题目： Genomic and evolutionary insights from molecular clocks 报告人： Simon Ho 教授 School of Life and Environmental Sciences, University of Sydney 时间： 2016年10月26日15:30 地 点： 中国科学院动物研究所 会议室： C101 联系人： 罗阿蓉（luoar@ioz.ac.cn）、朱朝东（zhucd@ioz.ac.cn） Molecular clocks are models that describe variation in rates of genetic change among organisms, allowing us to infer evolutionary timescales using phylogenetic analyses of DNAsequence data. A wide variety of clock models are now available, including those that allow rates to vary across branches in the tree. Over the past five decades, molecular clocks have been pivotal in resolving the timescale of the Tree of Life. Genome-scale data are now being produced at an astonishing rate, opening up exciting prospects for gaining detailed insights into the molecular evolutionary process. They also present anopportunity for refining our estimates of evolutionary timescales. I provide an overview of some of the approaches that have been used to estimate evolutionarytimescales from genome-scale data, drawing on several recent examples from mywork. I also describe how a phylogenetic approach can be used to provide insight into molecular evolutionary dynamics, with particular reference to the “pacemaker” models of genome evolution. About the speaker Simon is a Professor of Molecular Evolution at the University of Sydney. He received his PhD in 2006 (University of Oxford), then did postdoctoral work at Oxford and the Australian National University. Simon joined the University of Sydney in 2010, where he now leads the Molecular Ecology, Evolution, and Phylogenetics Lab. His research interests include phylogenetic methods, evolutionary models, and molecular clocks. The focus of Simon’s recent work has been on describing patterns of evolutionary rate variation across genomes and on phylogenomic estimation of evolutionary timescales. http://sydney.edu.au/science/people/simon.ho.php 看看Simon教授是哪位帅哥？ （图片来自：http://www.shsobu.org.au）
保护濒临灭绝的生物分类学家【原题】 近日英国伦敦自然历史博物馆启动了一个名为“Identification Trainers for the Future”的项目，旨在为英国培训一批年轻的物种鉴定专家，并希望将传统的物种鉴定方法得以传承。项目指出了目前能够掌握传统分类鉴定方法的专家正在急剧减少，许多生物类群的鉴定已无专家研究，这一趋势严重阻碍了生物多样性、保护生物学等方面的研究。 中国是生物多样性大国，与发达国家相比，很多类群的相关研究近乎空白。分类学家作为揭示生物多样性的主力军，在当前国内学术生态大环境下，正在以难以置信的速度濒临绝境。在昆虫分类圈子里，一些有很好研究基础的团队逐渐放弃传统分类而投入到了轰轰烈烈的所谓的生物系统学领域中，大批研究生不采标本，不懂分类，学了几年只学会了PCR、测序、建树，在缺乏对一个类群深入理解的基础上根据自己结果提出结论，以致高阶关系五花八门，分子种形态种分分合合。虽然论文点数越发越高，但最后的结果真的是我们需要的吗？前两年我在日本做博后的实验室教授退休，空出的位置全国招聘，大批做昆虫分子系统学的学者前来应聘，最后的位置却提供给了一个虽然年轻但形态分类做得很好的蚁类专家。在感叹其运气的同时，其背后的现象值得深思。 昨日惊悉中科院动物所著名鞘翅目分类学家虞佩玉先生辞世，哀叹又一位老先生离去的同时，却不免羡慕他们这一代人至少可以全身心的投入到自己挚爱的事业中去。而在80、90后这一代人中又能诞生多少这样的昆虫分类专家？还有多少年轻人愿意从事传统分类并能够坚持奋斗？昆虫分类学家就和他们热爱的昆虫一样，生境的破坏直接导致昆虫灭绝，而科研环境的巨变必然导致传统分类的衰亡。中国生物分类学科的发展何去何从？ 附“Identification Trainers for the Future”项目简介链接： http://www.nhm.ac.uk/our-science/our-work/science-society-and-skills/saving-species-experts-from-extinction.html 该网站可能打不开，具体内容如下： Saving species experts from extinction Max Barclay, Museum Coleoptera collection manager and species identification specialist, at work Species identification experts are a rare breed, but the Museum has a plan to train new specialists for the future. The UK’s plants and animals have never been under greater threat from environmental change and habitat loss. At the same time, critical skills for identifying organisms have been waning, hampering much-needed monitoring and conservation efforts. Fortunately scientists in the Museum’s Angela Marmont Centre for UK Biodiversity have designed a new work-based traineeship called Identification Trainers for the Future , which aims to pass on the complex skill of species identification to the next generation. The project is funded by a grant from the Heritage Lottery Fund ’s Skills for the Future programme and is being delivered in partnership with the Field Studies Council and the National Biodiversity Network Trust . The Museum is the ideal venue for the course because it has world-leading experts in species identification, along with fantastic specimen collections and training facilities. Project manager Stephanie West explains: 'The decline in identification skills is particularly true for some of the harder-to-reach groups, some of the more complex taxa. Groups like true flies and earthworms are often overlooked but vitally important to ecosystems.' A dying breed The species identification specialist is an endangered expert and increasingly this is being recognised across the ecological sector and beyond. In 2010, the Museum led a NERC -funded review of the current status of taxonomy and systematics within the UK. The review highlighted serious concerns over the training and recruitment of the next generation of taxonomists. More recently, The Chartered Institute for Ecology and Environmental Management (CIEEM) stressed the effects that declining skills in species identification are having on the professional ecology sector within its 2011 publication Ecological Skills: Shaping the profession for the 21st Century . West agrees with the institute’s bleak findings: ‘Our most highly skilled species identifiers and taxonomists are often amateurs and many of them are at, or beyond, retirement age. Younger ecologists are leaving universities with great qualifications but without the detailed knowledge of a true specialist. Expertise of course can only come with time and perseverance, but often graduates leave university with very little idea of how to start developing their skills in this area and very little exposure to field recording. We want to help turn this situation around via our traineeship scheme.’ Saving precious habitats The species identification skills gap is having a big impact on valuable habitats, ecosystems and biodiversity in the UK. For example, identification experts often act as ecological consultants - assessing the biodiversity value of land earmarked for development. The results of these consultations can often save a precious habitat, but West thinks the current skills gap and lack of experience in species identification can result in the loss of valuable sites. ‘The land can have value to biodiversity that is easy to miss if you do not know what you are looking for. There was one site I worked on where a high value acidic grassland was completely missed because the previous ecological consultancy did not recognise the particular species indicating the quality of the habitat. By identifying the grassland we were able to ensure the habitat was retained and enhanced through the development plans’. Species-rich lowland acidic grasslands are declining throughout the UK due both to increasing urbanisation and agricultural activity. Their classification relies on the identification of certain indicator species within the sward (an expanse of short grass) and they are also important ecosystems supporting a diverse range of specialist wildlife. Museum scientist inspecting botanical specimens on the Isles of Scilly A special passion As part of the project, the Museum will be offering 15 work-based traineeships over three years, training five students each year. West explains what is expected of each candidate: ‘We are looking for very motivated individuals, passionate about UK wildlife with the drive to become genuine experts.’ The traineeships are designed to do more than train a select group of individuals though. The project also aims to turn its trainees into trainers themselves, ready to pass on their skills through public outreach and the development of identification guides and toolkits. Training materials produced throughout the project will be made freely available to all and will be targeted at a range of interest groups, from beginners to experienced experts who are looking to further develop their skills. Plenty of amateur experience including involvement with national recording schemes and the ability to articulate concepts to others will help any applicant towards a place on the course. West is keen to point out that if a candidate has the passion and a flair for the subject it doesn’t matter if they have a degree or not. ‘We are looking for people with an underlying passion for species identification and who want to make it their career,’ she says. The Museum is investigating options to develop professional accreditation for identification skills. If successful, this will help to demonstrate and quantify identification expertise across the professional UK biodiversity sector. Future direction Once trainees have been accepted they will be taken through a series of workshops which will give them basic skills and knowledge that they will use throughout their work, including handling and using Museum collections, planning and undertaking field work, and an introduction to taxonomy. Throughout their time at the Museum, trainees will receive specialist training from Museum experts, concentrating on the identification of flowering plants, bryophytes, lichens and entomology groups such as true flies, earthworms, moths, bees, ants and wasps. Trainees will also get hands-on experience in the Museum’s Angela Marmont Centre for UK Biodiversity . Here, they will divide their time between working within the Identification and Advisory Service, taking calls from the public and the commercial sector, and working on the citizen science projects and events that are run by the centre. A student identifying species in the Museum's Angela Marmont Centre for UK Biodiversity The trainees will also spend time working with the Museum’s incredible collections in their chosen specialist area. They will handle specimens, collect material from the field and practice species identification with the curation team. This will give the trainees an unrivaled opportunity to develop their own specialism with their chosen group of species. Before the course is over the students will learn how to pass on their new skills to others, with help from our education and learning teams. The idea is that students will be able to communicate their scientific knowledge to audiences ranging from young children to adults, other scientists, and amateur and professional groups. The final challenge of the course is for the trainees to design and produce an identification training course (either to be delivered face to face or online), based on their species specialism. These resources would then be made freely available to anyone who wants to learn more about that specialist area of species identification. The goal of the course is ultimately to nurture and grow a new generation of species identification experts in the UK, passing on skills, knowledge and expertise for years to come. Apply here Museum team Primary investigator John Tweddle Co-investigator Lucy Robinson Project manager Stephanie West Publications The Management Standards Consultancy Ltd. (2011) Ecological Skills: Shaping the profession for the 21st Century . Institute of Ecology and Environmental Management: Hampshire 1- 9. Related information ID Trainers for the Future Angela Marmont Centre for UK Biodiversity Chartered Institute for Ecology and Environmental Management (CIEEM) National Biodiversity Network Trust Field Studies Council Funded by Related projects - See more at: http://www.nhm.ac.uk/our-science/our-work/science-society-and-skills/saving-species-experts-from-extinction.html#sthash.tknAeTmE.dpuf
张峰博士，是和我合作的第一个博士后。他主要研究弹尾虫的形态分类学。我2007年在昆仑山考察，发现了弹尾虫在特殊生境中驻花、访花的问题，需要有专人研究，但一直苦于找不到合适的合作者。 张峰研究生师从陈建秀教授攻读并获得博士学位，一直从事弹尾虫分类与生物学研究，对分子系统学也有浓厚兴趣。合作至今，虽然由于多种原因，我们没有能够做出来驻花、访花的工作，但是在分子系统学方面有了一些发现。张峰博士就形态性状（如： 鳞片 ） 发生和演化，结合形态学数据和分子数据，和国内外同行合作，整理了一篇论文，投稿到分子系统学经典杂志Molecular Phylogenetics and Evolution（MPE）。 该工作于今年1月投稿，审稿时间相对较长，且在我们给编辑部去信咨询进展后，又重新推荐了多位候选审稿人。 8月16日晚上收到编辑来信，告知该论文已经被接收（ acceptable for publication provided minor revisions are made ）。同时，编辑和审稿人也就该工作中存在的问题，点出了可以改进之处，为后续的相关研究提供了新的突破点。我们将尽快完成修改，争取早日在线，和同行分享。 感谢张峰博士和合作者的努力，并祝贺大家的辛勤劳动得到了回报！相信他能在形态分类学和分子系统学的基础上，不断拓展新的思路，获得新的成果。 题目： Molecular phylogeny shows independent origin of body scales in Entomobryidae (Hexapoda: Collembola) 摘要： Entomobryidae is the largest family in Collembola but relationships within the family have never been subjected to rigorous phylogenetic analyses. Within the family, body scales are present in many species, and are fundamental in the classification at the subfamilial and tribal levels. A molecular phylogeny was reconstructed using the nuclear 18SrRNA and partial 28SrRNA and the mitochondrial 16SrRNA to examine the evolution of scales across Entomobryidae subfamilies. These datasets were analyzed separately and combined, with parsimony, likelihood and Bayesian algorithms. Monophyly of Orchesellinae was not recovered, and it was split into a scaled clade and an unscaled clade, contradictiing to all recent taxonomic conceptions. The monophyly of Entomobryinae, Seirinae and Lepidocyrtinae is well supported, however within Entomobryinae, the polyphyly of Entomobryini and Willowsiini implies that classificationusing the presence/absence of scales is not valid. Analyses of ancestral character state reconstruction in Entomobryidae indicate that the presence of body scales have evolved independently at least five times, with a loss of scales occurring independently at least twice. A revision of the family Entomobryidae on molecular and morphological basis is clearly needed. 进度： 已正式接收并在线发表 - http://www.sciencedirect.com/science/article/pii/S1055790313003825。 2014-Feng ZHANG-Molecular phylogeny reveals independent origins of body scales .PDF 自2014年3月31日以来，该论文被下载或浏览了492次。
标签: 分子系统学
