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Geophylogenies Uniting space and time


Graphic images designed to interrelate evolutionary models and geography have been important in the development and illustration of evolutionary concepts and hypotheses (Hewitt 2001). Images have been particularly important in phylogeography (Avise et al. 1987, Avise 2000) and panbiogeography (Croizat 1958, Craw et al. 1999). The majority of images, with the exception of panbiogeography, have been cartographic in nature in that they are drawn with license with the specific purpose of depicting a particular aspect of the data rather than being directly rendered from the data itself. Recently there has been move toward direct rendering of visualizations from data using geographical information systems (GIS) (Kidd & Ritchie 2006) and Google Earth (Janies et al. 2007).This change has been stimulated by ever increasing data volumes and complexity, the desire for quick and simple data exploration, and a growing interest in integrating evolutionary models with external geographical information to identify and quantify the geographical flow of lineages, selection, niche evolution and population connectivity for conservation planning (Kidd & Ritchie 2006, Storfer et al. 2007). Direct rendering of visualizations from data has the advantage of reflecting current database state, uniform presentation of high numbers of graphic elements and flexible editing; however it may sometimes be difficult to create clear images, e.g. in areas of high data density, as graphical license is restricted. Geophylogenies are phylogenetic models transformed into spatial networks through the application of a biogeographical model (Kidd & Liu in press). Geographical coordinates are associated with the nodes and links of the phylogenetic tree; observed tip nodes are associated with coordinates defining where the entity (genotype or species) is observed while internal nodes and branch paths are inferred from a biogeographical model. The simplest biogeographical model is to place inferred nodes at the spatial centroid of observations of the subclade it defines. Alternative historical models could be derived from ecological niche models (Guisan & Zimmerman 2000) or historical biogeographical approaches, e.g DIVA (Ronquist 1997) or LaGrange (Ree et al. 2005).

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Example 1: Evolution of the Artiodactyla in Space and Time. My colleague Sam Price (NESCent) and I recently received third prize in a Visualizing Network Dynamics competition (http://vw.indiana.edu/07netsci/entries/) with a 2D visualization (Figure 1; and see http://vw.indiana.edu/07netsci/entries/#evolution for entire image).

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The IBS mission The International Biogeography Society (IBS) was founded in 2001 with the following mission: (1) Foster communication and collaboration between biogeographers in disparate academic fields - scientists who would otherwise have little opportunity for substantive interaction and collaboration. (2) Increase both the awareness and interests of the scientific community and the lay public in the contributions of biogeographers. (3) Promote the training and education
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of biogeographers so that they may develop sound strategies for studying and conserving the worlds biota. Join the IBS
Figure 1.- Geophylogeny of 174 extant species of Artiodactyla (eventoed hoofed mammals) with some ancestral nodes positioned on the basis of fossil evidence. Here the entire geophylogeny is displayed on a polar projection with arrows showing flow from geophylogeny root to extant tip species. Red dots are the spatial centroid of extant taxa ranges. The light red dot is the root node (positioned from fossil evidence). Form here the group extensively radiated across the Eurasian and African continents with the exception of arctic and desert ecosystems. A fewer lineages crossed the Bearing strait to radiate in the Americas. Care should be taken interpreting this image as extinct species, e.g. North America camels are fully incorporated.

Join the IBS, help support its mission, and receive member benefits, including free online access to Blackwell Publishing's four biogeography journals and the society's journal Frontiers of Biogeography, discounts on meeting fees, books, and access to two additional Blackwell Publishing journals. Frontiers of Biogeography

Example 2: H5N1 Bird Flu virus spread and evolution with Google Maps. Janies et al.(2007) provide an excellent example using Google Earth to trace the global spread and evolution of H1N5 avian influenza. Google Earth (http://earth.google.com/) is a freely available platformindependent global desk mapping client with a user friendly interface. The geophylogeny can be displayed in its entirety or by year illuminating temporal change. Terminal nodes are symbolized to indicate organism host to which description boxes are attached detaining key amino acid states, surface protein mutations, ancestral and sister nodes and the source of the data. Hyperlinks directly link to the corresponding GenBank record. Branches are colour coded to indicate genotype or host vector and also have linked description boxes detailing inferred mutational change along the branch. The model is downloadable from Systematic Biology online (aiTrees.kmz from http://systbio.org/?q=node/184).

Frontiers of Biogeography IBS officers http://www .biogeography.org/html/ About%20IBS/officers.html Disclaimer The views expressed on the blog are not necessarily those of the International Biogeography Society. The IBS reserves the right to delete comments that are inappropriate for the blog. Biogeography headlines Cryptozoology? No need for an The Conversation apology But given biogeography and population biology, such a species is not plausible. Bigfoot's biggest bunions are his biggest supporters, the Bigfoot hunters. Sightings of the creature have come from all over North America. Bigfoot sightings in Northern ... When 2 becomes 12: Cryptic species Deep-Sea News need some love like they've never needed ... is fundamental not only ... lineages for our advances in understanding speciation processes in meiofaunal taxa [microscopic multicellular animals <1mm long, such as nematodes, copepods, and tardigrades], but also to understanding historical biogeography. Antarctic Biodiversity Data Science Daily (press release) Gathered by 90 Expeditions Since 1956data will also be used for a The Summarized comprehensive Biogeography Atlas of the Southern Ocean project to be
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Figure 2. H5N1 Bird Flu phylogeny with branches colour-coded to indicate dispersal vector overlaid onto population density.

Resources For other examples and methodological details: http://evoviz.org/GeoPhyloBuilder. Includes Geophylobuilder The Movie a short animated video of geophylogenies. http://evoviz.org/GoogleEarth http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html http://iphylo.blogspot.com/2007/06/google-earth-phylogenies.html Creating geophylogenies: GeoPhyloBuilder for ArcGIS. ARC Geodatabases, shapefiles and KML for Google Earth (needs Arc license), http://www.nescent.org/informatics/software.php CIPRES Experimental Google Earth Phylogenetic Tree Server. Bill Piels (Yale) Internet service that builds geophylogenies in KML for display in Google Earth, http://www.treebase.org/getrees/

Pie Charts on Google Earth: Phylogeoviz Yi-Hsin Erica Tsais (Duke University) Internet service that puts pie charts on Google Earth, http://www.phylogeoviz.org/ Workshop: A Visualizing Evolution in Space and Time workshop is planned for the 4th International Biogeography Society Meeting, Mrida, Mexico, January 2009.

released during the XI SCAR Biology Symposium in Barcelona July 2013. Share this story on Facebook, Twitter and Google: Other social , bookmarking ... Spectacular Forcepfly Species Found Sci-News.com in Brazil The distribution and biogeography of the family are discussed and it is even proposed that Meropeidae originated before continental drift and then divided into two branches, northern and southern, with the breakup of the old supercontinent Pangea ...
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David Michael Kidd, National Evolutionary Synthesis Center (NESCent), Durham. North Carolina, USA.

References
Avise, J.C. (2000) Phylogeography Harvard University Press, Cambridge, Massachusetts. Avise, J.C., Arnold, J., Ball, R.A., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. & Saunders, N.C. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522. Craw, R.C., Grehan, J.R. & Heads, M.J. (1999) Panbiogeography: Tracking the History of Life. Oxford University Press. Croizat, L. (1958) Panbiogeography. Published by the Author, Caracas. Guisan, A. & Zimmerman, N.E. (2000) Predictive habitat distribution modelling in ecology. Ecological Modelling, 135, 147-86. Hewitt, G.M. (2001) Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology, 10, 537-49. Janies, D., Hill, A.W., Guralnick, R., Habib, F., Waltari, E. & Wheeler, W.C. (2007). Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1). Systematic Biology, 56, 321 - 29. Kidd, D.M. & Ritchie, M.G. (2006) Phylogeographic information systems; Putting the geography into phylogeography. Journal of Biogeography, 33, 1851-65. Kidd, D.M. & Liu, X. (in press) GEOPHYLOBUILDER 1.0: an ArcGIS extension for creating 'geophylogenies'. Molecular Ecology Notes. Ree, R., Moore, B.R., Webb, C.O. & Donoghue, M.J. (2005) A liklihood framework for inferring the evolution of geographic range on phlyogenetic trees. Evolution, 59(11), 2299-311. Ronquist, F. (1997) Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Systematic Biology, 46(1), 195-203. Storfer, A., Murphy, M.A., Evans, J.S., Goldberg, C.S., Robinson, S., Spear, S.F., Dezzani, R., Delmelle, E., Vierling, L. & Waits, L.P (2007) Putting the landscape in . landscape genetics. Heredity, 98(3), 128-42.

ScienceDaily: Ecology Research News Two new species of mushroom found in the Iberian Peninsula, Spain - Tuesday, February 26, 2013 Exurban residences impact bird communities up to 200 meters away, study finds - Monday, February 25, 2013 Science blogs ambio (in Portuguese) BioBLOG British Ecological Society Blog ESA blog Nature blog Panbiogeography Gate Prometheus Real Climate Scitizen Systematic Conservation Planning Contributors V A Funk Dan Gavin Richard Field Brett Riddle IBS Newsletter (Joaqun Hortal) Rob Whittaker Marten Winter Karen Faller Antje Ahrends Meral Avci Joaquin Hortal Dov Sax Nogus-Bravo Ana (Guida) Santos Jack Williams Miguel B. Araujo spyros Mike Dawson Richard Pearson
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Published by IBS Newsletter (Joaqun Hortal) Labels Biogeographical toolbox, Newsletter (Summer 2007)

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