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MICB 475
Assignment #3
Complete the following worksheet using the mouse dataset and submit to Canvas as a PDF.
TAXONOMIC ANALYSIS:
After you generate the taxabarplot, download the figure under download
à
SVG (bar) and paste
it here:
Ensure the taxonomic rank to set to at least 2 or higher. Rank 1 would not resolve anything
significant. Below is an example at rank 4:
recip.462.WT.PD3.D49
recip.466.ASO.PD3.D7
recip.460.WT.HC3.D21
recip.467.WT.HC3.D49.a
recip.463.WT.PD3.D7
recip.465.ASO.PD3.D7
recip.463.WT.PD3.D21
recip.411.ASO.HC2.D49
recip.539.ASO.PD4.D7
recip.459.WT.HC3.D14
recip.459.WT.HC3.D49
recip.465.ASO.PD3.D14
recip.456.ASO.HC3.D49
recip.411.ASO.HC2.D14
recip.539.ASO.PD4.D14
recip.413.WT.HC2.D7
recip.391.ASO.PD2.D14
recip.462.WT.PD3.D7
recip.412.ASO.HC2.D14
recip.540.ASO.HC4.D7
recip.538.WT.PD4.D21
recip.460.WT.HC3.D14
recip.462.WT.PD3.D14
recip.536.ASO.PD4.D49
recip.403.ASO.PD2.D21
recip.467.WT.HC3.D49.b
recip.461.ASO.HC3.D49
recip.540.ASO.HC4.D14
recip.537.WT.PD4.D21
recip.290.ASO.OB2.D1
recip.459.WT.HC3.D21
recip.463.WT.PD3.D14
recip.401.ASO.HC2.D7
recip.391.ASO.PD2.D7
recip.391.ASO.PD2.D21
recip.460.WT.HC3.D7
recip.462.WT.PD3.D21
recip.400.ASO.HC2.D14
recip.461.ASO.HC3.D21
recip.411.ASO.HC2.D21
recip.458.ASO.HC3.D21
recip.412.ASO.HC2.D7
recip.464.WT.PD3.D14
recip.389.WT.HC2.D21
recip.220.WT.OB1.D7
recip.458.ASO.HC3.D49
recip.461.ASO.HC3.D7
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Relative Frequency
Sample
Name:
ANS
MICB 475
DIVERSITY ANALYSIS:
What did you decide on for rarefaction depth (ie. Sequencing depth cutoff)? Explain why.
Explanation should include:
•
based on the research question, refer to table.qza file using the slider to optimize
sample size and maintain a good number of reads/features
•
based on the alpha rarefaction curve where it plateaus to ensure ASV saturation. You
should be a looking at the observed features in the alpha rarefaction curve.
Sampling depth should be between ~500 – 4400. Anything below does not reach saturation of
ASVs and anything above results in significant loss of reads (<50% features).
Pick one of the ALPHA diversity metrics and use the donor_status category to fill in the sections
below:
EXAMPLE
Which metric did you pick:
Piloue’s Evenness
Paste the graph output below (
in the qiime2 viewer, there is an option of downloading the
figure as a SVG file):
What was the q-value? Is this significant?
q-value = 0.000002, yes significant
Healthy (n=24)
PD (n=23)
0.58
0.60
0.62
0.64
0.66
0.68
0.70
0.72
0.74
0.76
0.78
0.80
0.82
0.84
0.86
donor_status
pielou_evenness
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Related Questions
List the “gold standard” taxonomic methods currently applied to species designation
arrow_forward
Remembering the order of the taxonomic system from Domain to species is something you will need to know. One method to memorize a list is to use a Mnenomic device. The two best devices for taxonomy are either an Acronym or an Acrostic. Please see this link OR ask instructor if you need help on this! Examples of Mnemonic devices
What is your Mnemonic device for the following list (in this order)?
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
arrow_forward
How to interpret this phylogenetic tree (Maximum Likelihood)?
arrow_forward
I can apply the knowledge of Basic Taxonomic Concepts and Principles, Description, Nomenclature, Identification, and Classification. Characteristics of a Specific Taxon Relative to other Taxa by?
arrow_forward
Please help
Write a short sentence summary about taxonomy (1-3 sentences) from the video below.
https://m.youtube.com/watch?v=F38BmgPcZ_I
arrow_forward
5) List the different levels of the taxonomic classification system, in the order of most inclusive to least inclusive:
6) When I was in college, I was taught a mnemonic (memory device) to remember the proper order of classification levels: Drunken Kings Play Chess On Fine-Grained S ? Create a mnemonic of your own that lists the levels in the order in which you listed them in question #5:
arrow_forward
Directions: For the following organisms below, you are to sort them into at least 4 different groupings. There must be at least 2 organisms in a grouping. You may place them into columns (in a chart of some sort) or simply Number or your groups and list the organism that are included. ALSO, you must include a written description (at least 2 sentences) describing the characteristics of EACH GROUP that apply to all organisms within that group.
Hint** A quick google search, or image search may provide you the visual data you need to categorize the organisms.
Sponges (Porifera)
Cnidarians (Cnidaria)
Comb jellies (Ctenophora)
Flatworms (Platyhelminthes)
Ribbon worms (Nemertea)
Nematodes (Nematoda)
Arrow worms (Chaetognatha)
Segmented worms (Annelida)
Sipunculans (Sipuncula)
Molluscs (Mollusca)
Arthropods (Arthropoda)
Bryozoans (Bryozoa)
Phoronids (Phoronida)
Lamp shells (Brachiopoda)
Echinoderms (Echinodermata)
Hemichordates (Hemichordata)
Chordates (Chordata)
arrow_forward
What changed would our scientific community experience without without a taxonomic naming system?
arrow_forward
Soalan / Question 3
a) Berikan fungsi utama kekunci dikotomi.
Give the main function of dichotomous key
b) Kenalpasti langkah-langkah untuk identifikasi spesis berdasarkan kekunci dikotomi.
Identify steps for species identification based on dichotomous key.
c) Berdasarkan kladogram pada Rajah 1, terangkan secara ringkas ciri-ciri pada label (i), (ii)
dan (ii)
Based on the cladogram in Figure 1, briefly describe the characteristics on (i), (ii) dan (ii)
label.
Conifers
Lilies
Mosses
Ferns
(outgroup)
(ii)
(ii)
Node
(i)
Rajah / Figure 1
arrow_forward
Please answer all (6)
arrow_forward
With the given name/s or situation, identify the appropriate rule or principle that must be or was considered.
Choices:
Principle of binomial nomenclature, principle of priority, principle of coordination, principle of the first reviser, principle of homonymy, principle of typification
When Rattus as a genus name was established, its species name, Rattus norvegicus was also automatically established.
Noctua Linnæus, 1758 (Lepidoptera) and Noctua Gmelin (Sauropsida)
Limax maculatus was established in 1837 by Nunneley. However, it was found that Wiktor has already established Limax maximus (Gastropoda) in 1758. Since L. maximus was the senior synonym, it takes precedence over L. maculatus and it was used for the species.
The species name of giraffe is Giraffa camelopardalis.
arrow_forward
Please explain in 10 sentences or in paragraph form. Please. Thank you in advance!
arrow_forward
elaborate the instruction for part V.
arrow_forward
This is not a writing assignment.
arrow_forward
FILL IN THE TABLE BELOW BY CLASSIFYING INFORMATION WRITTEN IN AN ENVELOPE WITH A RECIPIENT'S ADDRESS. (SEE THE PICTURE)
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
arrow_forward
Explain the advantages and disadvantages of using a model organism (include at least 3 of each).
Edit View
Insert
Format
Tools
Table
-| BI U AVe
A v &v T? v
12pt v
Paragraph v
arrow_forward
Please help to creating parsimonious treesFor the following DNA sequences determine the most parsimonious phylogeny.
Tree ASpecies 1 AATTGCGGGATATATCGCGGGGAAATTTACGACTSpecies 2 AATGTCGGGATATATCGCGGGGAAATTTACGACTSpecies 3 AATTGCGGGATATATCGCGGGGAAATTTACGACT
Tree BSpecies 1 AATTGCGGGATATATCGCGGGGAAATTTACGACTSpecies 2 AACTGCGGCATATATCGCGGGGAAATTAACGACTSpecies 3 AAGTGCGCCATATATCGCCCGGATAATTTCGAGA
Tree CSpecies 1 CCGTATGACCGGGTATAAATCGCGCCCGGGATCTGCSpecies 2 CCGTATGAGGGGGTATATATCGGGCGCGGGATCTGCSpecies 3 CCGTATGACCGGGTATAAATCGCGCCCGGGATCTGCSpecies 4 CCGTATGAGGGGGTATATATCGGGCGCGGGATCTGC
Tree DSpecies 1 GGGATATAGCGCACGATATCGTAGCCTAACGTTTTACGSpecies 2 GGGATATAGCGCACGATATCGTAAGCTAACGTTTTACGSpecies 3 AAAATATAGGCGTGGATATCGTAGCCTAACGTTGCATTSpecies 4 GGGATATACCGCACGTTATCGATCCCTAACGTTTTACG
arrow_forward
Sequence data from OTUs are provided in the table below with values provided as (percentage distance x 1000)
measurements. Determine the phylogenetic tree from the data in the table below using the UPGMA procedure mentioned in
class.
Berenstain Bear
Berentstain Bear Care Bear Gummi Bear Paddington Bear
Care Bear
160
Gummi Bear
150
40
Paddington Bear
80
130
120
Place each OTU in the correct box on the appropriate tree below. Do not label the incorrect tree.
Care Bear
Gummi Bear
Berenstain Bear
Paddington Bear
arrow_forward
A certain morphological trait is used to construct a phylogenetic tree of three species
(1, 2, and 3). Match each scenario with the correct corresponding tree.
Species 1: No
Species 2: Yes
1
1.
2
Species 3: Yes
3
Species 1: Yes
3
2.
Species 2: Yes
2
1
Species 3: No
1
3.
Species 1: Yes
3
2
Species 2: No
Species 3: Yes
Review Stuff
Question 26 (Mandatory) (4 points)
Species diversity is sometimes maintained or facilitated by... (CHOOSE ALL THAT
ARE CORRECT).
ر
8
DII
8
A
510
E
F11
3 €
F12
arrow_forward
A. Basic Phylogenetic Tree Construction: Create a phylogenetic tree which best represent the data provided:
Species
Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4
Guinca pir present
present
albsent
present
Camel
alosent
absent
present
absent
Capvbara prescnt
present
absent
present
Species
Enzyme 1 Enzyme 2 Enzyne 3 Enzyme 4
Opusurn present
presenl
pnesent
present
Plalypus
ppresent
present
pnesent
alsennt
Chit ken
prment
atrent
ataent
atrsent
B. Encircle Monophyletic groups that can be found in this tree.
Angus cattle
White-tailed deer
Blue whale
Pygmy hippopotamus
Extinct
Wild boar
Mammal
Alpaca
Based on the phylogenetic tree above, what species is most related to the blue whale?
arrow_forward
In minimum of 25 sentences, explain the concept of mimicry in relation to taxonomy and why it is important in the study of insect taxonomy. Provide a clear explanation and provide examples.
arrow_forward
Visit a specific area in your school or at home (e. g. garden). Using a pen and a clean sheet of paper, list down five (5) organisms found in that area and describe the value of each organism. Then, classify the value of the organisms by putting a check mark (/) on the space under the correct column. An example has been given. If you think that an organism has more than one value, put a check mark (/) on each.
arrow_forward
Activity 1.1: I Can Relate
Direction: Complete the graphic organizer below by relating each term to the
main idea or word. You may use a separate sheet of paper for your answers.
1. Deoxyribonucleic acid
(DNA)
6. Structure
2. Taxonomy
SYSTEMATICS
5. Binomial
3. Classification
nomenclature
4. Diversity
arrow_forward
For Meal Worm
This should include a header, in-text citation and give the reader background on the relevant science (the species, life cycle, habitat/niche of each stage, and metabolism.) Site your sources.
Roughly 1-2 pages, 1.5 spacing,
Avoid saying: GROW, PROVE, IN THIS EXPERIMENT
Can you please please answer I really need it please at least try to answer it’s very important please thank you
arrow_forward
Based on the information from the following table and the
provided phylogenetic tree, what kind of species classification is
shown?
A
B
C
D
E
F
G
H
1
J
K
L
M
N
O
Form of
Male
Genitalia
1
1
L
L
L
L
L
L
L
L
L
L
L
L
L
r
T
Pits) or
Tubercles
E
P
P
T
T
T
T
T
P
P
P
P
P
Р
P
P
O Phenetic Species Concept
O Blological Species Concept
O Phylogenetic Species Concept
O Sympatric Species Concept
Blayple (OUTGROUP)
beaver Dan, AZ
-Twentynine Paime, CA
-Harkavilla, UT
D-Chilchinbio, NM
-Vermilion Cas. AZ
64
-F-Mone Lake, CA
-G-Coral Pink Danes, UT
H-Pyramid Lake, N
-Crescent Dunes, MV
Meno Lake CA
-K-Olancha CA
-Olancha, CA
--Winnemucca, NV
-El Mirage, CA
Lo-Dumont Dunes, CA
Form of
dorsal
ridges
M₁
M₁
FFFFFFFFFF
M
Ma
M₂
M₂
arrow_forward
1.)List the levels of taxonomic hierarchy from Species to Domain:
2.)What levels are used in binomial naming system (scientific name)? What is the proper notation? Provide an example.
arrow_forward
Define the term taxonomy.
arrow_forward
A. Basic Phylogenetic Tree Construction: Create a phylogenetic tree which best represent the data provided:
Species
Enzyme 1
Enzyme 2
Enzyme 3
Enzyme 4
Guinea pig
present
present
absent
present
Camel
absent
absent
present
absent
Сарybara
present
present
absent
present
Species
Enzyme 1
Enzyme 2
Enzyme 3
Enzyme 4
Opossum
present
present
present
present
Platypus
present
present
present
absent
Chicken
present
absent
absent
absent
arrow_forward
1) For each of the organisms in the following table, complete the empty columns with an appropriate
answer for each taxon.
Organism
Green Algae
Fungi
Archaea
Sister
Taxa
Derived
Trait
Ancestral
Trait
Mode of
Reproduction
arrow_forward
Antonie van Leeuwenhoek was the first person to use a microscope and
describe tiny animalcules. What is an animalcule? Describe major
characteristics of an animalcule in terms of microbiology. Describe the size and
living state of these animalcules. Please include: How are animalcules
classified/identified? How do you form these classification groups?
Edit View Insert Format Tools Table
12pt ✓ Paragraph B IU А
VT² V
⠀
arrow_forward
Asap
arrow_forward
ny - Presenta...
Suggested Sites
Real-time HTML Edi.
2. Practicing Binomial Nomel
Use the classification tables below to write the scientific name correctly for each organism.
8.
9.
10
Common chimpanzee
Kingdom: Animalia
Phylum:
Class:
Order:
Family:
Genus:
African Bush Elephant
Kingdom:
Phylum:
Class:
Order:
Family:
Sloth
Animalia
Chordata
Kingdom:
Phylum:
Class:
Order:
Family:
Animalia
Chordata
Mammalia
Xenarthra
Chordata
Mammalia
Mammalia
Proboscidea
Elephantidae.
Loxodonta
africana
Primates
Hominidae
Bradypodidae
Bradypus
tridactylus
Pan
Genus:
Genus:
Species: troglodytes
Species:
Species:
9.
10.
arrow_forward
Can you please enumerate and explain how pesticides and Antibiotic Resistance Affect Genetic Diversity in Aquatic Organisms?
Please help me, I'm cramming for the presentation tomorrow. I'm a working student. just out from work.
arrow_forward
A taxonomist discovers a plant species that is unknown to science. Using your knowledge of the science of taxonomy gained through this course, discuss in a short essay how this taxonomist can go about describing the new species, and what would be important to do during this process.
You need to mention: Resources where he/she/they can study the plant and other plant collections, species concepts, taxonomic evidence that can be used and how these can be analysed, type specimens and also nomenclature (what is necessary for him/her/them to publish the name).
arrow_forward
Please help me answer this through an essay. Please clear handwriting.
arrow_forward
Describe the methods/procedures in naming new taxa.
arrow_forward
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Related Questions
- List the “gold standard” taxonomic methods currently applied to species designationarrow_forwardRemembering the order of the taxonomic system from Domain to species is something you will need to know. One method to memorize a list is to use a Mnenomic device. The two best devices for taxonomy are either an Acronym or an Acrostic. Please see this link OR ask instructor if you need help on this! Examples of Mnemonic devices What is your Mnemonic device for the following list (in this order)? Domain Kingdom Phylum Class Order Family Genus Speciesarrow_forwardHow to interpret this phylogenetic tree (Maximum Likelihood)?arrow_forward
- I can apply the knowledge of Basic Taxonomic Concepts and Principles, Description, Nomenclature, Identification, and Classification. Characteristics of a Specific Taxon Relative to other Taxa by?arrow_forwardPlease help Write a short sentence summary about taxonomy (1-3 sentences) from the video below. https://m.youtube.com/watch?v=F38BmgPcZ_Iarrow_forward5) List the different levels of the taxonomic classification system, in the order of most inclusive to least inclusive: 6) When I was in college, I was taught a mnemonic (memory device) to remember the proper order of classification levels: Drunken Kings Play Chess On Fine-Grained S ? Create a mnemonic of your own that lists the levels in the order in which you listed them in question #5:arrow_forward
- Directions: For the following organisms below, you are to sort them into at least 4 different groupings. There must be at least 2 organisms in a grouping. You may place them into columns (in a chart of some sort) or simply Number or your groups and list the organism that are included. ALSO, you must include a written description (at least 2 sentences) describing the characteristics of EACH GROUP that apply to all organisms within that group. Hint** A quick google search, or image search may provide you the visual data you need to categorize the organisms. Sponges (Porifera) Cnidarians (Cnidaria) Comb jellies (Ctenophora) Flatworms (Platyhelminthes) Ribbon worms (Nemertea) Nematodes (Nematoda) Arrow worms (Chaetognatha) Segmented worms (Annelida) Sipunculans (Sipuncula) Molluscs (Mollusca) Arthropods (Arthropoda) Bryozoans (Bryozoa) Phoronids (Phoronida) Lamp shells (Brachiopoda) Echinoderms (Echinodermata) Hemichordates (Hemichordata) Chordates (Chordata)arrow_forwardWhat changed would our scientific community experience without without a taxonomic naming system?arrow_forwardSoalan / Question 3 a) Berikan fungsi utama kekunci dikotomi. Give the main function of dichotomous key b) Kenalpasti langkah-langkah untuk identifikasi spesis berdasarkan kekunci dikotomi. Identify steps for species identification based on dichotomous key. c) Berdasarkan kladogram pada Rajah 1, terangkan secara ringkas ciri-ciri pada label (i), (ii) dan (ii) Based on the cladogram in Figure 1, briefly describe the characteristics on (i), (ii) dan (ii) label. Conifers Lilies Mosses Ferns (outgroup) (ii) (ii) Node (i) Rajah / Figure 1arrow_forward
- Please answer all (6)arrow_forwardWith the given name/s or situation, identify the appropriate rule or principle that must be or was considered. Choices: Principle of binomial nomenclature, principle of priority, principle of coordination, principle of the first reviser, principle of homonymy, principle of typification When Rattus as a genus name was established, its species name, Rattus norvegicus was also automatically established. Noctua Linnæus, 1758 (Lepidoptera) and Noctua Gmelin (Sauropsida) Limax maculatus was established in 1837 by Nunneley. However, it was found that Wiktor has already established Limax maximus (Gastropoda) in 1758. Since L. maximus was the senior synonym, it takes precedence over L. maculatus and it was used for the species. The species name of giraffe is Giraffa camelopardalis.arrow_forwardPlease explain in 10 sentences or in paragraph form. Please. Thank you in advance!arrow_forward
arrow_back_ios
SEE MORE QUESTIONS
arrow_forward_ios
Recommended textbooks for you
- Human Anatomy & Physiology (11th Edition)BiologyISBN:9780134580999Author:Elaine N. Marieb, Katja N. HoehnPublisher:PEARSONBiology 2eBiologyISBN:9781947172517Author:Matthew Douglas, Jung Choi, Mary Ann ClarkPublisher:OpenStaxAnatomy & PhysiologyBiologyISBN:9781259398629Author:McKinley, Michael P., O'loughlin, Valerie Dean, Bidle, Theresa StouterPublisher:Mcgraw Hill Education,
- Molecular Biology of the Cell (Sixth Edition)BiologyISBN:9780815344322Author:Bruce Alberts, Alexander D. Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter WalterPublisher:W. W. Norton & CompanyLaboratory Manual For Human Anatomy & PhysiologyBiologyISBN:9781260159363Author:Martin, Terry R., Prentice-craver, CynthiaPublisher:McGraw-Hill Publishing Co.Inquiry Into Life (16th Edition)BiologyISBN:9781260231700Author:Sylvia S. Mader, Michael WindelspechtPublisher:McGraw Hill Education
Human Anatomy & Physiology (11th Edition)
Biology
ISBN:9780134580999
Author:Elaine N. Marieb, Katja N. Hoehn
Publisher:PEARSON
Biology 2e
Biology
ISBN:9781947172517
Author:Matthew Douglas, Jung Choi, Mary Ann Clark
Publisher:OpenStax
Anatomy & Physiology
Biology
ISBN:9781259398629
Author:McKinley, Michael P., O'loughlin, Valerie Dean, Bidle, Theresa Stouter
Publisher:Mcgraw Hill Education,
Molecular Biology of the Cell (Sixth Edition)
Biology
ISBN:9780815344322
Author:Bruce Alberts, Alexander D. Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter
Publisher:W. W. Norton & Company
Laboratory Manual For Human Anatomy & Physiology
Biology
ISBN:9781260159363
Author:Martin, Terry R., Prentice-craver, Cynthia
Publisher:McGraw-Hill Publishing Co.
Inquiry Into Life (16th Edition)
Biology
ISBN:9781260231700
Author:Sylvia S. Mader, Michael Windelspecht
Publisher:McGraw Hill Education