Mitochondrial diversity of European pond turtles (Emys orbicularis) in Anatolia and the Ponto-Caspian Region: Multiple old refuges, hotspot of extant diversification and critically endangered endemics

Organisms Diversity and Evolution

Volumn 9, Issue 2, 2009, Pages 100-114

  Fritz, Uwe ^a   Ayaz, Dinçer ^b   Hundsdörfer, Anna K ^a   Kotenko, Tatiana ^c   Guicking, Daniela ^d   Wink, Michael ^d   Tok, C Varol ^e   Çiçek, Kerim ^b   Buschbom, Jutta ^f  

^a SENCKENBERG DEUTSCHES ENTOMOLOGISCHES INSTITUT   (Germany)

^b Faculty of Science   (Turkey)

^c SCHMALHAUSEN INSTITUTE OF ZOOLOGY   (Ukraine)

^d UNIVERSITY OF HEIDELBERG   (Germany)

^e ÇANAKKALE ONSEKIZ MART UNIVERSITY   (Turkey)

^f Federal Research Centre for Forestry and Forest Products   (Germany)

Author keywords

Cyt b; Glacial refuge; Isolation by distance; Phylogeography; Population genetics

Indexed keywords

ENDANGERED SPECIES; ENDEMIC SPECIES; GENETIC DIFFERENTIATION; MITOCHONDRIAL DNA; MITOCHONDRION; PHYLOGEOGRAPHY; POPULATION GENETICS; REFUGE; SPECIES DIVERSITY; TURTLE;

AEGEAN ISLANDS; ANATOLIA; ASIA; BLACK SEA; EURASIA; EUROPE; GREECE; IRAN; MIDDLE EAST; SOUTHERN EUROPE; TURKEY;

EMYS; EMYS ORBICULARIS; EMYS ORBICULARIS ORBICULARIS; TESTUDINES;

EID: 66549091450     PISSN: 14396092     EISSN: 16181077     Source Type: Journal    
DOI: 10.1016/j.ode.2009.02.002     Document Type: Article

References (56)

1. Ayaz D., Fritz U., Atatür M.K., Mermer A., Çiçek K., and Afsar M. Aspect of population structure of the European pond turtle (Emys orbicularis) in Lake Yayla, Western Anatolia, Turkey. J. Herpetol. 42 (2008) 518-522
2. Ayaz D., Fritz U., Tok C.V., Mermer A., Tosunoǧlu M., Afsar M., and Çiçek K. Population estimate and body size of European pond turtles (Emys orbicularis) from Pazaraǧaç (Afyonkarahisar/Turkey). Biologia 62 (2007) 225-227
3. Ballard J.W.O., and Whitlock M.C. The incomplete natural history of mitochondria. Mol. Ecol. 13 (2004) 729-744
4. Bandelt H.-J., Forster P., and Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16 (1999) 37-48
5. Bazin E., Glémin S., and Galtier N. Population size does not influence mitochondrial diversity in animals. Science 312 (2006) 570-572
6. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1660
7. Edwards S.V., Kingan S.B., Calkins J.D., Balakrishnan C.N., Jennings W.B., Swanson W.J., and Sorenson M.D. Speciation in birds: genes, geography and sexual selection. PNAS 102 (2005) 6550-6557
8. Eichwald E. Zoologia Specialis (1831), Zawadzki, Vilnius
9. Excoffier L., Laval G., and Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1 (2005) 47-50
10. Excoffier L., Smouse P.E., and Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131 (1992) 479-491
11. Fritz U. Zur innerartlichen Variabilität von Emys orbicularis (Linnaeus, 1758). 2. Variabilität in Osteuropa und Redefinition von Emys orbicularis orbicularis (Linnaeus, 1758) und E. o. hellenica (Valenciennes, 1832). Zool. Abh. 47 (1992) 37-77
12. Fritz U. Zur innerartlichen Variabilität von Emys orbicularis (Linnaeus, 1758). 4. Variabilität und Zoogeographie im pontokaspischen Gebiet mit Beschreibung von drei neuen Unterarten. Zool. Abh. 48 (1994) 53-93
13. Fritz U. Introduction to zoogeography and subspecific differentiation in Emys orbicularis (Linnaeus, 1758). Mertensiella 10 (1998) 1-27
14. Fritz U. Die Europäische Sumpfschildkröte (2003), Laurenti, Bielefeld
15. Fritz U., Baran I., Budak A., and Amthauer E. Some notes on the morphology of Emys orbicularis in Anatolia, especially on E. o. luteofusca and E. o. colchica, with the description of a new subspecies from southeastern Turkey. Mertensiella 10 (1998) 103-121
16. Fritz U., Cadi A., Cheylan M., Coïc C., Détaint M., Olivier A., Rosecchi E., Guicking D., Lenk P., Joger U., and Wink M. Distribution of mtDNA haplotypes (cyt b) of Emys orbicularis in France and implications for postglacial recolonization. Amphibia-Reptilia 26 (2005) 231-238
17. Fritz U., d'Angelo S., Pennisi M.G., and Lo Valvo M. Variation of Sicilian pond turtles, Emys trinacris - What makes a species cryptic?. Amphibia-Reptilia 27 (2006) 513-529
18. Fritz U., Fattizzo T., Guicking D., Tripepi S., Pennisi M.G., Lenk P., Joger U., and Wink M. A new cryptic species of pond turtle from southern Italy, the hottest spot in the range of the genus Emys. Zool. Scr. 34 (2005) 351-371
19. Fritz U., Guicking D., Kami H., Arakelyan M., Auer M., Ayaz D., Ayres Fernández C., Bakiev A.G., Celani A., Džukić G., Fahd S., Havaš P., Joger U., Khabibullin V.F., Mazanaeva L.F., Široký P., Tripepi S., Valdeón Vélez A., Velo Antón G., and Wink M. Mitochondrial phylogeography of European pond turtles (Emys orbicularis, Emys trinacris) - an update. Amphibia-Reptilia 28 (2007) 418-426
20. Fritz U., Guicking D., Lenk P., Joger U., and Wink M. When turtle distribution tells European history: mtDNA haplotypes of Emys orbicularis reflect in Germany former division by the Iron Curtain. Biologia 59 Suppl. 14 (2004) 19-25
21. Fu Y.-X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
22. Fu Y.-X., and Li W.-H. Statistical tests of neutrality of mutations. Genetics 133 (1993) 693-709
23. Goudet J., Raymond M., de Meeüs T., and Rousset F. Testing differentiation in diploid populations. Genetics 144 (1996) 1933-1940
24. Gustincich S., Manfioletti G., del Sal G., Schneider C., and Carninci C. A fast method for high-quality genomic DNA extraction from whole human blood. Bio Techniques 11 (1991) 298-302
25. Harmancioǧlu N., Alpaslan N., and Boelee E. Irrigation, Health and Environment: A Review of Literature from Turkey (2001), International Water Management Institute (IWMI), Colombo, Sri Lanka
26. Hewitt G.M. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol. J. Linn. Soc. 58 (1996) 247-276
27. Hewitt G.M. The genetic legacy of the Quaternary ice ages. Nature 405 (2000) 907-913
28. Hey J. The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations. Genetics 128 (1991) 831-840
29. Huelsenbeck J.P., and Ronquist F. MrBAYES. Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
30. ICZN [International Commission on Zoological Nomenclature]. International Code of Zoological Nomenclature. 4th ed. (1999), International Trust for Zoological Nomenclature, London
31. Irwin D.E. Phylogeographic breaks without geographic barriers to gene flow. Evolution 56 (2002) 2383-2394
32. Keane T.M., Creevey C.J., Pentony M.M., Naughton T.J., and McInerney J.O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6 (2006) 29
33. Keane T.M., Naughton T.J., and McInerney J.O. MULTIPHYL: a high-throughput phylogenomics webserver using distributed computing. Nucl. Acids Res. 35 (2007) W33-W37
34. Kiliç S., Evrendilek F., Berberoǧlu S., and Demirkesen A.C. Environmental monitoring of land-use and land-cover changes in a Mediterranean region of Turkey. Envir. Monit. Assess. 114 (2006) 157-168
35. Kiliç S., Evrendilek F., Şenol S., and Çelik I. Developing sustainability index for land uses and agricultural land covers: a case study in Turkey. Envir. Monit. Assess. 105 (2005) 323-335
36. Kotenko T., Zinenko O., Guicking D., Sauer-Guerth H., Wink M., and Fritz U. First data on the geographic variation of Emys orbicularis in Ukraine: mtDNA haplotypes, coloration, and size. In: Ananjeva N., and Tsinenko O. (Eds). Herpetologia Petropolitana (2005), Societas Europaea Herpetologica, St. Petersburg 43-46
37. Lenk P., Fritz U., Joger U., and Wink M. Mitochondrial phylogeography of the European pond turtle, Emys orbicularis (Linnaeus 1758). Mol. Ecol. 8 (1999) 1911-1922
38. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York
39. Paradis E., Claude J., and Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20 (2004) 289-290
40. Posada D., and Crandall K.A. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 16 (2001) 37-45
41. Praschag P., Hundsdörfer A.K., and Fritz U. Phylogeny and taxonomy of endangered South and South-east Asian freshwater turtles elucidated by mtDNA sequence variation (Testudines: Geoemydidae: Batagur, Callagur, Hardella, Kachuga, Pangshura). Zool. Scr. 36 (2007) 429-442
42. Ramos-Onsins S.E., and Rozas J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19 (2002) 2092-2100
43. Raymond M., and Rousset F. An exact test for population differentiation. Evolution 49 (1995) 1280-1283
44. Ronquist F., and Huelsenbeck J.P. MrBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
45. Rousset F. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145 (1997) 1219-1228
46. Rozas J., Sánchez-DelBarrio J.C., Messeguer X., and Rozas R. DNASP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
47. Schnute, J.T., Boers, N.M., Haigh, R., Couture-Beil, A., 2008. PBS Mapping 2.55: user's guide. Can. Tech. Rep. Fish. Aquat. Sci. 2549, i-vi+1-118.
48. Sommer R.S., Lindqvist C., Persson A., Bringsøe H., Rhodin A.G.J., Schneeweiß N., Široký P., Bachmann L., and Fritz U. Unexpected early extinction of the European pond turtle (Emys orbicularis) in Sweden and climatic impact on its Holocene range. Mol. Ecol. 18 (2009) 1252-1262 10.1111/j.1365-294X.2009.04096.x
49. Sommer R.S., Persson A., Wieseke N., and Fritz U. Holocene recolonization and extinction of the pond turtle, Emys orbicularis (L., 1758), in Europe. Quatern. Sci. Rev. 26 (2007) 3099-3107
50. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), ver. 4 (2002), Sinauer Associates, Sunderland, MA
51. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
52. Taşkavak E., and Ayaz D. Some investigations on the taxonomic status of Emys orbicularis from the Aegean and Central Anatolian Regions of Turkey. Pakistan J. Biol. Sci. 9 (2006) 574-581
53. Taşkavak E., and Reimann M. The present status of Emys orbicularis (Linnaeus, 1758) in southern Central Anatolia. Mertensiella 10 (1998) 267-278
54. Velo Antón G., García París M., and Cordero Rivera A. Patterns of nuclear and mitochondrial DNA variation in Iberian populations of Emys orbicularis (Emydidae): conservation implications. Conserv. Genet. 9 (2008) 1263-1274
55. Zink R.M., and Barrowclough G.F. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 17 (2008) 2107-2121
56. Zwickl, D.J., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. PhD dissertation, University of Texas, Austin, TX [Genetic Algorithm for Rapid Likelihood Inference software available from http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html].