1. A project on alignment of short tandem repeat loci between Homo Sapiens and Homo Neanderthalensis genomes Łukasz Olczak, Silesian University of Technology Rafał Pokrzywa, Silesian University of Technology Krzysztof Cyran, Silesian University of Technology Andrzej Polański, Silesian University of Technology

2. Aim: Align STR loci between human and neanderthal, and verify implications on: ▫Mechanisms of STR evolution ▫Quality of Neanderthal DNA assembly ▫Demographic scenarios between Homo Sapiens and Homo Neanderthalensis

3. Methods 1/3 BWtrs – Burrows-Wheeler transform based tool for searching tandem repeats in O(n log n) “BWtrs: A tool for searching for tandem repeats in DNA sequences based on the Burrows-Wheeler transform.” R. Pokrzywa, A. Polański Genomics 2010 We found: SpeciesNo. STR loci Human (hg19)11 834 083 Neanderthal (Vi33.16)2 529 812

4. Methods 2/3 STR alignment technique – extension of Needleman- Wunch algorithm Scoring function of aligned pair of tandem repeats – 1 – if STR motif of pair is the same and there is high similarity between aligned flanking sequences 0 - otherwise Example:

5. Dot plot (chr22)

6. Optimal path (chr22)

7. Methods 3/3 Mutability measure: Average squared divergence between binned orthologous – with correction for detecting threshold Affected by both mutation rate and variance in mutation step size

8. Results 1/5 Motif length Minimu m no. of repeats No. of orthologous loci Human = Neanderthal Human > Neanderthal Human < Neanderthal X 2 difference from 1:1P<0.05 Dinucleotide33802663795383333955.2802S Trinucleotide3424784241724372.7705NS Tetranucelotide39787968951470.1633NS Pentanucleotide32365231621281NS Hexanucleotide3560555320.2NS Total:435456

9. Results 2/5

10. Results 3/5

11. Results 4/5 We use regression model to explain variability in microsatellite mutability Predictors: ▫Motif size ▫No. repeats ▫Length in bp R 2 =0.72, p=3E-10

12. R 2 =0.71,p=4.15E-11

13. Conclusions 72% variation of mutability is explained by these 3 predictors There is a positive correlation between STR length, repeat number and mutability Motif size has negative effect on mutability The strongest predictor is microsatellite length in bp, next is motif size. Number of repeats has much more weaker influence on STRs mutability than length in bp

14. Conclusions We assumed generation time 20 years and divergence time between human and Neandertal 825000 y.a. Our estimates of microsatellite mutation are significantly lesser than estimates obtained for human-chimp alignment The more likely time of divergence is 500000 y.a. which is consistent with mitochondrial studies

15. Conclusions Neanderthal dinucleotide microsatellite lengths are significantly longer than their orthologous in human There are observations that microsatellite mutation rates are higher in population with higher fraction of heterozygotes This results confirms that in human history occurred a population bottleneck (70,000 y. a.) followed by exponential growth

16. Conclusions The quality of assembly of the Neanderthal’s nuclear DNA is very low, which caused by damage of ancient DNA There is tendency to assembly shorter STRs.

17. Thank you for your attention!!