A supertree is a single phylogenetic tree assembled from a combination of smaller phylogenetic trees, which may have been assembled using different datasets (e.g. morphological and molecular) or a different selection of taxa.[1] Supertree algorithms can highlight areas where additional data would most usefully resolve any ambiguities.[2] The input trees of a supertree should behave as samples from the larger tree.[3]

Construction methods

The construction of a supertree scales exponentially with the number of tax included; therefore for a tree of any reasonable size, it is not possible to examine every possible supertree and weigh its success at combining the input information. Heuristic methods are thus essential, although these methods may be unreliable; the result extracted is often biased or affected by irrelevant characteristics of the input data.[1]

The most well known method for supertree construction is Matrix Representation with Parsimony (MRP), in which the input source trees are represented by matrices with 0s, 1s, and ?s (i.e., each edge in each source tree defines a bipartition of the leafset into two disjoint parts, and the leaves on one side get 0, the leaves on the other side get 1, and the missing leaves get ?), and the matrices are concatenated and then analyzed using heuristics for maximum parsimony.[4] Another approach for supertree construction include a maximum likelihood version of MRP called "MRL" (matrix representation with likelihood), which analyzes the same MRP matrix but uses heuristics for maximum likelihood instead of for maximum parsimony to construct the supertree.

The Robinson-Foulds distance is the most popular of many ways of measuring how similar a supertree is to the input trees. It is a metric for the number of clades from the input trees that are retained in the supertree. Robinson-Foulds optimization methods search for a supertree that minimizes the total (summed) Robinson-Foulds differences between the (binary) supertree and each input tree.[1] In this case the supertree can hence be view as the median of the input tree according to the Robinson-Foulds distance. Alternative approaches have been developped to infer median supertree based on different metrics, e.g relying on triplet or quartet decomposition of the trees.[5]

A recent innovation has been the construction of Maximum Likelihood supertrees and the use of "input-tree-wise" likelihood scores to perform tests of two supertrees.[6]

Additional methods include the Min Cut Supertree approach,[7] Most Similar Supertree Analysis (MSSA), Distance Fit (DFIT) and Quartet Fit (QFIT), implemented in the software CLANN.[8][9]

Application

Supertrees have been applied to produce phylogenies of many groups, notably the angiosperms,[10] eukaryotes[11] and mammals.[12] They have also been applied to larger-scale problems such as the origins of diversity, vulnerability to extinction,[13] and evolutionary models of ecological structure.[14]

Further reading

References

  1. ^ a b c Bansal, M.; Burleigh, J.; Eulenstein, O.; Fernández-Baca, D. (2010). "Robinson-Foulds supertrees". Algorithms for Molecular Biology. 5: 18. doi:10.1186/1748-7188-5-18. PMC 2846952. PMID 20181274.
  2. ^ "Supertree: Introduction". genome.cs.iastate.edu.
  3. ^ Gordon, A. (1986). "Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves". Journal of Classification. 3 (2): 335–348. doi:10.1007/BF01894195. S2CID 122146129.
  4. ^ Mark A. Ragan (1992). "Phylogenetic inference based on matrix representation of trees". Molecular Phylogenetics and Evolution. 1 (1): 53–58. doi:10.1016/1055-7903(92)90035-F. ISSN 1055-7903. PMID 1342924.
  5. ^ Ranwez, Vincent; Criscuolo, Alexis; Douzery, Emmanuel J.P. (2010-06-15). "S uper T riplets : a triplet-based supertree approach to phylogenomics". Bioinformatics. 26 (12): i115–i123. doi:10.1093/bioinformatics/btq196. ISSN 1367-4811. PMC 2881381. PMID 20529895.
  6. ^ Akanni, Wasiu A.; Creevey, Christopher J.; Wilkinson, Mark; Pisani, Davide (2014-06-12). "L.U.St: a tool for approximated maximum likelihood supertree reconstruction". BMC Bioinformatics. 15 (1): 183. doi:10.1186/1471-2105-15-183. ISSN 1471-2105. PMC 4073192. PMID 24925766.
  7. ^ Semple, C. (2000). "A supertree method for rooted trees". Discrete Applied Mathematics. 105 (1–3): 147–158. CiteSeerX 10.1.1.24.6784. doi:10.1016/S0166-218X(00)00202-X.
  8. ^ Creevey, C. J.; McInerney, J. O. (2005-02-01). "Clann: investigating phylogenetic information through supertree analyses". Bioinformatics. 21 (3): 390–392. doi:10.1093/bioinformatics/bti020. ISSN 1367-4803. PMID 15374874.
  9. ^ Creevey, C. J.; McInerney, J. O. (2009-01-01). "Trees from Trees: Construction of Phylogenetic Supertrees Using Clann" (PDF). In Posada, David (ed.). Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. Vol. 537. Humana Press. pp. 139–161. doi:10.1007/978-1-59745-251-9_7. ISBN 978-1-58829-910-9. PMID 19378143.
  10. ^ Davies, T.; Barraclough, T.; Chase, M.; Soltis, P.; Soltis, D.; Savolainen, V. (2004). "Darwin's abominable mystery: Insights from a supertree of the angiosperms". Proceedings of the National Academy of Sciences of the United States of America. 101 (7): 1904–1909. Bibcode:2004PNAS..101.1904D. doi:10.1073/pnas.0308127100. PMC 357025. PMID 14766971.
  11. ^ Pisani, D.; Cotton, J.; McInerney, J. (2007). "Supertrees disentangle the chimerical origin of eukaryotic genomes". Molecular Biology and Evolution. 24 (8): 1752–1760. doi:10.1093/molbev/msm095. PMID 17504772.
  12. ^ Bininda-Emonds, O.; Cardillo, M.; Jones, K.; MacPhee, R.; Beck, R.; Grenyer, R.; Price, S.; Vos, R.; Gittleman, J.; Purvis, A. (2007). "The delayed rise of present-day mammals". Nature. 446 (7135): 507–512. Bibcode:2007Natur.446..507B. doi:10.1038/nature05634. PMID 17392779. S2CID 4314965.
  13. ^ Davies, T.; Fritz, S.; Grenyer, R.; Orme, C.; Bielby, J.; Bininda-Emonds, O.; Cardillo, M.; Jones, K.; Gittleman, J.; Mace, G. M.; Purvis, A. (2008). "Phylogenetic trees and the future of mammalian biodiversity". Proceedings of the National Academy of Sciences of the United States of America. 105 Suppl 1 (Supplement_1): 11556–11563. Bibcode:2008PNAS..10511556D. doi:10.1073/pnas.0801917105. PMC 2556418. PMID 18695230.
  14. ^ Webb, C. O.; Ackerly, D. D.; McPeek, M. A.; Donoghue, M. J. (2002). "Phylogenies and Community Ecology". Annual Review of Ecology and Systematics. 33: 475–505. doi:10.1146/annurev.ecolsys.33.010802.150448. S2CID 535590.
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