重建生命之树已经进入了组学时代。数据分析中存在的计算限制、问题和挑战依然存在。转载了Tandy Warnow教授在YouTube上的四个学术报告，和大家分享、共同学习。 注意：报告文件比较大，均在100-500MB左右。 http://user.qzone.qq.com/425414123/photo/V13qrwNW1ANlxg/ Tandy Warnow Founder Professor of Engineering Professor of the Departments of Computer Science and Bioengineering Institute for Genomic Biology, Biocomplexity Theme National Center for Supercomputing Applications Affiliate in the departments of Electrical and Computer Engineering, Mathematics, Statistics, Animal Biology, Entomology, and Plant Biology PhD (Mathematics) University of California at Berkeley, 1991 B.S. (Mathematics) University of California at Berkeley, 1984 Current NSF Funding : My research in currently funded by three grants from the National Science Foundation. Multiple sequence alignment , funded by NSF grant ABI-1458652, beginning August 2015. This project will develop new methods for multiple sequence alignment, building on our SATé, PASTA, and UPP methods. Metagenomics , funded by NSF grant III:AF:1513629. This is a collaborative grant with the University of Maryland, for new methods for metagenomic dataset analysis, building on our TIPP method for taxon identification of reads in a metagenomic sample. Graph-Theoretic Algorithms to Improve Phylogenomic Analyses , funded by NSF grant CCF-1535977. I am the overall PI, and this project is collaborative with Satish Rao (UC Berkeley PI) and Chandra Chekuri (UIUC). We are developing new theoretical computer science and discrete algorithms for improving the estimation of large species and gene trees, and specifically enabling statistical methods to scale to ultra-large datasets. Recent NSF funding has supported work in phylogenomics, described here . This is still an area of very active research in my group. I also recently benefited from support of the John P. Simon Guggenheim Foundation , and earlier support from the David and Lucile Packard Foundation , the Radcliffe Institute for Advanced Study at Harvard University , the Program for Evolutionary Dynamics at Harvard University , and Microsoft Research, New England . The Founder Professorship is funded through the Grainger Engineering Breakthroughs Initiative , which is supporting development of research in Big Data and Bioengineering at UIUC. I am grateful to the National Science Foundation for its continuous support since 1994. See this page for completed projects funded by NSF, starting in 2001. http://tandy.cs.illinois.edu
PLoS Biology发表了一篇关于生命之树与生物多样性的观点论文。题目是： Walking and talking the tree of life: Why and how to teach about biodiversity。想想就很浪漫的一件事，生命之树重构的是生命从发源到现在的历史长河。作为有幸从事分类学、系统发育研究的科研工作者，可以在这棵树的一个分支上做一点点工作。闲来无事，在咖啡时间还可以到其它分支上去漫步，和其他同行讨论、讨论。 多样性的分类学细节是生物学教育的关键骨架。但是现在生物教科书中关于生命之树的教学方法，虽早已过时，仍被广泛应用。作者在论文中比较了传统方法和分支方法的不同：前者展示的进化关系 模糊 、不能明确表示出重要的生命进化节点、过多依赖于对分类学阶元信息的记忆；后者则相反，关注共同祖先、单系类群和近裔功能性状。分支方法明确基于达尔文有变化的后裔“的观点，为学生掌握生物多样性结构性细节提供了理论框架，并有助于他们主动学习。作者提倡反映生命之树的系统发育分类系统，这样可以在 教学 逐渐增加 复杂性，展示 阶元并应用主动学习的技术和策略。 目前国内动物学、植物学、昆虫学等教科书，基本还是采取经典的分类学展示方法。以动物学为例，每个章节涉及一个门类，从形态结构功能到分类系统。一般在一个章节讨论进化关系。然而相较于形态学、分类学，系统发育在过去的50余年发展迅猛。很多类群的系统发育关系均有深入研究，至少部分改变了过去单纯从形态的角度提出的观点。但是这部分的内容比重却少有增加，和学科发展不相称，没有反映新思路、新学说和新技术。本科生和研究生对这些学科的理解，自然就停留在背诵记忆为主的水平，难以在进化生物学的框架内去开展科学思维和探索活动。 教科书只是知识集成和传播的一种形式，有助于提供标准答案，但少于创新思维启迪。我读硕士研究生期间，讲课好的老师基本上都用投影胶片的方式，尽量收集学科新进展。学生难以跟上授课，难以把握知识点，但确实培养了主动学习、主动探索的习惯和能力。现在，互联网时代，编著者和学生等受众互动，应该形成更加多元、多角度并可以及时更新的知识库。有了学科前沿的展示窗口，自然会吸引年轻人。 PERSPECTIVE Walking and talking the tree of life: Why and how to teach about biodiversity Cissy J. Ballen , Harry W. Greene （http://dx.doi.org/10.1371/journal.pbio.2001630） Abstract Taxonomic details of diversity are an essential scaffolding for biology education, yet outdated methods for teaching the tree of life (TOL), as implied by textbook content and usage, are still commonly employed. Here, we show that the traditional approach only vaguely represents evolutionary relationships, fails to denote major events in the history of life, and relies heavily on memorizing near-meaningless taxonomic ranks. Conversely, a clade-based strategy—focused on common ancestry, monophyletic groups, and derived functional traits—is explicitly based on Darwin’s “descent with modification,” provides students with a rational system for organizing the details of biodiversity, and readily lends itself to active learning techniques. We advocate for a phylogenetic classification that mirrors the TOL, a pedagogical format of increasingly complex but always hierarchical presentations, and the adoption of active learning technologies and tactics.
系统发育树是解决生态和进化问题的重要工具之一。构建较大的系统发育树的难点在于公共 DNA 序列的数据总量和数据结构。基因组数据和 DNA 条形码数据是两个不同类型的数据。目前它们还不太容易整合在一起，用于重新构建系统发育树。另外，两类数据的划分却也常常被研究人员忽视。 Douglas Chesters 博士通过生物信息学系统方法，重构了第一个昆虫（昆虫纲）物种水平的系统发育树。该工作对核转录组、线粒体基因组和 DNA 条形码分别建立了独立的数据矩阵；之后，逐级分析直至种一级进行系统发育树重建。该工作目前涉及的系统发育树包括了 760 科、 13,865 属和 49,358 个种。这个昆虫纲物种水平的系统发育树的基部部分与之前部分发表的工作相似。这项工作对昆虫物种树的实用性进行评估，比较了一些基于 DNA 分类学的分类方法。结果发现：当以大的生命树作为参考数据时， DNA 分类学思路的准确度较高。本文报道了如何将不同类型序列数据整合入超级矩阵这一技术难点的解决方法，将大大促进昆虫物种多样化的研究，并可以通过 DNA 更好描述来研究的群落的多样性。 此项工作是大数据库物种界定工作的延续和扩展，相关内容在首届全国生物系统学论坛上作特邀报告展示。 Douglas Chesters 博士目前是中国科学院动物研究所功能昆虫群进化研究组副研究员，独立承担国家自然科学基金委面上项目一项和外国青年科学家项目 1 项，并得到中国科学院 “ 国际人才计划 ” 的资助。 开源 软 件 ： A Linux implementation of the protocol described here ismade freely available under the GNU general public license athttps://sourceforge.net/projects/sophi/, and in supplementary material. 论文： Construction of a Species-Level Tree-of-Life for the Insects and Utility in Taxo.pdf ACCEPTED Construction of a Species-LevelTree-of-Life for the Insects and Utility in Taxonomic Profiling Douglas Chesters Syst Biol (2016) syw099. DOI: https://doi.org/10.1093/sysbio/syw099 While comprehensive phylogenies have proven an invaluabletool in ecology and evolution, their construction is made increasinglychallenging both by the scale and structure of publically available sequences.The distinct partition between gene-rich (genomic) and species-rich (DNAbarcode) data is a feature of data that has been largely overlooked, yetpresents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draftconstruction of a species-level phylogeny of insects (Class Insecta).Matrix-building requires separately optimized pipelines for nucleartranscriptomic, mitochondrial genomic, and species-rich markers, whereastree-building requires hierarchical inference in order to capturespecies-breadth while retaining deep-level resolution. The phylogeny of insectscontains 49358 species, 13865 genera, 760 families, 31 orders. Deep-levelsplits largely reflected previous findings for sections of the tree that aredata rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera,the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera,Brachycera (Diptera) and Cucujiformia (Coleoptera). However, analysis of bias,matrix construction and gene-tree variation suggests confidence in somerelationships (such as in Polyneoptera) is less than has been indicated by thematrix bootstrap method. To assess the utility of the insect tree as a tool inquery profiling, several tree-based taxonomic assignment methods are compared.Using mined test datasets of known species membership, a tendency is observedfor greater accuracy of species-level assignments where using a fixed,comprehensive tree-of-life in contrast to methods generating smaller de novoreference trees. Described herein is a solution to the discrepancy in the waydata is fit into supermatrices. The resulting tree facilitates wider studies ofinsect diversification and application of advanced descriptions of diversity incommunity studies, amongst other presumed applications. Data Integration , Data Mining , Insects , Phylogenomics , Phyloinformatics , Tree of Life IssueSection: Regular Manuscript
7月特刊：The Tree of Life: China Project 本期特刊研究内容 ：通过生命之树，将系统进化生物学与生态学结合在一起研究生物多样性格局及其形成机制是当前生命科学的研究热点，而这种结合需要一个地区的区域树不仅具有较高的分辨率，而且需要全的取样。本期特刊利用多基因序列构建的中国维管植物生命之树包括了中国95% 的属且置信度高，由于目前全球结合系统发育树的生物多样性研究，取样只能在科级水平上，因此本期特刊提供的属级生命之树对于未来研究中国植物区系的形成和发展具有重要的科学意义。 Wiley 特意开放了这期特刊中的所有文章，供感兴趣的读者免费阅读！ （ 点击文章标题阅读全文 ） The tree of life: China project 作者： Zhi-Duan Chen 等 Tree of life for the genera of Chinese vascular plants 作者： Zhi-Duan Chen, Tuo Yang, Li Lin 等 Embracing the pteridophyte classification of Ren-Chang Ching using a generic phylogeny of Chinese ferns and lycophytes 作者： Hong-Mei Liu Accelerated evolution of early angiosperms: Evidence from ranunculalean phylogeny by integrating living and fossil data 作者： Wei Wang, David L. Dilcher, Ge Sun, Hong-Shan Wang, Zhi-DuanChen Phylogenetic tree of vascular plants reveals the origins of aquatic angiosperms 作者： Zhi-Yuan Du, Qing-Feng Wang and China PhylogenyConsortium A molecular phylogeny of Chinese orchids 作者： Ming-He Li, Guo-Qiang Zhang, Si-Ren Lan 等 Phylogeny of the Rosidae: A dense taxon sampling analysis 作者： MiaoSun, Rehan Naeem, Jun-Xia Su 等 Global versus Chinese perspectives on the phylogeny of the N-fixing clade 作者： Hong-Lei Li, Wei Wang, Rui-Qi Li 等 A supermatrix approach provides a comprehensive genus-level phylogeny for Gentianales 作者： Lei-Lei Yang, Hong-Lei Li, Lei Wei 等 A comprehensive generic-level phylogeny of the sunflower family: Implications forthe systematics of Chinese Asteraceae 作者： Zhi-Xi Fu, Bo-Han Jiao, Bao Nie 等 Using nuclear genes to reconstruct angiosperm phylogeny at the species level: A case study with Brassicaceae species 作者： Liming Cai, Hong Ma Phylogeny and diversification of Chinese Araliaceae based on nuclear and plastid DNA sequence data 作者： Rong Li, Jun Wen Journal of Systematics and Evolution 由中国植物学会创办 ，目前由Wiley 出版。JSE 是一本植物学国际期刊，致力于对生物多样性进行研究。包括对新的植物种属的描述，对系统发生学、分子进化和基因组进化、进化发育生物学、进化生态学、种群生物学、保护生物学、生物地理学、古生物学、进化论和相关学科的研究。
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 Sciences o 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
标签: 生命之树
