Levels and distribution patterns of mitochondrial cox3 gene variation in brown seaweed,Sargassum polycystum C. Agardh (Fucales,Phaeophyceae) from Southeast Asia

Sargassum polycystum C. Agardh is one of the most abundant marine brown algae and is distributed widely in warm and temperate waters, particularly in the Indo-west Pacific region and Australia. Although its commercial potential and ecological and evolutionary importance are recognized, many pivotal aspects of its biology remain unexplored. Current knowledge of the historical biogeographical affinities and patterns is limited, but some data are available about its genetics, the genetic variation among populations, and spatial patterns. This study aimed to analyze the genetic population structure and distribution patterns of S. polycystum populations in 13 different locations from Indonesia to Japan using the mitochondrial gene cox3. The seven haplotypes of cox3 identified in this study indicated a low level of genetic diversity. Homogeneity of this haplotype was observed particularly in the Gulf of Thailand, Cambodia, and Japan, whereas higher haplotype diversity was found in Phuket (Thailand), Bali (Indonesia), and Singapore. Those data suggest that S. polycystum is likely to have expanded from the south of Indonesia and the west of the Malay Peninsula towards the northeast of the region. Geological studies showed that Sundaland, now corresponding to the Gulf of Thailand, was submerged due to sea level rises after the last glacial period. Therefore, the decrease in the genetic diversity of S. polycystum populations is interpreted here as a population expansion after the rise in sea levels.     

Anti-microfouling Activity of Lipidic Metabolites from the Invasive Brown Alga Sargassum muticum (Yendo) Fensholt

The purification of the chloroform extract from the brown invasive macroalga Sargassum muticum, through a series of chromatographic separations, yielded 12 fractions that were tested against strains of bacteria, microalgae, and fungi involved in marine biofilm formation. The chemical composition of four (a, c, g, and k) out of the six fractions that exhibited anti-microfouling activity was investigated. Fraction a contained saturated and unsaturated linear hydrocarbons (C₁₂–C₂₇). Arachidonic acid was identified as the major metabolite in fraction c whereas fraction g contained mainly palmitic, linolenic, and palmitoleic acids. Fraction k was submitted to further purification yielding the fraction kAcaF1e that was composed of galactoglycerolipids, active against the growth of two of the four bacterial strains (Shewanella putrefaciens and Polaribacter irgensii) and all tested fungi. These promising results, in particular the isolation and the activity of galactoglycerolipids, attest the potential of the huge biomass of S. muticum as a source of new environmentally friendly antifouling compounds.     

An Analysis of Age Structure and the Strategy for Asexual Propagation of Aneurolepidium chinense Population

Aneurolepidiurn chinense (Trin.) Kitag. is a rhizome grass. Among the total earing plants of the population in natural cutting grassland, 87 % was winterness plants. The oldest tillering node was four age, and its life time would reach five years. The plants of one and two age held the absolute dominant position and their proportion was 92.5% in the age structure of developing plants from the tillering nodes. The productivity of one age plants was the highest among plants of the total ages, whereas the vitalities of plants were evidently weakened by the third age. On the age structure, A. chinense population in the cutting grassland was a type of mixed population which was an expanding and a stable population. The strategy of asexual propagation, in which the age structure of the population would be regulated by developing plants from rhizome end, and the mechanism of biology and ecology on natural sustaining renovation of A. chinense grassland were comprehensively analysed.     

Genetic Admixture in the Culturally Unique Peranakan Chinese Population in Southeast Asia

The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300–500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.76–6.49%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.65–1.51%), southern Chinese (0.86%, 0.50–1.23%), and northern Chinese (0.25%, 0.18–0.32%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345–1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159–213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.     

Population structure and population history of Anopheles dirus mosquitoes in Southeast Asia

Separating the confounding effects of long-term population history from gene flow can be difficult. Here, we address the question of what inferences about gene flow can be made from mitochondrial sequence data in three closely related species of mosquitoes, Anopheles dirus species A, C, and D, from southeast Asia. A total of 84 sequences of 923 bp of the mitochondrial cytochrome oxidase I gene were obtained from 14 populations in Thailand, Myanmar, and Bangladesh. The genealogy of sequences obtained from two populations of AN: dirus C indicates no contemporary gene flow between them. The F(ST) value of 0.421 therefore probably represents a recent common history, perhaps involving colonization events. Anopheles dirus A and D are parapatric, yet no differentiation was seen either within or between species. The starlike genealogy of their haplotypes, smooth unimodal mismatch distributions, and excess of low frequency mutations indicate population expansion in An. dirus A and D. This, rather than widespread gene flow, explains their low within-species F(ST) values (0.018 and 0.022). The greater genetic diversity of An. dirus D suggests that expansion occurred first in species D and subsequently in species A. The current geographical separation and low hybrid fitness of these species also argue against ongoing interspecific gene flow. They suggest instead either historical introgression of mtDNA from An. dirus D into species A followed by independent range expansions, or a selective sweep of mtDNA that originated in An. dirus D. While not excluding contemporary gene flow, historical population processes are sufficient to explain the data in An. dirus A and D. The genealogical relationships between haplotypes could not be used to make inferences of gene flow because of extensive homoplasy due to hypervariable sites and possibly also recombination. However, it is concluded that this approach, rather than the use of fixation indices, is required in the future to understand contemporary gene flow in these mosquitoes. The implications of these results for understanding gene flow in another important and comparable group of malaria vector mosquitoes in Africa, the An. gambiae complex, are also discussed.     

Use of Expansion Factors to Estimate the Burden of Dengue in Southeast Asia: A Systematic Analysis

Background

Dengue virus infection is the most common arthropod-borne disease of humans and its geographical range and infection rates are increasing. Health policy decisions require information about the disease burden, but surveillance systems usually underreport the total number of cases. These may be estimated by multiplying reported cases by an expansion factor (EF).

Methods and Findings

As a key step to estimate the economic and disease burden of dengue in Southeast Asia (SEA), we projected dengue cases from 2001 through 2010 using EFs. We conducted a systematic literature review (1995–2011) and identified 11 published articles reporting original, empirically derived EFs or the necessary data, and 11 additional relevant studies. To estimate EFs for total cases in countries where no empirical studies were available, we extrapolated data based on the statistically significant inverse relationship between an index of a country''s health system quality and its observed reporting rate. We compiled an average 386,000 dengue episodes reported annually to surveillance systems in the region, and projected about 2.92 million dengue episodes. We conducted a probabilistic sensitivity analysis, simultaneously varying the most important parameters in 20,000 Monte Carlo simulations, and derived 95% certainty level of 2.73–3.38 million dengue episodes. We estimated an overall EF in SEA of 7.6 (95% certainty level: 7.0–8.8) dengue cases for every case reported, with an EF range of 3.8 for Malaysia to 19.0 in East Timor.

Conclusion

Studies that make no adjustment for underreporting would seriously understate the burden and cost of dengue in SEA and elsewhere. As the sites of the empirical studies we identified were not randomly chosen, the exact extent of underreporting remains uncertain. Nevertheless, the results reported here, based on a systematic analysis of the available literature, show general consistency and provide a reasonable empirical basis to adjust for underreporting.     

High Resolution Population Distribution Maps for Southeast Asia in 2010 and 2015

Spatially accurate, contemporary data on human population distributions are vitally important to many applied and theoretical researchers. The Southeast Asia region has undergone rapid urbanization and population growth over the past decade, yet existing spatial population distribution datasets covering the region are based principally on population count data from censuses circa 2000, with often insufficient spatial resolution or input data to map settlements precisely. Here we outline approaches to construct a database of GIS-linked circa 2010 census data and methods used to construct fine-scale (∼100 meters spatial resolution) population distribution datasets for each country in the Southeast Asia region. Landsat-derived settlement maps and land cover information were combined with ancillary datasets on infrastructure to model population distributions for 2010 and 2015. These products were compared with those from two other methods used to construct commonly used global population datasets. Results indicate mapping accuracies are consistently higher when incorporating land cover and settlement information into the AsiaPop modelling process. Using existing data, it is possible to produce detailed, contemporary and easily updatable population distribution datasets for Southeast Asia. The 2010 and 2015 datasets produced are freely available as a product of the AsiaPop Project and can be downloaded from: www.asiapop.org.     

Anti-obesity property of the brown seaweed,Sargassum polycystum using an in vivo animal model

Obesity has reached epidemic proportions in many countries around the world. Preventing and treating obesity is becoming an increasing priority due to dissatisfaction with high costs and hazardous side effects of anti-obesity drugs. This study was designed to investigate the anti-obesity properties of the Sabah brown seaweed, Sargassum polycystum, on body weight and blood plasma levels of rats fed a high-fat diet supplemented with different doses of the seaweed powder. Male Sprague Dawley rats were divided into five groups, representing control negative (CN) group, control positive (CP) group, low dosage group (LDG), medium dosage group (MDG) and high dosage group (HDG). The study duration was 8 weeks. All groups were fed high-fat diet throughout the study except for CN group, which was fed normal rat chow. LDG, MDG and HDG were supplemented high-fat diet with 2.5, 5.0 and 10.0 % seaweed powder, respectively. By comparing with the CP group, it was found that the HDG (10.0 % seaweed treatment diet) showed the greatest effect in suppressing weight gain, followed by the MDG (5.0 % seaweed treatment diet) and LDG (2.5 % seaweed treatment diet). The HDG decreased the levels of plasma total cholesterol and triglycerides. This finding shows that S. polycystum powder treatment had a positive effect on the inhibition of weight gain and has a promising value in preventing obesity.     

Seasonal studies on the alginate and its biochemical composition I: Sargassum polycystum (Fucales), Phaeophyceae

Investigations were made on the brown seaweed Sargassum polycystum C. Agardh collected from Rameswaram Coast, Tamil Nadu. The alginates extracted from ‘leaf’, ‘stem’ and entire thallus of S. polycystum were investigated for their viscosity and chemical constituents, namely β‐D‐mannuronic acid (M‐block), α‐L‐guluronic acid (G‐block) and alternating sequences of β‐D‐mannuronic acid and α‐L‐guluronic acid (MG‐block) for six different seasons between August 1998 and November 1999. Significant seasonal variation (P< 0.05) was observed with high yield of alginate in February. The alginate extracted from the ‘leaf’ region showed a maximum yield whereas the ‘stem’ region exhibited maximum viscosity. The amount of G‐block was found to be more than M‐ and MG‐blocks in all the samples tested. The amount of G‐block was high in ‘stem’ followed by leaf and entire thallus. A positive correlation was recorded between viscosity and G‐block. Among the three alginates, the ratio of M/G was low in the ‘stem’ followed by ‘leaf’ and entire thallus.     

Insight into the Peopling of Mainland Southeast Asia from Thai Population Genetic Structure

There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects.     

Immunohistochemical localization of endogenous D-Aspartate in the marine brown Alga Sargassum fusiforme

Immunohistochemical localization (cellular localization) of endogenous D-aspartate in the marine brown alga Sargassum fusiforme was investigated by the use of a specific polyclonal antibody raised against D-aspartate. D-Aspartate immunoreactivity was evident in the medullary layer in the blade of the alga, and weak staining was found in the cortical layer, whereas epidermal cells were found to lack D-aspartate. Within the cells of the layers, immunoreactivity was confirmed only in the cytosol and not in the cell wall, chloroplast, or vacuole. These results suggest that D-aspartate is present in S. fusiforme cells, and excludes the possibility that it is derived from attached or symbiotic organisms such as marine bacteria. This is the first report describing the localization of free D-aspartate in plant cells.     

Linking Up: The Role of Institutions and Farmers in Forage Seed Exchange Networks of Southeast Asia

Human Ecology - In Southeast Asia, access to improved forages remains a challenge for smallholder farmers and limits livestock production. We compared seed exchange networks supporting two...     

The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia

Background

Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning.

Methodology and Principal Findings

DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized.

Conclusions

DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.     

Artificial Seed Production and Cultivation of the Edible Brown Alga, Sargassum Fulvellum (Turner) C. Agardh: Developing a new Species for Seaweed Cultivation in Korea

Sargassum fulvellum is a brown alga recently introduced to the seaweed cultivation industry in Korea. There is current interest in the commercial scale of aquaculture of this species. For the artificial seeding and cultivation of this alga, growth and maturation were investigated from September 2002 to August 2003. Indoor culture experiments for maturation induction were also conducted at temperatures of 5, 10, 15, 20 and 25 ^∘C and irradiances of 20, 50, 80 and 100 μmol photons m⁻² s⁻¹ under 16:8 h (L:D) photoperiod. Within a given culture test range, higher temperature and irradiance levels favoured the maturation of receptacles in S. fulvellum. Using temperature and irradiance control for thalli, artificial seed production of this species could be done one month earlier than thalli matured in nature. Under natural condition, receptacle formation of the plants began in February, and the eggs were released from March to April. For mature thalli of 200 g wet wt., artificial seeding was complete enough for attachment on seed strings of 100 m. Mean production obtained from the artificial seeding technique in situ was 3.0 kg wet wt m⁻¹ of culture rope during the cultivation period.     

Expansion of Brown Bears (Ursus arctos) into the Eastern Alps: A Spatially Explicit Population Model

We present a spatially explicit population model for analysing the expansion of brown bears (Ursus arctos) after the reintroduction program in central Austria. The model is based on field investigations into brown bears in Austria and Slovenia and on current knowledge of brown bears. The landscape of the eastern Alps is represented by a GIS-derived raster map defining local habitat suitability and five major spatial barriers to dispersal. The population model follows the fate of individual bears and simulates reproduction, dispersal, home range establishment, and mortality in annual time steps. We indirectly adjust unknown or uncertain model parameters with 10-year data on the number of females with cubs in central Austria and determine key variables of population dynamics, such as population sizes and growth rates within different population nuclei, dispersal distances, or mortality rates, for model parameterisations that reproduce the data on females with cubs. We estimated a current (1996–2000) growth rate of the population in Austria and adjacent parts of Italy of some 14%; a high proportion of this growth was due toimmigration from Slovenia. Consequently, the growth rate of the subpopulation in central Austria, which probably is isolated functionally (i.e., no exchange of females) from the nuclei along the Austrian–Slovenian border, yielded some 7%. This subpopulation may comprise seven residents, and we estimated for females a 33% risk of extinction during the 1992–2000 period. Validation and confirmation of our model results with data on bear densities that were not used for model construction and parameterisation supported our findings. The high female mortality rates, together with the vulnerability of the small population to chance events (i.e., demographic stochasticity), are the most pressing threat for the population in the eastern Alps. Our approach could be widely applied for analysing dynamics of rare and endangered species in which the paucity of data precludes an appraisal of the state of the population using standard methods.     

Effects of Logging and Oil Palm Expansion on Stream Frog Communities on Borneo,Southeast Asia

The conversion of tropical rain forests to oil palm plantations is a major threat to Southeast Asia's rich biodiversity. Fostering forest species communities in secondary forests, agroforestry systems, and plantations is therefore increasingly becoming a conservation focus. This study uses standardized transect‐based sampling to compare species richness, density and community composition of stream anuran assemblages among primary forests, repeatedly logged forests and oil palm plantations in northern Borneo. In primary forest streams, we recorded an average of 19 frog species, compared to 15 species in logged forests and 11 species in oil palm plantation streams. However, the high percentage of canopy cover above the plantation streams mitigated this loss to some extent. This study corroborates numerous studies that oil palm plantations have mainly negative effects on the region's biodiversity. However, our results also demonstrate the high conservation value of logged forests for Bornean stream‐dependent anurans. We conclude that palm plantations have a largely unused potential to promote regional anuran biodiversity.     

Abnormal Fossil Upper Molar of Pongo from Thailand: Quaternary Climatic Changes in Southeast Asia as a Possible Cause

We interpret an unusual left M ³ attributed to Pongo from the Late Middle Pleistocene of Thailand to be an abnormal tooth rather than a supernumerary molar. Its peculiar morphology cannot be related to classical known causes that affect the dental germ: Gemination, schizodontia, synodontia. The ontogenic mechanism that might have led to the morphology of the tooth perhaps reflects stress related to a phase of marked climatic changes during the Late Middle Pleistocene in Southeast Asia.