메뉴 건너뛰기




Volumn 68, Issue 1, 2014, Pages 284-294

Recommendations for using msbayes to incorporate uncertainty in selecting an abc model prior: A response to oaks et al.

Author keywords

Approximate Bayesian computation; Mis specification; MsBayes; Prior; Synchronous divergence

Indexed keywords

BAYESIAN ANALYSIS; COMPARATIVE STUDY; ECOLOGICAL MODELING; SAMPLER; SAMPLING; UNCERTAINTY ANALYSIS; VERTEBRATE;

EID: 84890887584     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12241     Document Type: Article
Times cited : (29)

References (44)
  • 1
    • 0036909632 scopus 로고    scopus 로고
    • Estimating divergence times from molecular data on phylogenetic and population genetic timescales
    • Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli, and J. B. Slowinski 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Ann. Rev. Ecol. Syst. 33:707-740.
    • (2002) Ann. Rev. Ecol. Syst. , vol.33 , pp. 707-740
    • Arbogast, B.S.1    Edwards, S.V.2    Wakeley, J.3    Beerli, P.4    Slowinski, J.B.5
  • 2
    • 77956944519 scopus 로고    scopus 로고
    • Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna
    • Barber, B. R., and J. Klicka 2010. Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna. Proc. R. Soc. B: Biol. Sci. 1694:2675-2681.
    • (2010) Proc. R. Soc. B: Biol. Sci. , vol.1694 , pp. 2675-2681
    • Barber, B.R.1    Klicka, J.2
  • 3
    • 77956397064 scopus 로고    scopus 로고
    • A new model for extinction and recolonization in two dimensions: quantifying phylogeography
    • Barton, N. H., J. Kelleher, and A. M. Etheridge 2010. A new model for extinction and recolonization in two dimensions: quantifying phylogeography. Evolution 64:2701-2715.
    • (2010) Evolution , vol.64 , pp. 2701-2715
    • Barton, N.H.1    Kelleher, J.2    Etheridge, A.M.3
  • 4
    • 84890862957 scopus 로고    scopus 로고
    • Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model
    • Bazin, E., K. J. Dawson, and M. A. Beaumont 2010. Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model. Genet. Genet. 109:112391.
    • (2010) Genet. Genet , vol.109 , pp. 112391
    • Bazin, E.1    Dawson, K.J.2    Beaumont, M.A.3
  • 5
    • 78149388939 scopus 로고    scopus 로고
    • Approximate Bayesian computation in evolution and ecology
    • Beaumont, M. A. 2010. Approximate Bayesian computation in evolution and ecology. Ann. Rev. Ecol. Evol. Syst. 41:379-406.
    • (2010) Ann. Rev. Ecol. Evol. Syst. , vol.41 , pp. 379-406
    • Beaumont, M.A.1
  • 7
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont, M. A., W. Zhang, and D. J. Balding 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 9
    • 77954247262 scopus 로고    scopus 로고
    • ABC as a flexible framework to estimate demography over space and time: some cons, many pros
    • Bertorelle, G., A. Benazzo, and S. Mona 2010. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol. Ecol. 19:2609-2625.
    • (2010) Mol. Ecol. , vol.19 , pp. 2609-2625
    • Bertorelle, G.1    Benazzo, A.2    Mona, S.3
  • 10
    • 73549122582 scopus 로고    scopus 로고
    • Non-linear regression models for Approximate Bayesian Computation
    • Blum, M. G. B., and O. François 2010. Non-linear regression models for Approximate Bayesian Computation. Stat. Comput. 20:63-73.
    • (2010) Stat. Comput. , vol.20 , pp. 63-73
    • Blum, M.G.B.1    François, O.2
  • 11
    • 0003100554 scopus 로고
    • Robustness in the strategy of scientific model building
    • In R. L. Launer and G. Wilkinson, eds. Academic Press, New York.
    • Box, G. E. P. 1979. Robustness in the strategy of scientific model building. In R. L. Launer and G. Wilkinson, eds. Robustness in statistics. Academic Press, New York.
    • (1979) Robustness in statistics
    • Box, G.E.P.1
  • 12
    • 59849093347 scopus 로고    scopus 로고
    • Stability predicts genetic diversity in the Brazilian Atlantic Forest Hotspot
    • Carnaval, A., M. J. Hickerson, C. F. B. Haddad, M. T. Rodrigues, and C. Moritz 2009. Stability predicts genetic diversity in the Brazilian Atlantic Forest Hotspot. Science 323:785-789.
    • (2009) Science , vol.323 , pp. 785-789
    • Carnaval, A.1    Hickerson, M.J.2    Haddad, C.F.B.3    Rodrigues, M.T.4    Moritz, C.5
  • 13
    • 79955085425 scopus 로고    scopus 로고
    • Integrating statistical genetic and geospatial methods brings new power to phylogeography
    • Chan, Y. M., J. L. Brown, and A. D. Yoder 2011. Integrating statistical genetic and geospatial methods brings new power to phylogeography. Mol. Phylogenet. Evol. 59:523-537.
    • (2011) Mol. Phylogenet. Evol. , vol.59 , pp. 523-537
    • Chan, Y.M.1    Brown, J.L.2    Yoder, A.D.3
  • 14
    • 0042306266 scopus 로고    scopus 로고
    • The Practical implementation of Bayesian model selection
    • in Lahiri, ed. Vol. Institute of Mathematical Statistics, Beachwood, OH.
    • Chipman, H., E. George, and R. E. McCulloch 2001. The Practical implementation of Bayesian model selection. Pp. 65-134 in P. Lahiri, ed. IMS lecture notes-monograph series. Vol. 38. Institute of Mathematical Statistics, Beachwood, OH.
    • (2001) IMS lecture notes-monograph series , vol.38 , pp. 65-134
    • Chipman, H.1    George, E.2    McCulloch, R.E.3
  • 15
    • 33749668496 scopus 로고    scopus 로고
    • Validation of software for Bayesian models using posterior quantiles
    • Cook, S. R., A. Gelman, and D. B. Rubin 2006. Validation of software for Bayesian models using posterior quantiles. J. Comput. Graphical Stat. 15:675-692.
    • (2006) J. Comput. Graphical Stat. , vol.15 , pp. 675-692
    • Cook, S.R.1    Gelman, A.2    Rubin, D.B.3
  • 16
    • 77955493069 scopus 로고    scopus 로고
    • Inference on population history and model checking using DNA sequence and micro-satellite data with the software DIYABC(v1.0)
    • Cornuet, J.-M., V. Ravigné, and A. Estoup 2010. Inference on population history and model checking using DNA sequence and micro-satellite data with the software DIYABC(v1.0). BMC Bioinform. 11:401.
    • (2010) BMC Bioinform. , vol.11 , pp. 401
    • Cornuet, J.-M.1    Ravigné, V.2    Estoup, A.3
  • 18
    • 38649110663 scopus 로고    scopus 로고
    • Bayesian evolutionary analysis by sampling trees
    • Drummond, A. J., and A. Rambaut 2007. Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 19
    • 0034496840 scopus 로고    scopus 로고
    • Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
    • Edwards, S. V., and P. Beerli 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
    • (2000) Evolution , vol.54 , pp. 1839-1854
    • Edwards, S.V.1    Beerli, P.2
  • 20
    • 33646556408 scopus 로고    scopus 로고
    • Spatial modelling of biodiversity at the community level
    • Ferrier, S., and A. Guisan 2006. Spatial modelling of biodiversity at the community level. J. Appl. Ecol. 43:393-404.
    • (2006) J. Appl. Ecol. , vol.43 , pp. 393-404
    • Ferrier, S.1    Guisan, A.2
  • 22
    • 58149314233 scopus 로고    scopus 로고
    • Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach
    • Hickerson, M. J., and C. Meyer 2008. Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC Evol. Biol. 8:322.
    • (2008) BMC Evol. Biol. , vol.8 , pp. 322
    • Hickerson, M.J.1    Meyer, C.2
  • 23
    • 0242499432 scopus 로고    scopus 로고
    • Calibrating a molecular clock from phylogeographic data: moments and likelihood estimators
    • Hickerson, M. J., M. Gilchrist, and N. Takebayashi 2003. Calibrating a molecular clock from phylogeographic data: moments and likelihood estimators. Evolution 57:2216-2225.
    • (2003) Evolution , vol.57 , pp. 2216-2225
    • Hickerson, M.J.1    Gilchrist, M.2    Takebayashi, N.3
  • 24
    • 33645076038 scopus 로고    scopus 로고
    • Comparative phylogeographic summary statistics for testing simultaneous vicariance across taxon-pairs
    • Hickerson, M. J., G. Dolman, and C. Moritz 2006a. Comparative phylogeographic summary statistics for testing simultaneous vicariance across taxon-pairs. Mol. Ecol. 15:209-224.
    • (2006) Mol. Ecol. , vol.15 , pp. 209-224
    • Hickerson, M.J.1    Dolman, G.2    Moritz, C.3
  • 25
    • 33846875227 scopus 로고    scopus 로고
    • Test for simultaneous divergence using Approximate Bayesian computation
    • Hickerson, M. J., E. Stahl, and H. A. Lessios 2006b. Test for simultaneous divergence using Approximate Bayesian computation. Evolution 60:2435-2453.
    • (2006) Evolution , vol.60 , pp. 2435-2453
    • Hickerson, M.J.1    Stahl, E.2    Lessios, H.A.3
  • 26
    • 34548065664 scopus 로고    scopus 로고
    • msBayes: pipeline for testing comparative phylogeographic histories using hierarchical Approximate Bayesian computation
    • Hickerson, M. J., E. Stahl, and N. Takebayashi 2007. msBayes: pipeline for testing comparative phylogeographic histories using hierarchical Approximate Bayesian computation. BMC Bioinformatics 8:268.
    • (2007) BMC Bioinformatics , vol.8 , pp. 268
    • Hickerson, M.J.1    Stahl, E.2    Takebayashi, N.3
  • 27
    • 78650725611 scopus 로고    scopus 로고
    • MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity
    • Huang, W., Y. Qi, N. Takebayashi, and M. J. Hickerson 2011. MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. BMC Bioinform. 12:1.
    • (2011) BMC Bioinform. , vol.12 , pp. 1
    • Huang, W.1    Qi, Y.2    Takebayashi, N.3    Hickerson, M.J.4
  • 28
    • 78649302845 scopus 로고    scopus 로고
    • Inference of assemblage-level demographic histories of the North Atlantic intertidal
    • Ilves, K., W. Huang, J. Wares, and M. J. Hickerson 2010. Inference of assemblage-level demographic histories of the North Atlantic intertidal. Mol. Ecol. 19:4505-4519.
    • (2010) Mol. Ecol. , vol.19 , pp. 4505-4519
    • Ilves, K.1    Huang, W.2    Wares, J.3    Hickerson, M.J.4
  • 30
    • 77956572312 scopus 로고    scopus 로고
    • The discordance of diversification: evolution in the tropical-montane frogs of the Eastern Arc Mountains of Tanzania
    • Lawson, L. P. 2010. The discordance of diversification: evolution in the tropical-montane frogs of the Eastern Arc Mountains of Tanzania. Mol. Ecol. 19:4046-4060.
    • (2010) Mol. Ecol. , vol.19 , pp. 4046-4060
    • Lawson, L.P.1
  • 31
    • 37249005725 scopus 로고    scopus 로고
    • Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis
    • Leaché, A., S. A. Crews, and M. J. Hickerson 2007. Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis. Biol. Lett. 3:646-650.
    • (2007) Biol. Lett. , vol.3 , pp. 646-650
    • Leaché, A.1    Crews, S.A.2    Hickerson, M.J.3
  • 32
    • 0000810338 scopus 로고
    • A statistical paradox
    • Lindley, D. V. 1957. A statistical paradox. Biometrika 44:187-192.
    • (1957) Biometrika , vol.44 , pp. 187-192
    • Lindley, D.V.1
  • 33
    • 84875812122 scopus 로고    scopus 로고
    • Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events
    • Oaks, J. R., J. Sukumaran, J. A. Esselstyn, C. W. Linkem, C. D. Siler, M. T. Holder, and R. M. Brown 2012. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution 67:991-1010.
    • (2012) Evolution , vol.67 , pp. 991-1010
    • Oaks, J.R.1    Sukumaran, J.2    Esselstyn, J.A.3    Linkem, C.W.4    Siler, C.D.5    Holder, M.T.6    Brown, R.M.7
  • 34
    • 67649819681 scopus 로고    scopus 로고
    • Model criticism based on likelihood-free inference, with an application to protein network evolution
    • Ratmann, O., C. Andrieu, C. Wiuf, and S. Richardson 2009. Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc. Natl. Acad. Sci. 106:10576-10581.
    • (2009) Proc. Natl. Acad. Sci. , vol.106 , pp. 10576-10581
    • Ratmann, O.1    Andrieu, C.2    Wiuf, C.3    Richardson, S.4
  • 35
    • 0011890988 scopus 로고
    • A note on Jeffreys-Lindley paradox
    • Robert, C. 1993. A note on Jeffreys-Lindley paradox. Stat. Sin. 3:601-608.
    • (1993) Stat. Sin , vol.3 , pp. 601-608
    • Robert, C.1
  • 36
    • 80053069153 scopus 로고    scopus 로고
    • Lack of confidence in Approximate Bayesian computation model choice
    • Robert, C. P., J.-M. Cornuet, J.-M. Marin, and N. S. Pillai 2011. Lack of confidence in Approximate Bayesian computation model choice. Proc. Natl. Acad. Sci. 108:15112-15117.
    • (2011) Proc. Natl. Acad. Sci. , vol.108 , pp. 15112-15117
    • Robert, C.P.1    Cornuet, J.-M.2    Marin, J.-M.3    Pillai, N.S.4
  • 37
    • 33846939958 scopus 로고    scopus 로고
    • Sequential Monte Carlo without likelihoods
    • Sisson, D. 2007. Sequential Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. USA 104:1760-1765.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 1760-1765
    • Sisson, D.1
  • 39
    • 0036006020 scopus 로고    scopus 로고
    • Testing for genetic evidence of population expansion and contraction: an empirical analysis of micro-satellite DNA variation using a hierarchical Bayesian model
    • Storz, J. F., and B. A. Beaumont 2002. Testing for genetic evidence of population expansion and contraction: an empirical analysis of micro-satellite DNA variation using a hierarchical Bayesian model. Evolution 56:154-166.
    • (2002) Evolution , vol.56 , pp. 154-166
    • Storz, J.F.1    Beaumont, B.A.2
  • 41
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 42
    • 33644763127 scopus 로고    scopus 로고
    • Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster
    • Thornton, K., and P. Andolfatto 2005. Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172:1607-1619.
    • (2005) Genetics , vol.172 , pp. 1607-1619
    • Thornton, K.1    Andolfatto, P.2
  • 43
    • 67649804149 scopus 로고    scopus 로고
    • Genetic patterns of differentiation among five landbird species on the Queen Charlotte Islands, British Columbia
    • Topp, C., and K. Winker 2008. Genetic patterns of differentiation among five landbird species on the Queen Charlotte Islands, British Columbia. Auk 125:461-472.
    • (2008) Auk , vol.125 , pp. 461-472
    • Topp, C.1    Winker, K.2
  • 44
    • 70350136774 scopus 로고    scopus 로고
    • Efficient Approximate Bayesian computation coupled with Markov Chain Monte Carlo without likelihood
    • Wegmann, D., C. Leuenberger, and L. Excoffier 2009. Efficient Approximate Bayesian computation coupled with Markov Chain Monte Carlo without likelihood. Genetics 182:1207-1218.
    • (2009) Genetics , vol.182 , pp. 1207-1218
    • Wegmann, D.1    Leuenberger, C.2    Excoffier, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.