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">BLAST を使用して進化仮説を検定する
</a></li></ul>

<ul class="lab-items"><li data-lab-item="1">
								<div class="ingredient" data-value="空白のクラドグラム画像"><a target="_blank" href="/files/ftp_upload/10562/Blank_Cladogram.png">空白のクラドグラム画像</a></div>
								<div class="ingredient-amount">
									<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="インターネットに接続されたコンピュータ"></div>
								<div class="ingredient-amount">
									<span class="amount" data-value="-1">-1</span>
									<span class="unit" data-value="ラボのサイズに依存">ラボのサイズに依存</span>
								</div>
							</li></ul>

進化的関係

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">BLASTを使用して進化仮説を検証
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">学生が使用する各コンピューターでBLASTウェブサイトを開きます。<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">提供されたリンクに移動して、ニワトリ、ワニ、およびシマウマフィンチの遺伝子配列を見つけます。<a href="https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes" target="__blank" style="display:block;">https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes</a>注:これらの遺伝子配列は、謎の化石の生きた相対DNAサンプルとして使用されます。
</div></li><li data-sub-note-item="1-3"><div class="lab-step">最初のシーケンスをクリックして理解してください。
</div></li><li data-sub-note-item="1-4"><div class="lab-step">メインページに戻り、緑色の「クローンまたはダウンロード」ボタンをクリックしてください。
</div></li><li data-sub-note-item="1-5"><div class="lab-step">次に、「Download ZIP」を選択します。
</div></li><li data-sub-note-item="1-6"><div class="lab-step">学生が簡単にアクセスできるように、ファイルをコンピューターのデスクトップに保存します。各コンピューターで手順2〜6を繰り返します。
</div></li><li data-sub-note-item="1-7"><div class="lab-step">十分な数の空白のクラドグラムを印刷して、学生ごとに1つになるようにします。 注意: 予備のクラドグラムも印刷することをお勧めします。
</div></li></ul></li></ol>

<div class="section-question"><h4 class="question-sect">シナポモルフィとは何ですか?</h4><p>シナポモルフィアは、測定可能または定量化可能な物理的特徴であり、生物のグループを区別および分割するために使用できます。
</p></div><div class="section-question"><h4 class="question-sect">樹形図とは何ですか?</h4><p>樹形図は、生物のグループ間の進化的またはクラディスティックな関係を表す樹形図です。
</p></div><div class="section-question"><h4 class="question-sect">樹形図の2つの主要なタイプは何ですか、そしてそれらはどのように異なりますか?</h4><p>クラドグラムと系統群は、樹形図の2つの主要なタイプです。クラドグラムでは、枝の先端は種を表し、枝は単にそれらが互いにどのように関連しているかを示しています。ノードは、最後の共通の祖先を表します。系統群では、枝の長さはさまざまで、その長さは最後の共通の祖先からの分岐から経過した時間を表します。
</p></div><div class="secti...

BLASTを使用して進化仮説を検証する
拡大生徒が使用する各コンピューターでBLASTのWebサイトを開きます。...

Education

JoVE Lab Manual

生物学

Evolution

進化

Lab Manual Sub Articles

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>人間は何千年もの間、生物を分類し、組織化してきました。もともとは、主に生存に必要なオブジェクトを順序付けていました。人類の歴史が進むにつれて、これらの分類のスキルと詳細も進歩しました。紀元前4世紀、アリストテレスは正式な分類を開拓し、植物や動物をさまざまなグループに分類し、それらを物理的特性やそれらが占める生息地などの特性に基づいてさらに分類しました。その後、1700年代半ばに、リンネはアリストテレスのシステムに基づいて構築しました。彼は自分の最高レベルを王国のグループ化と呼び、そこから、枝を分割する決定的な物理的特徴であるシナポモルフィアを使用してグループを分割しました。たとえば、動物が背骨または同様の構造を持っている場合、それは脊索動物門に配置する必要があります。そうでない場合は、他にも多くの門があり、背骨のない動物は、昆虫を含む大きなグループである節足動物など、分割できます。リノーは、生物のグループをシナポモルフィアに基づいて、その後のレベルでクラス、目、科、属を通じて分割し続け、最終的な指定、一般的には種に到達しました。リンネの分類のタイプをクラディスティックスと呼び、物理的特性の違いに基づく生物の分類です。</p>
<p>今日、科学者は一般的に、これらの分割とグループを視覚的に表現するために、樹状図と呼ばれる木を構築します。この特定の形式の樹形図であるクラドグラムは、種間の系統的関係を視覚化するため、木の先端は種を表し、枝はそれらが互いにどのように関連しているかを示します。例えば、ここではチンパンジーとクマは、マンボウよりも互いに密接に関連しており、共通の特徴を共有しています。枝が出会う場所はノードと呼ばれ、後続の種に共通の祖先を示します。2番目の主要な樹形図タイプは系統です。これらはクラドグラムとは異なり、種間の枝の長さは異なり、それらの間の変化の程度を表します。したがって、分岐が長ければ長いほど、種が最後の共通の祖先から分岐してから経過した時間が長くなります。</p>
<p>樹木図は、生物の形態を単純に解析することによって構築されました。現代の技術の出現により、DNAの比較もツリーを構築する一般的な方法になりました。DNAは、4つの異なる塩基のいずれかに関連付けられたヌクレオチドで構成されています。アデニン、グアニン、シトシン、またはチミン。これらの塩基の順序がDNAコードです。このコードは親から子孫に渡されます。したがって、人間のように単一の種全体を見ると、私たちの遺伝暗号には非常に高い類似性があり、約99.9%です。また、私たちはチンパンジーやマウスなどの他の種とDNAコードの一部を共有していますが、私たちのDNAと彼らのDNAの全体的な類似性の程度は大きく異なります。これは、遺伝暗号間の類似性または相違点に基づいて種をグループ化する樹木を作成できることを意味します。統計学、数理モデリング、コンピュータサイエンスを組み合わせたこの分析分野は、バイオインフォマティクスと呼ばれています。DNA配列を比較するために、研究者は、National Center for Biotechnology Informationが作成し、維持しているBasic Local Alignment Search Tool(BLAST)と呼ばれるバイオインフォマティクスツールをよく使用します。</p>
<p>本研究室では、まず形態情報を用いて動物のクラドグラムを作成し、その形態に基づいてこのクラドグラム上に化石種を配置します。次に、化石とBLASTデータベースに関連する現代のいくつかの異なる親戚からのDNA配列を使用して、化石が樹木に位置付けていることを確認します。</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

人間は、紀元前4世紀にアリストテレスが初めて試みて以来、生物を適切に分類しようと試みてきました。アリストテレスの体系...

JoVE Lab ManualのこのBiology評価クイズで、進化的関係の理解をテストしてください。学生の学習を評価するために設計されたビデオベースの質問を通じて主要な概念をカバーしています。

Biology の 進化的関係 - 評価クイズ | JoVE Lab Manual

この 8 分間の学生プロトコル動画で、進化的関係 の手順をステップごとに学びましょう。JoVE Lab Manual の Biology コレクションの一部です。

Biology の 進化的関係 学生プロトコル - 5.4K+ 回の視聴 | 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

シナポモルフィとは何ですか?

樹形図とは何ですか?

樹形図の2つの主要なタイプは何ですか、そ...

Lab Prep

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