ANTH 270 Lab 3 Worksheet (1)

docx

School

University of Oregon *

*We aren’t endorsed by this school

Course

270

Subject

Anthropology

Date

Apr 3, 2024

Type

docx

Pages

Uploaded by GeneralSpider4171

Anthropology 270 Lab 3: Cladistics and Evolutionary Relationships Name: Diego Ryan Section Time: Thursday at 4PM Part 1: Introduction (read this before coming to labs) Humans are very good at recognizing patterns, which makes our species particularly fond of categorization and organization. To make sense of the natural world humans have long attempted to organize, catalog and classify Earth's “endless forms.” One of these famous organizers was the Swedish botanist and zoologist, Carolus Linnaeus. Known today as the Father of Modern Taxonomy, Linnaeus formalized the Latin-based naming system ( binomial nomenclature ) for categorizing plants, animals, and “minerals.” Although many of Linneaus’ original classifications have been reordered thanks to advancements in technology (e.g., we now know that manatees and whales are mammals, not fish), he was the first to correctly classify humans within the taxonomic order Primates, and was the first to classify bats as mammals (not birds). Another approach to biological classification, cladistics , focuses on grouping organisms based on shared derived traits (i.e., novel evolutionary traits that are unique to a particular species and all its descendants) in order to infer their "true" evolutionary relationships. These groupings are often visualized as a cladogram, or tree . Trees generally follow the Law of Parsimony , a scientific principle that states that the simplest explanation is the most likely, and therefore best, explanation. For example, if all members of a group were blue, the simplest explanation would be that they are blue because their common ancestor was also blue. In this case, the blue trait evolved once in the common ancestor and was passed on to all of its' descendants. To say that the blue trait evolved separately in each lineage is more complex and, therefore, less parsimonious. When organisms share a trait that was inherited from a common ancestor (e.g., the blue trait from the example above), the trait is called a homology . For example, although the arms of bats, humans, whales, and cats look very different on the outside (reflecting differences in locomotion), the bones on the inside are homologous. This is because they inherited these bones (i.e., humerus, radius, ulna, carpals, metacarpals and phalanges) from a common mammalian ancestor who possessed them. Trees made from homologous traits are called phylogenies . Phylogenies reflect evolutionary relationships because they are based on inheritance and common descent. It is important to note that not all trees show the “true” evolutionary history of organisms. Just because two species look alike or possess the same trait does not mean that they inherited that trait from a common ancestor. For example, both bats and birds can fly and have wings , but they did not inherit wings from their common ancestor. The bat-bird common ancestor did not fly or possess wings. Similarly, whales and seals are both aquatic mammals that possess flippers, but they didn’t inherit flippers from their common ancestor (their common ancestor was a terrestrial mammal). When organisms share a trait, but did not inherit it from a common ancestor (e.g., bat and bird wings), the trait is called an analogy . Analogous traits can arise through reversals (i.e., when a previously gained trait is lost) or convergent evolution , which occurs when species occupy the same ecological niche or live in similar environments (e.g., both whales and seals live in the ocean). Because analogies do not reflect evolutionary relationships, these traits should not be used to build trees! 1

In-Class Lab Activity During lab today you will watch Tree Diagrams and discuss how to build and interpret phylogenetic trees. Once we are familiar with making trees, we will put those skills to the test! For this lab activity we will be making two different types of trees; a cladogram based on phenotypic data (Part 1), and a phylogeny based on genetic data (Part 2). Part 2: Building a Tree from Phenotypic Data First, take a look at the 7 animals in the Lab section of our Week 3 module. The table below shows the presence/absence of 9 traits across the 7 mammals. Using only these traits, make the most parsimonious tree. You’ll need a piece of scratch paper and pencil. Hold onto your tree for the next step, but you will not turn in the tree. Your tree must abide by the following rules: 1. Your tree must be dichotomous (i.e., each branch of the tree must be split in two, usually with the organisms on one branch having the trait and the organisms on the other branch not having the trait), 2. You must put labeled tick-marks on the branches of your tree showing which traits you used to make your groupings (remember that all organisms past the tick-mark have this trait), and 3. Each branch of your tree must ultimately end in one species (i.e., each of the 7 mammals will end up on its own branch at the tip of the tree). Table 1. Presence or absence of 9 traits (rows) across the 7 mammals (columns) Trait Echidna Pangolin Slot h Armadillo Porcupine Lio n Human Produces milk Yes Yes Yes Yes Yes Yes Yes Live birth No Yes Yes Yes Yes Yes Yes Teeth No No Yes Yes Yes Yes Yes Fused ischium/sacrum No No Yes Yes No No No 4-chambered stomach No No Yes No No No No Tooth enamel No No No No Yes Yes Yes Continuously growing incisors No No No No Yes No No Increased sociality No No No No No Yes Yes Opposable thumb No No No No No No Yes 2

Part 2: Building a Phylogeny from Genetic Data Sometimes different datasets yield different results. This is especially true when making trees, as phenotypic data and genetic data can sometimes tell different evolutionary stories based on the specific combination of traits or genetic loci used. Here we will incorporate the genetic data from these 7 mammals to build a phylogeny showing their evolutionary relationships. We will then compare the trees that we made using the different datasets. To help you visualize this genetic data (in the form of nucleotide sequences), we have provided a table showing the first 15 nucleotide bases of a gene from each species below: Table 2 DNA sequences (rows) for 7 Mammals Echidna C A A T T C T G G C C G T C C Pangolin T C A T A G T C G T A T T A G Sloth C T A T G G T C G T A G T C T Armadillo C T A T G G T C G T A G T C T Porcupine T G A T C G T C G T A C T C A Lion T C A T A G T C G T A T T A G Human T G A T C G T C G T A C T C A You will notice that the colorful nucleotide sequences from the table above have been converted to FASTA format in the box below. FASTA format is a popular format for displaying sequence data and is required by many phylogenetic programs like the one we will use today. Table 3. Multiple Species Alignment for 7 Mammals. >Echidna CAATTCTGGCCGTCC >Pangolin TCATAGTCGTATTAG >Sloth CTATGGTCGTAGTCT >Armadillo CTATGGTCGTAGTCT >Porcupine TGATCGTCGTACTCA >Lion TCATAGTCGTATTAG >Human TGATCGTCGTACTCA 3

Your preview ends here

Eager to read complete document? Join bartleby learn and gain access to the full version

Access to all documents
Unlimited textbook solutions
24/7 expert homework help

1. Go to Simple Phylogeny . 2. Copy the entire multiple sequence alignment from the box above and paste it into the text box under “ STEP 1 - Enter your multiple sequence alignment. ” 3. Under " STEP 2 - Set your Phylogeny options, " change the clustering method to "UPGMA." 4. Click the “Submit” button under “ STEP 3 - Submit your job. ” A phylogeny showing the evolutionary relationships of these 7 species will show up on your screen in under 1 minute! 5. Again, keep your tree because you will need it to answer the questions below. However, you will not be turning in your trees. Part 3. Questions After you have completed the activity above, answer the following questions. You will need the trees you generated during the activity above to answer these questions. Use proper spelling, grammar and complete sentences. Each question will require about 1 paragraph. You can work as a group, but each person will turn in their own lab worksheet. You do not need to turn in your trees, but you will need to have completed them before answering the questions below. 1. How do the two trees compare to each other? What might be the benefit of looking at both phenotypic features and genotypes for establishing evolutionary relationships? The phonotype tree has lions being the closest relative to the humans. The genotype has the lion being more closely related to the pangolin and a human being closer related to a porcupine. The benefit of looking at both phenotypic features and genotypes is that we can follow closely and look to see who we share relationships with. We can also see that the genotype can give a clear genetic make-up of the development of different species. 2. Based on the character matrix (Table 1), all 7 mammals produce milk. Would it be more parsimonious to say that milk production is a homology or an analogy? Why? Milk production would be more a homology because all mammals had different functions and environments where they lived so milk production couldn’t be from evolution. This means milk production had to be inherited by a common ancestor since it has to be passed down and it’s coded in their DNA. 3. Both pangolins and armadillos have scales made of keratin (a protein that makes hairs, nails, horns and feathers). However, the gene tree (phylogeny inferred from genetic data) revealed some interesting evolutionary relationships. Given the results of your gene tree, are keratin scales a homology or an analogy? What would explain the appearance of this trait in these two lineages? Given the results of my gene tree keratin scales are a homology because many mammals hair is composed of keratin so it’s similar to milk production to where it has been passed down from generation to generation. The difference in appearance could be from from slight changes in dna due to their environment and what they need to live. 4

4. According to your gene tree, which species are more closely related: porcupines and humans or humans and lions? Explain how you came up with this answer. According to my gene tree the species that are more closely relates are humans and porcupines. I choose this because in the gene table humans and porcupines both have the exact same nucleotide sequence given the ones provided. This differs from the lion and human because humans and lions have slight difference in their nucleotide sequence provided. Website links noted in this Lab Worksheet: the arms of bats, humans, whales, and cats : https://qph.fs.quoracdn.net/main-qimg-1a9a91af16c994c5fe7fb1b5742840fe both bats and birds can fly and have wings : https://evolution.berkeley.edu/evolution-101/the-history-of-life-looking-at-the-patterns/homologies- and-analogies/ Tree Diagrams : https://learn.genetics.utah.edu/content/evolution/diagrams labeled tick-marks : https://cdn.kastatic.org/ka-perseus-images/491900ea3016ffa58693d3a4a8b594706661f648.png FASTA format https://blast.ncbi.nlm.nih.gov/Blast.cgi? CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp Simple Phylogeny : https://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny/ 5

ANTH 270 Lab 3 Worksheet (1)

Related Documents