Molecular Clock I. Evolutionary rate Xuhua Xia

Xuhua Xia Slide 2 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? Molecular clock hypothesis

Xuhua Xia Slide 3 Combined data for hemoglobins, cytochrome c & fibrinopeptide Fig 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 member within group should be equal K AC = K OA + K OC (1) K BC = K OB + K OC (2) K AB = K OA + K OB (3) So K OA = (K AC + K AB - K BC ) / 2 K OB = (K AB + K BC - K AC ) / 2 K OC = (K AC + K BC - K AB ) / 2 Fig Relative-rate test

Xuhua Xia Slide 5 Then according to molecular clock hypothesis: K OA = K OB so K OA – K OB = 0 and from equations (1) and (2) K OA – K OB = K AC – K BC Can compare rates of substitution in lineages A and B directly from K AC and K BC Fig Relative-rate test

Xuhua Xia Slide 6 A B C A B C Equal rates in lineages leading to A and B Slower rate in B lineage K AC = K BC K AC > K BC Rate difference

Xuhua Xia Slide 7 Relative-rate test Critical assumption: K AC, K BC and K AB are estimated without error. K’ AC = K OA + K OC +  AC K’ BC = K OB + K OC +  BC K’ AB = K OA + K OB +  AB K OA – K OB = K’ AC – K’ BC +  AC -  BC AC B O

Xuhua Xia Slide 8 How do you interpret the data shown in this table?

Xuhua Xia Slide 9 N r = number aa positions where human vs. rat different but human vs. chicken identical so replacement in rodent lineage N r = 600 N h = number of aa positions where human vs. rat different but rat vs. chicken identical So replacement in human lineage N h = 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:  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)

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 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 PhaseRate of AA replacementKA/Ks Slow phase 0.3  Ruminant rapid phase  0.30 Primate rapid phase  0.49

Xuhua Xia Slide 18 Fig 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 “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, (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, (2007).