# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz King and Wilson (1) inferred from this and other evidence that structural gene evolution and morphological evolution may proceed at independent rates. Some biologists, however, have been reluctant to agree with King and Wilson that there really is a contrast between the morphological and biochemical results of evaluating the difference between chimpanzee and human (3). Although these biologists are aware of the quantitative and objective nature of the biochemical comparisons, they are also aware that the chimpanzee-human, morphological difference has never been compared quantitatively with the morphological differences existing among other species. This lack of confidence in the morphologists' judgment that the chimpanzee-human difference is as big as that among the families of other animals is illustrated by Merrell (3). He stated, in essence, that if a nonmammalian creature were to classify animals on the basis of morphology, the chimpanzee-human difference might seem very small. In particular, he suggested that the chimpanzee-human difference might be no larger than that between two sibling species of frog (4). King 和 Wilson （ 1 ）基于这一点和其它证据推断，结构基因进化和形态进化可能以独立的速率进行。然而，一些生物学家不同意 King 和 Wilson 的观点，即在评估黑猩猩和人类之间差异中，形态学和生物化学结果之间确实存在着一种鲜明对比（ 3 ）。尽管这些生物学家知道生物化学的比较较为量化和相对客观的本质，但两个物种从未在形态进行过量化差异比较，就像其他物种之间存在的形态差异比较。 Merrell （ 3 ）证明，黑猩猩与人类的差异如果参照其它动物类群，已经达到了科级水平，致使把它们作为两个同属物种缺乏信心。他说，从本质上讲，如果一个非哺乳动物的生物要根据形态学对动物进行分类，那么黑猩猩与人类的区别可能看起来很小。特别是，他认为黑猩猩与人类的差异可能不大于两个蛙类姊妹种之间的差异（ 4 ）。 Cherty, L. M., S. M. Case, A. C. Wilson (1978). Frog perspective on the morphological difference between humans and chimpanzees. Science 200(4338): 209-211.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz The body shapes of humans and chimpanzees were compared quantitatively by criteria chosen for their capacity to discriminate well among the body shapes of frogs. By these criteria, the difference in body shape between humans and chimpanzees was found to be greater than that between the most dissimilar pairs of frogs examined —— that is, frogs classified in separate taxonomic suborders. Even though the morphological difference between the two primates is large by frog standards, the biochemical differences between the structural genes of these two species are small. The results of this study give quantitative support to the proposal that morphological evolution and biochemical evolution in structural genes can proceed at independent rates. 使用能够很好地区分不同蛙类物种的形态指标，来比较人类和黑猩猩的外形。根据这些标准，人类和黑猩猩的体形差异大于被检测的最不相似的蛙类（不同亚目）之间的差异。尽管按照蛙类的标准，两种灵长类动物的形态差异很大，但它们的结构基因之间的生化差异却很小。本研究的量化结果支持结构基因进化的形态进化可以不同速率进行的观点。 Cherty, L. M., S. M. Case, A. C. Wilson (1978). Frog perspective on the morphological difference between humans and chimpanzees. Science 200(4338): 209-211.
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）
刚刚收到澳大利亚Kim McKay女士来信，告知悉尼大学的Simon Ho博士荣获了Macquarie University Eureka Prize。2005年，DNA Barcoding第二届国际会议在英国自然历史博物馆召开。我认识了当时还在Oxford大学读博士的Simon。自此我们一直保持学术交流和合作。我很荣幸作为他申报该奖项的署名推荐人之一。祝贺Simon，他的工作被引目前已经超过7000次，果然是这个领域内快速升起的新星！ ASSOC PROF SIMON HO ARC QEII Research Fellow School of Biological Sciences THE UNIVERSITY OF SYDNEY Edgeworth David Building A11 Sydney, NSW 2006, Australia Simon在Sydney大学的网址： http://sydney.edu.au/science/people/simon.ho.php Simon的Google Scholar： http://scholar.google.com.cn/citations?user=Qr-P8DgAAAAJhl=en 发件人: Niall Byrne niall@scienceinpublic.com.au 日期: Wednesday, September 10, 2014 at 8:18 PM 至: Chao-Dong ZHU zhucd@ioz.ac.cn 主题: Tuning the clock of evolution: winner of 2014 Eureka Prize for Early Career Researcher announced Sent on behalf of Ms Kim McKay, Director and CEO, the Australian Museum Dear Chao-Dong, I’m pleased to announce that Simon Ho from the University of Sydney is the winner of the Macquarie University Eureka Prize for Outstanding Early Career Researcher . The other finalists were: · the Extremes Team, Drs Lisa Alexander, Sarah Perkins and Markus Donat of the University of New South Wales, who quantified what temperature extremes Australia can expect if we do not reduce carbon dioxide emissions · University of Sydney’s Associate Professor Richard Payne, who has developed synthetic vaccines to turn our own immune systems into cancer-destroying machines. If you’re on Twitter please share the news with the hashtag #eureka14 . Kind regards, Niall Byrne, Science in Public Tuning the clock of evolution Macquarie University Eureka Prize for Outstanding Early Career Researcher For those who work with ‘molecular clocks’, evolutionary biologist Simon Ho is the ultimate clockmaster. By using fossils to calibrate the molecular clock, comparing evolutionary rates in different species, and crunching huge genome data sets, Simon Ho from the University of Sydney has shown that modern humans separated from Neanderthals about 200,000 years later than we once thought. He’s also shown that the Irish Potato Famine fungus is still alive in the Americas, and has become potentially even more dangerous. For these and other contributions to evolutionary science, Simon has been awarded the Macquarie University Eureka Prize for Outstanding Early Career Researcher . Molecular clocks are how biologists explain how quickly different organisms evolve. By knowing the rate at which DNA mutates we can understand the ancient evolution of humans, predict how fast species will adapt to changing environments, and estimate the speed at which viruses and other pathogens could change and become dangerous. “Simon’s work has had a colossal impact on researchers’ understanding of the variation in evolutionary rates at the genetic level” Australian Museum Director and CEO Kim McKay said. Simon has had an extremely productive scientific career for such a young researcher, receiving two research fellowships from the Australian Research Council (2008-10 and 2011-15), as well as receiving Australian Research Council Discovery Project funding (2013-15). His scientific rigour and excellence was recognised with the Alan Wilton Award from the Genetics Society of Australasia (2011), rewarding outstanding contributions to the field of genetics research by early career scientists. Over the past five years, Simon’s work has produced 73 peer-reviewed journal articles and five encyclopaedia articles. His research also informs and enables many others in the field, reflected by the number of times that his work has been cited—over 7000 citations. The Australian Museum Eureka Prizes are the country’s most comprehensive national science awards. The Eureka Prizes have been rewarding science since 1990—celebrating 25 years in 2014. Further information: · Associate Professor Simon Ho, simon.ho@sydney.edu.au For media enquiries please contact the Australian Museum Eureka Prizes media team: · Niall Byrne, niall@scienceinpublic.com.au , 0417 131 977 · Errol Hunt, errol@scienceinpublic.com.au , 0423 139 210 Watch the winner’s video . For more information about all the winners visit australianmuseum.net.au/eureka . And you can watch all the finalist videos here .
http://bbs.sciencenet.cn/thread-1117412-1-3.html 中文版：《分子进化与系统发育》高等教育出版社 Molecular EvolutionEvolutionary Biology 【 http://bbs.sciencenet.cn/thread-1117412-1-3.html 】 英文版：《Molecular evoltion》 by LI WH, 《Molecular evolution and phylogenetics》by Nei and Kumar
论文题目： Transmission dynamics of rabies in China over the last 40 years: 1969–2009 发表刊物： Journal of Clinical Virology ， (2010) 49 ： 47–52 作者： Shengli Meng a , Gelin Xu a , ∗ , , ∗ , Xianfu Wu b , Yongliang Lei c , Jiaxin Yan a , Susan A. Nadin-Davis d , Hong Liu e , JieWu a , Dingming Wang f , Guanmu Dong g , Xiaoming Yang a , Charles E. Rupprecht b a Wuhan Institute of Biological Products, 9# Linjiang Ave., Wuhan, Hubei 430060, China b Centers for Disease Control and Prevention, Atlanta, GA, USA c Lishui Center for Disease Control and Prevention, Lishui, China d Rabies Center of Expertise, Ottawa Laboratory-Fallow Field, Canadian Food Inspection Agency, Ottawa, Ontario, Canada e Anhui Center for Disease Control and Prevention, Hefei, China f Guizhou Center for Disease Control and Prevention, Guiyang, China g National Institute for the Control of Pharmaceutical and Biological Products, Beijing, China 摘要 背景 ：狂犬病在中国是一种严重的重新出现的人畜共患病。依据历史数据推演狂犬病毒的分子进化和传播模式，可以为未来的疾病控制和预防提供更好的指导方针。 目的： 研究中国狂犬病毒的流行病学和进化动力学。 研究设计： 分析 1969 年至 2009 年间在 17 个省和 3 个区 ( 市 ) 收集到的 132 株狂犬病毒的糖蛋白基因序列的演变。 结果： 系统进化分析表明，中国狂犬病毒都属于基因 1 型，可细分为 A ～ F 共 6 个谱系。谱系 A 代表广泛分布的到处存在的谱系，而谱系 B 非常类似于北极狂犬病毒。剩余的谱系 C-F 主要在东南亚非常流行。中国狂犬病毒的进化速率是每年每位点 1.532×10 -4 个替代，相应的共同祖先大约存在于 1115 年。 结论： 该系统进化结构表明，中国狂犬病毒既在省内、也向省外传播，与人类的活动密切相关 。 Abstract Background: Rabies is a serious reemerging zoonosis in China. The molecular evolution and transmission patterns of rabies virus inferred from historical data can provide guidelines for better disease control and prevention in the future. Objectives: To investigate the epidemiology and evolutionary dynamics of the rabies virus in China. Study design: The molecular evolution of 132 viral glycoprotein gene sequences of Chinese rabies viruses collected in 17 provinces and 3 municipalities between 1969 and 2009 was analyzed. Results: Phylogenetic analysis revealed that Chinese rabies viruses are subdivided into 6 lineages (A–F) within Lyssavirus genotype 1. Lineage A represents the widely dispersed cosmopolitan lineage while lineage B is closely related to Arctic-like rabies viruses. The remaining lineages (C–F) are typical of those circulating across much of Southeast Asia. The evolutionary rate for Chinese rabies viruswas 1.532×10−4 substitutions per site per year, and the corresponding common ancestor was in about 1115. Conclusions: The phylogeographic structure demonstrated Chinese rabies viruses have been transmitted intra-provincially and extra-provincially due to human-related activities. 全文下载： Transmission dynamics of rabies in China over the last 40 years.pdf
科学网上头条“ 中国近十年论文总引用次数超过四百万 ”，其中报道了十几个国家近十年引用次数最多的文章，竟然发现有两篇文章是生物信息文章，啥是惊讶，如下。 5. 法国（近十年论文总引用次数6,660,630） 论文： A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood 被 引次数：2,995 领域：环境/生态学 发表期刊：《系统生物学》（ Systematic Biology 11. 西班牙（近十年论文总引用数3,256,075） 论文： DnaSP, DNA polymorphism analyses by the coalescent and other methods 被引次数：2,391 领域：计算机科学 发表期刊：《生物信息学》（ BIOINFORMATICS ） 两个都是生物信息学工具文章，还有一个生物信息学工具（MEGA）可能引用次数更多，就是因为这个工具使 Molecular Biology and Evolution 的09年的影响因子激增，当然Blast除外，这个是上世纪开发出来的。 这几个工具是做序列分析，分子进化等方面常用的工具。近几年随着测序的猛烈发展，也强烈推动这些工具的发展，估计在未来几年这些工具引用次数也会激增。 这几个工具我都用过，PHYML与MEGA很早就使用过，DnaSP还是最近接触。PHYML PhyML_3.0_win32.exe 主要是计算极大似然进化树，MEGA也是的,他还能计算NJ，MP等方法进化树，比PHYML强大很多。还有MEGA的最新版本MEGA5.03 MEGA5.03_Setup.exe 集中很多其他功能，能序列比对，集合了clustalw与MUSCLE，还有一些其他一些序列分析功能，比如计算祖先，序列之间的距离等等。DnaSP dnasp51001.msi 主要是序列分析，比如计算多态，序列间或各个位点的进化速度等等。 如果想学点生物信息与分子进化，或者想进这个领域，从学习MEGA和DnsSP是个不错的选择。 或者做分子方面的一些东西会使用这两个工具将会对工作有极大的帮助。这两个工具都有图形化界面，蛮傻瓜，比较好学。
标签: 分子进化
