Evolutionary Biology Concepts
-
Upload
kaydence-rojas -
Category
Documents
-
view
39 -
download
2
description
Transcript of Evolutionary Biology Concepts
![Page 1: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/1.jpg)
Evolutionary Biology Concepts
Molecular Evolution
Phylogenetic Inference
BIO520 Bioinformatics Jim Lund
Reading: Ch7
![Page 2: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/2.jpg)
Evolution
Evolution is a process that results in heritable changes in a population spread over many generations.
"In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next." - Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974
![Page 3: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/3.jpg)
Levels of Evolution
• Changes in allele frequencies within a species.
• Speciation.
Molecular changes:– Single bp changes.
– Genomic changes (alterations in large DNA segments).
![Page 4: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/4.jpg)
Branching Descent
Populations Individuals
![Page 5: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/5.jpg)
Phylogeny
Branching diagram showing the ancestral relations among species.
“Tree of Life”
History of evolutionary change
FRAMEWORK for INFERENCE
![Page 6: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/6.jpg)
The framework for phylogenetics
• How do we describe phylogenies?
• How do we infer phylogenies?
![Page 7: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/7.jpg)
Inheritance
DNA RNA Protein Function
![Page 8: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/8.jpg)
Ancestral Node or ROOT of
the TreeInternal Nodes orDivergence Points
(represent hypothetical ancestors of the taxa)
Branches or Lineages
Terminal Nodes
A
B
C
D
E
Represent theTAXA (genes,populations,species, etc.)used to inferthe phylogeny
Common Phylogenetic Tree Terminology
![Page 9: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/9.jpg)
Phylogenetic trees diagram the evolutionary relationships between the taxa
((A,(B,C)),(D,E)) = The above phylogeny as nested parentheses
Taxon A
Taxon B
Taxon C
Taxon E
Taxon D
No meaning to thespacing between thetaxa, or to the order inwhich they appear fromtop to bottom.
This dimension either can have no scale (for ‘cladograms’),can be proportional to genetic distance or amount of change(for ‘phylograms’ or ‘additive’ trees).
These say that B and C are more closely related to each other than either is to A,and that A, B, and C form a clade that is a sister group to the clade composed ofD and E. If the tree has a time scale, then D and E are the most closely related.
![Page 10: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/10.jpg)
Taxon A
Taxon B
Taxon C
Taxon D
1
1
6
5
genetic change
Taxon A
Taxon B
Taxon C
Taxon D
no meaning
Two types of trees
Cladogram Phylogram or additive tree
Meaning of branch length differs.
All show the same evolutionary relationships,or branching orders, between the taxa.
![Page 11: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/11.jpg)
Rooted vs Unrooted Trees
![Page 12: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/12.jpg)
More Trees
A B C D E F
![Page 13: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/13.jpg)
Trees-3
A B C D E F
![Page 14: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/14.jpg)
Extinction
A B C D E F
![Page 15: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/15.jpg)
Population Genetic Forces
• Natural Selection (fitness)• Drift (homozygosity by chance)
– much greater in small populations
• Mutation/Recombination (variation)• Migration
– homogenizes gene pools
Hardy-Weinberg Paradigmp+q=1
p2 + 2pq + q2 =1
![Page 16: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/16.jpg)
Modes of speciation
Many ways speciation can occur, among the most common are:
• Geographic isolation.
• Reproductive isolation.– Sexual selection.– Behavioral isolation.
![Page 17: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/17.jpg)
DNA, protein sequence change
![Page 18: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/18.jpg)
Multiple Changes/No Change
..CCU AUA GGG..
..CCC AUA GGG..
..CCC AUG GGG..
..CCC AUG GGC..
..CCU AUG GGC..
..CCU AUA GGC..
5 mutations1 DNA change
0 amino acid changes (net)
Enumerating bp/aa changes underestimates evolutionary change
![Page 19: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/19.jpg)
Mechanisms of DNA Sequence Change
Neutral Drift vs Natural Selection
Traditionalselectionmodel
Neutral(Kimura/Jukes)
Pan-neutralism
![Page 20: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/20.jpg)
Rate of change (evolution) of hemoglobin protein
Each point on the graph is for a pair of species, or groups of species. From Kimura (1983) by way of Evolution, Ridley, 3rd ed.
![Page 21: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/21.jpg)
Mutation rate varies Gene-to-Gene
Protein Rate (x 109 yr)
Lysozyme 2.0
Insulin 0.4
Histone H4 0.01
![Page 22: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/22.jpg)
Rate varies Site-to-Site
Protein Coding Silent
Albumin 0.9 6.7
Histone H4
0.03 6.1
Average 0.9 4.6
![Page 23: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/23.jpg)
Rate varies Site-to-Site
From Evolution. Mark Rdley, 3rd Ed.
![Page 24: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/24.jpg)
Constraints on “Silent” Changes
• Codon Biases-translation rates• Transcription elongation rates
– polymerase ‘pause’ sites
• “Silent” regulatory elements– select for or against
presence/absence
• Overall genome structure
![Page 25: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/25.jpg)
DNA, Protein Similarity
• Similarity by common descent– phylogenetic
• Similarity by convergence (rare)– functional importance
• Similarity by chance– random variation not limitless
– particular problem in wide divergence
![Page 26: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/26.jpg)
Homology-similar by common descent
CCCAGG
CCCAAGCCCAAA
CCTAAA
![Page 27: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/27.jpg)
Inferring Trees and Ancestors
CCCAGGCCCAAG->
CCCAAGCCCAAA->
CCTAAACCTAAA->
CCTAAC
Not always straightforward. The data doesn’t always give a single, correct answer.
![Page 28: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/28.jpg)
Homology, Orthology, Paralogy
![Page 29: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/29.jpg)
Paralogy Trap
![Page 30: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/30.jpg)
Improper Inference
Garbage in, garbage out!
![Page 31: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/31.jpg)
Our Goals
• Infer Phylogeny– Optimality criteria
– Algorithm
• Phylogenetic inference– (interesting ones)
![Page 32: Evolutionary Biology Concepts](https://reader035.fdocuments.us/reader035/viewer/2022070401/5681360c550346895d9d81f4/html5/thumbnails/32.jpg)
Watch Out
“The danger of generating incorrect results is inherently greater in computational phylogenetics than in many other fields of science.”
“…the limiting factor in phylogenetic analysis is not so much in the facility of software application as in the conceptual understanding of what the software is doing with the data.”