pbase/sheila/

1. human-chimp speciation~1. inferring the mode of speciation from genomic data: a study of the great apes 2. genetic evidence for complex speciation of humans and chimpanzees05.dec.06 – frank chanCS374 algorithms in biology

2. primates: a close family http://www.pbase.com/sheila/

3. human and chimps: how long ago have they split?

4. July 29, 2000 First unambiguous Brennifer anistonii sp. amigos identified Malib, California January 7, 2005 Allopatry reported for B. anistonii Los Angeles, California March 25, 2005 Population crash for B. anistonii (filed for divorce) Los Angeles, California July 2005, 2005 Printed literature (W magazine) makes mention of Condé Nast Brangelina jolieus sp. cryptovolerus October 2, 2005 Extinction (divorce) of B. anistonii Los Angeles, California December 2, 2005 Fossil of B. jolieus identified Santa Monica, California May 27, 2006 B. jolieus known to be reproductively viable Swakopmund, Namibia

5. he said, she said… have they, or have they not? Circa 2000 July 2005 Nov 2005 Brad Pitt denies relationship with Angelina Jolie “This particular story is completely untrue” –Pitt, Access Hollywood, 08.apr.05 sometimes it is hard to tell exactly when something happens…

6. speciation - terms "Species are groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups." Mayr, 1942 Sympatric- Greek sun-, from sun. together, with Allopatric Greek, from allos, other. Parapatric Greek, from para, beside.

7. speciation & divergence - implications • it all boils down to gene flow X no gene flow divergence time

8. “speciation” – an example from our daily lives indo-european german english french Vater unser im Himmel, geheiligt werde dein Name. Dein Reich komme. Dein Wille geschehe, wie im Himmel so auf Erden. Vater unser im Himmel, geheiligt werde deinName. DeinReichkomme. Dein Willegeschehe, wie im Himmel so auf Erden. Vater unser Our Father, Who art in heaven, Hallowed be Thy Name. Thy Kingdom come.Thy Will be done, on earth as it is in Heaven. Our Father, Who artin heaven, Hallowed be Thy Name. Thy Kingdomcome. Thy Willbe done, on earth as it is in Heaven. Our Father Notre Père Notre Père qui es aux cieux, que ton Nom soit sanctifié, que ton règne vienne, que ta volonté soit faite sur la terre comme au ciel. Notre Père qui es aux cieux, que ton Nom soit sanctifié, que ton règnevienne, que ta volonté soit faite sur la terre comme au ciel.

9. but what happens when “species” hybridize? indo-european X gene flow no gene flow german english french Es ist unserer Aufmerksamkeit nicht entgangen, dass die speziellen Paarungen... It has not escapedour notice that the specific pairing… Il n'a pas échappé à notre attention que l'appariement spécifique des bases… die wir als gegeben voraussetzen, unmittelbar auf... we have postulatedimmediatelysuggests… que nous avons proposésuggèreimmédiatement… einen möglichenVervielfältigungsmechanismus für die genetische Erbsubstanz schließen lassen. a possiblecopying mechanism for the genetic material. un mécanismepossible de réplication pour le matériel génétique.

10. Osada & Wu

11. divergence & constraints

12. how constraints may affect rates of hybridization indo-european german english french Das ist gut! Es ist unserer Aufmerksamkeit nicht entgangen... It has not escapedour notice… Il n'a pas échappé à notre attention… vs. That is good! Il est bon!

13. allopatric vs. parapatric speciation revisited

14. likelihood calculation τi = 2tui θi = 4Neui at equilibrium: uit uit

15. testing model Defining γ=τ/θ=t/2Ne γ1<< γ2 γ2 γ1

16. testing model the authors therefore rejected the γCDS = γIGSmodel

17. parapatry between chimps and gorilla? chimps gorilla http://pin.primate.wisc.edu/factsheets/entry/chimpanzee

19. primate lineage some ape divergence (τ) human chimp gorilla organutan macaque

20. the model τgenome τspecies human chimp

21. why might there be variations? τgenome τspecies human chimp

22. primate lineage some ape HCGO HCG M HC O G C H human chimp gorilla organutan macaque

23. sometimes local tree disagrees with species tree some ape chimpanzee human gorilla A T T

24. the most parsimonious solution some ape CG chimpanzee human gorilla A T A T T

25. other scenarios are possible, too some ape HG CG chimpanzee human gorilla T A T T

26. divergences help define relative branch lengths some ape HCGO HCG M HC O τgenome G C H CG human chimp gorilla organutan macaque HG

27. can we find these events? H+C+HG+CG H+C+HG+CG+HC+HCG+M

28. HCGOM HCGM 134% 124% HG/CG HC 88% 86% what does it look like near these events? H+C+HG+CG H+C+HG+CG+HC+HCG+M

29. where we find real incongruence, τdiffers Near sites with 2 HG/CG events within 200bp Measuring human-chimp divergence: b(d) Out of total events: n(d) Ratio: r(d) Parametric model: s(d) Near sites with 2 HC events within 200bp Quadratic function S over a defined window: L = 5000bp Measuring enrichment of human-chimp b(d) divergence:

30. even less divergence on the X chromosome human-chimp divergence chromosomal average human-chimp/human-macaque (5Mb) human-chimp/human-gorilla (10Mb) HG and CG sites over the X HCGOM shotgun (10Mb)

31. Model by Patterson et al.

32. controversy? you bet!

33. but did human and chimp hybridize??? some ape chimpanzee human gorilla

34. at HG sites [or CG sites] some ape τspecies chimpanzee human gorilla HCGOM HCGM HG/CG H+C+HG+CG H+C+HG+CG+HC+HCG+M HC τHG/CG

35. at HC sites some ape τspecies chimpanzee human gorilla HCGOM HCGM HG/CG H+C+HG+CG H+C+HG+CG+HC+HCG+M HC τHC

36. H+C+HG+CG H+C+G+HG+CG+HC+HCG+M is there a way to explain the X data? HG and CG sites over the X HCGOM shotgun (10Mb) human-chimp divergence chromosomal average some ape chimpanzee gorilla human τX chr.

37. what if I do the same for HG sites??? some ape τspecies chimpanzee human gorilla If I build a figure using HG/CG double sites, would I get a similar graph? Does that mean humans and gorillas have hybridized? H+G+HC+CG H+C+G+HG+CG+HC+HCG+M τHG

38. let’s take a closer look at the model τgenome τspecies human sympatric speciation! chimp is it possible, that the authors have it backwards???

39. allopatric speciation τspecies τgenome human chimp

40. parapatric speciation τgenome τspecies human chimp

41. authors’ conclusion:τgenome < τspecies in some regions HG/CG HC • based on problematic branch • length extrapolations • is it such a big deal? τgenome τspecies human chimp

42. call me a skeptic Such a scenario [that human lineage hybridised with the chimp lineage]— or a range of kinds of population subdivision—can indeed account for diversity among loci in divergence, but Patterson et al. do not test whether their data are consistent with the simple null model of abrupt allopatric speciation of a single well-mixed population. A simple calculation (H. Innan, personal communication) shows that their data are consistent with an ancestral effective population size of Ne ~45,000, which does not seem unreasonable, and is consistent with previous studies. Thus, there is no statistical evidence for hybridisation. Curr Biol. 2006 Aug 22;16(16):R647-50.

43. viability of hybrids • tend to be a question…

44. other unfortunate unions… Leopons Jaglion Tigon

45. more unfortunate unions… • zorse • grolar bear/pizzly bear • many of these animals don’t do all that well, let • alone reproduce…

46. primates: a close family http://www.pbase.com/sheila/

47. danke!thank you! merci!

48. 21 22 4 24 5,6 23 25 26 7,8,9,10,11 12 20 2,3 17,18,19 13 14 15 16 Other traits also evolve in parallel Completes Lows 1 Colosimo, et al., 2005

49. Control nuclear phylogeny indicates that local evolution of low populations from marine ancestors Low morphComplete morph Colosimo, et al., 2005

50. Eda tree reveals an ancient allele underlying the low-plated trait in far distant populations A similar tree from Pitx1 shows no shared allele, unlike the Eda tree Low morphComplete morph Reduced pelvisComplete pelvis Eda Colosimo, et al., 2005