Xishuangbanna Tropical Botanical Garden, (CAS) 中国科学院西双版纳热带植物园

Registration open for special course funded by NSF-USA: Next-gen forest surveys in Tropical Asia

admin — Mon, 14 May 2012 05:18:22 +0000

Next-gen forest surveys in Tropical Asia

This course will focus on the major issues surrounding tropical Asian forest management and the use of biotic surveys to monitor forest change. The course will consist of two parts: an on-line discussion course in Fall 2012 and a four week field course in July 2013 at the Xishuangbanna Tropical Botanical Garden (XTBG) in Yunnan, China, a research institute in the Chinese Academy of Sciences. Full scholarships will be provided for 12 students from any graduate degree granting institution in the U.S.A. and six students from similar nstitutions in tropical Asia. These scholarships are funded by the National Science Foundation (USA). Students will be accepted from Chinese institutions, who will pay course fees. Credit for the online course will be offered through Texas Tech University’s Graduate School. The course will be led by Chuck Cannon (Texas Tech University/Chinese Academy of Sciences, www.ecologicalevolution.org) and David Lohman (City College of New York-CUNY, www.sci.ccny.cuny.edu/lohman /) with additional support of the Program for Field Studies office based at XTBG.

For more information and to apply for a position, please visit the website below:

http://www.pfs-tropasia.org/courses/nsf-fieldcourse/

Dr. Cannon attends inception workshop on timber tracking

admin — Thu, 26 Apr 2012 01:24:11 +0000

A workshop hosted by Bioversity International, the German Ministry of Forest, Agriculture, and Consumer Protection, and the Forest Research Institute of Malaysia was held April 24-25 in Kuala Lumpur, Malaysia, to initiate a project on the “Identification of timber species and origins using DNA and stable isotope fingerprints”. Dr. Cannon has participated in the earliest stages of this project and contributed a presentation on “Reference-free approaches for comparative genomics”. The project will last three years and aims to create a database for roughly 20 timber species worldwide.

Exploiting sparseness in de novo genome assembly

admin — Mon, 16 Apr 2012 16:21:19 +0000

Mr. Ye Chengxi, formerly a member of the Ecology and Evolution of Plant-Animal Interactions at XTBG and now a PhD student in the Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland has just published an article in BMC Bioinformatics. The article demonstrates a novel and powerful approach to overcome the massive memory requirements of modern genome assembly by using a sparse version of the traditional de Bruijn graph, allowing the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. Mr Ye has produced a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. SparseAssembler was tested with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.

the article can be viewed at:

http://www.biomedcentral.com/1471-2105/13/S6/S1/abstract

We were hacked but we’re back!!

admin — Mon, 16 Apr 2012 15:09:33 +0000

Thanks to Loren Bell, working from the wilds of Borneo, the Ecological Evolution website should be fully functional again! We’ll run a tighter ship in the future. Cheers!! Official announcement about the new NSF field course to be released soon.

Genomic workshop announcement June 4-7, 2012

chuck — Mon, 26 Mar 2012 21:21:30 +0000

Workshop on Tropical Biodiversity and Genomics

Time and Venue
June 4-7 2012
Xishuangbanna Tropical Botanical Garden
Menglun, Yunnan, China

This small workshop will be organized in two sessions: a series of lectures and discussions with all participants, followed by two days of focused analysis of participant data. The Ecological Evolution group at XTBG has whole genome Illumina sequence data from numerous species of tropical tree, primarily in the genus Ficus (figs) and the family Fagaceae (oaks, stone oaks, chestnuts and beeches) and has several analyses and collaborations in progress. The group has primarily been developing reference-free analyses of this data from comparative and phylogenetic purposes.
The following participants have been confirmed:

Confirmed participants and their expertise
Chuck CANNON, XTBG and Texas Tech University
- Reference-free analytical approaches
- Tropical biodiversity and forests
Graham STONE, Edinburgh
- gall wasps
- transcriptomics
RUAN Jue, Beijing Institute of Genomics
- de novo analysis of next-gen data
SHI Su-Hua, San Yat Sen University, Guangzhou
- comparative genomics of mangrove species
WU Chung-I, Beijing Institute of Genomics, Beijing
- population genetics and diversification
Yann SURGET-GROBA, University of California, Santa Cruz and XTBG
- transcriptomes and biodiversity
YU Jun, Beijing Institute of Genomics
- biotechnology and next-gen sequencing

Registration

At the moment, we can still accept 4-5 additional participants but you must contact us before April 21st, 2011, when the participant list will be finalized. Please contact Chai-Shian KUA (kuacs@xtbg.ac.cn ) or Chuck CANNON (chuck@xtbg.ac.cn) to register.

Fees, due upon arrival
950 RMB for scientists from China and 550 USD for foreign scientists
500 RMB for students from China and 250 USD for foreign students

Accommodation: 200 RMB per night at the XTBG garden hotel. Other accommodation options are also available around XTBG

Field Trip : 200 RMB

Visit our website for more details, including a draft agenda and research topics: www.ecologicalevolution.org/training

Dr. Chen Xi (Cici) publishes on trade-off strategy in Lithocarpus seeds between physical and chemical defense

chuck — Sat, 24 Mar 2012 02:45:08 +0000

Dr. Chen Xi’s research on the chemical ecology of Lithocarpus seeds has just been published in PLoS ONE. The paper is entitled “Evidence for a trade-off strategy in stone oak (Lithocarpus) seeds between physical and chemical defense highlights fiber as an important antifeedant” and can be downloaded at the following link: http://dx.plos.org/10.1371/journal.pone.0032890

Expanding Capacity for Conservation Science Education in Tropical Asia

chuck — Sat, 10 Mar 2012 03:51:51 +0000

An invited article entitled “A Proposal for Expanding Capacity for Conservation Science Education in the Tropical Asia-Pacific Region” written by Charles Cannon, Rhett Harrison, Lan Qie, Ferry Slik and Jin Chen was just published in Biology International, the official journal of the International Union of Biological Sciences.

The full issue can be downloaded for free from the following link:

http://biologyinternational.org/

Field course in next-gen forest survey funded by U.S. NSF

chuck — Sat, 10 Mar 2012 03:45:11 +0000

A grant from the United States National Science Foundation has been awarded to Drs. Chuck Cannon and David Lohman (City College of New York) for a field course in next-gen forest survey techniques. Two years of funding have been awarded and the course will bring 12 graduates students from the United States, selected nationally, to work with 6 Chinese and 6 Asian students, selected from the East Asian region, in the forests managed by the Xishuangbanna Tropical Botanical Garden. The students will explore protocols for rapidly collecting field data, using widely available digital recording devices and advanced meta-genomic sequencing, and integrating that data into existing internet-based data-sharing platforms. Recruitment for the course will begin in April, 2012. The field course will be coupled with an online graduate level course to be offered through Texas Tech University, beginning in the fall. Please watch the Program for Field Studies – Tropical Asia for further announcements.

Dr. Cannon presents in webinar

chuck — Tue, 31 Jan 2012 17:23:58 +0000

Dr. Cannon will participate in an informative webinar on the topic of using flow cytometry to measure genome size entitled: “Using Flow Cytometry to Speed Determination of Eukaryotic Genome Sizes and Cell Type-Specific Gene Expression”

Broadcast Date: Wednesday, February 1, 2012
Time: 1:00 pm EST, 10:00 am PST

REGISTRATION IS FREE

http://www.genengnews.com/webinars/using-flow-cytometry-to-speed-determination-of-eukaryotic-genome-sizes-and-cell-type-specific-ge/151/

Dr. Cannon describes a new species of stone oak

chuck — Tue, 20 Dec 2011 14:32:10 +0000

A new species of stone oak (Lithocarpus pulongtauensis) has recently been published by the Annales Botanici Fennici. The species is named in honor of the recently gazetted protected area in the Kelabit Highlands, the Pulong Tau National Park, Sarawak, Malaysia. This species has been collected on the northern slopes of Mt. Kinabalu, where Dr. Cannon encountered a rather large population, and in the Kelabit Highlands. The nuts are enclosed in an unusual cupule, that is quite dark, the material is rather corky, and the large scales are fused.

Rubber and pulp are a double threat to Hainan forests

chuck — Wed, 07 Dec 2011 04:45:49 +0000

Zhai Deli’s study of land use change in the Changhua watershed on the island of Hainan was recently published in the Journal of Environmental Management. The article is entitled “Rubber and pulp plantations represent a double threat to Hainan’s natural tropical forests” and the work was completed with the following co-authors: Charles H. Cannon, J.W. Ferry Slik, Cui-Ping Zhang, and Zhi-Cong Dai.

Abstract

Hainan, the largest tropical island in China, belongs to the Indo-Burma biodiversity hotspot and harbors large areas of tropical forests, particularly in the uplands. The Changhua watershed is the cradle of Hainan’s main river and a center of endemism for plants and birds. The watershed contains great habitat diversity and is an important conservation area. We analyzed the impact of rubber and pulp plantations on the distribution and area of tropical forest in the watershed, using remote sensing analysis of Landsat images from 1988, 1995 and 2005. From 1988 to 1995, natural forest increased in area (979–1040 sq km) but decreased rapidly (763 sq km) over the next decade. Rubber plantations increased steadily through the study period while pulp plantations appeared after 1995 but occupied 152 sq km by 2005. Rubber and pulp plantations displace different types of natural forest and do not replace one another. Because pulp is not as profitable as rubber and existing pulp processing capacity greatly exceeds local supply, considerable pressure exists on remaining upland forests. We recommend for future management that these plantation forests be reclassified as ‘industrial’, making a clear policy distinction between natural and industrial forestry. Additionally, the local government should work to enforce existing laws preventing forest conversion on marginal and protected areas.

The article can be viewed and downloaded from this link – http://www.sciencedirect.com/science/article/pii/S0301479711003847

AFEC-X 2011 – our third year begins!

chuck — Wed, 26 Oct 2011 04:56:37 +0000

AFEC-X 2011 has started! On Oct 22, 25 participants from 12 countries (Thailand, Cambodia, Vietnam, Laos, India, Sri Lanka, Indonesia, Malaysia, Philippines, USA, DPR Korea, and of course China) arrived in XTBG. Deputy Director of XTBG, Dr Li Qingjun, gave a welcome address and introduction to XTBG at the course opening. Participants will spend the next two weeks in the beautiful botanical garden for lectures, discussions, and practicals over a range of topics, led by many leading experts. The course will then move to the field site in Mengsong, where the participants will spend more than two weeks designing and completing independent research projects.

My wordle

chuck — Sat, 22 Oct 2011 03:44:39 +0000

A wordle (http://www.wordle.net/) of the titles and abstracts from most of my publications. Cool!

Melissa Wong, visiting student from Malaysia, publishes in BMC Genomics

chuck — Tue, 06 Sep 2011 04:29:57 +0000

Melissa Wong, a PhD student from the National University of Malaysia and co-advised by Prof. Cannon and Prof. Wickneswari Ratnam, joined the Ecological Evolution group in 2009 for several months to learn bioinformatic techniques for analyzing next-gen sequencing techniques. Ms. Wong conducted her study on the whole transcriptome sequence from two parental species of Acacia to discover SNPs to use as breeding markers in a field-tested set of hybrids. The final published version of her paper is now available on the BMC Genomics website, where it is currently ‘Highly Accessed’.

http://www.biomedcentral.com/1471-2164/12/342

Ecological Evolution group passes its four year assessment

chuck — Sat, 13 Aug 2011 03:06:42 +0000

On Aug. 12, 2011, Dr. Cannon presented the achievements of the Ecological Evolution group over the first four years of its existence to an academic committee of 11 colleagues. The committee approved of the group’s efforts and agreed to continue XTBG’s support, including adding an additional staff member as a reward for our success! Thanks and congratulations to our staff, students, and colleagues!

XTBG scientists attend the 18th International Botanical Congress

chuck — Wed, 03 Aug 2011 08:33:49 +0000

Several faculty and students from XTBG attended the IBC 2011 meeting in Melbourne, Australia. Drs. Cannon and Slik presented in a special symposium on “Historical biogeography of Malesia and its effects on current patterns of plant diversity”. The International Botanical Congress is held every six years and is one of the biggest botanical meetings in the world. Almost two thousand people participated in the meeting and twenty concurrent symposia ran each afternoon.

Dr. Slik extends the analysis of Sundaland biogeography in PNAS

chuck — Tue, 12 Jul 2011 03:32:31 +0000

Dr. Ferry Slik, formerly of the Ecological Evolution group and now leading the Plant Geography group at XTBG, has published an analysis of 111 floristic inventory plots across the Sundaland region in the Proceedings of the National Academy of Sciences, USA. The major findings indicate that the marked biogeographic difference between western (Malay Peninsula and Sumatra) and eastern (Borneo) Sundaland was more related to plant species with coarse-soil tolerance rather than drought tolerance, suggesting that exposed sandy sea-bed soils acted as the major dispersal barrier in central Sundaland, not a savanna corridor. This finding makes it clear that proposed biogeographic explanations for plant and animal distributions within Sundaland, including possible migration routes for early humans, need to be reevaluated.

The article can be obtained at the following link: http://www.pnas.org/content/early/2011/07/08/1103353108.abstract

Visiting Professor Manuel Lerdau publishes in Nature

chuck — Thu, 07 Jul 2011 06:24:52 +0000

After a brief chat with Dr. Jacob Wickham at the Beijing meeting for Foreign Experts, Dr. Lerdau drafted a response to a recent article in Nature about invasive species. The article generated a great deal of response from the conservation community and Nature published three separate letters in response to the controversial article. These three articles will be included in the weekly press release by Nature. The article is available at the following website: http://www.nature.com/nature/journal/v475/n7354/full/475036d.html.

Dr. Yann Surget-Groba awarded a Visiting Foreign Junior Faculty Fellowship

chuck — Wed, 06 Jul 2011 07:03:47 +0000

Dr. Yann Surget-Groba, currently a postdoctoral researcher at the University of California, Santa Cruz, has been awarded a Visiting Foreign Junior Faculty Fellowship from the Chinese Academy of Sciences. He will join the Ecological Evolution group in March, 2012. He will be assisting the group to develop lab-based and bioinformatic techniques to study the genomic evolution and diversification of two model groups for the study of tropical rainforests, the stone oaks (Lithocarpus) and the figs (Ficus).

Workshop on Tropical Biodiversity and Genomics comes to a successful conclusion

chuck — Sun, 03 Jul 2011 06:46:46 +0000

WTBG@XTBG 2011 was a great start to an exciting new era in tropical biodiversity research in the Chinese Academy of Sciences. The workshop was organized into a series of excellent research talks presented by leading scientists and participants. Several working groups focused on transcriptomics, comparative genomics, reference-free analysis, and the detection of selective elements. The participants also discussed future directions, possible collaborations, and the structure of upcoming proposals. Invited speakers included Mike Arnold (Kunming Institute of Zoology and University of Georgia), Jeff Boore (Genome Project Solutions and University of California at Berkeley), Chuck Cannon (XTBG and Texas Tech University), David Galbraith (University of Arizona), Rhett Harrison (XTBG), Chai-Shian Kua (XTBG), Christian Lexer (University of Friborg, Switzerland), Hendrik-Jan Megens (Wageningen University), and Yann Surget-Groba (University of California, Santa Cruz). Three participants also gave presentations one evening: Ruan Jue (Beijing Institute of Genomics), Ye Cheng-Xi (XTBG), and Ye Sun (South China Botanical Garden).