生物演化 from Coursera

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第1讲序言——演化理论的发展史

大自然是美丽的，大自然的每个物种也是美丽的；而各个物种之间都存在某种关系，或近、或远、或互惠互利、或相互利用、或单方获益、或单方受害……而每个物种，以及物种之间的相互关系并不是一天之间就形成的，而是通过长期的演化慢慢地形成的。什么是生物演化？演化是从一个英文单词翻译过来，这个英文名词是：Evolution，动词是： Evolve。达尔文在《物种起源》中用的词是“descent with modification”，即“生物的特征代代相传，略有改变。”也就是说，演化是生物在形态、生理和行为上发生的世代之间十分缓慢的、可遗传的变化。Evolution更确切的翻译应该为“演化”。生物演化理论的发展史基本上是围绕着生物是否有变异、生物的变异是如何产生的、什么因素在推动生物演化及其机制是否什么等问题进行的，本序言将对生物演化理论做出直接或间接贡献的科学家做一系统介绍。最后将介绍生物演化研究的特点。

第2讲拉马克和达尔文的演化思想

拉马克（1744-1829）是一个非常有天赋的博物学家，他参过军、打过仗，退伍后拜著名植物学家Bernard de Jussieu为师学习植物学，并在著名博物学家Buffon（布冯）的资助下，出版了《法国植物志》。法国大革命后，拉马克到法国国家自然博物馆工作，负责昆虫和软体动物标本的整理和研究，在此工作基础上，他发表了“Philosophic Zoologique”（《动物学哲学》），系统地阐述了他的演化理论。拉马克认为所有生物物种都是在不断变化的，不断使用的器官得到加强，而不用的则退回；后天获得的性状能遗传；物种是多起源的。达尔文（1809-1882）是一位兴趣非常广泛、知识面非常广的博物学家，他自幼就对大自然有很强好奇心。随贝格尔号军舰5年的航海经历使得达尔文观察到很多现象，促使他对这些现象背后的规律进行深入的思考。达尔文的演化思想系统地被总结在他于1859年发表的《物种起源》中，其核心内容为：生物物种存在广泛的变异；自然选择，即在生物的变异中有一部分对生物生存和繁殖有益，含有这些有益变异的个体就能够在竞争当中占有优势，并留下后代，最重要的是这样变异能够被传给下一代；生命是单起源的，即所有物种起源于一个共同的祖先（生命之树）。拉马克和达尔文都是伟大的科学家，他们提出的生物演化理论不仅远远超出了他们所处时代的人们对生物普遍规律的理解，更为生命科学，甚至自然科学奠定了科学的基础。

第3讲达尔文演化理论的修订

达尔文发表《物种起源》时，人们对物种性状在世代之间传递规律的认识是错误的，达尔文也不能幸免。因此在达尔文生物演化理论中遗传机制是错误的。随着孟德尔遗传学的再发现和细胞生物学的发展，人们对遗传有了正确的认识，也就有了对达尔文演化理论中错误内容的修订。德国科学家魏兹曼（Weismann，1834－1914）对达尔文演化论进行了第一次修订，他还提出只有germ cells（生殖细胞）负责生殖，它不受环境、学习以及你形态改变的影响的；，而somatic cells（体细胞）执行身体的其他功能，它们有可能在整个生物成长发育的过程当中发生改变，环境会刺激它一些改变，但是这一改变是不可能遗传到下一代的；他甚至用实验来证明后天获得的性状是不可能遗传的。他特别强调自然选择，认为生物的所有性状都能归结于自然选择。随着分子生物学的发展，人们知道了遗传物质及其复制的机制，也就知道了遗传变异的机制。20世纪50年代研究生物演化理论的先驱们，如Sewall G. Wright (1889-1988)、Ronald A. Fisher (1890-1962)、John B.S. Haldane (1892-1964)、Theodosius G. Dobzhansky (1904-2005)、George L. Stebbins (1906-2000) 等将遗传学和统计学等方面紧密结合起来研究演化，开创了群体遗传学，并研发出各种模型来定量地“测量”基因突变、自然选择、个体的迁徙、遗传漂变以及交配系统对生物演化的具体影响。人们将这些科学家对达尔文演化理论的修订成为第二次修订。

第4讲自然选择和人工选择

自然选择是达尔文演化理论的核心内容之一。什么是自然选择？自然选择就是生物在自然界生存竞争当中，适应者能生存、能繁殖，而不适应者被淘汰的现象。自然选择的主要类型有：定向选择——某种性状特征被自然选择保留，传给下一代，使得这个性状特征在种群中不断得到加强。稳定选择——处于中间类型的性状特征得以保留，而处于两个极端的性状特征更易被淘汰。间断选择——与稳定选择相反，处于中间类型的性状特征更易被淘汰，而处于两个极端的性状特征得以保留。平衡选择——主要有两种类型：第一类为频率依赖型选择，即某种性状特征或基因型是否能够被保留下来，决定于它的频率；第二类为杂合子选择优势，及某个基因的杂合基因型比相应的纯合基因型个体的存活率或留下后代的可能性要高。正选择和负选择是在分子演化研究领域用得较多的术语，将在涉及分子演化课中详细解释。人工选择从宏观层面上是指人类根据自身的需求，针对一些生物的特殊表征或生理特征进行定向选择；而从微观的水平上来说，就是“选留”了决定我们人类所需要相关性状特征的等位基因，而其他的等位基因就被淘汰了。人工的选择很大程度上就是为了人类的需要，是为人类服务的，但对被选择对象来说，不一定是有利于生存或繁殖的。本节课将介绍一些具体的实例对上述概念进行解释。

第5讲适应

自然选择导致的结果就是生物对环境的适应。适应的定义就是生物的某种结构、行为或者是有机物质的功能，有利于生物在自然界成功地繁殖。衡量适应的一个定量指标是“适合度”（fitness），即某个基因型产生后代的相对生存力和繁殖能力。适合度的范围是1到0。适合度是一个相对的概念，一般将具有最强生存和繁殖能力基因型的适合度定为1。因为环境是在不断变化的，因此，生物对环境的适应是相对的。亲缘选择（kin selection）是一种特殊的选择形式，一些个体的行为是以降低自己的生存或繁殖能力为代价的，这样的行为的适应性意义是什么？本节课将对一些研究实例进行课堂讨论，启发同学们如何提出科学问题、如何提出假设，以及如何根据提出的假设设计科学实验、如何解释实验结果。这些问题包括“长颈鹿的长脖子是对取食的适应吗？”，“蝴蝶翅膀上的斑纹是用来迷惑其天敌的吗？”，以及“纹翅蝇具有条纹的翅及其震动是其天敌跳蛛的模仿吗？”。

第6讲中性演化理论及该理论提出的背景

随着分子生物学理论是技术的不断发展，人们发现生物种群中存在大量的遗传变异，而用达尔文的演化理论来解释分子水平的现象几乎是不可能的。在这个大背景下，日本科学家木村资生提出了“中性突变、随机固定”的中性演化理论，即生物体中产生的很多突变是“中性”的，它们对生物的生存和繁殖没有影响，因此这些突变被固定的概率是均等的，是随机的，且与种群大小无关。日本的另一位著名科学家太田朋子进一步完善了木村资生的中性演化理论，指出一些具有轻微危害的突变也可以被随机固定下来，而且这个过程与“有效种群”大小有关。分子演化的研究对象就是生物大分子，主要是DNA、RNA和蛋白质。相对于形态演化研究，分子演化研究所得到的数据量是巨大的，每个核苷酸或氨基酸就是一个特征。分子演化也有一些特殊的术语，在本节课的讲授中将给大家仔细讲解。

第7讲蛋白质演化速率和分子钟学说

分子演化研究都是基于一些数学的模型，而这些数学模型和公式的背后是要有一系列的假设的。计算蛋白质水平演化速率的假设就是：不同位点上的氨基酸的替代速率是相同的；即使不同，其平均替代速率也非常小。蛋白质演化速率的计算公式为k aa= K aa / (2T)，K aa 为每个位点的氨基酸平均替代率，K aa = - ln (1 – pd) ，pd ：两个序列中发生改变的氨基酸的比例，T：两个同源序列分歧的时间。以不同物种血红蛋白α链和β链的序列为例，分别得出其演化速率均约等于0.9 x 10E-9。基于这个结果，美国科学家L. Pauling和奥地利裔法国科学家E. Zuckerkandl提出了“分子钟”学说，认为生物大分子是按照一个恒定的速度在演化，就像一个时钟一样。人们用一些群岛上生物大分子演化速率的例子证实了分子钟的存在；但也有很多大分子并不符合分子钟的规律。现在人们知道，“分子钟”的应用有其局限性。

第8讲核酸演化速率和基因组学在演化研究中的应用

核酸演化速率的计算要比蛋白质演化速率计算复杂得多。首先将核酸分为蛋白质编码区和非编码区；还要将碱基的替代分为转换（同类碱基之间的替代）和颠换（不同类碱基之间的替代）；同时，有多种模型来定义单个碱基之间替代的速率。以2参数（K-2）模型为例，非编码区每个核苷酸位点的平均替代数计算公式为：K = (1/2)ln(x) + (1/4) ln(y)；x = 1/(1 – 2P – Q), y = 1/(1-2Q)，P为两序列中发生转换的碱基的比例，Q为两序列中发生颠换的碱基的比例，非编码区核酸的演化速率计算公式为：核酸的演化速率为r = K/2T，编码区的碱基替代又分为同义替代和非同义替代，其演化速率的公式不变，但K = Ks+ Ka；Ks为同义替代位点的平均替代数；Ka为非同义替代位点的平均替代数。Ka和Ks的比值，即Ka /Ks 是等于1、大于1或小于1可以用来判断所研究的基因所受到的选择压力类型。本节课还介绍了基因组学的研究进展，并具体介绍了将基因组研究用于几个物种演化研究的实例。

第9讲物种的形成和形成的速度

物种的定义，以及世界上是否有物种这个实体存在是一个人们长期争议的话题；而物种是如何形成的，则被达尔文称作“迷中之迷”。本节课将通过对一些科学家对采访录像，给大家介绍物种的几种定义，以及他们关于是否有物种这个实体存在的观点。新物种的产生最主要的原因是生殖隔离，生殖隔离分为不同的类型；根据地理分布的类型有异域隔离、邻域隔离和同域隔离；根据生殖生物学特征可分为合子前隔离和合子后隔离。但现实当中的情况会复杂得多，各类生物的特性也不尽相同，在做具体研究时，应针对具体情况进行具体分析。物种的形成是突发式的还是渐进式的，也是人们争论不休的问题。达尔文认为物种形成是十分缓慢的过程；但实际中有不少例外，如前面提到的埃迪卡拉生物群、澄江生物群，其演化速度是很快的；而这些化石是在达尔文提出其生物演化理论以后才发现的。哈佛大学古生物学家S. Gould教授基于这些化石证据提出了“间断平衡”学说，即物种的演化是以短期的快速演化和长期的静止状态交替进行的。尽管该学说还没有成熟的机制来支持，但它从化石的角度解释了一些现象，因此仍受到很多科学家的重视。

第10讲物种的灭绝

一个物种和一个生物个体一样，它有生、有死，它是有寿命的。什么叫灭绝？你怎么样给它来定一个义？有狭义的和广义的两种定义。狭义的物种灭绝的定义是，在过去50年内，野外再也没有发现这个物种的个体；该定义强调野外生存的个体。广义的定义是，一个物种最后一个个体的死亡就标志了该物种的灭绝；这个定义是一种绝对的定义，包括野外和圈养条件下的所有个体。人们从不同的角度将灭绝分为几种类型。如从谱系的角度分为“真灭绝”和“假灭绝”；从物种的角度可分为“全部灭绝”、“野外灭绝”、“局部灭绝”和“亚种灭绝”；从群体遗传学的角度可以分为“生态灭绝”。而物种灭绝的原因有内部和外部两种；内部原因是物种自身的特性决定的，而外部的原因则有大环境的变化，如火山爆发和外星体撞击地球引起的全球环境的改变等，现在最大的外部环境改变则为很多物种的生境受到了人类的活动的破坏和限制。我们应该约束我们的行为，维持大自然原有的平衡。

第11讲系统发生重建

“系统发生”（Phylogeny）就是指一类生物，或是物种，或是类群的演化历史。而系统发生树（phylogenetic tree）是指用图形的方式来描述一个类群的演化历史，以及其中各成员之间的相互关系。根据达尔文“生命之树”的原理，所有生物共享同一祖先，因此生物的系统发生关系是可以通过一些方法重新构建的。系统发生树的重建可以用形态性状、生理性状等，但现在用得最多的是DNA、RNA或蛋白质序列，或全基因组序列。本节课将用具体的实例如何用分子数据构建系统发生树，用这种方法来研究物种的起源和演化、物种之间的相互关系、一些特殊性状的起源、两类物种的协同演化等等；还可以用这种方法追溯病原体的来源、破解各种诉讼案件等。本节课还将给大家介绍一些系统发生重建中的术语和建树方法，以及如何对系统发生树的可靠性进行评估。

第12讲生命的起源和演化

自然选择驱动下的演化是生命最重要的特征之一。地球是一个具有46亿年历史的行星，其上最古老的岩石具有40到39亿年的年龄。现在人们知道最早记录有光合作用的岩石的年龄约为38亿年，而最早记录有原核细胞的化石的年龄则约为35亿年；真核生物的起源约为27亿年到12.5亿年之间。人们可以通过实验和想象力推测在这期间发生的事件，以及这些事件对地球上环境所带来的变化。现在人们还可以提供“合成生物学”的方法来“制造”生命，这些实验给研究生命起源带来的新的思路。化石记录了一些生命演化过程中发生的快速演化的事件，如埃迪卡拉生物群、布尔吉斯生物群、澄江生物群等；这些生物化石及其快速演化现象背后的机制吸引着众多的演化生物学家；而细胞生物学和分子生物学的证据则揭示了细胞中重要的细胞器——线粒体和叶绿体的起源，这两个重要的演化事件为真核细胞和绿色植物的演化提供了一个更高的平台。

第13讲家养动物的起源和现代智人的起源

狗是人类驯化的第一个动物，关于狗的起源和演化研究存在很多争议，其主要的问题集中在狗起源于何种动物，以及起源于何时、何地。科学家用形态数据、分子数据，如DNA片段和全基因组序列，甚至用了化石中的基因序列重建狗的系统发生，得出了不同的结论。而现代智人的演化则是演化生物学中一个热点问题。化石的证据已清晰的表明现代智人的祖先起源于非洲，但人类的祖先是如何迁徙和演化的、现代智人与已灭绝的人属中的其他物种是否存在基因交流则是人们研究的重点，也是争论的焦点。随着越来越多的人属物种化石的发现，特别是对这些化石中基因组进行序列测定的新技术发明后，人们将尼安德特人、丹尼萨瓦人等基因组序列与现代人基因组序列共同进行分析，发现其结果要比仅用现代人基因组分析所得的结果复杂得多。本节课将详细解释上述领域的各种学说和最新研究进展，给大家展示新的研究技术对演化研究领域所产生的巨大的影响。

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Provides an overview of molecular evolution, introducing bioinformatics and phylogenetic analysis techniques

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Learners who complete 生物演化 will develop knowledge and skills that may be useful to these careers:

Wildlife Biologist

Wildlife Biologists study wildlife populations. They may work for government agencies, non-profit organizations, or private companies. A course in Evolutionary Biology would be helpful for Wildlife Biologists because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Wildlife Biologists in their work, as they would be able to better understand the wildlife populations they are studying.

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Biologist

Biologists study living organisms. They may work in a variety of fields, including ecology, genetics, and evolution. A course in Evolutionary Biology would be helpful for Biologists because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Biologists in their work, as they would be able to better understand the living organisms they are studying.

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Policy Analyst

Policy Analysts develop and evaluate public policies. They may work for government agencies, non-profit organizations, or private companies. A course in Evolutionary Biology would be helpful for Policy Analysts because it would provide them with a strong understanding of the scientific method and the principles of evolution. This knowledge would be valuable for Policy Analysts in their work, as they would be able to better understand the impact of public policies on the environment and society.

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Museum curator

Museum Curators are responsible for the care and management of museum collections. They may also develop and lead educational programs. A course in Evolutionary Biology would be helpful for Museum Curators because it would provide them with a deep understanding of the theory of evolution and the history of life on Earth. This knowledge would be valuable for Museum Curators in their work, as they would be able to better interpret and display museum collections.

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Science Writer

Science Writers write about science for a variety of audiences, including the general public, students, and other scientists. A course in Evolutionary Biology would be helpful for Science Writers because it would provide them with a deep understanding of the theory of evolution. This knowledge would be valuable for Science Writers in their work, as they would be able to better communicate the science of evolution to their audiences.

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Forensic Scientist

Forensic Scientists collect and analyze evidence from crime scenes. They may also testify in court. A course in Evolutionary Biology would be helpful for Forensic Scientists because it would provide them with a strong understanding of the principles of evolution and the importance of DNA evidence. This knowledge would be valuable for Forensic Scientists in their work, as they would be able to better understand the evidence they are collecting and analyzing.

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Science Teacher

Science Teachers teach science to students at all levels, from elementary school to college. They develop lesson plans, conduct experiments, and grade assignments. A course in Evolutionary Biology would be helpful for Science Teachers because it would provide them with a deep understanding of the theory of evolution. This knowledge would be valuable for Science Teachers in their work, as they would be able to better teach their students about evolution.

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Science Communicator

Science Communicators communicate science to the public through a variety of media, including writing, speaking, and social media. A course in Evolutionary Biology would be helpful for Science Communicators because it would provide them with a deep understanding of the theory of evolution. This knowledge would be valuable for Science Communicators in their work, as they would be able to better communicate the science of evolution to their audiences.

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Conservationist

Conservationists work to protect the environment and its resources. They may work for government agencies, non-profit organizations, or private companies. A course in Evolutionary Biology would be helpful for Conservationists because it would provide them with a strong understanding of the principles of evolution and the importance of biodiversity. This knowledge would be valuable for Conservationists in their work, as they would be able to better understand the impact of human activities on the environment and develop strategies to protect it.

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Educator

Educators teach students at all levels, from elementary school to college. They develop lesson plans, conduct experiments, and grade assignments. A course in Evolutionary Biology would be helpful for Educators because it would provide them with a deep understanding of the theory of evolution. This knowledge would be valuable for Educators in their work, as they would be able to better teach their students about evolution.

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Consultant

Consultants provide advice and guidance to businesses and organizations. They may work in a variety of fields, including management, marketing, and finance. A course in Evolutionary Biology would be helpful for Consultants because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Consultants in their work, as they would be able to better understand the businesses and organizations they are advising.

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Technical Writer

Technical Writers create instruction manuals, technical reports, and other documents. They may work for a variety of industries, including software, manufacturing, and healthcare. A course in Evolutionary Biology would be helpful for Technical Writers because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Technical Writers in their work, as they would be able to better understand the technical concepts they are writing about.

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Medical Writer

Medical Writers create educational materials for patients and healthcare professionals. They may also write for medical journals and other publications. A course in Evolutionary Biology would be helpful for Medical Writers because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Medical Writers in their work, as they would be able to better understand the medical concepts they are writing about.

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Laboratory Technician

Laboratory Technicians work in a variety of settings, including research labs, hospitals, and clinics. They are responsible for conducting experiments, collecting data, and analyzing results. A course in Evolutionary Biology would be helpful for Laboratory Technicians because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Laboratory Technicians in their work, as they would be able to better understand the experiments they are conducting and the data they are collecting.

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Research Assistant

Research Assistants work with scientists to design and conduct research studies. They may also be responsible for collecting and analyzing data. A course in Evolutionary Biology would be helpful for Research Assistants because it would provide them with a strong foundation in the scientific method and in the principles of evolution. This knowledge would be valuable for Research Assistants in their work, as they would be able to better understand the research studies they are working on and the data they are collecting.

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