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

www.csmt.ewu.edu/.../ chem163/163LT1.html

Closely-related organisms have moresimilar protein sequences thandistant 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...”

www.whoi.edu/cms/images/oceanus/2005/4/v43n2-teske_edwards1en_8591.gif

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

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

Partiallywinged

Wingless

Morphological data Phylogeny based on molecular data

Male Female

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, http://www.ornl.gov/hgmis

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 afunctional 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 presentin 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 protistsuse 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

www.doc.ic.ac.uk/

- based on observed frequencies of amino acids replacing other amino acids during protein evolution, particularly within conserved regions

BLOSUM = BLOcks Substitution Matrix