Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. (English) Zbl 1210.92023
Summary: The application of phylogenetic inference methods, to data for a set of independent genes sampled randomly throughout the genome, often results in substantial incongruence in the single-gene phylogenetic estimates. Among the processes known to produce discord between single-gene phylogenies, two of the best studied in a phylogenetic context are hybridization and incomplete lineage sorting. Much recent attention has focused on the development of methods for estimating species phylogenies in the presence of incomplete lineage sorting, but phylogenetic models that allow for hybridization have been more limited. We propose a model that allows incongruence in single-gene phylogenies to be due to both hybridization and incomplete lineage sorting, with the goal of determining the contribution of hybridization to observed gene tree incongruence in the presence of incomplete lineage sorting. Using our model, we propose methods for estimating the extent of the role of hybridization in both a likelihood and a Bayesian framework. The performance of our methods is examined using both simulated and empirical data.
MSC:
| 92D15 | Problems related to evolution |
| 05C90 | Applications of graph theory |
| 62P10 | Applications of statistics to biology and medical sciences; meta analysis |
Keywords:
phylogenetics; hybridization; introgression; hybrid speciation; incomplete lineage sorting; coalescenceReferences:
| [1] | Arensburger, P.; Buckley, T. R.; Simon, C.; Moulds, M.; Holsinger, K. E., Biogeography and phylogeny of the New Zealand cicada genera (Hemiptera: Cicadidae) based on nuclear and mitochondrial DNA data, J. Biogeography, 31, 557-569 (2004) |
| [2] | Arnold, M. L., Natural hybridization and evolution (1997), Oxford University Press |
| [3] | Baack, E. J.; Rieseberg, L. H., A genomic view of introgression and hybrid speciation, Curr. Opin. Genetics Dev., 17, 1-6 (2007) |
| [4] | 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., 55, 3, 411-425 (2006) |
| [5] | Degnan, J.; Salter, L., Gene tree distributions under the coalescent process, Evolution, 59, 24-37 (2005) |
| [6] | Dowling, T. E.; Secor, C. L., The role of hybridization and introgression in the diversification of animals, Annu. Rev. Ecol. Syst., 28, 593-619 (1997) |
| [7] | Edwards, S. V.; Liu, L.; Pearl, D. K., High resolution species trees without concatenation, PNAS, 104, 5936-5941 (2007) |
| [8] | Gauthier, O.; Lapointe, F. J., Hybrid and phylogenetics revisited: A statistical test of hybridization using quartets, Syst. Botany, 32, 1, 8-15 (2007) |
| [9] | Gelman, A.; Rubin, D. B., Inference from iterative simulation using multiple sequences, Stat. Sci., 7, 457-511 (1992) · Zbl 1386.65060 |
| [10] | George, E. I.; McCulloch, R. E., Variable selection via Gibbs sampling, J. Am. Stat. Assoc., 88, 423, 881-889 (1993) |
| [11] | Guigo, R.; Muchnik, I.; Smith, T. F., Reconstruction of ancient molecular phylogeny, Mol. Phylogenet. Evol., 6, 189-213 (1996) |
| [12] | Hennig, W., Phylogenetic Systematics (1966), Illinios Press, Urbana-Champaign |
| [13] | Holder, M. T.; Anderson, J. A.; Holloway, A. K., Difficulties in Detecting Hybridization, Syst. Biol., 50, 6, 978-982 (2001) |
| [14] | Hudson, R. R., Testing the constant-rate neutral allele model with protein sequence data, Evolution, 37, 203-217 (1983) |
| [15] | Kingman, J. F.C., The coalescent, Stoch. Proc. Appl., 13, 235-248 (1982) · Zbl 0491.60076 |
| [16] | Legendre, P.; Makarenkov, V., Reconstruction of biogeographic and evolutionary networks using reticulograms, Syst. Biol., 51, 2, 199-216 (2002) |
| [17] | Liu, L.; Pearl, D. K., Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions, Syst. Biol., 56, 504-514 (2007) |
| [18] | Maddison, W. P., Gene trees in species trees, Syst. Biol., 46, 523-536 (1997) |
| [19] | Maddison, W. P.; Knowles, L. L., Inferring phylogeny despite incomplete lineage sorting, Syst. Biol., 55, 21-30 (2006) |
| [20] | Mallet, J., Hybridization as an invasion of the genome, TREE, 20, 5, 229-237 (2005) |
| [21] | Mallet, J., Hyrbid speciation, Nature, 446, 279-283 (2007) |
| [22] | Medigue, C.; Rouxel, T.; Vigier, P.; Henaut, A.; Danchin, A., Evidence for horizontal gene transfer in Escherichia coli speciation, J. Mol. Biol., 222, 851-856 (1991) |
| [23] | Mossel, E., Roch, S., 2008. Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci. http://arxiv.org/abs/0710.0262; Mossel, E., Roch, S., 2008. Incomplete lineage sorting: Consistent phylogeny estimation from multiple loci. http://arxiv.org/abs/0710.0262 |
| [24] | Nei, M., Molecular Evolutionary Genetics (1987), Columbia University Press, New York |
| [25] | Nordborg, M., Coalescent theory, (Balding, D.; Bishop, M.; Cannings, C., Handbook of Statistical Genetics (2001), Wiley: Wiley Chichester), 179-212 |
| [26] | Pamilo, P.; Nei, M., Relationships between gene trees and species trees, Mol. Biol. Evol., 5, 5, 568-583 (1988) |
| [27] | Posada, D., Evaluation of methods for detecting recombination from DNA sequences: Empirical data, Mol. Biol. Evol., 19, 708-717 (2002) |
| [28] | Rannala, B.; Yang, Z., Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci, Genetics, 164, 1645-1656 (2003) |
| [29] | Rieseberg, L. H., Hybrid origins of plant species, Annu. Rev. Ecol. Syst., 28, 359-389 (1997) |
| [30] | Rieseberg, L. H.; Morefield, J. D., Character expression, phylogenetic reconstruction, and the detection of reticulate evolution, (Hoch, P. C.; Stephenson, A. G., Experimental and Molecular Approaches to Plant Biosystematics (1995), Missouri Botanical Garden, St. Louis), 333-353 |
| [31] | Rieseberg, L. H.; Wendel, J. F., Introgression and its consequences in plants, (Harrison, R. G., Hybrid Zones and the Evolutionary Process (1993), Oxford University Press), 70-109 |
| [32] | Rosenberg, N. A., The probability of topological concordance of gene trees and species trees, Theor. Popul. Biol., 61, 225-247 (2002) · Zbl 1040.92032 |
| [33] | Sang, T.; Zhong, Y., Testing hybridization hypotheses based on incongruent gene trees, Syst. Biol., 49, 3, 422-434 (2000) |
| [34] | Self, S. G.; Liang, K. Y., Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions, J. Am. Stat. Assoc., 82, 398, 605-610 (1987) · Zbl 0639.62020 |
| [35] | Strimmer, K.; Moulton, V., Likelihood analysis of phylogenetic networks using directed graphical models, Mol. Biol. Evol., 17, 6, 875-881 (2000) |
| [36] | Tajima, F., Evolutionary relationship of DNA sequences in finite populations, Genetics, 105, 437-460 (1983) |
| [37] | Takahata, N., Gene genealogy in three related populations: Consistency probability between gene and population trees, Genetics, 122, 957-966 (1989) |
| [38] | Takahata, N.; Nei, M., Gene genealogy and variance of interpopulational nucleotide differences, Genetics, 110, 325-344 (1985) |
| [39] | Tateno, Y.; Nei, M.; Tajima, F., Accuracy of estimated phylogenetic trees from molecular data. I. distantly related species, J. Mol. Evol., 18, 387-404 (1982) |
| [40] | Tavaré, S., Line-of-descent and genealogical processes, and their applications in population genetics models., Theor. Popul. Biol., 26, 119-164 (1984) · Zbl 0555.92011 |
| [41] | Than, C.; Ruths, D.; Innan, H.; Nakhleh, L., Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions, J. Comp. Biol., 14, 4, 517-535 (2007) |
| [42] | Valdez, A. M.; Pinero, D., Phylogenetic estimation of plasmid exchange in bacteria, Evolution, 46, 3, 641-656 (1992) |
| [43] | Xu, S., Phylogenetic analysis under reticulate evolution, Mol. Biol. Evol., 17, 6, 897-907 (2000) |
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.
