![]() TipDate – depends on when isolated, i.e.Local Clock - default rate for all branches except for predefined branches.Global Clock – all braches have same rate (n-1) parameters ( (n-1) internal nodes).No Clock – each branch has an independent rate n sequences then (2n-3) parameters (branch lengths).1 A C T G 2 A C T G 3 A C A G 4 A C A CĪpplying a Clock “The molecular clock hypothesis postulates that for any given macromolecule (a protein or DNA sequence) the rate of evolution is approximately constant over time in all evolutionary lineages” Li 1997 Can be used similar to dating of geologic time using radioactive elements. Making a Tree: Methods (con’d) Maximum Likelihood: Best tree is most likely under model of the probability of mutations. Basis for determining tree topologies & branch lengths.High similarity strongly suggests homology.Predict character states of internal nodes.Making a Tree: Methods (con’d) n OTUs external nodes n-2 internal nodes Time Two methods to build trees: 1- Distance 2- Character.Making a Tree: Methods Phylogenetic Trees as NETWORKS Ancestral species vs. Making a Tree: Assumptions (con’d) Neutral Mutation Theory (Kimura and Ohta, 1974) 1- AA substitution rate is ~ constant 2- functionally less important evolves faster 3- deleterious and neutral more common 4- gene duplication precedes new function 5- deleterious and neutral mutation loss more often than positive beneficial fixation Making a Tree: Assumptions Natural Selection: 1- Hardy-Weinberg before selection 2- selection = survivorship (diploid) 3- Infinite population size Making a Tree: Basis (con’d) Mutations: 3 types 1- silent 2- missense (change in AA) 3- nonsense (termination codon) 4- indels- change length of codon Making a Tree: Basis Allele: alternative form of a gene N population size 2N gene copies (The video has a mouse, snake, squirrel, cat, monkey, elephant) After you have tried several rhymes, move onto the assessment section.Hickory Dickory Dock: Understanding the Molecular Clock Felisa Wolfe ERUPT: Biocomplexity Seminar Let's say the rhyme this time, but let's substitute a different animal and an different action word. This will help us remember which verb went with which animal. Since the word "run" is a verb, can you think of any other action words or verbs that describe how the animals in the video moved? Let's list these movements on the chart next to the the animal's name. If there was a fish in the video, we might say that the"fish swam up the clock." Swam is a verb. That means that these are words that describe how things move. ![]() Now that we have look at the video and made a list of all those animals, did you notice if they all "ran up the clock"? Do animals like cats and monkeys move in the same way? How about mice and elephants? Even if we said that they could all run, is that movement the same for each type of animal? This lesson includes a variety of animals and movement verbs. I really want the children to start to get a foundation for their language develop. Although they may be unable to read these words, they love expanding their vocabulary. My students love to use big, interesting words. ![]() What animals did you see? Did they all do the same thing? (yes, climbed the clock) I want you to remember this, so I have written down your responses on a chart. Play the video clip and have the children take notice of the different animals that come to climb the clock. The creator of the video changed a few things around from the nursery rhyme and I would like to see what you notice. Before we get to that, I have a short song video about "Hickory Dickory Dock". We are going to work with Hickory Dickory Dock again today, but we are going to focus on another piece about it. We worked on memorizing the rhyme and taking the poem and putting in the correct order. We have already been practicing the nursery rhyme of Hickory, Dickory Dock, but now we will focus on the idea of verb.īoys and girls, do you remember yesterday when we practiced the Nursery Rhyme, "Hickory Dickory Dock?" Let's say it now. When teaching a new concept, it is good practice to review something previously taught that can tie the children's schema to the new information.
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