Name: Evolutionary Relationships: Using BLAST to Test Evolutionary Hypotheses - Concept
Uploaded: 2019-01-29T11:04:45.000Z
Duration: 5 min 21 s
Channel: JoVE

K12 Standards

Virginia  Standards of Learning

HIgh School

Biology

BIO.7

BIO.7.d

Evolutionary Relationships

lab manual sub articles

Lab Manual Sub Articles

<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>

evolutionary relationships

<p>Humans have been attempting to properly classify living things since Aristotle made the first attempt during the 4<sup>th</sup> century BC. Aristotle&#8217;s system was improved upon during the Renaissance and then, subsequently, by Carolus Linnaeus in the mid 1700&#8217;s. These more formal classification and organization systems grouped species by their physical similarity to one another. For example, all vertebrates have a backbone, but invertebrates do not. Traits like the backbone are called synapomorphies, which are traits that are shared by a group of organisms, presumably because they were derived from a common ancestor. As we will explore, this method has been shown to have limitations and has more recently been amended to include genetic analysis. Still, scientists construct trees called dendrograms to create a visual representation of how species are related to one another and share common ancestors. These dendrograms can aid in our understanding of the evolutionary processes that drive these relationships. Genetic comparisons have added an important tool guiding the analysis of evolutionary relationships.</p>
<h4>Types of Dendrogram</h4>
<p>A type of dendrogram, called a cladogram, depicts the hypothetical genealogical relationships between species with the tips (or leaves) of the tree representing a species and the branches showing how species are related to each other. A slightly more complicated type of tree, called a phylogram, differs from a cladogram in that the branches leading to the species are of different lengths. The length of a branch in this type of tree represents the degree of change between species: the longer the branch, the more time since the species have diverged from a common ancestor. In both types of tree, the common ancestor of a group of species is indicated by a node, which is the point where a series of branches meet. Species that are more closely related to each other (most recently shared a common ancestor) will be located closest to the node. The two species that share a node are called a sister group<sup>1</sup>.</p>
<h4>Understanding Evolutionary Relationships using Genetic Data</h4>
<p>Historically, cladograms were constructed by comparing the morphology (physical structure) of organisms. This method is still practiced but the techniques have been modernized to include comparison of DNA (deoxyribonucleic acid) sequences between species. Using DNA for building trees has several advantages over relying solely on morphology, including being able to calculate an estimate of how long ago different species shared a common ancestor<sup>1</sup>. However, using DNA is not always feasible, especially when trees include extinct organisms. DNA is best found in soft tissues, which are not preserved during the fossilization process, and therefore it is uncommon for a DNA sample of an extinct species to be available.</p>
<p>DNA is passed on from parents to their offspring in hereditary units called genes. The nucleotide (A, G, C, and T) sequence of genes found in different species are frequently quite similar, likely due to their having come from a common ancestor. This fact allows researchers to align sequences from different species with one another to build the trees described above. Species with more similarity between their nucleotide sequences will be placed next to each other in a tree, and species with less sequence similarity will be placed further apart from each other.</p>
<p>Bioinformatics are the tools used by biologists to analyze large datasets using a combination of computer science, mathematical modeling, and statistics. One such tool is called BLAST (Basic Local Alignment Search Tool), which can be used to quickly search the entire genome of any species that is available in the NCBI (National Center for Biotechnology Information) database<sup>2</sup>. The NCBI database combines several different databases that hold different types of DNA sequence information. The process of a BLAST search includes complex computer algorithms, but basically, BLAST aligns sequences of each nucleotide base from a submitted DNA sequence (known as the <em>query</em> sequence) with sequences in the data base that most closely match it. The DNA sequences that are found will be listed in order of similarity to the sequence in question, and will therefore be from species closely related to the species containing the query gene. This comparison may or may not depict the actual evolutionary relationship between species because genes evolve at different rates. Additionally, genomes sometimes contain more than one instance of a similar sequence.</p>
<p>Comparison of DNA sequences of genes is valuable beyond consideration of evolutionary relationships. Frequently, genes are identified in model organisms, such as the fruit fly, <em>Drosophila melanogaster</em>, or the mouse<sup>3</sup>. Integral to studying a gene, the function of its product is commonly identified and analyzed. If a researcher is interested in studying that function in a different organism (humans for example), BLAST or other bioinformatic tools can be used to find candidate genes based on their similarities to the genes of known function from model organisms.</p>
<p>Human genes can also be used as the starting point to find homologs in model organisms. In fact, human disease research depends heavily on this. Once a human gene of interest is identified, mice can be genetically manipulated to have the homologous gene disrupted, or &#8220;knocked out,&#8221; creating a model of the human disease that can be studied in order to understand and treat the disease. There are many of these mouse strains currently available. For example, there is a mouse model for human Cystic Fibrosis (CF) called the <em>Cftr</em> knockout mouse and another modeling atherosclerosis, called the <em>Apoe</em> knockout<sup>3</sup>.<br />
 </p>
<h4>References:</h4>
<ol class="references">
	<li><strong>Annenberg Learner.</strong> Online Textbook: Unit 3 Evolution and Phylogenetics. <em>Rediscovering Biology. </em>[Online] 2017. [Cited: August 23, 2018.] https://www.learner.org/courses/biology/textbook/compev/compev_3.html.</li>
	<li><strong>National Center for Biotechnology Information, U.S. National Library of Medicine.</strong> BLAST: Basic Local Alignment Search Tool. [Online] https://blast.ncbi.nlm.nih.gov/Blast.cgi.</li>
	<li><strong>National Human Genome Research Institute.</strong> Background on Mouse as a Model Organism. <em>National Human Genome Research Institute. </em>[Online] December 2002. [Cited: August 23, 2018.] <a href="https://www.genome.gov/10005834/background-on-mouse-as-a-model-organism/" target="__blank">https://www.genome.gov/10005834/background-on-mouse-as-a-model-organism/</a>.</li>
</ol>

Evolutionary Relationships: Using BLAST to Test Evolutionary Hypotheses - Concept

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

Education

JoVE Lab Manual

Evolution

natural selection

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 ...

artificial selection

Artificial Selection

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

hardy-weinberg and genetic drift

Hardy-Weinberg and Genetic Drift

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Plant Diversity

From Water to Land
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microbial and fungal diversity

Microbial and Fungal Diversity

Bacteria and fungi are two highly diverse groups of organisms that can have significant beneficial or detrimental impacts on human health. For this ...

evolution

Learn how scientists use DNA, BLAST, and dendrograms to compare species, trace common ancestors, and study genes in model organisms.

DNA Evidence in Evolutionary Trees | JoVE K12

Texas Essential Knowledge and Skills

High School

Earth Systems Science

112.49.c.7.

112.49.c.7.F.

Next Generation Science Standards

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

BIO.9

BIO.9.A

south-carolina-college-and-career-ready-science-standards

South Carolina College and Career Ready Science Standards

Biological Evolution: Unity and Diversity

B-LS4-1.

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.a

SB4.b

Botany

SBO1.

coevolution-plant-morphological-anatomical-structures-with-animals-ie

Coevolution of plant morphological and anatomical structures with animals (i.e., pollination), Rhizobium (i.e., nitrogen fixation), and Mycorrhiza (i.e., fungi in rhizosphere).

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

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

<ul><li><a href="#" data-time="6">Forming an Evolutionary Hypothesis
</a></li><li><a href="#" data-time="92">Comparing Gene Sequences Using BLAST
</a></li><li><a href="#" data-time="405">Data Analysis
</a></li></ul>

<ol class="note-items"><li data-note-item="1" data-parent-collapse="">Forming an Evolutionary Hypothesis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="1-1"><div class="lab-step">NOTE: A cladogram is an important tool for forming an evolutionary hypothesis. A cladogram is a tree-shaped chart used to depict the hypothetical genealogical relationships between species. The tips or leaves of the chart represent specific species and the branches of the tree are different lengths. The different lengths represent the degree of change between each of the species. The common ancestor of all of the species that a specific line branches from is located at a node, where the branches intersect. Species that share a node are called a sister group.
</div></li><li data-sub-note-item="1-2"><div class="lab-step">To begin, look at the provided blank cladogram and make a hypothesis about where the assigned animals should be placed on the tree. If a blank cladogram has not been provided please <a target="_blank" href="/files/ftp_upload/10562/Blank_Cladogram.png">download one here</a>.
</div></li><li data-sub-note-item="1-3"><div class="lab-step">Next, observe the image of the fossilized animal.
</div></li><li data-sub-note-item="1-4"><div class="lab-step">Using the morphology, or physical characteristics, of the fossil, make a hypothesis about where on your cladogram it should be placed. Add a new line or mark to indicate your proposed position for the fossil.
</div></li></ul></li><li data-note-item="2" data-parent-collapse="">Comparing Gene Sequences Using BLAST
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="2-1"><div class="lab-step">NOTE: Historically, cladograms have been constructed through the comparison of morphology. Now, genetic sequences can also be compared between species of interest to construct cladograms. DNA sequences are not usually preserved in fossils, so for this lab you will use the BLAST database to compare the DNA sequences of living species that are closely related to the fossil to thousands of other living species.
</div></li><li data-sub-note-item="2-2"><div class="lab-step">Before beginning this lab, your instructor will have downloaded the three preserved gene sequences to a folder on your desktop.
</div></li><li data-sub-note-item="2-3"><div class="lab-step">Navigate to the BLAST homepage, which the instructor should have left open in your browser, and click on Saved Strategies from the menu at the top of the page.
</div></li><li data-sub-note-item="2-4"><div class="lab-step">Click Open on the Evolutionary_Relationships_Gene1.txt file.
</div></li><li data-sub-note-item="2-5"><div class="lab-step">Then, click View to go to the Standard Nucleotide BLAST search page. You should be able to see the DNA sequence in the Query Sequence box at the top-right of the screen.
</div></li><li data-sub-note-item="2-6"><div class="lab-step">Scroll to the bottom of the screen and click the BLAST button. Note: It will take a few moments to process and analyze the data. 
</div></li><li data-sub-note-item="2-7"><div class="lab-step">When the data has been processed, a graphic summary will appear.  NOTE: Your query sequence is represented by the blue line at the top of the box. Each of the lines below the blue line represents another sequence in the BLAST database that matches your query. The length and location of these bars represent where and how much of the sequence match up to the query. The color of the bar represents its score, or how identical the sequence is to the query. Below the graphic summary is the Sequences producing significant alignments list, which contains descriptions of the DNA sequences retrieved from the database that most closely align with the query sentence. These are listed in descending order, from the most similar at the top to the least similar at the bottom. On the right, there are several statistics on how closely related each database sequence is to the experimental sequence. The higher the Max, Total, Query Coverage, and Identity scores are, the more similar the query and retrieved sequences are to each other. Similarly, the lower the E value number, the less likely the sequences match was found by random chance and more significantly the alignment is accurate. An E value of 0 indicates a highly significant match.
</div></li><li data-sub-note-item="2-8"><div class="lab-step">Click on the name of the description of the most similar alignment listed. This will take you further down the page to the exact DNA sequence alignment between the retrieved sequence and the query sequence.
</div></li><li data-sub-note-item="2-9"><div class="lab-step">Click on the Sequence ID number. This will open a new tab with more specific information on the retrieved gene sequence.
</div></li><li data-sub-note-item="2-10"><div class="lab-step">Identify and record the scientific and common names of the organism, which should be listed next to Source.
</div></li><li data-sub-note-item="2-11"><div class="lab-step">Identify and record the protein that the gene codes for, which should be listed next to Definition.
</div></li><li data-sub-note-item="2-12"><div class="lab-step">Close the tab and hit Back to return to the Sequences producing significant alignments list.
</div></li><li data-sub-note-item="2-13"><div class="lab-step">Then, repeat steps 7 &#8211; 9 for the next most similar sequences.
</div></li><li data-sub-note-item="2-14"><div class="lab-step">After collecting several species names, return to the Sequences producing significant alignments list and click Select: All to check all of the boxes next to the names of each listed alignment sequence.
</div></li><li data-sub-note-item="2-15"><div class="lab-step">Click on Distance of tree results to create a phylogram based on the similarity of all of the BLAST result gene sequences to the query gene sequence.  Note: Your query fossil relative sequence will be highlighted in yellow.
</div></li><li data-sub-note-item="2-16"><div class="lab-step">Record your sequence&#8217;s location in relation to the other taxon groups shown in the tree.
</div></li><li data-sub-note-item="2-17"><div class="lab-step">Finally, return to the Saved Strategies tab and upload the next saved gene sequence.
</div></li><li data-sub-note-item="2-18"><div class="lab-step">Query the remaining two fossil relative DNA sequences as previously demonstrated (steps 1 &#8211; 16).
</div></li></ul></li><li data-note-item="3" data-parent-collapse="">Data Analysis
<button class="expand">Expand</button><ul class="lab-items"><li data-sub-note-item="3-1"><div class="lab-step">Based on your gene sequence results, come up with a second hypothesis about where your fossil specimen fit in the original cladogram.
</div></li><li data-sub-note-item="3-2"><div class="lab-step">Compare this placement with your first hypothesis.
</div></li><li data-sub-note-item="3-3"><div class="lab-step">Compare your tree with your classmates&#8217;. If any of your classmates put the fossil on a different branch, ask them how they came to that decision.
</div></li></ul></li></ol>

Learn by watching this video about Evolutionary Relationships: Using BLAST to Test Evolutionary Hypotheses - Procedure at JoVE.com

Evolutionary Relationships: Using BLAST to Test Evolutionary Hypotheses - Procedure

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

<p>An important tool in forming an evolutionary hypothesis is the construction of a cladogram, a tree-shaped chart used to depict the hypothetical genealogical relationships between species. In a cladogram, the tips or leaves of the chart represent specific species, and the branches of the tree are different lengths, to represent the degree of change between each species. The common ancestor of all of the species that a specific line branches from is located at the point where the branches intersect, and is called a node.</p><p>Species that share a node are called a sister group. In this first exercise, you have been given a copy of this cladogram. Looking at the groups of animals in the figure, what would be your hypothesis about where the animals should be placed on the tree?</p><p>Take time now to fill out the cladogram with your best guess as to where each animal fits. Now, look at this image of a fossilized animal. Based on the morphology, or physical characteristics of the fossil, where would you place this animal on your cladogram?</p><p>Add a new line or mark to indicate your proposed position for the fossil. Although historically, cladograms have been constructed through the comparison of morphological similarities and differences between species of interest, another method of creating cladograms is to compare the genetic sequences between species. As DNA sequences are not usually preserved in fossils, in this experiment, we will compare the DNA sequences of living species closely related to our fossil to those of thousands of other living species using the BLAST database.</p><p>The results will allow us to place the fossil into the cladogram based on DNA similarity. Before beginning this lab, your instructor will have downloaded the three preserved gene sequences, and these should be stored in a folder on your desktop. Go to the BLAST homepage, which your instructor should have left open in your browser, and click on Saved Strategies from the menu at the top of the page.</p><p>Under Upload Search Strategy, click on Choose File to browse your computer for the fossil relative DNA sequences, which should be located in a folder on the desktop. Click Open on the Evolutionary_Relationships_Gene1 dot text file. Click View to go to the Standard Nucleotide BLAST search page.</p><p>You should be able to see the DNA sequence in the Query Sequence box on the top-right of the screen. Scroll to the bottom of the screen and click the BLAST button. It will take a few moments to process and analyze the data.</p><p>When the data has been processed, a graphic summary will appear. Your query sequence is represented by the blue line at the top of the box. Each of the lines beneath it represents another sequence in the BLAST database which matches your query.</p><p>The length and location of these bars represent where and how much of the sequences match up to the query. Here, many of the bars match the whole query sequence across its length, while some are missing a little at the beginning of the sequence. The color of the bar represents its score, or how identical the sequences are to the query.</p><p>Below the graphic summary is the Sequences producing significant alignments list, which contains descriptions of the DNA sequences retrieved from the database that most closely align with the query sequence. The sequences are listed in descending order, from the most similar at the top, to the least similar at the bottom. On the right are several statistics on how closely related each database sequence is to the experimental sequence.</p><p>The higher the Max, Total, Query coverage, and Identity scores are, the more similar the query and retrieved sequences are to each other. Likewise, the lower the E value number, the less likely the sequence match was found by random chance, and the more significantly the alignment is accurate. Here, you will notice all E values are zero, meaning the matches are all highly significant.</p><p>Click on the name of the description of the most similar alignment listed. This will take you further down the page to the exact DNA sequence alignment between the retrieved sequence and the query sequence. Then, click on the Sequence ID number.</p><p>This will open a new tab with more specific information on the retrieved gene sequence. Identify and record the scientific and common names of the organism, which should be listed next to SOURCE, and then the protein that the gene codes for, which should be listed next to DEFINITION. Then, close this tab and hit Back to return to the Sequences producing significant alignments list, and repeat this process to identify and record this same information for the next several most similar sequences.</p><p>After collecting several species names, go back to the Sequences producing significant alignments list and click Select:All to check all of the boxes next to the names of each listed alignment sequence. Click on Distance tree of results to create a phylogram based on the similarity of all of the BLAST result gene sequences to the query gene sequence. Your query fossil relative sequence will be highlighted in yellow.</p><p>Record your sequence's location in relation to the other taxon groups shown in the tree. Finally, return to the Saved Strategies tab and upload the next gene sequence, and then query the other two fossil relative DNA sequences as just demonstrated. Based on your gene sequence results, come up with a second hypothesis about where your fossil specimen fits in the original cladogram.</p><p>Compare this placement with the first hypothesis. How similar are your DNA and morphology-based trees in their placement of the fossil specimen? What do your hypotheses say about the relative importance of morphology in predicting evolutionary relationships compared to DNA sequences?</p><p>Compare your tree with your classmates. How similar are your trees? Ask your classmates who put the fossil on a different branch how they came to that decision.</p>

<ul><li><a href="#" data-time="0.0">Using BLAST to Test Evolutionary Hypotheses
</a></li></ul>

<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 do they differ?</h4><p>Cladograms and phylograms are the two main types of dendrograms. In a cladogram, the tips of the branches represent the species, and the branches simply show how they relate to one another. Nodes represent the last common ancestor. In a phylogram, the branches vary in length, with the length representing the amount of time that has passed since divergence from the last common ancestor.
</p></div><div class="section-question"><h4 class="question-sect">What are the two main types of data used to create dendrograms?</h4><p>Measurements or quantification of morphological and/or physical characteristics, or genetic data, may be used to construct dendrograms.
</p></div><div class="section-question"><h4 class="question-sect">What is bioinformatics?</h4><p>Bioinformatics is a combination of statistics, mathematical modeling, and computer science applied to biological information &#8211; like DNA or protein sequences.
</p></div>

Evolutionary Relationships: Using BLAST to Test Evolutionary Hypotheses - Prep

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

<p>Before beginning the experiments, open the BLAST website, ready for the students to use on each computer. Then go to the provided GitHub link to find the chicken, alligator, and zebra finch gene sequences provided. These will be used as the living relative DNA samples for the mystery fossil.</p><p>When clicked, the first sequence should look like this. Go back to the main screen and click on the clone or download button which appears in green and then hit download ZIP. Save the files on the computer desktop for the students to access easily.</p><p>Finally, print out enough copies of the provided blank cladogram so that there should be one per student with a few spares.</p>

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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 ...

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 ...

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

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

Evolutionary Relationships

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