Molecular ClockI. Evolutionary rate

Xuhua Xia

xxia@uottawa.ca

http://dambe.bio.uottawa.ca

Xuhua Xia Slide 2

Within given gene (or DNA region), mutations (nt or aa sub) accumulateat an approximately equal rate in all evolutionary lineages

Rate constancy concept

Originally based on comparisons of protein sequences for hemoglobin, cytochrome c… from different organisms

Information can be used to estimate divergence times, reconstruct phylogenies…

BUT… Does it hold for all genes, all genomes… ?

How to reconcile with irregular rate of morphological evolution?

Molecular clock hypothesis

Xuhua Xia Slide 3

Combined data for hemoglobins, cytochrome c & fibrinopeptide

Fig. 4.15

Clock-like substitution rate

Xuhua Xia Slide 4

To compare rates in lineages A and B, use C as reference species

If constant rate, then “distance” from outgroup to each memberwithin group should be equal

KAC = KOA + KOC (1)

KBC = KOB + KOC (2)

KAB = KOA + KOB (3)

So KOA = (KAC + KAB - KBC ) / 2

KOB = (KAB + KBC - KAC ) / 2

KOC = (KAC + KBC - KAB ) / 2

Fig. 4.16

Relative-rate test

Xuhua Xia Slide 5

Then according to molecular clock hypothesis:

KOA = KOB so KOA – KOB = 0

and from equations (1) and (2)

KOA – KOB = KAC – KBC

Can compare rates of substitution in lineages A and B directly from KAC and KBC

Fig. 4.16

Relative-rate test

Xuhua Xia Slide 6

A B CA B C

Equal rates in lineagesleading to A and B

Slower rate in B lineage

KAC = KBCKAC > KBC

Rate difference

Xuhua Xia Slide 7

Relative-rate test

Critical assumption: KAC, KBC and KAB are estimated without error.

K’AC = KOA + KOC + AC

K’BC = KOB + KOC + BC

K’AB = KOA + KOB + AB

KOA – KOB = K’AC – K’BC + AC - BC

A C

B

O

Xuhua Xia Slide 8

How do you interpret the data shown in this table?

Xuhua Xia Slide 9

Nr = number aa positions where human vs. rat different

but human vs. chicken identicalso replacement in rodent lineage Nr = 600

Nh = number of aa positions where human vs. rat different

but rat vs. chicken identical So replacement in human lineage Nh = 416

How do you interpret these data?

Sub. rates between rodent and human

Xuhua Xia Slide 10

“They used amino acid sequences instead of DNA, because the chicken and mammalian lineages diverged about 300 million years ago…

… so it’d be difficult to obtain reliable estimates of divergence at synonymous sites.”

p.149

When to use AA sequence?

Xuhua Xia Slide 11

Beta hemoglobin gene cluster

Adult:

22(HbA)

22(HbA-2)

Fatal:

21 (HbF1)

22 (HbF2)

Embryonic:

22 (Hb Gower I)

22 (Hb Gower II)

Xuhua Xia Slide 12

Can use duplicated genes to test if rates are constant (Table 4.13)

How do you interpret the data in Table 4.13 ?

Cautionary note: there may be gene conversion events (“copy correction”) between sequences in multi-gene families

Xuhua Xia Slide 13

• Mutation rates– Generation time

– Metabolic rate (e.g., high aerobic respiration leads to mutagenic effects of oxygen free radicals)

– DNA repair

• Purifying selection or positive selection• Different genetic background

Causes of rate differences (p.152)

Xuhua Xia Slide 14

Martin PNAS 1993

Sub. rate, generation time, metabolic rate

Xuhua Xia Slide 15

For mammalian mitochondrial genes,

Ks ~ 5.7 x 10 -8 sub/ site/ year

~ 10 x higher than for mammalian nuclear genes

Mitochondrial DNA used extensively in taxonomic, forensic, conservation biology,… studies

But.. in plants, mitochondrial nt sub rate very slow…

Rate difference between nuc and mt DNA

Xuhua Xia Slide 16

An odd pattern in plants

Xuhua Xia Slide 17

Positive selection?

Tree based on growth hormone genes, with branch length proportional to the number of nucleotide substitutions

Fig. 4.19

Phase Rate of AA replacement KA/Ks

Slow phase 0.30.1 0.03

Ruminant rapid phase 0.30

Primate rapid phase 0.49

Xuhua Xia Slide 18

Fig. 4.18

Extant organisms

Ancestor

Lineage which has accumulated fewer substitutions, has retained more “primitive” ancestral state

But not necessarily any correlation between “primitive” appearance (morphological state) and amount of molecular change

“Primitive” vs. “advanced” (p.153)

Xuhua Xia Slide 19

- very rapid rate of evolution (Table 4.17)

HIV retrovirus ~ 10 6 x higher than mammalian nuclear genes

- error prone reverse transcription (RT)

- sequences may be useful in retracing spread through population

RNA viruses and retroviruses

Xuhua Xia Slide 20

- HIV virions harvested (blue vertical lines) at various times & sequenced

Freeman & Herron Fig. 1.10

“Each blue tick represents a virion sampled from the patient during the course of the infection; its horizontal position indicates when it was sampled and its vertical position indicates how genetically different it was from the first sample”.

Evolution of HIV population within an individual patient

Xuhua Xia Slide 21

Who brought HIV-1 to America?

Gilbert, M. T. et al. The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci U S A 104, 18566-70 (2007).

Xuhua Xia Slide 22

Who brought HIV-1 to America?

Gilbert, M. T. et al. The emergence of HIV/AIDS in the Americas and beyond. Proc Natl Acad Sci U S A 104, 18566-70 (2007).