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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老妈驾到

1986年到大港中学住校住高中开始,上大学、读研究生、留所工作、留学,离老妈老家越来越远。虽然京沪线很方便,但毕竟只能短时乡探亲。现在老妈终于来到北京,和我们住在一起。老岳母也有个谈伴,少有寂寞感。三十年了,又有老妈暖暖的感觉。恭祝老妈、老岳母老身康健、福寿绵长!恭祝您家老人福如东海、寿比南山!

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Spring is coming. Happy New Year of Monkey to you.

Finished almost all tasks in 2015, I left the IOZ at around 4:30 and walked into the Olympic Forest Park. It is quite windy and chilly, but the air is fresh and fantastic. It is not crowed as usual as many people left or, are leaving Beijing for their hometown to enjoy the Spring Festival holidays.
A few pictures to share my joy in this wonderful park nearby IOZ.
Happy New Year of Monkey. I wish you all have a very successful  and fruitfly New year in 2016!

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Biodiversity, Collaboration, Fellowship/Scholarship/Studentship, Phylogenetic, 未分类

Congratulations to Robert Dudley and Raphael Didham for their PIFI Professorship

Robert Dudley、Raphael Didham两位教授获得PIFI访问项目资助

      昨日收到所外事通知,我帮助申请的两位外籍教授获得了中国科学院PIFI访问项目(http://english.bic.cas.cn/AF/Fe/201408/t20140807_125680.html)资助。祝贺他们,并期待和他们的合作成功。

Robert Dudley教授

https://ib.berkeley.edu/people/faculty/dudleyr

他是世界知名的整合生物学学者,在动物飞行等多个领域做出了一系列开创性的成果。近年来,我课题组和Robert Dudley教授在昆虫飞行分析方面开展合作;古脊椎所徐星研究员和他在早期鸟类及其恐龙近亲飞行行为演化等研究方向开展了探讨与合作,在美国《科学》杂志上发表了一篇有关用整合手段探讨鸟类起源研究的综述文章,预计能够对这一学科的未来发展方向产生好的影响。

我研究组计划和Robert Dudley教授合作,在昆虫飞行分析研究方向展开更多工作,有望在蜜蜂飞行起源等方向取得一批重要成果。

Raphael Didham教授

http://www.web.uwa.edu.au/people/raphael.didham

他是西澳大学动物生物学学院的生物多样性教授,并在澳大利亚联邦科工委组织生态系统科学部有正式职位。他1997年从英国帝国理工学院获得博士学位,随后在美国做完博士后到新西兰Canterbury大学工作了10年。Raphael教授致力于量化研究全球变化背景下的生物多样性的动态驱动机制,尤其关注无脊椎动物多样性的保护和害虫防控功能。

Raphael Didham教授是世界知名的学者,在昆虫物种多样性、物种保护、群落生态学等多个领域做出了一系列重要的成果。近年来,我研究组和Raphael教授计划以野生蜜蜂物种多样性和中国昆虫多样性监测网络监测为重点开展合作,预计能够对这一学科的未来发展方向产生好的影响。

本文引用地址:http://blog.sciencenet.cn/blog-536560-954571.html  此文来自科学网朱朝东博客,转载请注明出处。

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Protocols for Biodiversity Monitoring

We are searching for protocols for biodiversity monitoring and observatory. Basically, data produced from potential protocols be scientific question-driven. We also expect results might help to link science and policy in China.

If you have any comments, please kindly input as comments following this post.

Thanks in advance.

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Equipments, Hymenopterists, Methodology, pollinator bees, 未分类

Preparing for nest traps for 2016

Nest trap has been identified as one of the major trapping methods for wild bees. It is not only standard for ecological or biodiversity studies, but also gather more information for bee natural history. Besides, it helps us to gather more experience to increase pollinator bees diversity and density for agriculture.

In the lab, Mr. Liang DING, Mr. Feng Yuan, Dr. Dun-Yuan HUANG, Dr. Chun-Ling HE, Mr. Qing-Tao WU, Mr. Peng-Fei GUO et al. did a lot in the field to apply nest traps for bee systematics and diversity studies. More thanks to Mr. Qing-Tao WU for his great efforts to develop equipments, which make many things possible to study bees.

为2016年野外工作准备原材料,制作野生蜂巢管。感谢丁亮、袁峰、黄敦元、贺春玲、吴清涛、郭鹏飞等大量前期实地调研,也为清涛积极投入工作点赞!

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CAS: deeper participation in global innovation

CAS: deeper participation in global innovation
(NO.112 January 2016)
Issue NO:Lead Updated:29-01-2016
International science and technology cooperation at Chinese Academy of Sciences (CAS)allows access to foreign ideas, helps to achieve major breakthroughs in research, and nurtures young scientists. It also expands China’s overseas influence, improves China’s international status and serves its diplomatic strategy of mutually beneficial cooperation.

During China’s 12th Five-Year Plan period (2011-15), international cooperation helped CAS deliver a series of major research achievements, resolve some key technical problems, and introduce and cultivate innovative talents in science and technology.

For instance, a third kind of neutrino oscillation was observed during the Daya Bay experiment jointly conducted by CAS and the US Department of Energy. The discovery was selected as one of the top 10 scientific breakthroughs by Science magazine. In 2015, Wang Yifang, who led the Daya Bay neutrino oscillation experiment in China, was awarded the Breakthrough Prize, the top prize in science.

In 2013, publication of the revised English edition of Flora of China, the largest-scale flora publication in the world, was completed, thanks to 25 years of collaborative efforts by China, the US and other countries.

Overseas footprint

In 2012, CAS initiated a plan of going international to enhance integration of international resources in science and technology, increase the academy’s overseas influence, raise its public profile, and sharpen its competitive edge.

In 2013, CAS launched expanded science and education cooperation with developing countries, with plans made in three core areas – overseas institutions, talent cultivation and Third World Academy of Sciences(TWAS) centers in China, which facilitated internal and external collaborations and boosted the developing world’s science and technology development in all aspects.

Eight overseas institutions under CAS – located in Africa, Central Asia, Southeast Asia, South Asia and South America – have become important platforms for talent cultivation, scientific and technological innovation, interdisciplinary research, and integration of industries, education and research.

Every year, CAS provides financial support to 200 doctoral students from the developing world and to nearly 200 visiting young scholars and postdoctoral fellows to study or work in China. In this way, CAS has helped developing countries construct their scientific and technological frameworks.

CAS-TWAS centers of excellence, based on China’s advantages and concerned with the developing world’s sustainable development, have cultivated more than 180 professionals in science and technology for over 40 developing countries.

Cooperation with “the Belt and Road” countries

During the 12th Five-Year Plan period, CAS carried out cooperation in science and technology with countries along “the Belt and Road”, which won wide domestic and foreign support.

Technological cooperation on the Silk Road Economic Belt has concentrated on fields like drug research and development, protection of ecological systems, sustainable development of the environment and resource capacity assessment.

As a contribution to the 21st-Century Maritime Silk Road, CAS has focused on areas such as protection of biodiversity, ocean environment and climate change, desertification control, prevention and control of infectious diseases, astronomical observation, and space weather monitoring.

In addition, CAS is actively promoting demonstrated applications and transfers of China’s advantageous science and technology achievements. For example, the academy has made use of China’s satellites and airborne remote sensing technology to assist decision-makers in the conservation of the Angkor World Heritage Site.

Talent programs

In the 12th Five-Year Plan period, CAS launched an international talent program, attracting nearly 3,000 top scientists and researchers to China from more than 80 countries.

Since 2007, a total of 69 experts from 20 countries including the US, Japan and Germany, have won the Award for International Scientific Cooperation and the CAS International Cooperation Award for Young Scientists due to outstanding achievements through cooperation with China.

International organizations

Accomplished CAS scientists are playing a leading role in the developing world as well as an increasingly prominent role in major international academic organizations that have traditionally been dominated by developed countries. More than 600 scientists have worked or are working for major international science and technology organizations, with about 160 appointed with senior positions.

CAS President Bai Chunli won a second term as TWAS president in 2015. Under Bai’s leadership, extensive science and technology cooperation networks were set up through the TWAS platform, which significantly boosted the developing world’s innovation capability in major disciplines, laid a new foundation for promoting South-North cooperation, and enhanced China’s reputation in science and technology.

In 2014, CAS hosted a successful Annual Global Meeting of the Global Research Council (GRC) in Beijing, at which Bai was elected as GRC president. Discussions were also held on global innovation management, with topics including the cultivation of young scientists.

A year later, CAS co-organized the International Summit on Human Gene Editing with US and British research institutions, which had a far-reaching influence on policies and decisions of countries across the world.

CAS has proposed and participated in many international science programs through the platform of international academic organizations. It initiated and took an active part in international programs including the International Space Weather Meridian Circle Program, the Third Pole Environment, and the International Thermonuclear Experimental Reactor (ITER). In doing so it joined the science and technology world’s efforts in researching and resolving major global issues.

Collaboration with world-class research institutions

The academy also joined hands with world-class research institutions in remarkable science and technology projects, including:

–construction of a joint nuclear research center with the US Department of Energy;

–enhanced cooperation with top universities including Harvard in frontier sciences and cultivation of postgraduates;

–construction of the Institute Pasteur of Shanghai jointly with France;

–construction of the CAS-MPG Partner Institute for Computational Biology with Germany;

–enhanced cooperation, with a focus on high technology, with Russia

–cooperation with small and medium-sized countries that are strong in science and technology, concentrating on giving full play to each other’s advantages, as well as on co-funded programs in selected areas.

Mega-science facilities

CAS owns 23 advanced mega-science facilities, accounting for 85 percent of the country’s total. Mega-science facilities, such as the Shanghai Synchrotron Radiation Facility and the Beijing Electron Positron Collider, as well as big data platforms, have attracted top scientists from around the world to participate in their design, construction, maintenance, operation and use. As international cooperation platforms, they are open to the whole world and have helped accomplish major research achievements.

CAS aspires to benefit all of humanity through deepened integration with global innovation and participation in global governance. The academy will always be committed to open-mindedness, self-confidence, equality and cooperation, while advancing toward the future in the world of science.

Source: China Science Daily

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