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昆虫纲物种水平生命之树重构
热度 2 zhuchaodong 2017-1-22 16:24
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
6095 次阅读|2 个评论
在中山大学生态与进化2016年暑期学校的授课幻灯片
热度 1 hypermarket 2016-7-8 21:47
1. Theoretical and technical thinking on phylogenomics 1Theoretical and technical thinking on phylogenomics-QX.pdf 2. Molecular Apomorphy: The lost part in molecular phylogenetics 2Molecular Apomorphy-QX.pdf
5488 次阅读|1 个评论
[转载]保护生物物种,更需要培育新一代分类学者(作者:刘星月)
zhuchaodong 2015-5-6 08:21
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
2140 次阅读|0 个评论
多基因DNA条形码系统MEE在线发表(Early View全文分享)
热度 1 zhuchaodong 2015-3-2 21:18
Early View全文分享: 2015-Douglas et al.-A DNA Barcoding system integrating multigene sequence data.pdf 自2003年在加拿大多伦多大学,了解了DNA条形码的理念后,我个人持续关注。2005年在伦敦自然历史博物馆参加第 二届世界DNA条形码大会后,自己更加希望做些工作,推动昆虫系统学工作。 基于 DNA 序列,学界已经开发了很多用于分类鉴定的方法和系统。但是,在真核生物中,大多数系统使用单个预设的基因片段,如 COI 、 16S 等。有限数据信息可能导致鉴定结果出现一定的偏差。这些系统也很难识别并分析基因组来源的大量基因数据。 今天收到 Methods in Ecology and Evolution 编辑部来信, Douglas Chesters 博士等整合多基因数据的 DNA 条形码系统的研究论文已经被正式接受,并将于近日在线发表。 在这篇论文中,我们实现了多个基因的 DNA 条形码功能: 1 )基于经常测定的基因位点数据,建立一个参考框架性数据集; 2 )其它基因数据和参考序列进行同源比对、剪切,同时在种内变异范围内对查询基因片段赋予物种分类阶元信息。我们把该方法和现有一些方法进行了比较,如“ bagpipe_phylo” 。后者在系统发育树上给序列重新赋予分类阶元信息。 上述建议的多基因系统正确推断了 GenBank 中节肢动物 78% 的物种和 94% 的属级阶元。尤为关键的是,物种鉴别的比例高于仅仅用 COI 的方法。测试数据中, 24% 的物种仅仅见于非 COI 基因,而且这些 COI 之外的基因的物种阶元信息赋予正确率并没有明显的降低。同法,我们应用非 COI 的数据栏对建立的宏基因组数据进行了额外的物种阶元信息赋予。通过测试 1 个 273 条蜜蜂基因序列的数据,我们通过改变遗传距离的计算方法,物种赋予正确率和基于系统发育的分类鉴定结果差异不明显。 标准的单基因片段 DNA 条形码仍然是基于 PCR 产生数据的物种鉴定的重要鉴定工具。对于已经建立的大量物种 DNA 条形码“骨干数据”而言,本文方法可以补充下列几点: 1 )基因组数据; 2 )通过整合其它独立的基因位点降低错误; 3 )对非条形码片段进行额外的物种鉴定。通过新一代测序平台,后面两点和群落基因组监测工作尤其相关。 学海无涯勤作舟。 Douglas 博士来组里以后,努力工作,取得了一系列的研究进展。 在基于基因序列的物种界别的方向上, Douglas 博士已经连续在 Systematic Biology ( 2 篇)和 Methods in Ecology and Evolution ( 2 篇)上发表论文,把单个基因的思路推广到多个基因,并实现了大数据库中基因物种信息的自动矫正和赋予。 功夫不负有心人:2014年, 他获得中国科学院院长国际学者1年期项目(PIFI),获得一项国家自然科学基金项目,并于年底成功竞聘为动物研究所副研究员。 后续我们计划在下面几个方面继续努力: 1 ) 把该方法推广到基因组。这个功能已经部分实现,但是还需要较多组学数据的实际测试。 2)把该方法推广到系统树上的一些关键节点。这是我个人最感兴趣的点。 3 )把该方法和其它学科,特别是昆虫多样性和物种互作研究结合起来。 4 )把该方法更系统地应用到蜜蜂物种较为丰富的几个属中,加快蜜蜂总科系统学研究工作。 原文摘要和全文将于在线后和大家分享: A DNA Barcoding system integrating multi-gene sequence data Douglas Chesters, Wei-Min Zheng and Chao-Dong Zhu Accepted manuscript online: 4 MAR 2015 04:41AM EST | DOI: 10.1111/2041-210X.12366 Abstract PDF(223K) Supporting Information Request Permissions
4991 次阅读|2 个评论
我研究组Systematic Biology在线发表面向DNA数据库物种界定规程
热度 1 zhuchaodong 2014-2-3 22:46
论文在线发表,引用信息如下: A Protocol for Species Delineation of Public DNA Databases, Applied to the Insecta. Douglas Chesters; Chao-Dong Zhu Systematic Biology 2014; doi: 10.1093/sysbio/syu038 论文全文下载: 相关数据: http://datadryad.org/resource/doi:10.5061/dryad.k7t50 论文在线发表: Abstract: http://sysbio.oxfordjournals.org/cgi/content/abstract/syu038?ijkey=tS8O8zuszBKwUulkeytype=ref PDF: http://sysbio.oxfordjournals.org/cgi/reprint/syu038?ijkey=tS8O8zuszBKwUulkeytype=ref 网站: phylolab.ioz.ac.cn 软件链接: 1、 Automated taxonomic identification of Apoidea (bee) DNA sequences 2、 Multi-Gene DNA Barcoding for Arthropods (beta) 介绍 大量 DNA 条形码数据为实现快速物种界定提供了可能性,也带来了两个问题:1)基于单个位点信息的物种界定是否可靠?2)依据公共数据库信息,实现物种界定的可靠性有多高? MEE 论文 (http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12104/abstract) 解决了多基因物种界定的全局参数优化 问题。我们 在提交MEE论文的前一天,也向另外一个专业杂志, Systematic Biology 提交了另外一篇论文。该论文最早的想法:飞速发展的测序技术至今测定了多少物种?公共数据库中有多少具有物种水平分类学信息的序列?这些分类学信息是否真实反映了物种界限?在无法完成形态分类学验证的情况下,如何基于多基因片段的信息,为无标记序列提供并验证物种分类信息? 为了实现上述想法, Douglas Chesters 博士开发并测试了一套流程,把 MEE 论文的方法从蜜蜂总科进一步推广到昆虫纲,从少数几个基因片段推广到n个,以期获得更加普遍而可靠的结论。经过审稿人、编辑、副主编和主编的3轮密集审阅,我们收获了很多建设性的建议和想法,并规划了下一步工作。 公共 DNA 数据库中昆虫物种界定规程 公共 DNA 数据库中包含很多生物类群,为系统学研究提供了大量数据来源。目前,基于分子数据的物种鉴别和界定工作已经逐步开展。现代测序技术的飞速发展,带来了海量分子数据的同时,也导致很多研究人员无法为相关数据提供准确的分类学信息。这些分类信息不够完整的分子数据,阻碍了在物种一级水平上开展精细的数据挖掘。同时,基于较大数据库进行物种聚类研究,也需要整合多个基因片段,从而在数据结构和计算过程中产生了很多问题。 作者研发了一种在分子序列数据库中界定物种的方法: 1) 首先获取所有昆虫的 DNA 序列,并对它们进行文本加工; 2) 根据一定的规则过滤掉重复数据; 3) 划分遗传位点 L ; 4) 根据每个位点信息,界定物种 S ; 5) 物种单元与位点相匹配,形成一组多位点物种界定的数据矩阵 L × S 。 作者应用马尔科夫聚类的方法将数据库划分为同源基因片段数据集。基于包含大部分物种多样性的基因,完成物种鉴定,并同时对物种单元名字赋予物种名。在物种聚类过程中,两两相似之处计算的复杂性的主要来源于线粒体基因组中的 COI 位点。自主研发的软件解决了这个复杂的过程:在分类的体系内执行序列两两比对,且为不同阶元的序列标注分类信息。 该工作研究了 GenBank 中超过 24 个不同同源基因, 194000 个未带分类标签的序列,包含 41 525 个带分类标签的物种( 98.7% 从昆虫数据库中获得)。通过对每个位点的分层聚类,利用独立的最优参数,这些序列被分组到 59173 个基于单个位点的分子分类单元( MOTU )中。来自不同位点的 MOTU ,由多部匹配算法进行匹配。这样,位点之间形成不一致性最低的多位点单元。匹配后,我们 发现了在目前的昆虫数据库中,存在 78091 个基于多位点信息的 MOTU 。其中, 38 574 个单元包含物种分类学信息,而 34 891 个则没有包含物种分类标签 。 除了可以估算物种多样性,我们开发的规程还将促进现代序列数据集的物种界定。特别是 L × S 矩阵代表了后分类学思路,将可以解构种级元基因组数据。这些方法将可以在多个基因位点,甚至基因组水平提取大量数据,产生更多研究物种多样性的 L × S 矩阵,从而整合到后续的系统发育的流程。 上述研究成果,已经被Systematic Biology接收: 17-Jan-2013 Submitted 18-Apr-2013 Reject; resubmission encouraged 08-Aug-2013 Resubmission 21-Nov-2013 Accept with major revisions 06-Jan-2014 Resubmission of R1 14-Apr-2014 Accept with minor revision 19-Apr-2014 Resubmission of R2 28-Apr-2014 Accept pending receipt of final changes 29-Apr-2014 Resubmission of R3 10-May-2014 Accept, Production Checklist 11-June-2014 Awaiting Assignment to Batch 15-June-2014 Published on-line
个人分类: 论文简介|7115 次阅读|4 个评论
2013年Douglas Chesters博士新发表论文
zhuchaodong 2013-2-17 11:12
今天早晨收到 Douglas 邮件,他的论文在线发表在 Systematic Biology 上。该论文 2011 年投稿,历经 3 次修稿。其中第三轮修改工作在我组做博士后期间完成。祝贺他和 Alfried 教授! Title: Resolving Ambiguity of Species Limits and Concatenation in Multi-locus Sequence Data for the Construction of Phylogenetic Supermatrices Authors: Douglas Chesters 1 , 2 , 3 and Alfried P. Vogler 1 , 2 Author Affiliations 1 Department of Entomology, Natural History Museum, London SW7 5BD, UK, 2 Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK, Email: apv@nhm.ac.uk 3 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China, Email: dc.1984@yahoo.co.uk Author for correspondence: Dr Alfried P. Vogler 论文链接如下: http://sysbio.oxfordjournals.org/content/early/2013/02/15/sysbio.syt011.abstract Douglas 在博士期间运用生物信息学手段研究了大规模系统发育分析过程中出现的系列问题。在 2009 年 7 月获得博士学位后,他分别在捷克和英国两所大学短暂工作,参与国际鞘翅目“生命之树”研究。 他于 2011 年 7 月 5 日受我邀请加入研究组,成为研究组信息分析员。 Douglas Chesters 博士在研究组中,在以前采用分子数据对动物物种实现分子分类的研究基础上,结合组内现有研究基础与在研项目,以膜翅目蜜蜂总科作为主要研究对象,建立生物信息平台,以期构建在物种水平上含最大信息量的分子序列数据集,开展分子分类与分子系统学研究,实现蜜蜂总科昆虫的物种智能鉴定,并探讨物种之间的系谱关系。 关键问题: 1 、 基于分子信息,建立传粉蜜蜂物种界定标准、方法、流程。目前中国已经定名约 1000 种蜜蜂,但是据吴燕如研究员和国外相关蜜蜂专家预估,中国可能存在约 3000 种蜜蜂留待进一步发现。另外一方面,蜜蜂总科普遍存在隐存种现象,而传统分类或者生物学观察尽管可能通过细致的研究能够解决这一问题,但是可能会非常缓慢。分子分类和传统分类相结合,可能加快物种发现的进程。 2 、 针对分子分类或系统发育分析中的重要环节,构建蜜蜂总科含最大信息量的性状矩阵。分子分类或者重构系统发育的必要前提是性状矩阵。在这个矩阵中,行,比较典型的可以代表物种;列,则代表不同分子序列中的同源位点。通常对于大规模系统发育分析,不论是对行还是列的构建都尤为关键:首先,由于大量物种的测序很难针对相同的基因片断或采用标准化的引物,选用合适的基因片断对构建性状矩阵即变的很重要。其次,虽然增加物种取样密度是可取的,但增加密度的同时则容易带来缺失的分子序列信息位点从而影响最终构建得到的系统发育树与真实进化树的相似度。 相关技能和研究经历: 1 、 Douglas 博士建立了一套流程,可以将单个或者多个基因整合到大数据集中的可行性。 2 、 他处理了一些系统发育信息学分析过程中利用分子数据进行物种分类的新问题。目前已经出现仅用分子数据设定物种界限的工作,但是在用多位点信息时不一致的结果带来了很多方法学上的问题。这些问题的解决方法已经投稿到系统学著名杂志 Systematic Biology ,并被接收。 3 、 他确定了大规模 COI 数据中不同变换速率的影响。目前,他和合作者已经发现在鞘翅目中, COI 的不同变换速率大量存在,但由于去掉它们不利于产生合理的比对结果,因此这些不同变换速率是有利的。 COI 的趋同性与异质性特点并没有影响它们的应用,因此存在一定的可能性将它们整合到分子分类与分子系统学工作中。 相关方法与流程, Douglas 博士通过和不同类群专家合作,逐步推广到膜翅目中几个大的总科中。下阶段,他将以蜜蜂总科为主要研究对象,更深入研究大数据集在分子分类与分子系统学中我们将面临的问题,并探讨解决方案。就这部分问题, Douglas 博士已经完成 2 篇论文,并于 2013 年春节前投稿到进化生物学领域杂志。
个人分类: 博士后合作|6800 次阅读|0 个评论

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