Lab 4 Reconstructing

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Isabella Moore Lab 4 Reconstructing Evolutionary Trees Phylogenetics is the field of study of evolutionary relationships and related methods, as used by biologists and paleontologists to reconstruct the relatedness among different species, populations and individuals. Although we often talk about phylogenetic methods for inferring relationships among different types of organisms, such as species of animals, plants and otherwise, phylogenetic methods are often used in various genetic analyses. Do you know anyone who had their DNA tested to figure out how they are related to someone else? Phylogenetic analysis is often used for that purpose, as well as figuring out the relationships among human viruses (like identifying different strains of COVID-19). Most phylogenetic methods take a large amount of character data, which are specific attributes or traits of organisms which are assumed to be potentially inheritable from generation to generation, or from an ancestral species to its descendants. Such characters can range widely in nature, from physical features to genetic sequences (such as individual base pairs), as well as behavioral traits and physiological properties. Extinct animals, such as non-avian dinosaurs, typically do not leave enough of their genetic material or other traces behind to do anything but use their physical characteristics of shape and form, also known as morphology , so to reconstruct how they are related to each other and to living species. Defining and tallying morphological characteristics requires less equipment and technical expertise than collecting genetic data, but does require a high degree of understanding about a group’s anatomy to recognize the many small differences in their structures and parts, as well as breaking complex differences down into multiple simpler characteristics. Each morphological character must be examined across all species to be analyzed, and the recording of the variation of each character as different states . Every variation of a given character is considered a different state of that character, with the simplest morphological characters simply having two states: the ‘presence’ or ‘absence’ of that feature. Once all the data is collected, phylogenetic trees can be constructed from the resulting character matrix . The aim to find trees that unite species together based on their shared character states. Most modern analyses computationally search the set of possible bifurcating evolutionary trees uniting a set of taxa, selecting the ‘best’ possible tree based on various criteria, with the most common criterion in paleontology being simply the trees with the smallest number of implied character changes, also called maximum parsimony . The resulting phylogenetic hypothesis typically lacks directionality, so the tree is rooted by always including one taxon in each analysis that is widely accepted as distantly related to all others, and thus can be assumed to provide information about the ancestral condition of each character. This taxon, known as the outgroup is used to root the phylogeny , which means the tree is drawn with first split in the tree being the split that separates the outgroup from all other species in the tree. Rooting a phylogenetic tree is important, as we should not group species based on ancestral traits, but rather based on those characters are shared and also derived , meaning they differ from the ancestral condition. For example, the ancestral dinosaur was likely bipedal, so we should not group two bipedal species such as Tyrannosaurus and Pachycephalosaurus based on that information alone. Groups identified through phylogenetic analysis of morphological data are considered to have strong support if they share multiple such shared derived characters, also referred to as synapomorphies .

Isabella Moore Lab 4 In this laboratory assignment, let’s be morphologists and define some characters that describe the arrangement and shape of the hip bones (also known as the ‘pelvic girdle’) of several vertebrates, record the states for each of those characters for a few taxa. We will use this information to mark character changes on several possible phylogenetic trees, and count how many character changes are necessary for each. Figures of the Vertebrate Hip At the end of the worksheet, you will find several images of the pelvic girdles for a number of vertebrates, oriented as seen from the side, where the leg bone attaches to the hip. On each hip, the three elements (ilium, ischium, pubis) are labeled. Note that the ilium is always more dorsal than the other three (closer to the back of the animal), and the pubis is always more cranial (closer to the head) than the ischium, which is instead more caudal (closer to the tail). Some of these figured hips also label the acetabulum , which is the socket for the hind-leg’s femur. The acetabulum is always present if a vertebrate has hind limbs, sometimes as a round depression or as a perforated opening, and the acetabulum is (almost) always located at the juncture of the ilium, ischium and pubis in terrestrial vertebrates. Some of the figures shown also have labels for other similar features such as the obturator foramen (an opening sometimes present between the ischium and pubis bones, which can get very small to non-existent in some animals) and the thyroid fenestra (a large gap between the ischium and Pubis, similar to the obturator foramen, sometimes in addition to the obturator foramen, or in replacement of the obturator foramen). Don’t worry about the distinction between the obturator foramen and thyroid fenestra in coding your character data. Pick Your Taxa 1) Choose five different vertebrate taxa whose pelvic girdle is shown at the end of the worksheet. You will analyze these five taxa as well as Icthyostega , a large amphibian that is the earliest and most distantly related of any of the taxa shown, and thus is the best stand-in for what a possible ‘ancestor’ of tetrapods looked like. Such ‘best guess for the ancestor’ taxa are often useful to include as outgroup taxa when we infer phylogenetic trees. (1 pt) A. (ingroup) - Tyrannosaurus B. (ingroup) - Stegosaurus C. (ingroup) - Alligator D. (ingroup) - Iguana E. (ingroup) - Dawndraco Icthyostega (outgroup) We recommend including taxa from both the bottom (dinosaurs) and the top (non-dinosaurs) of the sheet full of pelvic girdles.

Isabella Moore Lab 4 Pick Your Characters Paleontologists and other biologists who rely on morphology study the anatomy of organisms to define discrete traits which they call ‘characters’. These characters can be categorized as having different possible ‘states’, and then categorize different taxa (species) as having different ‘states’. Let’s take an example: the perforate acetabulum , a trait where the socket for the head of the leg’s 0femur actually thins to the degree that there no bone left in that socket, allowing those species that have a perforate acetabulum to have more mobility in their leg movement. This character exists across all the taxa – except in some species, the state is ‘perforate’ and in other species it is ‘not perforate’. This particular character is very binary – whether a species has a perforate acetabulum is a simple yes or no question with very little middle-ground. In Icthyostega , the taxon we have included for an idea of what the ancestor may have been like, the acetabulum is not perforate. The acetabulum is also not perforate in Eryops, Dimetrodon, the alligator, the iguana or Dawndraco . However, the acetabulum is perforated in Apteryx (the kiwi), Thescalosaurus, Tyrannosaurus, Stegosaurus, Diplodocus, and Velociraptor . 2) Below we have made a table for filling out with characters and their states. We have filled out the first character – whether the acetabulum is perforated or not, and described what the two possible states are. Come up with four different characters that describe variation in the form or arrangement of the bones that make up the hip of your five selected taxa. List these characters and their states below. Note that while I only give you room for listing four states, this was arbitrary and feel free to define characters with more than four states. (5 points) Character Description State 1 State 2 State 3 State 4 Char. 1 Orientation of the pubis relative to the ischium Pubis angled forward Pubis angled backward Pubis parallel to ischium Char. 2 Shape of the ilium crest: Crest projects cranially Crest projects caudally Crest projects dorsally Char. 3 Presence of a pre-pubis: Pre-pubis present Pre-pubis absent Char. 4 Shape of the acetabulum Round/circular Irregular and non-round Oval Elliptical Char. 5 Perforation of the Acetabulum Not perforated. Perforated. Preferably, when defining characters, you should select features that are shared by two or more of the hips in the ingroup, but are not shared by our ‘ancestral’ outgroup, Icthyostega . Those are the sorts of characters that are most useful for reconstructing evolutionary relationships. The perforate acetabulum might be such a character depending on which taxa you have chosen to analyze. Some example characters that you may feel free to ignore or steal, if they are applicable: the shape of the ilium (triangular, long and blade-like, crested, etc); ilium crest projects in a cranial direction or caudal direction or dorsally (‘upwards’); presence of an opening between the ischium and pubis; pubis is made of cartilage rather than bone; pubis angled forward or backwards making it parallel to the ischium; pubis has a ‘boot’ making it look like an upside down T; presence of a pre-pubis;

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Isabella Moore Lab 4 acetabulum is round/circular or irregular and non-round 3) Now fill out the character matrix below for your five characters, listing the respective state (which state number does this taxon have?), for each of your five selected vertebrate taxa. Your first character should be whether the acetabulum is perforated, so this state is already filled out for our outgroup, Icthyostega . (10 pts) Taxon Name Character 1 Character 2 Character 3 Character 4 Character 5 Taxon A Pubis angled forward Crest projects cranially Pre-pubis absent Round/circular acetabulum Taxon B Pubis angled backward Crest projects dorsally Pre-pubis absent Irregular and non-round acetabulum Taxon C Pubis parallel to ischium Crest projects cranially Pre-pubis present Oval acetabulum Taxon D Pubis angled forward Crest projects caudally Pre-pubis absent Round/circular acetabulum Taxon E Pubis parallel to ischium Crest projects dorsally Pre-pubis absent Elliptical acetabulum Icthyostega Not perforated. Mapping and Counting Character Changes 4) Below are four phylogenetic trees showing possible relationships among your six taxa. For each tree, map each character onto that tree – you can do this on the tree shown, or on a separate sheet of paper, or in your head). Typically, scientists do this ‘mapping’ by marking each branch where the state of that character changes with a dash. We can then count up the number of dashes to obtain the number of state transitions among tip taxa. Note that you do NOT need to show us these character mappings For example, consider if we were mapping the perforate acetabulum onto a tree with four taxa: Icthyostega , Dimetrodon , Stegosaurus and Velociraptor – note that only the last two are perforated. Then for two different phylogenetic hypotheses, we might map that character as such: In the above, only one character state change is needed to explain the known distribution of the perforated acetabulum in the first tree. In the second phylogenetic hypothesis, at least two character

Isabella Moore Lab 4 changes occurred: the dashes shown imply the perforated acetabulum is gained in the lineage leading to Velociraptor and Stegosaurus independently. Alternatively (not shown), the acetabulum was perforated in the lineage that was ancestral to Velociraptor , Stegosaurus and Dimetrodon , and the acetabulum became closed (unperforated) in a reversal on the lineage leading to Dimetrodon . Note that when mapping characters, we try to find the scenarios that require fewer changes of the character states rather than more states. There’s no strong historical reason for this (evolution can be as complicated as it wants to be, and it can often be very complicated), but scientists that work on phylogenetic relationships use the difference scenarios that imply the least character change to compare and contrast different evolutionary trees – this is the maximum parsimony mentioned at the start of this lab assignment. Once you’ve done these mappings for each character, count up the number of times that character changed on that specific tree and enter that number in the table below . Do this for all characters, on all trees, and then add up the total number of character changes observed on each tree. (10 pts) Phylogenetic Tree 1 Phylogenetic Tree 2 Phylogenetic Tree 3 Phylogenetic Tree 4 Number of Character State Changes for Character 1 0 0 1 1 Number of Character State Changes for Character 2 0 1 0 1 Number of Character State Changes for Character 3 0 0 0 1 Number of Character State Changes for Character 4 0 1 0 1 Number of Character State Changes for Character 5 0 0 0 0 Sum Total Number of Character State Changes 0 2 1 4

Isabella Moore Lab 4 5) Which of the four phylogenetic hypotheses infers the fewest character state changes? This is the most parsimonious tree (of the four we considered) and would be considered the best supported hypothesis under parsimony. (1 pts) Tree #3 has the least amount of changes of character state. This tree only has one character state change. 6) Create your own tree for these taxa. It cannot be identical to one of the four trees you just measured (but you can use those as inspiration) and it should be fully bifurcating (all lineages should split into two child lineages, such that there are no polytomies). Keep Icthyostega as an outgroup, so that the first split of your tree separates Icthyostega from the rest of the taxa in your analysis. Use what you’ve learned about your characters and the taxa involved to challenge yourself to find a tree that has fewer character state changes than the previous four. Paste an image of your tree below. (5 pts)

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Isabella Moore Lab 4 7) Using the tree you drew, map each character onto that tree, count the number of character state changes for each character, and count up the total number of character state changes. (1 pt) Phylogenetic Tree 5 Number of Character State Changes for Character 1 1 Number of Character State Changes for Character 2 1 Number of Character State Changes for Character 3 1 Number of Character State Changes for Character 4 1 Number of Character State Changes for Character 5 0 Sum Total Number of Character State Changes 4 8) Which phylogenetic hypothesis (of trees 1-5) is now the best supported tree under maximum parsimony? In a few sentences, describe the similarities and differences between your two most parsimonious trees (the “winner” and the “runner up”). Include information about sister taxa, monophyletic groups, and character changes in your description. (7 pts) As we see in question #7, the Phylogenetic Tree 5 is the most parsimonious hypothesis when compared to the other trees. This tree requires 0-character state changes. The tree’s optimal arrangement places the sister taxa based on the shared characteristics. When comparing tree 5 to the others, the others have to make more changes due to different taxon arrangements. Tree 5 is the only tree that provides a clear picture of evolutionary relationships. This makes it the best supported hypothesis under maximum parsimony. Caption for Pelvic Girdle Images Most of the pelvic girdles shown on the following page are taken Figure 9.22 from Kardong, based on Romer and Parsons. Note that one figure ( Dawndraco ) uses abbreviations for labels: the abbreviation ‘il’ indicates the ilium, ‘is’ indicates the ischium, ‘pu’ indicates the pubis, and ‘ac’ indicates the acetabulum. The Diplodocus and Stegosaur pelvises use colors: the bone in yellow is the ilium, the blue bone is the ischium and the red bone is the pubis. Key to Taxonomic Names Not in Common Use Dimetrodon → Quadrupedal Permian carnivore with a large sailback Thescelosaurus →Small Late Cretaceous herbivore, relative of Iguanodon Apteryx → Modern Kiwi (small ground-dwelling bird) Icthyostega → Aquatic quadrupedal Devonian carnivore Eryops → Quadrupedal semi-aquatic Permian carnivore Dawndraco – An early flying Pterosaur

Isabella Moore Lab 4

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