VNU Central Institute for Natural Resources and Environmental Studies

Traditionally, people have inhabited places with ready access to fresh water. Today, over 50% of the global population lives in urban areas, and water can be directed via tens of kilometres of pipelines. Still, however, a large part of the world's population is directly dependent on access to natural freshwater sources. So how are inhabited places related to the location of freshwater bodies today? We present a high-resolution global analysis of how close present-day populations live to surface freshwater. We aim to increase the understanding of the relationship between inhabited places, distance to surface freshwater bodies, and climatic characteristics in different climate zones and administrative regions. Our results show that over 50% of the world's population lives closer than 3 km to a surface freshwater body, and only 10% of the population lives further than 10 km away. There are, however, remarkable differences between administrative regions and climatic zones. Populations in Australia, Asia, and Europe live closest to water. Although populations in arid zones live furthest away from freshwater bodies in absolute terms, relatively speaking they live closest to water considering the limited number of freshwater bodies in those areas. Population distributions in arid zones show statistically significant relationships with a combination of climatic factors and distance to water, whilst in other zones there is no statistically significant relationship with distance to water. Global studies on development and climate adaptation can benefit from an improved understanding of these relationships between human populations and the distance to fresh water.

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

Abstract Noncoding DNA is central to our understanding of human gene regulation and complex diseases 1,2 , and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome 3–9 . Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA 10 , the relatively short timescales separating primate species 11 , and the previously limited availability of whole-genome sequences 12 . Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis -regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range dispersal. To examine the extent of seedling dispersal across oceans, we investigated the phylogeny and genetic structure among East Asiatic populations of Kandelia candel based on organelle DNAs. In total, three, 28 and seven haplotypes of the chloroplast DNA (cpDNA) atpB-rbcL spacer, cpDNA trnL-trnF spacer, and mitochondrial DNA (mtDNA) internal transcribed spacer (ITS) were identified, respectively, from 202 individuals. Three data sets suggested consistent phylogenies recovering two differentiated lineages corresponding to geographical regions, i.e. northern South-China-Sea + East-China-Sea region and southern South-China-Sea region (Sarawak). Phylogenetically, the Sarawak population was closely related to the Ranong population of western Peninsula Malaysia instead of other South-China-Sea populations, indicating its possible origin from the Indian Ocean Rim. No geographical subdivision was detected within the northern geographical region. An analysis of molecular variance (AMOVA) revealed low levels of genetic differentiation between and within mainland and island populations (phiCT = 0.015, phiSC = 0.037), indicating conspicuous long-distance seedling dispersal across oceans. Significant linkage disequilibrium excluded the possibility of recurrent homoplasious mutations as the major force causing phylogenetic discrepancy between mtDNA and the trnL-trnF spacer within the northern region. Instead, relative ages of alleles contributed to non-random chlorotype-mitotype associations and tree inconsistency. Widespread distribution and random associations (chi2 = 0.822, P = 0.189) of eight hypothetical ancestral cytotypes indicated the panmixis of populations of the northern geographical region as a whole. In contrast, rare and recently evolved alleles were restricted to marginal populations, revealing some preferential directional migration.

Compartmentation is a key strategy enacted by plants for the storage of specialized metabolites. The saffron spice owes its red color to crocins, a complex mixture of apocarotenoid glycosides that accumulate in intracellular vacuoles and reach up to 10% of the spice dry weight. We developed a general approach, based on coexpression analysis, heterologous expression in yeast (Saccharomyces cerevisiae), and in vitro transportomic assays using yeast microsomes and total plant metabolite extracts, for the identification of putative vacuolar metabolite transporters, and we used it to identify Crocus sativus transporters mediating vacuolar crocin accumulation in stigmas. Three transporters, belonging to both the multidrug and toxic compound extrusion and ATP binding cassette C (ABCC) families, were coexpressed with crocins and/or with the gene encoding the first dedicated enzyme in the crocin biosynthetic pathway, CsCCD2. Two of these, belonging to the ABCC family, were able to mediate transport of several crocins when expressed in yeast microsomes. CsABCC4a was selectively expressed in C. sativus stigmas, was predominantly tonoplast localized, transported crocins in vitro in a stereospecific and cooperative way, and was able to enhance crocin accumulation when expressed in Nicotiana benthamiana leaves.

Abstract Aim Unsustainable hunting is leading to widespread defaunation across the tropics. To mitigate against this threat with limited conservation resources, stakeholders must make decisions on where to focus anti‐poaching activities. Identifying priority areas in a robust way allows decision‐makers to target areas of conservation importance, therefore maximizing the impact of conservation interventions. Location Annamite mountains, Vietnam and Laos. Methods We conducted systematic landscape‐scale surveys across five study sites (four protected areas, one unprotected area) using camera‐trapping and leech‐derived environmental DNA. We analysed detections within a Bayesian multispecies occupancy framework to evaluate species responses to environmental and anthropogenic influences. Species responses were then used to predict occurrence to unsampled regions. We used predicted species richness maps and occurrence of endemic species to identify areas of conservation importance for targeted conservation interventions. Results Analyses showed that habitat‐based covariates were uninformative. Our final model therefore incorporated three anthropogenic covariates as well as elevation, which reflects both ecological and anthropogenic factors. Conservation‐priority species tended to found in areas that are more remote now or have been less accessible in the past, and at higher elevations. Predicted species richness was low and broadly similar across the sites, but slightly higher in the more remote site. Occupancy of the three endemic species showed a similar trend. Main conclusion Identifying spatial patterns of biodiversity in heavily defaunated landscapes may require novel methodological and analytical approaches. Our results indicate that to build robust prediction maps it is beneficial to sample over large spatial scales, use multiple detection methods to increase detections for rare species, include anthropogenic covariates that capture different aspects of hunting pressure and analyse data within a Bayesian multispecies framework. Our models further suggest that more remote areas should be prioritized for anti‐poaching efforts to prevent the loss of rare and endemic species.

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 344 described and undescribed species recovered a karst habitat preference occurring in 25.0% of the species, whereas that of the other eight specific habitat preferences occurred in only 0.2–11.0% of the species. The tenth category—general habitat preference—occurred in 38.7% of the species and was the ancestral habitat preference for Cyrtodactylus and the ultimate origin of all other habitat preferences. This study echoes the results of a previous study illustrating that karstic landscapes are generators of species diversity within Cyrtodactylus and not simply “imperiled arks of biodiversity” serving as refugia for relics. Unfortunately, the immense financial returns of mineral extraction to developing nations largely outweighs concerns for biodiversity conservation, leaving approximately 99% of karstic landscapes with no legal protection. This study continues to underscore the urgent need for their appropriate management and conservation. Additionally, this analysis supports the monophyly of the recently proposed 31 species groups and adds one additional species group.

DNA barcoding is a global initiative that provides a standardized and efficient tool to catalogue and inventory biodiversity, with significant conservation applications. Despite progress across taxonomic realms, globally threatened marine turtles remain underrepresented in this effort. To obtain DNA barcodes of marine turtles, we sequenced a segment of the cytochrome c oxidase subunit I (COI) gene from all seven species in the Atlantic and Pacific Ocean basins (815 bp; n = 80). To further investigate intraspecific variation, we sequenced green turtles (Chelonia mydas) from nine additional Atlantic/Mediterranean nesting areas (n = 164) and from the Eastern Pacific (n = 5). We established character-based DNA barcodes for each species using unique combinations of character states at 76 nucleotide positions. We found that no haplotypes were shared among species and the mean of interspecific variation ranged from 1.68% to 13.0%, and the mean of intraspecific variability was relatively low (0-0.90%). The Eastern Pacific green turtle sequence was identical to an Australian haplotype, suggesting that this marker is not appropriate for identifying these phenotypically distinguishable populations. Analysis of COI revealed a north-south gradient in green turtles of Western Atlantic/Mediterranean nesting areas, supporting a hypothesis of recent dispersal from near equatorial glacial refugia. DNA barcoding of marine turtles is a powerful tool for species identification and wildlife forensics, which also provides complementary data for conservation genetic research.

BACKGROUND: The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia. RESULTS: We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. Interestingly, we found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum. CONCLUSIONS: Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac.

Microplastics have turned into a key global environmental issue in the current decade because of their marine ubiquity, bioavailability and capability of carrying toxic chemicals. The study focuses, for the first time, on the existence of plastic debris in the stomach contents of some commercially important marine fishes caught from the lower Gulf of Thailand during August to November of 2017. Size and weight range of the samples were 8.5 to 37.1 cm and 8 to 133 g. Results highlighted the ingestion of plastics in the 66.67% samples (110 out of 165 samples). The plastics ingested were microplastics (79.52%) (<5 mm), mesoplastics (20.48%) (5-25 mm). No macroplastic was found during this study since the study dealt with small fishes only. Transparent color plastics were the most dominant colors found in the stomach of fishes examined. Net fibres were the major types of plastics found during this study. There was no relationship found between size of plastics and different biological features of the investigated fishes. These initial findings signify an imperative phase in exploring ecotoxicological perspectives such as the existence and impact of plastic debris on the food chain; the probable effects related to the transmission of contaminants on human health etc.

The chemical composition of PM2.5 was monitored simultaneously at two sites, one in a general area of the city center and one at a roadside, in Hanoi, Vietnam, during August 2019–July 2020 using 220 daily (24 h) filter samples. PM mass, water soluble ions, trace elements, organic and elemental carbon and sugar anhydrides were measured. The annual average PM2.5 concentrations, 49 and 46 μg m−3 at the traffic and the general urban site, respectively, exceeded the national (25 μg m−3) and 2021 WHO limit values (5 μg m−3). Daily PM2.5 concentrations were the highest in winter when stagnant meteorological conditions prevailed. On average, half of the resolved mass was organic matter, of which about 40% was attributable to biomass burning, most likely rice straw field burning and domestic fuel combustion. One third of PM2.5 was secondary inorganic aerosol which was dominated by sulphate hence indicating a high contribution of stationary sources like coal combustion. The elemental carbon level was higher at the traffic site, except in April 2020 during the COVID-19 restrictions. Zinc was the most common trace element with high daily variations and large differences between the sites, and it often peaked with Cd, Cl− and Pb indicating contribution of industrial sources and/or coal combustion. The highest zinc concentrations appeared on a few days and likely originated from open burning of municipal solid waste. It appeared that scattered open waste and biomass burning, as well as coal combustion, are important sources causing spikes of PM2.5 pollution in Hanoi above the general levels caused by routine industrial and traffic sources, especially during stagnant winter days. Source contributions were further studied with positive matrix factorization producing six source factors: traffic (12%), local secondary inorganic aerosol (SIA, 18%), biomass burning (19%), industry (9%), long-range transported SIA (25%) and dust (17%).

Abstract Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independently over time in different lineages. The gekkonid genus Cyrtodactylus is just such a lineage with approximately 300 species that range from South Asia to Melanesia and occupy a vast array of habitats. Ancestral state reconstructions using a stochastic character mapping analysis of nine different habitat preferences were employed across a phylogeny composed of 76% of the known species of Cyrtodactylus . This was done in order to ascertain which habitat preference is the ancestral condition and from that condition, the transition frequency to more derived habitat preferences. The results indicate that a general habitat preference is the ancestral condition for Cyrtodactylus and the frequency of transitioning from a general habitat preference to anything more specialized occurs approximately four times more often than the reverse. Species showing extreme morphological and/or ecological specializations generally do not give rise to species bearing other habitat preferences. The evolution of different habitat preferences is generally restricted to clades that tend to occur in specific geographic regions. The largest radiations in the genus occur in rocky habitats (granite and karst), indicating that the transition from a general habitat preference to a granite or karst‐dwelling life style may be ecologically uncomplicated. Two large, unrelated clades of karst‐associated species are centered in northern Indochina and the largest clade of granite‐associated species occurs on the Thai‐Malay Peninsula. Smaller, independent radiations of clades bearing other habitat preferences occur throughout the tree and across the broad distribution of the genus. With the exception of a general habitat preference, the data show that karst‐associated species far out‐number all others (29.6% vs. 0.4%–10.2%, respectively) and the common reference to karstic regions as “imperiled arcs of biodiversity” is not only misleading but potentially dangerous. Karstic regions are not simply refugia harboring the remnants of local biodiversity but are foci of speciation that continue to generate the most speciose, independent, radiations across the genus. Unfortunately, karstic landscapes are some of the most imperiled and least protected habitats on the planet and these data continue to underscore the urgent need for their conservation.

Coastal communities living in the low delta areas of Vietnam are increasingly vulnerable to tropical storms and related natural hazards of global climate change. Particularly in the Red River Delta Biosphere Reserve (RRDBR), farmers change the crop structure and diversify agricultural systems to adapt to the changing climate. The paper deals with a quantitative approach combined with behavior theories and surveyed data to analyze farmers’ intention to climate change adaptation in agriculture. Based on the Protection Motivation Theory (PMT), seven constructs are developed to a questionnaire surveying 526 local farmers: risk perception, belief, habit, maladaptation, subjective norm, adaptation assessment, and adaptation intention. Structural Equation Modeling (SEM) is implemented to extract eight factors and to quantify the relationship between protective behavior factors with the adaptation intention of the surveyed farmers. Two bootstrap samples of sizes 800 and 1200 are generated to estimate the coefficients and standard errors. The SEM result suggests a regional and three local structural models for climate change adaptation intention of farmers living in the RRDBR. Farmers show a higher adaptation intention when they perceive higher climate risks threatening their physical health, finances, production, social relationships, and psychology. In contrast, farmers are less likely to intend to adapt when they are subject to wishful thinking, deny the climate risks, or believe in fatalism.

Drought and related water scarcity have a significant impact on crop production. The purpose of this study was to predict the yield of pomegranate trees and palm trees in southern Iran based on the probability of future drought. We propose a novel meteorological drought-based approach that can predict yield of two crops in 2040 by using Cellular Automata (CA)-Markov chains. From these data in 2000, 2010, and 2020, the regression analysis of yield determination was done with the most important effective indicators that were identified by principal component analysis (PCA), thus leads to highly accuracy. The modelling results of remote-sensing indices (Standardized Precipitation Index-SPI, Standardized Precipitation Evapotranspiration Index-SPEI, Precipitation Condition Index-PCI, Vegetation Condition Index-VCI, Normalized Difference Vegetation Index-NDVI, and Temperature Condition Index-TCI) depicted the expansion of drought areas in southern parts than others regions, and the decreasing yield of two crops in 2000–2020. Additionally, the results of PCA showed that NDVI, PCI, and VCI indices were the most effective drought indices in determining palm’ yield, while SPEI and TCI indices were most effective in determining pomegranate’ yield. According to the results of the CA-Markov chain and regression, approximately 50–60% of the region will have low pomegranate and palm yields in 2040. The approach provides a framework to predict what the decreasing of crop yield is due to the drought effects, and for supporting the optimal decision-making on sustainable horticultural management.

The island of New Guinea lies in one of the most tectonically active regions in the world and has long provided outstanding opportunity for studies of biogeography. Several chelid turtles, of clear Gondwanal origin, occur in New Guinea; all species except one, the endemic Elseya novaeguineae, are restricted to the lowlands south of the Central Ranges. Elseya novaeguineae is found throughout New Guinea. We use mitochondrial and nuclear gene variation among populations of E. novaeguineae throughout its range to test hypotheses of recent extensive dispersal versus more ancient persistence in New Guinea. Its genetic structure bears the signature of Miocene vicariance events. The date of the divergence between a Birds Head (Kepala Burung) clade and clades north and south of the Central Ranges is estimated to be 19.8 Mya [95% highest posterior density (HPD) interval of 13.3–26.8 Mya] and the date between the northern and southern clades is estimated to be slightly more recent at 17.4 Mya (95% HPD interval of 11.0–24.5 Mya). The distribution of this endemic species is best explained by persistent occupation (or early invasion and dispersal) and subsequent isolation initiated by the dramatic landform changes that were part of the Miocene history of the island of New Guinea, rather than as a response to the contemporary landscape of an exceptionally effective disperser. The driving influence on genetic structure appears to have been isolation arising from a combination of: (1) the early uplift of the Central Ranges and establishment of a north-south drainage divide; (2) development of the Langguru Fold Belt; (3) the opening of Cenderawasih Bay; and (4) the deep waters of the Aru Trough and Cenderawasih Bay that come close to the current coastline to maintain isolation of the Birds Head through periods of sea level minima (−135 m). The dates of divergence of turtle populations north and south of the ranges predate the telescopic uplift of the central ranges associated with oblique subduction of the Australian Plate beneath the Pacific Plate. Their isolation was probably associated with earlier uplift and drainage isolation driven by the accretion of island terranes to the northern boundary of the Australian craton that occurred earlier than the oblique subduction. The opening of Cenderawasih Bay is too recent (6 Mya) to have initiated the isolation of the Birds Head populations from those of the remainder of New Guinea, although its deep waters will have served to sustain the isolation through successive sea level changes. The molecular evidence suggests that the Birds Head docked with New Guinea some time before the Central Ranges emerged as a barrier to turtle dispersal. Overall, deep genetic structure of the species complex reflects events and processes that occurred during Miocene, whereas structure within each clade across the New Guinea landscape relates to Pliocene and Pleistocene times.

Abstract Managing integrated social‐ecological systems to reduce risks to human and environmental well‐being remains challenging in light of the rate and extent of undesirable changes that are occurring. Developing frameworks that are sufficiently integrative to guide research to deliver the necessary insights into all key system aspects is an important outstanding task. Among existing approaches, resilience and nexus framings both allow focus on unpacking relationships across scales and levels in a system and emphasize the involvement of different groups in decision making to different extents. They also suffer weaknesses and neither approach puts social justice considerations explicitly at its core. This has important implications for understanding who wins and loses out from different decisions and how social and ecological risks and trade‐offs are shared and distributed, temporally and spatially. This paper conceptually integrates resilience and nexus approaches, developing a combined framework and indicating how it could effectively be operationalized in cases from mountain and mangrove social‐ecological systems. In doing so, it advances understanding of complex social‐ecological systems framings for risk‐based decision making beyond that which could be achieved through use of either resilience or nexus approaches alone. Important next steps in testing the framework involve empirical and field operationalization, requiring interdisciplinary, mixed method approaches.

A new species of Cyrtodactylus is described from the Truong Son (Annamite mountain range) of Quang Binh Province in central Vietnam. It is characterized by 3–5 transversal dorsal bands between the limb insertions, a neckband reaching the posterior margin of eye, 19–20 irregular longitudinal rows of dorsal tubercles, forelimbs with tubercles, 47–50 longitudinal rows of ventrals at midbody, 9–11 precloacal pores in an angular series in males and 16–27 enlarged precloacal scales in both sexes, 20–23 lamellae below the 4th toe, a segmented tail, and lacking of a distinct ventrolateral fold, a precloacal groove and femoral pores, as well as transversally enlarged subcaudal plates. The new species is known only from the karst forests of Phong Nha - Ke Bang National Park. Preliminary data on its natural history are provided.

Mangroves provide multiple benefits, from carbon storage and shoreline protection to food and energy for natural resource-dependent coastal communities. However, they are coming under increasing pressure from climate change, coastal development, and aquaculture. There is increasing need to better understand the changes mangroves face and whether these changes differ or are similar in different parts of the world. Using a multiple case study approach, focused on Vietnam, Zanzibar, and Brazil, this research analyzed the drivers, pressures, states, impacts, and responses (DPSIR) of mangrove systems. A qualitative content analysis was used on a purposively sampled document set for each country to identify and collate evidence under each of the DPSIR categories. Population growth and changing political and economic processes were key drivers across the three countries, leading to land use change and declining states of mangroves. This had an impact on the delivery of regulatory and provisioning ecosystem services from mangroves and on the welfare of coastal communities. Responses have been predominantly regulatory and aim to improve mangrove states, but without always considering ecosystem services or the consequences for welfare. The issue of scale emerged as a critical factor with drivers, pressures, impacts, and responses operating at different levels (from international to local), with consequences for response effectiveness.

Global agricultural by-products usually go to waste, especially in developing countries where agricultural products are usually exported as raw products. Such waste streams, once converted to "value-added" products could be an additional source of revenue while simultaneously having positive impacts on the socio-economic well-being of local people. We highlight the utilization of thermochemical techniques to activate and convert agricultural waste streams such as rice and straw husk, coconut fiber, coffee wastes, and okara power wastes commonly found in the world into porous activated carbons and biofuels. Such activated carbons are suitable for various applications in environmental remediation, climate mitigation, energy storage, and conversions such as batteries and supercapacitors, in improving crop productivity and producing useful biofuels.