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">Using BLAST to Test Evolutionary Hypotheses
</a></li></ul>

evolutionary relationships

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Using BLAST to Test Evolutionary Hypotheses
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">Open the BLAST website on each computer that the students will be using. <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">Navigate to the provided link to find the chicken, alligator, and zebra finch gene sequences. <a href="https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes" target="__blank" style="display:block;">https://github.com/EvolutionGenes/Evolutionary-Relationships-Genes</a> NOTE: These gene sequences will be used as the living relative DNA samples for the mystery fossil.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Click on the first sequence to familiarize yourself with it. 
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Return to the main page and click on the green &#8220;Clone or download&#8221; button. 
</div></li><li data-sub-note-item="1-5"><div class="lab-step">Then, select 'Download ZIP'. 
</div></li><li data-sub-note-item="1-6"><div class="lab-step">Save the files on the computer desktop for the students to access easily. Repeat steps 2 &#8211; 6 on each computer. 
</div></li><li data-sub-note-item="1-7"><div class="lab-step">Print out a sufficient number of blank cladograms so that there is one per student.  NOTE: It is recommended to also print spare cladograms.
</div></li></ul></li></ol>

<div class="section-question"><h4 class="question-sect">What are synapomorphies?</h4><p>Synapomorphies are measurable or quantifiable physical features which can be used to distinguish and split groups of living organisms.
</p></div><div class="section-question"><h4 class="question-sect">What are dendrograms?</h4><p>A dendrogram is a tree diagram representing the evolutionary or cladistical relationships between groups of organisms.
</p></div><div class="section-question"><h4 class="question-sect">What are two main types of dendrograms and how ...

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

Education

JoVE Lab Manual

Evolution

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

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>Humans have classified and organized biological organisms for thousands of years. Originally, primarily ordering objects necessary for survival. As human history progressed, so did the skill and detail in these classifications. In the fourth century B.C., Aristotle pioneered formal classifications, delineating plants and animals into different groups and then dividing these further based on their physical characteristics and traits like the habitats that they occupy. Later, in the mid 1700s, Linnaeus built on Aristotle&#39;s system. He called his highest level of grouping the kingdoms and, from there, divided the groups using synapomorphies, a defining physical feature which splits a branch. For example, if an animal possesses a backbone or a similar structure, it should be placed in the phylum chordata. If it doesn&#39;t, then there are many other phyla, which animals without backbones can be split into, including the arthropoda, a large group including insects. Linneaus continued splitting groups of organisms based on their synapomorphies at subsequent levels through the class, order, family, and genus, until reaching the final designation, generally, the species. We refer to Linnaeus&#39; type of classification as cladistics, the classification of organisms based on differences in physical characteristics.</p>
<p>Today, scientists commonly construct trees called dendrograms to give visual representations of these splits and groups. This particular form of dendrogram, the cladogram, visualizes the cladistic relationships between the species so that the tips of the tree represent the species and the branches show how they&#39;re related to one another. For example, here the chimpanzee and bear are more closely related to one another and share more common characteristics than either of them do with the sunfish. The places where the branches meet are referred to as nodes and denote common ancestors for the species that follow. A second major dendrogram type is the phylogram. These are different from cladograms because the length of the branches between species varies, representing the degree of change between them. So the longer the branch, the more time has passed since the species diverged from their last common ancestor.</p>
<p>Dendrograms were constructed by simply analyzing the morphology of organisms. With the advent of modern technology, comparing DNA has also become a common way to build trees. DNA is made up of nucleotides associated with one of four different bases. Adenine, guanine, cytosine, or thymine. The order of these bases is the DNA code. This code is passed from parent to offspring. Consequently, if you look across a single species like humans, there is a very high degree of similarity in our genetic code, around 99.9%. We also share some of our DNA code with other species, like chimpanzees and mice, but the degree of overall similarity between our DNA and theirs is vastly different. This means that we can create trees, which group species based on the similarities or difference between their genetic codes. This field of analysis, combining statistics, mathematical modeling, and computer science, is referred to as bioinformatics. To compare DNA sequences, researchers often use a bioinformatics tool called the Basic Local Alignment Search Tool, or BLAST, which was created, and is maintained by, the National Center for Biotechnology Information.</p>
<p>In this laboratory, you will first create a cladogram of animals using morphological information, and then place a fossil species onto this cladogram based on its morphology. You will then use DNA sequences from several different modern-day relatives of the fossil and the BLAST database to verify your positioning of the fossil onto the tree.</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

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

Test your understanding of Evolutionary Relationships with this Biology assessment quiz on JoVE Lab Manual. Covers key concepts through video-based questions designed to evaluate student learning.

Evolutionary Relationships in Biology - Assessment Quiz | JoVE Lab Manual

Use cladograms and BLAST to compare fossil traits and gene sequences, then test a fossil’s likely place on an evolutionary tree.

Testing Fossil Placement with Cladograms | JoVE K12

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

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

What are synapomorphies?

What are dendrograms?

Lab Prep

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