Unveiling an ancient biological invasion: Molecular analysis of an old European alien, the crested porcupine (Hystrix cristata)

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Trucchi, Emiliano ^a   Sbordoni, Valerio ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME B; RNA 12S; MITOCHONDRIAL DNA;

ARTICLE; BAYES THEOREM; CHEMICAL STRUCTURE; CONTROLLED STUDY; GENETIC ANALYSIS; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGEOGRAPHY; POPULATION GENETICS; POPULATION SIZE; PORCUPINE; SPECIES INVASION; AFRICA; ANIMAL; DNA SEQUENCE; GENETICS; GEOGRAPHY; HAPLOTYPE; ITALY; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT;

HYSTRIX CRISTATA;

AFRICA; ANIMALS; BAYES THEOREM; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; ITALY; PHYLOGENY; PORCUPINES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 66249107366     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-109     Document Type: Article

References (53)

1. HA Mooney RJ Hobbs, Invasive Species in a Changing World Washington, D.C.: Island Press 2000
2. Nonindigenous species: ecological explanation, environmental ethics, and public policy. DM Lodge K Shrader-Frechette, Conserv Biol 2003 17 31 37 10.1046/j.1523-1739.2003.02366.x
3. Introduction: Population biology, evolution, and control of invasive species. FW Allendorf LL Lundquist, Conserv Biol 2003 17 24 30 10.1046/j.1523-1739.2003.02365.x
4. Amassing efforts against alien invasive species in Europe. SM Shirley S Kark, PLoS Biol 2006 4 8 e279 DOI: 10.1371/journal.pbio.0040279 16895444 10.1371/journal.pbio.0040279
5. The population biology of invasive species. AK Sakai FW Allendorf JS Holt DM Lodge J Molofsky KA With S Baughman RJ Cabin JE Cohen NC Ellstrand DE McCauley P O'Neil IM Parker JN Thompson SG Weller, Annu Rev Ecol Syst 2001 32 305 332 10.1146/annurev.ecolsys.32.081501.114037
6. Phylogeography of Bufo marinus from its natural and introduced ranges. RW Slade C Moritz, Proc R Soc Lond B Biol Sci 1998 265 769 777 10.1098/rspb.1998.0359
7. The evolutionary consequences of biological invasions. AV Suarez ND Tsutsui, Mol Ecol 2008 17 351 360 10.1111/j.1365-294X.2007.03456.x 18173507
8. Understanding the long-term effects of species invasions. DL Strayer VT Eviner JM Jeschke ML Pace, Trends Ecol Evol 2006 21 645 651 10.1016/j.tree.2006. 07.007 16859805
9. Evolutionary responses of natives to introduced species: what do introductions tell us about natural communities? SY Strauss JA Lau SP Carroll, Ecol Lett 2006 9 357 374 10.1111/j.1461-0248.2005.00874.x 16958902
10. JC Avise, Phylogeography: The History and Formation of Species Cambridge, Massachusetts: Harvard University Press 2000
11. J Kingdon, The Kingdon Field Guide to African Mammals London: Academic press 1997
12. A porcupine find from roman Africa with a review of archaeozoological data from circummediterranean sites. JA Riquelme A Morales, Archaeofauna 1997 6 91 95
13. Morphometric variation in the skulls of the crested porcupine Hystrix cristata from mainland Italy, Sicily and northern Africa. FM Angelici D Capizzi G Amori L Luiselli, Mamm Biol 2003 68 165 173 10.1078/1616-5047-00078
14. Distribution of the Crested porcupine Hystrix cristata L., 1758 in peninsular Italy and Sicily. FM Angelici G Amori, Mus Reg Sci Nat Boll (Torino) 1999 16 83 88
15. Hystrix cristata Linnaeus, 1758 Stachelschwein. J Niethammer, Handbuck der Saugetiere Europas 2/I. Rodentia II Wiesbaden, Academische Verlagsgesellschaft, Niethammer J, Krapp F, 1982 588 605
16. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. AR Templeton KA Crandall CF Sing, Genetics 1992 132 619 633 1385266
17. Identifying the source of species invasions: sampling intensity vs. genetic diversity. JR Muirhead DK Gray DW Kelly SM Ellis DD Heath HJ MacIsaac, Mol Ecol 2008 17 1020 1035 10.1111/j.1365-294X.2008.03669.x 18261046
18. R Leighton, Sicily before History: An Archaeological Survey from the Palaeolithic to the Iron Age Ithaca, N.Y., Cornell University Press 1999
19. Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe. H Rajabi-Maham A Orth F Bonhomme, Mol Ecol 2008 17 627 641 18179435
20. Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages. U Saarma SYW Ho OG Pybus M Kaljuste IL Tumanov I Kojola AA Vorobiev NI Markov AP Saveljev H Valdmann EA Lyapunova AV Abramov P Männil M Korsten E Vulla SV Pazetnov VS Pazetnov SV Putchkovskiy AM Rkov, Mol Ecol 2007 16 401 413 10.1111/j.1365-294X.2006.03130.x 17217353
21. Island colonization and founder effects: the invasion of the Guadeloupe islands by ship rats (Rattus rattus). J Abdelkrim M Pascal S Samadi, Mol Ecol 2005 14 2923 2931 10.1111/j.1365-294X.2005.02604.x 16101763
22. Reduced genetic variation and the success of an invasive species. ND Tsutsui AV Suarez DA Holway TJ Case, Proc Natl Acad Sci USA 2000 97 5948 5953 10811892 10.1073/pnas.100110397
23. Dates from the molecular clock: how wrong can we be? MJF Pulquerio RA Nichols, Trends Ecol Evol 2007 22 180 184 10.1016/j.tree.2006.11.013 17157408
24. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. SYW Ho MJ Phillips A Cooper AJ Drummond, Mol Biol Evol 2005 22 1561 1568 10.1093/molbev/msi145 15814826
25. Rise and fall of the Beringian steppe bison. B Shapiro AJ Drummond A Rambaut MC Wilson PE Matheus AV Sher OG Pybus MTP Gilbert I Barnes J Binladen E Willerslev AJ Hansen GF Baryshnikov JA Burns S Davydov JC Driver DG Froese CR Harington G Keddie P Kosintsev ML Kunz LD Martin RO Stephenson J Storer R Tedford S Zimov A Cooper, Science 2004 306 1561 1565 10.1126/science.1101074 15567864
26. Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data. M Bonhomme A Blancher S Cuartero L Chikhi B Crouau-Roy, Mol Ecol 2008 17 1009 1019 10.1111/j.1365-294X.2007.03645.x 18261045
27. Increased genetic variation and evolutionary potential drive the success of an invasive grass. S Lavergne J Molofsky, Proc Natl Acad Sci USA 2007 104 3883 3888 17360447 10.1073/pnas.0607324104
28. Genetic bottleneck in invasive species: the potato tuber mothadds to the list. N Puillandre S Dupas O Dangles JL Zeddam C Capdevielle-Dulac K Barbin M Torres-Leguizamon JF Silvain, Biol Invasions 2008 10 319 333 10.1007/s10530-007-9132-y
29. Hydrological changes in the African tropics since the Last Glacial Maximum. F Gasse, Quat Sci Rev 2000 19 189 211 10.1016/S0277-3791(99)00061-X
30. African climate change and faunal evolution during the Pliocene-Pleistocene. PB deMenocal, Earth Planet Sci Lett 2004 220 3 24 10.1016/S0012-821X(04)00003-2
31. The genetic legacy of the Quaternary ice ages. GM Hewitt, Nature 2000 405 907 913 10.1038/35016000 10879524
32. Environmental change and rate of evolution: the phylogeographic pattern within the hartebeest complex as related to climatic variation. Flagstad PO Syvertsen NC Stenseth KS Jakobsen, Proc R Soc Lond B Biol Sci 2001 268 667 677 10.1098/rspb.2000.1416
33. Phylogeographical footprints of the Strait of Gibraltar and Quaternary climatic fluctuations in the Western Mediterranean: a case study with the greater white-toothed shrew, Crocidura russula (Mammalia: Soricidae). JF Cosson R Hutterer R Libois M Sara P Taberlet P Vogel, Mol Ecol 2005 14 1151 1162 10.1111/j.1365-294X.2005.02476.x 15773942
34. Development of primers to amplify mtDNA control region of Old World porcupines (subgenus Hystrix). E Trucchi G Gentile V Sbodoni, Mol ecol resour 2008 8 5 1139 1141 10.1111/j.1755-0998.2008.02201.x
35. Molecular systematic of Hystricognathi rodents: evidence from the mitochondrial 12S rRNA gene. MA Nedbal MW Allard RL Honeycutt, Mol Phylogenet Evol 1994 3 206 220 10.1006/mpev.1994.1023 7820285
36. Genotyping errors: causes, consequences and solutions. F Pompanon A Bonin E Bellemain P Taberlet, Nat Rev Gen 2005 6 847 846 10.1038/nrg1707
37. bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucl Acids Symp Ser 1999 41 95 98
38. M Nei, Molecular Evolutionary Genetics New York, Columbia University Press 1987
39. dnasp, DNA polymorphism analyses by the coalescent and other methods. J Rozas JC Sánchez-Del Barrio X Messeguer R Rozas, Bioinformatics 2003 19 2496 2497 10.1093/bioinformatics/btg359 14668244
40. On the number of segregating sites in genetical models without recombination. GA Watterson, Theor Popul Biol 1975 7 256 276 10.1016/0040-5809(75)90020-9 1145509
41. Some probabilistic and statistical problems in the analysis of DNA sequences. S Tavaré Lect Math Life Sc 1986 17 57 86
42. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetic. G Jobb A von Haesler K Strimmer, BMC Evol Biol 2004 4 18 15222900 10.1186/1471-2148-4-18
43. beast: Bayesian evolutionary analysis by sampling trees. AJ Drummond A Rambaut, BMC Evol Biol 2007 7 214 17996036 10.1186/1471-2148-7-214
44. Median-joining networks for inferring intraspecific phylogenies. HJ Bandelt P Forster A Rohl, Mol Biol Evol 1999 16 37 48 10331250 (Pubitemid 29024937)
45. arlequin ver. 3.0: an integrated software package for population genetics data analysis. L Excoffier G Laval S Schneider, Evol Bioinform Online 2005 1 47 50 19325852
46. Differences in rate of Cytochrome-b evolution among species of rodents. TA Spradling MS Hafner JW Demastes, J Mammal 2001 82 65 80 10.1644/1545- 1542(2001)082<0065:DIROCB>2.0.CO;2 (Pubitemid 32205474)
47. Statistical Properties of New Neutrality Tests Against Population Growth. SE Ramons-Onsins J Rozas, Mol Biol Evol 2002 19 2092 2100 12446801 (Pubitemid 35440445)
48. Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Y-X Fu, Genetics 1997 147 915 925 9335623 (Pubitemid 27418596)
49. Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to humanmitochondrial DNA. S Schneider L Excoffier, Genetics 1999 152 1079 1089 10388826 (Pubitemid 29330907)
50. Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. AJ Drummond A Rambaut B Shapiro OG Pybus, Mol Biol Evol 2005 22 1185 1192 10.1093/molbev/msi103 15703244
51. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. M Hasegawa H Kishino T Yano, J Mol Evol 1985 22 160 174 10.1007/BF02101694 3934395
52. Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models. MA Suchard RE Weiss JS Sinsheimer, Mol Biol Evol 2001 18 1001 1013 11371589 (Pubitemid 32520473)
53. beast user: A general user list for discussion about the BEAST MCMC program. http://groups.google.com/group/beast-users?hl=en