Evolutionary Biology Concepts

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Evolutionary Biology Concepts

• What is behind is not important!-
• or is it?
• Molecular Evolution
• Phylogenetic Inference

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Evolution
Change in living organisms via reproduction
"Change over time"-Kentucky School Boards
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Levels of Evolution

• Species
• Population
• gene frequencies
• Organismal
• genomic
• Molecular

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Branching Descent
Evolutionary Tree
Family Tree
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Phylogeny

• Branching diagram showing the ancestral relations
  among species.
• Tree of Life
• History of evolutionary change
• FRAMEWORK for INFERENCE

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Phylogenetic Inference
Mom's hair color?
Which form of reproduction?
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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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Inferring the Framework

• How do we describe phylogenies?
• How do we infer phylogenies?

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Inheritance
DNA
?RNA ?Protein ?Function
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Phylogenetic Trees
Sister Taxa
Terminal Taxa
Ancestor
Root
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More Trees
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Trees-3
Polyphyletic Group
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Rooted vs Unrooted Trees
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Extinction
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Speciation

• Poorly understood
• the mystery of mysteries-Darwin
• Reproductive isolation/divergence

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Population Genetic Forces
Hardy-Weinberg Paradigm pq1 p2 2pq q2 1

• Natural Selection (fitness)
• Drift (homozygosity by chance)
• much greater in small populations
• Mutation/Recombination (variation)
• Migration
• homogenizes gene pools

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DNA, protein sequence change
Rate1 change/6 aa sites per 108 yrs Rate0.16 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 mutations 1 DNA change 0 amino acid changes
(net)
Underestimate Evolution
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Mechanisms of DNA Sequence Change

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

Selection (Jukes)
Neutral (Kimura)
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Rate varies Gene-to-Gene
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Rate varies Site-to-Site
CodinggtSilent???
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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
Most non-coding sites are neutral? Coding/noncodin
g can be flexible?
Reconsider evolutionary mechanisms?
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Evolutionary Genetic Forces
Hardy-Weinberg Paradigm pq1 p2 2pq q2 1

• Natural Selection (fitness)
• Drift (homozygosity by chance)
• much greater in small populations
• Mutation/Recombination (variation)
• Migration
• homogenizes gene pools

Genome Recombination?
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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-similar by common descent
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Inferring Trees and Ancestors
CCCAGG CCCAAG-gt CCCAAG CCCAAA-gt
CCTAAA CCTAAA-gt CCTAAC
MANY traps, problems
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Homology, Orthology, Paralogy
Orthologs
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Paralogy Trap
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Improper Inference
Man is a mouse, not a rat!
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Convergence
Globin
Common Ancestor Convergence
Leghemoglobin
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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.