Name: blast practice for fossil dna clues
Uploaded: 2019-01-31T09:26:12.000Z
Duration: 1 min 2 s
Channel: JoVE

K12 Standards

Virginia  Standards of Learning

HIgh School

Biology

BIO.7

BIO.7.d

Evolutionary Relationships

<ul><li><a href="#" data-time="0.0">利用BLAST检验进化假说
</a></li></ul>

<ul class="lab-items"><li data-lab-item="1">
								<div class="ingredient" data-value="空白分支图图像"><a target="_blank" href="/files/ftp_upload/10562/Blank_Cladogram.png">空白分支图图像</a></div>
								<div class="成分量">
									<span class="amount" data-value="10">10</span>
									<span class="unit" data-value=""></span>
								</div>
							</li><li data-lab-item="1">
								<div class="ingredient" data-value="有互联网连接的计算机">有互联网连接的计算机</div>
								<div class="成分量">
									<span class="amount" data-value="-1">-1</span>
									<span class="unit" data-value="取决于实验室大小">取决于实验室大小</span>
								</div>
							</li></ul>

进化关系

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">使用 BLAST 验证进化假说
<button class="expand">展开</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">在每位学生使用的计算机上打开 BLAST 网站。<a target="__blank" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" style="display:block;">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a>
</div></li><li data-sub-note-item="1-2"><div class="lab-step">访问提供的链接，获取鸡、短吻鳄和斑胸草雀的基因序列。<a href="https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes" target="__blank" style="display:block;">https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes</a> 注意：这些基因序列将用作神秘化石的现生近缘物种 DNA 样本。
</div></li><li data-sub-note-item="1-3"><div class="lab-step">点击第一个序列，熟悉其格式和内容。
</div></li><li data-sub-note-item="1-4"><div class="lab-step">返回主页面，点击绿色的“Clone or download”按钮。
</div></li><li data-sub-note-item="1-5"><div class="lab-step">然后选择“Download ZIP”。
</div></li><li data-sub-note-item="1-6"><div class="lab-step">将文件保存在计算机桌面上，以便学生方便访问。在每台计算机上重复执行步骤 2 至 6。
</div></li><li data-sub-note-item="1-7"><div class="lab-step">打印足够数量的空白分支图，确保每位学生拥有一份。注意：建议额外打印若干备用分支图。
</div></li></ul></li></ol>

<div class="section-question"><h4 class="question-sect">什么是共有衍征？</h4><p>共有衍征是指可测量或可量化的物理特征，可用于区分和划分生物群体。</p></div><div class="section-question"><h4 class="question-sect">什么是树状图？</h4><p>树状图是一种表示生物类群之间进化关系或分支分类关系的树形图。</p></div><div class="section-question"><h4 class="question-sect">两种主要的树状图类型是什么？它们有何区别？</h4><p>分支图（cladogram）和系统发育图（phylogram）是两种主要的树状图。在分支图中，分支的末端代表物种，分支仅表示它们之间的相互关系，节点代表最近的共同祖先。在系统发育图中，分支的长度各不相同，分支长度表示自最近共同祖先分化以来所经过的时间。</p></div><div class="section-question"><h4 class="question-sect">构建树状图所使用的两种主要数据类型是什么？</h4><p>可用于构建树状图的数据包括形态学和/或...

使用 BLAST 验证进化假说  
在每位学生将要使用的计算机上打开 BLAST 网站。

Education

教育

JoVE Lab Manual

生物学

Evolution

进化

Lab Manual Sub Articles

实验手册子文章

blast practice for fossil dna clues

<p class="jove_content">Students use BLAST to test evolutionary hypotheses by comparing DNA sequences. BLAST, or Basic Local Alignment Search Tool, helps match a gene sequence to similar sequences in a database. In this activity, the comparison is used to investigate a mystery fossil and its possible living relatives.</p>

<p class="jove_content">The setup begins with the BLAST website opened on each student computer. Students then use the provided link to find the chicken, alligator, and zebra finch gene sequences. These sequences serve as the living relative DNA samples for the mystery fossil.</p>

<p class="jove_content">To prepare the files, the first sequence is opened so students can become familiar with it. Then the main page is used to click the green “Clone or download” button and choose “Download ZIP.” The files are saved on the desktop so students can access them easily. The same steps are repeated on each computer.</p>

<p class="jove_content">Blank cladograms are also printed for the class. Each student should have one cladogram to complete, and extra copies are recommended. The activity gives students a way to compare DNA evidence and build a simple model of evolutionary relationships.</p>

BLAST Practice for Fossil DNA Clues

evolutionary relationships

Testing Fossil Placement with Cladograms

Cladograms and BLAST help students test where a fossil may fit on an evolutionary tree. A cladogram is a tree-shaped chart that shows hypothetical genealogical relationships between species. The tips, or leaves, show specific species, and the branch lengths show the degree of change between them. A node is the point where branches meet and marks the common ancestor of the species that split from that line. Species that share a node are called a sister group.<br /><br />To start, students examine a blank...

Students use BLAST to test evolutionary hypotheses by comparing DNA sequences. BLAST, or Basic Local Alignment Search Tool, helps match a gene sequence to similar sequences in a database. In this activity, the comparison is used to investigate a mystery fossil and its possible living relatives.<br /><br />The setup begins with the BLAST website opened on each student computer. Students then use the provided link to find the chicken, alligator, and zebra finch gene sequences. These sequences serve as the...

lab manual sub articles

Set up a BLAST-based class activity with chicken, alligator, and zebra finch DNA samples to compare a mystery fossil and its living relatives.

BLAST Practice for Fossil DNA Clues | JoVE K12

Next Generation Science Standards

High School

Life Science

heredity-inheritance-and-variation-of-traits

Heredity: Inheritance and Variation of Traits

HS-LS3-3

HS-LS4-1

Florida Department of Education

SC.912.L.15

SC.912.L.15.4

SC.912.L.15.10

new-york-state-science-learning-standards

New York State Science Learning Standards

Inheritance and Variation of Traits

HS-LS3-3.

Natural Selection and Evolution

HS-LS4-1.

Georgia Standards of Excellence

9-12

SB4.b

<p>数千年来，人类一直在对生物有机体进行分类和归类。最初，这种分类主要针对生存所必需的物体。随着人类历史的发展，这些分类的技巧和精细程度也不断提高。公元前四世纪，亚里士多德开创了正式的分类体系，将植物和动物划分为不同的类群，然后根据它们的形态特征以及所占据的栖息地等性状进一步细分。后来，在18世纪中期，林奈（Linnaeus）在亚里士多德体系的基础上加以发展。他将其最高级别的分类单元称为“界”（kingdoms），并在此基础上依据共源性状（synapomorphies）——即能够划分分支的定义性形态特征——逐级细分。例如，若一种动物具有脊椎或类似结构，则应归入脊索动物门（phylum chordata）；若没有，则可将其归入其他多个无脊椎动物门类，例如节肢动物门（arthropoda），这是一个包含昆虫在内的庞大类群。林奈继续依据共源性状，在纲、目、科和属等逐级分类层级上对生物类群进行划分，直至最终的分类单元，通常是物种。我们将林奈这种基于形态特征差异的分类方式称为分支分类学（cladistics），即根据生物形态特征的差异对有机体进行分类。</p>
<p>如今，科学家通常构建一种称为树状图（dendrogram）的图形，以直观展示这些物种的分化与归类关系。这种特定形式的树状图，即分支图（cladogram），用于呈现物种之间的分支关系，其中树的末端代表物种，分支则显示它们之间的亲缘关系。例如，此处黑猩猩与熊之间的亲缘关系更近，它们共有的共同特征多于它们各自与翻车鱼之间的共同特征。分支交汇的位置称为节点（nodes），代表其后续物种的共同祖先。另一类主要的树状图类型是系统发育图（phylogram）。这类图与分支图不同之处在于，物种之间的分支长度各不相同，用以表示它们之间演化改变的程度。因此，分支越长，表明该物种自其最近共同祖先分化以来所经历的时间越久。</p>
<p>通过简单分析生物体的形态特征可构建系统发育树。随着现代技术的发展，比较DNA也已成为构建系统发育树的常用方法。DNA由核苷酸组成，每个核苷酸含有四种不同碱基之一：腺嘌呤（adenine）、鸟嘌呤（guanine）、胞嘧啶（cytosine）或胸腺嘧啶（thymine）。这些碱基的排列顺序构成了DNA编码。该编码由亲代传递给子代。因此，若观察同一物种（如人类），我们的遗传编码具有极高的相似性，约为99.9%。我们还与其它物种（如黑猩猩和小鼠）共享部分DNA序列，但我们的DNA与这些物种之间的总体相似程度存在显著差异。这意味着我们可以构建系统发育树，根据物种间遗传编码的相似性或差异性对物种进行归类。这一结合统计学、数学建模和计算机科学的分析领域被称为生物信息学。为了比较DNA序列，研究人员常使用一种名为“基本局部比对搜索工具”（Basic Local Alignment Search Tool，简称BLAST）的生物信息学工具，该工具由美国国家生物技术信息中心（National Center for Biotechnology Information）开发并维护。</p>
<p>在本实验中，您将首先利用形态学信息构建动物的系统发育树（分支图），然后根据化石物种的形态特征将其放置在该系统发育树上。接着，您将使用该化石若干现代近缘物种的 DNA 序列，并结合 BLAST 数据库，验证化石在进化树上的位置。</p>

dna evidence in evolutionary trees

<p class="jove_content">DNA evidence helps scientists map evolutionary relationships between living things. Early classification began with Aristotle in the 4th century BC and was later improved during the Renaissance and by Carolus Linnaeus in the mid-1700s. These systems grouped species by physical similarity, such as the presence or absence of a backbone in vertebrates and invertebrates. Traits like a backbone are called synapomorphies, which are shared traits that likely came from a common ancestor.</p>

<p class="jove_content">Physical traits are still useful, but they also have limits. To show how species are related, scientists build dendrograms, or branching diagrams. A cladogram is one type of dendrogram. It shows hypothetical family-like relationships, with the tips representing species and the branches showing how they are connected.</p>

<p class="jove_content">A phylogram is a more detailed tree. Its branch lengths are not the same. The length of a branch shows the amount of change between species, so a longer branch means more time since two species diverged from a common ancestor. In both cladograms and phylograms, a node marks the point where branches meet. Species that share the most recent common ancestor are closest to that node and are called sister groups.</p>

<p class="jove_content">Scientists used to make cladograms by comparing morphology, or body structure. That method is still used, but it now includes DNA sequence comparison. DNA evidence can also help estimate how long ago species shared a common ancestor. This is especially useful for understanding evolutionary history, although it does not always work for extinct organisms because DNA is usually found in soft tissue, and soft tissue is rarely preserved in fossils.</p>

<p class="jove_content">Genes carry DNA from parents to offspring. The nucleotide sequence in genes uses the bases A, G, C, and T. These sequences are often similar in different species because of common ancestry. Researchers can align them to build trees. Species with more similar sequences are placed closer together, while species with less similarity are placed farther apart.</p>

<p class="jove_content">Bioinformatics tools help scientists work with large DNA datasets. These tools combine computer science, math, and statistics. One example is BLAST, or Basic Local Alignment Search Tool. BLAST searches the NCBI database, which brings together several databases of DNA sequence information. It compares a query sequence against sequences in the database and lists the closest matches first.</p>

<p class="jove_content">A BLAST result can suggest which species are closely related to the source of the query gene. However, this comparison may not always show the exact evolutionary relationship. Genes can evolve at different rates, and genomes can contain more than one similar sequence. Even so, DNA comparisons are valuable for more than tree building. Scientists often use genes first found in model organisms such as the fruit fly Drosophila melanogaster or the mouse to study gene function in other species, including humans. Human genes can also be used to find homologs in model organisms. This approach is important in human disease research. For example, researchers can knock out a mouse version of a human gene to create disease models such as the Cftr knockout mouse for cystic fibrosis or the Apoe knockout mouse for atherosclerosis.</p>

DNA Evidence in Evolutionary Trees

人类自公元前4世纪亚里士多德首次尝试对生物进行分类以来，一直在努力完善生物分类体系。亚里士多德的分类系统……

使用 JoVE Lab Manual 上的这个Biology评估测验来测试你对进化关系的理解。通过视频问题涵盖关键概念，旨在评估学生的学习情况。

进化关系（Biology）- 评估测验 | JoVE Lab Manual

在这段 8 分钟的学生实验流程视频中，逐步学习 进化关系 的操作步骤。属于 JoVE Lab Manual 上的 Biology 系列。

Biology 中的 进化关系 学生实验流程 - 5.4K+ 观看次数 | JoVE Lab Manual

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches ...

Conditions on Early Earth

Around 4 billion years ago, oceans began to condense on earth while volcanic eruptions released nitrogen, carbon dioxide, methane, ammonia, and hydrogen ...

The Colonization of Land

Changes in the environment of the early Earth drove the evolution of organisms. As prokaryotic organisms in the oceans began to photosynthesize, they ...

What is Evolutionary History?

Scientists record evolutionary history by analyzing fossil, morphological, and genetic data. The fossil record documents the history of life on Earth and ...

The Evidence for Evolution

Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of ...

The Fossil Record

The fossil record documents only a small fraction of all organisms that have ever inhabited Earth. Fossilization is a rare process, and most organisms ...

Convergent Evolution

Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure ...

The student will investigate and understand that populations change through time. Key ideas include  evidence is found in fossil records and through DNA analysis;

BIO.7.a

What are Populations and Communities?

Populations are groups of individuals of the same species that inhabit a shared environment. Communities include multiple co-existing, interacting ...

Distribution and Dispersion

Ecology is the study of how organisms interact with their environment and with one another. An important aspect of ecology is understanding where species ...

Life Histories

Constrained by limited energy and resources, organisms must compromise between offspring quantity and parental investment. This trade-off is represented ...

Population Growth

Population size is dynamic, increasing with birth rates and immigration, and decreasing with death rates and emigration. In ideal conditions with ...

Ecological Niches

All organisms have a position within an ecosystem. The complete set of living and nonliving factors&#x2014;including food resources, climate, and ...

Ecological Succession

Ecological succession is influenced by the processes of facilitation, inhibition, and toleration. Facilitation occurs when early successional species ...

Keystone Species

Measures of species biodiversity, such as richness (i.e., the number of species present) and evenness (i.e., their relative abundance), describe an ...

Symbiosis

Symbiotic relationships are long-term, close interactions between individuals of different species that affect the distribution and abundance of those ...

Competition

When organisms require the same limited resources within an environment, they may have to compete for them. Competition is a net-negative interaction. ...

Predator-Prey Interactions

Predators consume prey for energy. Predators that acquire prey and prey that avoid predation both increase their chances of survival and reproduction ...

Ecological Disturbance

An ecological disturbance is a temporary disruption in the environment resulting from abiotic, biotic, or anthropogenic factors, causing a pronounced ...

The student will investigate and understand that populations change through time. Key ideas include  genetic variation, reproductive strategies, and environmental pressures affect the survival of populations;

BIO.7.b

What is Natural Selection?

Natural selection is an evolutionary process in which individuals with survival-promoting traits reproduce at higher rates. These favorable traits become ...

Types of Selection

Natural selection influences the frequencies of particular alleles and phenotypes within populations in several different ways. Primarily, natural ...

Frequency-dependent Selection

When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to ...

Limits to Natural Selection

Organisms that are well-adapted to their environment are more likely to survive and reproduce. However, natural selection does not lead to perfectly ...

Natural Selection

Fitness
Widespread variation of phenotypes in natural populations provides the raw material for evolution, which is the change in the inherited traits of ...

Simulating Natural Selection
ExpandTo prepare for the lab, set out workstations for each student pair containing 6 white, 6 black, and 13 gray 12 inch ...

Simulating Natural Selection
ExpandTo begin, cut the white, black, and gray pipe cleaners into quarters, which should produce a total of 100 pieces that ...

Artificial Selection

Natural Selection and Adaptive Evolution
In natural settings, adaptive evolution takes place by natural selection, a process in which differences in ...

Observing Artificial Selection in Plants
ExpandTwo weeks before beginning the pollination experiments, collect a sufficient amount of small pots with a ...

Observing Artificial Selection in Plants 
ExpandTo begin the experiment, collect five two-week old grown plants from the generation one population that ...

The student will investigate and understand that populations change through time. Key ideas include  natural selection is a mechanism that leads to adaptations and may lead to the emergence of new species; and

BIO.7.c

Humans have been attempting to properly classify living things since Aristotle made the first attempt during the 4th century BC. Aristotle&#8217;s system ...

Using BLAST to Test Evolutionary Hypotheses
ExpandOpen the BLAST website on each computer that the students will be using. ...

Forming an Evolutionary Hypothesis
ExpandNOTE: A cladogram is an important tool for forming an evolutionary hypothesis. A cladogram is a tree-shaped chart ...

The student will investigate and understand that populations change through time.Key ideas include  biological evolution has scientific evidence and explanations.

BLAST Practice for Fossil DNA Clues

Learning Objectives

什么是共有衍征？

什么是树状图？

两种主要的树状图类型是什么？它们有何区别？

Lab Prep

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