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Name Lab Section GEOL 126 Lab 4 Building Trees Geol 126 Friday 2PM Nathan In Phylogenetics in the fossil record Why should we care about the evolutionary relationships of organisms alive today and organisms that have been dead for millions of years Phylogenetic trees are like your family tree complete with your whacky uncle but on a broad biological scale They emphasize the connectedness of all living things and are the fundamental building blocks that scientists use to understand biodiversity in deep time Without phylogenetic trees we would know a lot less about the timing and tempo of mass extinctions diversification e g speciation events and the dispersal of organisms across oceans and landmasses in the fossil record So as we ll learn in this lab building and reading trees gives you cutting edge tools for reading the extensive story of life as we know it When it comes to assessing the evolutionary relationships of fossil organisms our options are limited by the fact that DNA decays relatively rapidly after an organism dies The oldest DNA ever found is from 1 6 million year old mammoths found in permafrost which means that most organisms to ever live during Earth s 4 6 billion year history do not have any DNA preserved in their fossil record This means we must rely on the physical characteristics i e morphology of the remains of fossil organisms to assess their evolutionary relationships A Cast of Characters So how do we go about finding the right criteria to assess shared ancestry in long dead organisms We start by observing common physical traits in other words characters and recording differences in their morphology Below is a character table that illustrates the basics of assessing the presence and absence of traits among 4 different animals Building an evolutionary tree To build our tree a k a cladogram and assess who is more closely related to whom we will focus on the frequency of shared traits between each critter mouse bat robin carp that are tabulated above Examine the tree labeled A and compare it to the tree labeled B Which tree based on the character table above provides the best support for the evolutionary relationships of these animals Let s walk through the possibilities on the next page In Tree A the bat and the robin are shown to be the most closely related based on their shared trait of wings Tree A could be a plausible hypothesis of evolutionary relationships but it isn t the best i e most parsimonious tree because it suggests that the bat and the mouse independently acquired the presence of milk glands and hair OR that the robin lost the presence of hair and milk glands and acquired feathers This is a fairly complicated hypothesis If we look at the character table we can find a simpler hypothesis of the evolutionary relationships of these 4 critters First we observe that the mouse and the bat share 6 of the 7 possible character states presence of 1 lungs 2 four boney limbs 3 milk glands 4 hair and 5 Jaws absence of 6 Feathers On the other hand the robin and the bat share 4 of the 7 possible character states presence of 1 lungs 2 four boney limbs 3 Wings 4 Jaws The robin and the mouse only share 3 of the 7 possible character states presence of 1 Lungs 2 Four boney limbs 3 Jaws Lastly the carp only shares one character state with the other 3 critters the presence of jaws Based on those shared characteristics Tree B would be the tree that represents most parsimonious explanation for the evolutionary relationships of these critters Exercise 1 The Evolutionary Relationships of Candy We ll divide the class into four pods Your TA will pick four candy brands and pass representative specimens from each brand among each pod Each pod will use the space below to determine 4 characters that they observe in all 4 of their candy specimens Then using those characters your pod will determine the evolutionary relationships of the candy specimens Note the acquisition loss of character states homologues on their corresponding branches on the tree When every pod has completed their tree they will present their tree to the class and we will briefly discuss commonalities and differences between each pod s tree Helpful Terminology Clade a group of species descended from one ancestral species Phylogeny an evolutionary pathway Cladogram a hypothetical phylogeny Parsimony a parsimonious phylogenetic tree requires the least evolutionary change the fewest character state changes to explain all your observations Homolog ue Shared derived character evolutionary novelty Names of your pod members Nathan Grete Tour Character Table Character Candy 1 Candy 3 Candy 4 Candy2 Hershey s 100 Grand Milley Way Hershey s Cookies Milk 1 2 3 4 1 Stuff Inside V Candy Bar v V V N N n Cream White Chocolate x M Candy Phylogenetic Tree Hershey s Cookies a Cream 100 Grand Milky Way White Chocolate Caramel Hershey s Stuff inside camely Bar Milk Questions 1 What defined your candy clade as a whole The componentofMilkdefined our clade as a whole 2 Were any traits lost among your candy species No traits were lostamong our candy species 3 Was there any homoplasy independently derived characters as a result of convergent evolution cookies or Cream had an independently derived characteristic of white chocolate 4 What is your favorite candy species Hershey s Exercise 2 Assessing the phylogenetic relationships of animal groups Using the skills we have developed as a class determining the evolutionary relationships of candy we will now split among the four stations with specimens from different parts of the animal tree of life Your pod will choose one of these groups and use the same process of character selection scoring to sort out who is more closely related to whom among your group The four groups are as follows 1 Invertebrates 2 General Vertebrates 3 Reptiles and 4 Mammals Animal Group Mammals Character Table Taxon 2 Character Taxon 1 Taxon 3 Taxon 4 Polar Bear SubenTooth Dolphin Giant Extinet Beaver 1 2 HoleinFrontent W w r X Carnassial Tooth v WxX Teeth Function vrX Nostril Position X X v w Tearing Crushing 4 Head Muzzle X 3 Saber Tooth cast Dolphin Beaver I CHend Carnassial Teeth Phylogenetic Tree Polar Bear Nose Hole in front Questions ofeye socket 1 earing Teeth Nose Muzle 1 Which animals in your group shared the most character states How was this reflected in your evolutionary tree Polar Bear ISuber Tooth Cut 2 The outgroup is the animal that shares the least amount of character states with the rest of

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USC GEOL 126 - Lab 4- Building Trees

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