SMBE 2015: Rapid Identification of Phylogenetically Informative Data from Next-Gen Sequencing
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Talk on SISRS and multiple datasets and resulting phylogenies that can be produced.
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SMBE 2015: Rapid Identification of Phylogenetically Informative Data from Next-Gen Sequencing
- 1. Rapid identification of phylogenetically informative data from next-gen sequencing Rachel Schwartz The Biodesign Institute Arizona State University Rachel.Schwartz@asu.edu July 16, 2015
- 2. Big data for phylogenetics
- 3. Phylogenomics requires a lot of time and money
- 4. SISRS: Site Identification from Short Read Sequences
- 5. A composite genome for reference Shotgun sequencingShotgun sequencing Shotgun sequencing Assemble composite genome
- 6. A composite genome for reference
- 7. A composite genome for reference Shotgun sequencingShotgun sequencing Shotgun sequencing Assemble composite genome Align reads to composite genome
- 8. A composite genome for reference Shotgun sequencingShotgun sequencing Shotgun sequencing Assemble composite genome Align reads to composite genome Call genotype at each site for each sample
- 9. A composite genome for reference Shotgun sequencingShotgun sequencing Shotgun sequencing Assemble composite genome Align reads to composite genome Call genotype at each site for each sample Remove sites with missing data
- 10. A composite genome for reference Shotgun sequencingShotgun sequencing Shotgun sequencing Assemble composite genome Align reads to composite genome Call genotype at each site for each sample Remove sites with missing data Output alignment
- 11. Simulations A B C D E F G H Laddertrees Equal branch length A B C D E F G H Long deep branches A B C D E F G H Short deep branches A B C D E F G H Balancedtrees A B C D E F G H A B C D E F G H
- 12. Simulation Results: 1 million bp genome A B C D E F G H Laddertrees Equal branch length A B C D E F G H Long deep branches A B C D E F G H Short deep branches G H G H G H Coverage Numberofcorrectmappablesites 1 10 100 1000 10000 100000 1 2 4 8 10 20 50 ● ● ● ● ● ● ● Slow genes Fast genes ● Schwartz et al. (2015) BMC Bioinformatics
- 13. Simulation Results: by depth Coverage Numberofcorrectmappablesites 1 10 100 1000 10000 100000 1 2 4 8 10 20 50 q q q q q q q q q q q q q A B C D E F G H Laddertrees Equal branch length Long C D E F G H Balancedtrees Depth 1 Depth 2 Depth 3 Depth 4 ∗ Depth 5 • Depth 6 Schwartz et al. (2015) BMC Bioinformatics
- 14. Phylogeny of apes from SISRS data Bonobo Human Gorilla Orangutan Rhesus macaque Crab macaque Chimp
- 15. Phylogeny of mammals from SISRS data treeshrew horse pig cow toothed whale baleen whale pangolin dog cat bat megabat shrew star nosed mole aardvark tenrec elephant shrew manatee elephant sloth armadillo opossum wallaby rabbit pika rat mouse colugo lemur human macaque 100 90 100 91 61 100 100 100 100 100 86 51 100 100 100 100 100 100 100 100 72 100 100 100 100 100 100 Schwartz et al. (2015) BMC Bioinformatics
- 16. Phylogeny of mammals from SISRS data colugo sn mole shrew horse pig cow baleenwhale toothedwhale pangolin dog cat bat megabat aardvark tenrec e shrew elephant manatee opossum wallaby sloth armadillo treeshrew rat mouse rabbit pika lemur human macaque 100 60 100 100 100 100 100 100 100 100 53 100 100 100 100 100 100 100 99 100 100 75 100 100 100 100 treeshrew horse pig cow toothedwhale baleenwhale pangolin dog cat bat megabat shrew sn mole aardvark tenrec e shrew manatee elephant sloth armadillo opossum wallaby rabbit pika rat mouse colugo lemur human macaque 100 90 100 91 61 100 100 100 100 100 86 51 100 100 100 100 100 100 100 100 72 100 100 100 100 100 100 lemur colugo bat megabat horse pig cow toothedwhale baleenwhale pangolin dog cat sn mole shrew manatee elephant tenrec aardvark e shrew wallaby opossum armadillo sloth treeshrew rabbit pika rat mouse human macaque 100 100 61 62 61 100 100 100 100 100 87 80 100 100 100 100 100 100 100 100 100 100 92 100 100 100 100 Schwartz et al. (2015) BMC Bioinformatics
- 17. Phylogeny of mammals from SISRS data Opossum Wallaby aardvarkG armadillo baleenwhaleG bat cat colugoG cow dog elephant eshrewG horse human lemur macaque manateeG megabatG mouse pangolinG pig pika rabbit ratT shrew slothG sn moleG tenrecG toothedwhale treeshrew
- 18. Phylogenies of angiosperms from SISRS data q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q 50 75 100 125 20 40 60 Number of Gaps Allowed At A Site Robinson−FouldsDistance q q Distance Nodes In Tree Comparing Trees Generated With Varying Amounts of Missing Data Adam Orr
- 19. SISRS rapidly identifies phylogenetically informative data from next-gen sequencing reads Apes: 3 days Mammals: 7 days Leishmania: 12 hours No reference genome is required. Minimal assembly required (completely automated). Results are comparable to slower, labor-intensive methods.
- 22. Branch length estimation T5 T4 T2 T1 T8 T3 T6 T7 T9 T8 T4 T1 T2 T7 T6 T9 T5 T3 T9 T7 T6 T3 T8 T1 T2 T4 T5 T8 T4 T1 T2 T7 T6 T9 T3 T9 T7 T6 T3 T8 T1 T2 T4 T5 Tree height = 1 q q q qq q qq q qq q q q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q qq q q qq q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q 0.0 0.2 0.4 0.6 0.8 1.0 0.00.20.40.60.81.0 Simulated branch length Estimatedbranchlength
- 23. Branch length estimation T5 T4 T2 T1 T8 T3 T6 T7 T9 T8 T4 T1 T2 T7 T6 T9 T5 T3 T9 T7 T6 T3 T8 T1 T2 T4 T5 T8 T4 T1 T2 T7 T6 T9 T3 T9 T7 T6 T3 T8 T1 T2 T4 T5 Height = Sim height q qq qqqqqq qq q q q qqq q q q qq q q q qq q q qq q qq q q q q q q q q q q q q q q q q q q q q qq q q q q q q q qq q q qqqq q qqq qqq qq q q q q qq q q q q q q q q q q q q q q q q 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.00.10.20.30.40.50.6 Simulated branch length Estimatedbranchlength
- 24. Branch length estimation: most variable loci qq q q qqq q q q qq q q q q q 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.00.10.20.30.40.50.6 Simulated branch length Estimatedbranchlength Slope / Cor / Max Brlen 2.06 1 0.03 1.3 0.99 0.05 0.7 0.99 0.08 0.29 1 0.28 0.24 0.93 0.29 0.21 0.61 0.52
- 25. Branch length estimation: most conserved loci qqq q qq qq qq qqqq qq q 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.00.10.20.30.40.50.6 Simulated branch length Estimatedbranchlength Slope / Cor / Max Brlen 0.85 0.72 0.03 0.73 0.96 0.05 0.73 0.9 0.08 0.3 0.97 0.28 0.19 0.58 0.29 0.17 0.78 0.52
- 26. Conclusions SISRS rapidly identifies data for phylogenetics from next-gen sequencing reads Different (SISRS) data = alternative topologies Use SISRS data to estimate branch lengths and divergence dates accurately
- 27. Acknowledgements Co-authors / Collaborators Reed Cartwright (ASU) Kelly Harkins (ASU and UCSC) Anne Stone (ASU) Kael Dai (ASU) Adam Orr (ASU) Mike Miller (Villanova) Funding NSF DBI-1356548 NIH R01-GM101352-01A1 NSF DDIG BCS-1232582 ASU Startup Funds SISRS is available at https://github.com/rachelss/SISRS