Lab 3 - Phylogenetics

docx

School

Texas A&M University, Corpus Christi *

*We aren’t endorsed by this school

Course

3411

Subject

Computer Science

Date

Apr 3, 2024

Type

docx

Pages

Uploaded by ProfessorOryx1942

Phylogenetics Lab Turn in all 7 trees you generated in class, including the one you drew by hand and the 6 done on the computer. Be sure two of them have traits (apomorphies) noted on them (the hand- drawn one and one of the computer generated trees). Also turn in a trait matrix for the mammals and answer the following review questions in depth. Review Questions 1. What differences and similarities did you notice between the trees you generated? In particular, how did the trees generated with DNA differ than the one you made with physical traits? - In all the trees I generated, the platypus stayed relatively in the same place as an outgroup with the least amount of branch points and divergence from the species’s common ancestor. I also noticed that the trees based on physical traits were less accurate than the ones generated by DNA. I think this is most likely due to the trees based on physical traits being subjective to opinion and bias. Whereas the trees generated based on DNA are based on data and facts. 2. Were any of your physical traits autapomorphic or synapomorphic when plotted on the gene trees? Which ones and for which species? Phylogeneticists often refer to these physical traits as “evolutionarily significant,” what do you suppose they mean by this? - The automorphic traits are 10,8,6,5,2. These autotrophic traits include Diastema unique to Deer, Occipital crest unique to Cats, Large braincase unique to coyotes, extended rostrum unique to platypus, and >12 incisors unique to opossums. The rest of the traits listed are synapomorphic and shared with the other species. These physical traits can be referred to as “evolutionary significant” because these developed traits can be unique to species that need them to survive whereas other species can survive without them. Therefore making the derived traits significant to the species' survival and contributing to the process of evolution. 3. Were any of your physical traits analogous? Which ones? Why do you suppose some traits can occur multiple times on a tree while others don’t? - An analogous trait according to class lecture, arises due to environmental constraints causing common adaptions. An example of a physical trait being analogous is cutting/shredding cheek teeth shared between the European rabbit and American mink. Both the rabbit and mink have cutting/shredding cheek teeth, but in terms of the tree generated with physical traits, they are one of the most unrelated species. Traits can occur multiple on a tree if they are needed for survival. Traits in various species may not be related, but they can have a similar function.

4. Given your results from two genes and physical traits, what relationships between species are you certain of? Which ones are you uncertain of? Why? - Given my results from two genes and physical traits, I am most certain that the American mink and domestic cat are related. The mink and cat share the majority of the physical traits and the most DNA traits than any of the other species. I am also certain that the platypus is the most unrelated species to the others because it shares no physical or DNA traits with the other species, therefore making it the outgroup. I am uncertain of all the other relationships because I feel that the data my partners collected is not entirely accurate. Also, the physical tree varies from the DNA tree greatly except for the information regarding the mink and cat species. Also, the physical traits tree varies depending on the observer. With all of these factors considered, I feel uncertain of all the relationships between the other species I did not mention. 5. If gene trees have more information in terms of base pairs for generating phylogenies, why do you suppose phylogeneticists even bother using and including physical traits in their analyses? - Phylogeneticists include physical traits in their analysis because DNA can change over time in a variety of ways such as random mutations. Relying solely on DNA for interpretation could cause the information to be accurate and the mistake of species being closely related when they are really not. Accounting for species' physical traits will help determine whether or not the data aligns with evolution and is showing accurate lineage. Required materials: Responses (1 pt. for each question) 1 hand-drawn tree with traits on it (1 pt.) 1 character matrix (0.5 pts.) 6 computer generated trees, 1 with traits on it (3.5 pts. total) Hand-drawn tree:

UPGMA Tree - Bootstrap Consensus tree for RAG1: Original Tree - RAG1: Rag1 Bootstrap Tree w/traits on it:

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

Bootstrap Tree - OPNSW: Original Tree - OPNSW: Bootstrap Tree - 2gene:

Original Tree - 2gene:

Name: Section: Species Traits (Write in trait below number) 1 Teeth 2 >12 incisors 3 canine teeth longer than incisors 4 Cutting/ shredding cheek teeth 5 large braincase 6 occipital crest 7 sagittal crest 8 extended rostrum 9 peg teeth 10 diastema Cat 1 0 1 1 0 1 1 0 1 1 Deer 1 0 0 1 0 0 1 0 0 1 Mink 1 0 1 1 0 0 1 0 0 0 Monkey 1 0 1 1 0 0 1 0 0 0 Opossum 1 1 1 1 0 0 1 0 1 1 Platypus 0 0 0 0 0 0 0 0 0 0 6

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

Coyote 1 0 1 1 1 0 1 0 1 0 Rabbit 1 0 0 1 0 0 0 0 0 0 Matrix: Platypus Cat Deer Mink Monkey Opossum Coyote Rabbit Platypus 0 Cat 7 0 Deer 4 3 0 Mink 4 3 2 0 Monkey 4 3 2 0 0 Opossum 7 2 3 3 3 0 Coyote 6 3 4 2 2 3 0 Rabbit 2 5 2 2 2 5 4 0 7

Related Documents

SP24 Exercise Answers 3.pdf

hw3-released.pdf

Python Exercise.html

ITSS4352_Assignment10-Arsh D..docx

ITSS4352_Assignment10- Arsh D..pdf

AZA video- complete.docx

WrittenReport02.docx

Week 4 Mini Individual Assignment.docx

BIA 580-A Python-Mid Exam.pdf

CS570 Spring 2024 Exam 1 Solutions Rubrics.pdf

workshop-week2.pdf

Journal 1-1 Identifying Empirical Evidence.docx

Recommended textbooks for you

Systems Architecture

Computer Science

ISBN:9781305080195

Author:Stephen D. Burd

Publisher:Cengage Learning

COMPREHENSIVE MICROSOFT OFFICE 365 EXCE

Computer Science

ISBN:9780357392676

Author:FREUND, Steven

Publisher:CENGAGE L

Principles of Information Systems (MindTap Course...

Computer Science

ISBN:9781285867168

Author:Ralph Stair, George Reynolds

Publisher:Cengage Learning

Fundamentals of Information Systems

Computer Science

ISBN:9781305082168

Author:Ralph Stair, George Reynolds

Publisher:Cengage Learning

Oracle 12c: SQL

Computer Science

ISBN:9781305251038

Author:Joan Casteel

Publisher:Cengage Learning

New Perspectives on HTML5, CSS3, and JavaScript

Computer Science

ISBN:9781305503922

Author:Patrick M. Carey

Publisher:Cengage Learning

SEE MORE TEXTBOOKS

Recommended textbooks for you

Systems Architecture
Computer Science
ISBN:9781305080195
Author:Stephen D. Burd
Publisher:Cengage Learning
COMPREHENSIVE MICROSOFT OFFICE 365 EXCE
Computer Science
ISBN:9780357392676
Author:FREUND, Steven
Publisher:CENGAGE L
Principles of Information Systems (MindTap Course...
Computer Science
ISBN:9781285867168
Author:Ralph Stair, George Reynolds
Publisher:Cengage Learning
Fundamentals of Information Systems
Computer Science
ISBN:9781305082168
Author:Ralph Stair, George Reynolds
Publisher:Cengage Learning
Oracle 12c: SQL
Computer Science
ISBN:9781305251038
Author:Joan Casteel
Publisher:Cengage Learning
New Perspectives on HTML5, CSS3, and JavaScript
Computer Science
ISBN:9781305503922
Author:Patrick M. Carey
Publisher:Cengage Learning