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How to date

How to date. Xuhua Xia xxia@uottawa.ca http://dambe.bio.uottawa.ca. Objectives. Two major objectives of molecular phylogenetics Branching patterns (speciation or gene duplication events) Dating of the speciation or gene duplication events Classification of methods Criteria used

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How to date

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  1. How to date Xuhua Xia xxia@uottawa.ca http://dambe.bio.uottawa.ca

  2. Objectives • Two major objectives of molecular phylogenetics • Branching patterns (speciation or gene duplication events) • Dating of the speciation or gene duplication events • Classification of methods • Criteria used • Maximum likelihood (ML) method (e.g., PAML) • Bayesian methods (e.g., BEAST) • Least-squares (LS) method based on distance-based matrices (e.g., DAMBE) • Hard- or soft-bound • Global or local clock • Data needed • A topology • A set of aligned sequences OR a distance matrix satisfying the molecular clock hypothesis (either globally or locally) • Calibration points • One or more from fossil record • From sampling time for rapidly evolving species (e.g., RNA viruses) Slide 2

  3. The LS method in linear regression Y = a + b x RSS = 0 means a perfect fit of the linear model to the data. A large RSS means a poor fit. Slide 3

  4. The rational of the LS method 1 t3 2 t2 3 T1 4 4 Sp1 Sp2 d12 Sp3 d13 d23 Sp4 d14 d24 d34 Slide 4

  5. Multiple calibration points 1 T3 2 t2 3 T1 4 4 Sp1 Sp2 d12 Sp3 d13 d23 Sp4 d14 d24 d34 Slide 5

  6. Slide 6

  7. gibbon sumatran 20.655±1.221 3.104±0.273 orangutan 14±0 gorilla Hard calibration point = 14 million years bonobo 7.079±0.527 1.754±0.184 a) chimpanzee 7±0 Hard calibration point = 7 million years human gibbon sumatran 20.903±1.503 3.206±0.280 orangutan 14.757±0.217 gorilla Soft calibration point = 14 million years bonobo 7.258±0.530 1.818±0.180 b) chimpanzee Soft calibration point = 7 million years 5.487±0.434 human

  8. Dating with local clocks OTU1 OTU2 7 OTU3 10 7 OTU4 16 13 12 a) b) 6 OTU4 T1 = 10 3 OTU3 3 2r2 t2 = 5 OTU2 2 RSS = 0 r0 = 0.6, r1 = 3, r2 = 1.2 t3 = 1.6667 5r1 OTU1 c) OTU4 T1 = 10 OTU3 t2 = 6.2195 OTU2 RSS = 13.1667 r = 0.6833 t3 = 5.1220 OTU1

  9. Method comparison RY07 BEAST Slide 9

  10. Pan calibration time = 10 Myr 7.890±1.308 Homo calibration time = 35 Myr 9.450±1.522 Gorilla 12.988±2.053 Pongo 32.564±4.103 Macaca 56.059±5.436 Callithrix Daubentonia Cheirogaleus 26.761±3.528 Mirza calibration time = 77 Myr M.ravelobensis 7.9±1.4 M.tavaratra 21.639±2.906 78.210±1.871 M.berthae 49.231±4.101 2.2±0.4 M.myoxinus 5.3±0.9 2.3±0.4 M.rufus1 4.617±0.808 37.682±3.785 M.rufus2 9.7±1.3 4.348±0.845 M.sambiranensis M.griseorufus 7.089±1.119 M.murinus 66.992±5.038 Lepilemur 36.351±2.849 Propithecus Hapalemur 9.608±1.533 26.049±2.955 Lemur 14.668±1.861 Eulemur 18.125±2.285 Varecia Loris 46.073±5.575 Galago

  11. Galago [31.6677,53.3297] Loris Varecia [14.5445,23.4733] Eulemur [10.9426,17.9562] Lemur [20.9195,33.1815] [6.8351,11.8498] Hapalemur Propithecus [25.534,38.8127] [53.26,79.827] Lepilemur M.murinus [4.8645,8.6395] M.griseorufus calibration time = 77 my M.sambiranensis [7.3,11.7] [2.7447,4.8025] M.rufus2 [22.6131,34.6002] [3.3,5.3] M.rufus1 [3.7,6.0] [1.6314,2.9896] M.myoxinus [13.8197,21.595] [1.3,2.6] [39.2193,60.6649] [68.927,92.9419] M.berthae M.tavaratra M.ravelobensis [5.7784,9.3783] Mirza [18.7945,29.488] Cheirogaleus Daubentonia Callithrix [46.4962,69.6653] Macaca [27.9235,37.5614] Pongo [11.2396,17.6519] calibration time = 35 my Gorilla calibration time = 10 my [8.059,12.1832] Homo [5.5629,9.3534] Pan

  12. Rationale of Tip-Dating s6@1965 25 yr t4=? s5@1960 30 yr t5=? s4@1970 20 yr t2=? s3@1980 10 yr t3=? s2@1975 15 yr t1=? s1@1990 40 50 30 40 20 RSS=(d12/r+15-2*t1)2+(d13/r+10-2*t3)2+(d14/r+20-2*t3)2 +(d15/r+30-2*t5)2+(d16/r+25-2*t5)2+(d23/r+15+10-2*t3)2 +(d24/r+15+20-2*t3)2+(d25/r+15+30-2*t5)2+(d26/r+15+25-2*t5)2 +(d34/r+10+20-2*t2)2+(d35/r+10+30-2*t5)2+(d36/r+10+25-2*t5)2 +(d45/r+20+30-2*t5)2+(d46/r+20+25-2*t5)2+(d56/r+30+25-2*t4)2 r = 0.01 Slide 13

  13. Final dated tree s6@1965 1950 s5@1960 1940 s4@1970 1960 s3@1980 1950 s2@1975 1970 s1@1990 Slide 14

  14. Dates with standard deviation S8@1985 1,792.77±22.00 S7@1962 S4@1968 1,770.96±24.30 1,817.23±16.71 S3@1945 1,791.98±21.08 S5@2000 1,766.78±25.64 1,875.51±13.38 S6@1970 1,902.81±8.42 S2@1965 S1@1980 Slide 15

  15. Dating and cospeciation H14 H13 H12 H11 H10 H9 H8 H7 H6 H5 H4 H3 H2 H1 P14 P13 P12 P11 P10 P9 P8 P7 P6 P5 P4 P3 P2 Slide 16 P1

  16. Dating and cospeciation P14 P13 P12 H14 H13 P11 H12 H11 P10 H10 H9 P9 H8 H7 P8 H6 H5 P7 H4 H3 P6 H2 H1 P5 P4 P3 P2 P1 12 10 8 6 4 2 0 0 2 4 6 8 10 12

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