Phylogenetics: The “E” word in disguise

1. Phylogenetics: The “E” word in disguise Keith A. Crandall, Brigham Young University http://biology.byu.edu/Faculty/kac/crandall_lab/

2. Phylogeny - What is it? • How do you reconstruct them? • What are they good for? • Is evolution important?

3. Molecular Evolution of HIV: A teaching model for evolution • Over 22 million people have died from AIDS • Over 42 million people are living with HIV/AIDS - 74% in sub-Saharan Africa • Over 19 million women are living with HIV/AIDS • 14,000 new infections every day (half occurring among people ages 15-24 • Over 14 million AIDS orphans

5. Where Did HIV Originate? • Geographic location? • Previous host? • Timing of transmission?

6. HIV-1 and HIV-2 HIV-1 group O and M HIV-1 group M Type 2 HIV Group M Type 1 Group O Geographic Origins & Distribution of HIV

7. Number of Trees?

8. HIV-1 Whole Genomes 1993 - 15 HIV-1 Whole Genomes 2003 (JAN) - 397

9. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

10. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

11. Working Tree sp2 sp1 c2 sp3 sp5 sp4

12. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

13. Working Tree sp2 sp1 c2 sp3 c4 sp5 sp4

14. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

15. Working Tree sp2 sp1 c7 c2 sp3 c4 sp5 sp4

16. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

17. Working Tree sp2 sp1 c7 c2 sp3 c4 c9 sp5 sp4

18. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

19. Working Tree sp2 sp1 c10 c7 c2 sp3 c4 c9 sp5 sp4

20. Estimate a Phylogeny Sp1 ACCGTCTTGTTA Sp2 AGCGTCATCAAA Sp3 AGCGTCATCAAA Sp4 ACCGTCTTGATA Sp5 AGCCTCTTCATA

21. Final Tree sp2 sp1 c10 c11 c2 c7 sp3 c4 c9 sp5 sp4

23. Previous Host • Phylogeny!

24. Full Length Gag A A / G A Group M Group O DJ264 U455 DJ263 UG037 G G IbNG ANT70 H HH8793 MVP5180 CAR402 G6165 A /E 100 CM240 A 100 100 TH253 100 B C CAR402 RU520 K89 CM240 UG037 DJ263 D RU131 CM243 DJ264 F U455 G6165 IbNG .10 G HH8793 100 100 LBV21-7 LAI VI557 H VI191 MN VI525 C 100 BR025 100 SF2 VI997 B 100 100 ETH2220 RF 100 F NDK 100 F9363 ELI UG268 D Z2Z6 VI850 DJ259 100 HAN ETH2220 SF2 BR025 92 100 .10 BK132 SM145 C BZ167 LAI ZAM18 MN B RF VI69 ELI VI174 SG365 NDK BZ162 UG274 K31 F9363 Env A F D UG273 UG037 .10 E SF170 DJ264 IbNG DJ263 CM235 CM240 C CAR402 5 ’ Pol ETH2220 G C BR025 DJ263 UG268 100 ZAM18 IbNG 100 DJ264 HH8793 100 SE364 RU131 100 100 CM240 G G6165 G6165 TH253 100 CAR402 LBV21-7 A VI991 H 84 U455 95 UG975 VI997 LAI 100 97 UG037 100 100 MN B SF2 100 99 HAN F F9363 NDK BR020 Z2Z6 RF VI850 BZ126 ELI RF F9363 D SF2 F LAI ELI SE365 B D UG269 .10 .10

25. A B HIV-1 B,C,E HIV-1 A,G HIV-2 A,B HIV-1 A,C,D,E,F,G,H,O HIV-1 E,B HIV-1 C HIV-1 A,D HIV-1 C HIV-2 A HIV-1 A,C,D HIV-1 B, C C D HIV-1 B HIV-1 B A,C,D,E,F,G,H,O HIV-1 B A,C,E,O HIV-1 B,F,C HIV-1 B A,C,E O HIV-1 B,E

26. Why Estimating Phylogenetic Relationships? • Designating Subtypes - Classification • Establishing Transmission Patterns • Evolution of Drug Resistance • Estimating Population Genetic Parameters - • Migration rates, Recombination rates, etc.

27. Transmission Patterns • Louisiana Murder Trial • Expectations? • Samples from Victim • Samples from patients of the accused • Samples from local controls

28. P P P V P P P V LC V V LC LC LC V LC LC V LC LC LC LC LC LC GUILTY! Not! VS Alternative Hypotheses VS or

32. Genetic Questions • What is this? - DNA Barcoding • Where did it come from? • When did it get here? • What’s its function? • Molecular, Ecological, Phenotypic • Correlations between form and function • Correlations between genotype and phenotype

33. River One Population Subdivision River Two Single Species Phylogeography 11 0 0 13 16 10 12 2 1 7 4 14 0 5 9 3 8

34. Comparative Phylogeography 11 0 0 13 2 16 10 12 1 7 4 14 0 5 9 Historical Isolation/ Fragmentation 3 8 11 River One 8 7 10 3 0 4 1 6 0 0 0 13 12 14 5 2 9 Recurrent Restricted Gene Flow

35. Cambarus hamulatus Cambarus jonesi Cambarus sp. nov. 1 Cambarus sp. nov. 2 Cambarus veitchorum Sampled site Western Escarpment Sequatchie Valley Jackson County Mountains Highland Rim Southern Appalachian species

36. 86 77 97 85 Phylogeny Cambarus hamulatus 74 42 68 44 84 38 86 75 82 Cambarus jonesi 100 100 55 100 99 58 48 100 97 Cambarus sp. nov. 1 91 65 100 100 93 99 Cambarus sp. nov. 2 100 100 100

37. Cambarus jonesi 3-3 2-6 1-10 20 1-7 2-5 14 1-8 1-9 18 13 19 1-11 15 17 16 3-2 1-4 2-3 1-5 9 Cambarus hamulatus 2-4 1-6 12 3-1 2-2 1-3 6 7 10 3-4 8 11 2-7 1-12 22 21 23 Cambarus sp nov 1 1-2 1-1 2-1 4 5 23 steps Cambarus sp nov 2 3 2 2-2A 2-1A 1-1A 25 1-2A 24 1 26 Genealogy 1-2, 1-5 CRE 2-1 LDC 2-3 RGF w/ IBD 2-6, 3-1, 3-3 CRE 3-2 LDC Total PF & LDC

38. Molecular Evolution

39. OPSIN: Model System for Molecular Evolution UV IR 400 500 600 700 Wavelength (nm) CRLAKIAMTTVALWFIAWT PYLLINWVGMFARSYLSPV YTIWGYVFAKANAVYNPIV YAISHPKYRAAMEKKLPCL SCKTESDDVSESASTTTSS ENVIRONMENT PHENOTYPE GENOTYPE

40. Is max Correlated with Ecological Differences? INPUT OUTPUT microscopic thin beam of spectral light Detect light not absorbed by the photopigment INPUT – OUTPUT = pigment absorbance 400 – 700 nm at 1nm intervals

41. Coil Tendencies, Compressibility, Alpha-Helix

42. Summary • Evolutionary histories provide great insights into the biology of infectious diseases • Indeed, we use these same approaches in conservation genetics, endangered species studies, etc. • HIV provides a unique model system for teaching evolution since you can experience evolution in real time • Research Experience - GET SOME! • NSF RET - Research Experience for Teachers

43. Acknowledgements • NSF • Arkansas Game & Fish • BYU • Colleagues • Students • Family