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Molecular Clock I. Evolutionary rate. Xuhua Xia [email protected] http://dambe.bio.uottawa.ca. 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.

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Molecular clock i evolutionary rate

Molecular ClockI. Evolutionary rate

Xuhua Xia

[email protected]

http://dambe.bio.uottawa.ca


Molecular clock hypothesis
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?


Clock like substitution rate
Clock-like substitution rate

Fig. 4.15

Combined data for hemoglobins, cytochrome c & fibrinopeptide


Relative rate test
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)

KOA = (KAC + KAB - KBC ) / 2

So

KOB = (KAB + KBC - KAC ) / 2

KOC = (KAC + KBC - KAB ) / 2


Relative rate test1
Relative-rate test

Then according to molecular clock hypothesis:

so KOA – KOB = 0

KOA = KOB

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


Rate difference
Rate difference

A

C

B

A

C

B

Equal rates in lineages

leading to A and B

Slower rate in B lineage

KAC > KBC

KAC = KBC


Relative rate test2
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

O

A

C

KOA – KOB = K’AC – K’BC + AC - BC

B



Sub rates between rodent and human
Sub. rates between rodent and human

Nr = number aa positions where human vs. rat different

but human vs. chicken identical

Nr = 600

so replacement in rodent lineage

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?


When to use aa sequence
When to use AA sequence?

“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


Beta hemoglobin gene cluster
Beta hemoglobin gene cluster

Adult:

22(HbA)

22(HbA-2)

Fatal:

21 (HbF1)

22 (HbF2)

Embryonic:

22 (Hb Gower I)

22 (Hb Gower II)


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


Causes of rate differences p 152
Causes of rate differences (p.152) (Table 4.13)

  • 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


Sub rate generation time metabolic rate
Sub. rate, generation time, metabolic rate (Table 4.13)

Martin PNAS 1993


Rate difference between nuc and mt dna
Rate difference between nuc and mt DNA (Table 4.13)

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…



Positive selection
Positive selection? (Table 4.13)

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

Fig. 4.19


Primitive vs advanced p 153
“Primitive” vs. “advanced” (p.153) (Table 4.13)

Ancestor

Extant organisms

Fig. 4.18

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


Rna viruses and retroviruses
RNA viruses and retroviruses (Table 4.13)

- 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


Evolution of hiv population within an individual patient
Evolution of HIV population within an individual patient (Table 4.13)

- 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 positionindicates when it was sampled and its vertical position indicates how genetically different it was from the first sample”.

Freeman & Herron Fig. 1.10


Who brought hiv 1 to america
Who brought HIV-1 to America? (Table 4.13)

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).


Who brought hiv 1 to america1
Who brought HIV-1 to America? (Table 4.13)

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).


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