Mitochondrial phylogeography of the black rat supports a single invasion of the western Mediterranean basin

Biological Invasions

Volumn 17, Issue 6, 2015, Pages 1859-1868

  Colangelo, P ^a,e   Abiadh, A ^b   Aloise, G ^c   Amori, G ^a   Capizzi, D ^d   Vasa, E ^e   Annesi, F ^e   Castiglia, R ^e  

^a CNR   (Italy)

^b Eco conservation Society   (Tunisia)

^c UNIVERSITY OF CALABRIA   (Italy)

^d Agenzia Regionale per i Parchi   (Italy)

^e SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Italian peninsula; Mediterranean basin; North Africa; Phylogeography; Rattus rattus; Roof rat

Indexed keywords

EID: 84939992906     PISSN: 13873547     EISSN: 15731464     Source Type: Journal    
DOI: 10.1007/s10530-015-0842-2     Document Type: Article

References (45)

1. Aplin KP, Suzuki H, Chinen AA, Chesser RT, ten Have J, Donnellan SC, Austin J, Frost A, Gonzalez JP, Herbreteau V, Catzeflis F, Soubrier J, Fang Y-P, Robins J, Matisoo-Smith E, Bastos ADS, Maryanto I, Sinaga MH, Denys C, Van Den Bussche RA, Conroy C, Rowe K, Cooper A (2011) Multiple geographic origins of commensalism and complex dispersal history of black rats. PLoS ONE 6:e26357
2. Armitage P, West B, Steedman K (1984) New evidence of the black rat in Roman London. Lond Archaeol 4:375–383
3. Armitage PL (1993) Commensal rats in the New World, 1492–1992. Biologist 40:174–178
4. Bastos ADS, Nair D, Taylor PJ, Brettschneider H, Kirsten F, Mostert ME, von Maltitz E, Lamb JM, van Hooft P, Belmain SR, Contrafatto G, Downs S, Chimimba CT (2011) Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in south Africa. BMC Genet 12:26
5. Bonhomme F, Orth A, Cucchi T, Rajabi-Maham H, Catalan J, Boursot P, Auffray JC, Britton-Davidian J (2011) Genetic differentiation of the house mouse around the Mediterranean basin: matrilineal footprints of early and late colonization. Proc R Soc B 278:1034–1043
6. Chinen AA, Suzuki H, Aplin KP, Tsuchiya K, Suzuki S (2005) Preliminary genetic characterization of two lineages of black rats (Rattus rattus sensu lato) in Japan, with evidence for introgression at several localities. Genes Genet Syst 80:367–375
7. Clement M, Posada D, Crandall K (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1660
8. Conroy CJ, Rowe KC, Rowe KMC, Kamath PL, Aplin KP, Hui L, James DK, Moritz C, Patton JL (2013) Cryptic genetic diversity in Rattus of the San Francisco Bay region, California. Biol Invasions 15:741–758
9. De Grossi Mazorin J (1987) La fauna. In: Ghini G (ed) Archeologia Laziale VIII. CNR, Roma, pp 234–235
10. Ervynck A (2002) Sedentism or urbanism? On the origin of the commensal black rat (Rattus rattus). In: Dobney K, O’Connor T (eds) Bones and the man. Studies in honour of Don Brothwell. Oxbow, Oxford, pp 95–109
11. Facon B, Genton BJ, Shykoff J, Jarne P, Estoup A, David P (2006) A general eco-evolutionary framework for understanding bioinvasions. Trends Ecol Evol 21:130–135
12. Gage KL, Kosoy MY (2005) Natural history of plague: perspectives from more than a century of research. Annu Rev Entomol 50:505–528
13. Gratz NG (1999) Control of plague transmission. In: Dennis DT, Gage KL, Gratz N, Poland J, Tikhomirov E (eds) Plague manual: epidemiology, distribution, surveillance and control. WHO, Geneva, pp 97–131
14. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321
15. Hingston M, Goodman SM, Ganzhorn JU, Sommer S (2005) Reconstruction of the colonization of southern Madagascar by introduced Rattus rattus. J Biogeogr 32:1549–1559
16. Hirst LF (1953) The conquest of plague. A study of the evolution of epidemiology. Oxford University Press, Oxford
17. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO (2006) 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 6:29
18. Konkola K (1992) More than a coincidence? The arrival of arsenic and the disappearance of plague in early modern Europe. J Hist Med Allied Sci 47:186–209
19. Kotsakis T, Ruschioni E (1984) I microvertebrati di un insediamento dell’Età del Ferro presso Tortoreto (Teramo, Italia centrale). Rend Accad Naz Lincei 76:295–304
20. Lack JB, Greene DU, Conroy CJ, Hamilton MJ, Braun JK, Mares MA, Van Den Bussche RA (2012) Invasion facilitates hybridization with introgression in the Rattus rattus species complex. Mol Ecol 21:3545–3561
21. Lack JB, Hamilton MJ, Braun JK, Mares MA, Den Bussche RA (2013) Comparative phylogeography of invasive Rattus rattus and Rattus norvegicus in the U.S. reveals distinct colonization histories and dispersal. Biol Invasions 15:1067–1087
22. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452
23. López M, Foronda P, Feliu C, Hernández M (2013) Genetic characterization of black rat (Rattus rattus) of the Canary Islands: origin and colonization. Biol Invasions. doi:10.1007/s10530-013-0466-3
24. Lowe S, Browne M, Boudjelas S, De Poorter M (2000) 100 of the World’s Worst Invasive Alien Species A selection from the Global Invasive Species Database. The Invasive Species Specialist Group (ISSG) a specialist group of the Species Survival Commission (SSC) of the World Conservation Union (IUCN), 12 pp
25. McCormick M (2003) Rats, communications, and plague: towards an ecological history. J Interdiscip Hist 34:1–25
26. Musser GG, Carleton MD (2005) Superfamily Muroidea. In: Wilson DE, Reeder DM (eds) Mammal species of the world: a taxonomic and geographic reference, 3rd edn. Johns Hopkins University Press, Baltimore, pp 894–1600
27. Prugnolle F, Théron A, Pointier JP, Jabbour-Zahab R, Jarne P, Durand P, Meeûs TD (2005) Dispersal in a parasitic worm and its two hosts: consequence for local adaptation. Evolution 59:296–303
28. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–2100
29. Robins JH, McLenachan PA, Phillips MJ, Craig L, Ross HA, Matisoo-Smith E (2008) Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Mol Phylogenet Evol 49:460–466
30. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569
31. Rowe KC, Aplin KP, Baverstock PR, Moritz C (2011) Recent and rapid speciation with limited morphological disparity in the genus Rattus. Syst Biol 60:188–203
32. Ruffino L, Vidal E (2010) Early colonization of Mediterranean islands by Rattus rattus: a review of zooarcheological data. Biol Invasions 12:2389–2394
33. Russell JC, Gleeson DM, Le Corre M (2011) The origin of Rattus rattus on the Îles Éparses, Western Indian Ocean. J Biogeogr 38:1834–1836
34. Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, Baughman S, Cabin RJ, Cohen JE, Ellstrand NC, McCauley DE, O’Neil P, Parker IM, Thompson JN, Weller SG (2001) The Population Biology of Invasive Species. Annu Rev Ecol Syst 32:305–332
35. Salah MA, Martinez I (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res 25:4692–4693
36. Saunders EAC, Reumer JWF (1984) The influence of prehistoric and Roman migrations on the vertebrate fauna of Menorca (Spain). Br Archaeol Rep Int Ser 229:119–144
37. Solano E, Franchini P, Colangelo P, Capanna E, Castiglia R (2013) Multiple origins of the western European house mouse in the Aeolian Archipelago: clues from mtDNA and chromosomes. Biol Invasions 15:729–739
38. Strayer DL, Eviner VT, Jeschke JM, Pace ML (2006) Understanding the long-term effects of species invasions. Trends Ecol Evol 31:645–651
39. Suzuki H, Tsuchiya K, Takezaki N (2000) A Molecular Phylogenetic Framework for the Ryukyu Endemic Rodents Tokudaia osimensis and Diplothrix legata. Mol Phylogenet Evol 15:15–24
40. Tchernov E (1968) Succession of rodent faunas during the Upper Pleistocene of Israel (Mammalia depicta). Paul Parey, Verlag, Hamburg
41. Tollenaere C, Brouat C, Duplantier JM, Rahalison L, Rahelinirina S, Pascal M, Moné H, Mouahid G, Leirs H, Cosson JF (2010) Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar. J Biogeogr 37:398–410
42. Twigg GI, Buckle AP, Bullock DJ (2008) Ship rat Rattus rattus. In: Harris S, Yalden DW (eds) Mammals of the British Isles: handbook, 4th edn. The Mammal Society, Southampton, pp 155–158
43. Vigne JD, Valladas H (1996) Small mammal fossil assemblages as indicators of environmental change in Northern Corsica during the last 2,500 years. J Archaeol Sci 23:199–215
44. Von den Driesch A, Boessneck J (1983) A Roman cat skeleton from Quseir on the Red Sea Coast. J Archaeol Sci 10:205–212
45. Weissbrod L, Malkinson D, Cucchi T, Gadot Y, Finkelstein I, Bar-Ozet G (2014) Ancient urban ecology reconstructed from archaeozoological remains of small mammals in the near east. PLoS ONE 9(3):e91795 l.pone.0091795