1. Molecular Clock: Lineage-specific evolutionary rate
Xuhua Xia

2. Molecular clock hypothesis
Within given gene (or DNA region), mutations (nt or aa sub) accumulate
at 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?
Xuhua Xia

3. Clock-like substitution rate
Fig. 4.15
Linear relationship
What does slope represent?
# subs/site per unit time
= rate
Combined data for hemoglobins, cytochrome c & fibrinopeptide
several apparent deviations: slowdown in rate after divergence of ape/monkey lineages & acceleration after split of horse/donkey lineages
What would figure look like without combining genes

4. Different rates among genes
Linear relationship between # substitutions
and geological time
Rates of aa substitution vary among proteins
… so slopes will differ
Alberts Fig. 5.1
Xuhua Xia

5. Relative-rate test
To compare rates in lineages A and B, use C as reference species
If constant rate, then “distance” from outgroup to each member
within group should be equal
KAC = KOA + KOC (1)
KBC = KOB + KOC (2)
Fig. 4.16
KAB = KOA + KOB (3) So
KOA = (KAC + KAB - KBC ) / 2
KOB = (KAB + KBC - KAC ) / 2
KOC = (KAC + KBC - KAB ) / 2
Xuhua Xia

6. Relative-rate test Then according to molecular clock hypothesis:
KOA = KOB
so KOA – KOB = 0
and from equations (1) and (2)
KOA – KOB = KAC – KBC
Fig. 4.16
Can compare rates of substitution in lineages A and B
directly from KAC and KBC
The importance of chooing a good outgrout: a long OC could obscure the difference between OA and OB
Xuhua Xia

7. Rate difference Equal rates in lineages Slower rate in B lineage
leading to A and B
Slower rate in B lineage
KAC > KBC
KAC = KBC
Xuhua Xia

8. Relative-rate test K’AC = KOA + KOC + AC K’BC = KOB + KOC + BC O
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 O A C
KOA – KOB = K’AC – K’BC + AC - BC B
The longer the branch, the more substitution saturation and the more difficult to arrive at an accurate estimate.
Another reason for chooing a good outgrout wisely: a long OC could obscure the difference between OA and OB
Xuhua Xia

9. How do you interpret the data shown in this table?
Tip: Title of this section in text:
“Nearly equal rates in mice and rats”
Xuhua Xia

10. Sub. rates between rodent and human
P. 149: "The number of gaps was also higher in humans (44 gaps) than in rodents (31 gaps)" Switch "humans" and "rodents"
Nr = number aa positions where human vs. rat different
but human vs. chicken identical
so replacement in rodent lineage
Nr = 600
Nh = number of aa positions where human vs. rat different
but rat vs. chicken identical
Growth hormone is one of the exceptions. It evolves faster in human than in rodents.
So replacement in human lineage
Nh = 416
Tip: p section is called “Higher rates in rodents than in primates”
The reason for using AA: lower mutiple hits than nucleotide sequence, essential for inferring Nr and Nh

11. Beta hemoglobin gene cluster
Adult:
22(HbA)
22(HbA-2)
Fatal:
A136 22(HbF1)
G136 22 (HbF2)
Embryonic:
22 (Hb Gower I)
22 (Hb Gower II)
Xuhua Xia

12. Can use duplicated genes to test if rates are constant (Table 4.13)
Human b-globin genes
Mouse b-globin genes
embryonic
fetal
adult
embryonic
fetal
adult
Score numbers of nt subs per syn site (KS) and per non-syn site (KA) between duplicated genes in humans & rodents
How do you interpret these data?
“Duplicate copies in mouse are all more divergent than [counterpart copies] in humans”
Cautionary notes: (1) there may be gene conversion events (“copy correction”) between sequences in multi-gene families (Topic 11), (2) the mouse genes may be in genome regions with high mutation rate
“Higher rates in rodents than in primates” p
Xuhua Xia

13. Causes of rate differences (p.152)
Mutation rates
Generation time
Metabolic rate (e.g., high aerobic respiration leads to mutagenic effects of oxygen free radicals)
DNA repair
Gene conversion in multi-gene families
Substitution rates:
population size
genetic variation
purifying selection or positive selection
Different genomic background (known different rates at different genomic regions)
Xuhua Xia

14. Sub. rate, generation time, metabolic rate
Martin PNAS 1993
Xuhua Xia

15. Rate difference between nuc and mt DNA
For mammalian mitochondrial genes,
Ks ~ 5.7 x 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…
This explains why the maximum parsimony method is used widely by plant phylogeneticists but rarely by animal phylogeneticists

16. Relative rates for nuclear, chloroplast
and mitochondrial genes in plant cells?
In plants, mitochondrial rates of nt sub are much slower than nuclear (or chloroplast)
… whereas mammalian mito rate ~ 10x faster than nuclear
L = # sites

17. Positive selection? Fig. 4.19
Tree based on growth hormone genes, with branch length proportional to the number of nucleotide substitutions, and number of AA replacement shown under branch
Didn't we just conclude that rodents evolve faster than humans?
Phase
Rate of AA replacement
KA/Ks
Slow phase
0.3±0.1
0.03
Ruminant rapid phase
5.6±1.4
0.30
Primate rapid phase
10.8±1.3
0.49
Fig. 4.19
Xuhua Xia

18. RNA viruses and retroviruses
- 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
Xuhua Xia

19. Evolution of HIV population within an individual patient
The rapid evolution makes it possible to do tip-dating.
- HIV virions harvested (blue vertical lines) at various times & sequenced
“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”.
Freeman & Herron Fig. 1.10
Xuhua Xia

20. 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, (2007).
Xuhua Xia

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, (2007).
Xuhua Xia