Phylogeographic information systems: Putting the geography into phylogeography

Journal of Biogeography

Volumn 33, Issue 11, 2006, Pages 1851-1865

  Kidd, David M ^a,b   Ritchie, Michael G ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

Author keywords

Bioinformatics; Coalescent; Geographical information system; GeoPhylo data standards; Historical biogeography; Phylogeography; Phyloinformatics; Population genetics; Visualization

Indexed keywords

BIODIVERSITY; EVOLUTIONARY BIOLOGY; GENOTYPE; GIS; INFORMATION SYSTEM; PHYLOGENETICS; PHYLOGEOGRAPHY; SPATIAL DISTRIBUTION; VISUALIZATION;

PHYLO;

EID: 33749539880     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2006.01574.x     Document Type: Article

References (109)

1. Anderson, F.E. (2002) Phylogeny and historical biogeography of the Loliginid squids (Mollusca: Cephalopoda) based on mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution, 15, 191-214.
2. Arbogast, B.S. & Kenagy, G.J. (2001) Comparative phylogeography as an integrative approach to historical phylogeography. Journal of Biogeography, 28, 819-825.
3. Avise, J.C. (1998) The history and purview of phylogeography: a personal reflection. Molecular Ecology, 7, 371-379.
4. Avise, J.C. (2000) Phylogeography. Harvard University Press, Harvard.
5. Barbujani, G. (2000) Geographic patterns: how to identify them and why. Human Biology, 72, 133-153.
6. Barton, N.H. & Baird, S.J.E. (1998) Analyse. http://helios.bto.edsac. uk/evolgen/Mac/Analyse.
7. Bermingham, E. & Martin, A.P. (1998) Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America. Molecular Ecology, 7, 499-517.
8. Bermingham, E. & Moritz, C. (1998) Comparative phylogeography: concepts and applications. Molecular Ecology, 7, 367-369.
9. Bohonak, A.J. (2002) IBD (Isolation By Distance): a program for analyses of isolation by distance. Journal of Heredity, 93, 154-155.
10. Bowser, G. (1996) Integrating ecological tools with remotely sensed data: modeling animal dispersal on complex landscapes. Proceedings, Third International Conference/Workshop on Integrating GIS and Environmental Modeling, Santa Fe, NM, January 21-26, 1996. National Center for Geographic Information and Analysis, Santa Barbara, CA. Available on CD or from http://www.ncgia.ucsb. edu/conf/SANTA_FE_CD-ROM/main.html.
11. Bremer, K. (1992) Ancestral areas: a cladistic reinterpretation of the center of origin concept. Systematic Biology, 41, 436-445.
12. Bremer, K. (1995) Ancestral areas: optimization and probability. Systematic Biology, 44, 255-259.
13. Bridle, J.R., Baird, S.J.E. & Butlin, R.K. (2001) Spatial structure and habitat variation in a grasshopper hybrid zone. Evolution, 55, 1832-1843.
14. Brooks, D.R. (1985) Historical ecology: a new approach to studying the evolution of ecological associations. Annals of the Missouri Botanical Garden, 72, 660-680.
15. Brooks, D.R. (1990) Parsimony analysis in historical biogeography and coevolution: methodological and theoretical update. Systematic Zoology, 39, 14-30.
16. Brooks, D.R., van Veller, M.G.P. & McLennan, D.A. (2001) How to do BPA, really. Journal of Biogeography, 28, 345-358.
17. Buckler, E.S., IV. (1999) Phylogeographer: software for the analysis of phylogeographic hypotheses. http://statgen.ncsu.edu/buckler/.
18. Cavalli-Sforza, L.L., Menozzi, P. & Piazza, A. (1994) The history and geography of human genes. Princeton University Press, Princeton.
19. Cesaroni, D., Matarazzo, P., Allegrucci, G. & Sbordoni, V. (1997) Comparing patterns of geographic variation in cave crickets by combining geostatistic methods and Mantel tests. Journal of Biogeography, 24, 419-431.
20. Clark, P.J. & Evans, F.C. (1954) Distance to nearest neighbor as a measure of spatial relationships in populations. Ecology, 35, 445-453.
21. Clarke, D.G. & Clark, D.M. (1995) Lineage. Elements of spatial data quality (ed. by S.C. Guptill and J.L. Morrison), pp. 13-30. Elsevier Science, Oxford.
22. Cleland, C.E. (2001) Historical science, experimental science, and the scientific method. Geology, 29, 987-990.
23. Cox, D.D., Cox, L.H. & Ensor, K.B. (1997) Spatial sampling and the environment: some issues and directions. Environmental and Ecological Statistics, 4, 219-233.
24. de Cserna, Z. & Alvarez, R. (1995) Quaternary drainage development in central Mexico and the threat of an environmental disaster; a geological appraisal. Environmental and Engineering Geoscience, 1, 29-34.
25. Di Zio, S., Fontanella, L. & Ippoliti, L. (2004) Optimal spatial sampling schemes for environmental surveys. Environmental and Ecological Statistics, 11, 397-414.
26. Dufayard, J.F., Duret, L., Penel, S., Gouy, M., Rechenmann, F. & Perriere, G. (2005) Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics, 21, 2596-2603.
27. Dupanloup, I., Schneider, S. & Excoffier, L. (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571-2581.
28. Epperson, B.K. (2003) Geographical genetics. Princeton University Press, Princeton.
29. Excoffier, L., Smouse, P.E. & Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotyes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
30. Goodchild, M.F. (1992) Geographical information science. International Journal of Geographical Information Science, 6, 31-45.
31. Graham, C.H., Ron, S.R., Santos, J.C., Schneider, C.J. & Moritz, C. (2004) Integrating phylogenetics and environmental niche models to explore speciation mechanisms in Dendrobatid frogs. Evolution, 58, 1781-1793.
32. Hale, M.L., Lurz, P.W.W., Hirley, M.D.F., Rushton, S., Fuller, R.M. & Wolff, K. (2001) Impact of landscape management on the genetic structure of red squirrel populations. Science, 293, 2246-2248.
33. Hewitt, G.M. (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 78-112.
34. Hewitt, G.M. (2001) Speciation, hybrid zones and phylogeography - or seeing genes in space and time. Molecular Ecology, 10, 537-549.
35. Hey, J. & Machado, C.A. (2003) The study of structured populations - new hope for a difficult and divided science. Nature Reviews Genetics, 4, 535-543.
36. Hoffmann, M.H., Glaß, A.S., Tomiuk, J., Schmuths, H., Fritsch, R.M. & Bachman, K. (2003) Analysis of molecular data of Arabidopsis thaliana (L.) Heynh. (Brassicaceae) with Geographical Information Systems (GIS). Molecular Ecology, 12, 1007-1019.
37. Hovencamp, P. (2001) A direct method for the analysis of vicariance patterns. Cladistics, 17, 260-265.
38. Hugall, A., Moritz, C., Moussalli, A. & Stanisic, J. (2002) Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Sciences USA, 99, 6112-6117.
39. Hugall, A., Stanisic, J. & Moritz, C. (2003) Trans-species phylogeography of the Sphaerospira lineage and history of Queensland rainforests: extinctions and speciation in a biogeographical context. The Molecular Systematics and Phylogeny of Mollusks (ed. by C. Lydeard and D. Linburg), pp. 270-301. Smithsonian Institution Press, Washington.
40. Humphries, C.J. (2000) Form, space, and time; which came first? Journal of Biogeography, 27, 11-15.
41. Kidd, D.M. (2001) Interpolation in a heterogeneous world. Innovations in GIS 8: spatial information and the environment (ed. by P.E. Halls), pp. 199-212. Taylor and Francis, London.
42. Kidd, D.M. & Ritchie, M.G. (2000) Inferring the patterns and causes of geographic variation in Ephippiger ephippiger (Orthoptera, Tettigoniidea) using Geographical Information Systems. Biological Journal of the Linnaean Society, 71, 269-295.
43. Kidd, D.M. & Ritchie, M.G. (2001) A geographical information science (GISci) approach to exploring variation in the bushcricket Ephippiger ephippiger. GIS and Remote Sensing Applications in Biogeography and Ecology (ed. by A.C. Millington, S.J. Walsh and P.E. Osborne), pp. 193-212. Kluwer Academic Publishers, Dordrecht.
44. Kingman, J.F.C. (1982) On the genealogy of large populations. Journal of Applied Probability, 19A, 27-43.
45. Knowles, L.L. (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691-701.
46. Knowles, L.L. & Maddison, W.P. (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
47. Lam, N. (1983) Spatial interpolation methods: a review. The American Cartographer, 10, 129-149.
48. Lange, A.F. & Gilbert, C. (1999) Using GPS for GIS data capture. Geographical Information Systems (ed. by P.A. Longley, M.F. Goodchild, D.J. Maguire and D.W. Rhind), 2nd edn, pp. 467-476. John Wiley and Sons, New York.
49. Longley, P.A., Goodchild, M.F., Maguire, D.J. & Rhind, D.W. (eds) (1999) Geographical Information Systems, 2nd edn. John Wiley and Sons, New York.
50. Machado, C.A., Kliman, R.M., Markert, J.A. & Hey, J. (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution, 19, 472-488.
51. Maddison, D.R. & Maddison, W.P. (2005) Cartographer, a Mesquite module for plotting geographic data. Version 1.0. http://mesquiteproject.org/ packages/cartographer.
52. Manel, S., Schwartz, M.K., Luikart, G. & Taberlet, P. (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology and Evolution, 18, 189-197.
53. Mark, D.M. (2003) Geographical information science: defining the field. Foundations of geographic information science (ed. by M. Duckham, M.F. Goodchild and M.F. Worboys), pp. 1-15. Taylor and Francis, London.
54. Martínez-Meyer, E., Peterson, A.T. & Hargrove, W.W. (2004) Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity. Global Ecology and Biogeography, 13, 305-314.
55. Mateos, M., Sanjur, O.I. & Vrijenhoek, R.C. (2002) Historical biogeography of the livebearing fish genus Poeciliopsis (Poeciliidae: Cyprinodontiformes). Evolution, 56, 972-984.
56. Miller, M.P. (2005) Alleles In Space (AIS): computer software for the joint analysis of interindividual spatial and genetic information. Journal of Heredity, 96, 722-724.
57. Miller, M. P, Bellinger, M.R., Forsman, E. D. & Haig, S.M. (2006) Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States. Molecular Ecology, 15, 145-159.
58. Mitas, L. & H. Mitasova (1999) Spatial Interpolation. Geographical information systems: principles, techniques, management and applications (ed. by P. Longley, M.F. Goodchild, D.J. Maguire and D.W. Rhind), pp. 481-492. John Wiley & Sons, New York.
59. Monmonier, M.S. (1973) Maximum-difference barriers: an alternative numerical regionalization method. Geographical Analysis, 5, 245-261.
60. Morell, V. (1996) TreeBASE: the roots of phylogeny. Science, 273, 569.
61. Muehrcke, P.C. & Muehrcke, J.O. (1998) Map use: reading, analysis, interpretation. JP Publications, Madison, WI.
62. Nakhleh, L., Miranker, D., Barbancon, F., Piel, W.H. & Donoghue, M.I. (2002) Requirements of phylogenetic data bases. Department of Computer Sciences, University of Texas at Austin, USA. http://www.acsu.buffalo.edu/ ~wpiel/pdfs/bibe2003.pdf.
63. Nichols, R.A. (1988) Genetical and ecological differentiation across a hybrid zone. Ecological Entomology, 13, 39-49.
64. Open GIS Consortium, Inc. (2004) OpenGIS® Geography Markup Language (GML) Implementation specification (ed. by S. Cox, P. Daisey, R. Lake, C. Portele and A. Whiteside). OpenGIS® Recommendation Paper OGC 03-105r1 Version: 3.1.0. http://www.opengeospatial.org/.
65. 10 concentrations in Rio de Janeiro. Environmental and Ecological Statistics, 12, 169-193.
66. Page, R.D.M. (1993) COMPONENT, version 2.0. Natural History Museum, London. http://taxonomy.zoology.gla.ac.uk/rod/cpw.html.
67. Peng, Z.-R. & Tsou, M.-H (2003) Internet GIS: distributed geographic information services for the internet and wireless networks. John Wiley & Sons, New Jersey.
68. Perez, T., Albornoz, J. & Domínguez, A. (2002) Phylogeography of Chamois inferred from microsatellites. Molecular Phylogenetics and Evolution, 25, 524-534.
69. Peterson, A.T., Soberón, J. & Sánchez-Cordero, V. (1999) Conservation of ecological niches in evolutionary time. Science, 285, 1265-1267.
70. Petit, R.J., Pineau, E., Demesure, B., Bacilieri, R., Ducousso, A. & Kremer, A. (1997) Chloroplast DNA footprints of post-glacial recolonization by oaks. Proceedings of the National Academy of Sciences USA, 94, 9996-10001.
71. Petit, R.J., Aguinagalde, I., de Beaulieu, J.L., Bittkau, C., Brewer, S., Cheddadi, R., Ennos, R., Fineschi, S., Grivet, D., Lascoux, M., Mohanty, A., Muller-Starck, G., Demesure-Musch, B., Palme, A., Martin, J.P., Rendell, S. & Vendramin, G.G. (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science, 300, 1563-1565.
72. Pullan, M.R., Watson, M.F., Kennedy, J.B., Raguenaud, C. & Hyam, R. (2000) The Prometheus Taxonomic Model: a practical approach to representing multiple taxonomies. Taxon, 49, 55-75.
73. Ree, R.H., Moore, B.R., Webb, C.O. & Donoghue, M.J. (2005) A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution, 59, 2299-2311.
74. Remington, C.L. (1968) Suture-zones of hybrid interaction between recently joined biotas. Evolutionary biology (ed. by T. Dobzhansky, M.K. Hecht and W.C. Steere), pp. 321-428. Plenum Press, New York.
75. Rempel, R.S. & Kushneriuk, R.S. (2003) The influence of sampling scheme and interpolation method on the power to detect spatial effects of forest birds in Ontario (Canada). Landscape Ecology, 18, 741-757.
76. Rendine, S., Piazza, A., Menozzi, P. & Cavalli-Sforza, L.L. (1999) A problem with synthetic maps: reply to Sokal et al. Human Biology, 71, 15-25.
77. Rice, N.H., Martínez-Meyer, E. & Peterson, A.T. (2003) Ecological niche differentiation in the Aphelocoma jays: a phylogenetic perspective. Biological Journal of the Linnaean Society, 80, 369-383.
78. Riddle, B.R. (2005) Is biogeography emerging from its identity crisis? Journal of Biogeography, 32, 185-186.
79. Riddle, B.R. & Funk, V. (2004) Introduction to Part II: phylogeography and diversification. Frontiers in biogeography: new directions in the geography of nature (ed. by M.V. Lomolino and L.R. Heaney), pp. 87-91. Sinauer Associates, Inc., Sunderland, MA.
80. Riddle, B.R. & Hafner, D.J. (2004) The past and future roles of phylogeography in historical biogeography. Frontiers in biogeography: new directions in the geography of nature (ed. by M.V. Lomolino and L.R. Heaney), pp. 93-110. Sinauer Associates, Inc., Sunderland, MA.
81. Ritchie, M.G., Kidd, D.M. & Gleason, J.M. (2001) Mitochondrial DNA variation and GIS analysis confirm a secondary origin of geographic variation in the bushcricket Ephippiger ephippiger (Orthoptera: Tettigonioidea), and resurrect two subspecies. Molecular Ecology, 10, 603-612.
82. Ronquist, F. (1994) Ancestral areas and parsimony. Systematic Biology, 43, 267-274.
83. Ronquist, F. (1995) Ancestral areas revisited. Systematic Biology, 44, 572-575.
84. Ronquist, F. (1997) Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Systematic Biology, 46, 195-203.
85. Rosenburg, N.A. & Nordborg, M. (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics, 3, 380-390.
86. Rosser, Z.H., Zerjal, T., Hurles, M.E., Adojaan, M., Alavantic, D., Amorim, A., Amos, W., Armenteros, M., Arroyo, E., Barbujani, G., Beckman, G., Beckman, L., Bertranpetit, J., Bosch, E., Bradley, D.G., Brede, G., Cooper, G., Corte-Real, H.B., de Knijff, P., Decorte, R., Dubrova, Y.E., Evgrafov, O., Gilissen, A., Glisic, S., Golge, M., Hill, E.W., Jeziorowska, A., Kalaydjieva, L., Kayser, M., Kivisild, T., Kravchenko, S.A., Krumina, A., Kucinskas, V., Lavinha, J., Livshits, L.A., Malaspina, P., Maria, S., McElreavey, K., Meitinger, T.A., Mikelsaar, A.V., Mitchell, R.J., Nafa, K., Nicholson, J., Norby, S., Pandya, A., Parik, J., Patsalis, P.C., Pereira, L., Peterlin, B., Pielberg, G., Prata, M.J., Previdere, C., Roewer, L., Rootsi, S., Rubinsztein, D.C., Saillard, J., Santos, F.R., Stefanescu, G., Sykes, B.C., Tolun, A., Villems, R., Tyler-Smith, C. & Jobling, M.A. (2000) Y-Chromosomal diversity in Europe in clinal and influenced primarily by geography, rather than language. American Journal of Human Genetics, 67, 1526-1534.
87. Sanderson, M.J., Baldwin, B.G., Bharathan, G., Campbell, C.S., Vondohlen, C., Ferguson, D., Porter, J.M., Wojciechowski, M.F. & Donoghue, M.J. (1993) The growth of phylogenetic information and the need for a phylogenetic database. Systematic Biology, 42, 562-568.
88. Schönhuth, S. & Doadrio, I. (2003) Phylogenetic relationships of the Mexican minnows of the genus Notropis (Actinopterygii, Cyprinidae). Biological Journal of the Linnaean Society, 80, 323-337.
89. Scott, J.M., Heglund, P.J., Morrison, M.L., Haufler, J.B., Raphael, M.G., Wall, W.A. & Samson, F.B. (eds) (2002) Predicting species occurrences: issues of accuracy and scale. Island Press, Washington.
90. Sites, J.W., Jr & Marshall, J.C. (2003) Delimiting species: a Renaissance issue in systematic biology. Trends in Ecology and Evolution, 18, 462-470.
91. Sivasundara, A. & Hey, J. (2003) Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species. Molecular Biology and Evolution, 19, 472-488.
92. Slatkin, M. & Maddison, W.P. (1989) A cladistic measure of gene flow inferred from the phylogeny of alleles. Genetics, 123, 603-613.
93. Sokal, R.R., Oden, N.I. & Thomson, B.A. (1999a) A problem with synthetic maps. Human Biology, 71, 1-13.
94. Sokal, R.R., Oden, N.I. & Thomson, B.A. (1999b) Problems with synthetic maps remain: reply to Rendine et al. Human Biology, 71, 447-453.
95. Sork, V.L., Nason, J., Campbell, D.R. & Fernandez, J.F. (1999) Landscape approaches to historical and contemporary gene flow in plants. Trends in Ecology and Evolution, 14, 219-224.
96. Sujatha, S., Balaji, S. & Srinivasan, N. (2001) PALI: a database of alignments and phylogeny of homologous protein sequences. Bioinformatics, 17, 375-376.
97. Swenson, N.G. & Howard, D.J. (2004) Do suture zones exist? Evolution, 58, 2391-2397.
98. Taberlet, P., Fumagalli, L., Wust-Saucy, A.-G. & Cosson, J.-F. (1998) Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology, 7, 453-464.
99. Templeton, A.R. (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381-397.
100. Templeton, A.R. (2001) Using phylogeographic analysis of gene trees to test species status and process. Molecular Ecology, 10, 779-792.
101. Templeton, A.R. (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789-809.
102. Templeton, A.R., Routman, E. & Phillips, C.A. (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the Tiger Salamander, Ambystoma tigrinum. Genetics, 140, 767-782.
103. Thompson, J.N. (2005) The geographical mosaic of coevolution. The University of Chicago Press, Chicago.
104. Thorpe, R.S. (1996) The use of DNA divergence to help determine the correlates of evolution of morphological characters. Evolution, 50, 524-551.
105. Webb, S.A., Graves, J.A., Marcias-Garcia, C., Magurran, A.E., ó Foighil, D. & Ritchie, M.G. (2004) Molecular phylogeny of the live-bearing Goodeidae (Cyprinodontiformes). Molecular Phylogenetics and Evolution, 30, 527-544.
106. Whelan, S., de Bakker, P.I. & Goldman, N. (2003) Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics, 19, 1556-1563.
107. White, D. & Sifneos, J.C. (2002) Regression tree cartography. Journal of Computational and Graphical Statistics, 11, 600-614.
108. Womble, W.H. (1951) Differential systematics. Science, 114, 315-322.
109. Zhong, Y., Pramanik, S. & Beaman, J.H. (1999) HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees. Bioinformatics, 15, 149-156.