Biodiversity, Collaboration, Scientific Meetings, Symposia, Workshops, Taxonomy, 未分类

A Workshop to Explore Enhancing Collaboration between US and Chinese Researchers in Systematic Biology, Guangzhou, Feb. 23-28

中美生命之树研讨班

已有 231 次阅读 2016-3-1 09:34 |系统分类:科研笔记|关键词:研讨会;生物系统学;生物多样性;生命之树     推荐到群组

2月23-26日,我有幸受邀参加了中美生命之树研讨班,并作两个讨论小组发言。此次会议由基金委主办,华南植物园协办的会议。会议目的是促进中美在生物系统学领域的合作。

个人最大的感受:1)会议形式非常灵活;2)会议考虑到合作研究中普遍受到关注的问题(见加下划线部分);3)会议代表来自病毒学、微生物学、动物学、植物学等多个学科领域;4)美方Pat、Karl等是会议讨论的灵魂人物,牢牢把握了研讨会的方向。

中国每个学科领域都有专业学会、专业委员会及其例会,但是缺乏跨类群关注系统学或进化生物学的专业组织。相信此次会议会启发部分代表,并酝酿启动中国系统学与进化生物学学术组织(Association of Systematic and Evolutionary Biology, China)。

A Workshop to Explore Enhancing Collaboration between US and Chinese Researchers in Systematic Biology

Workshop Agenda

Tuesday 23 February 2016.

8:30am-11:00pm. Registration, Yanling Hotel Lobby
12:30am. Lunch, Chinese Restaurant, Yanling Hotel (the first floor)
4:00pm-6:00pm. Informal mixer. Western Restaurant, Yanling Hotel (the first floor), Informal gathering for those who will arrive by late afternoon

6:30pm-7:30pm. Welcome Banquet. Western Restaurant, Yanling Hotel (the first floor)

Wednesday 24 February 2016. The First Meeting Room, South China Botanical Garden

8:15-8:45. Bus from hotel to botanic garden

8:45-10:00. Welcome, introductions, goals
Why are we here? What is a “workshop”? What do we want to accomplish?Introductions of participants from China and US
Introductions of program officers from NSFC and US NSF

Each participant should briefly explain: name, position, institution, taxonomic group or habitat ofinterest, methods used in research, geographic area of focus, what would do you hope to get out ofthe workshop.

10:00-10:30. Break and group photo

10:30-11:30. Short presentations on active US-China collaborations. Focus of the presentationsshould be on who is involved, how did the collaboration begin, how is the research supported,what are most positive outcomes, what problems had to be solved? What were the importantlessons learned. (6 presentations @ 10 minutes each; 3 from US, 3 from China)

o Anthony Cognato, Michigan State University.
o Ying Huang, Institute of Microbiology, Chinese Academy of Scienceso Karl Kjer, University of California Davis
o Xi-jun Ni, Department of Paleomammalogy, Beijing
o Greg Mueller, Chicago Botanic Garden
o Jian-quan Liu, Sichuan University

11:30-12:00. Discussion

12:00-1:00. Lunch. Informal discussions.

1:00-2:00. Small group discussions (form four groups): Benefits and challenges of international collaboration. Each group should discuss benefits and challenges. Think about communication, funding, sharing data, training, permissions

Four meeting room: The Second Meeting Room, The Third Meeting Room, The 427 Meeting Room,The 527 Meeting Room

2:00-3:00. Small discussion groups report to full workshop group (15 minutes each), The First MeetingRoom

3:00-3:30. Break

3:30-5:00. Small group discussions (form four groups): What are the most exciting questions andrapidly developing fields in systematics that would benefit from collaboration? Possible topicscould include:

  •   Environmental genomics, integration of environmental data in systematics and taxonomy
  •   Phylogenomics
  •   Single cell genomics, phylogenetic taxonomy,
  •   Collections-based bioinformatics (collaboration between iDigBio, and Chinese counterparts)
  •   Monography in the bioinformatics era
  •   The “microbial black box” – how do we get from metagenomics to cultivated species and back?
  •   Combining molecular and morphological data (and extant and fossil)
  •   Macroevolutionary analysis of traits. How to capture and analyze diverse data in sensible ways to address evolutionary questions
  •   Expanding the role and relevance of ecological and historical biogeography in understanding climate change

    Four meeting room: The Second Meeting Room; The Third Meeting Room; The 427 Meeting Room;The 527 Meeting Room

    5:00-6:00. Small discussion groups report to full workshop group. General discussion.Preview for Thursday (panel discussions). The First Meeting Room

    6:00. End of discussions for today, bus from SCBG to Yanling Hotel6:30-7:30. Dinner. Western Restaurant, Yanling Hotel (the first floor)

    Thursday, 25 February 2016. The First Meeting Room, South China Botanical Garden

    8:15-8:45. Bus from hotel to botanic garden

    8:45-9:30. Panel discussion on data and collections, including methods and toolsfor data sharing.Collaborative projects depend on the ability to share data and collections among members ofthe team. This is more challenging for long distance collaborations. How have you solved these challenges in collaborative research?(not necessary to be US-China collaborationexample)

o Rüdiger Bieler, Field Museum
o Paul Marek, Virginia Polytechnic Institute and State University
o Fabiany Herrera, Chicago Botanic Garden
o Xin Zhou, China National GeneBank, BGI-Shenzhen
o Chao-Dong Zhu, Institute of Zoology, Chinese Academy of Sciences
o Fumin Lei, Key Laboratory of Zoological Systematics and Evolution, Beijing

All workshop participants: What are the big challenges that your discipline faces for datasharing? What formats and repositories should be used for character data, publishedphylogenies, specimen vouchers and records to ensure their re-use potential? What are thebest tools for sharing data within the research team?

9:30-10:30. Discussion of sharing data and collections

10:30-11:00. Break

11:00-12:00. Panel discussion on field work and permits. Many projects require field work and permits.In addition material use agreements are often required. The panel discussion should explorechallenges and solutions to field work and permission challenges.

o Melanie Hopkins, American Museum of Natural History (paleontology)o Ken Halanych, Auburn University
o Zhiwei Liu, Eastern Illinois University (insects)
o Zhu-Liang Yang, Kunming Institute of Botany

o Gongle Shi, Nanjing Institute of Geology and Palaeontology
o Shunping He, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan

12:00-1:00. Working lunch. Small group discussion of field work and permits. Form six groups fordiscussion.

1:00-2:00. Breakout groups report to full workshop group (10 minutes each)3

2:00-3:45. Panel discussion on publishing and sharing credit. It is very important in collaborativeresearch to discuss how the team will publish the results of the research and how the team members will share credit and be listed in the authorship of the publications. This is especiallyimportant for graduate students and postdocs, who need to be recognized for theircontributions so that they can find jobs!

o Aaron Bauer, Villanova University
o Debashish Bhattacharya, Rutgers University
o Petra Sierwald, Field Museum
o De-Zhu Li, Kunming Institute of Botany
o Jing Che, Kunming Institute of Zoology
o Chao-Dong Zhu, Institute of Zoology, Chinese Academy of Sciences

3:45-4:00. Break

4:00-4:30. Discussion on training opportunities. Collaborative projects provide great opportunities forteam members to learn new skills. This open discussion session will focus on examples oftraining opportunities in collaborative projects.

o AJ Harris and Yundong Gao (early career collaboration)

o Patrick Herendeen, graduate training in the US
o Wenjun Bu, graduate training in China

4:30-5:30. Discussion on funding opportunities. Discussion lead by program officers from NSF andNSFC

Funding system in USA (focus in NSF). What can and cannot be included in budget?Howdoes NSF proposal process work? Presented by NSF program officers Funding system in China. What can and cannot be included in budget? How does NSFCproposal process work? Presented by NSFC program officers

Discussion of Genealogy of Life Program (“GoLife”) at NSF
5:30-6:00. General discussion. Any subjects needing more time for discussion?

What would we like to see as products from this workshop? Should we write an article for ajournal to discuss US-China collaboration in systematics? Possible topics to consider in apaper:

o What is the value for Sino – US collaborations? What strengths does each sidecontribute?

o What are the opportunities and challenges?
o What is the role of conservation or other practical consideration?

6:00. End of discussions for today, bus from SCBG to Yanling Hotel6:30-7:30. Dinner. Western Restaurant, Yanling Hotel (the first floor)

Friday, 26 February 2016. South China Botanical Garden and Post-Workshop Excursion

8:15-8:45. Bus from hotel to botanic garden. Note: participants attending the excursion should checkout before breakfast and bring their luggage with them to the garden!

8:45-11:30. Conclusions: identify opportunities and actions that can be taken immediately andoutcomes that will require additional work.
Do we have recommendations that can be developed into a manuscript for publication?

11:30-1:00. Lunch and free time to see conservatory. Please take your delegate card with you.

1:00. Depart for excursion.
Dinghushan National Nature Reserve, Zhaoqing city (a World Network of BiosphereReserves).This reserve has been protected for 400 years as it contains the Qingyu Buddhist Temple. It is 1133 ha and the local vegetation is characterized by evergreen broadleaf forest.There are 1993 vascular plants, of which 700 woody species.

1:00. Bus from SCBG to Yanling Hotel (Who do not attend excursion), check out before 2:30pm6:00 pm. Check in to hotel in Zhaoqing city.

Saturday, 27 February 2016. Post-Workshop Excursion

After breakfast (about 8:00 am), depart for Fengkai county, Zhaoqing city. We will visitHeishiding Nature Reserve as well as the Fengkai national geological park. The HeishidingNature Reserve is located at the Tropic of Cancer and covers about 4200 ha evergreenbroadleaf forest. There are 1900 species of seed plants, 118 families, 670 genera, 1000species of insect, and 42 families, 122 species of birds.

3: 00 pm. Depart for Guangzhou
6: 30 pm, check in Guangdong Hotel, downtown Guangzhou

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Biodiversity, DNA Barcoding, DNA Taxonomy, Methodology, Phylogenetic, Taxonomy

The minimum sample size for DNA Barcoding

We recently published a paper on the minimum sample size in DNA Barcoding in the journal Ecology and Evolution (doi: 10.1002/ece3.1846). It tried to use simulated datasets to examine the effects of sample size on four estimators of genetic diversity, mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. As found by the previous project by Ai-Bing ZHANG et al. (2010, doi:10.1016/j.ympev.2009.09.014), this project confirms again that larger sample size helps to find the better results from DNA Barcoding. Besides, we found the minimum sample size of 20 individuals is required for each subsample.

Dr A-Rong LUO led the project. She collaborated with researchers and student in Yunnan University, Beijing University of Chemical Technology, Capital Normal University and University of Sydney. Mr. Hai-Qiang LAN, the joint graduate student between Yunnan University of Finance and Economics and Institute of Zoology, Chinese Academy of Sciences finished his thesis during the project. The project was mainly supported by grants from the National Science Foundation, China, and partially supported by the Program of Ministry of Science and Technology of the People’s Republic of China.

我们最近在Ecology and Evolution上发表了一篇论文,研究了DNA Barcoding的最小取样量问题(doi: 10.1002/ece3.1846)。该工作用模拟数据,对错配分布、核苷酸多样性、单倍型数量和最大配对距离等四个遗传多样性的取样量效应进行了比较分析。和张爱兵等(2010, doi:10.1016/j.ympev.2009.09.014)发现的一样,我们发现取样量越大,DNA Barcoding的结果越好;同时,我们的结果发现每个亚群取样量至少为21个个体。

罗阿蓉博士为第一作者。她和云南财经大学、北京化工大学、首都师范大学、悉尼大学等研究人员合作完成。通过这个项目,云南大学和中国科学院动物研究所联合培养了一名硕士研究生,蓝海强完成一篇学位论文。该工作主要得到自然科学基金委面上和特殊学科点项目,部分得到科学与技术部基础专项的支持。

Luo, A., Lan, H., Ling, C., Zhang, A., Shi, L., Ho, S. Y. W. and Zhu, C. (2015), A simulation study of sample size for DNA barcoding. Ecol Evol, 5: 5869–5879. doi:10.1002/ece3.1846

English Abstract:

For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. Our results showed that mismatch distributions derived from subsamples of ≥20 individuals usually bore a close resemblance to that of the full dataset. Estimates of nucleotide diversity from subsamples of ≥20 individuals tended to be bell-shaped around that of the full dataset, whereas estimates from smaller subsamples were not. As expected, greater sampling generally led to an increase in the number of haplotypes. We also found that subsamples of ≥20 individuals allowed a good estimate of the maximum pairwise distance of the full dataset, while smaller ones were associated with a high probability of underestimation. Overall, our study confirms the expectation that larger samples are beneficial for the efficacy of DNA barcoding and suggests that a minimum sample size of 20 individuals is needed in practice for each population.

中文摘要:

DNA条形码可以为某些生物类群分类、进化生物学和物种多样性评估等研究提供有效的辅助性作用。但是,条形码的效力取决于每个物种的取样程度。只有足够的取样量才能可靠地估计遗传多样性,从而精确界定物种。我们通过数据模拟,对4个影响DNA条形码相关的遗传多样性变量进行了分析:错配分布、核苷酸多样性、单倍型数量和最大配对距离。我们的结果表明:20个(包括)以上的个体组成亚组得到的错配分布和全数据集的相似;20个以上个体亚组的核苷酸多样性估值在全数据集附近形成钟形分布,而20个以下个体亚组则非钟形分布;加大取样量通常会提高单倍型数量;20个以上个体亚组可以较好估计全数据集的最大配对距离。综上,我们的研究确认DNA条形码取样量的重要性,每个种群至少取样20个。

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Taxonomy, 未分类

Being a taxonomist, how and what do you contribute to teams or projects in other fields?

I’m conceiving a few paragraphs to discuss on contributions from taxonomists, demands from other topics and gaps between taxonomists and other researchers. Here, taxonomists are not limited to alpha level who focus mainly on species identification and classification.

Certainly, taxonomists have been spending much valuable time and rich expertise to contribute a lot to some important projects, especially those on biodiversity, ecology, evolutionary biology, invasion biology, plant protection, conservation biology, and emerging genome biology. Also, governments demands more for quarantine of pests. However, there is a trend that more and more teams appreciate taxonomists’ contributions only in the acknowledgement part of papers.

Why?

How to fill in the gaps?

How to optimise the interactions between taxonomists and other researchers?

Your answers/comments are mostly welcome. If you are willing to act as the coauthor(s) of this potential manuscript to Zoological Systematics, please kindly email me at zhucd@ioz.ac.cn. 

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