in logged forest, but the effect amounted to <0.1°C difference between forest types. We therefore conclude that selectively logged forests are similar to primary forests in their potential for thermal buffering, and subsequent ability to retain temperature-sensitive species under climate change. Selectively logged forests can play a crucial role in the long-term maintenance of global biodiversity.
Animals can have both positive (e.g. via seed dispersal) and negative (e.g. via herbivory) impacts on plants. The net effects of these interactions remain difficult to predict and may be affected by overhunting and habitat disturbance, two widespread threats to tropical forests. Recent studies have documented their separate effects on plant recruitment but our understanding of how defaunation and logging interact to influence tropical tree communities is limited. From 2013 to 2016, we followed the fate of marked tree seedlings (n = 1489) from 81 genera in and outside experimental plots. Our plots differentially excluded small, medium and large-bodied mammal herbivores in logged and unlogged forest in Malaysian Borneo. We assessed the effects of experimental defaunation and logging on taxonomic diversity and plant trait (wood density, specific leaf area, fruit size) composition of seedling communities. Although seedling mortality was highest in the presence of all mammal herbivores (44%), defaunation alone did not alter taxonomic diversity nor plant trait composition. However, herbivores (across all body sizes) significantly reduced mean fruit size across the seedling community over time (95% confidence interval (CI): -0.09 to -0.01), particularly in logged forest (95% CI: -0.12 to -0.003). Our findings suggest that impacts of mammal herbivores on plant communities may be greater in forests with a history of disturbance and could subsequently affect plant functional traits and ecological processes associated with forest regeneration.
Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests.
Decline in forest productivity due to forest conversion is defining the Bornean landscape. Responses of bacterial communities due to land-use changes are vital and could define our understanding of ecosystem functions. This study reports the changes in bacterial community structure in organic soil (0-5 cm; O-Horizon) and organic-mineral soil (5-15 cm; A-Horizon) across Maliau Basin Conservation Area old growth forest (MBOG), Fragment E logged forest (FELF) located in Kalabakan Forest Reserve to Benta Wawasan oil palm plantation (BWOP) using two-step PCR amplicon analysis of bacteria DNA on Illumina Miseq next generation sequencing. A total of 30 soil samples yielded 893,752-OTU reads at ≥97% similarity from 5,446,512 good quality sequences. Soil from BWOP plantation showed highest unshared OTUs for organic (49.2%) and organic-mineral (50.9%) soil. MBOG soil showed a drop in unshared OTUs between organic (48.6%) and organic-mineral (33.9%). At phylum level, Proteobacteria dominated MBOG but shifted to Actinobacteria in logged and plantation soil. Present findings also indicated that only FELF exhibited change in bacterial communities along the soil depth, moving from the organic to the organic-mineral layer. Both layers of BWOP plantation soils deviated from other forests' soil in β-diversity analysis. To our knowledge, this is the first report on transitions of bacterial community structures with different soil horizons in the tropical rainforest including Borneo, Sabah. Borneo tropical soils form a large reservoir for soil bacteria and future exploration is needed for fully understanding the diversity structure and their bacterial functional properties.
Over half of globally threatened animal species have experienced rapid geographic range loss. Identifying the parts of species' distributions most vulnerable to local extinction would benefit conservation planning. However, previous studies give little consensus on whether ranges decline to the core or edge. We built on previous work by using empirical data to examine the position of recent local extinctions within species' geographic ranges, address range position as a continuum, and explore the influence of environmental factors. We aggregated point-locality data for 125 Galliform species from across the Palearctic and Indo-Malaya into equal-area half-degree grid cells and used a multispecies dynamic Bayesian occupancy model to estimate rates of local extinctions. Our model provides a novel approach to identify loss of populations from within species ranges. We investigated the relationship between extinction rates and distance from range edge by examining whether patterns were consistent across biogeographic realm and different categories of land use. In the Palearctic, local extinctions occurred closer to the range edge than range core in both unconverted and human-dominated landscapes. In Indo-Malaya, no pattern was found for unconverted landscapes, but in human-dominated landscapes extinctions tended to occur closer to the core than the edge. Our results suggest that local and regional factors override general spatial patterns of recent local extinction within species' ranges and highlight the difficulty of predicting the parts of a species' distribution most vulnerable to threat.
Resting strategies of planktonic organisms are important for the ecological processes of coastal waters and their impacts should be taken into consideration in management of water bodies used by multiple industries. We combined different approaches to evaluate the importance of resting stages in Singapore coastal waters. We used molecular approaches to improve the knowledge on Singapore biodiversity, we sampled and extracted cysts from sediments to evaluate the density of resting stages in Johor Strait, and we compared systematically information on Singapore planktonic biodiversity to existing published information on resting stages from these reported organisms. This is the first study evaluating the importance of resting stages in Singapore waters. Above 120 species reported in Singapore are known to produce resting stages though no previous work has ever been done to evaluate the importance of these strategies in these waters. The results from the resting stage survey confirmed 0.66 to 5.34 cyst g-1 dry weight sediment were present in the Johor Strait suggesting that cysts may be flushed by tidal currents into and out of the strait regularly. This also suggest that the blooms occurring in Singapore are likely due to secondary growth of Harmful Algae Bloom species in the water rather than from direct germination of cysts from sediment. Finally, we discuss the importance of these resting eggs for three main national industries in Singapore (shipping, marine aquaculture and provision of drinking water through seawater desalination). We argue that this study will serve as a baseline for some of the future management of Singapore waters.
The Mamut Copper Mine (MCM) located in Sabah (Malaysia) on Borneo Island was the only Cu-Au mine that operated in the country. During its operation (1975-1999), the mine produced 2.47 Mt of concentrate containing approximately 600,000 t of Cu, 45 t of Au and 294 t of Ag, and generated about 250 Mt of overburden and waste rocks and over 150 Mt of tailings, which were deposited at the 397 ha Lohan tailings storage facility, 15.8 km from the mine and 980 m lower in altitude. The MCM site presents challenges for environmental rehabilitation due to the presence of large volumes of sulphidic minerals wastes, the very high rainfall and the large volume of polluted mine pit water. This indicates that rehabilitation and treatment is costly, as for example, exceedingly large quantities of lime are needed for neutralisation of the acidic mine pit discharge. The MCM site has several unusual geochemical features on account of the concomitant occurrence of acid-forming sulphide porphyry rocks and alkaline serpentinite minerals, and unique biological features because of the very high plant diversity in its immediate surroundings. The site hence provides a valuable opportunity for researching natural acid neutralisation processes and mine rehabilitation in tropical areas. Today, the MCM site is surrounded by protected nature reserves (Kinabalu Park, a World Heritage Site, and Bukit Hampuan, a Class I Forest Reserve), and the environmental legacy prevents de-gazetting and inclusion in these protected area in the foreseeable future. This article presents a preliminary geochemical investigation of waste rocks, sediments, secondary precipitates, surface water chemistry and foliar elemental uptake in ferns, and discusses these results in light of their environmental significance for rehabilitation.
Selective logging that is commonly conducted in tropical forests may change tree species diversity. In rarely disturbed tropical forests, locally rare species exhibit higher survival rates. If this non-random process occurs in a logged forest, the forest will rapidly recover its tree species diversity. Here we determined whether a forest in the Pasoh Forest Reserve, Malaysia, which was selectively logged 40 years ago, recovered its original species diversity (species richness and composition). To explore this, we compared the dynamics of secies diversity between unlogged forest plot (18.6 ha) and logged forest plot (5.4 ha). We found that 40 years are not sufficient to recover species diversity after logging. Unlike unlogged forests, tree deaths and recruitments did not contribute to increased diversity in the selectively logged forests. Our results predict that selectively logged forests require a longer time at least than our observing period (40 years) to regain their diversity.
The extent to which distinct bacterial endophyte communities occur between different plant organs and species is poorly known and has implications for bioprospecting efforts. Using the V3 region of the bacterial 16S ribosomal RNA (rRNA) gene, we investigated the diversity patterns of bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes plus rhizosphere soil community. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species. The non-metric multidimensional scaling (NMDS) analysis highlighted an extensively overlapping bacterial community structure, and the β-nearest taxon index (βNTI) analysis revealed dominance of stochastic processes in community assembly, suggesting that bacterial endophyte operational taxonomic units (OTUs) were randomly distributed among plant species and organs and rhizosphere soil. Percentage turnover of OTUs within pairs of samples was similar both for plant individuals of the same species and of different species at around 80-90%. Our results suggest that sampling extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. These observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.
The aim of this study is to examine the impact of air pollutants, including mono-nitrogen oxides (NOx), nitrous oxide (N2O), sulfur dioxide (SO2), carbon dioxide emissions (CO2), and greenhouse gas (GHG) emissions on ecological footprint, habitat area, food supply, and biodiversity in a panel of thirty-four developed and developing countries, over the period of 1995-2014. The results reveal that NOx and SO2 emissions both have a negative relationship with ecological footprints, while N2O emission and real GDP per capita have a direct relationship with ecological footprints. NOx has a positive relationship with forest area, per capita food supply and biological diversity while CO2 emission and GHG emission have a negative impact on food production. N2O has a positive impact on forest area and biodiversity, while SO2 emissions have a negative relationship with them. SO2 emission has a direct relationship with per capita food production, while GDP per capita significantly affected per capita food production and food supply variability across countries. The overall results reveal that SO2, CO2, and GHG emissions affected potential habitat area, while SO2 and GHG emissions affected the biodiversity index. Trade liberalization policies considerably affected the potential habitat area and biological diversity in a panel of countries.
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.