Evolutionary change involves genetic change   Phenotype   Genotype Study of evolution of macromolecules - nature of changes (in DNA, protein) & their impact BIO 3102 MOLECULAR EVOLUTION M.C. Escher “Sky & water”

cenancestor - most recent common ancestor of extant organisms extinct lineages primordial life form modern species Brown Fig.16.1 Use of molecular data to help reconstruct evolutionary history - phylogenetic trees

Ottawa Citizen December 3, 2010 Science December 2, 2010 Building blocks of DNA, proteins & lipids (for life on earth) carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur Nature December 9, 2010

chem163/163LT1.html Closely-related organisms have more similar protein sequences than distant organisms MOLECULAR CLOCKS

“Taking an axe to the Tree of Life...” “... far more complex scenario than Darwin could have imagined... “Web-of-life” Dalhousie University News July 11, 2007 Ford Doolittle Many [microbes] swap genes back and forth, or engage in gene duplication, recombination, gene loss or gene transfers...”

2. Is the frog more closely related to the fish or to the human, based on this tree? 1. Which tree is more accurate? “The tree-thinking challenge” Science 310:979, 2005 A B

Volpe & Rosenbaum Fig.14.3 Schopf PNAS 91:6735, 1994 Extant Fossil

Mass extinctions, as well as radiations leading to taxonomic diversity App1.Fig.2

“Loss and recovery of wings in stick insects” Nature 421: 264, 2003 Winged Partially winged Wingless Morphological dataPhylogeny based on molecular data MaleFemale

GENE - sequence of DNA (or RNA) that is essential for a specific function EVOLUTIONARY INFORMATION FROM DNA SEQUENCES? 1. Protein-coding genes 2. RNA-specifying genes - structural - regulatory U.S. Dept of Energy Human Genome Program, Do not use term in text (p.9): “Untranscribed genes” for #3 3. Functional DNA elements

PSEUDOGENE - non-functional DNA with high degree of similarity to a functional gene How can pseudogenes arise during evolution? “SILENT” GENE - untranscribed, but potentially functional at DNA level Orthologous genes - descendants of an ancestral gene that was present in the last common ancestor of two or more species Paralogous genes - arose by gene duplication within a lineage

Fig.1.4 “TYPICAL” EUKARYOTIC PROTEIN-CODING GENE Is there an error in this figure? Where is the promoter? 5’ UTR ?3’ UTR ? What regions will be present in the mRNA?

“TYPICAL” BACTERIAL GENE ORGANIZATION Fig.1.6 Operon = cluster of co-transcribed genes How many promoters in this region? How many proteins encoded? Evolutionary advantages of operon organization?

- DNA usually shown as single-stranded with coding strand in 5’ to 3’ orientation PROTEIN-CODING GENES 5’ …. AUG GGA UUG CCC GCC …. 3’ 3’.… TAC CCT AAC GGG CGG …. 5’ 5’ …. ATG GGA TTG CCC GCC …. 3’ “coding strand” DNA “template strand” mRNA … so genetic code table can be used directly

Codon families have 1 – 6 members 5’ …. AUG GGA UUG CCC CAC …. 3’ For the 61 sense codons, how many substitution mutations are possible?

Genetic code is not “universal” Some mitochondria, a few bacteria, a few protists use a non-standard code Table 1.4 Vertebrate mitochondrial code UGA = Trp (instead of stop codon) AGA, AGG = stop codons AUA, AUG = Met Possible implications of different codes in nature?

AMINO ACIDS – Venn diagram showing properties Fig. 1.9

Table 4.7 Conservative Ile Amino acid substitutions: Radical Cys Amino acid substitution matrices

BLOSUM62 matrix - based on observed frequencies of amino acids replacing other amino acids during protein evolution, particularly within conserved regions BLOSUM = BLOcks Substitution Matrix