Population genetic structure and diversity of the Apennine endemic stream frog, Rana italica - Insights on the Pleistocene evolutionary history of the Italian peninsular biota

Molecular Ecology

Volumn 17, Issue 17, 2008, Pages 3856-3872

  Canestrelli, Daniele ^a   Cimmaruta, Roberta ^a   Nascetti, Giuseppe ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

Author keywords

Allozymes; Italian peninsula; mtDNA; Multiple refugia; Phylogeography; Rana italica

Indexed keywords

CYTOCHROME B; ISOENZYME; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; DNA SEQUENCE; FROG; GEL ELECTROPHORESIS; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; ITALY; MOLECULAR EVOLUTION; PHYLOGENY; POLYMERASE CHAIN REACTION; POPULATION GENETICS;

ANIMALS; BAYES THEOREM; CLUSTER ANALYSIS; CYTOCHROMES B; DNA, MITOCHONDRIAL; ELECTROPHORESIS, STARCH GEL; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; ISOENZYMES; ITALY; PHYLOGENY; POLYMERASE CHAIN REACTION; RANIDAE; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

ANURA; PTYCHOHYLA; RANA ITALICA;

EID: 50049090586     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03870.x     Document Type: Article

References (99)

1. Acquafredda P, Palmentola G (1986) Il glacialismo quaternario nell'Italia meridionale dal Massiccio del Matese all'Aspromonte. Biogeographia, 10, 13 18.
2. Audisio P (1984) I Kateretidae e i Nitidulidae (Coleoptera) dell'Italia meridionale: distribuzione ed ipotesi sul popolamento. Biogeographia, 10, 605 623.
3. Austin JD, Lougheed SC, Boag PT (2004) Controlling for the effects of history and nonequilibrium conditions in gene flow estimates in northern bullfrog (Rana catesbeiana) populations. Genetics, 168, 1491 1506.
4. Ayala FJ (1997) Vagaries of the molecular clock. Proceeding of the National Academy of Sciences, USA, 94, 7776 7783.
5. Ayala FJ (1999) Molecular clock mirages. Bioassays, 21, 71 75.
6. Babik W, Branicki W, Sandera M et al 2004) Mitochondrial phylogeography of the moor frog, Rana arvalis. Molecular Ecology, 13, 1469 1480.
7. Bella JL, Serrano L, Orellana J, Maso PL (2007) The origin of Chorthippus parallelus hybrid zone: chromosomal evidence of multiple refugia for Iberian populations. Journal of Evolutionary Biology, 20, 568 576.
8. Blondel J, Aronson JC (1999) Biology and Wildlife of the Mediterranean Region. Oxford University Press, Oxford, UK.
9. Böhme MU, Fritz U, Kotenko T et al 2007) Phylogeography and cryptic variation within the Lacerta viridis complex (Lacertidae, Reptilia). Zoologica Scripta, 36, 119 131.
10. Bologna MA, Mazzotti S (2006) Biogeography. In: Atlas of Italian Amphibian and Reptiles (eds Sindaco R, Doria G, Razzetti E, Bernini F), pp. 654 677. Edizioni Polistampa, Florence, Italy.
11. Bonfiglio L, Mangano G, Marra AC, Masini F, Pavia M, Petruso D (2002) Pleistocene Calabrian and Sicilian bioprovinces. Geobios, 35, 29 39.
12. Bonnet E, Van de Peer Y (2002) zt: a software tool for simple and partial Mantel tests. Journal of Statistical Software, 7, 1 12.
13. Borkin LJ (1999) Distribution of Amphibians in North Africa, Europe, Western Asia, and the Former Soviet Union. In: Patterns of Distribution of Amphibians: a Global Perspective (ed. Duellmann WE), pp. 329 420. The Johns Hopkins University Press, Baltimore, Maryland.
14. Brewer S, Cheddadi R, de Beaulieau JL, Reille M, Data contributors (2002) The spread of deciduous Quercus throughout Europe since the last glacial period. Forest Ecology and Management, 156, 27 48.
15. Burridge CP, Craw D, Fletcher D, Waters JM (2008) Geological dates and molecular rates: fish DNA sheds lights on time dependency. Molecular Biology and Evolution, 25, 624 633.
16. Caloi L, Malatesta A, Palombo RM (1989) Biogeografia della Calabria meridionale durante il Quaternario. Atti Accademia Peloritana dei Pericolanti Classe I, Scienze Matematiche Fisiche e Naturali, 67, 261 278.
17. Canestrelli D, Cimmaruta R, Costantini V, Nascetti G (2006a) Genetic diversity and phylogeography of the Apennine yellow-bellied toad Bombina pachypus, with implications for conservation. Molecular Ecology, 15, 3741 3754.
18. Canestrelli D, Zangari F, Nascetti G (2006b) Genetic evidence for two distinct species within the Italian endemic Salamandrina terdigitata Bonnaterre, 1789 (Amphibia: Urodela: Salamandridae). Herpetological Journal, 16, 221 227.
19. Canestrelli D, Verardi A, Nascetti G (2007a) Genetic differentiation and history of populations of the Italian treefrog: lack of concordance between mitochondrial and nuclear genes. Genetica, 130, 241 255.
20. Canestrelli D, Cimmaruta R, Nascetti G (2007b) Phylogeography and historical demography of the Italian treefrog Hyla intermedia reveals multiple refugia, population expansions and secondary contacts within peninsular Italy. Molecular Ecology, 16, 4808 4821.
21. Canestrelli D, Nascetti G (2008) Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear-mitochondrial discordance. Journal of Biogeography, doi
22. Capula M, Ceccarelli A (2003) Distribution on genetic variation and taxonomy of insular and mainland populations of the Italian wall lizard, Podarcis sicula. Amphibia-Reptilia, 24, 483 495.
23. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1660.
24. Comes HP (2004) The Mediterranean region - a hotspot for plant biogeographic research. New Phytologist, 164, 11 14.
25. Corander J, Waldmann P, Sillanpaa MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367 374.
26. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959 969.
27. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry Bulletin, 19, 11 15.
28. Drummond AJ, Rambaut A (2006) beast, Version 1.4. University of Oxford, Oxford, UK.
29. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185 1192.
30. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Molecular Ecology, 11, 2571 2581.
31. Eckert CG, Samis KE, Lougheed SC (2008) Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond. Molecular Ecology, 17, 1170 1188.
32. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479 491.
33. Excoffier L, Laval G, Schneider S (2005) arlequin (version 3.0): an integrated software package for population genetic data analysis. Evolutionary Bioinformatics Online, 1, 47 50.
34. Felsenstein J (1993) Phylogeny Inference Package (phylip Version 3.5c. University of Washington, Seattle.
35. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
36. Ghisetti F (1979) Evoluzione neotettonica dei principali sistemi di faglie della Calabria centrale. Bollettino della Società Geologica Italiana, 98, 387 430.
37. Ghisetti F (1981) L'evoluzione strutturale del bacino plio-pleistocenico di Reggio Calabria nel quadro geodinamico dell'arco calabro. Bollettino Geologico Italiano, 100, 433 466.
38. Gibbons A (1998) Calibrating the mitochondrial DNA clock. Science, 279, 38 39.
39. Giovannotti M, Nisi Cerioni P, Kalboussi M, Aprea G, Caputo V (2007) Phylogeographic inferences from the mtDNA variation of the three-toed skink, Chalcides chalcides (Reptilia: Scincidae). Journal of Experimental Zoology Part B Molecular and Developmental Evolution, 308, 3 297.
40. Gómez A, Lunt DH (2006) Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. In: Phylogeography in Southern European Refugia: Evolutionary Perspectives on the Origins and Conservation of European Biodiversity (eds Weiss S, Ferrand N), pp. 155 188. Springer Verlag, Dordrecht, The Netherlands.
41. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available at http://www.unil.ch/izea/ softwares/fstat.html.
42. Grivet D, Petit RJ (2003) Chloroplast DNA phylogeography of the hornbeam in Europe: evidence for a bottleneck at the outset of postglacial colonization. Conservation Genetics, 4, 47 56.
43. Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: the rear edge matters. Ecology Letters, 8, 461 467.
44. Harris H, Hopkinson DA (1976) Handbook of Enzyme Electrophoresis in Human Genetics. North-Holland Publishing, Amsterdam.
45. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160 174.
46. Hewitt GM (1996) Some genetic consequences of ice ages and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247 276.
47. Hewitt GM (1999) Postglacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 87 112.
48. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907 913.
49. Hewitt GM (2004a) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 183 195.
50. Hewitt GM (2004b) The structure of biodiversity - insights from molecular phylogeography. Frontiers in Zoology, 1, 4.
51. Hewitt GM, Ibrahim KM (2001) Inferring glacial refugia and historical migrations with molecular phylogenies. In: Integrating Ecology and Evolution in a Spatial Context. BES Symposium Volume (eds Silvertown J, Antonovics J, Blackwells), pp. 271 294. Cambridge University Press, Cambridge, UK.
52. Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Reviews in Ecology and Systematics, 28, 437 466.
53. Hutchinson DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898 1914.
54. Kocher TD, Thomas WK, Meyer A et al 1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceeding of the National Academy of Sciences, USA, 86, 6196 6200.
55. Krystufek B, Buzan EV, Hutchinson WF, Hänfling B (2007) Phylogeography of the rare Balkan endemic Martino's vole, Dinaromys bogdanovi, reveals strong differentiation within the western Balkan Peninsula. Molecular Ecology, 16, 1221 1232.
56. Kumar S, Tamura K, Nei M (2004) mega 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, 150 163.
57. Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OE Jr (2006) Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conservation Genetic, 7, 295 302.
58. Legendre L, Legendre P (1983) Numerical Ecology. Elsevier Scientific Publishing, Amsterdam.
59. Magri D (2008) Patterns of post-glacial spread and the extent of glacial refugia of European beech (Fagus sylvatica). Journal of Biogeography, 35, 450 463.
60. Martínez-Solano I, Teixeira J, Buckley D, Garcìa- Parìs M (2006) Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic. Molecular Ecology, 15, 3375 3388.
61. Mattoccia M, Romano A, Sbordoni V (2005) Mitochondrial DNA sequence analysis of the spectacled salamander, Salamandrina terdigitata (Urodela: Salamandridae), supports the existence of two distinct species. Zootaxa, 995, 1 19.
62. Moritz C, Schneider CJ, Wake DB (1992) Evolutionary relationships within Ensatina eschscholtzi complex confirm the ring species interpretation. Systematic Zoology, 41, 273 291.
63. Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853 858.
64. Nascetti G, Zangari F, Canestrelli D (2005) The spectacled salamanders, Salamandrina terdigitata Lacépède, 1788 and S. perspicillata Savi, 1821: 1) genetic differentiation and evolutionary history. Rendiconti Lincei: Scienze Fisiche e Naturali, 16, 159 169.
65. Nei M (1972) Genetic distance between populations. American Naturalist, 106, 283 292.
66. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 83, 583 589.
67. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
68. Nieberding C, Libois R, Douady CJ, Morand S, Michaux JR (2005) Phylogeography of a Nematode (Heligmosomoides polygyrus) in the Western Palearctic region: persistence of Northern cryptic populations during ice ages? Molecular Ecology, 14, 765 779.
69. Paulo OS, Dias C, Bruford MW, Jordan WC, Nichols RA (2001) The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard. Proceedings Royal Society B: Biological Sciences, 268, 1625 1630.
70. Petit RJ, Aguinagalde I, de Beaulieu JL et al 2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science, 300, 1563 1565.
71. Pierpaoli M, Riga F, Trocchi V, Randi E (1999) Species distinction and evolutionary relationships of the Italian hare (Lepus corsicanus) as described by mitochondrial DNA sequencing. Molecular Ecology, 8, 1805 1817.
72. Pignatti S (1984) La flora dell'Appennino meridionale: distribuzione attuale ed ipotesi sull'origine. Biogeographia, 10, 89 100.
73. Podnar M, Mayer W, Tvrtković N (2005) Phylogeography of the Italian wall lizard, Podarcis sicula, as revealed by mitochondrial DNA sequences. Molecular Ecology, 14, 575 588.
74. Posada D, Crandall KA (1998) modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
75. Posada D, Crandall KA (2001) Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology & Evolution, 16, 37 45.
76. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
77. Ragghianti M, Wake DB (1986) Genic variation and its evolutionary implications in the Italian newt, Triturus italicus. Herpetologica, 42, 206 214.
78. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092 2100.
79. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223 225.
80. Richardson BJ, Bayerstock PR, Adams M (1986) Allozyme Electrophoresis: A Handbook for Animal Systematics and Population Studies. Academic Press, San Diego, California.
81. Riddle BR, Hafner DJ, Alexander LF, Jaeger JR (2000) Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. Proceeding of the National Academy of Sciences, USA, 97, 14438 14443.
82. Santucci F, Nascetti G, Bullini L (1996) Hybrid zones between two genetically differentiated forms of the pond frog Rana lessonae in southern Italy. Journal of Evolutionary Biology, 9, 429 450.
83. Schmitt T (2007) Molecular biogeography of Europe: Pleistocene cycles and postglacial trends. Frontiers in Zoology, 4, 11.
84. Schmitt T, Habel JC, Zimmermann M, Müller P (2006) Genetic differentiation of the marbled white butterfly, Melanargia galathea, accounts for glacial distribution patterns and postglacial range expansion in southeastern Europe. Molecular Ecology, 15, 1889 1901.
85. Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264 279.
86. Smith MA, Green DM (2005) Are all amphibian populations metapopulations? Dispersal and the metapopulation paradigm in amphibian ecology and conservation. Ecography, 28, 110 128.
87. Sneath PHA, Sokal RR (1973) Numerical Taxonomy. W.H. Freeman, San Francisco, California.
88. Steinfartz S, Veith M, Tautz D (2000) Mitochondrial sequence analysis of Salamandra taxa suggests old splits of major lineages and postglacial recolonizations of Central Europe from distinct source populations of Salamandra salamandra. Molecular Ecolology, 9, 397 410.
89. Stuart S, Chanson JS, Cox NA et al 2004) Status and trends of amphibian declines and extinctions worldwide. Science, 306, 1783 1786.
90. Swenson NG, Howard DJ (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. American Naturalist, 166, 581 591.
91. Swofford DL, Selander RB (1999) biosys-2: A Computer Program for the Analysis of Allelic Variation in Population Genetics and Biochemical Systematics (Release 2.0). University of Illinois, Urbana, Champaign, Illinois.
92. Taberlet P (1998) Biodiversity at the intraspecific level: the comparative phylogeographic approach. Journal of Biotechnology, 64, 91 100.
93. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512 526.
94. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619 633.
95. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustal _x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876 4882.
96. Tortorici L (1981) Analisi delle deformazioni fragili dei sedimenti postorogeni della Calabria settentrionale. Bollettino della Società Geologica Italiana, 100, 291 308.
97. Ungaro A, Cecchetti S, Aloise G, Nascetti G (2001) Paleogeographic events in southern Italy and the genetic structure of Talpa romana. 8th Congress European Society Evolutionary Biology, Aarhus, Denmark 20-26 August 2001. Abstracts: 88.
98. Ursenbacher S, Conelli A, Golay P et al 2006) Phylogeography of the asp viper (Vipera aspis) inferred from mitochondrial DNA sequence data: Evidence for multiple Mediterranean refugial areas. Molecular Phylogenetics and Evolution, 38, 546 552.
99. Weiss S, Ferrand N, eds (2006) Phylogeography in Southern European Refugia: Evolutionary Perspectives on the Origins and Conservation of European Biodiversity. Springer Verlag, Dordrecht, The Netherlands.