Phylogenetic trees: Phylogenetic trees: Computer models of Computer models of

evolution evolution Dr Dan EverettDr Dan Everett

CSCI 1210CSCI 1210

Gene sequence and active sitesGene sequence and active sites

This diagram represents the amino acid This diagram represents the amino acid sequence of the gene for sequence of the gene for Yeast Ubiquitin Yeast Ubiquitin Activating EnzymeActivating Enzyme, UBA-1, UBA-1

Colored regions are Colored regions are conservedconserved – no random – no random mutations observedmutations observed

Triosephosphate Isomerase Triosephosphate Isomerase

SpinachSpinach CNGTCNGTKESITKESITKKLLVVSDSDLNLNSATLEADSATLEAD

RiceRice CNGTCNGTTDQVDTDQVDKKIIVVKIKILNLNEGQIASTEGQIAST

MonkeyMonkey MNGRKQMNGRKQNNLGELIGTLNAAKVPADLGELIGTLNAAKVPAD

HumanHuman MNGRKQMNGRKQSSLGELIGTLNAAKVPADLGELIGTLNAAKVPAD

MosquitoMosquito MNGDKASIADLCKVLTTGPLNADMNGDKASIADLCKVLTTGPLNAD

Sequence differencesSequence differences

The sequences are peptides, not DNA The sequences are peptides, not DNA codonscodons

The sequences must be The sequences must be alignedaligned to correct to correct for insertions and deletions (hard problem)for insertions and deletions (hard problem)

Monkey Monkey vs.vs. human proteins show fewer human proteins show fewer differences than spinach differences than spinach vs.vs. rice rice

Sequence distance matrixSequence distance matrix

SpinachSpinach RiceRice MosquitoMosquito MonkeyMonkey HumanHuman

SpinachSpinach 0.00.0 84.984.9 105.6105.6 90.890.8 86.386.3

RiceRice 84.984.9 0.00.0 117.8117.8 122.4122.4 122.6122.6

MosquitoMosquito 105.6105.6 117.8117.8 0.00.0 84.784.7 80.880.8

MonkeyMonkey 90.890.8 122.4122.4 84.784.7 0.00.0 3.33.3

HumanHuman 86.386.3 122.6122.6 80.880.8 3.33.3 0.00.0

First step in the tree First step in the tree constructionconstruction

Humans and Humans and monkeys are most monkeys are most closely related of all closely related of all pairs of species in the pairs of species in the table.table.

Create an initial Create an initial subtree. (Hypothetical subtree. (Hypothetical common ancestors in common ancestors in green)green)

Revised distance matrix:Revised distance matrix:

SpinachSpinach RiceRice MosquitoMosquito PrimatePrimate

SpinachSpinach 0.00.0 84.984.9 105.6105.6 88.5588.55

RiceRice 84.984.9 0.00.0 117.8117.8 122.5122.5

MosquitoMosquito 105.6105.6 117.8117.8 0.00.0 82.7582.75

PrimatePrimate 88.5588.55 122.5122.5 82.7582.75 0.00.0

Second subtree:Second subtree:

Revised distance matrix, againRevised distance matrix, again

SpinachSpinach RiceRice AnimalAnimal

SpinachSpinach 0.00.0 84.984.9 97.197.1

RiceRice 84.984.9 0.00.0 120.2120.2

AnimalAnimal 97.197.1 120.2120.2 0.00.0

The Final tree…The Final tree…

Why this result is significant…Why this result is significant…

Before DNA techniques, biologists Before DNA techniques, biologists constructed phylogenetic trees using constructed phylogenetic trees using traditional tools (fossils, anatomy, traditional tools (fossils, anatomy, etcetc))

DNA tools provide an independent method DNA tools provide an independent method for constructing phylogenetic treesfor constructing phylogenetic trees

Trees constructed with different methods Trees constructed with different methods match quite well!match quite well!

A common human ancestor…A common human ancestor…

Can the scenario on the right happen?Can the scenario on the right happen? Can the scenario on the left happen?Can the scenario on the left happen? M1 must be smaller than H!M1 must be smaller than H!

… … must exist! But when and must exist! But when and where?where?

Mitochondrial DNAMitochondrial DNA

MitochondriaMitochondria are the “energy factories” are the “energy factories” of the cellof the cell

Mitochondria float in the cytoplasm Mitochondria float in the cytoplasm They have their own DNA and reproduce They have their own DNA and reproduce

independently of the cell nucleusindependently of the cell nucleus Passed by mother to child in the eggPassed by mother to child in the egg Not subject to sexual recombination, so Not subject to sexual recombination, so

simpler to tracksimpler to track

The “Out of Africa” HypothesisThe “Out of Africa” Hypothesis

This phylogenetic tree This phylogenetic tree constructed using constructed using mitochondrial DNA mitochondrial DNA from 145 humansfrom 145 humans

Consistent with Consistent with migration of original migration of original humans from Africahumans from Africa

Numbers represent Numbers represent thousands of years thousands of years since common since common ancestorancestor

““Mitochondrial Eve”Mitochondrial Eve”

Existed about 200,000 years ago in AfricaExisted about 200,000 years ago in Africa Was the common female ancestor of all Was the common female ancestor of all

living humansliving humans Was NOT the only living female at the Was NOT the only living female at the

time!time! Use mitochondrial DNA because we Use mitochondrial DNA because we

inherit it from our mothers onlyinherit it from our mothers onlyRebecca Cann Rebecca Cann et alet al, Nature 1987, Nature 1987

Critique of “Mitochondrial Eve”Critique of “Mitochondrial Eve”

Rates of ‘neutral’ mutation are not constantRates of ‘neutral’ mutation are not constant In some cases mitochondrial DNA has combined In some cases mitochondrial DNA has combined

with nuclear DNA from the fatherwith nuclear DNA from the father Do these problems invalidate the theory?Do these problems invalidate the theory?http://www.apologeticspress.org/docsdis/2003/dc-03-01.htmhttp://www.apologeticspress.org/docsdis/2003/dc-03-01.htm

AcknowledgementsAcknowledgements

Human family tree: Dr Curtis Human family tree: Dr Curtis Strobeck, University of AlbertaStrobeck, University of Albertahttp://www.biology.ualberta.ca/courses/biol380/uplohttp://www.biology.ualberta.ca/courses/biol380/uplo

ads/winter03/lecture/b1/curt_strobeck/public/lectureads/winter03/lecture/b1/curt_strobeck/public/lectures/Lecture_26_Tree_of_Individuals.pdfs/Lecture_26_Tree_of_Individuals.pdf

UAB-1 gene sequence:UAB-1 gene sequence: http://www.nottingham.ac.uk/biochemcourses/shttp://www.nottingham.ac.uk/biochemcourses/s

tudents/ub/e1.htmltudents/ub/e1.html Phylogentic tree Phylogentic tree computation example: computation example: Gaston Gaston Gonnet,Gonnet,Institute for Scientific ComputingInstitute for Scientific ComputingZurich, SwitzerlandZurich, Switzerland