Colonization time of Arabia by the White-tailed Mongoose Ichneumia albicauda as inferred from mitochondrial DNA sequences

References

• Almada V. C. Pereira A. M. Robalo J. I. Fonseca J. P. Levy A. Maia C. Valente A. (2008): Mitochondrial DNA fails to reveal genetic structure in sea-lampreys along European shores. – Molecular Phylogenetics and Evolution 46: 391–396
   Google Scholar
• Aubry K. B. Statham M. J. Sacks B. N. Perrine J. D. Wisely S. M. (2009): Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia. – Molecular Ecology 18: 2668–2686
   Google Scholar
• Austerlitz F. Jung-Muller B. Godelle B. Gouyon P-H. (1997): Evolution of coalescence times, genetic diversity and structure during colonization. – Theoretical Population Biology 51: 148–164
   Google Scholar
• Bailey G. (2009): The Red Sea, coastal landscapes, and hominin dispersals. p. 15–37. In: M. D. Petraglia & J. I. Rose (Eds), The evolution of human populations in Arabia: Paleoenvironments, Prehistory and Genetics. – Dordrecht
   Google Scholar
• Bray H. E. Stokes S. (2004): Temporal patterns of arid-humid transitions in the south-eastern Arabian peninsula based on optical dating. – Geomorphology 59: 271–280
   Google Scholar
• Dehghani R. Wanntorp L. Pagani P. Kallersjo M. Werdelin L. Veron G. (2008): Phylogeography of the white-tailed mongoose (Herpestidae, Carnivora, Mammalia) based on partial sequences of the mtDNA control region. – Journal of Zoology 276: 385–393
   Google Scholar
• Delany M. J. (1989): The zoogeography of the mammal fauna of southern Arabia. – Mammal Review 19: 133–152
   Google Scholar
• De Queiroz A. (2005): The resurrection of oceanic dispersal in historical biogeography. – Trends in Ecology and Evolution 20: 68–73
   Google Scholar
• Drummond A. J. Rambaut A. (2007): BEAST: Bayesian evolutionary analysis by sampling trees. – BMC Evolutionary Biology 7: 214
   Google Scholar
• Excoffier L. Laval G. Schneider S. (2005): Arlequin (version 3.0): an integrated software package for population genetics data analysis. – Evolutionary Bioinformatics Online 1: 47–50
   Google Scholar
• Fernandes C. A. Rohling E. J. Siddall M. (2006): Absence of post-Miocene Red Sea land bridges: biogeographic implications. – Journal of Biogeography 33: 961–966
   Google Scholar
• Fernandes C. A. (2009): Bayesian coalescent inference from mitochondrial DNA variation of the colonization time of Arabia by the hamadryas baboon (Papio hamadryas hamadryas). p. 89–100. In: M. D. Petraglia & J. I. Rose (Eds), The evolution of human populations in Arabia: Paleoenvironments, Prehistory and Genetics. – Dordrecht
   Google Scholar
• Gaggiotti O. E. Excoffier L. (2000): A simple method of removing the effect of a bottleneck and unequal population sizes on pairwise genetic distances. – Proceedings of the Royal Society of London B 267: 81–87
   Google Scholar
• Geraads D. Alemseged Z. Reed D. Wynn J. Roman D. C. (2004): The Pleistocene fauna (other than Primates) from Asbole, lower Awash Valley, Ethiopia, and its environmental and biochronological implications. – Géobios 37: 697–718
   Google Scholar
• Glennie K. W. Singhvi A. K. (2002): Event stratigraphy, paleoenvironment and chronology of SE Arabian deserts. – Quaternary Science Reviews 21: 853–869
   Google Scholar
• Griswold C. K. Baker A. J. (2002): Time to most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration. – Evolution 56: 143–153
   Google Scholar
• Guillaumet A. Crochet P. A. Pons J. M. (2008): Climate-driven diversification in two widespread Galerida larks. – BMC Evolutionary Biology 8: 32
   Google Scholar
• Harpending H. C. (1994): Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. – Human Biology 66: 591–600
   Google Scholar
• 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
   Google Scholar
• Hey J. Nielsen R. (2004): Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. – Genetics 167: 747–760
   Google Scholar
• Hey J. Nielsen R. (2007): Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. – Proceedings of the National Academy of Sciences of the United States of America 104: 2785–2790
   Google Scholar
• Ibrahim K. M. Nichols R. A. Hewitt G. M. (1996): Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. – Heredity 77: 282–291
   Google Scholar
• Jobb G. Von Haeseler A. Strimmer K. (2004): TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. – BMC Evolutionary Biology 4: 18
   Google Scholar
• Johnson J. A. Dunn P. O. Bouzat J. L. (2007): Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens. – Molecular Ecology 16: 2203–2222
   Google Scholar
• Kass R. E. Raftery A. E. (1995): Bayes factors. – Journal of the American Statistical Association 90: 773–795
   Google Scholar
• Kocher T. D. Thomas W. K. Meyer A. Edwards S. V. Paabo S. Villablanca F. X. Wilson A. C. (1989): Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. – Proceedings of the National Academy of Sciences of the United States of America 86: 6196–6200
   Google Scholar
• Kuhner M. K. (2009): Coalescent genealogy samplers: windows into population history. – Trends in Ecology and Evolution 24: 86–93
   Google Scholar
• Lahr M. Foley R. (1998): Towards a theory of modern human origins: geography, demography, and diversity in recent human evolution. – American Journal of Physical Anthropology Suppl 27: 137–176
   Google Scholar
• Leonard J. A. Vilà C. Wayne R. K. (2005): Legacy lost: genetic variability and population size of extirpated US grey wolves (Canis lupus). – Molecular Ecology 14: 9–17
   Google Scholar
• Leschen R. A. B. Buckley T. R. Harman H. M. Shulmeister J. (2008): Determining the origin and age of the Westland Beech (Nothofagus) gap, New Zealand, using fungus beetle genetics. – Molecular Ecology 17: 1256–1276
   Google Scholar
• Lessios H. A. Garrido M. J. Kessing B. D. (2001): Demographic history of Diadema antillarum, a keystone herbivore on Caribbean reefs. – Proceedings of the Royal Society of London B 268: 2347–2353
   Google Scholar
• McFadden K. W. Gompper M. E. Valenzuela D. G. Morales J. C. (2008): Evolutionary history of the critically endangered Cozumel dwarf carnivores inferred from mitochondrial DNA analyses. – Journal of Zoology 276: 176–186
   Google Scholar
• Moeyersons J. Vermeersch P. M. Peer P. V. (2002): Dry cave deposits and their palaeoenvironmental significance during the last 115ka, Sodmein Cave, Red Sea Mountains, Egypt. – Quaternary Science Reviews 21: 837–851
   Google Scholar
• Nei M. Li W. H. (1979): Mathematical model for studying genetic variation in terms of restriction endonucleases. – Proceedings of the National Academy of Sciences of the United States of America 76: 5269–5273
   Google Scholar
• Nielsen R. Wakeley J. (2001): Distinguishing migration from isolation: a Markov chain Monte Carlo approach. – Genetics 158: 885–896
   Google Scholar
• Patou M. L. McLenachan P. A. Morley C. G. Couloux A. Jennings A. P. Veron G. (2009): Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes. – Molecular Phylogenetics and Evolution 53: 69–80
   Google Scholar
• Pesole G. Sbisá E. Preparata G. Saccone C. (1992): The evolution of the mitochondrial d-loop region and the origin of modern man. – Molecular Biology and Evolution 9: 587–598
   Google Scholar
• Pook C. E. Joger U. Stumpel N. Wuster W. (2009): When continents collide: phylogeny, historical biogeography and systematics of the medically important viper genus Echis (Squamata: Serpentes: Viperidae). – Molecular Phylogenetics and Evolution 53: 792–807
   Google Scholar
• Posada D. Buckley T. R. (2004): Model selection and model averaging in phylogenetics: advantages of Akaike Information criterion and Bayesian approaches over likelihood ratio tests. – Systematic Biology 53: 793–808
   Google Scholar
• Rambaut A. (2009): FigTree v1.3.1, Available from ttp://tree.bio.ed.ac.uk/software/figtree
   Google Scholar
• Rambaut, A A. J. Drummond (2007): Tracer v1.5, Available from http://tree.bio.ed.ac.uk/software/tracer
   Google Scholar
• Rieder M. J. Taylor S. L. Tobe V. O. Nickerson D. A. (1998): Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. – Nucleic Acids Research 26: 967–973
   Google Scholar
• Riley S. P. Pollinger J. P. Sauvajot R. M. York E. C. Bromley C. Fuller T. K. Wayne R. K. (2006): A southern California freeway is a physical and social barrier to gene flow in carnivores. – Molecular Ecology 15: 1733–1741
   Google Scholar
• Robinson T. J. Matthee C. A. (1999): Molecular genetic relationships of the extinct ostrich, Struthio camelus syriacus: consequences for ostrich introductions into Saudi Arabia. – Animal Conservation 2: 165–171
   Google Scholar
• Rogers A. R. Harpending H. (1992): Population growth makes waves in the distribution of pair-wise genetic differences. – Molecular Biology and Evolution 9: 552–569
   Google Scholar
• Rogers R. R. Hartman J. H. Krause D. W. (2000): Stratigraphic analysis of Upper Cretaceous Rocks in the Mahajanga Basin, northwestern Madagascar: implications for ancient and modern faunas. – Journal of Geology 108: 275–301
   Google Scholar
• Rohling E. J. Fenton M. Jorissen F. J. Bertrand P. Ganssen G. Caulet J. P. (1998): Magnitude of sea-level lowstands of the past 500,000 years. – Nature 394: 162–165
   Google Scholar
• Ronquist F. Huelsenbeck J. P. (2003): MrBayes3: Bayesian phylogenetic inference under mixed models. – Bioinformatics 19: 1572–1574
   Google Scholar
• Savolainen P. Zhang Y. P. Luo J. Lundeberg J. Leitner T. (2002): Genetic evidence for an East Asian origin of domestic dogs. – Science 298: 1610–1613
   Google Scholar
• Schneider S. Excoffier L. (1999): Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. – Genetics 152: 1079–1089
   Google Scholar
• Shields G. F. Kocher T. D. (1991): Phylogenetic relationships of North American ursids based on analysis of mitochondrial DNA. – Evolution 45: 218–221
   Google Scholar
• Siddall M. Rohling E. J. Almogi-Labin A. Hemleben C. Meischner D. Schmelzer I. Smeed D. A. (2003): Sea-level fluctuations during the last glacial cycle. – Nature 423: 853–858
   Google Scholar
• Stoneking M. Sherry S. T. Redd A. J. Vigilant L. (1992): New approaches to dating suggest a recent age for the human mtDNA ancestor. – Philosophical Transactions of the Royal Society of London B 337: 167–175
   Google Scholar
• Suchard M. A. Weiss R. E. Sinsheimer J. S. (2001): Bayesian selection of continuous-time Markov chain evolutionary models. – Molecular Biology and Evolution 18: 1001–1013
   Google Scholar
• Taberlet P. Bouvet J. (1994): Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. – Proceedings of the Royal Society of London B 255: 195–200
   Google Scholar
• 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
   Google Scholar
• Tamura K. Dudley J. Nei M. Kumar S. (2007): MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. – Molecular Biology and Evolution 24: 1596–1599
   Google Scholar
• Tchaicka L. Eizirik E. De Oliveira T. G. Cândido J. F. Jr. Freitas T. R. (2007): Phylogeography and population history of the crab-eating fox (Cerdocyon thous). – Molecular Ecology 16: 819–838
   Google Scholar
• Van den Bergh G. D. de Vos J. Sondaar P. Y. (2001): The late Quaternary palaeogeography of mammal evolution in the Indonesian Archipelago. – Palaeogeography, Palaeoclimatology, Palaeoecology 171: 385–408
   Google Scholar
• Van Vuuren B. J. Robinson T. J. (1997): Genetic population structure in the yellow mongoose, Cynictis penicillata. – Molecular Ecology 6: 1147–1153
   Google Scholar
• Wakeley J. Hey J. (1997): Estimating ancestral population parameters. – Genetics 145: 847–855
   Google Scholar
• Wildman D. E. Bergman T. J. al-Aghbari A. Sterner K. N. Newman T. K. Phillips-Conroy J. E. Jolly C. J. Disotell T. R. (2004): Mitochondrial evidence for the origin of hamadryas baboons. – Molecular Phylogenetics and Evolution 32: 287–296
   Google Scholar
• Wilson D. E. Mittermeier R. A. (2009): Handbook of the Mammals of the World, Volume 1: Carnivores. – Barcelona
   Google Scholar
• Winney B. J. Hammond R. L. Macasero W. Flores B. Boug A. Biquand V. Biquand S. Bruford M. W. (2004): Crossing the Red Sea: phylogeography of the hamadryas baboon, Papio hamadryas hamadryas. – Molecular Ecology 13: 2819–2827
   Google Scholar
• Won Y. Young C. R. Lutz R. A. Vrijenhoek R. C. (2003): Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents. – Molecular Ecology 12: 169–184
   Google Scholar
• Woods W. W. Imes J. L. (1995): How wet is wet? Precipitation constraints on late Quaternary climate in the southern Arabian Peninsula. – Journal of Hydrology 164: 263–268
   Google Scholar
• Xia Y. Xie Z. (2001): DAMBE: software package for data analysis in molecular biology and evolution. – Journal of Heredity 92: 371–373
   Google Scholar
• Yan Z. Petit-Maire N. (1994): The last 140 ka in the Afro-Asian arid/semi-arid transitional zone. – Palaeogeography, Palaeoclimatology, Palaeoecology 110: 217–233
   Google Scholar
• Yoder A. D. Burns M. N. Zehr S. Delefosse T. Veron G. Goodman S. M. Flynn J. J. (2003): Single origin of Malagasy Carnivora from an African ancestor. – Nature 421: 734–737
   Google Scholar