Tutorial 2 Student Guide Phylogenetic Trees Summer 2020 PDF

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Download Tutorial 2 Student Guide Phylogenetic Trees Summer 2020 PDF

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Biology 1M03

TUTORIAL 2| PHYLOGENETIC TREES Student Package Objectives

● Be able to use morphological and molecular information to construct phylogenetic trees. ● Be able to discuss the advantages and disadvantages of various methods for creating phylogenetic trees.

Preparation

; Read the Introduction in this lab manual. ; Read section 25.1 (pages 514-520) from Biological Science 3rd Canadian Edition. ; Read Bioskills 11 in the Bioskills section at the back of Biological Science 3rd Canadian Edition (B42  B43). ; View the pre-lab AVENUE Powerpoint lesson. ; Complete the AVENUE pre-lab quiz.

INTRODUCTION: Evolutionary theory postulates that organisms on earth are related by common ancestry, which inevitably results in species with common characteristics. The evolutionary history of a group of organisms is known as a phylogeny and can be illustrated in the form of a phylogenetic tree. This is a means of depicting ancestor-descendant relationships and who is related who (Freeman, 3rd Canadian edition section 25.1). The cladistic approach to deriving phylogentic trees is based on identifying shared, derived characteristics (or synapomorphies) in the species being studied. Morphological traits that consist of the shape and appearance of an organism’s body and counterparts, is one method of identifying derived characteristics that can then be used to create a phylogenetic tree to relate the species. Derived traits can also be identified by observing phenotypic characteristics. The cladistic approach relies on accurate observation and determines visible or observable differences between the species. Observable changes in morphology are the end result of changes happening at the gene level. Mutations in DNA can result in changes in the function of the encoded protein which can then bring about changes at the cellular and morphological level. With the advent of techniques that allow rapid sequencing of the DNA of many organisms, changes in the DNA sequence of a particular gene or conserved region of DNA can also be used to derive phylogenetic trees. In addition, the use of DNA sequences as the basis for determining phylogenies also allows the determination of “genetic distance” between the different species. This is a measurement of the average percentage of bases in a particular DNA sequence that differs between two species.

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The ability to taste some or all of the five basic tastes will be used to create phylogenetic trees during this week’s tutorial. It is currently believed that mammals are only able to distinguish between a maximum of five different tastes. These tastes are classified as bitter, salty, sour, sweet, and umami. Umami is the associated with the enhanced tasting sensation of compounds that contains glutamate when mixed with ribonucleotides that are often contain in meats. A recent decision to include umami as one of the five basic taste was the result of the discovery of a receptor for umami in taste cells (Reed and Knaapila, 2010). PTC is considered to be a bitter substance. Many primates have derived the ability to be non-tasters. PRE-TUTORIAL ASSIGNMENT In lecture you will have discussed phylogenetic trees (Freeman, 3rd Canadian Edition, section 25.1), for a review of the terminology watch the PowerPoint presentation entitled “Phylogenetic Trees: PowerPoint Lesson”. Complete the pre-lab AVENUE quiz which contains information about creating and interpreting phylogenetic trees. IN-CLASS ACTIVITY: PHYLOGENETIC TREES AND MONOPHYLETIC GROUPS Draw the phylogenetic tree that is provided in the box below. Draw all possible equivalent trees.

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Using the “snip-test”, determine the number of monophyletic groups that are present in the phylogenetic tree.

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IN-CLASS ACTIVITY: CONSTRUCTING A PHYLOGENETIC TREE Your TAs will give a brief overview of how to draw a phylogenetic tree based on the information in the table on page 4. You will then be shown how to analyze the different derived traits by means of a PowerPoint presentation and discussion in the class. You will then use this information to complete the table of traits (page 3) and draw a phylogenetic tree on page 4. The second phylogenetic tree to be constructed will be done by examining the differing abilities of some mammals to recognise the five basic tastes. The construction of these phylogenetic trees will aid during the completion of this week’s post-tutorial assignment

IN-CLASS ACTIVITY: CONSTRUCTING A PHYLOGENETIC TREE Use this page to follow along during the presentation. This is for information only, do not hand it in. Fill in the missing traits.

Text Character Trait

Species Amnion

Legs

Warm Blood

Hemipenes

Gizzard

Vertebrate

Snake

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Gecko

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Frog

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Alligator

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Bird

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Draw your tree in the space below:

Gecko

Bird Snake

Alligator Warm-blodded Gizzard Snake

Frog Hemipenes Amnion Legs

Vertebrate

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Hemipenes

CONSTRUCTING A PHYLOGENETIC TREE : ASSESSING DERIVED TRAITS Mammalian Trait Chart Look at the table below and identify the traits that are important in distinguishing each organism. If the organism possesses the trait, ‘’ will be present in the cell, and if it does not the cell will contain a ‘’. Fill in this table, including the missing numbers and traits. Traits Species

Sweet

Umami

Sour

Salty

Mouse

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Whale

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Human

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Cat

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Panda

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Chimpanzee

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On the following page create the corresponding phylogenetic tree. Make sure to identify the origin of the traits and label all the organisms locations found on the tree (on the end of branches).

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CONSTRUCTING A PHYLOGENETIC TREE USING MORPHOLOGICAL CHARACTERISTICS Hadassah Annor 400260899 Name: _________________________________________________ Student number: ______________________ Phylogenetic Tree: Mammalian Trait Chart Draw your tree in the space provided. Clearly label traits and species names in their corresponding locations. Attempt to create the most parsimonious solution.

Mouse Humans Panda Chimpanzee Umami Cat Sweet Whale Sour

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TUTORIAL 2: POST -T UTORIAL ASSIGNMENT Hadassah Annor Name:________________________________________

Student #:____________________________ 400260899

T05 Tutorial Section: __ ____________________________

Michelle Brown TA:________________________

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1. How many unique phylogenetic trees can be created from 3 species when any 2 of the 3 species are sister taxa? Construct the trees in the space below. (3 marks) Draw your trees in the space below:

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2. How many monophyletic groups are present in phylogenetic tree seen below? (1 mark)

13 Number of monophyletic groups:____________

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3. Use the table and space below to construct a phylogenetic tree. “” indicates the presence of the trait, “” indicates the absence of the trait. Ensure that the tree reflects the principle of maximum parsimony (5 marks). Traits

Species

PTC

Sweet

Umami

Sour

Salty

Mouse

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1

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Whale

0

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Human

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Cat

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Panda

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Chimpanzee

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Draw your tree in the space below:

Human Chimpanzee

Mouse Loss of PTC

Panda Sweet

Cat

Sweet Whale

Umami PTC PTC

Sour Salty

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Umami

4. Gorillas, chimpanzees, and humans are able to taste PTC, but chimpanzees and humans have also derived the capacity to be a non-taster via convergent evolution. Using the information in the table below, construct a phylogenetic tree that reflects these derived traits. “” indicates the presence of the trait, “” indicates the absence of the trait  marks). Traits Species

PTC Taster

Loss of PTC Taste

Similar teeth, skull and genitals

Gorilla

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0

0

Chimpanzee

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Human

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Draw your tree in the space below:

Human Chimpanzee Loss of PTC taster

Loss of PTC taste

Gorilla

Similar teeth, skull and genitals PTC Taster

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TA Initials _____ 9...