View attached explanation and answer. Let me know if you have any questions.hey buddy. Here is the completed workbook of the answer. In case you have any more questions of me, do not hesiate to ask anytime😀
Lab Bioinformatics Fly Lab
(Created by Benjamin Carone, Yong Chen and Marina Bogush)
A hypothesis driven, Molecular Phylogenetics Exercise in Drosophila
Learning Objectives:
● Identify morphological differences between species and recognize the process of
evolution driving these differences
Pre-lab:
Learn how to generate a phylogenetic tree by watching the video:
https://www.youtube.com/watch?v=09eD4A_HxVQ
Section 1: Introduction to Phylogeny and Hypothesis Generation
●
●
●
●
Part I – Identify Morphological Differences in Fruit Flies
Part II – Generating a Hypothesis-driven Phylogeny
Part III – Identifying Drosophila Cytochrome b gene using Flybase.org
Part IV – Getting the cytochrome B gene sequence for the remaining 5 species
using Flybase.org BLAST
Section 2: Performing DNA and Protein Alignments and
Phylogenies
● Part I – Perform a DNA alignment using “MUSCLE Alignment” (online
program)
● Part II – Generate a phylogeny using the MUSCLE output and compare to
predicted phylogeny
● Part III – Translate the first 500bp of D. melanogaster cytochrome b gene from
DNA to protein (online program)
● Part IV – Navigate to NCBI and perform a Protein BLAST
● Part V – Identify a total of 7 different cytochrome b sequences from students
choice of species from BLAST results and download into Microsoft Word
● Part VI – Perform an amino acid alignment using “MUSCLE Alignment” (online
program)
● Part VII – Generate a phylogeny using the MUSCLE output and compare to
DNA phylogeny and predictions
Section 1:
●
●
●
●
Part I – Identify Morphological Differences in Fruit Flies
Part II – Generating a Hypothesis-driven Phylogeny
Part III – Identifying Drosophila Cytochrome b gene using Flybase.org
Part IV – Getting the cytochrome B gene sequence for the remaining 5 species
using Flybase.org BLAST
Hypothesis Generation
In this section of the lab, students will compare the trait of 5 different species of fruit fly,
Drosophila and the common housefly, Musca domestica. In order to do so, students will
utilize the Drosophila web resource flybase.org, which houses a wide selection of
scientific tools including an image database of fruit fly strains as well as genomic data for
a variety of species. During the hypothesis generation portion of this laboratory students
will navigate to Flybase.org, identify traits and make a hypothesis as to their evolutionary
relationship in the form of a phylogenetic tree prediction.
Geographic distribution of commonly studied Drosophila species
Part I – Identifying Morphological Differences in Fruit Flies.
1
Figure S1. Habitat distributions of Drosophila species. The coloured regions indicate the
Climatic environment for each Drosophila species based on the rainfall, temperature and
vegetation: red, yellow, green and purple roughly correspond to equatorial, arid, warm
and snowy climates, respectively (Kottek et al. 2006).
You will be using Flybase.org
1. Open a Chrome Browser window and navigate to flybase.org.
Part I – Identifying Morphological Differences in Fruit Flies.
You will be using Flybase.org
1. Open a Chrome Browser window and navigate to flybase.org.
2. Click on the drop-down menu “Species” on the top, select the “Color
Illustrations” (you can also reach the page by this link
https://flybase.org/static/Drosophilidae ). Click the “Illustrations” at the bottom to
expand it.
3. Find the species in the table below, compare, and fill in Morphological Character
section of the table with your observations. (there is no image of M. domestica,
you can find from https://en.wikipedia.org/wiki/Housefly )
2
4. Using Figure 1 on the previous page fill in the Geographical distribution (Wet vs.
Dry habitat). Note: D. melanogaster is in North America (Philly)
Fly Species
Geographical
Distribution
Habitat –(Wet/
Dry/Temperate)
D. ananassae
(Fruit Fly)
Wet habitats
D. melanogaster
(Fruit Fly)
Temperate habitats
D. virilis
(Fruit Fly)
Dry habitats
D. mojavensis
(Fruit Fly)
Dry habitats
D willistoni
(Fruit Fly)
Temperate habitats
M. domestica
(House Fly)
Wet habitats
Morphological Character
Eye Color (Red/White)
Thorax (Long/Short)
Body Color (Light/Dark & Striped/Plain
Eye Color: Red
Thorax: long
Body Color: Light and Plain
Eye Color: Red
Thorax: Short
Body Color: Light with dark stripes
Eye Color: Red
Thorax: Long
Body Color: Dark & Striped
Eye Color: Red
Thorax: Short
Body Color: Light & Striped
Eye Color: Red
Thorax: Short
Body Color: Light & Striped
Eye Color: Red
Thorax: Short
Body Color: Dark & Striped
Part II – Generating a hypothesis-driven phylogeny.
Some organisms share common features and characteristics. The more similar
characteristics two organisms share the more likely they are to be close to each other in
evolutionary relationship. When comparing multiple organisms and trying to identify
their evolutionary relationship we will often create a “tree” depicting their relationship.
This “tree” is called a phylogeny. In this part of the lab, you will individually create
your own phylogeny based on the observations of traits that recorded in Part I of this lab.
Example phylogenies:
3
U…
