Displaying publications 81 - 100 of 394 in total

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  1. Effect of condensed tannins on bovine rumen protist diversity based on 18S rRNA gene sequences
    Tan HY, Sieo CC, Abdullah N, Liang JB, Huang XD, Ho YW
    J. Eukaryot. Microbiol., 2013 Jan-Feb;60(1):98-100.
    PMID: 23205499 DOI: 10.1111/jeu.12011
    Molecular diversity of protists from bovine rumen fluid incubated with condensed tannins of Leucaena leucocephala hybrid-Rendang at 20 mg/500 mg dry matter (treatment) or without condensed tannins (control) was investigated using 18S rRNA gene library. Clones from the control library were distributed within nine genera, but clones from the condensed tannin treatment clone library were related to only six genera. Diversity estimators such as abundance-based coverage estimation and Chao1 showed significant differences between the two libraries, although no differences were found based on Shannon-Weaver index and Libshuff.
    Matched MeSH terms: Biodiversity
  2. Fulltext Risk assessment for living modified organisms
    S.L. Tan
    ASM Science Journal, 2013;7(2):129-138.
    MyJurnal
    The paper seeks to assuage the fears and worries over living modified organisms (LMOs). It describes how any research carried out on LMOs as well as any release activity on LMOs for public use in Malaysia is controlled by the Biosafety Act 2007. Stringent risk assessment of the LMO and its product/s is carried out to eradicate or minimize the negative effects of these on animal and human health, and to biological diversity and the environment. In contrast, no such risk assessment is carried out on introduced exotic species, or on the products of other types of technology, with the exception of pharmaceuticals. Examples are given comparing risk assessment on LMOs and exotic species.
    Matched MeSH terms: Biodiversity
  3. Conservation gap analysis of dipterocarp hotspots in Sarawak using GIS, remote sensing and herbarium data
    Stephen P. Teo, Paul P.K. Chai, Mui-How Phua
    Sains Malaysiana, 2013;42:1237-1246.
    Dipterocarpaceae is the dominant tree family in the tropical rain forests of Southeast Asia. Borneo is the centre of diversity for the dipterocarps. Identification of hotspots is important for forest and biodiversity conservation efforts. Species Occurrence Models (SOMs) were generated for all 247 species of dipterocarps recorded in Sarawak using herbarium occurrence data and based on the best model selected. The species occurrence density map for each genus and category (endemic and non endemic) was generated by overlaying the SOMs of all species in each genus or category. The species occurrence density maps were analyzed with land cover map from Landsat 7-EMT+ images and protected forest areas for identifying hotspots for conservation in Sarawak. Overlaying the SOM maps revealed that areas in central Sarawak and the southwest region (northwest Borneo around Kuching) are the main hotspots of dipterocarp diversity in Sarawak while the coastal lowland areas in the lower Rejang and Baram River which are mainly peat swamp forest are poorer in species occurrence density. In terms of endemism, as with dipterocarp diversity, the mixed diptercarp forest of central Sarawak is also the most important hotspot. Gap analysis revealed that most protected forest areas are in southwest Sarawak (Bako, Kubah, Tanjung Datu and Gunung Gading National Parks) and in the northern part of Sarawak (Niah, Lambir Hills and Mt Mulu National Parks). This leaves the hotspot in the central part of Sarawak least protected. Protected areas only cover between 2 and 4% of the total areas for the different hotspots (75% species density) while majority of the hotspots that are still forested are outside the protected areas.
    Matched MeSH terms: Biodiversity
  4. Soil bacterial community structure in five tropical forests in Malaysia and one temperate forest in Japan revealed by pyrosequencing analyses of 16S rRNA gene sequence variation
    Miyashita NT, Iwanaga H, Charles S, Diway B, Sabang J, Chong L
    Genes Genet Syst, 2013;88(2):93-103.
    PMID: 23832301
    Bacterial community structure was investigated in five tropical rainforests in Sarawak, Malaysia and one temperate forest in Kyoto, Japan. A hierarchical sampling approach was employed, in which soil samples were collected from five sampling-sites within each forest. Pyrosequencing was performed to analyze a total of 493,790 16S rRNA amplicons. Despite differences in aboveground conditions, the composition of bacterial groups was similar across all sampling-sites and forests, with Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes accounting for 90% of all Phyla detected. At higher taxonomic levels, the same taxa were predominant, although there was significant heterogeneity in relative abundance of specific taxa across sampling-sites within one forest or across different forests. In all forests, the level of bacterial diversity, estimated using the Chao1 index, was on the order of 1,000, suggesting that tropical rainforests did not necessarily have a large soil bacterial diversity. The average number of reads per species (OTUs) per sampling-site was 8.0, and more than 40-50% of species were singletons, indicating that most bacterial species occurred infrequently and that few bacterial species achieved high predominance. Approximately 30% of species were specific to one sampling-site within a forest, and 40-60% of species were uniquely detected in one of the six forests studied here. Only 0.2% of species were detected in all forests, while on average 32.1% of species were detected in all sampling-sites within a forest. The results suggested that bacterial communities adapted to specific micro- and macro-environments, but macro-environmental diversity made a larger contribution to total bacterial diversity in forest soil.
    Matched MeSH terms: Biodiversity*
  5. Fulltext Building a DNA barcode reference library for the true butterflies (Lepidoptera) of Peninsula Malaysia: what about the subspecies?
    Wilson JJ, Sing KW, Sofian-Azirun M
    PLoS One, 2013;8(11):e79969.
    PMID: 24282514 DOI: 10.1371/journal.pone.0079969
    The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.
    Matched MeSH terms: Biodiversity
  6. Building a discovery partnership with Sarawak Biodiversity Centre: a gateway to access natural products from the rainforests
    Yeo TC, Naming M, Manurung R
    Comb Chem High Throughput Screen, 2014 Mar;17(3):192-200.
    PMID: 24409959
    The Sarawak Biodiversity Centre (SBC) is a state government agency which regulates research and promotes the sustainable use of biodiversity. It has a program on documentation of traditional knowledge (TK) and is well-equipped with facilities for natural product research. SBC maintains a Natural Product Library (NPL) consisting of local plant and microbial extracts for bioprospecting. The NPL is a core discovery platform for screening of bioactive compounds by researchers through a formal agreement with clear benefit sharing obligations. SBC aims to develop partnerships with leading institutions and the industries to explore the benefits of biodiversity.
    Matched MeSH terms: Biodiversity*
  7. Distinct bacterial communities dominate tropical and temperate zone leaf litter
    Kim M, Kim WS, Tripathi BM, Adams J
    Microb Ecol, 2014 May;67(4):837-48.
    PMID: 24549745 DOI: 10.1007/s00248-014-0380-y
    Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.
    Matched MeSH terms: Biodiversity*
  8. Monitoring in the Western Pacific region shows evidence of seagrass decline in line with global trends
    Short FT, Coles R, Fortes MD, Victor S, Salik M, Isnain I, et al.
    Mar Pollut Bull, 2014 Jun 30;83(2):408-16.
    PMID: 24746094 DOI: 10.1016/j.marpolbul.2014.03.036
    Seagrass systems of the Western Pacific region are biodiverse habitats, providing vital services to ecosystems and humans over a vast geographic range. SeagrassNet is a worldwide monitoring program that collects data on seagrass habitats, including the ten locations across the Western Pacific reported here where change at various scales was rapidly detected. Three sites remote from human influence were stable. Seagrasses declined largely due to increased nutrient loading (4 sites) and increased sedimentation (3 sites), the two most common stressors of seagrass worldwide. Two sites experienced near-total loss from of excess sedimentation, followed by partial recovery once sedimentation was reduced. Species shifts were observed at every site with recovering sites colonized by pioneer species. Regulation of watersheds is essential if marine protected areas are to preserve seagrass meadows. Seagrasses in the Western Pacific experience stress due to human impacts despite the vastness of the ocean area and low development pressures.
    Matched MeSH terms: Biodiversity
  9. Fulltext Polyherbal formulation: Concept of ayurveda
    Parasuraman S, Thing GS, Dhanaraj SA
    Pharmacogn Rev, 2014 Jul;8(16):73-80.
    PMID: 25125878 DOI: 10.4103/0973-7847.134229
    Ayurveda is one of the traditional medicinal systems of Indian. The philosophy behind Ayurveda is preventing unnecessary suffering and living a long healthy life. Ayurveda involves the use of natural elements to eliminate the root cause of the disease by restoring balance, at the same time create a healthy life-style to prevent the recurrence of imbalance. Herbal medicines have existed world-wide with long recorded history and they were used in ancient Chinese, Greek, Egyptian and Indian medicine for various therapies purposes. World Health Organization estimated that 80% of the word's inhabitants still rely mainly on traditional medicines for their health care. The subcontinent of India is well-known to be one of the major biodiversity centers with about 45,000 plant species. In India, about 15,000 medicinal plants have been recorded, in which the communities used 7,000-7,500 plants for curing different diseases. In Ayurveda, single or multiple herbs (polyherbal) are used for the treatment. The Ayurvedic literature Sarangdhar Samhita' highlighted the concept of polyherbalism to achieve greater therapeutic efficacy. The active phytochemical constituents of individual plants are insufficient to achieve the desirable therapeutic effects. When combining the multiple herbs in a particular ratio, it will give a better therapeutic effect and reduce the toxicity. This review mainly focuses on important of the polyherbalism and its clinical significance.
    Matched MeSH terms: Biodiversity
  10. Distribution of detritivores in tropical forest streams of peninsular Malaysia: role of temperature, canopy cover and altitude variability
    Che Salmah MR, Al-Shami SA, Abu Hassan A, Madrus MR, Nurul Huda A
    Int J Biometeorol, 2014 Jul;58(5):679-90.
    PMID: 23483291 DOI: 10.1007/s00484-013-0648-9
    The diversity and abundance of macroinvertebrate shredders were investigated in 52 forested streams (local scale) from nine catchments (regional scale) covering a large area of peninsular Malaysia. A total of 10,642 individuals of aquatic macroinvertebrates were collected, of which 18.22% were shredders. Biodiversity of shredders was described by alpha (αaverage), beta (β) and gamma diversity (γ) measures. We found high diversity and abundance of shredders in all catchments, represented by 1,939 individuals (range 6-115 and average per site of 37.29±3.48 SE) from 31 taxa with 2-13 taxa per site (αaverage=6.98±0.33 SE) and 10-15 taxa per catchment (γ=13.33±0.55 SE). At the local scale, water temperature, stream width, depth and altitude were correlated significantly with diversity (Adj-R2=0.205). Meanwhile, dissolved oxygen, stream velocity, water temperature, stream width and altitude were correlated to shredder abundance (Adj-R2=0.242). At regional scale, however, water temperature was correlated negatively with β and γ diversity (r2=0.161 and 0.237, respectively) as well as abundance of shredders (r2=0.235). Canopy cover was correlated positively with β diversity (r2=0.378) and abundance (r2=0.266), meanwhile altitude was correlated positively with β (quadratic: r2=0.175), γ diversity (quadratic: r2=0.848) as well as abundance (quadratic: r2=0.299). The present study is considered as the first report describing the biodiversity and abundance of shredders in forested headwater streams across a large spatial scale in peninsular Malaysia. We concluded that water temperature has a negative effect while altitude showed a positive relationship with diversity and abundance of shredders. However, it was difficult to detect an influence of canopy cover on shredder diversity.
    Matched MeSH terms: Biodiversity*
  11. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests
    Tripathi BM, Lee-Cruz L, Kim M, Singh D, Go R, Shukor NA, et al.
    Microb Ecol, 2014 Aug;68(2):247-58.
    PMID: 24658414
    Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.
    Matched MeSH terms: Biodiversity*
  12. Fulltext A baseline measure of tree and gastropod biodiversity in replanted and natural mangrove stands in malaysia: langkawi island and sungai merbok
    Hookham B, Shau-Hwai AT, Dayrat B, Hintz W
    Trop Life Sci Res, 2014 Aug;25(1):1-12.
    PMID: 25210584 MyJurnal
    THE DIVERSITIES OF MANGROVE TREES AND OF THEIR ASSOCIATED GASTROPODS WERE ASSESSED FOR TWO MANGROVE REGIONS ON THE WEST COAST OF PENINSULAR MALAYSIA: Langkawi Island and Sungai Merbok. The mangrove area sampled on Langkawi Island was recently logged and replanted, whereas the area sampled in Sungai Merbok was part of a protected nature reserve. Mangrove and gastropod diversity were assessed in four 50 m(2) (10 × 5 m) sites per region. The species richness (S), Shannon Index (H') and Evenness Index (J') were calculated for each site, and the mean S, H' and J' values were calculated for each region. We report low tree and gastropod S, H' and J' values in all sites from both regions. For Langkawi Island, the mean S, H' and J' values for mangrove trees were S = 2.00±0, H' = 0.44±0.17 and J' = 0.44±0.17; the mean S, H' and J' values for gastropods were S = 4.00±1.63, H' = 0.96±0.41 and J' = 0.49±0.06. In Sungai Merbok, the mean S, H' and J' values for mangrove trees were S = 1.33±0.58, H' = 0.22±0.39 and J' = 0.22 ±0.39; the mean S, H' and J' values for gastropods were S = 4.75±2.22, H' = 1.23±0.63 and J' = 0.55±0.12. This study emphasises the need for baseline biodiversity measures to be established in mangrove ecosystems to track the impacts of anthropogenic disturbances and to inform management and restoration efforts.
    Matched MeSH terms: Biodiversity
  13. Succession patterns of fungi associated to wound-induced agarwood in wild Aquilaria malaccensis revealed from quantitative PCR assay
    Mohamed R, Jong PL, Nurul Irdayu I
    World J Microbiol Biotechnol, 2014 Sep;30(9):2427-36.
    PMID: 24840100 DOI: 10.1007/s11274-014-1668-2
    Aquilaria malaccensis produces agarwood in response to wounding and fungal attack. However, information is limited regarding Aquilaria's interaction with its diverse fungal community. In this study, time-related changes of three natural fungal colonizers in two wounded wild A. malaccensis were tracked, beginning a few hours after wounding up to 12 months. Using species-specific primers derived from their nrITS sequences in quantitative real-time PCR (qPCR), we quantified the amount of Cunninghamella bainieri, Fusarium solani and Lasiodiplodia theobromae. Because time is a major factor affecting agarwood quantity and quality, 14 wood samples were collected at different time points, i.e., 0-18 h, 2-13 days, 2-18 weeks, and 6-12 months after wounding. qPCR data revealed that the abundance of the three species decreased over time. The fungi were detected in high numbers during the first few hours and days after wounding (40- to 25,000-fold higher levels compared with initial counts) and in low numbers (<1- to 3,200-fold higher than initially) many months later. Consistent with its role in defense response, the accumulation of secondary metabolites at the wounding site could have caused the decline in fungal abundance. Succession patterns of the two trees were not identical, indicating that fungal populations may have been affected by tree environment and wound microclimate. Our results are important for understanding the diversity of microbial community in wild Aquilaria species and their association to wound-induced agarwood formation. Fungi could be secondary triggers to agarwood production in situations where trees are wounded in attempt to induce agarwood.
    Matched MeSH terms: Biodiversity
  14. A global strategy for road building
    Laurance WF, Clements GR, Sloan S, O'Connell CS, Mueller ND, Goosem M, et al.
    Nature, 2014 Sep 11;513(7517):229-32.
    PMID: 25162528 DOI: 10.1038/nature13717
    The number and extent of roads will expand dramatically this century. Globally, at least 25 million kilometres of new roads are anticipated by 2050; a 60% increase in the total length of roads over that in 2010. Nine-tenths of all road construction is expected to occur in developing nations, including many regions that sustain exceptional biodiversity and vital ecosystem services. Roads penetrating into wilderness or frontier areas are a major proximate driver of habitat loss and fragmentation, wildfires, overhunting and other environmental degradation, often with irreversible impacts on ecosystems. Unfortunately, much road proliferation is chaotic or poorly planned, and the rate of expansion is so great that it often overwhelms the capacity of environmental planners and managers. Here we present a global scheme for prioritizing road building. This large-scale zoning plan seeks to limit the environmental costs of road expansion while maximizing its benefits for human development, by helping to increase agricultural production, which is an urgent priority given that global food demand could double by mid-century. Our analysis identifies areas with high environmental values where future road building should be avoided if possible, areas where strategic road improvements could promote agricultural development with relatively modest environmental costs, and 'conflict areas' where road building could have sizeable benefits for agriculture but with serious environmental damage. Our plan provides a template for proactively zoning and prioritizing roads during the most explosive era of road expansion in human history.
    Matched MeSH terms: Biodiversity
  15. Simulium (Simulium) lomkaoense, a New Species of Black Fly (Diptera: Simuliidae) From Thailand
    Takaoka H, Srisuka W, Saeung A, Otsuka Y
    J Med Entomol, 2014 Nov 01;51(6):1109-15.
    PMID: 26309295 DOI: 10.1603/ME14039
    Simulium (Simulium) lomkaoense sp. nov. is described from females, males, pupae, and larvae in Thailand. This new species is assigned to the Simulium malyschevi Dorogostaisky, Rubtsov & Vlasenko species-group of the subgenus Simulium, and appears to be closely related to Simulium baimaii Kuvangkadilok & Takaoka from Thailand in having a similar shape of the female and male genitalia, pupal gill with two inflated filaments, and simple wall-pocket-shaped cocoon. This new species is compared taxonomically with S. baimaii and other related species. It represents the third species of the S. malyschevi species-group known from Thailand.
    Matched MeSH terms: Biodiversity
  16. Fulltext Host-specific microbial communities in three sympatric North Sea sponges
    Naim MA, Morillo JA, Sørensen SJ, Waleed AA, Smidt H, Sipkema D
    FEMS Microbiol Ecol, 2014 Nov;90(2):390-403.
    PMID: 25088929 DOI: 10.1111/1574-6941.12400
    The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An α-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86-92% similar to known sequences.
    Matched MeSH terms: Biodiversity*
  17. Fulltext Female black flies of Simulium (Diptera: Simuliidae) collected on humans in Tam Dao National Park, Vietnam: description of a new species and notes on four species newly recorded from Vietnam
    Takaoka H, Sofian-Azirun M, Ya'cob Z, Chen CD, Lau KW, Pham HT
    Trop Biomed, 2014 Dec;31(4):742-8.
    PMID: 25776600 MyJurnal
    A total of 29 female black flies were captured by a hand net as they swarmed around humans in Tam Dao National Park, Vinh Phuc Province, Vietnam. They included one species of the subgenus Gomphostilbia (Simulium (Gomphostilbia) asakoae Takaoka & Davies) and five species of the subgenus Simulium, of which one species is described as Simulium (Simulium) vietnamense sp. nov. and the other four species (S. (S.) chungi Takaoka & Huang, S. (S.) grossifilum Takaoka & Davies, S. (S.) maenoi Takaoka & Choochote, and S. (S.) rufibasis Brunetti) are newly recorded from Vietnam.
    Matched MeSH terms: Biodiversity*
  18. Fulltext Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora
    Chung KF, Leong WC, Rubite RR, Repin R, Kiew R, Liu Y, et al.
    Bot Stud, 2014 Dec;55(1):1.
    PMID: 28510906 DOI: 10.1186/1999-3110-55-1
    BACKGROUND: The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species.

    RESULTS: Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.

    CONCLUSIONS: Based on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.

    Matched MeSH terms: Biodiversity
  19. Fulltext Spatially explicit trends in the global conservation status of vertebrates
    Rodrigues AS, Brooks TM, Butchart SH, Chanson J, Cox N, Hoffmann M, et al.
    PLoS One, 2014;9(11):e113934.
    PMID: 25426636 DOI: 10.1371/journal.pone.0113934
    The world's governments have committed to preventing the extinction of threatened species and improving their conservation status by 2020. However, biodiversity is not evenly distributed across space, and neither are the drivers of its decline, and so different regions face very different challenges. Here, we quantify the contribution of regions and countries towards recent global trends in vertebrate conservation status (as measured by the Red List Index), to guide action towards the 2020 target. We found that>50% of the global deterioration in the conservation status of birds, mammals and amphibians is concentrated in <1% of the surface area, 39/1098 ecoregions (4%) and eight/195 countries (4%) - Australia, China, Colombia, Ecuador, Indonesia, Malaysia, Mexico, and the United States. These countries hold a third of global diversity in these vertebrate groups, partially explaining why they concentrate most of the losses. Yet, other megadiverse countries - most notably Brazil (responsible for 10% of species but just 1% of deterioration), plus India and Madagascar - performed better in conserving their share of global vertebrate diversity. Very few countries, mostly island nations (e.g. Cook Islands, Fiji, Mauritius, Seychelles, and Tonga), have achieved net improvements. Per capita wealth does not explain these patterns, with two of the richest countries - United States and Australia - fairing conspicuously poorly. Different countries were affected by different combinations of threats. Reducing global rates of biodiversity loss will require investment in the regions and countries with the highest responsibility for the world's biodiversity, focusing on conserving those species and areas most in peril and on reducing the drivers with the highest impacts.
    Matched MeSH terms: Biodiversity
  20. Fulltext Succession of bacterial community structure and diversity in soil along a chronosequence of reclamation and re-vegetation on coal mine spoils in China
    Li Y, Wen H, Chen L, Yin T
    PLoS One, 2014;9(12):e115024.
    PMID: 25502754 DOI: 10.1371/journal.pone.0115024
    The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation.
    Matched MeSH terms: Biodiversity*
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