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Explore the evolution of dinosaurs in the tree of life. Learn how to use BLAST and MAB Phylogeny Analysis to place the T-Rex in relation to modern animals. Understand phylogenetics, read phylogenetic trees, and discover where extinct animals fit in evolution. Unravel the mysteries of T-Rex classification using cutting-edge bioinformatics tools.
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What we know so far.. • We already know how scientists were able to use mass spectrometry to identify peptide sequences from the bone of a Tyrannosaurus rex. • In Activity 3-BLAST we learned how peptide sequences can help identify the animal, as well as the animals most closely related to it. • We also learned how to use bioinformatics tool (BLAST) to compare DNA or protein sequences among animals.
Today’s goal • Using BLAST and MAB Phylogeny Analysis, we can determine how the T. rex is related to present-day animals. • The final result will be your own phylogenetic tree depicting how animals relate to each other.
What you will learn • What is phylogenetics? • Why is phylogenetics important? • How do you read a phylogenetic tree? • What is MAB?
What is phylogenetics? • Phylogenetics is the study of evolutionary relationships among a set of taxa. • Taxa(taxon for singular) refers to one or more groups of organisms. • For example, primates could be a taxa referring to all monkeys and apes. However, monkeys on their own could also be a taxon. (taxa classification to the left) • Evolution is the natural process in which taxa diverges from its ancestors to form new groups of animals.
Why is it important? Phylogenetics allows scientists to understand how organisms are related, how to classify living things, and how certain features evolved. Understanding these relationships is beneficial in conservation of species and ecosystems, as well as biomedical research.
How to read a phylogenetic tree To the left is a basic phylogenetic tree, sometimes called a cladogram. The symbols at the bottom of the tree represent the taxa that have evolved (called tips). • The animals at the bottom of the tree represent the taxa (groups of plants or animals) that have evolved (called tips) • The marks a node as well as the most recent common ancestor(MRCA) to the taxa it’s connected to. A node is the MRCA and all of its descendants, or the letters that follow the branches. • The branches are the physical lines that connect ancestors to their descendants. • The marks the root of the tree, where the shared common ancestor of all taxa is found.
Example of phylogenetic trees The numbers on each node are depicting the specific trait that has evolved in this new lineage. #1 is depicting that every group of animals after this point has jaws. After #2, all animals have developed lungs. For example, lizards have claws/nails and lungs, but they do not have fur or feathers. 5. 4. 3. 2. 1.
Example of Phylogenetic trees Sister clades (or groups) are the most closely related taxa on the tree. Here, chimps are sister to mice. The outgroup is the most distantly related group to the rest. On this tree the outgroup would be hagfish.
Vertebrate Phylogenetic Tree Before creating your phylogenetic tree, it is helpful to understand a few main characteristics of the animals on the tree and the groups they belong too. There are five main groups of vertebrates: mammals, birds, fish, reptiles, and amphibians. • Mammals are classified by the presence of hair, mammary glands, and they must be endothermic (“warm-blooded”). • Birds are classified by the presence of feathers, and toothless-beaked jaws. • Fish are classified by uptaking oxygen through gills, ectothermic (“cold-blooded”), and live in water. • Reptiles are classified by being covered in scales, ectothermic, and breathing with lungs. • Amphibians are classified by permeable skin, ectothermic, and they live part of their lives in the water and part on land.
Where does the Tyrannosaurus Rex fit in? • Recent studies show that the T-Rex might have been mesothermic, which is a mixture of warm-blooded and cold-blooded. They were capable of internally adjusting their body temperature, but not to the same extent as birds and mammals. (LA) • Scientists also believe that the T-Rex had scaly skin, rather than feathers. • The main difference that sets the T-Rex apart from lizards and amphibians is their large size. The T-Rex was up to 40 feet long and 15 to 20 feet tall, whereas the largest lizard is a mere 10 feet, but on average are less than a foot long. This leaves scientists with one main question, is the T. rex more closely related to birds, reptiles, or crocodiles?
Where does the Tyrannosaurus rex fit in? (pt. 2) Using MAB (Methods and Algorithms for Bioinformatics) you will discover where extinct animals, like the T-rex fit in evolutionarily with modern animals. Follow the instructions on the PDF to learn how MAB works, and to create your very own phylogenetic tree using peptide sequences.
