To refer to this article use this url: http://dpc.uba.uva.nl/ctz/vol81/nr03/art02
References
Anisimova M, Gascuel O. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Systematic Biology 55: 539-552.
Avise JC, Bowen BW, Lamb T, Meylan AB, Bermingham E. 1992. Mitochondrial DNA evolution at a turtle’s pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines. Molecular Biology and Evolution 9: 457-473.
Barley AJ, Spinks PQ, Thomson RC, Schaffer HB. 2010. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Molecular Phylogenetics and Evolution 55: 1189-1194.
Bininda-Emonds ORP. 2004. The evolution of supertrees. Trends in Ecology and Evolution 19: 315-322.
Bisby FA, Roskov YR, Orrell TM, Nicolson D, Paglinawan LE, Bailly N, Kirk, PM, Bourgoin T, Baillargeon G. 2009. Species 2000 & ITIS Catalogue of Life: 2009 Annual Checklist. Available via http://www.catalogueoflife.org/annual-checklist/2009/ [visited on 15 Oct 2009].
Buhlmann KA, Akre TSB, Iverson JB, Karapatakis D, Mittermeier RA, Georges A, Rhodin AGJ, van Dijk PP, Gibbons JW. 2009. A global analysis of tortoise and freshwater turtle distributions and identification of priority conservation areas. Chelonian Consevation Biology 8: 116-149.
Caccone A, Gentile G, Burns CE, Sezzi E, Bergman W, Ruelle M, Saltonstall K, Powell JR. 2004. Extreme difference in rate of mitochondrial and nuclear DNA evolution in a large ectotherm, Galapagos tortoises. Molecular Phylogenetics and Evolution 31: 794-798.
Cervelli M, Oliverio M, Bellini A, Bologna M, Cecconi F, Mariottini P. 2003. Structural and sequence evolution of U17 small nucleolar RNA (snoRNA) and its phylogenetic congruence in chelonians. Journal of Molecular Evolution 57: 73-84.
Chandler CH, Janzen FJ. 2009. The phylogenetic position of the snapping turtles (Chelydridae) based on nucleotide sequence data. Copeia 2009: 209-213.
Engstrom TN, Shaffer HB, McCord WP. 2004. Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines : Trionychidae). Systematic Biology 53: 693-710.
Feldman CR, Parham JF. 2002. Molecular phylogenetics of emydine turtles: taxonomic revision and the evolution of shell kinesis. Molecular Phylogenetics and Evolution 22: 388-398.
Fritz U, Guicking D, Auer M, Sommer RS, Wink M, Hundsdörfer, AK. 2008. Diversity of the Southeast Asian leaf turtle genus Cyclemys: how many leaves on its tree of life? Zoologica Scripta 37: 367-390.
Fritz U, Daniels SR, Hofmeyr MD, González J, Barrio-Amorós CL, Siroky P, Hundsdörfer AK, Stuckas H. 2010. Mitochondrial phylogeography and subspecies of the wide-ranging sub-Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae) - a case study for the pitfalls of pseudogenes and GenBank sequences. Journal of Zoological Systematics and Evolutionary Research 48: 348-359.
Fritz U, Schmidt C, Ernst CH. 2011. Competing generic concepts for Blanding’s, Pacific and European pond turtles (Emydoidea, Actinemys and Emys) - Which is best? Zootaxa 2791: 41-53.
Fujita MK, Engstrom TN, Starkey DE, Shaffer HB. 2004. Turtle phylogeny: insights from a novel nuclear intron. Molecular Phylogenetics and Evolution 31: 1031-1040.
Gaffney ES. 1984. Historical analysis of theories of chelonian relationship. Systematic Zoology 33: 283-301.
Georges A, Birrell J, Saint KM, McCord WP, Donnellan S. 1998. A phylogeny for side-necked turtles (Chelonia: Pleurodira) based on mitochondrial and nuclear gene sequence variation. Biological Journal of the Linnean Society 67: 213-246.
Goloboff PA. 1999. Analysing large data sets in reasonable times: solutions for composite optima. Cladistics 15, 415-428.
Goloboff PA, Pol D. 2002. Semi-strict supertrees. Cladistics 18: 514-525.
Guindon S, Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
Harris DJ. 2003 Can you bank on GenBank? Trends in Ecology and Evolution 18: 317-319.
He J, Zhou T, Rao D, Zhang Y. 2007. Molecular identification and phylogenetic position of Cuora yunnanensis. Chinese Science Bulletin 52: 3305-3309.
Honda M, Yasukawa Y, Hirayama R, Ota H. 2002. Phylogenetic relationships of the Asian box turtles of the genus Cuora sensu lato (Reptilia: Bataguridae) inferred from mitochondrial DNA sequences. Zoological Science 17: 1305-1312.
Janzen FJ, Krenz JG. 2004. Phylogenetics: which was first, TSD or GSD? Pp. 121-130 in: Valenzuela N, Lance VA, eds, Temperature-dependent sex determination in vertebrates. Washington: Smithsonian Books.
Joyce WG, Parham JF, Gauthier JA. 2004. Developing a protocol for the conversion of rank-based taxon names to phylogenetically defined clade names, as exemplified by turtles. Journal of Paleontology 78: 989-1013.
Kälersjö M, Albert VA, Farris JS. 1999. Homoplasy increases phylogenetic structure. Cladistics 15: 91-93.
Krenz JG, Naylor GJP, Shaffer HB, Janzen FJ. 2005. Molecular phylogenetics and evolution of turtles. Molecular Phylogenetics and Evolution 37: 178-191.
Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution 20: 86-93.
Laurin M. 2010. The subjective nature of Linnean categories and its impact in evolutionary biology and biodiversity studies. Contributions to Zoology 79: 131-146.
Laurin M, Reisz RR. 1995. A reevaluation of early amniote phylogeny. Zoological Journal of the Linnean Society 113: 165-223.
Le M, McCord WP, Iverson JB. 2007. On the paraphyly of the genus Kachuga (Testudines: Geoemydidae). Molecular Phylogenetics and Evolution 45: 398-404.
Lee MSY. 1997. Reptile relationships turn turtles. Nature 389: 245-246.
Lee MSY. 2001. Molecules, morphology, and the monophyly of diapsid reptiles. Contributions to Zoology 70: 1-22.
Lourenço JM, Claude J, Galtier N, Chiari Y. 2012. Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Molecular Phylogenetics and Evolution 62: 496-507.
Lyson TR, Bever GS, Bhullar B-AS, Joyce WG, Gauthier JA. 2010. Transitional fossils and the origin of turtles. Biology Letters 6: 830–833.
Marjanović D, Laurin, M. 2007. Fossils, molecules, divergence times, and the origin of Lissamphibians. Systematic Biology 56: 369-388.
Naro-Maciel E, Le M, FizSimmons NN, Amato G. 2008. Evolutionary relationships of marine turtles: a molecular phylogeny based on nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 49: 659-662.
Parham JF, Simison BW, Kozak KH, Feldman CR, Shi H. 2001. New Chinese turtles: endangered or invalid. A reassessment of two species using mitochondrial DNA, allozyme electrophoresis and known-locality specimens. Animal Conservation 4: 357-367.
Parham JF, Feldman CR, Boore, JL. 2006. The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA. BMC Evolutionary Biology 6: 11.
Posada D. 2008. jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
Praschag P, Hundsdörfer AK, Fritz U. 2007a. Phylogeny and taxonomy of endangered South and South-east Asian freshwater turtles elucidated by mtDNA sequence variation (Testudines: Geoemydidae: Batagur, Callagur, Hardella, Kachuga, Pangshura). Zoologica Scripta 36: 429-442.
Praschag P, Hundsdörfer AK, Reza AHM, Fritz U. 2007b. Genetic evidence for wild-living Aspideretes nigricans and a molecular phylogeny of South Asian softshell turtles (Reptilia: Trionychidae: Aspideretes, Nilssonia). Zoologica Scripta 36: 301-310.
Praschag P, Hundsdörfer AK, Fritz U. 2009. Further specimens and phylogenetic position of the recently described leaf turtle species Cyclemys gemeli (Testudines: Geoemydidae). Zootaxa 2008: 29-37.
Reisz RR, Laurin M. 1991. Owenetta and the origin of turtles. Nature 349: 324-326.
Sanderson MJ, Donoghue MJ. 1996. The relationship between homoplasy and confidence in a phylogenetic tree. Pp. 67-89 in: Sanderson MJ, Hufford L, eds, Homoplasy: The recurrence of similarity in evolution. San Diego: Academic Press.
Sanderson MJ, Shaffer BH. 2002. Troubleshooting molecular phylogenetics analyses. Annual Review of Ecology and Systematics 33: 49-72.
Sanderson MJ, Purvis A, Henze C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends in Ecology and Evolution 13: 105-109.
Seddon JM, Georges A, Baverstock PR, McCord WP. 1997. Phylogenetic relationships of chelid turtles (Pleurodira : Chelidae) based on mitochondrial 12S rRNA gene sequence variation. Molecular Phylogenetics and Evolution 7: 55-61.
Shaffer HB, Meylan PA, McKnight ML. 1997. Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. Systematic Biology 46: 235-268.
Spinks PQ, Shaffer HB. 2007. Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgressions, numts, and inferences from multiple nuclear loci. Conservation Genetics 8: 641-657.
Spinks PQ, Shaffer HB. 2009. Conflicting mitochondrial and nuclear gene phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridisation. Systematic Biology 58: 1-20.
Spinks PQ, Shaffer HB, Iverson JB, McCord WP. 2004. Phylogenetic hypotheses for the turtle family Geoemydidae. Molecular Phylogenetics and Evolution 32: 164-182.
Spinks PQ, Thomson RC, Lovely GA, Shaffer HB. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. BMC Evolutionary Ecology 9: 56.
Stephens PR, Wiens JJ. 2003. Ecological diversification and phylogeny of emydid turtles. Biological Journal of the Linnean Society 79: 577-610.
Stephens PR, Wiens JJ. 2009. Evolution of sexual size dimorphisms in emydid turtles; ecological dimorphism, Rensch’s rule, and sympatric divergence. Evolution 63: 910-925.
Sterli J. 2010. Phylogenetic relationships among extinct and extant turtles: the position of Pleurodira and the effects of the fossils on rooting crown-group turtles. Contributions to Zoology 79: 93-106.
Stuart BL, Parham JF. 2004. Molecular phylogeny of the critically endangered Indochinese box turtle (Cuora galbinifrons). Molecular Phylogenetics and Evolution 31: 164-177.
Stuart BL, Parham JF. 2007. Recent hybrid origin of three rare Chinese turtles. Conservation Genetics 8: 169-175.
Stuart BL, Fritz U. 2008. Historical DNA from museum type specimens clarifies diversity of Asian leaf turtles (Cyclemys). Biological Journal of the Linnean Society 94: 131-141.
The Reptile Database. 2011. Available at http://www.reptile-database.org/ [visited on 15 Oct 2009].
Thomson RC, Shaffer HB. 2010. Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Systematic Biology 59: 42-58.
Thomson S, Georges A. 2009. Myuchelys gen. nov. - a new genus for Elseya latisternum and related forms of Australian freshwater turtle (Testudines: Pleurodira: Chelidae). Zootaxa 2053: 32-42.
Vargas-Ramirez M, Castano-Mora OV, Fritz U. 2008. Molecular phylogeny and divergence times of ancient South American and Malagasy river turtles (Testudines: Pleurodira: Podocnemididae). Organisms, Diversity & Evolution 8: 388-398.
Vilgalys R. 2003. Taxonomic misidentification in public DNA databases. New Phytologist 160: 4-5.
Wiens JJ, Kuczynski CA, Stephens PR. 2010. Discordant mitochondrial and nuclear genes phylogenies in emydid turtles: implications for speciation and conservation. Biological Journal of the Linnean Society 99: 445-461.
Wink M, Guiking D, Fritz U. 2001. Molecular evidence for hybrid origins of Mauremys iversoni Pritchard and McCoy, 1991, and Mauremys pritchardi McCord, 1997 (Reptilia: Testudines: Bataguridae). Zoologische Abahndlungen (Dresden) 52: 41-49.
Zardoya R, Meyer A. 1998. Complete mitochondrial genome suggests diapsid affinities of turtles. Proceedings of the National Academy of Sciences of the USA 95: 14226-14231.
Zardoya R, Meyer A. 2001. The evolutionary position of turtles revised. Naturwissenschaften 88: 193-200.