Evolutionary Biology Concepts “What is behind is not important!”- or is it? Molecular Evolution Phylogenetic Inference 2/23/2019 Chuck Staben

Change in living organisms via reproduction Evolution Change in living organisms via reproduction "Change over time"-Kentucky School Boards 2/23/2019 Chuck Staben

Levels of Evolution Species Population Organismal Molecular gene frequencies Organismal genomic Molecular 2/23/2019 Chuck Staben

Branching Descent Evolutionary Tree Family Tree 2/23/2019 Chuck Staben

FRAMEWORK for INFERENCE Phylogeny Branching diagram showing the ancestral relations among species. “Tree of Life” History of evolutionary change FRAMEWORK for INFERENCE 2/23/2019 Chuck Staben

Phylogenetic Inference Mom's hair color? Which form of reproduction? 2/23/2019 Chuck Staben

courtesy, Ms. J. Rae Staben Mom-Inferred vs Real “Blonde” Phenotype Recombination Male/hair color Multigenic hair color? Potential Asexual Propagation Date of vasectomy? courtesy, Ms. J. Rae Staben 2/23/2019 Chuck Staben

Inferring the Framework How do we describe phylogenies? How do we infer phylogenies? 2/23/2019 Chuck Staben

DNA Inheritance RNA Protein Function Classical Phylogeny Molecular Phylogeny Classical Phylogeny 2/23/2019 Chuck Staben

Phylogenetic Trees Sister Taxa Terminal Taxa Node Internode Ancestor B C D E F Terminal Taxa Internode Node Ancestor Root 2/23/2019 Chuck Staben

More Trees Paraphyletic Group Clade Monophyletic Group A B C D E F 2/23/2019 Chuck Staben

Trees-3 A B C D E F Polyphyletic Group 2/23/2019 Chuck Staben

Rooted vs Unrooted Trees Add Root 2/23/2019 Chuck Staben

Extinction A B C D E F 2/23/2019 Chuck Staben

Speciation Poorly understood Reproductive isolation/divergence “…the mystery of mysteries…”-Darwin Reproductive isolation/divergence 2/23/2019 Chuck Staben

Population Genetic Forces Hardy-Weinberg Paradigm p+q=1 p2 + 2pq + q2 =1 Natural Selection (fitness) Drift (homozygosity by chance) much greater in small populations Mutation/Recombination (variation) Migration homogenizes gene pools 2/23/2019 Chuck Staben

DNA, protein sequence change Rate=1 change/6 aa sites per 108 yrs Rate=0.16 x 10-9 yrs (normal ~ 1 per 10-9 yrs per site) 2/23/2019 Chuck Staben

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 2/23/2019 Chuck Staben

Mechanisms of DNA Sequence Change Neutral Drift vs Natural Selection For a 1000 base gene, 41000 sequences! Selection (Jukes) Neutral (Kimura) 2/23/2019 Chuck Staben

Rate varies Gene-to-Gene 2/23/2019 Chuck Staben

Rate varies Site-to-Site Coding>Silent??? 2/23/2019 Chuck Staben

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 2/23/2019 Chuck Staben

Coding/noncoding can be flexible? Neutralism in Eukaryotes vs Prokaryotes- “Slightly deleterious mutations” Models Most non-coding sites are neutral? Coding/noncoding can be flexible? Reconsider evolutionary mechanisms? 2/23/2019 Chuck Staben

Evolutionary Genetic Forces Hardy-Weinberg Paradigm p+q=1 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? 2/23/2019 Chuck Staben

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 2/23/2019 Chuck Staben

Homology-similar by common descent 2/23/2019 Chuck Staben

Inferring Trees and Ancestors CCCAGG CCCAAG-> CCCAAG CCCAAA-> CCTAAA CCTAAA-> CCTAAC MANY traps, problems 2/23/2019 Chuck Staben

Homology, Orthology, Paralogy Paralogs Orthologs 2/23/2019 Chuck Staben

Paralogy Trap 2/23/2019 Chuck Staben

Improper Inference Man is a mouse, not a rat! 2/23/2019 Chuck Staben

Convergence Globin Common Ancestor Convergence Leghemoglobin 2/23/2019 Chuck Staben

Our Goals Infer Phylogeny Phylogenetic inference Optimality criteria Algorithm Phylogenetic inference (interesting ones) 2/23/2019 Chuck Staben

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.” 2/23/2019 Chuck Staben