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Phylogenetics in the cloud Brian O’Meara

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1 Phylogenetics in the cloud Brian O’Meara

2 Understand what phylogenetics is and its utility for life scientists (briefly) Know some of the computational pitfalls Identify some of the available resources Become ok with just saying yes to being a user (sometimes) Learning objectives

3 © Doug Stone 7 origins of agriculture AngiospermConifer origins of inbreeding

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5 ©David Cannatella Ryan & Rand, 1995

6 H5N1 bird flu: phylogeography & evolution Wallace et al, 2007

7 Organ et al. Origin of avian genome size and structure in non-avian dinosaurs. Nature (2007) vol. 446 (7132) pp Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5-12% of the total genome size in the saurischian dinosaur lineage, but was 7-19% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage.

8 Alfaro et al. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. P Natl Acad Sci Usa (2009) vol. 106 (32) pp

9 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

10 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

11 sequinr, ape, rentrez,...

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14 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

15 N N Number of atoms in the universe >1 million species

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17 Smith et al ,533 species Needed 32 GB of RAM to run

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19 Reuse! treebase, rdryad

20 Coming soon

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22 96% of published trees are available only as pictures of trees 4% of published trees are available as actuall y reusable trees Stoltzfus et al. 2013

23 241,465 TeraGrid/XSEDE jobs submitted by 8,598 unique users. Average of 171 new XSEDE Users registered in every month. 5,216 CPU years of TeraGrid/XSEDE time. 241,465 TeraGrid/XSEDE jobs submitted by 8,598 unique users. Average of 171 new XSEDE Users registered in every month. 5,216 CPU years of TeraGrid/XSEDE time.

24 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

25 Copyright © All Rights Reserved. Substantial duplication is not permitted. We encourage wide use of this resource, but until it is complete it should not be used to represent a synthesis for any taxonomic group. Currently large scale, automated, data-mining is not permitted. Consult the authors if you have any questions about appropriate use, or if you plan to publish results from the database.

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27 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

28 HD TV: 1920 × ,533 names largest computer monitors: 3280×2048 (can be tiled) Laser printer: effectively 3600 × 4725 (can be tiled)

29 OneZoom Video from Imperial College London https://www.youtube.com/watch?v=LZ3n3mV4uVc

30 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

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32 Get sequence data Build tree Calibrate tree to time Look at tree Get cool data Answer question

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35 Coming soon

36 Understand what phylogenetics is and its utility for life scientists (briefly) Know some of the computational pitfalls Identify some of the available resources Become ok with just saying yes to being a user (sometimes) Learning objectives


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