Biased Substitutions in the Human Genome: Sex, Gambling and Non-Darwinian Evolution

1. Biased Substitutions in the Human Genome:Sex, Gambling and Non-Darwinian Evolution Tim Dreszer, Katie Pollard and David Haussler

2. Dreszer T. R., Wall G.D., Haussler D. and Pollard K.S.Biased Substitutions in the Human Genome: The Footprints of Male-Driven Biased Gene ConversionGenome Res. 17:1420-1430 Epub: September 4, 2007. ISSN 1088-9051/07.

3. Where this Began: Fastest Evolving Regions of the Human Genome Show a Surprising “Bias” In Top 4 Regions: • AT pair replaced by GC or CG pair 33 times • GC replaced by AT pair only once [1] 1Pollard K.S., Salama S.R., King B., Kern A., Dreszer T., Katzman S., Siepel A., Pedersen J., Bejerano G., Baertsch R., Rosenbloom K.R., Kent J. and Haussler D. Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genetics. 2(10):e168 Oct. 13, 2006.

4. Initial Terms • AT pairs bond with 2 hydrogen bonds and are here referred to as “Weak” Pairs • GC bond with 3 and are referred to as “Strong” Pairs • SNPs are single nucleotide polymorphisms while “substitutions” are single pair changes that have been “fixed” in the genome. • “Bias” here specifically refers to “Weak to Strong” SNPs or substitutions. This work finds surprising biased substitution patterns.

5. Large Scale Bias: Isochores • In warm blooded vertebrate genomes, regions as large as 300 kilobases dubbed “isochores” can be strikingly higher or lower in GC content.[2] • Isochores stretch across conserved and non-conserved sequences. • The content of GC in genes is correlated with the isochores they are within[3], and one study suggests that the genes may lead the selection.[4] 2 Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. May 24, 1985. The mosaic genome of warm-blooded vertebrates. Science. 228(4702):953-8. 3 Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 228(4702):953-8. May 24, 1985. 4 Press W.H. and Robins H. Oct. 2006. Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic Environment. Genetics, 174:1029-1040.

6. Three Possible Causes of Current Human Bias and of Isochores [5] • Mutation Bias: variation in mutation rates in different regions of the genome.[6] • Natural Selection (fitness selection) for GC alleles may have driven isochore formation[7], and may be behind local GC content as well. • Biased Gene Conversion (BGC) may result in a pressure that pushes GC pairs to fixation at recombination hot spots.[8] 5 Eyre-Walker A. and Hurst L.D. July 2001. The evolution of isochores. Nat Rev Genet. 2(7):549-55. 6 Sueoka N. April 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci.85(8):2653-7. 7 Bernardi G, Bernardi G. 1986. Compositional constraints and genome evolution. J. Mol Evol. 24(1-2):1-11. 8 Eyre-Walker A. June 22 1993. Recombination and mammalian genome evolution.Proc Biol Sci. 252(1335):237-43.

7. Mismatched SNP Repair in Heteroduplex During Recombination T G GCTGTAGATCGTTG ACGTA GATTACGTCGT CGACATCTAGCAAT TGCAT CTAATGCAGCA C A Both mismatches are converted to “strong” G-C pairs, replacing “weak” SNPs. [9] Biased Gene Conversion: 9 Brown, T. C., and J. Jiricny. 1988. Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell54:705–711.

8. Distinguishing between the Three Models • Mutation bias should result in similar patterns of bias between SNPs and substitutions.[10] • Natural Selection may result in a correlation between biased substitutions and conservation. • BGC may result in a correlation between biased substitutions and current recombination hot spots or rates.[11] • BGC should be most easily recognized in clusters of closely spaced substitutions. Clusters are not, however, inconsistent with fitness selection. 10 Lercher M.J., Urrutia A.O., Pavlícek A. and Hurst L.D. 2003. A unification of mosaic structures in the human genome. Hum. Mol. Genetics, 12(19):2411-2415. 11 Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G., Shlien, A., Palsson, S.T., Frigge, M.L., Thorgeirsson, T.E., Gulcher, J.R., and Stefansson, K. . 2002. A high-resolution recombination map of the human genome, Nature Genetics, 31(3):241-247.

9. Mutation Bias?

10. Bias by Window: G+C Content

11. Windows: Bias by Conservation?

12. Windows: Bias At Hotspots?

13. Bias Near Telomeres?

14. Bias by Substitution Density

15. Bias as a Social Disease: Zippers

16. Bias as a Social Disease: Heat

17. Biased Gang Members are Recruited From Unbiased Individuals SNPs: Substitutions:

18. Mutation Bias is Rejected. • Assuming the rate of mutation and fixation have not changed over the last 6my, biased mutations are fixed in the genome in greater proportion than they occur. • When examining clusters of biased differences, the evidence is strikingly against the biased mutation hypothesis. • Clusters are predicted by the BGC hypothesis but are not contrary to a natural selection model.

19. The Story is in the Data, but How to Look At It? • Individual Weak to Strong Substitutions don’t show the story well: too much noise. • Comparing windows of fixed size results in comparing apples to oranges: a cluster of 3 with 2 WtoS compared to a cluster of 7 with 7 WtoS. • What is Needed: A measure of the degree to which a single substitution is biased and clustered. • With such a measure, mapping where this phenomenon occurs might be revealing.

20. Geography of a Chromosome

21. UBCS or UC BS? • Clusters are 5 or more substitutions within 300bp. • Biased Clusters are at least 80% Weak to Strong substitutions. • Biased Clustered Substitutions (BCS) are substitutions within biased clusters. • Expected BCS is the binomial probability of BCS within each 1mbp bin. Actual BCS – Expected BCS = Unexpected BCS UBCS is Unexpected Biased Clusters Substitutions

22. Geography of a Chromosome Take 2

23. UBCS is Predictable

24. UBCS Rises Near the Telomeres of All Human Autosomes

25. Chromosome 5 is Typical

26. Chromosome Y is an Exception

27. No Signal on Chromosome Y is what would be expected if Biased Gene Conversion is the Driving force of UBCS. • Recombination doesn’t occur on chromosome Y. • Fitness Selection isn’t ruled out, but it doesn’t predict a missing signal on Y.

28. Chromosome X is an Enigma

29. Is it Just that Sex is Mysterious? • The BGC model doesn’t predict a missing signal on X: Chromosome X recombines so there should be a signal. • Natural Selection doesn’t predict the missing signal either. However, there may be fitness based reasons for selecting GC SNPs near the telomeres of autosomes that do not apply to the sex chromosomes.

30. Is there a Clue in the Pseudo-Autosomal Regions?

31. Fun with Correlations

32. Conservative Bias?

33. Recruitment?

34. Recombination Hot Spots

35. Recombination Rate

36. Males are the Troublemakers!

37. Rank Troublemakers

38. History vs. Geography

39. BGC Model is Accepted • While fitness selection cannot be ruled out, there is no process known that would explain a fitness advantage of increasing the GC content of mega-base regions by selecting localized clusters of GC SNPs. • Fitness selection cannot explain the correlation with recombination rates or the lack of correlation with conserved regions. • Biased Gene Conversion explains all the observed data: • Clusters of biased substitutions within 300 bases of each other. • Selection of Biased Substitutions from Unbiased SNPs • Correlation of UBCS with recombination rate. • Lack of signal on the Y chromosome. • Lack of signal on the X chromosome. • Even the correlation of UBCS with GC content makes sense.

40. Why is this Striking? These datasets are mutually exclusive! They represent a pattern in substitutions occurring since humans and chimps diverged approximately 6mya.

41. UBCS Rises Near the Telomeres of All Chimp Autosomes

42. UBCS Signal is Remarkably Similar Between Human and Chimp Genomes

43. Stable BCS Accumulation is Revealing • Moderate correlation between current recombination hotspots but strong correlation with male recombination rates agrees with models of hot spots moving[12,13] while regional recombination rates remain steady.[14] • The similarity of human and chimp UBCS profiles attests to a stable force across 12 my of genetic divergence. • The highly localized bias suggests an explanation for the origin of isochores. The telomeres of autosomes may be Duret’s GC factories[15], allowing the build up of isochores over millions of years. • The borders between high and low GC regions seen today may represent the historical record of chromosomal rearrangements. 12 Pineda-Krch M. and Redfield R.J.April 2005. Persistence and Loss of Meiotic Recombination Hotspots. Genetics, 169:2319-2333. 13 Winckler W., Myers S.R., Richter D.J., Onofrio R.C., McDonald G.J., Bontrop R.E., McVean G.A.T., Gabriel S.B., Reich D., Donnelly P., Altshuler D. April 1, 2005. Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees. Science 308(5718):107-111. 14 Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. Oct. 14 2005.A fine-scale map of recombination rates and hotspots across the human genome. Science. 310(5746):321-4. 15 Duret L., Eyre-Walker A. and Galtier N. Aug. 2006. A new perspective on isochore evolution. Gene385:71–74.

44. Chromosome 2 is an Exception

45. Current Recombination Rate is not High in Zone of Fusion

46. Two Autosomes on a Date Assuming: • The internal peak was created while the regions were still telomeric. • Since fusion the region is no longer accumulating UBCS. • The force creating UBCS has been constant over the past 6my. Then the fusion might be dated. Using the ability to predict the UBCS signal at human telomeres from the UBCS signal at chimpanzee telomeres, then the predicted height minus the actual height of the chr2 peak may proportional to the time that has elapsed since the fusion. Estimated Fusion Date is 740,000 years ago with a CI95 of no more than 2.71 mya.

47. Chromosome 2 Fusion Dating

48. Non-Darwinian Selection • BGC acts as a selection pressure[16], separate from fitness. It selects GC SNPs over AT SNPs with enough pressure that some of them are fixed into the genome. • While the individual SNPs may have already been tested as not too harmful, a newly selected cluster may be a novel allele never before seen. • If a single point mutation is far more likely to be harmful than beneficial, what about a cluster of them? • BGC selection can be expected to accelerate positive selection. • BGC selection can also be expected to compete with and slow negative selection. 16 Nagylaki T. Oct. 1983. Evolution of a finite population under gene conversion. Proc. Natl. Acad. Sci. USA.80(20):6278–6281.

49. Non-Darwinian EvolutionTake 1 Despite a lack of correlation betweenUBCS and transcription density genome-wide, the most extremelybiased regions of the genome contain a disproportionate numberof genes.

50. Non-Darwinian Evolution has Sculpted Humans Of the 10 top scoring regions of biased clustered substitutions4 are involved in brain development or function!Eight of 10 are transcribed, while the other 2 are predicted genes, transcribed in mammals.