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">Utilisation de BLAST pour tester des hypothèses évolutives
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								<div class="ingrédient » data-value="Image de cladogramme vide"><a target="_blank » href="/files/ftp_upload/10562/Blank_Cladogram.png">Image de cladogramme vide</a></div>
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									<span class="montant » data-value="10">10</span>
									<span class="unité » data-value=""></span>
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							</li><li data-lab-item="1">
								<div class="ingrédient » data-value="Ordinateur avec connexion internet">Ordinateur avec connexion internet</div>
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									<span class="quantité » data-value= »-1">-1</span>
									<span class="unité » data-value="Dépend de la taille du laboratoire">Dépend de la taille du labo</span>
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relations évolutives

<ol class="note-items"><li data-note-item="1 » data-parent-collapse=">Utilisation de BLAST pour tester des hypothèses évolutives
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">Ouvrez le site web BLAST sur chaque ordinateur que les étudiants utiliseront. <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">Naviguez jusqu’au lien fourni pour trouver les séquences des gènes du poulet, de l’alligator et du pinson zébré. <a href="https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes » target="__blank » style="display :block ;">https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes</a> REMARQUE : Ces séquences de gènes seront utilisées comme échantillons d’ADN parent vivant pour le fossile mystérieux.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Cliquez sur la première séquence pour vous familiariser avec elle. 
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Retournez à la page principale et cliquez sur le bouton vert « Cloner ou télécharger ». 
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Ensuite, sélectionnez 'Télécharger ZIP'. 
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Enregistrez les fichiers sur le bureau de l’ordinateur pour que les élèves puissent y accéder facilement. Répétez les étapes 2 à 6 sur chaque ordinateur. 
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Imprimez un nombre suffisant de cladogrammes vierges pour qu’il y en ait un par élève.  REMARQUE : Il est recommandé d’imprimer également des cladogrammes de rechange.
</div></li></ul></li></ol>

<div class="section-question"><h4 class="question-sect">Que sont les synapomorphies ?</h4><p>Les synapomorphies sont des caractéristiques physiques mesurables ou quantifiables qui peuvent être utilisées pour distinguer et diviser des groupes d’organismes vivants.
</p></div><div class="section-question"><h4 class="question-sect">Que sont les dendrogrammes ?</h4><p>Un dendrogramme est un diagramme arborescent représentant les relations évolutives ou cladistiques entre des groupes d’organismes.
</p></div><div class="section-question"><h4 class="qu...

Relations évolutives

Utilisation de BLAST pour tester des hypothèses évolutives
ExpandOuvrez le site Web BLAST sur chaque ordinateur que les élèves utiliseront. ...

Education

Enseignement

JoVE Lab Manual

Biologie

Evolution

Évolution

Lab Manual Sub Articles

Sous-articles du manuel de laboratoire

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>Les humains ont classé et organisé les organismes biologiques pendant des milliers d’années. À l’origine, il s’agissait principalement de commander des objets nécessaires à la survie. Au fur et à mesure que l’histoire de l’humanité progressait, les compétences et les détails de ces classifications augmentaient également. Au IVe siècle av. J.-C., Aristote a été le pionnier des classifications formelles, délimitant les plantes et les animaux en différents groupes, puis les divisant davantage en fonction de leurs caractéristiques physiques et de leurs traits tels que les habitats qu’ils occupent. Plus tard, au milieu des années 1700, Linné s'est appuyé sur le système d'Aristote. Il a appelé son plus haut niveau de regroupement les royaumes et, à partir de là, a divisé les groupes à l’aide de synapomorphies, une caractéristique physique déterminante qui divise une branche. Par exemple, si un animal possède une colonne vertébrale ou une structure similaire, il doit être placé dans le chordata de l’embranchement. Si ce n'est pas le cas, il existe de nombreux autres embranchements, dans lesquels les animaux sans colonne vertébrale peuvent être divisés, y compris les arthropodes, un grand groupe comprenant des insectes. Linné a continué à diviser des groupes d’organismes en fonction de leurs synapomorphies aux niveaux ultérieurs à travers la classe, l’ordre, la famille et le genre, jusqu’à ce qu’il atteigne la désignation finale, généralement, l’espèce. Nous nous référons au type de classification de Linné comme cladistique, la classification des organismes basée sur les différences de caractéristiques physiques.</p>
<p>Aujourd’hui, les scientifiques construisent couramment des arbres appelés dendrogrammes pour donner des représentations visuelles de ces divisions et groupes. Cette forme particulière de dendrogramme, le cladogramme, visualise les relations cladistiques entre les espèces de sorte que les pointes de l'arbre représentent l'espèce et que les branches montrent comment elles sont liées les unes aux autres. Par exemple, ici, le chimpanzé et l’ours sont plus étroitement liés l’un à l’autre et partagent plus de caractéristiques communes que l’un ou l’autre avec le poisson-lune. Les endroits où les branches se rencontrent sont appelés nœuds et désignent des ancêtres communs pour les espèces qui suivent. Un deuxième type majeur de dendrogramme est le phylogramme. Ceux-ci sont différents des cladogrammes car la longueur des branches entre les espèces varie, représentant le degré de changement entre elles. Ainsi, plus la branche est longue, plus le temps s’est écoulé depuis que l’espèce a divergé de son dernier ancêtre commun.</p>
<p>Les dendrogrammes ont été construits en analysant simplement la morphologie des organismes. Avec l’avènement de la technologie moderne, la comparaison de l’ADN est également devenue un moyen courant de construire des arbres. L’ADN est composé de nucléotides associés à l’une des quatre bases différentes. Adénine, guanine, cytosine ou thymine. L’ordre de ces bases est le code ADN. Ce code est transmis du parent à la progéniture. Par conséquent, si vous regardez une seule espèce comme les humains, il y a un très haut degré de similitude dans notre code génétique, environ 99,9 %. Nous partageons également une partie de notre code ADN avec d’autres espèces, comme les chimpanzés et les souris, mais le degré de similitude globale entre notre ADN et le leur est très différent. Cela signifie que nous pouvons créer des arbres, qui regroupent les espèces en fonction des similitudes ou de la différence entre leurs codes génétiques. Ce domaine d’analyse, combinant les statistiques, la modélisation mathématique et l’informatique, est appelé bioinformatique. Pour comparer les séquences d’ADN, les chercheurs utilisent souvent un outil bio-informatique appelé Basic Local Alignment Search Tool, ou BLAST, qui a été créé et est maintenu par le National Center for Biotechnology Information.</p>
<p>Dans ce laboratoire, vous créerez d’abord un cladogramme d’animaux à l’aide d’informations morphologiques, puis vous placerez une espèce fossile sur ce cladogramme en fonction de sa morphologie. Vous utiliserez ensuite les séquences d’ADN de plusieurs parents modernes du fossile et la base de données BLAST pour vérifier votre positionnement du fossile sur l’arbre.</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

Les humains tentent de classer correctement les êtres vivants depuis qu’Aristote a fait la première tentative au 4ème siècle avant JC. Le système d’Aristote ...

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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

Que sont les synapomorphies ?

Que sont les dendrog...

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