Abstract
The usual approach to organising human knowledge in any field is to invent an intuitive, often hierarchical system of classification. Perhaps uniquely to natural history, humans did not so much invent such a system as discover one: the tree of life. This now iconic object has utility, not only in biodiversity research but also in conservation and science communication. For example, engagement in conservation requires highlighting the scale of biodiversity and what we stand to lose; this can be communicated very effectively by showing people the complete tree of life. Here we discuss the challenges involved in making the complete tree of life accessible to a broad audience. The first challenge relates to data curation, which is marred by the lack of a universally recognised database of species names. Different species can have the same name, different names can refer to the same species, and spelling errors are rife. The second challenge is tree visualisation. While many visualisation methods already exist, few are able to represent the complete tree of life. We argue that scaling up any method to the extent necessary for showing the whole tree of life is bound to expose inescapable trade-offs in the prominence given to each aspect of the underlying data. For example, should topology or species richness be prioritised when displaying clades that contain an insignificant proportion of species but which occupy a prominent position in the tree topology? We conclude with an optimistic outlook for using the tree of life in science communication.
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Notes
- 1.
Actually, even then they would find many points of interest including unicorn fishes, unicorn beetles, unicorn plants, and ‘Unicorn’ – a genus of goblin spiders.
References
Adams D (1995) The restaurant at the end of the universe. Ballantine, New York
Balzer M, Deussen O and Lewerentz C (2005) Voronoi treemaps for the visualization of software metrics. Proceedings of the 2005 ACM symposium on software visualization 165–172. https://doi.org/10.1145/1056018.1056041
Block F, Horn MS, Phillips BC, et al (2012) The DeepTree exhibit: visualizing the tree of life to facilitate informal learning. IEEE Trans Vis Comput Graph 18:2789–2798. https://doi.org/10.1109/TVCG.2012.272 – also see to.pbs.org/1J8YBfl
Borkin MA, Vo AA, Bylinskii Z et al (2013) What makes a visualization memorable? IEEE Trans Vis Comput Graph 19:2306–2315. https://doi.org/10.1109/TVCG.2013.234
Bouckaert RR (2010) DensiTree: making sense of sets of phylogenetic trees. Bioinformatics (Oxford, England) 26:1372–1373. https://doi.org/10.1093/bioinformatics/btq110
Boyle B, Hopkins N, Lu Z et al (2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics 14:16. https://doi.org/10.1186/1471-2105-14-16
Brown CT, Hug LA, Thomas BC et al (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523:208–211. https://doi.org/10.1038/nature14486
Chase MW et al (2016) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc 181(1):1–20. https://doi.org/10.1111/boj.12385
Crahen A (2016) Alaska and Hawaii – Why you ruin my maps? The Data Duo – available at https://thedataduo.com/2016/09/28/alaska-and-hawaii-why-you-ruin-my-maps/
Dawkins R, Wong Y (2016) The Ancestor’s tale, 2nd edn. Orion Publishing Co, UK
de Vienne DM (2016) Lifemap: exploring the entire tree of life. PLoS Biol 14:e2001624. https://doi.org/10.1371/journal.pbio.2001624
Federhen S (2011) The NCBI taxonomy database. Nucleic Acids Res 40:D136–D143. https://doi.org/10.1093/nar/gkr1178
Felsenstein J (2004) Inferring Phylogenies, 2nd edn. Sinauer Associates, Sunderland
Gouy R, Baurain D, Philippe H (2015) Rooting the tree of life: the phylogenetic jury is still out. Philos Trans R Soc Lond Ser B Biol Sci 370:20140329. https://doi.org/10.1098/rstb.2014.0329
Green DM (1991) Chaos, fractals and nonlinear dynamics in evolution and phylogeny. Trends Ecol Evol 6:333–337. https://doi.org/10.1016/0169-5347(91)90042-V
Hawksworth DL, Greuter W, Stalpers JA et al (2009) Registration of scientific names of plants, fungi, bacteria, cultivated plants, and animals: approaches and experiences across disciplines. Bull Zool Nomencl 66:109–124
Hinchliff CE, Smith SA, Allman JF et al (2015) Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl Acad Sci U S A 112:12764–12769. https://doi.org/10.1073/pnas.1423041112
Hug LA, Baker BJ, Anantharaman K et al (2016) A new view of the tree of life. Nat Microbiol 1:16048. https://doi.org/10.1038/nmicrobiol.2016.48
Isaac NJB, Turvey ST, Collen B et al (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS One 2:e296–e296. https://doi.org/10.1371/journal.pone.0000296
Kleiberg E, van de Wetering H, van Wijk J (2001) Botanical visualization of huge hierarchies. In: IEEE symposium on information visualization, 2001. INFOVIS 2001. IEEE, pp 87–94
Koike H, Yoshihara H (1993) Fractal approaches for visualizing huge hierarchies. In: Proceedings 1993 I.E. symposium on visual languages. IEEE Comput. Soc. Press, pp 55–60. https://doi.org/10.1109/VL.1993.269566
Kumar S, Stecher G, Suleski M, Hedges SB (2017) TimeTree: a resource for timelines, timetrees, and divergence times. Mol Biol Evol 34:1812–1819. https://doi.org/10.1093/molbev/msx116
Lamping J, Rao R (1996) The hyperbolic browser: a focus+context technique for visualizing large hierarchies. J Vis Lang Comput. https://doi.org/10.1006/jvlc.1996.0003
Maddison DR, Maddison WP (1996) The tree of life project
Mitchell KJ, Llamas B, Soubrier J et al (2014) Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science (New York, NY) 344:898–900. https://doi.org/10.1126/science.1251981
Nater A, Mattle-Greminger MP, Nurcahyo A et al (2017) Morphometric, behavioral, and genomic evidence for a new orangutan species. Curr Biol: CB 27:3487–3498.e10. https://doi.org/10.1016/j.cub.2017.09.047
O’Meara B (2017) DateLife – available at datelife.org
Mesibov B (2018) “The Not problem” iPhylo guest post. Available at iphylo.blogspot.co.uk/2018/01/guest-post-not-problem.html
Page RDM (2012) Space, time, form: viewing the tree of life. Trends Ecol Evol 27:113–120. https://doi.org/10.1016/j.tree.2011.12.002
Patterson DJ, Cooper J, Kirk PM et al (2010) Names are key to the big new biology. Trends Ecol Evol 25:686–691. https://doi.org/10.1016/j.tree.2010.09.004
Patterson DJ, Egloff W, Agosti D et al (2014) Scientific names of organisms: attribution, rights, and licensing. BMC Res Notes 7:79. https://doi.org/10.1186/1756-0500-7-79
Purvis A, Agapow P-MM (2002) Phylogeny imbalance: taxonomic level matters. Syst Biol 51:844–854. https://doi.org/10.1080/10635150290102546
Rees T (2015) 10 years of global biodiversity databases: are we there yet? iPhylo blog
Rees JA (2018) How many described species are sampled in published phylogenetic trees? Odontomachus’s Blog. Available at odontomachus.wordpress.com/author/odontomachus/
Rosindell J, Harmon LJ (2012) OneZoom: a fractal explorer for the tree of life. PLoS Biol 10:e1001406. https://doi.org/10.1371/journal.pbio.1001406
Sanderson MJ (2014) Ceiba: scalable visualization of phylogenies and 2D/3D image collections. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu315
Schulz H-J (2011) Treevis.net: a tree visualization reference. IEEE Comput Graph Appl 31:11–15. https://doi.org/10.1109/MCG.2011.103
Shalchian-Tabrizi K, Minge MA, Espelund M et al (2008) Multigene phylogeny of choanozoa and the origin of animals. PLoS One 3:e2098. https://doi.org/10.1371/journal.pone.0002098
Shapiro LH, Strazanac JS, Roderick GK (2006) Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. Mol Phylogenet Evol 41:53–63. https://doi.org/10.1016/j.ympev.2006.04.006
Snyder JP (1987) Map projections – a working manual. U.S. Geological Survey. United States Government Printing Office, Washington, DC
Srivastava M, Begovic E, Chapman J et al (2008) The Trichoplax genome and the nature of placozoans. Nature 454:955–960. https://doi.org/10.1038/nature07191
Stoltzfus A, Lapp H, Matasci N et al (2013) Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics 14:158. https://doi.org/10.1186/1471-2105-14-158
Stoltzfus A, O’Meara B, Whitacre J et al (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes 5:574. https://doi.org/10.1186/1756-0500-5-574
Stribling J, Krohn M, Aguayo D (2005) SCIgen – an automatic CS paper generator. pdos.csail.mit.edu/archive/scigen
Tittensor DP, Walpole M, Hill SLL et al (2014) A mid-term analysis of progress toward international biodiversity targets. Science:241–244
Vliegen R, van Wijk JJ, van der Linden EJ (2006) Visualizing business data with generalized Treemaps. IEEE Trans Vis Comput Graph 12(5):789–796. https://doi.org/10.1109/TVCG.2006.200
Zimmer C (2009) Crunching the data for the tree of life. The New York Times see nytimes.com/2009/02/10/health/10iht-10tree.20079116.html
Acknowledgements
We would like to thank Dan Faith and Rosa Scherson for inviting us to write this chapter and for editing the volume as a whole; Alexandra Freeman for comments on the text; Luke Harmon for his role in supporting the OneZoom project and non-profit organisation from inception; many photographers and illustrators for providing public domain material used in OneZoom imagery within this chapter; Chris Jenord and Damian Belson from the Ancestor’s Trail team for their work on that project and for granting permission to use the trail map in Fig. 3.1; Josh Wolfe for the use of his maze generation software under an MIT licence to create a maze base for Fig. 3.2, the complete puzzle is also available under a Creative Commons Attribution licence – Version 3.0 – and is attributable to James Rosindell and OneZoom; David R. Maddison for the left panel of Fig. 3.3 downloaded from Tolweb.org and licensed under a Creative Commons Attribution licence – Version 3.0; Remco Bouckaert for granting permission to use the image from DensiTree as the right panel of our Fig. 3.3; the One Tree, One Planet team (Doug Soltis, Pam Soltis, Rob Guralnick and Naziha Mestaoui) for permitting us to use a screenshot of their projection project and for using OneZoom as part of that work; the University of Florida for their support of the One Tree, One Planet project; T. Michael Keesey (vectorization) and Tony Hisgett (photography) for the PhyloPic image of a chimpanzee in Fig. 3.9, licensed under a Creative Commons Attribution 3.0 Unported licence; and Rod Page for his thought-provoking comments on the OneZoom software both as a reviewer and since initial publication. This work was supported by the Natural Environment Research Council via an Independent Research Fellowship NE/L011611/1 grant to James Rosindell.
Maze of Life Solution
The solution to the problem in Fig. 3.1: human, does not fit anywhere (trick question); olympic torrent salamander, 3; tardigrade, 6; chocolate chip starfish, 5; Pacific dampwood termite, 1; house mouse louse, 2; blue-black spider wasp, 4; and cactus sea squirt, 7.
URLs for Resources Mentioned
Ancestor’s Trail | |
DateLife | |
DeepTree | |
Encyclopedia of life | |
GlobalNames | |
Lifemap | |
OneZoom | |
OneZoom code (GitHub) | |
Open Tree of Life | |
Tree of Life Web Project | |
WikiProject Taxonomy | |
ZooBank |
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Rosindell, J., Wong, Y. (2018). Biodiversity, the Tree of Life, and Science Communication. In: Scherson, R., Faith, D. (eds) Phylogenetic Diversity. Springer, Cham. https://doi.org/10.1007/978-3-319-93145-6_3
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