Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting

Systematic Biology

Volumn 62, Issue 3, 2013, Pages 467-478

  Jones, Graham ^a,b   Sagitov, Serik ^b   Oxelman, Bengt ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

Allopolyploid; Bayesian; hybridization; network; phylogenetics

Indexed keywords

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BRASSICACEAE; GENETICS; HYBRIDIZATION; MOLECULAR EVOLUTION; POLYPLOIDY; SILENE;

BAYES THEOREM; BRASSICACEAE; EVOLUTION, MOLECULAR; HYBRIDIZATION, GENETIC; MODELS, GENETIC; POLYPLOIDY; SILENE;

BRASSICACEAE; CARYOPHYLLACEAE; EMBRYOPHYTA; PACHYCLADON; SILENE;

EID: 84876251356     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt012     Document Type: Article

References (32)

1. Brysting A.K., Oxelman B., Huber K.T., Moulton V., Brochmann C. 2007. Untangling complex histories of genome mergings in high polyploids. Syst. Biol. 56:467-476.
2. Cai D., Rodríguez F., Teng Y., Ané C., Bonierbale M., Mueller L.A., Spooner D.M. 2012. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evol. Biol. 12:70.
3. Chen Z.-Z., Wang L. 2010. Hybridnet: A tool for constructing hybridization networks. Bioinformatics 26:2912-2913.
4. Chen Z.-Z., Wang L. 2012. Algorithms for reticulate networks of multiple phylogenetic trees. IEEE/ACM Trans. Comput. Biol. Bioinform. 9:372-384.
5. Cui L., Wall P.K., Leebens-Mack J.H., Lindsay B.G., Soltis D.E., Doyle J.J., Soltis P.S., Carlson J.E., Arugumanathan K., Barakat A., Albert VA., Ma H., dePamphilis C.W. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16:738-749.
6. Drummond A.J., Rambaut A. 2007. BEAST:Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
7. Drummond A.J., Suchard MA., Xie D., Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29:1969-1973.
8. Fujita M., Leaché A., Burbrink F., McGuire J., Moritz C. 2012. Coalescent-based species delimitation in an integrative taxonomy Trends Ecol. Evol. 27:480-488.
9. Gerard D., Gibbs H., Kubatko L. 2011. Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling. BMC Evol. Biol. 11:291.
10. Gernhard T. 2008. The conditioned reconstructed process. J. Theo. Biol. 253:769-778.
11. Green P.J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732.
12. Heled J., Drummond A. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
13. Huber K.T., Moulton V. 2006. Phylogenetic networks from multilabelled trees. J. Math. Biol. 52:613-632.
14. Huber K.T., Oxelman B., Lott M., Moulton V. 2006. Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol. Biol. Evol. 23:1784-1791.
15. Joly S., Heenan P.B., Lockhart P.J. 2009. A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand. Mol. Phylogenet. Evol. 51:365-372.
16. Kubatko L. 2009. Identifying hybridization events in the presence of coalescence via model selection. Syst. Biol. 58:478-488.
17. Lanier H.C., Knowles L.L. 2012. Is recombination a problemfor species- tree analyses? Syst. Biol. 61:691-701.
18. Lott M., Spillner A., Huber K.T., Moulton V. 2009a. Padre: A package for analyzing and displaying reticulate evolution. Bioinformatics 25:1199-1200.
19. Lott M., Spillner A., Huber K.T., Petri A., Oxelman B., Moulton V. 2009b. Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evol. Biol. 9:216.
20. Marcussen T., Jakobsen K.S., Danihelka J., Ballard H.E., Blaxland K., Brysting A.K., Oxelman B. 2012. Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae). Syst. Biol. 61:107-26.
21. Mau B., Newton M.A., Larget B. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1-12.
22. Petri A., Oxelman B. 2011. Phylogenetic relationships within silene (caryophyllaceae) section physolychnis. Taxon 60:953-968.
23. Popp M., Erixon P., Eggens F., Oxelman B. 2005. Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae) inferred from low copy nuclear RNA polymerase introns, rDNA, and chloroplast DNA. Syst. Bot. 30:302-313.
24. R Development Core Team. 2008. R: A language and environment for statistical computing. Vienna (Austria):R Foundation for Statistical Computing Vienna.
25. Rambaut A., Grassly N.C. 1997. Seq-Gen:an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
26. Rannala B., Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
27. Smedmark J.E.E., Eriksson T., Evans R.C., Campbell C.S. 2003. Ancient allopolyploid speciation in geinae (rosaceae):evidence from nuclear granule-bound starch synthase (gbssi) gene sequences. Syst. Biol. 52:374-385.
28. Tate J.A., Soltis D.E., Soltis P.S. 2005. Polyploidy in plants. In:Gregory T.R., editor. The evolution of the genome. London:Elsevier Academic Press. p. 371-426.
29. Wendel J.F., Doyle J.J. 2005. Polyploidy and evolution in plants. In:Henry R.J., editor. Plant diversity and evolution:genotypic and phenotypic variation in higher plants. Cambridge (MA):CABI Publishing. p. 97-117.
30. Wood T.E., Takebayashi N., Barker M.S., Mayrose I., Greenspoon P.B., Rieseberg L.H. 2009. The frequency of polyploid speciation in vascular plants. Proc. Natl Acad. Sci. U S A 106:13875-13879.
31. Yang Z., Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proc. Natl Acad. Sci. U S A 107:9264-9269.
32. Yu Y., Degnan J., Nakhleh L. 2012. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genet. 8:e1002660.