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Evolutionary Biology Concepts

Evolutionary Biology“What is behind is not important!”-

or is it?Phylogenetic Inference

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Evolution

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Branching Descent

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Phylogeny

Branching diagram showing the ancestral relations among species.

“Tree of Life”

History of evolutionary change

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Phylogenetic Inference

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Mom-Inferred vs Real

•“Blonde” Phenotype•Recombination

•Male/hair color•Multigenic hair color?•Potential Asexual Propagation

•Date of vasectomy?

courtesy, Ms. J. Rae Staben

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Inheritance

DNARNA Protein Function

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Phylogenetic TreesA B C D E F

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More TreesA B C D E F

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Trees-3A B C D E F

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Rooted vs Unrooted Trees

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ExtinctionA B C D E F

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Evolutionary 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

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DNA, protein sequence change

Rate=1 change/6 aa sites per 108 yrsRate=0.16 x 10-9 yrs

(normal ~ 1 per 10-9 yrs per site)

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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)

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Mechanisms of DNA Sequence Change

Neutral Drift vs Natural Selection• For a 1000 base gene, 41000 sequences!

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Rate varies Gene-to-Gene

Protein Rate (x 109 yr)

Lysozyme 2.0

Insulin 0.4

Histone H4 0.01

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Rate varies Site-to-Site

Protein Coding Silent

Albumin 0.9 6.7

HistoneH4

0.03 6.1

Average 0.9 4.6

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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

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Neutralism in Eukaryotes vs Prokaryotes-“Slightly deleterious mutations” Models

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Evolutionary 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

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DNA, Protein Similarity

• Similarity by common descent– phylogenetic

• Similarity by convergence– functional importance

• Similarity by chance– random variation not limitless– particular problem in wide divergence

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Homology, Orthology, Paralogy

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Paralogy Trap

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Improper Inference

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Convergence

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Our Goals

• Infer Phylogeny– Optimality criteria– Algorithm

• Phylogenetic inference– (interesting ones)

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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 applicaition as in the conceptual understanding of what the software is doing with the data.”