The big questions for biodiversity informatics

References

• Ackerly , D. D. 2003 . Community assembly, niche conservatism, and adaptive evolution in changing environments . International Journal of Plant Sciences , 164 : S165 – S184 .
   Web of Science ®Google Scholar
• Araújo , M. B. and New , M. 2007 . Ensemble forecasting of species distributions . Trends in Ecology & Evolution , 22 : 42 – 47 .
   PubMed Web of Science ®Google Scholar
• Ausubel , J. H. 2009 . A botanical macroscope . Proceedings of the National Academy of Sciences USA , 106 : 12569 – 12570 .
   PubMedGoogle Scholar
• Butler , D. 2006 . Mashups mix data into global service . Nature , 439 : 6 – 7 .
   PubMed Web of Science ®Google Scholar
• Carstens , B. C. and Richards , C. L. 2007 . Integrating coalescent and ecological niche modeling in comparative phylogeography . Evolution , 61 : 1439 – 1454 .
   PubMed Web of Science ®Google Scholar
• Cracraft , J. 2002 . The seven great questions of systematic biology: An essential foundation for conservation and the sustainable use of biodiversity . Annals of the Missouri Botanical Garden , 89 : 127 – 144 .
   Web of Science ®Google Scholar
• Croizat , L. 1962 . Space, Time, Form: The Biological Synthesis , Caracas, Venezuela : Published by the author .
   Google Scholar
• Edwards , J. L. 2008 . Research and societal benefits of the Global Biodiversity Information Facility . BioScience , 54 : 486 – 487 .
   Google Scholar
• Fitzpatrick , B. M. , Fordyce , J. A. and Gavrilets , S. 2009 . Pattern, process and geographic modes of speciation . Journal of Evolutionary Biology , 22 : 2342 – 2347 .
   PubMedGoogle Scholar
• Gotelli , N. J. , Anderson , M. J. , Arita , H. T. , Chao , A. , Colwell , R. K. , Connolly , S. R. , Currie , D. J. , Dunn , R. R. , Graves , G. R. , Green , J. L. , Grytnes , J.-A. , Jiang , Y.-H. , Jetz , W. , Lyons , K. , McCain , C. M. , Magurran , A. E. , Rahbek , C. , Rangel , T. F.L.V.B. , Soberón , J. , Webb , C. O. and Willig , M. R. 2009 . Patterns and causes of species richness: A general simulation model for macroecology . Ecology Letters , 12 : 873 – 886 .
   PubMed Web of Science ®Google Scholar
• Gotmark , F. and Nilsson , C. 1992 . Criteria used for protection of natural areas in Sweden 1909–1986. . Conservation Biology , 6 : 220 – 231 .
   Google Scholar
• Graham , C. H. , Ferrier , S. , Huettman , F. , Moritz , C. and Peterson , A. T. 2004 . New developments in museum-based informatics and applications in biodiversity analysis . Trends in Ecology and Evolution , 19 : 497 – 503 .
   PubMed Web of Science ®Google Scholar
• Grayman , W. M. , Males , R. M. , Gates , W. E. and Hadder , A. W. 1975 . Land-based modeling system for water quality management studies . Journal of the Hydraulics Division, ASCE , 101 : 567 – 580 .
   Google Scholar
• Guralnick , R. and Hill , A. 2009 . Biodiversity informatics: Automated approaches for documenting global biodiversity patterns and processes . Bioinformatics , 25 : 421 – 428 .
   PubMed Web of Science ®Google Scholar
• Hamid , J. S. , Hu , P. , Roslin , N. M. , Ling , V. , Greenwood , C. M.T. and Beyene , J. 2009 . Data integration in genetics and genomics: Methods and challenges . Human Genomics and Proteomics , 2009 : 869093
   PubMedGoogle Scholar
• Hey , T. , Tansley , S. and Tolle , K. 2009 . The Fourth Paradigm: Data-intensive Scientific Discovery , Redmond, Washington : Microsoft Research .
   Google Scholar
• Hickerson , M. , Carstens , B. , Cavender-Bares , J. , Crandall , K. , Graham , C. , Johnson , J. , Rissler , L. , Victoriano , P. and Yoder , A. 2009 . Phylogeography's past, present, and future: 10 years after Avise 2000 . Molecular Phylogenetics and Evolution , 54 : 291 – 301 .
   PubMedGoogle Scholar
• Hijmans , R. J. , Cameron , S. E. , Parra , J. L. , Jones , P. G. and Jarvis , A. 2005 . Very high resolution interpolated climate surfaces for global land areas . International Journal of Climatology , 25 : 1965 – 1978 .
   Web of Science ®Google Scholar
• Jackson , S. T. and Overpeck , J. T. 2000 . Responses of plant populations and communities to environmental changes of the Late Quaternary . Palaeobiology , 26 (supplement) : 194 – 220 .
   Google Scholar
• Janies , D. , Hill , A. , Guralnick , R. , Habib , F. , Waltari , E. and Wheeler , W. 2007 . Genomic analysis and geographic visualization of the spread of avian influenza (H5N1) . Systematic Biology , 56 : 321 – 329 .
   PubMed Web of Science ®Google Scholar
• Jetz , W. and Rahbek , C. 2001 . Geometric constraints explain much of the species richness pattern in African birds . Proceedings of the National Academy of Sciences USA , 98 : 5661 – 5666 .
   PubMedGoogle Scholar
• Kearney , M. and Porter , W. P. 2004 . Mapping the fundamental niche: Physiology, climate, and the distribution of a nocturnal lizard . Ecology , 85 : 3119 – 3131 .
   Web of Science ®Google Scholar
• Kim , J. H. 2002 . Bioinformatics and genomic medicine . Genetics in Medicine , 4 : 62S – 65S .
   PubMed Web of Science ®Google Scholar
• Knowles , L. L. , Carstens , B. C. and Keat , M. L. 2007 . Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence . Current Biology , 17 : 940 – 946 .
   PubMed Web of Science ®Google Scholar
• Koleff , P. , Tambutti , M. , March , I. , Esquivel , R. , Cantú , C. and Lira-Noriega , A. 2009 . “ Identificación de prioridades y análisis de vacíos para la conservación de la biodiversidad de México ” . In Capital Natural de México. Estado de Conservación y Tendencias de Cambio , Edited by: Dirzo , R. , González , R. and March , I. 651 – 718 . Mexico, D.F. : Comision Nacional para el Conocimiento y Uso de la Biodiversidad .
   Google Scholar
• Koning , D. , Sarkar , I. and Moritz , T. 2005 . TaxonGrab: Extracting taxonomic names from text . Biodiversity Informatics , 2 : 79 – 82 .
   Google Scholar
• Koslow , S. and Hirsch , M. 2004 . Celebrating a decade of neuroscience databases . Neuroinformatics , 2 : 267 – 269 .
   PubMedGoogle Scholar
• Kozak , K. H. , Wiens , J. J. and Pfennig , D. 2009 . Does niche conservatism promote speciation? A case study in North American salamanders . Evolution , 60 : 2604 – 2621 .
   Google Scholar
• Losos , J. B. and Glor , R. E. 2003 . Phylogenetic comparative methods and the geography of speciation . Trends in Ecology and Evolution , 18 : 220 – 227 .
   Google Scholar
• Ludascher , B. , Altintas , I. , Berkley , C. , Higgins , D. , Jaeger , E. , Jones , M. , Lee , E. A. , Tao , J. and Zhao , Y. 2006 . Scientific workflow management and the Kepler system . Concurrency and Computation: Practice and Experience , 18 : 1039 – 1065 .
   Web of Science ®Google Scholar
• Lynch , J. D. 1989 . “ The gauge of speciation: On the frequency of modes of speciation ” . In Speciation and its Consequences , Edited by: Otte , D. and Endler , J. A. 527 – 553 . Sunderland, MA : Sinauer Associates .
   Google Scholar
• Manso , M.-Á. and Wachowicz , M. 2009 . GIS design: A review of current issues in interoperability . Geography Compass , 3 : 1105 – 1124 .
   Google Scholar
• Martínez-Meyer , E. , Peterson , A. T. and 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 .
   Web of Science ®Google Scholar
• Martinez Del Rio , C. 2008 . Metabolic theory or metabolic models? . Trends in Ecology and Evolution , 25 : 256 – 260 .
   Google Scholar
• Nelson , G. O. and Platnick , N. I. 1981 . Systematics and Biogeography: Cladistics and Vicariance , New York : Columbia University Press .
   Google Scholar
• Page , R. D.M. 2008 . Biodiversity informatics: The challenge of linking data and the role of shared identifiers . Briefings in Bioinformatics , 9 : 345 – 354 .
   PubMedGoogle Scholar
• Peterson , A. T. , Ortega-Huerta , M. A. , Bartley , J. , Sanchez-Cordero , V. , Soberon , J. , Buddemeier , R. H. and Stockwell , D. R.B. 2002 . Future projections for Mexican faunas under global climate change scenarios . Nature , 416 : 626 – 629 .
   PubMed Web of Science ®Google Scholar
• Peterson , A. T. , Soberón , J. and Sánchez-Cordero , V. 1999 . Conservatism of ecological niches in evolutionary time . Science , 285 : 1265 – 1267 .
   PubMed Web of Science ®Google Scholar
• Porter , W. , Sabo , J. , Tracy , C. , Reichman , O. and Ramankutty , N. 2002 . Physiology on a landscape scale: Plant-animal interactions . Integrative and Comparative Biology , 42 : 431 – 453 .
   PubMed Web of Science ®Google Scholar
• Rahbek , C. , Gotelli , N. J. , Colwell , R. K. , Entsminger , G. L. , Rangel , T. F.L.V.B. and Graves , G. R. 2007 . Predicting continental-scale patterns of bird species richness with spatially explicit models . Proceedings of the Royal Society B , 274 : 165 – 174 .
   PubMed Web of Science ®Google Scholar
• Rangel , T. F. , Diniz-Filho , J. A. and Colwell , R. 2007 . Species-richness and evolutionary niche dynamics: A spatial pattern-oriented simulation experiment . American Naturalist , 170 : 602 – 616 .
   PubMedGoogle Scholar
• Ricklefs , R. E. and Schluter , D. 1993 . Species Diversity in Ecological Communities: Historical and Geographical Perspectives , Chicago : University of Chicago Press .
   Google Scholar
• Ridgely , R. S. , Allnutt , T. F. , Brooks , T. , Mcnicol , D. K. , Mehlman , D. W. , Young , B. E. and Zook , J. R. 2005 . Digital Distribution Maps of the Birds of the Western Hemisphere, version 2.1 , Arlington, Virginia : NatureServe .
   Google Scholar
• Roos , D. S. 2001 . Bioinformatics—Trying to swim in a sea of data . Science , 291 : 1260 – 1261 .
   PubMed Web of Science ®Google Scholar
• Sarkar , S. , Pressey , R. L. , Faith , D. P. , Margules , C. R. , Fuller , T. , Stoms , D. M. , Moffett , A. , Wilson , K. A. , Williams , K. J. , Williams , P. H. and Andelman , S. 2006 . Biodiversity conservation planning tools: Present status and challenges for the future . Annual Review of Environment and Resources , 31 : 123 – 159 .
   Web of Science ®Google Scholar
• Sautter , G. , Boehm , K. and Agosti , D. 2006 . A combining approach to find all taxon names (FAT) . Biodiversity Informatics , 3 : 46 – 58 .
   Google Scholar
• Schalk , P. H. 1998 . Management of marine natural resources through biodiversity informatics . Marine Policy , 22 : 269 – 280 .
   Google Scholar
• Soberón , J. and Nakamura , M. 2009 . Niches and distributional areas: Concepts, methods, and assumptions . Proceedings of the National Academy of Sciences USA , 106 : 19644 – 19650 .
   PubMed Web of Science ®Google Scholar
• Soberón , J. and Peterson , A. T. 2005 . Interpretation of models of fundamental ecological niches and species’ distributional areas . Biodiversity Informatics , 2 : 1 – 10 .
   Google Scholar
• Sonnhammer , E. L.L. 2004 . Genome informatics: Taming the avalanche of genomic data . Genome Research , 6 : 301
   Google Scholar
• Stein , B. R. and Wieczorek , J. 2004 . Mammals of the world: MaNIS as an example of data integration in a distributed network environment . Biodiversity Informatics , 1 : 14 – 22 .
   Google Scholar
• Thomas , C. D. , Cameron , A. , Green , R. E. , Bakkenes , M. , Beaumont , L. J. , Collingham , Y. C. , Erasmus , B. F.N. , Ferreira De Siqueira , M. , Grainger , A. , Hannah , L. , Hughes , L. , Huntley , B. , Van Jaarsveld , A. S. , Midgely , G. E. , Miles , L. , Ortega-Huerta , M. A. , Peterson , A. T. , Phillips , O. L. and Williams , S. E. 2004 . Extinction risk from climate change . Nature , 427 : 145 – 148 .
   PubMed Web of Science ®Google Scholar
• Vogler , A. P. and Monaghan , M. T. 2006 . Recent advances in DNA taxonomy . Journal of Zoological Systematics and Evolutionary Research , 45 : 1 – 10 .
   Web of Science ®Google Scholar
• Waltari , E. , Perkins , S. , Hijmans , R. , Peterson , A. T. , Nyári , Á. and Guralnick , R. 2007 . Locating Pleistocene refugia: Comparing phylogeographic and ecological niche model predictions . PLoS ONE , 2 : e563
   PubMed Web of Science ®Google Scholar
• Wells , P. V. 1983 . Palaeobiogeography of montane islands in the Great Basin since the last glaciopluvial . Ecological Monographs , 53 : 341 – 382 .
   Web of Science ®Google Scholar
• Williams , J. W. and Jackson , S. T. 2007 . Novel climates, no-analogue communities, and ecological surprises . Frontiers in Ecology and the Environment , 5 : 475 – 482 .
   Web of Science ®Google Scholar
• Yesson , C. , Brewer , P. W. , Sutton , T. , Caithness , N. , Pahwa , J. S. , Burgess , M. , Gray , W. A. , White , R. J. , Jones , A. C. , Bisby , F. A. and Culham , A. 2007 . How global is the Global Biodiversity Information Facility? . PLoS ONE , 2 : e1124
   PubMed Web of Science ®Google Scholar