Orthologous loci for phylogenomics from raw NGS data

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1 Orthologous loci for phylogenomics from raw NS data Rachel Schwartz The Biodesign Institute Arizona State University May 2, 205

2 Big data for phylogenetics

3 Phylogenomics requires a lot of time and money

4 Phylogenomics with big data Output alignment

5 Phylogenomics with big data Align reads to reference Call genotypes Output alignment

6 Phylogenomics with big data Assemble genomes Align reads to reference Find orthologous loci Call genotypes Output alignment

7 SISRS: Site Identification from Short Read Sequences Fast and efficient Accurate topologies Accurate divergence dates

8 A composite genome for reference Assemble composite genome

9 A composite genome for reference

10 A composite genome for reference Assemble composite genome Align reads to composite genome

11 A composite genome for reference Assemble composite genome Align reads to composite genome Call genotype at each site for each sample

12 A composite genome for reference Assemble composite genome Align reads to composite genome Call genotype at each site for each sample Remove sites with missing data

13 A composite genome for reference Assemble composite genome Align reads to composite genome Call genotype at each site for each sample Remove sites with missing data Output alignment

14 Simulations A B C D E F Ladder trees Equal branch length A B C D E F Long deep branches A B C D E F Short deep branches A B C D E F Balanced trees A B C D E F A B C D E F

15 Simulation Results: million bp genome Ladder trees Equal branch length F E D C B A Long deep branches Number of correct mappable sites F E D C Short deep branches Coverage B B Slow genes Fast genes A A F E D C

16 Simulation Results: by depth 000 Equal branch length F Long Number of correct mappable sites Coverage Ladder trees Depth Depth 2 Depth 3 Depth 4 Depth 5 Depth 6 Balanced trees E D C B A F E D C

17 Phylogeny of apes from SISRS data Crab macaque Rhesus macaque Chimp Bonobo uman orilla Orangutan

18 Phylogeny of mammals from SISRS data wallaby opossum mouse rat pika rabbit macaque human lemur 72 colugo treeshrew star nosed mole shrew megabat bat cat dog pangolin baleen whale 86 toothed whale cow 5 pig horse armadillo sloth 90 elephant manatee elephant shrew 6 9 tenrec aardvark Schwartz et al. (205) BMC Bioinformatics

19 Phylogeny of Leishmania from SISRS data L. lainsoni L. naiffi L. panamensis L. guyanensis L. shawii L. braziliensis (genome) L. braziliensis L. enrietti Endotrypanum sp. L. deanei L. hertigi L. adleri L. pifanoi L. tropica L. aeithiopica L. donovani L. donovani 2

20 SISRS rapidly identifies phylogenetically informative data from next-gen sequencing reads Apes: 3 days Mammals: 7 days Leishmania: 2 hours No reference genome is required. Minimal assembly required (completely automated). Results are comparable to slower, labor-intensive methods.

21 Divergence dating

22 Divergence dating T5 T T T5 T T5 T T T5 Tree height =

23 Divergence dating T5 T5 T5 T T5 Estimated branch length T T T Tree height = T Simulated branch length

24 Divergence dating T5 T5 T5 T T5 Estimated branch length T T T eight = Sim height T Simulated branch length

25 SISRS rapidly identifies phylogenetically informative data from next-gen sequencing reads Fast and efficient Accurate topologies Accurate divergence dates

26 Acknowledgements Collaborators Reed Cartwright Kelly arkins and Anne Stone Kael Dai Undergraduates Dominic Nicacio Nick Ingle Emily Thompson Adam Orr Funding NSF DBI NI R0-M0352-0A NSF DDI BCS NSF Bioinformatics Fellowship

27 SISRS: Site Identification from Short Read Sequences Fast and efficient Accurate topologies Accurate divergence dates