Erratum: Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades (Systematic Biology 63 (951-970) 10.1093/sysbio/syu056));Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades

Systematic Biology

Volumn 63, Issue 6, 2014, Pages 951-970

  Matzke, Nicholas J ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; FOUNDER EFFECT; PHYLOGENY; PHYLOGEOGRAPHY; PROCEDURES; PSYCHOTRIA; REPRODUCIBILITY; SPECIES DIFFERENTIATION;

COMPUTER SIMULATION; FOUNDER EFFECT; GENETIC SPECIATION; MODELS, BIOLOGICAL; PHYLOGENY; PHYLOGEOGRAPHY; PSYCHOTRIA; REPRODUCIBILITY OF RESULTS;

EID: 84921863746     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu091     Document Type: Erratum

References (78)

1. Baldwin B.G., Sanderson M.J. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc. Nat. Acad. Sci., 95:9402-9406.
2. Benavides E., Baum R., Snell H.M., Snell H.L., Sites J.W. 2009. Island biogeography of galápagos lava Lizards (Tropiduridae: Microlophus): species diversity and colonization of the Archipelago. Evolution, 63:1606-1626.
3. Bennett G.M., O'Grady P.M. 2013. Historical biogeography and ecological opportunity in the adaptive radiation of native Hawaiian leafhoppers (Cicadellidae: Nesophrosyne). J. Biogeogr., 40:1512-1523.
4. Box G.E.P., Draper N.R. 1987. Empirical model-building and response surfaces. New York (NY): Wiley.
5. Bremer K. 1992. Ancestral areas: a cladistic reinterpretation of the center of origin concept. Syst. Biol. 41:436-445.
6. Buerki S., Forest F., Alvarez N., Nylander J.A.A., Arrigo N., Sanmartín I. 2011. An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae. J. Biogeogr. 38:531-550.
7. nd ed. New York (NY): Springer.
8. Byrd R.H., Lu P., Nocedal J., Zhu C. 1995. A limited memory algorithmfor bound constrained optimization. SIAMJ. Sci. Comput. 16:1190-1208.
9. Carlquist S.J. 1974. Island biology. New York (NY): Columbia University Press.
10. Carson H.L., Templeton A.R. 1984. Genetic revolutions in relation to speciation phenomena: the founding of new populations. Annu. Rev. Ecol. Syst. 15:97-131.
11. Clague D.A. 1996. The growth and subsidence of the Hawaiian-Emperor volcanic chain. In: Keast A., Miller S.E., editors. The origin and evolution of Pacific Island Biotas, New Guinea to Eastern Polynesia: patterns and processes. Amsterdam: SPB Academic Publishing. p. 35-50.
12. Clark J.R., Ree R.H., Alfaro M.E., King M.G., Wagner W.L., Roalson E.H. 2008. A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages. Syst. Biol. 57:693-707.
13. Clark JR, Wagner WL, Roalson EH. 2009. Patterns of diversification and ancestral range reconstruction in the southeast Asian-Pacific angiosperm lineage Cyrtandra (Gesneriaceae). Mol. Phylogenet. Evol., 53:982-994.
14. Cowie R.H., Holland B.S. 2006. Dispersal is fundamental to biogeography and the evolution of biodiversity on oceanic islands. J. Biogeogr. 33:193-198.
15. Coyne J.A., Orr H.A. 2004. Speciation. Sunderland (MA): Sinauer Associates.
16. Davis M.P., Midford P.E., Maddison W. 2013. Exploring power and parameter estimation of the BiSSE method for analyzing species diversification. BMC Evol. Biol. 13:38.
17. de Queiroz A. 2005. The resurrection of oceanic dispersal in historical biogeography. Trends Ecol. Evol. 20:68-73.
18. Dunbar-Co S. 2008. Island evolution: phylogeny, adaptive radiation, and biogeography of Plantago (Plantaginaceae) in the Hawaiian Islands. Ph.D., University of Hawai'i.
19. de Queiroz A. 2014. The monkey's voyage: how improbable journeys shaped the history of life. New York (NY): Basic Books.
20. Eddelbuettel D, Francois R. 2013. Rcpp: Seamless R and C++ Integration, CRAN: The Comprehensive R Archive Network, Vienna, Austria. http://cran.r-project.org/package=Rcpp, (last accessed August 7, 2014).
21. Escoto B. 2011. Marginal likelihood computation via arrogance sampling. arXiv.org:1-12.
22. Felsenstein J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35:1229-1242.
23. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
24. FitzJohn R.G. 2012. Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol. Evol. 3:1084-1092.
25. Gillespie R.G., Baldwin B.G. 2010. Island biogeography of remote archipelagos: Interplay between ecological and evolutionary processes. In: Losos J.B., Ricklefs R.E., MacArthur R.H., editors. The theory of island biogeography revisited. Princeton, Princeton University Press, p. 358-387.
26. Gillespie R.G., Baldwin B.G., Waters J.M., Fraser C.I., Nikula R., Roderick G.K. 2012. Long-distance dispersal: a framework for hypothesis testing. Trends Ecol. Evol. 27:47-56.
27. Goldberg E.E., Igi?c B. 2012. Tempo and mode in plant breeding system evolution. Evolution 66:3701-3709.
28. Goldberg E.E., Lancaster L.T., Ree R.H. 2011. Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Syst. Biol. 60:451-465.
29. Gould S.J., Eldredge N. 1972. Punctuated equilibria: an alternative to phyletic gradualism. In: Thomas J. M. Schopf, editor., Models in paleobiology. San Francisco: Freeman & Cooper, p. 82-115.
30. Green P.J. 1995. Reversible jump Markov Chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732.
31. Harmon L.J., Weir J.T., Brock C.D., Glor R.E., Challenger W. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.
32. Heads M.J. 2012. Molecular panbiogeography of the tropics. Berkeley: University of California Press.
33. Hormiga G., Arnedo M., Gillespie R.G. 2003. Speciation on a conveyor belt: sequential colonization of the Hawaiian Islands by Orsonwelles Spiders (Araneae, Linyphiidae). Syst. Biol., 52:70-88.
34. Huelsenbeck J.P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
35. Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
36. Jordan S., Simon C., Polhemus D. 2003. Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus megalagrion (Odonata: Coenagrionidae). Syst. Biol., 52:89-109.
37. Kambysellis M.P., Ho K.-F., Craddock E.M., Piano F., Parisi M., Cohen J. 1995. Pattern of ecological shifts in the diversification of Hawaiian Drosophila inferred from a molecular phylogeny. Curr. Biol. 5:1129-1139.
38. Kodandaramaiah U. 2010. Use of dispersal-vicariance analysis in biogeography - a critique. J. Biogeogr. 37:3-11.
39. Landis M., Matzke N.J., Moore B.R., Huelsenbeck J.P. 2013. Bayesian analysis of biogeography when the number of areas is large. Syst. Biol. 62(6): 789-804.
40. Lapoint R.T., O'Grady P.M., Whiteman N.K. 2013. Diversification and dispersal of the Hawaiian Drosophilidae: the evolution of Scaptomyza. Mol. Phylogenet. Evol. 69:95-108.
41. Lerner H.R.L., Meyer M., James H.F., Hofreiter M., Fleischer R.C. 2011. Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian Honeycreepers. Curr. Biol., 21:1838-1844.
42. Link W.A., Barker R.J. 2009. Bayesian inference: with ecological applications. Boston: Elsevier/Academic.
43. th ed. Sunderland (MA): Sinauer Associates.
44. Maguire K.C., Stigall A.L. 2008. Paleobiogeography of miocene equinae of North America: a phylogenetic biogeographic analysis of the relative roles of climate, vicariance, and dispersal. Palaeogeogr. Palaeoclimatol. Palaeoecol. 267:175-184.
45. Matos-Maraví P.F., Peña C., Willmott K.R., Freitas A.V.L., Wahlberg N. 2013. Systematics and evolutionary history of butterflies in the "Taygetis clade" (Nymphalidae: Satyrinae: Euptychiina): towards a better understanding of Neotropical biogeography. Mol. Phylogenet. Evol. 66:54-68.
46. Matzke N.J. 2013a. BioGeoBEARS: BioGeography with Bayesian (and likelihood) evolutionary analysis in R Scripts, CRAN: The Comprehensive R Archive Network, Vienna, Austria. http://cran.r-project.org/package=BioGeoBEARS (last accessed August 7, 2014).
47. Matzke N.J. 2013b. cladoRcpp: C++ implementations of phylogenetic calculations, CRAN: The Comprehensive R Archive Network, Vienna, Austria. http://cran.r-project.org/package=cladoRcpp (last accessed August 7, 2014).
48. Matzke N.J. 2013c. TreeRogue: R code for digitizing trees. https://stat.ethz.ch/pipermail/r-sig-phylo/2010-October/000816.html (last accessed August 7, 2014).
49. Matzke N.J., Sidje R.B. 2013. rexpokit: R wrappers for EXPOKIT; other matrix functions, CRAN: The Comprehensive R Archive Network, Vienna, Austria. http://cran.r-project.org/package=rexpokit (last accessed August 7, 2014).
50. Mayr E. 1954. Change of genetic environment and evolution. In: Huxley J., Hardy A.C., Ford E.B., editors. Evolution as a process. London: Allen & Unwin. p. 157-180.
51. Moler C., Van Loan C. 2003. Nineteen dubious ways to compute the exponential of a matrix, twenty-five years later. SIAM Rev. 45:3-49.
52. Mooers A. 2004. Effects of tree shape on the accuracy of maximum likelihood-based ancestor reconstructions. Syst. Biol. 53: 809-814.
53. Mooers A., Schluter D. 1999. Reconstructing ancestor states with maximum likelihood: support for one-and two-rate models. Syst. Biol. 48:623-633.
54. Nash J.C., Varadhan R. 2011. Unifying optimization algorithms to aid software system users: optimx for R. J. Stat. Softw. 43:1-14.
55. Nash J.C., Varadhan R. 2012. optimx: a replacement and extension of the optim() function, CRAN: The Comprehensive R Archive Network, Vienna, Austria. http://cran.r-project.org/package=optimx (last accessed August 7, 2014).
56. Nepokroeff M., Sytsma K.J., Wagner W.L., Zimmer E.A. 2003. Reconstructing ancestral patterns of colonization and dispersal in the Hawaiian understory tree genus Psychotria (Rubiaceae): a comparison of parsimony and likelihood approaches. Syst. Biol. 52:820-838.
57. Nicholson K.E., Crother B.I., Guyer C., Savage J.M. 2012. It is time for a newclassification of anoles (Squamata: Dactyloidae). Zootaxa, 3477:1-108.
58. Paulay G., Meyer C. 2002. Diversification in the tropical pacific: comparisons between marine and terrestrial systems and the importance of founder speciation. Integr. Comp. Biol. 42: 922-934.
59. Posada D., Crandall K.A. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50:580-601.
60. Pyron R.A. 2014. Biogeographic analysis reveals ancient continental vicariance and recent oceanic dispersal in amphibians. Syst. Biol. Available online 19 June 2014.
61. Ree R.H. 2013. Lagrange configurator version 20130526 (beta). http://www.reelab.net/lagrange/configurator/index (last accessed August 7, 2014).
62. Ree R.H., Sanmartín I. 2009. Prospects and challenges for parametric models in historical biogeographical inference. J. Biogeogr. 36:1211-1220.
63. Ree R.H., Smith S.A. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 57:4-14.
64. Ree R.H., Moore B.R., Webb C.O., Donoghue M.J. 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59:2299-2311.
65. Ronquist F. 1997. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst. Biol. 46:195-203.
66. Ronquist F., Sanmartín I. 2011. Phylogenetic methods in biogeography. Annu. Rev. Ecol. Evol. Syst. 42:441-464.
67. Sanderson M.J. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of amolecular clock. Bioinformatics 19:301-302.
68. Sanmartín I. 2012. Historical biogeography: evolution in time and space. Evo. Edu. Outreach. 5:555-568.
69. Santos C.M.D. 2007. On basal clades and ancestral areas. J. Biogeogr. 34:1470-1469.
70. Sidje R.B. 1998. Expokit: a software package for computing matrix exponentials. ACM Trans. Math. Softw. 24:130-156.
71. Smith S.A., Donoghue, M.J. 2010. Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales). Syst. Biol. 59:322-341.
72. Smith S.A., Ree R.H. 2010. Lagrange: likelihood analysis of geographic range evolution, https://code.google.com/p/lagrange/ (last accessed August 7, 2014).
73. Statisticat L. 2013a. LaplacesDemon Tutorial. Statisticat, Hot Springs, South Dakota. http://www.bayesian-inference.com/softwaredownload (last accessed August 7, 2014).
74. Statisticat L. 2013b. LaplacesDemon: complete environment for Bayesian inference. Statisticat, Hot Springs, South Dakota. http://www.bayesian-inference.com/softwaredownload (last accessed August 7, 2014).
75. Templeton A.R. 2008. The reality and importance of founder speciation in evolution. BioEssays 30:470-479.
76. Waters J.M., Trewick S.A., Paterson A.M., Spencer H.G., Kennedy M., Craw D., Burridge C.P., Wallis G.P. 2013. Biogeography off the tracks. Syst. Biol. 62:494-498.
77. Webb C.O., Ree R.H. 2012. Historical biogeography inference in Malesia. In: Gower D., Johnson K., Richardson J., Rosen B., Ruber L., Williams S. editors. Biotic evolution and environmental change in Southeast Asia. Cambridge, Cambridge University Press, p. 191-215.
78. Wiley E.O. 1981. Phylogenetics: the theory and practice of phylogenetic systematics. New York (NY): Wiley.