Genes and Evolution

Molecular clocks and phylogenies

Adam Price

Systematics A definition of taxonomyPhylogenies Characters and traits

Homology and homoplastySimple PhylogeniesMolecular evolution

SubstitutionsSynonymous and nonsynonymous Selection and neutral theory

Molecular phylogeniesMolecular clocks

Defining Systematics and Taxonomy

Systematics- the study of the diversity of organisms

Taxonomy- the science of classification of organismstaxis = Greek to arrange, classify

Why?Explains evolutionary relationshipsIntrinsically interestedUnderpins an understanding of biology- e.g. ecology, conservationImportant in applications to human life

Phylogeny- the history of descent of a group of organisms from a common ancestor

from Greek- phylon = tribe, race genesis = source

Conventionally represented by a phylogeneic treeMonkey

Gorilla

Chimpanzee

Human

Ferns

Conifers

Peas

Rice

Phylogenic trees

Phylogentic trees are based on comparison of traitsindividuals with common traits are placed together

Traits inherited from a common ancestor are termed homologous

Traits that differs from the ancestor are termed derived

Phylogenies are trees that best explain the distribution of homologous and derived traits in the organisms studied (the focal group).

Character = a feature of the organisms (e.g. flower colour, height)Trait = one form of a character (blue flower colour, short height)

Derived trait

TaxonJaws Lungs Claws or

nailsFeathers Fur Mammary

glandsFour-chambered

heartHagfish - - - - - - -Perch + - - - - - -Salamander + + - - - - -Lizard + + + - - - -Crocodile + + + - - - +Pigeon + + + + - - +Mouse + + + - + + +Chimpanzee + + + - + + +

Scoring traits to make a simple phylogeny

Hagfish

Perch

Salamander

Lizard

Crocodile

Pigeon

Mouse

Chimpanzee

Jaws

Lungs

Claws ornails

Four-chamberedheart

Fur, mammaryglands

Feathers

A simple phylogeny

Relative evolutionary time

Ancient events Recent events

Monophyletic

Paraphyletic

Polyphyletic

Monophyletic taxa include all descendants of a common ancestorParaphyletic taxa include some, but not all, descendants of a common ancestorPolyphyletic taxa includes members with more than one recent common ancestor

Outgroup

Outgroup a lineage closely related to the focal group

Phylogenetic trees

The problem of homoplastic traitstraits that appear similar but are not related through ancestry

Convergent evolution- independent evolution of similar traits due to similar selection pressure (e.g. wings in birds and bats)

Parallel evolution- independent evolution of common traits in organisms sharing distant relatives (e.g. patterns of butterfly wings).

Evolutionary reversals- the loss of a derived trait (e.g. limbs of snakes, teeth of frogs).

Traits used in phylogenetics

Morphology and developmentalthe importance of fossils

MolecularProtein sequencesGenetic markersDNA sequences

The advantages of molecular traits

Disadvantages ?

1/ They directly reflect the underlying process of evolution- changes in the hereditary material

2/ There are a vast number of potential traits

3/ They can detect difference between very closely related organism (even those that show no phenotypic difference)

4/ They are not effected by the environment (unlike some morphological traits)

5/ Since mutations generally occur as random events with specific probabilities, the number of mutations can be used to calibrate evolutionary time (molecular clocks)

Transitions and Transversions in nucleotide substitutions

Transitions replace a purine base with the other purine base, or a pyrimidine base with the other pyrimidine base

Pyrimidines T C C TPurines A G G A

Transversions replace a purine with a pyrimidine or vice versa

T A T G C A C GA T A C G T G C

Transition mutations are about 2 x more common than transversions

A

TC

G Transition

Transition

Transversion

Mutation in Coding vs Noncoding DNA

Mutations in noncoding DNA do not generally effect phenotype and therefore are not subjected to selection

A substantial part of the DNA of eukaryotes is noncoding- introns, repetitive sequences, pseudogenes

Some mutations in coding regions do not change amino acid sequence because of the degenerate codon system

Some mutations in coding regions change amino acid sequence to a similar type of amino acid, therefore having little or no effect on protein function

Synonymous vs nonsynonymous substitutions

Substitutions in Coding regions

Synonymous substitutions are those that do not change the amino acid that is specified by the gene

There are various degrees of nonsynonymous mutations depending on there effect on protein function. When the mutation changes the amino acid to a similar type then function may be little effected. Some amino acids of proteins are more important than others- active sites for example.

CUU ----> AUU = Leucine -----> Isoleucine

Nonsynonymous substitutions are those that change the amino acid chain specified

CUU ----> CUC = Leucine -----> Leucine

Miss-sense substitutions

Substitutions in Coding regions

Miss-sense substitutions are those that prematurely terminate the gene

UAU ----> UAG = Tyrosine -----> Stop

UUA ----> UAA = Leucine -----> Stop

Generally rare since nearly always involved change in protein activity

U C A GUUU UCU UAU UGUUUC

Phenyl-alanineF UCC UAC

TyrosineYUGC

CystineC

UUA UCA UAA UGA Stop

U

UUGLeucineL

UCG

SerineS

UAGStop

UGG TryptophanWCUU CCU CAU CGUCUC CCC CAC

HistidineHCGC

CUA CCA CAA CGA

C

CUG

LeucineL

CCG

ProlineP

CAGGlutamineQ

CGG

ArginineR

AUU ACU AAU AGUAUC ACC AAC

AsparagineNAGC

SerineS

AUAIsoleucineI

ACA AAA AGA

A

AUG MethionineM ACG

ThreonineT

AAGLysineK

AGGArginineR

GUU GCU GAU GGUGUC GCC GAC

AspaticacidD GGC

GUA GCA GAA GGA

G

GUG

ValineV

GCG

AlanineA

GAGGlutamicacidE GGG

GlycineG

Second Letter

Fir

st L

ette

r

Codon usage

0

2

4

6

8

10

12S

ub

stit

uti

on

s p

er

site

pe

r 10

00,0

00,0

00 y

ea

rsSynonymous mutationsNonsynonymous mutations

Synonymous mutations are more commonly fixed in evolution

0

1

2

3

4

5

6

7

8

9

10

Su

bst

itu

tio

ns

pe

r si

te p

er

1000

,000

,000

ye

ars

Ups

trea

m r

egio

ns

Dow

nstr

eam

reg

ions

Non

-deg

ener

ate

site

s

Tw

ofol

d de

gene

rate

sit

es

Fou

rfol

d de

gene

rate

sit

es

Intr

ons

Pse

udog

enes

Ani

mal

mtD

NA

Different types of sequence evolve at different rates

Comparing amino acid sequences

leu arg phe cys ser arg

leu gap phe cys phe arg

leu gap phe cys phe arg

leu arg ile cys ser argleu arg ile cys ser arg

leu arg phe cys ser arg

ser

ser

ser

serala

ile

Sequence 1Sequence 2Sequence 3Sequence 4Sequence 5Sequence 6

leu arg phe cys ser arg

leu gap phe cys ser arg

ser

ser

Sequence 1Sequence 2

leu arg phe cys ser arg

leu phe cys ser arg

ser

ser

Sequence 1Sequence 2

leu arg phe cys ser arg

leu gap phe cys phe arg

leu gap phe cys phe arg

leu arg ile cys ser argleu arg ile cys ser arg

leu arg phe cys ser arg

ser

ser

ser

serala

ile

Sequence 1Sequence 2Sequence 3Sequence 4Sequence 5Sequence 6

1 2 3 4 5 6

1 2 2 1 2 1

2 5 0 3 4 3

3 5 7 3 4 3

4 6 4 4 1 2

5 5 3 3 6 2

6 6 4 4 5 5

Sequence NumberDifferences

Similarities

Comparing amino acid sequences

Human/chimp G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G Y S YRhesus monkey G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G Y S Y

Horse G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F T YDonkey G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F S Y

Cow G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F S YDog G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A P G F S Y

Rabbit G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A V G F S YGray whale G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A V G F S Y

Grey kangaroo G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L N G L F G R K T G Q A P G F T Y

Chicken G D I E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A E G F S YPigeon G D I E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A E G F S YDuck G D V E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A E G F S YTurtle G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L N G L I G R K T G Q A E G F S YSnake G D V E K G K K I F T M K C S Q C H T V E K G G K H K T G P N L H G L F G R K T G Q A V G Y S YFrog G D V E K G K K I F V Q K C A Q C H T C E K G G K H K V G P N L Y G L I G R K T G Q A A G F S YTuna G D V A K G K K T F V Q K C A Q C H T V E N G G K H K V G P N L W G L F G R K T G Q A E G Y S Y

Dogfish G D V E K G K K V F V Q K C A Q C H T V E N G G K H K T G P N L S G L F G R K T G Q A Q G F S Y

Samia moth G N A E N G K K I F V Q R C A Q C H T V E A G G K H K V G P N L H G F Y G R K T G Q A P G F S YHornworm moth G N A D N G K K I F V Q R C A Q C H T V E A G G K H K V G P N L H G F F G R K T G Q A P G F S YScrew worm fly G D V E K G K K I F V Q R C A Q C H T V E A G G K H K V G P N L H G L F G R K T G Q A A G F A Y

Fruit fly G D V E K G K K L F V Q R C A Q C H T V E A G G K H K V G P N L H G L I G R K T G Q A A G F A YBakers yeast G S A K K G A T L F K T R C E L C H T V E K G G P H K V G P N L H G I F G R H S G Q A P G Y S Y

Candida krusei (yeast) G S A K K G A T L F K T R C A E C H T V E A G G P H K V G P N L H G I F G R H S G Q A P G Y S YNeursopora (mold) G D S K K G A N L F K T R C A E C H E N L T Q K I G P A L H G L F G R K T G Q A D G Y A Y

Wheat G N P D A G A K I F K T K C A Q C H T V E A G A H K Q G P N L H G L F G R Q S G S T A G Y S YSunflower G D P T T G A K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T A G Y S Y

Mung bean G D S K S G E K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T A G Y S YRice G N P K A G E K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T P G Y S Y

Sesame G D V K S G E K I F K T K C A Q C H T V E K G A H K Q G P N L N G L F G R Q S G T T P G Y S Y

Cytochrome C- a highly conserved gene

Acidic side chains Basic side chainsHydrophobic side

chains

0

10

20

30

40

50

60

0 200 400 600 800 1000 1200

Time since divergence (millions of years)

Am

ino

acid

sub

stit

utio

ns (

per

100

resi

dues

) in

cyt

ochr

ome

c

Yeast vs mould

Angiosperms vs animals

Insects vs vertebrates

Fish vs land vertebrates

Amphibians vs birds and mammals

Birds vs mammals

Mammals vs reptiles

Birds vs reptiles

A molecular clock for Cytochrome c

The Neutral Theory of molecular evolution

Most mutations are either selectively neutral or nearly so.

Thus, the genetic variation within species results from random genetic drift

Consider population of size N with a neutral mutation rate at a locus of mutations per gamete per generation

No. of new mutations = x 2N

Probability of fixation by genetic drift = frequency, p = 1/2N

Number of new mutations per generation that are likely to become fixed by genetic drift = no. of mutations x probability of fixation

=

The rate of fixation of neutral mutations is equal to the neutral mutation rate

Molecular clocks

Thus, sequences diverge in evolution at a constant rate

Thus, the divergence between two sequences can be used to say when the two organisms diverged from each other

But remember•Not all mutations are neutral•Not all loci change at the same rate•Transitions are more common than transversions•Rates are strictly based on generations (not years), and reproductive rates vary between species

Therefore, all molecular clocks need calibrating

600

500

400

300

200

100

0

Mil

lion

yea

rsag

o

Species

Divergence based on molecular clockDivergence based on fossil record

Divergence of humans from other species based on -globin molecular clock calibrated on fossil evidence of divergence from cows

Calibration of -globin molecular clock

Shark

Carp

Frog

AlligatorChicken

QuollCow

Baboon