Who is Who in Phylogenetic Networks

Publications related to 'lineage sorting'   Order by:   Type | Year

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AIC bayesian BIC bootstrap branch-length coalescent explicit-network from-network from-rooted-trees from-species-tree from-unrooted-trees hybridization lateral-gene-transfer likelihood lineage-sorting model-selection parsimony phylogenetic-network phylogeny Program-JML Program-PhyloNet reconstruction software statistical-model supernetwork

2013

1 Yun Yu, R. Matthew Barnett and Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013. Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.         Toggle abstract "Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators of hybridization. However, methods that follow this approach mostly ignore population effects, such as incomplete lineage sorting (ILS). Given that hybridization occurs between closely related organisms, ILS may very well be at play and, hence, must be accounted for in the analysis framework. To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections of gene-tree topologies under this criterion. This framework enables phylogenetic analyses while accounting for both hybridization and ILS. Further, we propose two techniques for incorporating information about uncertainty in gene-tree estimates. Our simulation studies demonstrate the good performance of our framework in terms of identifying the location of hybridization events, as well as estimating the proportions of genes that underwent hybridization. Also, our framework shows good performance in terms of efficiency on handling large data sets in our experiments. Further, in analysing a yeast data set, we demonstrate issues that arise when analysing real data sets. Although a probabilistic approach was recently introduced for this problem, and although parsimonious reconciliations have accuracy issues under certain settings, our parsimony framework provides a much more computationally efficient technique for this type of analysis. Our framework now allows for genome-wide scans for hybridization, while also accounting for ILS. [Phylogenetic networks; hybridization; incomplete lineage sorting; coalescent; multi-labeled trees.] © 2013 The Author(s). All rights reserved."

2012

2 Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179-184, 2012. Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model. Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.         Toggle abstract "I introduce the software jml that tests for the presence of hybridization in multispecies sequence data sets by posterior predictive checking following Joly, McLenachan and Lockhart (2009, American Naturalist e54). Although their method could potentially be applied on any data set, the lack of appropriate software made its application difficult. The software jml thus fills a need for an easy application of the method but also includes improvements such as the possibility to incorporate uncertainty in the species tree topology. The jml software uses a posterior distribution of species trees, population sizes and branch lengths to simulate replicate sequence data sets using the coalescent with no migration. A test quantity, defined as the minimum pairwise sequence distance between sequences of two species, is then evaluated on the simulated data sets and compared to the one estimated from the original data. Because the test quantity is a good predictor of hybridization events, departure from the bifurcating species tree model could be interpreted as evidence of hybridization. Software performance in terms of computing time is evaluated for several parameters. I also show an application example of the software for detecting hybridization among native diploid North American roses. © 2011 Blackwell Publishing Ltd." 3 Yun Yu and Luay Nakhleh. Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting. 2012. Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software. Note: http://arxiv.org/abs/1212.1909.

2011

4 Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011. Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model. Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.         Toggle abstract "Analyses of the increasingly available genomic data continue to reveal the extent of hybridization and its role in the evolutionary diversification of various groups of species. We show, through extensive coalescent-based simulations of multilocus data sets on phylogenetic networks, how divergence times before and after hybridization events can result in incomplete lineage sorting with gene tree incongruence signatures identical to those exhibited by hybridization. Evolutionary analysis of such data under the assumption of a species tree model can miss all hybridization events, whereas analysis under the assumption of a species network model would grossly overestimate hybridization events. These issues necessitate a paradigm shift in evolutionary analysis under these scenarios, from a model that assumes a priori a single source of gene tree incongruence to one that integrates multiple sources in a unifying framework. We propose a framework of coalescence within the branches of a phylogenetic network and show how this framework can be used to detect hybridization despite incomplete lineage sorting. We apply the model to simulated data and show that the signature of hybridization can be revealed as long as the interval between the divergence times of the species involved in hybridization is not too small. We reanalyze a data set of 106 loci from 7 in-group Saccharomyces species for which a species tree with no hybridization has been reported in the literature. Our analysis supports the hypothesis that hybridization occurred during the evolution of this group, explaining a large amount of the incongruence in the data. Our findings show that an integrative approach to gene tree incongruence and its reconciliation is needed. Our framework will help in systematically analyzing genomic data for the occurrence of hybridization and elucidating its evolutionary role. [Coalescent history; incomplete lineage sorting; hybridization; phylogenetic network.]. © 2011 The Author(s)."

2009

5 Laura S. Kubatko. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. In Systematic Biology, Vol. 58(5):478-488, 2009. Keywords: AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1093/sysbio/syp055.         6 Chen Meng and Laura S. Kubatko. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. In Theoretical Population Biology, Vol. 75(1):35-45, 2009. Keywords: bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1016/j.tpb.2008.10.004.         Toggle abstract "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. Here 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. © 2008 Elsevier Inc. All rights reserved." 7 Simon Joly, Patricia A. McLenachan and Peter J. Lockhart. A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting. In The American Naturalist, Vol. 174(2):E54-E70, 2009. Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://www.plantevolution.org/pdf/Joly&al_2009_AmNat.pdf.         Toggle abstract "The extent and evolutionary significance of hybridization is difficult to evaluate because of the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present a novel parametric approach for statistically distinguishing hybridization from incomplete lineage sorting based on minimum genetic distances of a nonrecombining locus. It is based on the idea that the expected minimum genetic distance between sequences from two species is smaller for some hybridization events than for incomplete lineage sorting scenarios. When applied to empirical data sets, distributions can be generated for the minimum interspecies distances expected under incomplete lineage sorting using coalescent simulations. If the observed distance between sequences from two species is smaller than its predicted distribution, incomplete lineage sorting can be rejected and hybridization inferred. We demonstrate the power of the method using simulations and illustrate its application on New Zealand alpine buttercups (Ranunculus). The method is robust and complements existing approaches. Thus it should allow biologists to assess with greater accuracy the importance of hybridization in evolution. © 2009 by The University of Chicago."

2008

8 Barbara R. Holland, Steffi Benthin, Peter J. Lockhart, Vincent Moulton and Katharina Huber. Using supernetworks to distinguish hybridization from lineage-sorting. In BMCEB, Vol. 8(202), 2008. Keywords: explicit network, from unrooted trees, hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, supernetwork. Note: http://dx.doi.org/10.1186/1471-2148-8-202.         Toggle abstract "Background. A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence. However, this approach may be confounded by factors such as poor taxon-sampling and/or incomplete lineage-sorting. Results. Using coalescent simulations, we investigated the potential of supernetwork methods to differentiate between gene tree incongruence arising from taxon sampling and incomplete lineage-sorting as opposed to hybridization. For few hybridization events, a large number of independent loci, and well-sampled taxa across these loci, we found that it was possible to distinguish incomplete lineage-sorting from hybridization using the filtered Z-closure and Q-imputation supernetwork methods. Moreover, we found that the choice of supernetwork method was less important than the choice of filtering, and that count-based filtering was the most effective filtering technique. Conclusion. Filtered supernetworks provide a tool for detecting and identifying hybridization events in phylogenies, a tool that should become increasingly useful in light of current genome sequencing initiatives and the ease with which large numbers of independent gene loci can be determined using new generation sequencing technologies. © 2008 Holland et al; licensee BioMed Central Ltd."

2001

9 Mark T. Holder, Jennifer A. Anderson and Alisha K. Holloway. Difficulties in Detecting Hybridization. In Systematic Biology, Vol. 50(6):978-982, 2001. Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://dx.doi.org/10.1080/106351501753462911.         Toggle abstract [No abstract available]

2000

10 Tao Sang and Yang Zhong. Testing Hybridization Hypotheses Based on Incongruent Gene Trees. In Systematic Biology, Vol. 49(3):422-434, 2000. Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://dx.doi.org/10.1080/10635159950127321.