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Michael Matschiner University of Zurich @m_matschiner evoinformatics.eu

Accuracy and precision of phylogenomic divergence-time estimates. Michael Matschiner University of Zurich @m_matschiner www.evoinformatics.eu. Accuracy and precision of phylogenomic divergence-time estimates. Michael Matschiner University of Zurich @m_matschiner www.evoinformatics.eu.

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Michael Matschiner University of Zurich @m_matschiner evoinformatics.eu

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  1. Accuracy and precision of phylogenomic divergence-time estimates • Michael Matschiner • University of Zurich • @m_matschiner • www.evoinformatics.eu

  2. Accuracy and precision of phylogenomic divergence-time estimates • Michael Matschiner • University of Zurich • @m_matschiner • www.evoinformatics.eu

  3. AGCGTA AGCCTA AGCCTG AGCCTG Divergence-time estimation Time

  4. AGCGTA AGCCTA AGCCTG AGCCTG Divergence-time estimation Unprecise estimate Time

  5. AGCGTATCAGTCA AGCCTGTCAGTCA AGCCTGTCAGTCA AGCCTATCAGTCA GCTACACGTCTCAG GCTACAAGTCTAAG GCTACAAGTCTAAG GCTACACGTCTCAG Divergence-time estimation GTGTCCAATCAGT CTGTCCAATCAGT CTGTCCAATCAGT CTGTCCGATCAGT GCTACACGTCGAAG GCTACACGTCTAAG GCCACAAGTCTAAG GCCACAAGTCTAAC Time Precise estimate

  6. AGCGTATCAGTCA AGCCTGTCAGTCA AGCCTGTCAGTCA AGCCTATCAGTCA GCTACACGTCTCAG GCTACAAGTCTAAG GCTACAAGTCTAAG GCTACACGTCTCAG Divergence-time estimation GTGTCCAATCAGT CTGTCCAATCAGT CTGTCCAATCAGT CTGTCCGATCAGT GCTACACGTCGAAG GCTACACGTCTAAG GCCACAAGTCTAAG GCCACAAGTCTAAC Time Inaccurate estimate

  7. Tree discordance Species tree Gene trees

  8. Tree discordance Incomplete lineage sorting

  9. Tree discordance Introgression

  10. Tree discordance recombination recombination recombination

  11. Tree discordance recombination recombination c-gene recombination Doyle (1995) Syst Bot

  12. Tree discordance c-gene Doyle (1995) Syst Bot

  13. c-gene Tree discordance c-gene c-gene c-gene Doyle (1995) Syst Bot

  14. Tree discordance Alignment Doyle (1995) Syst Bot

  15. How long are c-genes?

  16. Simulations Stick spiders 5 million years Notothenioid fishes 20 species Stick spiders: Gillespie et al. (2018) Curr Biol, notothenioid fishes: Ceballos et al. (2019) BMC Evol Biol

  17. Simulations

  18. Simulations Ne = 100,000 5 million years 20 species msprime: Kelleher et al. (2016) PLoS Comput Biol

  19. Simulations Ne = 50,000 5 million years 20 species msprime: Kelleher et al. (2016) PLoS Comput Biol

  20. Simulations Ne = 200,000 5 million years 20 species msprime: Kelleher et al. (2016) PLoS Comput Biol

  21. Simulations Ne = 100,000 r = 5×10-9/g 5 million years 20 species msprime: Kelleher et al. (2016) PLoS Comput Biol

  22. Simulations Ne = 100,000 r = 5×10-9/g r = 10-8/g 5 million years 20 species msprime: Kelleher et al. (2016) PLoS Comput Biol

  23. Simulations Ne = 100,000 r = 10-8/g r = 2×10-8/g 5 million years 20 species msprime: Kelleher et al. (2016) PLoS Comput Biol

  24. c-gene sizes 25 20 15 Mean size (bp) 10 5 0 Ne = 50,000 100,000 200,000 r = 10-8/g c-genie: Malinsky & Matschiner (2019) https://github.com/mmatschiner/c-genie

  25. c-gene sizes 25 20 15 Mean size (bp) 10 5 0.0 0 r = 5×10-9/g 10-8/g 2×10-8/g Ne = 100,000 c-genie: Malinsky & Matschiner (2019) https://github.com/mmatschiner/c-genie

  26. c-genes are short. * *in rapidly diverging groups

  27. Tree discordance c-gene Doyle (1995) Syst Bot

  28. Tree discordance Single-topology tract Doyle (1995) Syst Bot

  29. Single-topology tract sizes 600 500 400 Mean size (bp) 300 200 100 0 Ne = 50,000 100,000 200,000 r = 10-8/g c-genie: Malinsky & Matschiner (2019) https://github.com/mmatschiner/c-genie

  30. Single-topology tract sizes 200 150 Mean size (bp) 100 50 0 r = 5×10-9/g 10-8/g 2×10-8/g Ne = 100,000 c-genie: Malinsky & Matschiner (2019) https://github.com/mmatschiner/c-genie

  31. How bad is this?

  32. Divergence-time estimation

  33. Concatenation Long alignment (100,000 bp) BEAST2.5: Bouckaert et al. (2019) PLoS Comput Biol

  34. Concatenation 5 5 4 4 3 3 Estimated node age 2 2 1 1 Ne = 200,000 r = 10-8/g Ne = 50,000 0 0 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age BEAST2.5: Bouckaert et al. (2019) PLoS Comput Biol

  35. Concatenation 4 4 2 2 Overestimated Overestimated Estimated node age / true node age 1 1 Underestimated Underestimated Ne = 50,000 Ne = 200,000 0.5 0.5 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age BEAST2.5: Bouckaert et al. (2019) PLoS Comput Biol

  36. Concatenation 4 4 2 2 Estimated node age / true node age 1 1 r = 2×10-8/g Ne = 100,000 r = 5×10-9/g 0.5 0.5 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age BEAST2.5: Bouckaert et al. (2019) PLoS Comput Biol

  37. Gene tree / species tree “Gene” alignments (20 × 5,000 bp) StarBEAST2: Ogilvie et al. (2018) Mol Biol Evol

  38. Gene tree / species tree 4 4 2 2 Estimated node age / true node age 1 1 Ne = 200,000 r = 10-8/g Ne = 50,000 0.5 0.5 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age StarBEAST2: Ogilvie et al. (2018) Mol Biol Evol

  39. Gene tree / species tree 4 4 2 2 Estimated node age / true node age 1 1 r = 2×10-8/g Ne = 100,000 r = 5×10-9/g 0.5 0.5 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age StarBEAST2: Ogilvie et al. (2018) Mol Biol Evol

  40. SNAPP Individual SNPs (5,000 SNPs) SNAPP: Bryant et al. (2012) Mol Biol Evol, Stange et al. (2018) Syst Biol

  41. SNAPP 4 4 2 2 Estimated node age / true node age 1 1 Ne = 200,000 r = 10-8/g Ne = 50,000 0.5 0.5 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age SNAPP: Bryant et al. (2012) Mol Biol Evol, Stange et al. (2018) Syst Biol

  42. SNAPP 4 4 2 2 Estimated node age / true node age 1 1 r = 2×10-8/g Ne = 100,000 r = 5×10-9/g 0.5 0.5 0 1 2 3 4 5 0 1 2 3 4 5 True node age True node age SNAPP: Bryant et al. (2012) Mol Biol Evol, Stange et al. (2018) Syst Biol

  43. 0.5 Precision 0.4 Gene tree / species tree Concatenation SNAPP 0.3 0.5 0.5 0.2 0.4 0.4 0.3 0.3 Mean precision 0.1 0.2 0.2 0.1 0.1 0 0 0 0-1 1-2 2-3 3-4 4-5 0-1 1-2 2-3 3-4 4-5 0-1 1-2 2-3 3-4 4-5 True node age True node age True node age

  44. 0.5 Accuracy 0.4 Gene tree / species tree Concatenation SNAPP 0.3 0.5 0.5 0.2 0.4 0.4 0.3 0.3 Mean accuracy 0.1 0.2 0.2 0.1 0.1 Ne = 200,000 Ne = 200,000 0 0 0 0-1 1-2 2-3 3-4 4-5 0-1 1-2 2-3 3-4 4-5 0-1 1-2 2-3 3-4 4-5 True node age True node age True node age

  45. The Bright Side of Phylogenetics

  46. Relate / tsinfer Ancestral recombination graph Relate: Speidel et al. (2019) bioRxiv, tsinfer: Kelleher et al. (2018) bioRxiv

  47. Thanks Milan Malinsky University of Basel, Switzerland Marcelo Sanchez University of Zurich, Switzerland

  48. Code https://github.com/mmatschiner/evol2019 Slides http://evoinformatics.eu/presentations.htm

  49. Code https://github.com/mmatschiner/evol2019 Slides http://evoinformatics.eu/presentations.htm

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