Learning Activities: The Tree of Life

| Ecological Niche Modeling of Florida Temperature Changes and Endangered Rabbit Survival |

 

Ecological Niche Models (ENMs) can be used to show many biological and environmental relationships. Applications can be used to promote conservation of species by making predictions of the future status of organisms due to climate changes, environmental changes and human impact. The Florida Marsh Rabbit is a species of concern while a subspecies that is native to the Florida Keys – Sylvilagus palustris hefneri – is endangered. This rabbit lives in shallow water environments. This species of rabbit may be adversely impacted by changing water levels along Florida coasts. Layering information on Florida sea level data with marsh rabbit abundance data may show a relationship between the productivity of the marsh rabbit. Since the Florida Keys subspecies is now endangered, it would be expected that data shows a greater impact due to more intense sea level change in that region of Florida. QGIS 2.18 software program will be used to analyze and layer data with maps in order to unite multiple data bases. Students will learn that many data bases containing useful information for scientific analysis are available for public use as well as a model example of how such databases may be used for research application.

 

Grade: High School

Author: R. Allen

Program: Tree of Life 2018

| How Biodiverse Is Your Environment? |

 

Students will identify as many plant species in a given area. The NCBI BLAST site will be used to find the DNA sequence for the gene rbcL which is common to most plants. The DNA sequences will then be uploaded into the Mega site which will generate a phylogenic tree showing the relationships of the plants in the area.

 

Grade: High School

Author: R. Bartenslager

Program: Tree of Life 2018

| Identifying and Acting To Mitigate an Environmental Problem  |

 

Students identify an enviromental problem of personal concern, research the topic, plan an action to help resolve/mitigate the problem, carry it out, write it up, and present it.

 

Grade: High School

Author: B. Breil

Program: Tree of Life 2018

| The Use of Natural History Collections Data to Learn About Ecosystems and Biodiversity |

 

This activity aims at engaging students in learning about species distributions, co-occurrence and conservation using institutional collections of data. A computational tool called iDigBio can be used to show on a map the spatial distribution of species through georeferencing. Gray bat whose scientific name is Myotis griserscens (mammal) is one of the endangered and threatened species in Florida. Using the provided data, students are going to use iDigBio to see how spatially distributed these species are hence analyze the data and come up with ways to protect them.

 

Grade: Middle School

Author: J. Chiomadzi

Program: Tree of Life 2018

| Kissing Cousins? From Cladogram to Phylogenetic Tree |

 

Kissing Cousins? From Cladogram to Phylogenetic Tree is a collection of activities that may be completed in class, assigned as homework, or a combination of the two. A variety of methods and resources are presented that can be used to clarify the concepts of evolution and the methods used to support the ideas of evolutionary relationships. NOTE: The computational analysis section is designed to facilitate the use of Chromebooks, therefore the analysis of DNA sequences requires internet access.

 

Grade: High School

Author: L. DeLuera

Program: Tree of Life 2018

| Plant Phylogenies Pathway through Florida |

 

Evolutionary biologist Theodosius Dobzhansky once said, “Nothing in biology makes sense except in the light of evolution.” Phylogenetic trees are means of hypothesizing the evolutionary relatedness of life. Consequently, a corollary was developed saying that, “Everything in biology makes more sense in light of a tree of relationships.” Using common Florida species native to a specific locale (in this case, Seminole County was used), students will explore evolutionary trends by developing phylogenetic trees and homology tables using sequence alignment tools. Each student groups’ species list will be a subset of a larger class set. Groups will have overlapping information and will see how their trees compare based on species differences. In summary of the activity, the class will attempt to compile their data into one larger tree; the result is that students will see that science doesn’t always involve clean data and emphasizes the need for more powerful computational methods to handle the vast amount of data available.

 

Grade: High School

Author: W. Furiosi 

Program: Tree of Life 2018

| DNA to Phylogeny |

 

DNA is universal. Every living organism on earth shares the same molecules, including DNA. The same processes are used by all living things in order to grow, reproduce, metabolize, etc. The Human Genome project mapped all of our genes and since then we can determine which genes are responsible for which traits. This has led to amazing medical treatments and will continue to do so. Because of the universality of genetics, genes can be swapped between organisms, evolutionary relationships can be seen, medical advancements have been made. Restriction enzymes have been used to cut and paste genes within an organism’s genome. DNA can be extracted and used for medical research, forensics and showing evolutionary relationships. All of this can lead to a better understanding of ourselves and how the rest of the living world works.

 

Grade: High School

Author: C. Goldenberg

Program: Tree of Life 2018

| Using DNA data to Generate Phylogenetic Trees |

 

This activity can be a stand-alone activity to demonstrate how DNA sequence is used to generate a phylogenetic tree. The intended use of the lesson is as a final activity of a Comparative Proteomics unit that explores alternative methods for analyzing evolutionary relationships between various species of fish. Students will first analyze potential evolutionary relationships based on environmental niche and morphology. Generating protein profiles using extraction and SDS-PAGE becomes a second method for considering species differences that students can utilize to develop their own cladograms. As a final activity, DNA and a web based bioinformatics tool will be used to generate a final version of a phylogenetic tree. DNA can be isolated and used for sequencing, the DNA sequence used in the online tool DNA Subway. Alternatively, DNA sequence obtained from NCBI can be loaded. Students can generate DNA sequence to be analyzed using NCBI-BLAST. DNA sequence for mitochondrial cytochrome c oxidase 1 gene for six common fish is provided. Cytochrome c oxidase was chosen because of its use in DNA barcoding.

 

Grade: High School

Author: K. Kehoe

Program: Tree of Life 2018

| DNA,RNA, and Protein Synthesis |

 

DNA is the carrier of the genetic information that determines everything about living organisms. Everyone’s hair color, height, blood type and skin color are all determined by the DNA. To convert the information from the DNA to the characteristics in the genes, a process referred to in biology as the “central dogma” occurs. This process involves the transcribing of DNA into RNA, and then the translating of RNA into a protein.
DNA is made up of building blocks called nucleotides. The nucleotides are made of nitrogen bases called Adenine, Thymine, Cytosine, and Guanine, (A, T, C, G) whose arrangements will determine the types of genes found in living organisms. Translating the DNA sequences into an amino acid sequence which are the building blocks of proteins will determine the expression of a gene.
The activity in this lab involves a simplified way of transcribing DNA to RNA, and then translating RNA into a sentence that would represent an amino acid sequence that results in a protein. Following the simplified hands on activity, a computational method, BLAST, will be used to illustrate the process in a “real world” manner using a real DNA strand from a national database and translating it to a protein found in various animals. By observing similar animal species with this specific protein, and preparing a phylogenic tree using these animals, one could identify the relatedness of different organisms in the Tree of Life.

 

Grade: High School

Author: M. Lawrence

Program: Tree of Life 2018

| Ecological Niche Modeling: What Processes do Scientist Use? |

 

Ecological niche modeling is a method of using digitized species information, perhaps from collections, and making maps of a biological species’ potential distribution. Using technology allows scientists to use large data sets to get more accurate models as data is added. Ecological niche mapping is a means of showing speciation and biodiversity. Modeling thousands of species and piling distribution maps on top of each other allow scientists to get species richness data. In addition, scientists can compare current and future data models to make predictions on species distribution based on climate models or other ecological projects. It is important to note that ecological modeling looks only at the organism’s fundamental niche. Interactions with other organisms and other elements may not be considered. In this activity, students will simulate actual processes used by scientists to create ecological niche predictive models. This is a computer-based activity.

 

Grade: High School

Author: V. Ledford

Program: Tree of Life 2018

| Ecological Niche Modeling for Hula Hoop Ecosystems |

 

Biodiversity is not limited to large scale ecosystems, scientists can measure species diversity in small areas. An organism serves roles in their ecosystems through and are indirectly connected to the abiotic and biotic materials/beings with the ecosystem. Phylogenetic trees help scientists predict the degree of relatedness between organisms and can help indicate relationships evolutionary relatedness or coevolution among organisms in similar environments. In this activity, students will use a hula hoop to mark a random area of land from which they will collect data to identify small scale biodiversity, species relatedness, and then map the locations of those organisms within the given area. Students will also produce a cladogram or phylogenetic tree to demonstrate how relatedness among the organisms.

 

Grade: High School

Author: L. Mabour

Program: Tree of Life 2018

| Can We Predict Invasive Species |

 

Invasive species can harm the environment, the economy, or even human health. How can an invasive species so easily take over? Can we predict invasive species? In this activity students will use QGIS and Maxent software to model niches and distributions of a chosen species in their native habitat. The model expresses a probability distribution where each grid cell has a predicted suitability of conditions for the species. Students will then analyze other regions using the same bioclimatic variables to determine if their chosen species could potentially inhabit the new region or become invasive.

 

Grade: High School

Author: E. Miller

Program: Tree of Life 2018

| Branching Out: Using NCBI, BLAST, and MEGA to Construct a Phylogenetic Tree |

 

In this lesson, there are two different levels available for students: a basic application (part 1) and a more difficult extension (part 2). In part 1, students will use a data set provided (FASTA formatted nucleotides) to BLAST in the NCBI database to find homologs (homologous organisms) to make a phylogenetic tree using blast. In part one, students may choose to do an extension where they find the common name and images of the organisms to add to the tree. In part 2, students will do an extension where they locate a different common gene and find the nucleotide sequence to BLAST and make a new phylogenetic tree.

 

Grade: High School

Author: J. Rankin and C. Reedy

Program: Tree of Life 2018

| Understanding the Tree of Life: A Framework for Building Ecosystem Resilience |

 

This lesson plan explores biodiversity and its role in sustaining life on Earth. It begins by introducing students to the key concepts in ecology, biology, and environmental science at the root of speciation and natural selection, and leads them into engaging collaborative learning group activities on interdependence. Students will develop a conceptual understanding of this lesson by participating in a guided classroom discussion on TreeTender- a short film advocating eco-awareness and the significance of phylogenetic diversity and the environmental-societal factors threatening the health and balance of Earth’s system. This type of open dialogue and debate over these topics will allow students to construct and share their knowledge of what they believe is contributing to the current state of our planet, and our planet’s response to these conditions. To emphasize the importance of building ecosystem resilience, students will then move into an eco-survey of endangered species to demonstrate how human activity and the degradation of suitable habitats is interfering with the distribution and diversification of ecological communities.

 

Grade: Middle School

Author: M. Rivas-Reyes

Program: Tree of Life 2018

| Using Computational Biology  |

 

Students will have previously done an activity with Land use’s around their neighborhood and compare maps created by their peers prior to watching tree tender. Categories for land uses will be constructed by each group. Students will create a class mural on long sheet of paper and incorporated ecosystems services . Groups will be assembled per categories ex: parks and recreation, power and waste water treatment plants, how to deal with trash etc. visual representations on small pieces of papers and select areas to “place” their land use on the class mural. As each group attaches their specific land use members will explain the pros and cons of choosing specific sites. A lottery system will be devised so first come first serve. An extension of this will be to explore the term ecosystem services.

 

Grade: High School

Author: M. Torres

Program: Tree of Life 2018