For all researches, please visit our "Peer-reviewed publications" page.
Cao B, Bai C, Zhang L, Li G, Mao M (2016)
Journal of Plant Ecology rtw009.
AimsPredicting suitable habitat distribution is an effective way to protect rare or endangered medicinal plants. Cornus officinalis is a perennial tree growing in forest edge and its air-dried pericarp is one of the traditional Chinese medicines (TCM) with significant medicinal values. In recent years, C. officinalis has undergone severe degeneration of its natural habitat owing to growing market demands and unprecedented damage to the forests. Moreover, the degeneration of suitable habitat has threatened the supply of medicinal materials, and even led to the extinction of some engendered medicinal plant species. In this case, there is a great risk to introduce and cultivate medicinal plants if planners determine the suitable cultivation regions based on personal subjective experience alone. Therefore, predicting suitable potential habitat distribution of medicinal plants (e.g. C. officinalis) and revealing the environmental factors determining such distribution patterns are important to habitat conservation and environmental restoration. MethodsIn this paper, we report the results of a study on the habitat distribution of C. officinalis using maximum entropy (Maxent) modeling and fuzzy logics together with loganin content and environmental variables. The localities of 106 C. officinalis in China were collected by our group and other researchers and used as occurrence data. The loganin content of 234 C. officinalis germplasm resources were tested by high-performance liquid chromatography (HPLC) and used as content data. 79 environmental variables were selected and processed with multi-collinearity test by using Pearson Correlation Coefficient (r) to determine a set of independent variables. The chosen variables were then processed in the fuzzy linear model according to the cell values (maximum, minimum) of localities with estimated loganin content. The SDMtoolbox was used to spatially rarefy occurrence data and prepare bias files. Furthermore, combined Maxent modeling and fuzzy logics were used to predict the suitable habitat of C. officinalis. The modeling result was validated using null-model method. Important findingsAs a result, six environmental factors including tmin3, prec3, bio4, alt, bio12 and bio3 were determined as key influential factors that mostly affected both the habitat suitability and active ingredient of C. officinalis. The highly suitable regions of C. officinalis mainly "core distribution zone" of the east-central China. The statistically significant AUC value indicated that combined Maxent modeling and fuzzy logics could be used to predict the suitable habitat distribution of medicinal plants. Furthermore, our results confirm that ecological factors played critical roles in assessing suitable geographical regions as well as active ingredient of plants, highlighting the need for effective habitat rehabilitation and resource conservation.
Keywords: Cornus officinalis, Maxent modeling, fuzzy logics, habitat distribution, medicinal plant
Duan R, Kong X, Huang M, Varela S, Ji X (2016)
The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
Many studies predict that climate change will cause species movement and turnover, but few studies have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change will cause a major shift in the spatial patterns of amphibian diversity. Suitable habitats for over 90% of species will be located in the north of the current range, for over 95% of species in higher altitudes, and for over 75% of species in the west of the current range. The distributions of species predicted to move westwards, southwards and to higher altitudes will contract, while the ranges of the species not showing these trends will expand. Amphibians will lose 20% of their original ranges on average; the distribution outside current ranges will increase by 15%. Climate change will likely modify the spatial configuration of climatically suitable areas. Changes in area and fragmentation of climatically suitable patches are related, which means that species may be simultaneously affected by different stressors as a consequence of climate change.
Keywords: Amphibians, Climate impacts, Dispersal, Distribution, Fragmentation, MaxEnt, Range shifts, Turnover
Escobar L, Qiao H, Peterson A (2016)
Parasites & vectors 9(1) 112.
BACKGROUND: Chikungunya virus (CHIKV) is endemic to Africa and Asia, but the Asian genotype invaded the Americas in 2013. The fast increase of human infections in the American epidemic emphasized the urgency of developing detailed predictions of case numbers and the potential geographic spread of this disease. METHODS: We developed a simple model incorporating cases generated locally and cases imported from other countries, and forecasted transmission hotspots at the level of countries and at finer scales, in terms of ecological features. RESULTS: By late January 2015, >1.2 M CHIKV cases were reported from the Americas, with country-level prevalences between nil and more than 20 %. In the early stages of the epidemic, exponential growth in case numbers was common; later, however, poor and uneven reporting became more common, in a phenomenon we term "surveillance fatigue." Economic activity of countries was not associated with prevalence, but diverse social factors may be linked to surveillance effort and reporting. CONCLUSIONS: Our model predictions were initially quite inaccurate, but improved markedly as more data accumulated within the Americas. The data-driven methodology explored in this study provides an opportunity to generate descriptive and predictive information on spread of emerging diseases in the short-term under simple models based on open-access tools and data that can inform early-warning systems and public health intelligence.
Keywords: Entomology, Infectious Diseases, Parasitology, Tropical Medicine
Guan B, Chen W, Gong X, Wu T, Cai Q, Liu Y et al. (2016)
Landscape connectivity of Cercidiphyllum japonicum, an endangered species and its implications for conservation
Ecological Informatics 33 51-56.
Cercidiphyllum japonicum, a Tertiary relict, recolonized areas north of the Yangtze River after the last glacial; however, little is known about its specific colonization corridors. Together with distribution models, the least cost path (LCP) analysis has been used to reveal the landscape connectivity of species. In this study, we utilized the categorical LCP method, combining the species distribution with genetic data from cpDNA and nuclear markers, to identify the possible dispersal routes of C. japonicum after the LGM. Across time periods and genetic markers, the results revealed that the species generally spread from the western edge of the Sichuan Basin, while the highest degree of dispersal potential corresponds with the year 2080 and the cpDNA haplotype. Furthermore, shifts in the species' range and the indication of an area of low genetic divergence further support the existence of a dispersal corridor. Overall, we believe that a dispersal route from the western edge of the Sichuan Basin through the Qinling Mountains and further to the northeast could exist, and therefore, the results are an important supplement to the evolutionary history of C. japonicum. In the future, we believe species distribution models (SDM) and connectivity assessment in relation to climate change will provide increasingly useful information and new implications for prioritizing the conservation of the endangered species.
Keywords: Dispersal corridors, Genetic landscape, Least cost path, Shared haplotypes, Species distribution models
Huang D, Hoeksema B, Affendi Y, Ang P, Chen C, Huang H et al. (2016)
Biodiversity and Conservation.
The South China Sea in the Central Indo-Pacific is a large semi-enclosed marine region that supports an extraordinary diversity of coral reef organisms (including stony corals), which varies spatially across the region. While one-third of the world’s reef corals are known to face heightened extinction risk from global climate and local impacts, prospects for the coral fauna in the South China Sea region amidst these threats remain poorly understood. In this study, we analyse coral species richness, rarity, and phylogenetic diversity among 16 reef areas in the region to estimate changes in species and evolutionary diversity during projected anthropogenic extinctions. Our results show that richness, rarity, and phylogenetic diversity differ considerably among reef areas in the region, and that their outcomes following projected extinctions cannot be predicted by species diversity alone. Although relative rarity and threat levels are high in species-rich areas such as West Malaysia and the Philippines, areas with fewer species such as northern Vietnam and Paracel Islands stand to lose disproportionately large amounts of phylogenetic diversity. Our study quantifies various biodiversity components of each reef area to inform conservation planners and better direct sparse resources to areas where they are needed most. It also provides a critical biological foundation for targeting reefs that should be included in a regional network of marine protected areas in the South China Sea
Keywords: IUCN Red List, Marine biodiversity, Phylogenetic diversity, Rarity, Scleractinia, Species richness
Jia S, Zhang M, Raab-Straube E, Thulin M (2016)
Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia
Biological Journal of the Linnean Society.
Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid-late Miocene significantly affected the diversification of the genus in these areas.
Keywords: 2016, CN, China, DE, GBIF_used, Germany, SE, Sweden, phylogenetic analysis, phylogenetics
Ke Z, Zhang X, Cao Z, Ding Y, Li N, Cao L et al. (2016)
Biomedicine & Pharmacotherapy 78 272-279.
Neurodegenerative diseases, referring to as the progressive loss of structure and function of neurons, constitute one of the major challenges of modern medicine. Traditional Chinese herbs have been used as a major preventive and therapeutic strategy against disease for thousands years. The numerous species of medicinal herbs and Traditional Chinese Medicine (TCM) compound formulas in nervous system disease therapy make it a large chemical resource library for drug discovery. In this work, we collected 7362 kinds of herbs and 58,147 Traditional Chinese medicinal compounds (Tcmcs). The predicted active compounds in herbs have good oral bioavailability and central nervous system (CNS) permeability. The molecular docking and network analysis were employed to analyze the effects of herbs on neurodegenerative diseases. In order to evaluate the predicted efficacy of herbs, automated text mining was utilized to exhaustively search in PubMed by some related keywords. After that, receiver operator characteristic (ROC) curves was used to estimate the accuracy of predictions. Our study suggested that most herbs were distributed in family of Asteraceae, Fabaceae, Lamiaceae and Apocynaceae. The predictive model yielded good sensitivity and specificity with the AUC values above 0.800. At last, 504 kinds of herbs were obtained by using the optimal cutoff values in ROC curves. These 504 herbs would be the most potential herb resources for neurodegenerative diseases treatment. This study would give us an opportunity to use these herbs as a chemical resource library for drug discovery of anti-neurodegenerative disease.
Keywords: Drug discovery, Network pharmacology, Neurodegenerative diseases, Virtual screening
Li G, Xu G, Guo K, Du S (2016)
Geographical boundary and climatic analysis of Pinus tabulaeformis in China: Insights on its afforestation
Ecological Engineering 86 75-84.
Pinus tabulaeformis, as an endemic species in China, is one of the main tree species for afforestation. For rational cultivation planning and conservation, it is necessary to understand the geographical boundaries and the ecological characteristics of P. tabulaeformis, and to explore its priority afforestation areas. In this study, maximum entropy modeling (MaxEnt) was used to identify and prioritize suitable habitats of P. tabulaeformis, based on 13 climatic variables and GlobCover 2009 data. The results show that the MaxEnt model performs better than random prediction, with an average test area under the curve (AUC) value of 0.93 (0.91–0.94). Precipitation of wettest month (PWM), annual biotemperature (ABT), mean temperature of the coldest month (MTCM), annual mean temperature (AMT), precipitation of driest month (PDM), coldness index (CI), annual precipitation (AP), and mean temperature of the warmest month (MTWM) are identified as dominant variables which explain 94.6% of variability the geographical distribution of P. tabulaeformis. Climatic conditions of P. tabulaeformis in the core area of its distribution are as follows: PWM, 100–246mm; ABT, 3.0–4.7°C; MTCM, −20.2 to −1.1°C; AMT, 2.9–14.7°C; PDM, 2–11mm; CI, −49.4–0°C; AP, 431–1122mm; and MTWM, 19.6–31.2°C. The suitable areas for afforestation are 2.6×104km2 (patches with an area >1km2), 1.6×104km2 (patches with an area >10km2), and 1.2×104km2 (patches with an area >100km2), which are mainly located in north Shaanxi, south Ningxia, and the middle of Gansu and Liaoning provinces with serious landscape fragmentation caused by human agricultural activities. Our simulation results can improve our understanding of the geographical and ecological characteristics of P. tabulaeformis and provide prediction of priority areas for afforestation of this species under current and future climate change scenarios in China.
Keywords: Afforestation, Climate change, Ecological niche, Geographical boundary, Species distribution model, Vegetation mapping
Lv X, Xia L, Ge D, Wu Y, Yang Q (2016)
Climatic niche conservatism and ecological opportunity in the explosive radiation of arvicoline rodents (Arvicolinae, Cricetidae).
Evolution; international journal of organic evolution.
Climatic niche conservatism shapes patterns of diversity in many taxonomic groups, while ecological opportunity (EO) can trigger rapid speciation that is less constrained by the amount of time a lineage has occupied a given habitat. These two processes are well studied, but limited research has considered their joint and relative roles in shaping diversity patterns. We characterized climatic and biogeographic variables for 102 species of arvicoline rodents (Arvicolinae, Cricetidae), testing the effects of climatic niche conservatism and EO on arvicoline diversification as lineages transitioned between biogeographic regions. We found that the amount of time a lineage has occupied a precipitation niche is positively correlated with diversity along a precipitation gradient, suggesting climatic niche conservatism. In contrast, shift in diversification rate explained diversity patterns along a temperature gradient. Our results suggest that an indirect relationship exists between temperature and diversification that is associated with EO as arvicoline rodents colonized warm Palearctic environments. Climatic niche conservatism alone did not fully explain diversity patterns under density-dependence, highlighting the additional importance of EO-related processes in promoting the explosive radiation in arvicoline rodents and shaping diversity pattern among biogeographic regions and along climatic gradients. This article is protected by copyright. All rights reserved.
Keywords: Diversification rate, ecological opportunity, historical biogeography, macroevolution, time-for-speciation effect
Shang H, Wang Y, Zhu X, Zhao G, Wang F, Lu J et al. (2016)
Journal of Systematics and Evolution.
Adiantum × meishanianum F. S. Hsu ex Y. C. Liu & W. L. Chiou was regarded as an endemic species in Meishan Village, Kaohsiung, Taiwan, China and a hybrid between A. malesianum Ghatak (the maternal parent) and a sexually reproducing diploid cryptic species of A. philippense L. (the paternal parent), as revealed by chloroplast and nuclear markers. However, morphological research revealed that A. × meishanianum is also disjunctively distributed in Yunnan and that its paternal parent is possibly A. menglianense Y. Y. Qian. Thus, this study aimed to confirm these findings by using two chloroplast regions and a low-copy nuclear marker in DNA barcoding and phylogenetic analyses, spore measurement, and flow cytometry. Our results indicated that A. × meishanianum in Yunnan is triploid and abortive, the same as A. × meishanianum in Taiwan, and they both originated from the hybridization between the maternal parent of A. malesianum and the paternal parent of A. menglianense, but not A. philippense. In conclusion, A. × meishanianum probably originated from multiple hybridizations in Taiwan and Yunnan.
Keywords: A. menglianense, Adiantum × meishanianum, cryptic species, disjunctive distribution, multiple hybrids