Show simple item record

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories

dc.contributor.authorKnowles, L. Lacey
dc.contributor.authorHuang, Huateng
dc.contributor.authorSukumaran, Jeet
dc.contributor.authorSmith, Stephen A.
dc.date.accessioned2018-05-15T20:15:34Z
dc.date.available2019-05-13T14:45:28Zen
dc.date.issued2018-03
dc.identifier.citationKnowles, L. Lacey; Huang, Huateng; Sukumaran, Jeet; Smith, Stephen A. (2018). "A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories." American Journal of Botany 105(3): 376-384.
dc.identifier.issn0002-9122
dc.identifier.issn1537-2197
dc.identifier.urihttps://hdl.handle.net/2027.42/143759
dc.publisherWiley‐Blackwell
dc.subject.otherlateral gene transfer
dc.subject.otherspecies tree
dc.subject.otherCLASSIPHY
dc.subject.othercoalescence
dc.subject.othergene‐tree discord
dc.subject.otherincomplete lineage sorting
dc.titleA matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories
dc.typeArticleen_US
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiology
dc.subject.hlbsecondlevelBotany
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/143759/1/ajb21064_am.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/143759/2/ajb21064.pdf
dc.identifier.doi10.1002/ajb2.1064
dc.identifier.sourceAmerican Journal of Botany
dc.identifier.citedreferenceRuprecht, C., R. Lohaus, K. Vanneste, M. Mutwil, Z. Nikoloski, Y. Van de Peer, and S. Persson. 2017. Revisiting ancestral polyploidy in plants. Science Advances 3: e1603195.
dc.identifier.citedreferenceMcCormack, J. E., H. Huang, and L. L. Knowles. 2009. Maximum‐likelihood estimates of species trees: How accuracy of phylogenetic inference depends upon the divergence history and sampling design. Systematic Biology 58: 501 – 508.
dc.identifier.citedreferenceMeng, C., and L. S. Kubatko. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Theoretical Population Biology 75: 35 – 45.
dc.identifier.citedreferenceMorgan, C. C., P. G. Foster, A. E. Webb, D. Pisani, J. O. McInerney, and M. J. O’Connell. 2013. Heterogeneous models place the root of the placental mammal phylogeny. Molecular Biology and Evolution 30: 2145 – 2156.
dc.identifier.citedreferenceMirarab, S., M. S. Bayzid, B. Boussau, and T. Warnow. 2014. Statistical binning enables an accurate coalescent‐based estimation of the avian tree. Science 346: 1337.
dc.identifier.citedreferencePrum, R. O., J. S. Berv, A. Dornburg, D. J. Field, J. P. Townsend, E. M. Lemmon, and A. R. Lemmon. 2015. A comprehensive phylogeny of birds (Aves) using targeted next‐generation DNA sequencing. Nature 526: 569 – 573.
dc.identifier.citedreferenceRobin, X., N. Turck, A. Hainard, N. Tiberti, F. Lisacek, J. C. Sanchez, and M. Müller. 2011. pROC: an open‐source package for R and S plus to analyze and compare ROC curves. BMC Bioinformatics 12: 77.
dc.identifier.citedreferenceRobinson, D. F., and L. R. Foulds. 1981. Comparison of phylogenetic trees. Mathematical Biosciences 53: 131 – 147.
dc.identifier.citedreferenceRambaut, A., and N. C. Grassly. 1997. SEQ‐GEN: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences 13: 235 – 238.
dc.identifier.citedreferenceRichards, E. J., J. M. Brown, A. J. Barley, R. A. Chong, and R. C. Thomson. 2017. Unexpected variation across mitochondrial gene trees and evidence for systematic error: How much gene tree variation is biological? BioRxiv. https://doi.org/10.1101/171413.
dc.identifier.citedreferenceShen, X.‐X., C. T. Hittinger, and A. Rokas. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology and Evolution 1: 126.
dc.identifier.citedreferenceSolís‐Lemus, C., and C. Ané. 2016. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLOS Genetics 12: e1005896.
dc.identifier.citedreferenceSolís‐Lemus, C., P. Bastide, and C. Ané. 2017. PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution 34: 3292 – 3298.
dc.identifier.citedreferenceSmith, S. A., M. J. Moore, J. W. Brown, and Y. Yang. 2015. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology 15: 150.
dc.identifier.citedreferenceStamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics 30: 1312 – 1313.
dc.identifier.citedreferenceSukumaran, J., E. P. Economo, and L. L. Knowles. 2016. Machine learning biogeographic processes from biotic patterns: a new trait‐dependent dispersal and diversification model with model choice by simulation‐trained discriminant analysis. Systematic Biology 65: 525 – 545.
dc.identifier.citedreferenceWen, D., and L. Nakhleh. 2017. Coestimating reticulate phylogenies and gene trees from multilocus sequence data. Systematic Biology 67: 439 – 457.
dc.identifier.citedreferenceWickett, N. J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, USA 111: E4859 – 4868.
dc.identifier.citedreferenceXi, Z., R. K. Bradley, K. J. Wurdack, K. M. Wong, M. Sugumaran, K. Bomblies, J. S. Rest, and C. C. Davis. 2012. Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics 13: 227.
dc.identifier.citedreferenceXi, Z. X., L. Liu, J. S. Rest, and C. C. Davis. 2014. Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Systematic Biology 63: 919 – 932.
dc.identifier.citedreferenceYang, Y., M. J. Moore, S. F. Brockington, D. E. Soltis, G. K.‐S. Wong, E. J. Carpenter, Y. Zhang, et al. 2015. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution 32: 2001 – 2014.
dc.identifier.citedreferenceZhang, C., H. A. Oglivie, A. J. Drummond, and T. Stadler. 2018. Bayesian inference of species networks from multilocus sequence data. Molecular Biology and Evolution 35: 504 – 517.
dc.identifier.citedreferenceZhong, B., L. Liu, Z. Yan, and D. Penny. 2013. Origin of land plants using the multispecies coalescent model. Trends in Plant Science 18: 492 – 495. https://doi.org/10.1016/j.tplants.2013.04.009.
dc.identifier.citedreferenceBlischak, P., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2017. HyDe: a Python package for genome‐scale hybridization detection. bioRXiv. https://doi.org/10.1016/10.1101/188037.
dc.identifier.citedreferenceBoussau, B., G. J. Szollosi, L. Duret, M. Gouy, E. Tannier, and V. Daubin. 2013. Genome‐scale coestimation of species and gene trees. Genome Research 23: 323 – 330.
dc.identifier.citedreferenceBrown, J. M., and R. C. Thomson. 2017. Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses. Systematic Biology 66: 517 – 530.
dc.identifier.citedreferenceCox, C. J., B. Li, P. G. Foster, T. M. Embley, and P. Civan. 2014. Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Systematic Biology 63: 272 – 279.
dc.identifier.citedreferencede Queiroz, A., and J. Gatesy. 2007. The supermatrix approach to systematics. Trends in Ecology & Evolution 22: 34 – 41.
dc.identifier.citedreferenceEdwards, S. V. 2009. Is a new and general theory of molecular systematics merging? Evolution 63: 1 – 19.
dc.identifier.citedreferenceFontaine, M. C., J. B. Pease, A. Steele, R. M. Waterhouse, D. E. Neafsey, I. V. Sharakhov, X. Jiang, et al. 2015. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347: 1258524 – 1258524.
dc.identifier.citedreferenceFoster, P. G. 2004. Modeling compositional heterogeneity. Systematic Biology 53: 485 – 495.
dc.identifier.citedreferenceGatesy, J., and M. Springer. 2014. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Molcular Phylogenetics and Evolution 80: 231 – 266.
dc.identifier.citedreferenceGori, K., T. Suchan, N. Alvarez, N. Goldman, and C. Dessimoz. 2016. Clustering genes of common evolutionary history. Molecular Biology and Evolution 33: 1590 – 1605.
dc.identifier.citedreferenceHuang, H., Q. He, L. S. Kubatko, and L. L. Knowles. 2010. Sources of error for species‐tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. Systematic Biology 59: 573 – 583.
dc.identifier.citedreferenceHuang, H., J. Sukumaran, S. A. Smith, and L. L. Knowles. 2018. Cause of gene tree discord? CLASSIPHY, a procedure for distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics. Peer J, in review. Available at https://peerj.com/preprints/3489/.
dc.identifier.citedreferenceHuang, H., L. Tran, and L. L. Knowles. 2014. Do estimated and actual species phylogenies match? Evaluation of African cichlid radiations. Molecular Phylogenetics and Evolution 78: 56 – 65.
dc.identifier.citedreferenceHuang, W., G. Zhou, M. Marchand, J. Ash, D. Morris, P. Van Dooren, J. M. Brown, et al. 2016. TreeScaper: visualizing and extracting phylogenetic signal from sets of trees. Molecular Biology and Evolution 33: 3314 – 3316.
dc.identifier.citedreferenceJarvis, E. D., S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. Ho, et al. 2014. Whole‐genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320 – 1331.
dc.identifier.citedreferenceJombart, T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403 – 1405.
dc.identifier.citedreferenceJombart, T., S. Devillard, and F. Balloux. 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11: 94 – 109.
dc.identifier.citedreferenceKnowles, L. L. 2009. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Systematic Biology 58: 463 – 467.
dc.identifier.citedreferenceKnowles, L. L. 2010. Sampling strategies for species‐tree estimation. In L. L. Knowles and L. S. Kubatko [eds.], Estimating species trees: practical and theoretical aspects, 163 – 172. Wiley‐Blackwell, Hoboken, NJ, USA.
dc.identifier.citedreferenceKnowles, L. L., and L. S. Kubatko [eds.], 2010. Estimating species trees: practical and theoretical aspects. Wiley‐Blackwell, Hoboken, NJ, USA.
dc.identifier.citedreferenceKubatko, L. S. 2009. Identifying hybridization events in the presence of coalescence via model selection. Systematic Biology 58: 478 – 488.
dc.identifier.citedreferenceKubatko, L. S., and J. H. Degnan. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56: 17 – 24.
dc.identifier.citedreferenceLanier, H. C., H. Huang, and L. L. Knowles. 2013. How low can you go? The effects of mutation rate on the accuracy of species‐tree reconstruction. Molecular Phylogenetics and Evolution 70: 112 – 119.
dc.identifier.citedreferenceLewitus, E., and H. Morlon. 2016. Characterizing and comparing phylogenies from their Laplacian spectrum. Systematic Biology 65: 495 – 507.
dc.identifier.citedreferenceLiu, L., Z. Xi, and C. C. Davis. 2014. Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting. Molecular Biology and Evolution 32: 791 – 805.
dc.identifier.citedreferenceMaddison, W. P. 1997. Gene trees in species trees. Systematic Biology 46: 523 – 536.
dc.identifier.citedreferenceMallo, D., L. D. Martins, and D. Posada. 2016. SimPhy: Phylogenomic simulation of gene, locus, and species trees. Systematic Biology 65: 334 – 344.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe its collections in a way that respects the people and communities who create, use, and are represented in them. We encourage you to Contact Us anonymously if you encounter harmful or problematic language in catalog records or finding aids. More information about our policies and practices is available at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.