Extracted from the Mendeley GBIF Public Library.
Cai, T., Guo, Y., Huettmann, F., Lee, K., 2015.
"presence only" information for Hooded Cranes during spring and fall migration in Asia
Lim, H. C., Zou, F. S., Sheldon, F., 2015.
Microsoft Word - LIM Genetic differentiation in two widespread, open-forest bird species of Southeast Asia ( Copsychus saularis and Megalaima haemacephala ): Insights from ecological niche modeling - LIM1.pdf
Current Zoology 61(5) 1-21.
cological niche modeling has emerged as an useful tool in the investigation of the phylogeographic histories of species or communities in a region. The high biodiversity (oftentimes cryptic), and complex geogra phy and geological history of Southeast Asia particularly call for multipronged approaches in phylogeographic inve stigations. Past studies have focused on taxa that are ass ociated with lowland rainforests, which is the dominant natural vegetation type. Here, we combine published phylogenetic data, ecological ni che modeling and paleo-climate models to reveal potential drivers of divergence in two ope n-forest bird species, the oriental magpi e-robin Copsychus saularis and Coppersmith barbet Megalaima haemacephala . In spite of broad overlap in current distributions, there are subtle differences in their climatic niches, which result in different responses to past climatic changes. For C. saularis , both Last Glacial Maximum climate models indicated that the entire Sundaland was climati cally suitable, while phylogenetic analyses found divergent easte rn and western Sundaland lineages. We thus postulate that this genetic divergence was a result of past separations of coastal habitats into eastern and western portions due to the emergence of Sunda shelf as s ea-level fell. The current separation of morphological subspecies in Borneo is maintained by low climatic suitab ility (high annual rainfall) in certain regions. The extirpation of M. haemacephala from Borneo and southern Malay Peninsula might have been driven by unsuitable conditions (high temperature seasonality) in central Sundaland an d/or the lack of open woodlands. Our study shows that ecological niche m odeling adds a powerful dimension to our attempt to understand l ineage evolution in space
Keywords: Barbet, Indo-Burma, Magpie -ro, Malay Archipelago
Luo, Z., Jiang, Z., Tang, S., 2015.
Ecological Applications 25(1) 24-38.
Climate change has significant impacts on species' distributions and diversity patterns. Understanding range shifts and changes in richness gradients under climate change is crucial for conservation. The Tibetan Plateau, home to wild yak, chiru, and kiang, contains a biome with many endemic ungulates. It is highly sensitive to climate change and a region that merits particular attention with regard to the impacts of global climate change on its biomes. Maximum entropy approaches were used to estimate current and future potential distributions, in response to climate change, for 22 ungulate species. We used three general circulation (MK3, HADCM3, MIROC3_2-MED) and three emissions scenarios (B1, A1B, A2) to derive estimated future measurements of 14 environmental variables over three time periods (2020, 2050, 2080), and then modeled species distributions using these predicted environmental measurements for each time period under two dispersal hypotheses (full and zero, respectively). This resulted in a tota...
Keywords: Maxent (maximum entropy), Tibetan Plateau, ecological niche models, ensemble forecasting models, environmental suitability, global climate change, range shifts, species richness patterns, ungulates
Parsa, S., Hazzi, N., Chen, Q., Lu, F., Herrera Campo, B., Yaninek, J., Vásquez-Ordóñez, A., 2015.
Experimental & applied acarology 65(2) 195-204.
The cassava green mites Mononychellus tanajoa and M. mcgregori are highly invasive species that rank among the most serious pests of cassava globally. To guide the development of appropriate risk mitigation measures preventing their introduction and spread, this article estimates their potential geographic distribution using the maximum entropy approach to distribution modeling. We compiled 1,232 occurrence records for M. tanajoa and 99 for M. mcgregori, and relied on the WorldClim climate database as a source of environmental predictors. To mitigate the potential impact of uneven sampling efforts, we applied a distance correction filter resulting in 429 occurrence records for M. tanajoa and 55 for M. mcgregori. To test for environmental biases in our occurrence data, we developed models trained and tested with records from different continents, before developing the definitive models using the full record sets. The geographically-structured models revealed good cross-validation for M. tanajoa but not for M. mcgregori, likely reflecting a subtropical bias in M. mcgregori's invasive range in Asia. The definitive models exhibited very good performance and predicted different potential distribution patterns for the two species. Relative to M. tanajoa, M. mcgregori seems better adapted to survive in locations lacking a pronounced dry season, for example across equatorial climates. Our results should help decision-makers assess the site-specific risk of cassava green mite establishment, and develop proportional risk mitigation measures to prevent their introduction and spread. These results should be particularly timely to help address the recent detection of M. mcgregori in Southeast Asia.
Keywords: Cassava green mite, Manihot esculenta, Mononychellus mcgregori, Mononychellus tanajoa, Pest risk map, Species distribution modeling
Zhao, L., Hou, P., Zhu, G., Li, M., Xie, T., Liu, Q., 2015.
Agricultural and Forest Entomology n/a-n/a.
Eastern China was once listed as an area infested with the invasive codling moth Cydia pomonella L. (Lepidoptera: Tortricide). Intensive efforts later revealed the absence of such infestation. Currently, the majority of the population is distributed in western China. A disjunct population is also observed in the north east. In present study, the disjunct distribution was interpreted by mapping the climate dimension and potential distribution using an ecological niche modelling approach. The preferred niche models were utilized to identify the relative roles of climate, human influence and vegetation with respect to the present distribution and also to extrapolate the climate dimensions suitable for the codling moth in China. The results of the present study suggest that a combination of climate suitability and human influence explain the range expansion. Undistributed areas in eastern China were found to have low to medium climate suitability. Nonetheless, these areas belong to apple-growing regions that have high propagule pressure; thus, eventual establishment appears to be possible because of host plant availability, human activity and the wide ecological flexibility of the moth. Highly suitable habitats were found to be strongly related to high temperature and low precipitation throughout the year, whereas areas with low temperature and plenty of rainfall are unfavourable.
Keywords: China, codling moth (Cydia pomonella), disjunct population, ecological niche modelling, potential distribution
Barnes, M., Jerde, C., Wittmann, M., Chadderton, W., Ding, J., Zhang, J., Purcell, M., Budhathoki, M., Lodge, D., 2014.
Geographic selection bias of occurrence data influences transferability of invasive Hydrilla verticillata distribution models
Ecology and Evolution.
Due to socioeconomic differences, the accuracy and extent of reporting on the occurrence of native species differs among countries, which can impact the per- formance of species distribution models. We assessed the importance of geo- graphical biases in occurrence data on model performance using Hydrilla verticillata as a case study. We used Maxent to predict potential North Ameri- can distribution of the aquatic invasive macrophyte based upon training data from its native range. We produced a model using all available native range occurrence data, then explored the change in model performance produced by omitting subsets of training data based on political boundaries. We also com- pared those results with models trained on data from which a random sample of occurrence data was omitted from across the native range. Although most models accurately predicted the occurrence of H. verticillata in North America (AUC > 0.7600), data omissions influenced model predictions. Omitting data based on political boundaries resulted in larger shifts in model accuracy than omitting randomly selected occurrence data. For well-documented species like H. verticillata, missing records from single countries or ecoregions may mini- mally influence model predictions, but for species with fewer documented occurrences or poorly understood ranges, geographic biases could misguide pre- dictions. Regardless of focal species, we recommend that future species distribu- tion modeling efforts begin with a reflection on potential spatial biases of available occurrence data. Improved biodiversity surveillance and reporting will provide benefit not only in invaded ranges but also within under-reported and unexplored native ranges.
Keywords: aquatic macrophyte, biological invasion, habitat model, maximum entropy, model, niche, prediction, spatial bias
Bystriakova, N., Ansell, S., Russell, S., Grundmann, M., Vogel, J., Schneider, H., 2014.
Present, past and future of the European rock fern Asplenium fontanum: combining distribution modelling and population genetics to study the effect of climate change on geographic range and genetic diversity
Annals of Botany 113(3) 453-65.
BACKGROUND AND AIMS: Climate change is expected to alter the geographic range of many plant species dramatically. Predicting this response will be critical to managing the conservation of plant resources and the effects of invasive species. The aim of this study was to predict the response of temperate homosporous ferns to climate change. METHODS: Genetic diversity and changes in distribution range were inferred for the diploid rock fern Asplenium fontanum along a South-North transect, extending from its putative last glacial maximum (LGM) refugia in southern France towards southern Germany and eastern-central France. This study reconciles observations from distribution models and phylogeographic analyses derived from plastid and nuclear diversity. KEY RESULTS: Genetic diversity distribution and niche modelling propose that genetic diversity accumulates in the LGM climate refugium in southern France with the formation of a diversity gradient reflecting a slow, post-LGM range expansion towards the current distribution range. Evidence supports the fern's preference for outcrossing, contradicting the expectation that homosporous ferns would populate new sites by single-spore colonization. Prediction of climate and distribution range change suggests that a dramatic loss of range and genetic diversity in this fern is possible. The observed migration is best described by the phalanx expansion model. CONCLUSIONS: The results suggest that homosporous ferns reproducing preferentially by outcrossing accumulate genetic diversity primarily in LGM climate refugia and may be threatened if these areas disappear due to global climate change.
Keywords: Chloroplast, Chloroplast: genetics, Climate Change, Conservation of Natural Resources, DNA, Demography, Ferns, Ferns: genetics, Genetic Loci, Genetic Markers, Genetic Markers: genetics, Genetic Variation, Genetics, Isoenzymes, Isoenzymes: genetics, Models, Phylogeography, Plant Leaves, Plant Leaves: genetics, Plant Proteins, Plant Proteins: genetics, Population, Reproduction, Software, Statistical
Chen, C., Qi, Z., Xu, X., Comes, H., Koch, M., Jin, X., Fu, C., Qiu, Y., 2014.
Understanding the formation of Mediterranean-African-Asian disjunctions: evidence for Miocene climate-driven vicariance and recent long-distance dispersal in the Tertiary relict Smilax aspera (Smilacaceae)
The New Phytologist 204(1) 243-55.
Tethyan plant disjunctions, including Mediterranean-African-Asian disjunctions, are thought to be vicariant, but their temporal origin and underlying causes remain largely unknown. To address this issue, we reconstructed the evolutionary history of Smilax aspera, a hypothesized component of the European Tertiary laurel forest flora. Thirty-eight populations and herbarium specimens representing 57 locations across the species range were sequenced at seven plastid regions and the nuclear ribosomal internal transcribed spacer region. Time-calibrated phylogenetic and phylogeographic inferences were used to trace ancestral areas and biogeographical events. The deep intraspecific split between Mediterranean and African-Asian lineages is attributable to range fragmentation of a southern Tethyan ancestor, as colder and more arid climates developed shortly after the mid-Miocene. In the Mediterranean, climate-induced vicariance has shaped regional population structure since the Late Miocene/Early Pliocene. At around the same time, East African and South Asian lineages split by vicariance, with one shared haplotype reflecting long-distance dispersal. Our results support the idea that geographic range formation and divergence of Tertiary relict species are more or less gradual (mostly vicariant) processes over long time spans, rather than point events in history. They also highlight the importance of the Mediterranean Basin as a centre of intraspecific divergence for Tertiary relict plants.
Keywords: african, analyses, ancestral area reconstruction, chloroplast dna, disjunctions, eurasian, molecular dating, phylogenetic, phylogeographical inference
Ding, W., Gu, J., Cao, L., Li, N., Ding, G., Wang, Z., Chen, L., Xu, X., Xiao, W., 2014.
Traditional Chinese herbs as chemical resource library for drug discovery of anti-infective and anti-inflammatory.
Journal of Ethnopharmacology 155(1) 589-98.
ETHNOPHARMACOLOGICAL RELEVANCE: Infection is a major group of diseases which caused significant mortality and morbidity worldwide. Traditional Chinese herbs have been used to treat infective diseases for thousands years. The numerous clinical practices in disease therapy make it a large chemical resource library for drug discovery. MATERIALS AND METHODS: In this study, we collected 1156 kinds of herbs and 22,172 traditional Chinese medicinal compounds (Tcmcs). The chemical informatics and network pharmacology were employed to analyze the anti-infective effects of herbs and Tcmcs. In order to evaluate the drug likeness of Tcmcs, the molecular descriptors of Tcmcs and FDA-approved drugs were calculated and the chemical space was constructed on the basis of principal component analysis in the eight descriptors. On purpose to estimate the effects of Tcmcs to the targets of FDA-approved anti-infective or anti-inflammatory drugs, the molecular docking was employed. After that, docking score weighted predictive models were used to predict the anti-infective or anti-inflammatory efficacy of herbs. RESULTS: The distribution of herbs in the phylogenetic tree showed that most herbs were distributed in family of Asteraceae, Fabaceae and Lamiaceae. Tcmcs were well coincide with drugs in chemical space, which indicated that most Tcmcs had good drug-likeness. The predictive models obtained good specificity and sensitivity with the AUC values above 0.8. At last, 389 kinds of herbs were obtained which were distributed in 100 families, by using the optimal cutoff values in ROC curves. These 389 herbs were widely used in China for treatment of infection and inflammation. CONCLUSION: Traditional Chinese herbs have a considerable number of drug-like natural products and predicted activities to the targets of approved drugs, which would give us an opportunity to use these herbs as a chemical resource library for drug discovery of anti-infective and anti-inflammatory.
Keywords: Anti-infection, Anti-inflammatory, Chemical informatics, Network pharmacology, Traditional Chinese herb
Haibin, Y., Yili, Z., Jungang, G., Wei, Q., 2014.
Visualizing Patterns of Genetic Landscapes and Species Distribution of Taxus wallichiana (Taxaceae), Based on GIS and Ecological Niche Models
Journal of Resources and Ecology 5(3) 193-202.
The Chinese yew ( China, is now on the edge of extinction. In order to understand the evolutionary processes that control the current Taxus ), which is widely distributed in the Himalayas and in southern diversity within this species at the genetic and ecological levels, its genetic patterns and range dynamics must first wallichiana be identified and mapped. This knowledge can then be applied in the development of an effective conservation strategy. Based on molecular data obtained from 48 populations of T. , we used GIS-based interpolation approach for the explicit visualization of patterns of genetic divergence and diversity, and a number of potential evolutionary hotspots have been specifically identified within the genetic landscape maps. Within the maps of wallichiana genetic divergence and diversity, five areas of high inter-population genetic divergence and six areas of high intra-population genetic diversity have been highlighted in a number of separate mountain regions, and these evolutionary hotspots should have the priority to be protected. Furthermore, four geographical barriers have been identified: the eastern Himalayas, the Yunnan Plateau, the Hengduan Mountains and the Taiwan Strait. According to ecological niche modeling (ENM), the populations of T. within the Sino-Himalayan Forest floristic subkingdom experienced westward expansion from the periods of Last Inter-glacial to Last Glacial Maximum (LGM). Following the LGM, the distribution range overall became reduced and fragmented. These findings challenge the wallichiana classic mode of contraction-expansion in response to the last glaciation. In conclusion, our findings suggest that the changes in geographical landscapes and climate that occurred during the Quaternary resulted in current genetic landscape patterns.
Keywords: ecological niche models, enms, genetic landscape, gis, himalayas, phylogeography