Inference of population history by coupling exploratory and model-driven phylogeographic analyses

International Journal of Molecular Sciences

Volumn 11, Issue 4, 2010, Pages 1190-1227

  Garrick, Ryan C ^a   Caccone, Adalgisa ^a   Sunnucks, Paul ^b  

^a YALE UNIVERSITY   (United States)

^b MONASH UNIVERSITY   (Australia)

Author keywords

Cladistic analysis; Landscape history; Molecular markers; Population structure; Statistical phylogeography; Temporal contrasts

Indexed keywords

ANALYTIC METHOD; CLADISTICS; DNA SEQUENCE; GENETIC VARIABILITY; HISTORY; NONHUMAN; PHYLOGENETIC TREE; PHYLOGEOGRAPHY; POPULATION BIOLOGY; REVIEW; SPECIES DIFFERENTIATION;

CLADISTIC ANALYSIS; LANDSCAPE HISTORY; MOLECULAR MARKERS; POPULATION STRUCTURE; STATISTICAL PHYLOGEOGRAPHY; TEMPORAL CONTRASTS;

GENE FREQUENCY; GENEALOGY AND HERALDRY; GENETIC VARIATION; GENOTYPE; MODELS, GENETIC; PHYLOGEOGRAPHY; POPULATION DENSITY;

EID: 77951913552     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms11041190     Document Type: Review

References (197)

1. Avise, J.C.; Arnold, J.; Ball, R.M.; Bermingham, E.; Lamb, T.; Neigel, J.E.; Reeb, C.A.; Saunders, N.C. Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 1987, 18, 489-522.
2. Avise, J.C. Phylogeography: The History and Formation of Species; Harvard University Press: Cambridge, MA, USA, 2000.
3. Schneider, C.; Moritz, C. Rainforest refugia and evolution in Australia's Wet Tropics. Proc. R. Soc. Lond. B: Biol. Sci. 1999, 266, 191-196.
4. Brisson, J.A.; De Toni, D.C.; Duncan, I.; Templeton, A.R. Abdominal pigmentation variation in Drosophila polymorpha: Geographic variation in the trait, and underlying phylogeography. Evolution 2005, 59, 1046-1059.
5. Hoskin, C.J.; Higgie, M.; McDonald, K.R.; Moritz, C. Reinforcement drives rapid allopatric speciation. Nature 2005, 437, 1353-1356.
6. Palkovacs, E.P.; Dion, K.B.; Post, D.M.; Caccone, A. Independent evolutionary origins of landlocked alewife populations and rapid parallel evolution of phenotypic traits. Mol. Ecol. 2008, 17, 582-597.
7. DeChaine, E.G.; Martin, A.P. Using coalescent simulations to test the impact of Quaternary climate cycles on divergence in an alpine plant-insect association. Evolution 2006, 60, 1004-1013.
8. Smith, C.I.; Godsoe, W.K.W.; Tank, S.; Yoder, J.B.; Pellmyr, O. Distinguishing coevolution from covicariance in an obligate pollination mutualism: Asynchronous divergence in Joshua tree and its pollinators. Evolution 2008, 62, 2676-2687.
9. Schneider, C.J.; Cunningham, M.; Moritz, C. Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Mol. Ecol. 1998, 7, 487-498.
10. Riddle, B.R.; Hafner, D.J.; Alexander, L.F.; Jaeger, J.R. Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. Proc. Natl. Acad. Sci. USA 2000, 97, 14438-14443.
11. Trewick, S.A.; Wallis, G.P. Bridging the beech-gap: New Zealand invertebrate phylogeography implicates Pleistocene glaciation and Pliocene isolation. Evolution 2001, 55, 2170-2180.
12. Carstens, B.C.; Brunsfeld, S.J.; Demboski, J.R.; Good, J.M.; Sullivan, J. Investigating the evolutionary history of the pacific northwest mesic forest ecosystem: Hypothesis testing within a comparative phylogeographic framework. Evolution 2005a, 59, 1639-1652.
13. Garrick, R.C.; Rowell, D.M.; Simmons, C.S.; Hillis, D.M.; Sunnucks, P. Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails. Evolution 2008a, 62, 1103-1118.
14. Moritz, C. Defining 'evolutionarily significant units' for conservation. Trends Ecol. Evol. 1994, 9, 373-375.
15. Moritz, C. Strategies to protect biological diversity and the evolutionary processes that sustain it. Syst. Biol. 2002, 51, 238-254.
16. Moritz, C.; Faith, D.P. Comparative phylogeography and the identification of genetically divergent areas for conservation. Mol. Ecol. 1998, 7, 419-429.
17. Crandall, K.A.; Bininda-Emonds, O.R.R.; Mace, G.M.; Wayne, R.K. Considering evolutionary processes in conservation biology. Trends Ecol. Evol. 2000, 15, 290-295.
18. Fraser, D.J.; Bernatchez, L. Adaptive evolutionary conservation: Towards a unified concept for defining conservation units. Mol. Ecol. 2001, 10, 2741-2752.
19. Palsbøll, P.J.; Berube, M.; Allendorf, F.W. Identification of management units using population genetic data. Trends Ecol. Evol. 2007, 22, 11-16.
20. McLachlan, J.S.; Clark, J.S.; Manos, P.S. Molecular indicators of tree migration capacity under rapid climate change. Ecology 2005, 86, 2088-2098.
21. Cordellier, M.; Pfenninger, M. Inferring the past to predict the future: Climate modelling predictions and phylogeography for the freshwater gastropod Radix balthica (Pulmonata, Basommatophora). Mol. Ecol. 2009, 18, 534-544.
22. Norgate, M.; Chamings, J.; Pavlova, A.; Bull, J.K.; Murray, N.D.; Sunnucks, P. Mitochondrial DNA indicates Late Pleistocene divergence of populations of Heteronympha merope, an emerging model in environmental change biology. PLoS ONE, 2009, 11, e7950.
23. Templeton, A.R.; Routman, E.; Phillips, C.A. Separating population structure from population history: A cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 1995, 140, 767-782.
24. Templeton, A.R. Nested clade analyses of phylogeographic data: Testing hypotheses about gene flow and population history. Mol. Ecol. 1998, 7, 381-397.
25. Slatkin, M.; Maddison, W.P. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 1989, 123, 603-613.
26. Slatkin, M.; Hudson, R.R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 1991, 129, 555-562.
27. Rogers, A.R.; Harpending, H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992, 9, 552-569.
28. Felsenstein, J. Estimating effective population size from samples of sequences: Inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet. Res. 1992, 59, 139-147.
29. Hey, J.; Machado, C.A. The study of structured populations - New hope for a difficult and divided science. Nat. Rev. Genet. 2003, 4, 535-543.
30. Knowles, L.L. The burgeoning field of statistical phylogeography. J. Evol. Biol. 2004, 17, 1-10.
31. Nielsen, R.; Beaumont, M.A. Statistical inferences in phylogeography. Mol. Ecol. 2009, 18, 1034-1047.
32. Hickerson, M.J.; Carstens, B.C.; Cavender-Bares, J.; Crandall, K.A.; Graham, C.H.; Johnson, J.B.; Rissler, L.; Victoriano, P.F.; Yoder, A.D. Phylogeography's past, present, and future: 10 years after Avise, 2000. Mol. Phylogenet. Evol. 2010, 54, 291-301.
33. Kuhner, M.K.; Yamato, J.; Felsenstein, J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 1998, 149, 429-434.
34. Smouse, P.E.; Peakall, R. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 1999, 82, 561-573.
35. Pritchard, J.K.; Stephens, M.; Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 2000, 155, 945-959.
36. 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. USA 2001, 98, 4563-4568.
37. Templeton, A.R. Out of Africa again and again. Nature 2002, 416, 45-51.
38. Hey, J.; Nielsen, R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 2004, 167, 747-760.
39. Drummond, A.J.; Rambaut, A.; Shapiro, B.; Pybus, O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 2005, 22, 1185-1192.
40. Drummond, A.J.; Ho, S.Y.W.; Phillips, M.J.; Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4, e88.
41. Edwards, S.; Beerli, P. Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 2000, 54, 1839-1854.
42. Arbogast, B.S.; Edwards, S.V.; Wakeley, J.; Beerli, P.; Slowinski, J.B. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 2002, 33, 707-740.
43. Hudson, R.R.; Turelli, M. Stochasticity overrules the three-times rule: Genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondrial DNA. Evolution 2003, 57, 182-190.
44. Knowles, L.L. Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Mol. Ecol. 2001, 10, 691-701.
45. Knowles, L.L.; Maddison, W.P. Statistical phylogeography. Mol. Ecol. 2002 11, 2623-2635.
46. Carstens, B.C.; Degenhardt, J.D.; Stevenson, A.L.; Sullivan, J. Accounting for coalescent stochasticity in testing phylogeographical hypotheses: Modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Mol. Ecol. 2005b, 14, 255-265.
47. Carstens, B.C.; Knowles, L.L. Shifting distributions and speciation: Species divergence during rapid climate change. Mol. Ecol. 2007, 16, 619-627.
48. Garrick, R.C.; Nason, J.D.; Meadows, C.A.; Dyer, R.J. Not just vicariance: Phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Mol. Ecol. 2009, 18, 1916-1931.
49. Sunnucks, P. Efficient genetic markers for population biology. Trends Ecol. Evol. 2000, 15, 199-203.
50. Manel, S.; Gaggiotti, O.E.; Waples, R.S. Assignment methods: Matching biological questions with appropriate techniques. Trends Ecol. Evol. 2005, 20, 136-142.
51. Waples, R.S.; Gaggiotti, O. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol. Ecol. 2006, 15, 1419-1439.
52. Cruzan, M.B.; Templeton, A.R. Paleoecology and coalescence: Phylogeographic analysis of hypotheses from the fossil record. Trends Ecol. Evol. 2000, 15, 491-496.
53. Hugall, A.; Moritz, C.; Moussalli, A.; Stanisic, J. Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proc. Natl. Acad. Sci. USA 2002, 99, 6112-6117.
54. Carstens, B.C.; Richards, C.L. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 2007, 61, 1439-1454.
55. Excoffier, L.; Heckel, G. Computer programs for population genetics data analysis: A survival guide. Nat. Rev. Genet. 2006, 7, 745-758.
56. Kuhner, M.K. Coalescent genealogy samplers: Windows into population history. Trends Ecol. Evol. 2009, 24, 86-93.
57. Garrick, R.C.; Sunnucks, P. Development and application of three-tiered nuclear genetic markers for basal Hexapods using single-stranded conformation polymorphism coupled with targeted DNA sequencing. BMC Genet. 2006, 7, 11.
58. Stow, A.J.; Sunnucks, P. Briscoe, D.A.; Gardner, M.G. The impact of habitat fragmentation on dispersal in Cunningham's skink (Egernia cunninghami): Evidence from allelic and genotypic analyses of microsatellites. Mol. Ecol. 2001, 10, 867-878.
59. Stow, A.J.; Sunnucks, P. High mate and site fidelity in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat. Mol. Ecol. 2004a, 13, 419-430.
60. Stow, A.J.; Sunnucks, P. Inbreeding avoidance in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat. Mol. Ecol. 2004b, 13, 443-447.
61. Hartl, D.L. Principles of Population Genetics. Sinauer Associates: Sunderland, MA, USA, 1980.
62. Guillot, G.; Estoup, A.; Mortier, F.; Cosson, J.F. A spatial statistical model for landscape genetics. Genetics 2005, 170, 1261-1280.
63. Lancaster, M.L.; Gemmell, N.J.; Negro, S.; Goldsworthy, S.; Sunnucks, P. Ménage à trois on Macquarie Island: Hybridization among three species of fur seal (Arctocephalus spp.) following historical population extinction. Mol. Ecol. 2006, 15, 3681-3692.
64. Ciofi, C.; Wilson, G.A.; Beheregaray, L.B.; Marquez, C.; Gibbs, J.P.; Tapia, W.; Snell, H.L.; Caccone, A.; Powell, J.R. Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela island. Genetics 2006, 172, 1727-1744.
65. Russello, M.A.; Beheregaray, L.B.; Gibbs, J.P.; Fritts, T.; Havill, N.; Powell, J.R.; Caccone, A. Lonesome George is not alone among Galápagos tortoises. Curr. Biol. 2007, 17, R317-R318.
66. Poulakakis, N.; Glaberman, S.; Russello, M.; Beheregaray, L.B.; Ciofi, C.; Powell, J.R.; Caccone, A. Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proc. Natl. Acad. Sci. USA 2008, 105, 15464-15469.
67. Curach, N.; Sunnucks, P. Molecular anatomy of an onychophoran: Compartmentalized sperm storage and heterogeneous paternity. Mol. Ecol. 1999, 8, 1375-1385.
68. Lada, H.; Mac Nally, R.; Taylor, A.C. Distinguishing past from present gene flow along and across a river: The case of the carnivorous marsupial (Antechinus flavipes) on southern Australian floodplains. Cons. Genet. 2008, 9, 569-580.
69. Weir, B.S.; Cockerham, C.C. Estimating F-statistics for the analysis of population structure. Evolution 1984, 38, 1358-1370.
70. Cavalli-Sforza, L.L.; Edwards, A.W.F. Phylogenetic analysis: Models and estimation procedures. Evolution 1967, 21, 550-570.
71. Nei, M. Genetic distance between populations. Am. Nat. 1972, 106, 283-292.
72. Comps, B.; Gömöry, D.; Letouzey, J.; Thiébaut, B.; Petit, R.J. Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics 2001, 157, 389-397.
73. Nason, J.D.; Hamrick, J.L.; Fleming, T.H. Historical vicariance and postglacial colonization effects on the evolution of genetic structure in Lophocereus, a Sonoran Desert columnar cactus. Evolution 2002, 56, 2214-2226.
74. Cornuet, J.M.; Luikart, G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 1996, 144, 2001-2014.
75. Tallmon, D.A.; Koyuk, A.; Luikart, G.; Beaumont, M.A. ONeSAMP: A program to estimate effective population size using approximate Bayesian computation. Mol. Ecol. Res. 2008, 8, 299-301.
76. Dyer, R.J.; Nason, J.D. Population Graphs: The graph theoretic shape of genetic structure. Mol. Ecol. 2004, 13, 1713-1727.
77. Dyer, R.J. The evolution of genetic topologies. Theor. Popul. Biol. 2007, 71, 71-79.
78. Giordano, A.R.; Ridenhour, B.J.; Storfer, A. The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym). Mol. Ecol. 2007, 16, 1625-1637.
79. Rozenfeld, A.F.; Arnaud-Haond, S.; Hernández-García, E.; Eguíluz, V.M.; Serrão, E.A.; Duarte, C.M. Network analysis identifies weak and strong links in a metapopulation system. Proc. Natl. Acad. Sci. USA 2008, 105, 18824-18829.
80. Amos, W.; Manica, A. Global genetic positioning: Evidence for early human population centers in coastal habitats. Proc. Natl. Acad. Sci. USA 2006, 103, 820-824.
81. Cullingham, C.I.; Pond, B.A.; Kyle, C.J.; Rees, E.E.; Rosatte, R.C.; White, B.N. Combining direct and indirect genetic methods to estimate dispersal for informing wildlife disease management decisions. Mol. Ecol. 2008, 17, 4874-4886.
82. Wilding, C.S.; Butlin, R.K.; Grahame, J. Differential gene exchange between parapatric morphs of Littorina saxatilis detected using AFLP markers. J. Evol. Biol. 2001, 14, 611-619.
83. Umina, P.A.; Weeks, A.R.; Kearney, M.R.; McKechnie, S.W.; Hoffmann, A.A. A rapid shift in a classic clinal pattern in Drosophila reflecting climate change. Science 2005, 308, 691-693.
84. Hardy, O.J.; Charbonnel, N.; Freville, H.; Heuertz, M. Microsatellite allele sizes: A simple test to assess their significance on genetic differentiation. Genetics. 2003, 163, 1467-1482.
85. Beckman, J.; Banks, S.C.; Sunnucks, P.; Lill, A.; Taylor, A.C. Phylogeography and environmental correlates of a cap on reproduction: Teat number in a small marsupial. Antechinus agilis. Mol. Ecol. 2007, 16, 1069-1083.
86. Swofford, D.L.; Olsen, G.J.; Waddell, P.J.; Hillis, D.M. Phylogeneic inference. In Molecular Systematics, 2nd ed.; Hillis, D.M., Moritz, C., Mable, B.K., Eds.; Sinauer Associates: Sunderland, MA, USA, 1996; pp. 407-514.
87. Templeton, A.R.; Crandall, K.A.; Sing, C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 1992, 132, 619-633.
88. Bandelt, H.-J.; Forster, P.; Röhl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16, 37-48.
89. Posada, D.; Crandall, K.A. Intraspecific gene genealogies: Trees grafting into networks. Trends Ecol. Evol. 2001, 16, 37-45.
90. Crandall, K.A.; Templeton, A.R. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 1993, 134, 959-969.
91. Pfenninger, M.; Posada, D. Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): Fragmentation, corridor migration, and secondary contact. Evolution 2002, 56, 1776-1788.
92. Excoffier, L.; Smouse, P.E.; Quattro, J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 1992, 131, 479-491.
93. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123, 585-595.
94. Fu, Y.-X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147, 915-925.
95. Beaumont, M.A. Detecting population expansion and decline using microsatellites. Genetics 1999, 153, 2013-2029.
96. Garza, J.C.; Williamson, E.G. Detection of reduction in population size using data from microsatellite loci. Mol. Ecol. 2001, 10, 305-318.
97. Ramos-Onsins, S.E.; Rozas, J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 2002, 19, 2092-2100.
98. Schmuki, C.; Vorburger, C.; Runciman, D.; MacEachern, S.; Sunnucks, P. When log-dwellers meet loggers: Impacts of forest fragmentation on two endemic log-dwelling beetles in southeastern Australia. Mol. Ecol. 2006, 15, 1481-1492.
99. Beheregaray, L.B.; Caccone, A. Cryptic biodiversity in a changing world. J. Biol. 2007, 6, 9.
100. Kuo, C.-H.; Avise, J.C. Phylogeographic breaks in low-dispersal species: The emergence of concordance across gene trees. Genetica 2005, 124, 179-186.
101. Hickerson, M.J.; Dolman, G.; Moritz, C. Comparative phylogeographic summary statistics for testing simultaneous vicariance. Mol. Ecol. 2006a, 15, 209-223.
102. Galbreath K.E; Hafner, D.J.; Zamudio, K.R.; Agnew, K. Isolation and introgression in the Intermountain West: Contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps). J. Biogeog. 2010, 37, 344-362.
103. Hickerson, M.J.; Stahl, E.A.; Lessios, H.A. Test for simultaneous divergence using approximate Bayesian computation. Evolution 2006b, 60, 2435-2453.
104. Leaché, A.D.; Crews, S.C.; Hickerson, M.J. Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis. Biol. Lett. 2007, 3, 646-650.
105. Hickerson, M.J.; Meyer, C.P. Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC Evol. Biol. 2008, 8, 322.
106. Hurt, C.; Anker, A.; Knowlton, N. A multilocus test of simultaneous divergence across the Isthmus of Panama using snapping shrimp in the genus Alpheus. Evolution 2009, 63, 514-530.
107. Templeton, A.R. Statistical hypothesis testing in intraspecific phylogeography: Nested clade phylogeographical analysis vs. approximate Bayesian computation. Mol. Ecol. 2009, 18, 319-331.
108. Lessa, E.P.; Cook, J.A.; Patton, J.L. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc. Natl. Acad. Sci. USA 2003, 100, 10331-10334.
109. Beheregaray, L.B.; Ciofi, C.; Geist, D.; Gibbs, J.P.; Caccone, A.; Powell, J.R. Genes record a prehistoric volcano eruption in the Galápagos. Science 2003, 302, 75.
110. Carstens, B.C.; Stevenson, A.L.; Degenhardt, J.D.; Sullivan, J. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Syst. Biol. 2004, 53, 781-792.
111. Smith, C.I.; Farrell, B.D. Range expansions in the flightless longhorn cactus beetles, Moneilema gigas and Moneilema armatum, in response to Pleistocene climate changes. Mol. Ecol. 2005, 14, 1025-1044.
112. Sunnucks, P.; Blacket, M.J.; Taylor, J.M.; Sands, C.J.; Ciavaglia, S.A.; Garrick, R.C.; Tait, N.N.; Rowell, D.M.; Pavlova, A. A tale of two flatties: Different responses of two terrestrial flatworms to past environmental climatic fluctuations at Tallaganda in montane southeastern Australia. Mol. Ecol. 2006, 15, 4513-4531.
113. Garrick, R.C.; Sands, C.J.; Rowell, D.M.; Hillis, D.M.; Sunnucks, P. Catchments catch all: Longterm population history of a giant springtail from the southeast Australian highlands-a multigene approach. Mol. Ecol. 2007, 16, 1865-1882.
114. Dupanloup, I.; Schneider, S.; Excoffier, L. A simulated annealing approach to define the genetic structure of populations. Mol. Ecol. 2002, 11, 2571-2581.
115. Manni, F.; Guérard, E.; Heyer, E. Geographic patterns of (genetic, morphologic, linguistic) variation: How barriers can be detected by using Monmonier's algorithm. Hum. Biol. 2004, 76, 173-190.
116. Crandall, K.A.; Posada, D.; Vasco, D. Effective population sizes: Missing measures and missing concepts. Anim. Conserv. 1999, 2, 317-319.
117. Rosenberg, N.A.; Tao, R. Discordance of species trees with their most likely gene trees: The case of five taxa. Syst. Biol. 2008, 57, 131-140.
118. Althoff, D.M.; Pellmyr, O. Examining genetic structure in a bogus yucca moth: A sequential approach to phylogeography. Evolution 2002, 56, 1632-1643.
119. Buckley, D. Toward an organismal, integrative, and iterative phylogeography. BioEssays 2009, 31, 784-793.
120. Kingman, J.F.C. The coalescent. Stoch. Proc. Appl. 1982, 13, 235-248.
121. Nordborg, M. Coalescent theory. In Handbook of Statistical Genetics; Balding, D.J., Bishop, M.J., Cannings, C., Eds.; John Wiley and Sons: Chichester, UK, 2001; pp. 213-238.
122. Wakeley, J. The effects of subdivision on the genetic divergence of populations and species. Evolution 2000, 54, 1092-1101.
123. Kuhner, M.K. LAMARC 2.0: Maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 2006, 22, 768-770.
124. Beerli, P. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol. Ecol. 2004, 13, 827-836.
125. Congdon, B.C.; Piatt, J.F.; Martin, K.; Friesen, V.L. Mechanisms of population differentiation in marbled murrelets: Historical versus contemporary processes. Evolution 2000, 54, 974-986.
126. Morando, M.; Avila, L.J.; Baker, J.; Sites, J.W., Jr. Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): Evidence for introgression and incomplete lineage sorting. Evolution 2004, 58, 842-861.
127. Buckley, T.R.; Cordeiro, M.; Marshall, D.C.; Simon, C. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst. Biol. 2006, 55, 411-425.
128. Nielsen, R.; Wakeley, J. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 2001, 158, 885-896.
129. Hey, J.; Nielsen, R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 2007, 104, 2785-2790.
130. Strasburg, J.L.; Rieseberg, L.H. How robust are "Isolation with Migration" analyses to violations of the IM model? A simulation study. Mol. Biol. Evol. 2010, 27, 297-310.
131. Becquet, C.; Przeworski, M. Learning about modes of speciation by computational approaches. Evolution 2009, 63, 2547-2562.
132. Lee, J.Y.; Edwards, S.V. Divergence across Australia's Carpentarian barrier: Statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution 2008, 62, 3117-3134.
133. Dolman, G.; Moritz, C. A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia). Evolution 2006, 60, 573-582.
134. Muster, C.; Maddison, W.P.; Uhlmann, S.; Berendonk, T.U.; Vogler, A.P. Arctic-alpine distributions - Metapopulations on a continental scale? Am. Nat. 2009, 173, 313-326.
135. Garrick, R.C.; Dyer, R.J.; Beheregaray, L.B.; Sunnucks, P. Babies and bathwater: A comment on the premature obituary for nested clade phylogeographical analysis. Mol. Ecol. 2008b, 17, 1401-1403.
136. Jesus, F.F.; Wilkins, J.F.; Solferini, V.N.; Wakeley, J. Expected coalescence times and segregating sites in a model of glacial cycles. Genet. Mol. Res. 2006, 5, 466-474.
137. Anderson, E.C.; Dunham, K.K. The influence of family groups on inferences made with the program Structure. Mol. Ecol. Resour. 2008, 8, 1219-1229.
138. Goldberg, C.S.; Waits, L.P. Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure. Mol. Ecol. Resour. 2010, 10, 304-313.
139. Rosenblum, E.B.; Novembre, J. Ascertainment bias in spatially structured populations: A case study in the Eastern Fence Lizard. J. Hered. 2007, 98, 331-336.
140. Harwood, T.D. The circular definition of populations and its implications for biological sampling. Mol. Ecol. 2009, 18, 765-768.
141. Steele, C.A.; Storfer, A. Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution. Mol. Phylogenet. Evol. 2007, 43, 468-479.
142. Anderson, D.R.; Burnham, K.P.; Thompson, W.L. Null hypothesis testing: Problems, prevalence, and an alternative. J. Wildl. Manage. 2000, 64, 912-923.
143. Anderson, D.R.; Burnham, K.P. Avoiding pitfalls when using information-theoretic methods. J. Wildl. Manage. 2002, 66, 912-918.
144. Johnson, J.B.; Omland, K.S. Model selection in ecology and evolution. Trends Ecol. Evol. 2004, 19, 101-108.
145. Sullivan, J.; Joyce, P. Model selection in phylogenetics. Annu. Rev. Ecol. Evol. Syst. 2005, 36, 445-466.
146. Carstens, B.C.; Stoute, H.N.; Reid, N.M. An information-theoretical approach to phylogeography. Mol. Ecol. 2009, 18, 4270-4282.
147. Beadell, J.S.; Hyseni, C.; Abila, P.; Enyaru, J.C.K.; Ouma, J.; Mohammed, Y.O.; Okedi, L.M.; Aksoy, S.; Caccone, A. Fine-scale population structure of Glossina fuscipes: Implications for control of tsetse in Uganda. PLoS Negl. Trop. Dis. 2010, 4, e636.
148. Lemmon, A.R.; Lemmon, E.M. A likelihood framework for estimating phylogeographic history on a continuous landscape. Syst. Biol. 2008, 57, 544-561.
149. Edwards, D.L.; Roberts, J.D.; Keogh, J.S. Climatic fluctuations shape the phylogeography of a mesic direct-developing frog from the south-western Australian biodiversity hotspot. J. Biogeogr. 2008, 35, 1803-1815.
150. Garrick, R.C.; Sands, C.J.; Rowell, D.M.; Tait, N.N.; Greenslade, P.; Sunnucks, P. Phylogeography recapitulates topography: Very fine-scale local endemism of a saproxylic 'giant' springtail at Tallaganda in the Great Dividing Range of south-east Australia. Mol. Ecol. 2004, 13, 3329-3344.
151. Caccone, A.; Sbordoni, V. Molecular biogeography of cave life: A study using mitochondrial DNA from Bathysciine beetles. Evolution 2001, 55, 122-130.
152. Ketmaier, V.; Argano, R.; Caccone, A. Phylogeography and molecular rates of subterranean aquatic Stenasellid Isopods with a peri-Tyrrhenian distribution. Mol. Ecol. 2003, 12, 547-555.
153. Beheregaray, L.B.; Gibbs, J.P.; Havill, N.; Fritts, T.H.; Powell, J.R.; Caccone, A. Giant tortoises are not so slow: Rapid diversification and biogeographic consensus in the Galápagos. Proc. Natl. Acad. Sci. USA 2004, 101, 6514-6519.
154. Strasburg, J.L.; Kearney, M.; Moritz, C.; Templeton, A.R. Integrating phylogeography with distribution modeling: Multiple Pleistocene range expansions in a parthenogenetic gecko. PLoS ONE 2007, 2, e760.
155. Gifford, M.E.; Larson, A. In situ genetic differentiation in a Hispaniolan lizard (Ameiva chrysolaema): A multilocus perspective. Mol. Phylogenet. Evol. 2008, 49, 277-291.
156. Kearney, M.; Blacket, M.J. The evolution of sexual and parthenogenetic Warramaba: A window onto Plio-Pleistocene diversification processes in an arid biome. Mol. Ecol. 2008, 17, 5257-5275.
157. DeChaine, E.G.; Martin, A.P. Historic cycles of fragmentation and expansion in Parnassius smintheus (Papilionidae) inferred using mitochondrial DNA. Evolution 2004, 58, 113-127.
158. DeChaine, E.G.; Martin, A.P. Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains. Am. J. Bot. 2005, 92, 477-486.
159. Caccone, A.; Milinkovitch, M.C.; Sbordoni, V.; Powell, J.R. Mitochondrial DNA rates and biogeography in European newts (genus Euproctus). Syst. Biol. 1997, 46, 126-144.
160. Phillips, B.L.; Baird, S.J.E.; Moritz, C. When vicars meet: A narrow contact zone between morphologically cryptic phylogeographic lineages of the rainforest skink, Carlia rubrigularis. Evolution 2004, 58, 1536-1548.
161. Zamudio, K.R.; Savage, W.K. Historical isolation, range expansion, and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum). Evolution 2003, 57, 1631-1652.
162. Huelsenbeck, J.P.; Hillis, D.M.; Jones, R. Parametric bootstrapping in molecular phylogenetics: Applications and performance. In Molecular Zoology: Advances, Strategies and Protocols; Ferraris, J.D., Palumbi, S.R., Eds.; Wiley-Liss: New York, NY, USA, 1996; pp. 19-45.
163. Sullivan, J.; Arellano, E.; Rogers, D.S. Comparative phylogeography of Mesoamerican highland rodents: Concerted versus independent response to past climatic fluctuations. Am. Nat. 2000, 155, 755-768.
164. Jacquez, G.M. The map comparison problem: Tests for the overlap of geographic boundaries. Stat. Med. 1995, 14, 2343-2361.
165. Sun, J.X.; Mullikin, J.C.; Patterson, N.; Reich, D.E. Microsatellites are molecular clocks that support accurate inferences about history. Mol. Biol. Evol. 2009, 26, 1017-1027.
166. Excoffier, L. Patterns of DNA sequence diversity and genetic structure after a range expansion: Lessons from the infinite-island model. Mol. Ecol. 2004, 13, 853-864.
167. Wegmann, D.; Currat, M.; Excoffier, L. Molecular diversity after a range expansion in heterogeneous environments. Genetics 2006, 174, 2009-2020.
168. Benavides, E.; Baum, R.; Snell, H.M.; Snell, H.L.; Sites, J.W., Jr. Island biogeography of Galápagos lava lizards (Tropiduridae: Microlophus): Species diversity and colonization of the archipelago. Evolution 2009, 63, 1606-1626.
169. Ho, S.Y.W.; Phillips, M.J.; Cooper, A.; Drummond, A.J. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 2005, 22, 1561-1568.
170. Burridge, C.P.; Craw, D.; Fletcher, D.; Waters, J.M. Geological dates and molecular rates: Fish DNA sheds light on time dependency. Mol. Biol. Evol. 2008, 25, 624-633.
171. Excoffier, L.; Ray, N. Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol. Evol. 2008, 23, 347-351.
172. Beheregaray, L.B. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Mol. Ecol. 2008, 17, 3754-3774.
173. Wiedmann, R.T.; Smith, T.P.L.; Nonneman, D.J. SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genet. 2008, 9, 81.
174. Sunnucks, P.; Wilson, A.C.C.; Beheregaray, L.B.; Zenger, K.; French, J.; Taylor, A.C. SSCP is not so difficult: The application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol. Ecol. 2000, 9, 1699-1710.
175. Stephens, M.; Smith, N.J.; Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 2001, 68, 978-989.
176. Svensson, E.M.; Anderung, C.; Baubliene, J.; Persson, P.; Malmström, H.; Smith, C.; Vretemark, M.; Daugnora, L.; Götherström, A. Tracing genetic change over time using nuclear SNPs in ancient and modern cattle. Anim. Genet. 2007, 38, 378-383.
177. Allentoft, M.E.; Schuster, S.C.; Holdaway, R.N.; Hale, M.L.; McLay, E.; Oskam, C.; Gilbert, M.T.P.; Spencer, P.; Willerslev, E.; Bunce, M. Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. Biotechniques 2009, 46, 195-200.
178. Symula, R.; Schulte, R.; Summers, K. Molecular phylogenetic evidence for a mimetic radiation in Peruvian poison frogs supports a Müllerian mimicry hypothesis. Proc. R. Soc. Lond. B: Biol. Sci. 2001, 268, 2415-2421.
179. Hillis, D.M.; Huelsenbeck, J.P. Support for dental HIV transmission. Nature 1994, 369, 24-25.
180. Godinho, R.; Mendonca, B.; Crespo, E.G.; Ferrand, N. Genealogy of the nuclear β-fibrinogen locus in a highly structured lizard species: Comparison with mtDNA and evidence for intragenic recombination in the hybrid zone. Heredity 2006, 96, 454-463.
181. Vaughan, I.P.; Ormerod, S.J. Improving the quality of distribution models for conservation by addressing shortcomings in the field collection of training data. Conserv. Biol. 2003, 17, 1601-1611.
182. McPherson, J.M.; Jetz, W.; Rogers, D.J. Using coarse-grained occurrence data to predict species distributions at finer spatial resolutions-possibilities and limitations. Ecol. Modell. 2006, 192, 499-522.
183. Moya, O.; Contreras-Díaz, H.G.; Oromí, P.; Juan, C. Phylogeography of a ground beetle species in La Gomera (Canary Islands): The effects of landscape topology and population history. Heredity 2007, 99, 322-330.
184. Eckert, A.J.; Carstens, B.C. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 2008, 49, 832-842.
185. McRae, B.H. Isolation by resistance. Evolution 2006, 60, 1551-1561.
186. Zellmer, A.J.; Knowles, L.L. Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence. Mol. Ecol. 2009, 18, 3593-3602.
187. Lee-Yaw, J.A.; Davidson, A.; McRae, B.H.; Green, D.M. Do landscape processes predict phylogeographic patterns in the wood frog? Mol. Ecol. 2009, 18, 1863-1874.
188. Kearney, M.; Porter, W. Mechanistic niche modelling: Combining physiological and spatial data to predict species' ranges. Ecol. Lett. 2009, 12, 334-350.
189. Rosauer, D.; Laffan, S.W.; Crisp, M.D.; Donnellan, S.C.; Cook, L.G. Phylogenetic endemism: A new approach for identifying geographical concentrations of evolutionary history. Mol. Ecol. 2009, 18, 4061-4072.
190. Havill, N.P.; Montgomery, M.E.; Yu, G.; Shiyake, S.; Caccone, A. Mitochondrial DNA from hemlock woolly adelgid (Hemiptera: Adelgidae) suggests cryptic speciation and pinpoints the source of the introduction to eastern North America. Ann. Entomol. Soc. Am. 2006, 99, 195-203.
191. Goldstein, D.B.; Ruiz Linares, A.; Cavalli-Sforza, L.L.; Feldman, M.W. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA 1995, 92, 6723-6727.
192. Zhivotovsky, L.A. Estimating divergence time with the use of microsatellite genetic distances: Impacts of population growth and gene flow. Mol. Biol. Evol. 2001, 18, 700-709.
193. Knowles, L.L. Statistical Phylogeography. Annu. Rev. Ecol. Evol. Syst. 2009, 40, 593-612.
194. Kerstens, H.H.D.; Crooijmans, R.P.M.A.; Veenendaal, A.; Dibbits, B.W.; Chin-A-Woeng, T.F.C.; den Dunnen, J.T.; Groenen, M.A.M. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: Applied to Turkey. BMC Genomics 2009, 10, 479.
195. Rasmussen, D.A.; Noor, M.A.F. What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics 2009, 10, 382.
196. Caccone, A.; Gentile, G.; Burns, C.E.; Sezzi, E.; Bergman, W.; Ruelle, M.; Saltonstall, K.; Powell, J.R. Extreme difference in rate of mitochondrial and nuclear DNA evolution in a large ectotherm, Galápagos tortoises. Mol. Phylogenet. Evol. 2004, 31, 794-798.
197. Wiedmann, R.T.; Smith, T.P.L.; Nonneman, D.J. SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genet. 2008, 9, 81.