Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa: SUPERSMART
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Slides for my lightning talk on the SUPERSMART platform to the SSB/SSE/ASN annual meeting, Austin, TX, USA. SSB Spotlight Session: "Next generation phylogenetic inference 2". Monday, June 20th 2016, 3:20PM, Ballroom A.
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Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa: SUPERSMART
- 1. h#p://www.supersmart-‐project.org Self-‐Updating Platform for the Estimation of Rates of Speciation, Migration, And Relationships of Taxa Rutger Vos, Naturalis Biodiversity Center, Leiden, the Netherlands @rvosa
- 2. Methods to construct large species trees !"#$%&'()*+),- .+,$/0$1(+)+2$,3++- !"#$%&%$$ 4%&'53%,+ Tree inference !"#$%&'()*+),- Tree inference (same study) Supertree methods (e.g. MRP) .67+3*%,3'8 !"#$%'(&%)* 4%&'53%,+ Concatenation Tree inference (e.g. ML, Bayesian) 9'-,$/0$-7+4'+-$ 1/3$3//,$,%8%2 4%&'53%,+ :%4;5/)+$,3++ 1(+)6-$&+<+&2 =6&&$%&'()*+), 1-7+4'+-$/3$5+&/>2 !+,-.!/0.1 3+?4%&'53%,+ Identify & align orthologous sequences; Tree inference Decompose & add markers Infer trees & place in backbone !! " # # # # # $ $ $ $ $ % % % % % " " " " " && & & &&&& # # # # # # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " ! ! ! % % % % % $ $ $ $ $ " " " " " !! " # # # # # $ $ $ $ $ % % % % % " " " " " !! " & & & &&&&&&&& ! $ &&& & && !! " # # # # # $ $ $ $ $ % % % % % " " " " " & & & & &&&& # # # # # # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " ! ! ! % % % % % $ $ $ $ $ " " " " " !! " # # # # # $ $ $ $ $ % % % % % " " " " " !! " & & & &&&&&&&& ! $ && & & && !! " # # # # # $ $ $ $ $ % % % % % " " " " " ! # # # # # # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " ! ! % % % % % $ $ $ $ $ " " " " " ! " # # # # # $ $ $ $ $ % % % % % " " " " " !! " ! ! ! $ ! ! !! " !! " # # # # # $ $ $ $ $ % % % % % " " " " " ! # # # # # # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " ! ! % % % % % $ $ $ $ $ " " " " " ! " # # # # # $ $ $ $ $ % % % % % " " " " " !! " ! ! ! $ ! ! !! " # # # # # # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " ! ! ! ! % % % % % $ $ $ $ $ " " " " " !! " # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " !! ! ! #" # # # # $ $ $ $ % % % % " " " " !! " # # # # # # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " ! ! ! ! % % % % % $ $ $ $ $ " " " " " !! " # # # # # $ $ $ $ $ % % % % % $ $ $ $ $ % % % % % $ $ $ $ $ " " " " " !! ! ! #" # # # # $ $ $ $ % % % % " " " " !! " h#p://www.supersmart-‐project.org -‐ @rvosa
- 3. The SUPERSMART algorithm !" #" $" #% &% &" !% $% &% &' &" #% #" #' !' !" !% $% $' $" !' $" &' $' !" #% #" !% &% &" #' $% !" #" $" 80 0 Time (Ma) 80 0 Time (Ma)Relative time 1 0 h#p://www.supersmart-‐project.org -‐ @rvosa
- 4. Data mining h#p://www.supersmart-‐project.org -‐ @rvosa taxon coverage data available A1 A4 A7 A2 !"## $# #%$#! !" #" "" "$! $%%% S1 S2 S6 S5 S3 S7 !"# %$% "$!" & & & & & & & & & & & & & "!"# %% $! "#" $& & & & & & & & & & & !" #" #" " & & & & & && & & & & & & & & & %!" % #" " ! #" $$& & & & & & & & & & !"## $# "# $! !"""& & & & & & & & & A3 S1 S2 S6 S5 S3 S7 S4 A1 A 3A 2 A 4 A 5A6A 7 !"##%$ !"# %$% "!"# %% !"##%$# !"##%$# !" #" !" #" !""" %!" % $! "#" $ $! #" $$ #" " $! $%%% #" " "" " #%$#! "# $! "$!" %$#!" $ %$!" $ $#" $#" Alignments Exemplarspecies Minimally sparse supermatrix (minimum of two markers per exemplar species) $
- 5. Effect of data mining parameterization h#p://www.supersmart-‐project.org -‐ @rvosa 0 5 10 15 20 0.050.100.150.20 Averaged posterior probabilities on nodes Minimum marker coverage per taxon Maximumaverageduncorrectedpairwisedistance p < 0.8 0.8 < p < 0.95 p > 0.95
- 6. Recovering a simulated tree Simulated Tree Re-estimated Tree data sim 0.000.10 data sim 60708090 % of invariant sites per alignment % data sim 0102030 Number of indels per alignment count data sim 04080120 data sim 0200400 data sim 02040 average distance within alignment relativeeditdistance Average size of indels per alignment size(nucleotides) Number of gaps per sequence gapcount % gaps per sequence % !" #" time (myr) 80 0 0 80 h#p://www.supersmart-‐project.org -‐ @rvosa
- 7. Install a vagrant box, then: $ smrt [COMMAND] [OPTIONS] h#p://www.supersmart-‐project.org -‐ @rvosa
- 8. Acknowledgements h#p://www.supersmart-‐project.org -‐ @rvosa The smar,es: • Alexandre Antonelli • Rutger Vos • Hannes He#ling • Mike Sanderson • Bengt Oxelman • Karin Nilsson • Mats Töpel • Hervé Sauquet • Henrik Nilsson • Daniele Silvestro • Fabien Condamine • Ruud Scharn Thank you to: • Erick Matsen • Meg Pirrung • You, the audience!