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18 - A critical appraisal of the meaning and diagnosability of cryptic evolutionary diversity, and its implications for conservation in the face of climate change

from Section 4 - Conservation

Published online by Cambridge University Press:  16 May 2011

J. Bernardo
Affiliation:
Cornell University, Roan Mountain, TN, USA
Trevor R. Hodkinson
Affiliation:
Trinity College, Dublin
Michael B. Jones
Affiliation:
Trinity College, Dublin
Stephen Waldren
Affiliation:
Trinity College, Dublin
John A. N. Parnell
Affiliation:
Trinity College, Dublin
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Summary

Abstract

Accurate species delimitation is a foundational assumption of biological research. It is especially relevant to conservation, because species names are the currency for conservation policy. Cryptic species are species that are deeply genetically divergent from other such lineages, but that have escaped detection and description because they lack obvious morphological discontinuities. They are not necessarily closely related. Genetic data have revealed surprising amounts of cryptic diversity, which has provoked numerous criticisms concerning their taxonomic recognition and relevance to conservation. I critically examine these and other concerns in the context of a hypothetico-deductive framework (HDF) for species delimitation and conclude that they are unfounded. I explore links between taxonomy and systematics with respect to cryptic species recognition, claims about the relative usefulness of morphological versus genetic data for species delimitation, and the kinds of inferential errors that attach to the process of inferring species boundaries. The balance of the chapter shows that the description of cryptic diversity is an important enterprise and considers its implications for conservation biology, especially in the context of global warming.

Introduction

Biodiversity conservation is a multidisciplinary enterprise that seeks to preserve species diversity in the form of ecologically and evolutionarily viable populations.

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Publisher: Cambridge University Press
Print publication year: 2011

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References

Adams, D. C., Berns, C. M., Kozak, K.H. and Wiens, J. J. (2009). Are rates of species diversification correlated with rates of morphological evolution? Proceedings of the Royal Society of London B, 276, 2729–2738.CrossRefGoogle ScholarPubMed
Agapow, P. M. (2005). Species: demarcation and diversity. In Phylogeny and Conservation, ed. Purvis, A., Gittleman, J. L. and Brooks, T. M.. Cambridge: Cambridge University Press.Google Scholar
Agapow, P. M. and Sluys, R. (2005). The reality of taxonomic change. Trends in Ecology and Evolution, 20, 278–280.CrossRefGoogle ScholarPubMed
Agapow, P. M., Bininda-Emonds, O. R. P., Crandall, K. A. et al. (2004). The impact of species concept on biodiversity studies. Quarterly Review of Biology, 79, 161–179.CrossRefGoogle ScholarPubMed
Agnarsson, I. and Kuntner, M. (2007). Taxonomy in a changing world: seeking solutions for a science in crisis. Systematic Biology, 56, 531–539.CrossRefGoogle Scholar
Alizon, S., Kucera, M. and Jansen, V. A. A. (2008). Competition between cryptic species explains variations in rates of lineage evolution. Proceedings of the National Academy of Sciences of the USA, 105, 12382–12386.CrossRefGoogle ScholarPubMed
Allen, B., Kon, M. and Bar-Yam, Y. (2009). A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. American Naturalist, 174, 236–243.CrossRefGoogle ScholarPubMed
Anderson, J. and Tilley, S. G. (2003). Systematics of the Desmognathus ochrophaeus complex in the Cumberland Plateau of Tennessee. Herpetological Monographs, 17, 75–110.CrossRefGoogle Scholar
Andreone, F., Carpenter, A. I., Cox, N. et al. (2008). The challenge of conserving amphibian megadiversity in Madagascar. PLoS Biology, 6, e118.CrossRefGoogle ScholarPubMed
Austin, M. (2007). Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecological Modeling, 200, 1–19.CrossRefGoogle Scholar
Avise, J. C. (1989). A role for molecular genetics in the recognition and conservation of endangered species. Trends in Ecology and Evolution, 4, 279–281.CrossRefGoogle ScholarPubMed
Avise, J. C. (1996). Introduction: the scope of conservation genetics. In Conservation Genetics: Case Histories from Nature, ed. Avise, J. C. and Hamrick, J. L.. New York, NY: Chapman and Hall, pp. 1–9.CrossRefGoogle Scholar
Avise, J. C. (2000). Phylogeography. Cambridge, MA: Harvard University Press.Google ScholarPubMed
Avise, J. C. (2007). Twenty-five key evolutionary insights from the phylogeographic revolution in population genetics. In Phylogeography of Southern European Refugia, ed. Weiss, S. and Ferrand, N.. Dordrecht: Springer, pp. 7–21.Google Scholar
Avise, J. C. (2008). Three ambitious (and rather unorthodox) assignments for the field of biodiversity genetics. Proceedings of the National Academy of Sciences of the USA, 105, 11564–11570.CrossRefGoogle ScholarPubMed
Avise, J. C. and Aquadro, C. F. (1982). A comparative summary of genetic distances in the vertebrates: patterns and correlations. Evolutionary Biology, 15, 151–185.CrossRefGoogle Scholar
Avise, J. C. and Johns, G. C. (1999). Proposal for a standardized temporal scheme of biological classification for extant species. Proceedings of the National Academy of Sciences of the USA, 96, 7358–7363.CrossRefGoogle ScholarPubMed
Avise, J. C. and Mitchell, D. (2007). Time to standardize taxonomies. Systematic Biology, 56, 130–133.CrossRefGoogle ScholarPubMed
Avise, J. C. and Walker, D. (1999). Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome. Proceedings of the National Academy of Sciences of the USA, 96, 9929–95.CrossRefGoogle ScholarPubMed
Avise, J. C. and Walker, D. (2000). Abandon all species concepts? A response. Conservation Genetics, 1, 77–80.CrossRefGoogle Scholar
Baker, R. J. (1984). A sympatric cryptic species of mammal: a new species ofRhogeessa (Chiroptera: Vespertilionidae). Systematic Zoology, 33, 178–183.Google Scholar
Baker, R. J. and Bradley, R. D. (2006). Speciation in mammals and the genetic species concept. Journal of Mammalogy, 87, 643–662.CrossRefGoogle ScholarPubMed
Balmford, A., Green, R. E. and Jenkins, M. (2003). Measuring the changing state of nature. Trends in Ecology and Evolution, 18, 326–330.CrossRefGoogle Scholar
Bateman, R. M. and DiMichele, W. A. (2003). Genesis of phenotypic and genotypic diversity in land plants: the present as the key to the past. Systematics and Biodiversity, 1, 13–28.CrossRefGoogle Scholar
Baum, D. A. and Shaw, K. L. (1995). Genealogical perspectives on the species problem. In Monographs in Systematic Botany: Experimental and Molecular Approaches to Plant Biosystematics, ed. Hoch, P. and Stephenson, A.. St Louis, MO: Missouri Botanical Garden, pp. 289–303.Google Scholar
Beale, C. M., Lennon, J. J. and Gimona, A. (2008). Opening the climate envelope reveals no macroscale associations with climate in European birds. Proceedings of the National Academy of Sciences of the USA, 105, 14908–14912.CrossRefGoogle ScholarPubMed
Beheregaray, L. and Caccone, A. (2007). Cryptic biodiversity in a changing world. Journal of Biology, 6, 9.CrossRefGoogle Scholar
Bell, M. A. and Foster, S. A. (1994). The Evolutionary Biology of the Threespine Stickleback. London: Oxford University Press.Google Scholar
Bernardo, J. (1994). Experimental analysis of allocation in two divergent, natural salamander populations. American Naturalist, 143, 14–38.CrossRefGoogle Scholar
Bernardo, J. and Agosta, S. (2003). Clinal variation in the larval life history of mountain dusky salamanders: ecological limits on foraging time and prey abundance restrict opportunities for larval growth. Journal of Zoology, 259, 411–421.CrossRefGoogle Scholar
Bernardo, J. and Reagan-Wallin, N. L. (2002). Plethodontid salamanders do not conform to ‘general rules’ for ectotherm life histories: insights from allocation models about why simple models do not make accurate predictions. Oikos, 97, 398–414.CrossRefGoogle Scholar
Bernardo, J. and Spotila, J. (2006). Physiological constraints on organismal response to global warming; mechanistic insights from clinally varying populations and implications for assessing endangerment. Biology Letters, 2, 135–139.CrossRefGoogle ScholarPubMed
Bernardo, J., Ossola, R. J., Spotila, J. and Crandall, K. A. (2007). Interspecies physiological variation as a tool for cross-species assessments of global warming-induced endangerment: validation of an intrinsic determinant of macroecological and phylogeographic structure. Biology Letters, 3, 695–698.CrossRefGoogle ScholarPubMed
Bickford, D., Lohman, D. J., Sodhi, N. S. et al. (2006). Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution, 22,148–155.CrossRefGoogle ScholarPubMed
Biju, S. D. and Bossuyt, F. (2003). New frog family from India reveals an ancient biogeographical link with the Seychelles. Nature, 425, 711–714.CrossRefGoogle ScholarPubMed
Blackburn, T. M. and Gaston, K. J., eds. (2003). Macroecology: Concepts and Consequences. British Ecological Society Annual Symposium Series. Oxford: Blackwell Science.
Blaxter, M. L. (2004). The promise of DNA taxonomy. Philosophical Transactions of the Royal Society of London B, 359, 669–679.CrossRefGoogle ScholarPubMed
Boissin, E., Féral, J. P. and Chenuil, A. (2008). Defining reproductively isolated units in a cryptic and syntopic species complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholis squamata (Ophiuroidea). Molecular Ecology, 17, 1732–1744.CrossRefGoogle Scholar
Botkin, D. B., Saxe, H., Araújo, M. B. et al. (2007). Forecasting the effects of global warming on biodiversity. Bioscience, 57, 227–236.CrossRefGoogle Scholar
Bradley, R. D. and Baker, R. J. (2001). A test of the genetic species concept: cytochrome-b sequences and mammals. Journal of Mammalogy, 82, 960–973.2.0.CO;2>CrossRefGoogle Scholar
Brown, D. M., Brenneman, R. A., Georgiadis, N. J. et al. (2007). Extensive population genetic structure in the giraffe. BMC Biology, 5, 57.CrossRefGoogle ScholarPubMed
Brown, J. H. (1995). Macroecology. Chicago, IL: University of Chicago Press.Google Scholar
Bruce, R. C. (2005). Did Desmognathus salamanders reinvent the larval stage?Herpetological Review, 36, 107–112.Google Scholar
Burbrink, F. T. (2001). Systematics of the North American rat snake complex (Elaphe obsoleta). Herpetological Monographs, 15, 1–53.CrossRefGoogle Scholar
Burbrink, F. T. (2002). Phylogeographic analysis of the cornsnake (Elaphe guttata) complex as inferred from maximum likelihood and Bayesian analyses. Molecular Phylogenetics and Evolution, 25, 465–476.CrossRefGoogle ScholarPubMed
Burbrink, F. T., Lawson, R. and Slowinski, J. B. (2000). Molecular phylogeography of the North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution, 54, 2107–2114.CrossRefGoogle ScholarPubMed
Burns, J. M., Janzen, D. H., Hajibabaei, M., Hallwachs, W. and Hebert, P. D. N. (2008). DNA and cryptic species of skipper butterflies in the genus Perichares in Area de Conservacion Guanacaste, Costa Rica. Proceedings of the National Academy of Sciences of the USA, 105, 6350–6355.CrossRefGoogle ScholarPubMed
Camp, C. D., Marshall, J. L., Landau, K. R., Austin, R. M. and Tilley, S. G. (2000). Sympatric occurrence of two species of the two-lined salamander (Eurycea bislineata) complex. Copeia, 2000, 572–578.CrossRefGoogle Scholar
Camp, C. D., Peterman, W. E., Milanovich, J. R. et al. (2009). A new genus and species of lungless salamander (family Plethodontidae) from the Appalachian highlands of the south-eastern United States. Journal of Zoology, 279, 86–94.CrossRefGoogle Scholar
Casu, M. and Curini-Galletti, M. (2006). Genetic evidence for the existence of cryptic species in the mesopsammic flatworm Pseudomonocelis ophiocephala (Rhabditophora: Proseriata). Biological Journal of the Linnean Society, 87, 553–576.CrossRefGoogle Scholar
Ceballos, G. and Ehrlich, P. R. (2009). Discoveries of new mammal species and their implications for conservation and ecosystem services. Proceedings of the National Academy of Sciences of the USA, 106, 3841–3846.CrossRefGoogle ScholarPubMed
Chaitra, M. S., Vasudevan, K. and Shanker, K. (2004). The biodiversity bandwagon: the splitters have it. Current Science, 86, 897–899.Google Scholar
Chek, A. A., Austin, J. D. and Lougheed, S. C. (2003). Why is there a tropical-temperate disparity in the genetic diversity and taxonomy of species? Evolutionary Ecology Research, 5, 69–77.Google Scholar
Chen, G. andHare, M. P. (2008). Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa. Molecular Ecology, 17, 1451–1468.CrossRefGoogle ScholarPubMed
Chown, S. L. andGaston, K. J. (1999). Exploring links between physiology and ecology at macro-scales: the role of respiratory metabolism in insects. Biological Reviews, 74, 87–120.CrossRefGoogle Scholar
Chown, S. L. andGaston, K. J. (2008). Macrophysiology for a changing world. Proceedings of the Royal Society of London B, 275, 1469–1478.CrossRefGoogle ScholarPubMed
Chown, S. L., Gaston, K.J. and Robinson, D. (2004). Macrophysiology: large-scale patterns in physiological traits and their ecological implications. Functional Ecology, 18, 159–167.CrossRefGoogle Scholar
Clausen, J., Keck, D. D. and Heisey, W. M. (1940). Experimental Studies on the Nature of Species. I. Effects of Varied Environments on Western North American Plants. Carnegie Institute of Washington Publications, 520. Washington, DC: Carnegie Institute.Google Scholar
Clausen, J., Keck, D. D. and Heisey, W. M. (1948). Experimental Studies on the Nature of Species. III. Environmental Responses of Climatic Races of Achillea. Carnegie Institute of Washington Publications, 581. Washington, DC: Carnegie Institute.Google Scholar
Clausen, J., Keck, D. D. and Heisey, W. M. (1958). Experimental Studies on the Nature of Species. IV. Genetic Structure of Ecological Races. Carnegie Institute of Washington Publications, 615. Washington, DC: Carnegie Institute.Google Scholar
Cohen, J. (1977). Statistical Power Analysis for the Behavioral Sciences. New York, NY: Academic Press.Google Scholar
Collins, J. P. andHalliday, T. (2005). Forecasting changes in amphibian biodiversity: aiming at a moving target. Philosophical Transactions of the Royal Society of London B, 360, 309–314.CrossRefGoogle Scholar
Cooper, N., Bielby, J., Thomas, G. H. et al. (2008). Macroecology and extinction risk correlates of frogs. Global Ecology and Biogeography, 17, 211–221.CrossRefGoogle Scholar
Cracraft, J., Feinstein, J., Vaughn, J. and Helm-Bychowski, K. (1998). Sorting out tigers (Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics. Animal Conservation, 1, 139–150.CrossRefGoogle Scholar
Craig, M. T., Graham, R. T., Torres, R. A. et al. (2008). How many species of goliath grouper are there? Cryptic genetic divergence in a threatened marine fish and the resurrection of a geopolitical species. Endangered Species Research, 7, 167–174.CrossRefGoogle Scholar
Crandall, K. A., Bininda-Emonds, O. R. P., Mace, G. M. and Wayne, R. K. (2000). Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution, 15, 290–295.CrossRefGoogle ScholarPubMed
Crandall, K. A., Robison, H. W. and Buhay, J. E. (2009). Avoidance of extinction through nonexistence: the use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater crayfish. Conservation Genetics, 10, 177–189.CrossRefGoogle Scholar
Craul, M., Zimmermann, E., Rasoloharijaona, S., Randrianambinina, B. and Radespiel, U. (2007). Unexpected species diversity of Malagasy primates (Lepilemur spp.) in the same biogeographical zone: a morphological and molecular approach with the description of two new species. BMC Evolutionary Biology, 7, 83.CrossRefGoogle ScholarPubMed
Cree, A. andButler, D. (1993). Tuatara recovery plan (Sphenodon spp.). Threatened Species Recovery Plan 9. Wellington: New Zealand Department of Conservation.
Crozier, R. H. (1997). Preserving the information content of species: genetic diversity, phylogeny and conservation worth. Annual Review of Ecology and Systematics, 28, 243–268.CrossRefGoogle Scholar
Crozier, R. H., Dunnett, D. J. and Agapow, P. M. (2005). Phylogenetic biodiversity assessment based on systematic nomenclature. Evolutionary Bioinformatics Online, 1, 11–36.Google Scholar
Cruse, M., Telerant, R., Gallagher, T., Lee, T. and Taylor, J. W. (2002). Cryptic species inStachybotrys chartarum. Mycologia, 94, 814–822.CrossRefGoogle ScholarPubMed
Darlington, C. D. (1940). Taxonomic systems and genetic systems. In The New Systematics, ed. Huxley, J.. Oxford: Clarendon Press, pp. 137–160.Google Scholar
Darwin, C. R. (1859). On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray.Google Scholar
Daugherty, C. H., Cree, A., Hay, J. M. and Thompson, M. B. (1990). Neglected taxonomy and continuing extinction of the tuatara (Sphenodon). Nature, 347, 177–179.CrossRefGoogle Scholar
Daugherty, C. H., Patterson, G. B. and Hitchmough, R. A. (1994). Taxonomic and conservation review of the New Zealand herpetofauna. New Zealand Journal of Zoology, 21, 317–323.CrossRefGoogle Scholar
Queiroz, K. (1998). The general lineage concept of species, species criteria and the process of speciation. In Endless Forms: Species and Speciation, ed. Howard, D. and Berlocher, S.. Oxford: Oxford University Press, pp. 57–75.Google Scholar
Queiroz, K. (1999). The general lineage concept of species and the defining properties of the species category. In Species: New Interdisciplinary Essays, ed. Wilson, R. A.. Cambridge, Massachusetts, MA: MIT Press, pp. 49–89.Google Scholar
Queiroz, K. (2005a). A unified species concept and its consequences for the future of taxonomy. Proceedings of the California Academy of Sciences, 56, 196–215.Google Scholar
Queiroz, K. (2005b). Different species problems and their resolution. BioEssays, 27, 1263–1269.CrossRefGoogle ScholarPubMed
Queiroz, K. (2006). The PhyloCode and the distinction between taxonomy and nomenclature. Systematic Biology, 55, 160–162.CrossRefGoogle ScholarPubMed
Queiroz, K. (2007a). Toward an integrated system of clade names. Systematic Biology, 56, 956–974.CrossRefGoogle ScholarPubMed
Queiroz, K. (2007b). Species concepts and species delimitation. Systematic Biology, 56, 879–886.CrossRefGoogle ScholarPubMed
Quieroz, K. andDonoghue, M. J. (1988). Phylogenetic systematics and the species problem. Cladistics, 4, 317–338.CrossRefGoogle Scholar
Quieroz, K. andDonoghue, M. J. (1990). Phylogenetic systematics and species revisited. Cladistics, 6, 83–90.CrossRefGoogle Scholar
Queiroz, K. andGauthier, J. (1992). Phylogenetic taxonomy. Annual Review of Ecology and Systematics, 23, 449–480.CrossRefGoogle Scholar
Derycke, S., Remerie, T., Backeljau, T. et al. (2008). Phylogeography of the Rhabditis (Pellioditis) marina species complex: evidence for long-distance dispersal, and for range expansions and restricted gene flow in the northeast Atlantic. Molecular Ecology, 17, 3306–3322.CrossRefGoogle ScholarPubMed
DeSalle, R., Egan, M. G. and Siddall, M. (2005). The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society of London B, 360, 1905–1916.CrossRefGoogle ScholarPubMed
Deutsch, C. A., Tewksbury, J. J., Huey, R. B. et al. (2008). Impacts of climate warming on terrestrial ectotherms across latitude. Proceedings of the National Academy of Sciences of the USA, 105, 6668–6672.CrossRefGoogle ScholarPubMed
Dobzhansky, T. (1937a). Genetic nature of species differences. American Naturalist, 71, 404–420.Google Scholar
Dobzhansky, T. (1937b). Genetics and the Origin of Species. New York, NY: Columbia University Press.Google Scholar
Dobzhansky, T. (1950). Mendelian populations and their evolution. American Naturalist, 84, 401.CrossRefGoogle Scholar
Donoghue, M. J. (1985). A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist, 88, 172–181.CrossRefGoogle Scholar
Dubois, A. (2003). The relationships between taxonomy and conservation biology in the century of extinctions. Comptes Rendus Biologies, 326, S9-S21.CrossRefGoogle ScholarPubMed
Dunham, A. E., Smith, G. R. and Taylor, J. N. (1979). Evidence for character displacement in western American catostomid fishes. Evolution, 33, 877–896.CrossRefGoogle ScholarPubMed
Dunn, C. P. (2003). Keeping taxonomy based in morphology. Trends in Ecology and Evolution, 18, 270–271.CrossRefGoogle Scholar
Dytham, C. (2009). Evolved dispersal strategies at range margins. Proceedings of the Royal Society of London B, 276, 1407–1413.CrossRefGoogle ScholarPubMed
Echelle, A. A.,Bussche, R. A., Malloy, T. P., Haynie, M. L. and Minckley, C. O. (2000). Mitochondrial DNA variation in pupfishes assigned to the species Cyprinodon macularius (Atherinomorpha: Cyprinodontidae): taxonomic implications and conservation genetics. Copeia, 2000, 353–364.CrossRefGoogle Scholar
Egge, J. J.D. andSimons, A. M. (2006). The challenge of truly cryptic diversity: diagnosis and description of a new madtom catfish (Ictaluridae:Noturus). Zoologica Scripta, 35, 581–595.CrossRefGoogle Scholar
Estes, S. andArnold, S. J. (2007). Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales. American Naturalist, 169, 227–244.CrossRefGoogle ScholarPubMed
Felsenstein, J. (2004). Inferring Phylogenies. Sunderland, MA: Sinauer Associates.Google Scholar
Felsenstein, J. (2009). Phylogeny programs. http://evolution.genetics.washington.edu/phylip/software.html.
Ferguson, J. W. H. (2002). On the use of genetic divergence for identifying species. Biological Journal of the Linnean Society, 75, 509–516.CrossRefGoogle Scholar
Forsman, Z. H., Barshis, D. J., Hunter, C. L. and Toonen, R. J. (2009). Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites. BMC Evolutionary Biology, 9, 45.CrossRefGoogle ScholarPubMed
Fouquet, A., Gilles, A., Vences, M. et al. (2007). Underestimation of species richness in Neotropical frogs revealed by mtDNA analyses. PLoS ONE, 2, e1109.CrossRefGoogle ScholarPubMed
Franz, N. M. (2005). On the lack of good scientific reasons for the growing phylogeny/classification gap. Cladistics, 21, 495–500.CrossRefGoogle Scholar
Freckleton, R. P., Pagel, M. and Harvey, P. H. (2003). Comparative methods for adaptive radiations. In Macroecology Concepts and Consequences, ed. Blackburn, T. M. and Gaston, K. J.. Oxford: Blackwell, pp. 391–407.Google Scholar
Funk, D. J. andOmland, K. E. (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics, 34, 397–423.CrossRefGoogle Scholar
Gaston, K. J. andBlackburn, T. M. (2000). Pattern and Process in Macroecology. Oxford: Blackwell Science.CrossRefGoogle Scholar
Gaston, K. J., Chown, S. L., Calosi, P. et al. (2009). Macrophysiology: a conceptual reunification. American Naturalist, 174, 595–612.CrossRefGoogle ScholarPubMed
Gentile, G., Fabiani, A., Marquez, C. et al. (2009). An overlooked pink species of land iguana in the Galápagos. Proceedings of the National Academy of Sciences of the USA, 106, 507–511.CrossRefGoogle ScholarPubMed
Glaw, F. and Köhler J. (1998). Amphibian species diversity exceeds that of mammals. Herpetological Review, 29, 11–12.Google Scholar
Glaw, F. and Vences, M. (2003). Introduction to amphibians. In The Natural History of Madagascar, ed. Goodman, S. M. and Benstead, J. P.. Chicago, IL: University of Chicago Press, pp. 883–898.Google Scholar
Gómez, A., Wright, P. J., Lunt, D. H. et al. (2007). Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon. Proceedings of the Royal Society of London B, 274, 199–207.CrossRefGoogle ScholarPubMed
Good, D. A. (1994). Species limits in the genus Gerrhonotus (Squamata: Anguidae). Herpetological Monographs, 8, 180–202.CrossRefGoogle Scholar
Gower, D. J., Bhatta, G., Giri, V. et al. (2004). Biodiversity in the Western Ghats: the discovery of new species of caecilian amphibians. Current Science, 87, 739–740.Google Scholar
Groeneveld, L. F., Weisrock, D. W., Rasoloarison, R. M., Yoder, A. D. and Kappeler, P. M. (2009). Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genusCheirogaleus. BMC Evolutionary Biology, 9, 30.CrossRefGoogle ScholarPubMed
Grube, M. andKroken, S. (2000). Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycological Research, 104, 1284–1294.CrossRefGoogle Scholar
Guilhaumon, F., Gimenez, O., Gaston, K. J. and Mouillot, D. (2008). Taxonomic and regional uncertainty in species-area relationships and the identification of richness hotspots. Proceedings of the National Academy of Sciences of the USA, 105, 15458–15463.CrossRefGoogle ScholarPubMed
Gum, B., Gross, R. and Geist, J. (2009). Conservation genetics and management implications for European grayling, Thymallus thymallus: synthesis of phylogeography and population genetics. Fisheries Management and Ecology, 16, 37–51.CrossRefGoogle Scholar
Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W. and Hebert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the USA, 103, 968–971.CrossRefGoogle ScholarPubMed
Hanken, J. (1999). Why are there so many new amphibian species when amphibians are declining? Trends in Ecology and Evolution, 14, 7–8.CrossRefGoogle ScholarPubMed
Harris, D. J. andFroufe, E. (2005). Taxonomic inflation: species concept or historical geopolitical bias. Trends in Ecology and Evolution, 20, 6–7.Google Scholar
Harrison, R. G. (2002). Species concepts. In Encyclopedia of Evolution, ed. Pagel, M.. Oxford: Oxford University Press, pp. 1078–1083.Google Scholar
Harvey, P. H. andRambaut, A. (2000). Comparative analyses for adaptive radiations. Philosophical Transactions of the Royal Society of London B, 355, 1599–1606.CrossRefGoogle ScholarPubMed
Heath, T. A., Zwickl, D. J., Kim, J. and Hillis, D. M. (2008a). Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology, 57, 160–166.CrossRefGoogle ScholarPubMed
Heath, T. A., Hedtke, S. M. and Hillis, D. M. (2008b). Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution, 46, 239–257.Google Scholar
Hebert, P. D. N. andGregory, T. R. (2005). The promise of DNA barcoding for taxonomy. Systematic Biology, 54, 852–859.CrossRefGoogle ScholarPubMed
Hebert, P. D. N., Cywinska, A., Ball, S. L. and de Waard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B, 270, 313–321.CrossRefGoogle ScholarPubMed
Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. and Hallwachs, W. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterflyAstraptes fulgerator. Proceedings of the National Academy of Sciences of the USA, 101, 14812–14817.CrossRefGoogle ScholarPubMed
Heckman, K. L., Rasoazanabary, E., Machlin, E., Godfrey, L. R. and Yoder, A. D. (2006). Incongruence between genetic and morphological diversity inMicrocebus griseorufus. BMC Evolutionary Biology, 6, 98.CrossRefGoogle ScholarPubMed
Hedin, M. (1997). Speciational history in a diverse clade of habitat-specialized spiders (Araneae: Nesticidae: Nesticus): inferences from geographic-based sampling. Evolution, 51, 1927–1943.Google Scholar
Hedin, M. andWood, D. L. (2002). Genealogical exclusivity in geographically proximate populations of Hypochilus thorelli Marx (Araneae, Hypochilidae) on the Cumberland Plateau of North America. Molecular Ecology, 11, 1975–1988.CrossRefGoogle ScholarPubMed
Hedtke, S. M., Townsend, T. and Hillis, D. M. (2006). Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Systematic Biology, 55, 522–529.CrossRefGoogle ScholarPubMed
Heinicke, M. P., Duellman, W. E., Trueb, L. et al. (2009). A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny. Zootaxa, 2211, 1–35.Google Scholar
Hemmerter, S., Šlapeta, J., Hurk, A. et al. (2007). A curious coincidence: mosquito biodiversity and the limits of the Japanese encephalitis virus in Australasia. BMC Evolutionary Biology, 7, 100.CrossRefGoogle ScholarPubMed
Hendry, A. P., Vamosi, S. M., Latham, S. J., Heilbuth, J. C. and Day, T. (2000). Questioning species realities. Conservation Genetics, 1, 67–76.CrossRefGoogle Scholar
Highton, R. (1990). Taxonomic treatment of genetically differentiated populations. Herpetologica, 46, 114–121.Google Scholar
Highton, R. (2000). Detecting cryptic species using allozyme data. In The Biology of Plethodontid Salamanders, ed. Bruce, R. C., Jaeger, R. G. and Houck, L. D.. New York, NY: Kluwer Academic/Plenum Publishers, pp. 215–241.Google Scholar
Highton, R. and Peabody, R. (2000). Geographic protein variation and speciation in salamanders of the Plethodon jordani and Plethodon glutinosus complexes in the southern Appalachian Mountains with the description of four new species. In The Biology of Plethodontid Salamanders, ed. Bruce, R. C., Jaeger, R. G. and Houck, L. D.. New York, NY: Kluwer Academic/Plenum Publishers, pp. 31–93.Google Scholar
Hoffmann, A. A. and Blows, M. W. (1993). Evolutionary genetics and climate change: will animals adapt to global warming? In Biotic Interactions and Global Change, ed. Kareiva, P. M., Kingsolver, J. G. and Huey, R. B.. Sunderland, MA: Sinauer Associates, pp. 165–178.Google Scholar
Huey, R. B.Deutsch, C., Tewksbury, J. J. et al. (2009). Climate warming puts the heat on tropical forest lizards. Proceedings of the Royal Society of London B, 276, 1939–1948.CrossRefGoogle Scholar
Huxley, J. S., ed. (1940). The New Systematics. Oxford: The Clarendon Press.Google Scholar
Hyde, J. R., Kimbrell, C. A., Budrick, J. E., Lynn, E. A. and Vetter, R. D. (2008). Cryptic speciation in the vermilion rockfish (Sebastes miniatus) and the role of bathymetry in the speciation process. Molecular Ecology, 17, 1122–1136.CrossRefGoogle ScholarPubMed
Irwin, D. E. (2002). Phylogeographic breaks without geographic barriers to gene flow. Evolution, 56, 2383–2394.CrossRefGoogle ScholarPubMed
,International Union for the Conservation of Nature (IUCN) (2001). The IUCN Red List Categories and Criteria, version 3.1. www.iucnredlist.org/technical-documents/categories-and-criteria.
Isaac, N. J. B., Mallet, J. and Mace, G. M. (2004). Taxonomic inflation: its influence on macroecology and conservation. Trends in Ecology and Evolution, 19, 464–469.CrossRefGoogle ScholarPubMed
Johns, G. C. andAvise, J. C. (1998). A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution, 15, 1481–1490.CrossRefGoogle ScholarPubMed
Kankare, M. andShaw, M. R. (2004). Molecular phylogeny of Cotesia (Hymenoptera: Braconidae: Microgastrinae) parasitoids associated with Melitaeini butterflies (Lepidoptera: Nymphalidae: Melitaeini). Molecular Phylogenetics and Evolution, 32, 207–220.CrossRefGoogle Scholar
Kastin, A. J. (2006). Handbook of Biologically Active Peptides. New York, NY: Academic Press.Google Scholar
Kearney, M. andPorter, W. P. (2009). Mechanistic niche modeling: combining physiological and spatial data to predict species' ranges. Ecology Letters, 12, 334–350.CrossRefGoogle Scholar
Kelt, D. A. andBrown, J. H. (2000). Species as units in ecology and biogeography: are the blind leading the blind? Global Ecology and Biogeography, 9, 213–217.CrossRefGoogle Scholar
Kim, K. C., Brown, B. W. and Cook, E. F. (1966). A quantitative taxonomic study of the Hoplopleura hesperomydis complex (Anoplura, Hoplopleuridae), with notes on a posteriori taxonomic characters. Systematic Zoology, 15, 24–45.CrossRefGoogle Scholar
King, R. A., Tibble, A. L. and Symondson, W. O. C. (2008). Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms. Molecular Ecology, 17, 4684–4698.CrossRefGoogle Scholar
King, T. L., Switzer, J. F., Morrison, C. L. et al. (2006). Comprehensive genetic analyses reveal evolutionarily distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the U.S. Endangered Species Act. Molecular Ecology, 15, 4331–4359.CrossRefGoogle Scholar
Knowlton, N. (1993). Sibling species in the sea. Annual Review of Ecology and Systematics, 24, 189–216.CrossRefGoogle Scholar
Knowlton, N. (2000). Molecular genetic analyses of species boundaries in the sea. Hydrobiologia, 420, 73–90.CrossRefGoogle Scholar
Köhler, J., Vietes, D. R., Bonett, R. M. et al. (2005). New amphibians and global conservation: a boost in species discoveries in a highly endangered vertebrate group. BioScience, 55, 693–696.CrossRefGoogle Scholar
Kong, L. andLi, Q. (2009). Genetic evidence for the existence of a cryptic species in an endangered clam Coelomactra antiquata. Marine Biology, 156, 1507–1515.CrossRefGoogle Scholar
Lamoreaux, J. F., Morrison, J. C., Ricketts, T. H. et al. (2006). Global tests of biodiversity concordance and the importance of endemism. Nature, 440, 212–214.CrossRefGoogle Scholar
LeDuc, R. G., Robertson, K. M. and Pitman, R. L. (2008). Mitochondrial sequence divergence among Antarctic killer whale ecotypes is consistent with multiple species. Biology Letters, 4, 426–429.CrossRefGoogle ScholarPubMed
Lee, M. S. Y. (2004). The molecularisation of taxonomy. Invertebrate Systematics, 18, 1–6.CrossRefGoogle Scholar
Lee, T., Burch, J. B., Coote, T. et al. (2009). Moorean tree snail survival revisited: a multi-island genealogical perspective. BMC Evolutionary Biology, 9, 204.CrossRefGoogle ScholarPubMed
Lefébure, T., Douady, C. J., Gouy, M. and Gibert, J. (2006). Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution, 40, 435–447.CrossRefGoogle ScholarPubMed
Linnaeus, C. (1758). Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Stockholm.Google Scholar
Lipscomb, D., Platnick, N. and Wheeler, Q. (2003). The intellectual content of taxonomy: a comment on DNA taxonomy. Trends in Ecology and Evolution, 18, 65–66.CrossRefGoogle Scholar
Loehle, C. (1987). Hypothesis testing in ecology: psychological aspects and the importance of theory maturation. Quarterly Review of Biology, 62, 397–409.CrossRefGoogle ScholarPubMed
Losos, J. B., Schoener, T. W., Warheit, K. I. and Creer, D. A. (2001). Experimental studies of adaptive differentiation in Bahamian Anolis lizards. Genetica, 112–113, 399–415.CrossRefGoogle ScholarPubMed
Lubischew, A. A. (1962). On the use of discriminant functions in taxonomy. Biometrics, 18, 455–477.CrossRefGoogle Scholar
MacArthur, R. andLevins, R. (1967). The limiting similarity, convergence, and divergence of coexisting species. American Naturalist, 101, 377–385.CrossRefGoogle Scholar
Mace, G. M. (2004). The role of taxonomy in species conservation. Philosophical Transactions of the Royal Society of London B, 359, 711–719.CrossRefGoogle ScholarPubMed
Mace, G. M. andPurvis, A. (2008). Evolutionary biology and practical conservation: bridging a widening gap. Molecular Ecology, 17, 9–19.CrossRefGoogle ScholarPubMed
Malhotra, A. andThorpe, R. S. (1997). Size and shape variation in a Lesser Antillean anole, Anolis oculatus (Sauria: Iguanidae) in relation to habitat. Biological Journal of the Linnean Society, 60, 53–72.Google Scholar
Mallet, J. andWillmott, K. (2003). Taxonomy: renaissance or Tower of Babel?Trends in Ecology and Evolution, 18, 57–59.CrossRefGoogle Scholar
Mayer, F. andHelversen, O. (2001). Sympatric distribution of two cryptic bat species across Europe. Biological Journal of the Linnean Society, 74, 365–374.CrossRefGoogle Scholar
Mayr, E. (1940). Speciation phenomena in birds. American Naturalist, 74, 249–278.CrossRefGoogle Scholar
Mayr, E. (1942). Systematics and the Origin of Species. New York, NY: Columbia University Press.Google Scholar
McCune, A. R. (1997). How fast is speciation: molecular, geological and phylogenetic evidence from adaptive radiations of fishes. In Molecular Evolution and Adaptive Radiation, ed. Givnish, T. and Sytsma, K.. Cambridge: Cambridge University Press, pp. 585–610.Google Scholar
McDiarmid, R. W. and Donnelly, M. A. (2005). The herpetofauna of the Guayana Highlands: amphibians and reptiles of the Lost World. In Ecology and Evolution in the Tropics: a Herpetological Perspective, ed. Donnelly, M. A., Crother, B. I., Guyer, C., Wake, M. H. and White, M. E.. Chicago, IL: University of Chicago Press, pp. 461–560.Google Scholar
McPeek, M. A. andBrown, J. M. (2007). Clade age and not diversification rate explains species richness among animal taxa. American Naturalist, 169, E97–E106.CrossRefGoogle Scholar
Mead, L. S., Clayton, D. R., Nauman, R. S., Olsen, D. H. and Pfrender, M. E. (2005). Newly discovered populations of salamanders from Siskiyou County, California, represent a species distinct fromPlethodon stormi. Herpetologica, 61, 158–177.CrossRefGoogle Scholar
Means, D. B. andSavage, J. M. (2007). Three new malodorous rainfrogs of the genus Pristimantis (Anura:= Brachycephalidae) from the Wokomung Massif, in west-central Guyana, South America. Zootaxa, 1658, 39–55.Google Scholar
Meegaskumbura, M., Bossuyt, F., Pethiyagoda, R. et al. (2002). Sri Lanka: an amphibian hotspot. Science, 298, 379.
Meiri, S. and Mace, G. M. (2007). New taxonomy and the origin of species. PLOS Biology, 5, e194,1385–1386.CrossRefGoogle ScholarPubMed
Mendelson, J. R., Lips, K. R., Gagliardo, R. W. et al. (2006). Confronting amphibian declines and extinctions. Science, 313, 48.CrossRefGoogle ScholarPubMed
Menegon, M., Doggart, N. and Owen, N. (2008). The Nguru mountains of Tanzania, an outstanding hotspot of herpetofaunal diversity. Acta Herpetologica, 3, 107–127.Google Scholar
Merriam, C. H. (1918). Review of the grizzly and big brown bears of North America (genus Ursus) with the description of a new genus, Vetularctos. North American Fauna, 41, 1–136.CrossRefGoogle Scholar
Meyer, A. (1987). Phenotypic plasticity and heterochrony in Cichlasoma managuense (Pisces, Cichlidae) and their implications for speciation in cichlid fishes. Evolution, 41, 1357–1369.Google ScholarPubMed
Miles, D. B., Noecker, R., Roosenburg, W. M. and White, M. M. (2002). Genetic relationships among populations of Sceloporus undulatus fail to support subspecific designations. Herpetologica, 58, 277–292.CrossRefGoogle Scholar
Milinkovitch, M. C., Monteyne, D., Russello, M. et al. (2007). Molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon. BMC Ecology, 7, 2.CrossRefGoogle Scholar
Miller, K. J. andBenzie, J. A. H. (1997). No clear genetic distinction between morphological species within the coral genusPlatygyra. Bulletin of Marine Science, 61, 907–917.Google Scholar
Min, M. S., Yang, S. Y., Bonett, R. M. et al. (2005). Discovery of the first Asian plethodontid salamander. Nature, 435, 87–90.CrossRefGoogle ScholarPubMed
Molbo, D., Machado, C. A., Sevenster, J. G., Keller, L. and Herre, E. A. (2003). Cryptic species of fig pollinating wasps: implications for the evolution of the fig-wasp mutualism, sex allocation, and the precision of adaptation. Proceedings of the National Academy of Sciences of the USA, 100, 5867–5872.CrossRefGoogle ScholarPubMed
Morando, M., Avila, L. J. and Sites, J. W. (2003). Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata; Liolaemidae) in Andean–Patagonian South America. Systematic Biology, 52, 159–185.CrossRefGoogle ScholarPubMed
Moritz, C. (2002). Strategies to protect biological diversity and the processes that sustain it. Systematic Biology, 51, 238–254.CrossRefGoogle Scholar
Moritz, C. andCicero, C. (2004). DNA barcoding: promise and pitfalls. PLoS Biology, 2, e279.CrossRefGoogle ScholarPubMed
Myers, P., Lundrigan, B. L., Gillespie, B. W. and Zelditch, M. L. (1996). Phenotypic plasticity in skull and dental morphology in the prairie deer mouse (Peromyscus maniculatus bairdii). Journal of Morphology, 229, 229–237.3.0.CO;2-W>CrossRefGoogle Scholar
Nelson, N. J., Keall, S. N., Brown, D. and Daugherty, C. H. (2002). Establishing a new wild population of Tuatara (Sphenodon guntheri). Conservation Biology, 16, 887–894.CrossRefGoogle Scholar
Ohlemüller, R., Anderson, B. J., Araújo, M. B. et al. (2008). Coincidence of climatic and species rarity: high risk to small-range species from climate change. Biology Letters, 4, 568–572.CrossRefGoogle ScholarPubMed
Omland, K. E. (1997). Correlated rates of molecular and morphological evolution. Evolution, 51, 1381–1393.CrossRefGoogle ScholarPubMed
Omland, K. E., Lanyon, S. M. and Fritz, S. J. (1999). A molecular phylogeny of the New World Orioles (Icterus): the importance of dense taxon sampling. Molecular Phylogenetics and Evolution, 12, 224–239.CrossRefGoogle ScholarPubMed
Orme, C. D. L., Davies, R. G., Burgess, M. et al. (2005). Global hotspots of species richness are not congruent with endemism or threat. Nature, 436, 1016–1019.CrossRefGoogle ScholarPubMed
Padial, J. M. andRiva, I. (2006). Taxonomic inflation and the stability of species lists: the perils of ostrich's behavior. Systematic Biology, 55, 859–867.CrossRefGoogle ScholarPubMed
Page, T., Choy, S. C. and Hughes, J. (2005). The taxonomic feedback loop: symbiosis of morphology and molecules. Biology Letters, 1, 139–142.CrossRefGoogle ScholarPubMed
Parham, J. F., Türkozan, O., Stuart, B. L. et al. (2006). Genetic evidence for premature taxonomic inflation in Middle Eastern tortoises. Proceedings of the California Academy of Sciences, 57, 955–964.Google Scholar
Parra-Olea, G., García-París, M., Papenfuss, T. J. and Wake, D. B. (2005). Systematics of the Pseudoeurycea bellii species complex. Herpetologica, 61, 145–158.CrossRefGoogle Scholar
Perez, K. E. andMinton, R. L. (2008). Practical applications for systematics and taxonomy in North American freshwater gastropod conservation. Journal of the North American Benthological Society, 27, 471–483.CrossRefGoogle Scholar
Pérez-Losada, M. and Crandall, K. A. (2003). Can taxonomic richness be used as a surrogate for phylogenetic distinctness indices for ranking areas for conservation?Animal Biodiversity and Conservation, 26, 77–84.Google Scholar
Peterson, A. T. and Navarro-Siguënza, A. G. (1999). Alternate species concepts as bases for determining priority conservation areas. Conservation Biology, 13, 427–431.CrossRefGoogle Scholar
Pfenniger, M. andSchwenk, K. (2007). Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evolutionary Biology, 7, 6.Google Scholar
Platt, J. R. (1964). Strong inference. Science, 146, 347–353.CrossRefGoogle ScholarPubMed
Pörtner, H. O. andFarrell, A. P. (2008). Physiology and climate change. Science, 322, 690–692.CrossRefGoogle ScholarPubMed
Poulakakis, N., Glaberman, S., Russello, M. et al. (2008). Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proceedings of the National Academy of Sciences of the USA, 105, 15464–15469.CrossRefGoogle ScholarPubMed
Price, T. (1997). Correlated evolution and independent contrasts. Philosophical Transactions of the Royal Society of London B, 352, 519–529.CrossRefGoogle ScholarPubMed
Price, T. andKirkpatrick, M. (2009). Evolutionarily stable range limits set by interspecific competition. Proceedings of the Royal Society of London B, 276, 1429–1434.CrossRefGoogle ScholarPubMed
Pringle, A., Baker, D. M., Platt, J. L. et al. (2005). Cryptic speciation in the cosmopolitan and clonal human pathogenic fungusAspergillus fumigatus. Evolution, 59, 1886–1899.CrossRefGoogle ScholarPubMed
Quesada, H., Posada, D., Caballero, A., Morán, P. and Rolán-Alvarez, E. (2007). Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution, 61, 1600–1612.CrossRefGoogle Scholar
Ramey, R. R., Liu, H. P., Epps, C. W., Carpenter, L. and Wehausen, J. D. (2005). Genetic relatedness of the Preble's meadow jumping mouse (Zapus hudsonius preblei) to nearby subspecies of Z. hudsonius as inferred from variation in cranial morphology, mitochondrial DNA, and microsatellite DNA: implications for taxonomy and conservation. Animal Conservation, 8, 329–346.CrossRefGoogle Scholar
Ramey, R. R., Wehausen, J. D., Liu, H. P., Epps, C. W. and Carpenter, L. (2006). Response to Vignieri et al. (2006): Should hypothesis testing or selective post hoc interpretation of results guide the allocation of conservation effort?Animal Conservation, 9, 244–247.CrossRefGoogle Scholar
Ramey, R. R., Wehausen, J. D., Liu, H. P., Epps, C. W. and Carpenter, L. M. (2007). How King et al. (2006) define an ‘evolutionarily distinct’ subspecies: a response. Molecular Ecology, 16, 3518–3521.CrossRefGoogle Scholar
Riddle, B. R. andHafner, D. J. (1999). Species as units of analysis in ecology and biogeography: time to take the blinders off. Global Ecology and Biogeography, 8, 433–441.CrossRefGoogle Scholar
Riddle, B. R., Hafner, D. J., Alexander, L.F. and Jaeger, J. R. (2000). Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. Proceedings of the National Academy of Sciences of the USA, 97, 14438–14443.CrossRefGoogle ScholarPubMed
Robalo, J. I., Sousa-Santos, C., Cabral, H., Castilho, R. and Almada, V. C. (2009). Genetic evidence fails to discriminate between Macroramphosus gracilis Lowe 1839 and Macroramphosus scolopax Linnaeus 1758 in Portuguese waters. Marine Biology, 156, 1733–1737.CrossRefGoogle Scholar
Roca, A. L., Georgiadis, N., Pecon-Slattery, J. and O'Brien, S. J. (2001). Genetic evidence for two species of elephant in Africa. Science, 293, 1473–1477.CrossRefGoogle ScholarPubMed
Roy, V., Demanche, C., Livet, A. and Harry, M. (2006). Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers. BMC Evolutionary Biology, 6, 102.CrossRefGoogle ScholarPubMed
Russello, M. A., Glaberman, S., Gibbs, J. P. et al. (2005). A cryptic taxon of Galápagos tortoises in conservation peril. Biology Letters, 1, 287–290.CrossRefGoogle ScholarPubMed
Schlick-Steiner, B. C., Seifert, B., Stauffer, C. et al. (2007). Without morphology cryptic species stay in taxonomic crypsis following discovery. Trends in Ecology and Evolution, 22, 391–392.CrossRefGoogle ScholarPubMed
Schluter, D. (2000a). The Ecology of Adaptive Radiation. Oxford: Oxford University Press.Google Scholar
Schluter, D. (2000b). Ecological character displacement in adaptive radiation. American Naturalist, 156, S4–S16.CrossRefGoogle Scholar
Sechrest, W., Brooks, T. M., da Fonseca, G. A. B. et al. (2002). Hotspots and the conservation of evolutionary history. Proceedings of the National Academy of Sciences of the USA, 99, 2067–2071.CrossRefGoogle ScholarPubMed
Sever, D. M., Dundee, H. A. and Sullivan, C. D. (1976). A new Eurycea (Amphibia: Plethodontidae) from southwestern North Carolina. Herpetologica, 32, 26–29.Google Scholar
Shaffer, H. B., Pauly, G. B., Oliver, J. C. and Trenham, P. C. (2004a). The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense. Molecular Ecology, 13, 3033–3049.CrossRefGoogle ScholarPubMed
Shaffer, H. B., Fellers, G. M., Voss, S. R., Oliver, J. C. and Pauly, G. B. (2004b). Species boundaries, phylogeography, and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex. Molecular Ecology, 13, 2667–2677.CrossRefGoogle ScholarPubMed
Siddall, M. E., Trontelj, P., Utevsky, S. Y., Nkamany, M. and Macdonald, K. S. (2007). Diverse molecular data demonstrate that commercially available medicinal leeches are notHirudo medicinalis. Proceedings of the Royal Society of London B, 274, 1481–1487.CrossRefGoogle ScholarPubMed
Simpson, G. G. (1943). Criteria for genera, species and subspecies in zoology and paleontology. Annals of the New York Academy of Science, 44, 145–178.CrossRefGoogle Scholar
Simpson, G. G. (1945). The principles of classification and a classification of mammals. Bulletin of the American Museum of Natural History, 85, 1–350.Google Scholar
Sinclair, E. A., Pérez-Losada, M. and Crandall, K. A. (2005). Molecular phylogenetics for conservation biology. In Phylogeny and Conservation, ed. Purvis, A., Gittleman, J. L. and Brooks, T.. Cambridge: Cambridge University Press, pp. 19–56.Google Scholar
Sites, J. W. andCrandall, K. A. (1997). Testing species boundaries in biodiversity studies. Conservation Biology, 11, 1289–1297.CrossRefGoogle Scholar
Sites, J. W. andMarshall, J. C. (2003). Species delimitation: a Renaissance issue in systematic biology. Trends in Ecology and Evolution, 18, 462–470.CrossRefGoogle Scholar
Sites, J. W. and Marshall, J. C. (2004). Operational criteria for delimiting species. Annual Review of Ecology, Evolution, and Systematics, 35, 199–229.CrossRefGoogle Scholar
Smith, M. A., Woodley, N. E., Janzen, D. H., Hallwachs, W. and Hebert, P. D. N. (2006). DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Academy of Sciences of the USA, 103, 3657–3662.CrossRefGoogle Scholar
Smith, M. A., Rodriguez, J. J., Whitfield, J. B. et al. (2008). Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections. Proceedings of the National Academy of Sciences of the USA, 105, 12359–12364.CrossRefGoogle ScholarPubMed
Song, H., Buhay, J. E., Whiting, M. F. and Crandall, K. A. (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences of the USA, 105, 13486–13491.CrossRefGoogle ScholarPubMed
Spicer, J. I. andGaston, K. J. (1999). Physiological Diversity and Its Ecological Implications. Oxford: Blackwell Science.Google Scholar
Starrett, J. and Hedin, M. (2007). Multilocus genealogies reveal multiple cryptic species and biogeographic complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodieatidae). Molecular Ecology, 16, 583–604.CrossRefGoogle Scholar
Stillman, J. H. (2002). Physiological tolerance limits in intertidal crabs. Integrative and Comparative Biology, 42, 790–796.CrossRefGoogle Scholar
Stillman, J. H. (2003). Acclimation capacity underlies climate change susceptibility. Science, 301, 65.CrossRefGoogle ScholarPubMed
Stillman, J. H. (2004). A comparative analysis of plasticity of thermal limits in porcelain crabs across latitudinal and intertidal zone clines. International Congress Series, 1275C, 267–275.CrossRefGoogle Scholar
Strathmann, R. R., Fenaux, L. and Strathmann, M. F. (1992). Heterochronic developmental plasticity in larval sea urchins and its implications for evolution of nonfeeding larvae. Evolution, 46, 972–986.CrossRefGoogle ScholarPubMed
Stuart, B. L., Inger, R. F. and Voris, H. K. (2006). High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs. Biology Letters, 2, 470–474.CrossRefGoogle ScholarPubMed
Stuart, S. N., Chanson, J. S., Cox, N. A. et al. (2004). Status and trends of amphibian declines and extinctions worldwide. Science, 306, 1783–1786.CrossRefGoogle ScholarPubMed
Suatoni, E., Vicario, S., Rice, S., Snell, T. and Caccone, A. (2006). An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer –Brachionus plicatilis. Molecular Phylogenetics and Evolution, 41, 86–98.CrossRefGoogle Scholar
Swatdipong, A., Vasemägi, A., Koskinen, M. T., Piironen, J. and Primmer, C. R. (2009). Unanticipated population structure of European grayling in its northern distribution: implications for conservation prioritization. Frontiers in Zoology, 6, 6.CrossRefGoogle ScholarPubMed
Tarjuelo, I., Posada, D., Crandall, K. A., Pascual, M. and Turon, X. (2001). Cryptic species of Clavelina (Ascidiacea: Aplousobranchiata, Polycitoridae) in two different habitats: harbours and rocky littoral zones in the northwestern Mediterranean. Marine Biology, 139, 455–462.Google Scholar
Tattersall, I. (2007). Madagascar's lemurs: cryptic diversity or taxonomic inflation? Evolutionary Anthropology, 16, 12–23.CrossRefGoogle Scholar
Tautz, D., Arctander, P., Minelli, A., Thomas, R. H. and Vogler, A. P. (2003). A plea for DNA taxnomy. Trends in Ecology and Evolution, 18, 70–74.CrossRefGoogle Scholar
Templeton, A. R., Routman, E. and Phillips, C. A. (1995). Separating population structure from history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander. Ambystoma tigrinum. Genetics, 140, 767–782.Google ScholarPubMed
Templeton, A. R., Robertson, R. J., Brisson, J. and Strasburg, J. (2001). Disrupting evolutionary processes: the effect of habitat fragmentation on collared lizards in the Missouri Ozarks. Proceedings of the National Academy of Sciences of the USA, 98, 5426–5432.CrossRefGoogle ScholarPubMed
Thomas, C. D., Cameron, A., Green, R. E. et al. (2004). Extinction risk from climate change. Nature, 427, 145–148.CrossRefGoogle ScholarPubMed
Thorpe, J. P. (1982). The molecular clock hypothesis: biochemical evolution, genetic differentiation and systematics. Annual Review of Ecology and Systematics, 13, 139–168.CrossRefGoogle Scholar
Thorpe, J. P., Smartt, J. and Allcock, A. L. et al. (1995). Genetic diversity as a component of biodiversity. In Global Biodiversity Assessment, ed. Heywood, V. H. and Watson, R. T.. Cambridge: Cambridge University Press, pp. 57–87.Google Scholar
Tilley, S. G. (1981). A new species of Desmognathus (Amphibia: Caudata: Plethodontidae) from the southern Appalachian Mountains. Occasional Papers of the Museum of Zoology, University of Michigan, 695, 1–23.Google Scholar
Tilley, S. G. andMahoney, M. J. (1996). Patterns of genetic differentiation in salamanders of the Desmognathus ochrophaeus complex(Amphibia: Plethodontidae). Herpetological Monographs, 10, 1–42.Google Scholar
Tilley, S. G., Merritt, R. B., Wu, B. and Highton, R. (1978). Genetic differentiation in salamanders of the Desmognathus ochrophaeus complex. Evolution, 32, 93–115.CrossRefGoogle Scholar
Toda, M., Hikida, T. and Ota, H. (2001). Discovery of sympatric cryptic species within Gekko hokouensis (Gekkonidae: Squamata) from the Okinawa Islands, Japan, by use of allozyme data. Zoologica Scripta, 30, 1–11.CrossRefGoogle Scholar
Todd, P. A. (2008). Morphological plasticity in scleractinian corals. Biological Reviews, 83, 315–337.CrossRefGoogle ScholarPubMed
Toews, D. P. L. andIrwin, D. E. (2008). Cryptic speciation in a Holarctic passerine revealed by genetic and bioacoustic analyses. Molecular Ecology, 17, 2691–2705.CrossRefGoogle Scholar
Toft, C. A. andShea, P. J. (1983). Detecting community-wide patterns: estimating power strengthens statistical inference. American Naturalist, 122, 618–625.CrossRefGoogle Scholar
Trewick, S. A. (1998). Sympatric cryptic species in New Zealand Onychophora. Biological Journal of the Linnean Society, 63, 307–329.CrossRefGoogle Scholar
Trontelj, P. andFiser, C. (2009). Cryptic species diversity should not be trivialised. Systematics and Biodiversity, 7, 1–3.CrossRefGoogle Scholar
Trontelj, P., Douady, C. J., Fiser, C. et al. (2009). A molecular test for cryptic diversity in ground water: how large are the ranges of macro-stygobionts? Freshwater Biology, 54, 727–744.CrossRefGoogle Scholar
Meijden, A., Vences, M., Hoegg, S. and Meyer, A. (2005). A previously unrecognized radiation of ranid frogs in southern Africa revealed by nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 37, 674–685.CrossRefGoogle ScholarPubMed
Vences, M. and Köhler, J. (2008). Global diversity of amphibians (Amphibia) in freshwater. Hydrobiologia, 595, 569–580.CrossRefGoogle Scholar
Vences, M. andWake, D. B. (2007). Speciation, species boundaries and phylogeography of amphibians. In Amphibian Biology, Vol. 6, Systematics, ed. Heatwole, H. H. and Tyler, M.. Chipping Norton, Australia: Surrey Beatty & Sons, pp. 2613–2669.Google Scholar
Vieites, D. R., Wollenberg, K. C., Andreone, F. et al. (2009). Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory. Proceedings of the National Academy of Sciences of the USA, 106, 8267–8272.CrossRefGoogle ScholarPubMed
Vignieri, S. N, Hallerman, E. M., Bergstrom, B. J. et al. (2006). Mistaken view of taxonomic validity undermines conservation of an evolutionarily distinctive mouse: A response to Ramey et al. Animal Conservation, 9, 237–243.CrossRef
Wake, D. B. andVredenburg, V. T. (2008). Are we in the midst of the sixth mass extinction? A view from the world of amphibians. Proceedings of the National Academy of Sciences of the USA, 105, 11466–11473.CrossRefGoogle ScholarPubMed
Wheeler, Q. D. (2004). Taxonomic triage and the poverty of phylogeny. Philosophical Transactions of the Royal Society of London B, 359, 571–583.CrossRefGoogle ScholarPubMed
Wheeler, Q. D. (2008). Undisclosed thinking: morphology and Hennig's unfinished revolution. Systematic Entomology, 33, 2–7.CrossRefGoogle Scholar
Whittaker, R. H. (1972). Evolution and measurement of species diversity. Taxon, 21, 213–251.CrossRefGoogle Scholar
Wiens, J. J. (2004). The role of morphological data in phylogeny reconstruction. Systematic Biology, 53, 653–661.CrossRefGoogle ScholarPubMed
Wiens, J. J. andPenkrot, T. (2002). Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology, 51, 69–91.CrossRefGoogle Scholar
Will, K. W. andRubinoff, D. (2004). Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics, 20, 47–55.CrossRefGoogle Scholar
Wullschleger, E. B. andJokela, J. (2002). Morphological plasticity and divergence in life-history traits between two closely related freshwater snails, Lymnaea ovata and Lymnaea peregra. Journal of Molluscan Studies, 68, 1–5.CrossRefGoogle Scholar
Wynn, A. H., Highton, R. and Jacobs, J. F. (1988). A new species of rock-crevice dwelling Plethodon from Pigeon Mountain, Georgia. Herpetologica, 44, 135–143.Google Scholar
Yoder, A. D., Rasoloarison, R. M., Goodman, S. M. et al. (2000). Remarkable species diversity in Malagasy mouse lemurs (Primates, Microcebus). Proceedings of the National Academy of Sciences of the USA, 97, 11325–11330.CrossRefGoogle ScholarPubMed
Yoder, A. D., Burns, M. M. and Genin, F. (2002). Molecular evidence of reproductive isolation in sympatric sibling species of mouse lemurs. International Journal of Primatology, 23, 1335–1343.CrossRefGoogle Scholar
Yoder, A. D., Olson, L. E., Hanley, C. et al. (2005). A multidimensional approach for detecting species patterns in Malagasy vertebrates. Proceedings of the National Academy of Sciences of the USA, 102, 6587–6594.CrossRefGoogle ScholarPubMed
Zwickl, D. J. and Hillis, D. M. (2002). Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology, 51, 588–589.CrossRefGoogle ScholarPubMed

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