RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

Molecular Phylogenetics and Evolution

Volumn 87, Issue , 2015, Pages 46-49

  Yu, Yan ^a,b   Harris, Alan J ^c   Blair, Christopher ^b,d   He, Xingjin ^a  

^a SICHUAN UNIVERSITY   (China)

^b DUKE UNIVERSITY   (United States)

^c OKLAHOMA STATE UNIVERSITY   (United States)

^d NEW YORK CITY COLLEGE OF TECHNOLOGY   (United States)

Author keywords

Ancestral state reconstruction; Historical biogeography; Software

Indexed keywords

COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; SPECIES DIFFERENTIATION; STATISTICAL MODEL; UNCERTAINTY;

COMPUTER GRAPHICS; GENETIC SPECIATION; MODELS, STATISTICAL; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; SOFTWARE; UNCERTAINTY; USER-COMPUTER INTERFACE;

EID: 84964253057     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2015.03.008     Document Type: Article

References (26)

1. Ali S.S., Pfosser M., Wetschnig W., et al. Out of Africa: Miocene dispersal, vicariance, and extinction within Hyacinthaceae Subfamily Urgineoideae. J. Integr. Plant Biol. 2013, 55(10):950-964.
2. Beaulieu J.M., Tank D.C., Donoghue M.J. A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana. BMC Evol. Biol. 2013, 13(1):80.
3. Buerki S., Forest F., Alvarez N., et al. An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae. J. Biogeogr. 2011, 38(3):531-550.
4. Comas I., Coscolla M., Luo T., et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet. 2013, 45(10):1176-1182.
5. Harris A.J., Xiang Q.Y. Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to dispersal vicariance analysis and a case using Aesculus L. (Sapindaceae) including fossils. J. Syst. Evol. 2009, 47:349-368.
6. Harris A.J., Wen J., Xiang Q.J. Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA Approach. J. Syst. Evol. 2013, 51:117-133.
7. Johns M.V. Non-parametric empirical Bayes procedures. Ann. Math. Statist. 1957, 28:649-669.
8. Kodandaramaiah U. Use of dispersal-vicariance analysis in biogeography-a critique. J. Biogeogr. 2010, 37(1):3-11.
9. Landis M.J., Matzke N.J., Moore B.R. Bayesian analysis of biogeography when the number of areas is large. Syst. Biol. 2013, 62:789-804.
10. Link-Pérez M.A., Watson L.E., Hickey R.J. Redefinition of Adiantopsis Fée (Pteridaceae): systematics, diversification, and biogeography. Taxon 2011, 60(5):1255-1268.
11. Matzke, N.J., 2013. BioGeoBEARS: BioGeography with Bayesian (and Likelihood). Evolutionary Analysis in R Scripts. Release R package version 0.2.1.http://CRAN.R-project.org/package=BioGeoBEARS.
12. Matzke, N.J., 2014. Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Systematic Biology. syu056.
13. Miraldo A., Hanski I. Competitive release leads to range expansion and rampant speciation in Malagasy dung beetles. Syst. Biol. 2014, syu011.
14. Moreau C.S., Bell C.D. Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants. Evolution 2013, 67(8):2240-2257.
15. Moyle R.G., Andersen M.J., Oliveros C.H., et al. Phylogeny and biogeography of the core babblers (Aves: Timaliidae). Syst. Biol. 2012, 61(4):631-651.
16. Nylander J.A.A., Olsson U., Alström P., Sanmartín I. Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Syst. Biol. 2008, 57:257-268.
17. Razo-Mendivil U., de León G.Pérez-Ponce Testing the evolutionary and biogeographical history of Glypthelmins (Digenea: Plagiorchiida), a parasite of anurans, through a simultaneous analysis of molecular and morphological data. Mol. Phylogenet. Evol. 2011, 59(2):331-341.
18. Ree R.H., Smith S.A. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 2008, 57(1):4-14.
19. Ronquist, F., 1996. Dispersal Vicariance Analysis (DIVA) 1.1. User's manual.
20. Ronquist F. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst. Biol. 1997, 46:195-203.
21. Ronquist, F., 2001. Dispersal Vicariance Analysis (DIVA), version v. 1.2.
22. Schenk J.J., Rowe K.C., Steppan S.J. Ecological opportunity and incumbency in the diversification of repeated continental colonizations by muroid rodents. Syst. Biol. 2013, 62(6):837-864.
23. Smith S.A. Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae. J. Biogeogr. 2009, 36(12):2324-2337.
24. Smith, S.A., 2010. Lagrange C++ Manual.
25. Xiang Q.Y., Thomas D.T. Tracking character evolution and biogeographic history through time in Cornaceae - does choice of methods matter?. J. Syst. Evol. 2008, 46:349-374.
26. Yu Y., Harris A.J., He X.J. S-DIVA (statistical dispersal-vicariance analysis): a tool for inferring biogeographic histories. Mol. Phylogenet. Evol. 2010, 56:848-850.