Three roads diverged? Routes to phylogeographic inference

Trends in Ecology and Evolution

Volumn 25, Issue 11, 2010, Pages 626-632

  Bloomquist, Erik W ^a   Lemey, Philippe ^b   Suchard, Marc A ^c,d  

^a OHIO STATE UNIVERSITY   (United States)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDEMIC; HISTORICAL GEOGRAPHY; MIGRATION; NUMERICAL MODEL; PHYLOGEOGRAPHY;

ANIMAL; BIOLOGICAL MODEL; DEMOGRAPHY; GENETIC VARIABILITY; PHYLOGEOGRAPHY; SHORT SURVEY;

ANIMALS; DEMOGRAPHY; GENETIC VARIATION; MODELS, BIOLOGICAL; PHYLOGEOGRAPHY;

EID: 77957923165     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2010.08.010     Document Type: Short Survey

References (86)

1. Searle J., et al. Of mice and (Viking?) men: phylogeography of British and Irish house mice. Proc. R. Soc. B Biol. Sci. 2009, 276:201-207.
2. Fagundes N., et al. Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. U. S. A 2007, 104:17614-17619.
3. Li J., et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008, 319:1100-1104.
4. von Holdt B., et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 2010, 464:898-902.
5. Biek R., et al. A virus reveals population structure and recent demographic history of its carnivore host. Science 2006, 311:538-541.
6. Biek R., et al. A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:7993-7998.
7. Smith G., et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 2009, 459:1122-1125.
8. Lemey P., et al. Reconstructing the initial global spread of a human influenza pandemic: a Bayesian spatial--temporal model for the global spread of H1N1. PLoS Curr. Influenza 2009, RRN1031.
9. Nielsen R., Beaumont M. Statistical inferences in phylogeography. Mol. Ecol. 2009, 18:1034-1047.
10. Knowles L. Statistical phylogeography. Annu. Rev. Ecol. Evol. Syst. 2009, 40:593-612.
11. Avise J. Phylogeography: retrospect and prospect. J. Biogeog. 2009, 36:3-15.
12. Hickerson M., et al. Phylogeography's past, present, and future: 10 years after Avise, 2000. Mol. Phylogenet. Evol. 2010, 54:291-301.
13. Brooks S., et al. Assessing the effect of genetic mutation: a Bayesian framework for determining population history from DNA sequence data. Bayesian Statistics 2007, Vol.8:1-26. Oxford University Press.
14. Templeton A. Coalescent-based, maximum likelihood inference in phylogeography. Mol. Ecol. 2010, 19:431-435.
15. Lemey P., et al. Bayesian phylogeography finds its roots. PLoS Comput. Biol. 2009, 5:e1000520.
16. Lemey P., et al. Phylogeography takes a relaxed random walk in continuous space and time. Mol. Biol. Evol. 2010, 27:1877-1885.
17. Hey J. Isolation with migration models for more than two populations. Mol. Biol. Evol. 2010, 27:905-920.
18. Heled J., Drummond A. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
19. Beerli P., Palczewski M. Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 2010, 185:313-326.
20. Beaumont M., et al. In defence of model-based inference in phylogeography. Mol. Ecol. 2010, 19:436-446.
21. Camargo A., et al. Phylogeography of the frog Leptodactylus validus (Amphibia: Anura): patterns and timing of colonization events in the Lesser Antilles. Mol. Phylogenet. Evol. 2009, 53:571-579.
22. Phillipsen I., Metcalf A. Phylogeography of a stream-dwelling frog ( Pseudacris cadaverina) in southern California. Mol. Phylogenet. Evol. 2009, 53:152-170.
23. Gante H., et al. Diversification within glacial refugia: tempo and mode of evolution of the polytypic fish Barbus sclateri. Mol. Ecol. 2009, 18:3240-3255.
24. Felsenstein J. Phylogenies and the comparative method. Am. Nat. 1985, 125:1-15.
25. Harvey P., Pagel D. The Comparative Method in Evolutionary Biology 1991, Oxford University Press.
26. Templeton A. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol. Ecol. 1998, 7:381-397.
27. Panchal M., Beaumont M. The automation and evaluation of nested clade phylogeographic analysis. Evolution 2007, 61:1466-1480.
28. Templeton A., et al. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. III. Cladogram estimation. Genetics 1992, 134:659-669.
29. Clement M., et al. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 2000, 9:1657-1659.
30. Posada D., Crandall K. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 2001, 16:37-45.
31. Templeton A., et al. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophilia. Genetics 1987, 117:343-351.
32. Templeton A., et al. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 1993, 134:659-669.
33. Cassens I., et al. Evaluating intraspecific " network" construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach?. Syst. Biol. 2005, 54:363-372.
34. Knowles L. Why does a method that fails continue to be used?. Evolution 2008, 62:2713-2717.
35. Templeton A. A maximum likelihood framework for cross validation of phylogeographic hypotheses. Evolutionary Theory and Processes: Modern Horizons 2004, 209-230. Kluwer Academic Publishers. S. Wasser (Ed.).
36. Panchal M., Beaumont M. Evaluating nested clade phylogenetic analysis under models of restricted gene flow. Syst. Biol. 2010, 59:415-432.
37. Wong K., et al. Alignment uncertainty and genomic analysis. Science 2008, 319:473-476.
38. Redelings B., Suchard M. Robust inferences from ambiguous alignments. Sequence Alignment: Methods, Models, Concepts, and Strategies 2009, 209-271. University of California Press. M. Rosenberg (Ed.).
39. Suchard M., et al. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 2001, 18:1001-1013.
40. Redelings B., Suchard M. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 2005, 54:401-418.
41. Novák A., et al. StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics 2008, 24:2403-2404.
42. Drummond A., et al. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 2005, 22:1185-1192.
43. Minin V., et al. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 2008, 25:1459-1471.
44. Beerli P., Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:4563-4568.
45. Zarate S., et al. Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Virology 2007, 81:6643-6651.
46. Swofford D., Maddison W. Parsimony, character-state reconstructions and evolutionary inferences. Systematics, Historical Ecology, and North American Freshwater Fishes 1992, 186-223. Stanford University Press. R. Mayden (Ed.).
47. Wallace R., et al. A statistical phylogeography of influenza A H5N1. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:4473-4478.
48. Cunningham C., et al. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 1998, 13:361-366.
49. Ronquist F. Bayesian inference of character evolution. Trends Ecol. Evol. 2004, 19:475-481.
50. Sanmartin I., et al. Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. J. Biogeog. 2008, 35:428-449.
51. Kuo L., Mallick B. Variable selection for regression models. Sankhya B 1998, 60:65-81.
52. Lemmon A., Lemmon E. A likelihood framework for estimating phylogeographical history on a continuous landscape. Syst. Biol. 2008, 57:544-561.
53. Drummond A., et al. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4:e88.
54. Paradis E., et al. Modeling large-scale dispersal distances. Ecol. Model. 2002, 151:279-292.
55. Viswanathan G., et al. Lévy flight search patterns of wandering albatrosses. Nature 1996, 381:413-415.
56. Reynolds A., Rhodes C. The Lévy flight paradigm: random search patterns and mechanisms. Ecology 2009, 90:877-887.
57. Edwards A., et al. Revisiting Lévy flight search patterns of wandering albatrosses, bumblebees and deer. Nature 2007, 449:1044-1048.
58. Schluter D., et al. Likelihood of ancestral states in adaptive radiation. J. Org. Evol. 1997, 51:1699-1711.
59. Drummond A., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
60. Mavárez J., et al. Evolutionary history and phylogeography of the schistosome-vector freshwater snail Biomphalaria glabrata based upon nuclear and mitochondrial DNA sequences. Heredity 2002, 89:266-272.
61. Avise J. Phylogeography: The History and Formation of Species 2000, Harvard University Press.
62. Hey J., Machado C. The study of structured populations -- a new hope for a difficult and divided science. Nat. Rev. Genet. 2003, 4:535-543.
63. Kingman J. The coalescent. Stochastic Processes Appl. 1982, 13:235-248.
64. Felsenstein, J. et al. (1999) Likelihoods on coalescents: a Monte Carlo sampling approach to inferring parameters from populations samples of molecular data. In Statistics in Molecular Biology (Seillier-Moiseiwitsch, F., ed.) IMS Lecture Notes, Vol. 33, pp. 163-184, Institute of Mathematical Statistics.
65. Liu L., Pearl D. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 2007, 56:504-514.
66. Edwards S. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
67. Degnan J., Rosenberg N. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
68. Templeton A., et al. Separating population structure from population history - a cladisitic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 1995, 140:767-782.
69. Knowles L., Maddison W. Statistical phylogeography. Mol. Ecol. 2002, 11:2623-2635.
70. Templeton A. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 2004, 13:789-809.
71. Petit R. The coup de grâce for nested clade phylogeographic analysis. Mol. Ecol. 2008, 17:516-518.
72. Beaumont M., Panchal M. On the validity of nested clade phylogeographic analysis. Mol. Ecol. 2008, 17:2563-2565.
73. Garrick R., et al. Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis. Mol. Ecol. 2008, 17:1401-1403.
74. Templeton A. Nested clade analysis: an extensively validated method for strong phylogeographic inference. Mol. Ecol. 2008, 17:1877-1880.
75. Templeton A. Why does a method that fails continue to be used? The answer. Evolution 2009, 63:807-812.
76. Templeton A. Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographic analysis vs. approximate Bayesian computation. Mol. Ecol. 2009, 18:319-331.
77. Templeton A. Coherent and incoherent inference in phylogeography and human evolution. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:6376-6381.
78. Paraense W. A survey of planorbid molluscs in the Amazonian region of Brazil. Mem. Inst. Oswaldo Cruz 1983, 78:343-361.
79. Mavárez J., et al. Fine-scale population structure and dispersal of Biomphalaria glabrata, the intermediate snail host of Schistosoma mansoni, in Venezuela. Mol. Ecol. 2002, 11:879-899.
80. Mavárez J., et al. Genetic differentiation, dispersal and mating system in the schistosome-transmitting freshwater snail Biomphalaria glabrata. Heredity 2002, 89:258-265.
81. Janies D., et al. Genomic analysis and geographic visualization of the spread of avian influenza (H5N1). Syst. Biol. 2007, 56:321-329.
82. Parks D., et al. GenGIS: a geospatial information system for genomic data. Genome Res. 2009, 19:1896-1904.
83. Kidd D., Ritchie M. Phylogeographic information systems: putting the geography into phylogeography. J. Biogeog. 2006, 33:1851-1865.
84. O'Brien J., et al. Learning to count: robust estimates for labeled distances between molecular sequences. Mol. Biol. Evol. 2009, 26:801-814.
85. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 1988, 22:521-565.
86. Smouse P. To tree or not to tree. Mol. Ecol. 1998, 7:399-412.