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Sundaland Dipterocarp forests during Quaternary glacial maxima

In findings published in the Proceedings of the National Academy of Sciences (U.S.A.), the persistence of Dipterocarp forests on the greatly expanded Sunda Shelf during the brief glacial maxima of the Quaternary Period was supported by the largest database of collections of Dipterocarpaceae specimens in the world and advanced niche modeling techniques.  The team of scientists, including Drs. Cannon and Slik (both formerly at XTBG), expand the evidence that strongly suggests that the current Southeast Asian forests have been greatly fragmented and reduced in their extent, although forests of the glacial maxima might have been less species-rich with many species having smaller geographic distributions.  Most importantly, current forests must have experienced a great deal of mixture and migration from the slightly drier and cooler conditions of the Last Glacial Maximum which ended roughly 12,000 years ago.  Little evidence was found for the existence of a savanna region on any substantial portion of the Sunda Shelf.

Genomic data reveals patterns in the regulation of transpiration in Ficus

Protein Domain Analysis of Genomic Sequence Data Reveals Regulation of LRR Related Domains in Plant Transpiration in Ficus.  Tiange Lang, Kangquan Yin, Jinyu Liu, Kunfang Cao, Charles H. Cannon, and Fang K. Du.  PLoS One.

Predicting protein domains is essential for understanding a protein’s function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated withde novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

Borneo and Indochina are evolutionary hotspots

A recent publication in Systematic Biology highlights the role of Borneo and Indochina as exceptional evolutionary hotspots in Southeast Asia.  Compiling and reanalyzing a large amount of data, a team of 13 experts representing a wide range of scientific fields demonstrate that for a diverse range of fauna and flora, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo’s biota since at least the early Miocene.  Dr. Cannon participated in this study and was a co-author on the publication.


The pdf is available for free download from

Dr. Cannon speaks at evolutionary genomics meeting

Dr. Charles Cannon gave an invited presentation at the “Evolutionary Genetics and Genomics” workshop at Cold Spring Harbor, Asia in Suzhou, China on Oct 10, 2014.  His talk was entitled “Tropical Diversification and Genomic Mutualisms”.

The workshop site is at the following link:

While in China, he was also invited to make a presentation at Sun Yat Sen University in Guangzhou, China.  His talk was entitled “See the forest through the trees” and was given to the research groups of Prof. Chung-I Wu and Prof. Suhua Shi.

Peter Alele publishes study on soils in Uganda

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda?

  • Peter O. Alele mail,
  • Douglas Sheil,
  • Yann Surget-Groba,
  • Shi Lingling,
  • Charles H. Cannon
  • Published: August 12, 2014
  • DOI: 10.1371/journal.pone.0104818

Footprints of divergent selection in tropical chestnut

Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

C Li, Y Sun, H W Huang and C H Cannon

Given predicted rapid climate change, an understanding of how environmental factors affect genetic diversity in natural populations is important. Future selection pressures are inherently unpredictable, so forest management policies should maintain both overall diversity and identify genetic markers associated with the environmental factors expected to change most rapidly, like temperature and rainfall. In this study, we genotyped 648 individuals in 28 populations of Castanopsis fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived microsatellite markers. After removing six loci that departed from Hardy–Weinberg equilibrium, we measured genetic variation, population structure and identified candidate loci putatively under selection by temperature and precipitation. We found that C. fargesii populations possessed high genetic diversity and moderate differentiation among them, indicating predominant outcrossing and few restrictions to gene flow. These patterns reduce the possible impact of stochastic effects or the influence of genetic isolation. Clear footprints of divergent selection at four loci were discovered. Frequencies of five alleles at these loci were strongly correlated with environmental factors, particularly extremes in precipitation. These alleles varied from being near fixation at one end of the gradient to being completely absent at the other. Our study species is an important forest tree in the subtropical regions of China and could have a major role in future management and reforestation plans. Our results demonstrate that the gene flow is widespread and abundant in natural populations, maintaining high diversity, while diversifying selection is acting on specific genomic regions.

Field Methods in Tropical Ecology, Evolution, and Conservation – north Sulawesi, Indonesia

Dr. Cannon taught in a field course organized by Myron Shekelle and Maryati Abiduna.  The course was funded primarily by the Ewha Woman’s University of South Korea.


Genome size variation in Fagaceae and its implications for trees

CHEN Sichong, now pursuing a PhD at the University of New South Wales with Angela Moles, has published her research on genome size variation in the Fagales in the journal Tree Genetics and Genomes.


Polyploidization is a major source of diversification among plants, particularly during cladogenesis, but most evidence involves herbaceous temperate species. The prevalence of polyploidy among woody taxa is largely unknown, especially among tropical groups. In this study, we examined genome size variation globally and at several taxonomic levels within the Fagaceae. This family has diversified in the northern temperate zone (Quercus) and at least twice in the Asian tropics (Lithocarpus andCastanopsis), allowing us to examine genomic size evolution across a broad latitudinal range. We compared nuclear DNA contents from 78 species in six genera, including new measurements for 171 individuals from 47 Chinese species using standard flow cytometry methods. No evidence suggests that polyploidization or whole genome duplication has occurred in the family. Genome size varied among genera, but limited variation was present in each genus and species. In general, tropical species had larger genomes than temperate species, but the ancestral state cannot be determined given current evidence. Partial duplication does seem to occur among species as within genus variation was larger than within species variation. A review of the literature suggests that genome size and even chromosome structure is highly conserved among woody plants and trees. We propose that ploidy level and genome size are conserved among trees because they participate in diverse syngameons. This behavior would provide similar benefits to polyploidization but avoid exclusion from the syngameon. This conservatism in genome size and structure should enhance ongoing whole genome studies.

Dr. Yi Zhuangfang publishes another paper concerning the ecological economics of forests in Xishuangbanna

Can carbon-trading schemes help to protect China’s most diverse forest ecosystems? A case study from Xishuangbanna, Yunnan

authors: Zhuang-Fang Yi , Grace WongCharles H. CannonJianchu XuPhilip Beckschäfer, and Ruth D. Swetnamg

published in Land Use and Policy



Xishuangbanna has been largely transformed from biodiverse natural forests and mixed-use farms into monoculture rubber plantations in just twenty years. This conversion has expanded into forests previously protected by the community and onto marginal sites at high-elevation. Market-based ecosystem payments, especially carbon financing, are potential tools to prevent further forest loss in China. Here, we compare rubber net present value (NPV), carbon sequestration, and seed-plant species diversity for Xishuangbanna given three land-use scenarios: Business-As-Usual (BAU), Economic Oriented Scenario (EOS) and Conservation Oriented Scenario (COS) using a previously published spatial map of rubber profitability. The EOS achieved the greatest rubber profit but caused substantial reductions in natural forest area, biodiversity and carbon stocks. The EOS also requires substantial immigration of workers into a remote and ecologically important region with little social infrastructure for basic security, food security, health-care and education, causing frequently ignored costs. As expected, the COS will maintain the highest levels of natural forest area, sequester 57% more carbon, and 71% more biodiversity than EOS. Given the conservation value of the carbon stores and rich biodiversity residing in Xishuangbanna’s natural forests, reducing rubber NPV only marginally would probably cost less than attempting to recover these resources. We recommend that rubber plantations be limited to established, productive lowland areas whilst protecting intact high-elevation forest and reforesting low-productivity plantations. These actions will enhance carbon sequestration and biodiversity conservation. Management policies focused solely on profits, like the EOS scenario, will fail to sustain the entire range of natural resources and ecosystem services. The prices in the carbon market would have to be considerably larger than they are currently to compete with the profitability of rubber.



Free downloads until Mar 26th of Dr. Yi’s Ecological Indicators paper

Elsevier Press is offering a personal link for sharing our new article “Developing indicators of economic value and biodiversity loss for rubber plantations in Xishuangbanna, southwest China: A case study from Menglun township” in Ecological Indicators:

This link will provide free access to your article, and is valid for 50 days, until 26th March, 2014.

Get it while it’s free!!

Signs of Change: crowd-sourcing time-lapse photography

A new crowd-funding effort has just launched at, organized by the great people at the SciFund Challenge.

Check out my proposal: or

The idea is to create sites where anyone can snap a photo of the landscape from a fixed position and contribute to a time-lapse movie of the location.  In this way, we can monitor environmental change together, watch the seasons change, see the effect of management and natural events, like fires or droughts.  The idea is a simple but exciting one.  Please consider contributing, even small amounts can help get this idea started!

Topics in Tropical Asian Forestry: technology meets conservation – applications being accepted now!

Topics in Tropical Asian Forestry: technology meets conservation

Applications for full scholarships are now being accepted until Nov. 15, 2013!  
For a full course description and instructions on how to apply, please visit the “Training” tab on this site.

“Magic” mushrooms observed in Xishuangbanna

Taylor Lockwood, professional mushroom photographer and official media specialist for the NSF-NSFC field course in digital forestry techniques, discovered a previously unreported bio-luminescent mushroom growing in XTBG.  Read the full report at the following link:

Dr. Cannon presents at Flora Malesiana IX in Bogor, Indonesia

Dr. Cannon made two presentations at the Ninth meeting of the Flora Malesiana project: “Near-sensing tropical Asian forests” and “Land area dynamics of the Southeast Asian archipelago during the Quaternary Period”.  The meeting was held from Aug 27-31, 2013 in Bogor, Indonesia.

Dr. Cannon presents at Sun Yat-Sen University and South China Botanical Garden

On August 22, 2013, Dr. Cannon presented talks on the “Historical Distribution of Tropical Rainforest in Sundaland during the Quaternary Period” at Sun Yat-Sen University in Guangzhou, Guangdong, China at the invitation of Dr. HE Fangliang.  The same day, he also presented the same talk at the South China Botanical Garden at the invitation of Dr. GE Xuejun.

Song of the near-sensing tribe

Click on the link below and listen to the rhythmic but primitive farewell song of the near-sensers in their native habitat (which is everywhere).

Rainforest party jamz

Topics in Tropical Asian Forestry field course underway

The field course on “Near-sensing and forest monitoring techniques” has now finished its second week and the students are busy working on their independent projects. Part of the Topics in Tropical Asian Forestry course, jointly funded by the U.S. National Science Foundation and the Natural Science Foundation of China, the course is being held from July 26 until Aug 21, 2013.  The course is led by Dr. Chuck Cannon (XTBG-Texas Tech) and Dr. Dave Lohman (City University New York) and is attended by 28 students from the USA. China, and seven other countries.

Guest speakers have included Dr. Luo Shu-jin (Beijing University), Dr. Doug Yu (KIZ-Univ East Anglia), Dr. He Fangliang (Univ. Alberta-Sun Yat-Sen Univ), Dr. Richard Corlett (XTBG), Dr. Ferry Slik (XTBG), Dr. Doug Schaefer (XTBG), Dr. Chen Jin (XTBG), Dr. Chen Hui (XTBG) and Mr. Wang Ximin (XTBG).  We will be making an announcement about how to apply for next year’s course shortly!

The group after the culture show in Jinghong!  The dancing elephants with the water pipes were the best!


Gaining tree cover while losing forest in Hainan

Dr. Zhai, now at the Kunming Institute of Botany and the World Agroforestry Institute, has published an article that points out the importance of accurately classifying forests and making the distinction between ‘industrial forest’ and ‘natural forest’ in government reforestation programs. While this important distinction, plantations can be used to increase tree cover while losing natural diverse forests, as has happened in Hainan.

Zhai, D.L., J.C. Xu, Z.C. Dai, C.H. Cannon, and R. E. Grumbine. 2013. Increasing tree cover but losing diverse natural forests in Hainan, China. Regional Environmental Change. DOI 10.1007/s10113-013-0512-9.

To protect biodiversity and improve environmental conditions, China has invested billions of dollars in reforestation and payments for ecosystem service programs. Here, we examine the Sloping Land Conversion Program, the largest such program in the world and found that after 13 years of implementation at our study site, it has had negative impacts on natural tropical forests. GIS and remote sensing techniques revealed that both natural forests and natural shrub and grasslands were replaced by non-native monocultural plantations on Hainan Island, China, a key tropical biodiversity hotspot. Under current Chinese policy, these plantations are classified simply as “forests”, with the assumption that they are equivalent to natural forests. This lack of a distinction in forest quality has led to substantial deforestation and plantation expansion, including encroachment into protected areas on Hainan. Additional social and economic drivers of these changes were identified by examining the participants in this program and their actions. Without a new ecologically based definition of forests and new goals for reforestation, such programs designed to improve ecosystem services, and forest quality may actually threaten remaining natural forests and other vegetation types in Hainan and in other areas of mainland China.

Prof. Cannon and Assoc. Prof. Surget-Groba receive fellowships

Associate Professor Yann Surget-Groba, leader of the Ecological Evolution group, received another year’s extension for his Junior Visiting Professorship at the Chinese Academy of Sciences, based at XTBG.

Professor Chuck Cannon also received a Senior Visiting Professorship from the Chinese Academy of Sciences for several months in 2013 to develop the international training courses in the Program for Field Studies office, in collaboration with the Center for Integrative Conservation, led by Prof. Richard Corlett.

Topics in Tropical Asian Forestry – online material available

The online material, including lectures, discussions, and interviews, are available through the TiTAF2012 tab at the top of the Ecological Evolution web page.  This course was held in the fall semester of 2012 with the participation of 18 students from almost as many universities from across the US and Asia.  It was supported by the U.S. National Science Foundation and Texas Tech University.