Correction
2010; University of Chicago Press; Volume: 175; Issue: 5 Linguagem: Inglês
10.1086/652725
ISSN1537-5323
AutoresSimon Joly, Bernard E. Pfeil, Bengt Oxelman, Patricia A. McLenachan, Peter J. Lockhart,
Tópico(s)Yeasts and Rust Fungi Studies
ResumoPrevious article FreeCorrectionSimon Joly, Bernard E. Pfeil, Bengt Oxelman, Patricia A. McLenachan, and Peter J. LockhartSimon Joly, Bernard E. Pfeil, Bengt Oxelman, Patricia A. McLenachan, and Peter J. Lockhart1. Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, 4101 Sherbrooke Est, Montreal, Quebec H1X 2B2, Canada;2. Department of Plant and Environmental Sciences, Gothenburg University, Box 461, 405 30 Gothenburg, Sweden;3. Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New ZealandOriginal articleA Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting.PDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmailPrint SectionsMoreFollowing the publication of "A statistical approach for distinguishing hybridization and incomplete lineage sorting" by Simon Joly, Patricia A. McLenachan, and Peter J. Lockhart (American Naturalist 174:E54–E70), we noticed an inversion in one of the sequence data sets analyzed. The inversion occurs in the psbA‐trnH spacer between positions 91 and 116 (TreeBase accession S2284, matrix 4341). Overlooking this inversion resulted in inferring 18 nucleotide substitutions between sequences that differ by this inversion. In this correction, we reanalyze the data on New Zealand alpine Ranunculus when treating this inversion as a single evolutionary event.The new concatenated chloroplast data set (with the inversion removed) resulted in a different gene tree (fig. 1). Although the inversion is present in all taxa from breeding group 1 and in the two individuals that were inferred to contain an introgressed chloroplast in the original study (Ranunculus crithmifolius from Mount Lyndon and Ranunculus insignis from Mount Hutt), these two individuals are now nested within sequences of breeding group 2. The presence of the inversion in R. crithmifolius and R. insignis thus probably represents an independent evolutionary event. A species tree search by gene tree parsimony using this modified chloroplast phylogeny resulted in two most parsimonious unrooted trees that differ from each other only by the relative positioning of species of breeding group 2: one tree was identical to that of the original publication, with Ranunculus enysii and R. insignis being sister species, whereas in the other, R. crithmifolius and R. insignis grouped together. We ran MCMCcoal on both species trees and tested for the presence of hybridization using both species tree topologies following the exact same procedures as in Joly et al. (2009), with one exception. We used a heredity scalar of 0.5 for chloroplast markers for estimating population sizes and divergence times, which is the correct heredity scalar for plastid DNA in hermaphrodites (we thank M. Lascoux for pointing out this problem). This reanalysis could not reject the hypothesis that the observed distances were the result of lineage sorting alone ($$P> .05$$). The presence of hybridization in the New Zealand alpine Ranunculus thus remains inconclusive.Figure 1: Maximum likelihood phylogeny (TVM + I) obtained by heuristic search in PAUP*. The asterisks indicate individuals in which the psbA‐trnH inversion is present. Bootstrap proportions were obtained from 1,000 replicates.View Large ImageDownload PowerPointThe fact that hybridization could not be detected in this Ranuculus data set does not undermine the ability of our method to identify hybridization events, as simulation studies have shown that it is efficient. It also does not rule out the presence of hybridization in this group because some species are still nonmonophyletic in the chloroplast tree and it is possible that sequencing more nucleotides would reveal instances of hybridization. Previous article DetailsFiguresReferencesCited by The American Naturalist Volume 175, Number 5May 2010 Published for The American Society of Naturalists Article DOIhttps://doi.org/10.1086/652725 Views: 232Total views on this site Citations: 10Citations are reported from Crossref HistoryReceived February 18, 2010 © 2010 by The University of Chicago.PDF download Crossref reports the following articles citing this article:Meng‐Ting Wang, Zhen‐Yu Hou, Chao Li, Jia‐Peng Yang, Zhi‐Tao Niu, Qing‐Yun Xue, Wei Liu, Xiao‐Yu Ding Rapid structural evolution of Dendrobium mitogenomes and mito‐nuclear phylogeny discordances in Dendrobium (Orchidaceae), Journal of Systematics and Evolution 61, no.55 (Nov 2022): 790–805.https://doi.org/10.1111/jse.12912Belen Escobari, Thomas Borsch, Taylor S. Quedensley, Michael Gruenstaeudl Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif‐based sequence alignment amid low genetic distances, American Journal of Botany 108, no.1111 (Nov 2021): 2235–2256.https://doi.org/10.1002/ajb2.1775Kunal Arekar, Abhijna Parigi, K. Praveen Karanth Understanding the convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae)†, Journal of Genetics 100, no.22 (Nov 2021).https://doi.org/10.1007/s12041-021-01329-8Narjara Lopes de Abreu, Ruy José Válka Alves, Sérgio Ricardo Sodré Cardoso, Yann J.K. Bertrand, Filipe Sousa, Climbiê Ferreira Hall, Bernard E. Pfeil, Alexandre Antonelli The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss), PeerJ 6 (Jun 2018): e4916.https://doi.org/10.7717/peerj.4916F. Sousa, Y. J. K. Bertrand, J. J. Doyle, B. Oxelman, B. E. Pfeil Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L., Systematic Biology 66, no.66 (Feb 2017): 934–949.https://doi.org/10.1093/sysbio/syx035Pedro Jiménez‐Mejías, Mario Fernández‐Mazuecos, María Elena Amat, Pablo Vargas Narrow endemics in European mountains: high genetic diversity within the monospecific genus Pseudomisopates (Plantaginaceae) despite isolation since the late Pleistocene, Journal of Biogeography 42, no.88 (Apr 2015): 1455–1468.https://doi.org/10.1111/jbi.12507Bruno Maia-Carvalho, Helena Gonçalves, Nuno Ferrand, Iñigo Martínez-Solano Multilocus assessment of phylogenetic relationships in Alytes (Anura, Alytidae), Molecular Phylogenetics and Evolution 79 (Oct 2014): 270–278.https://doi.org/10.1016/j.ympev.2014.05.033Hamid Moazzeni, Shahin Zarre, Bernard E. Pfeil, Yann J. K. Bertrand, Dmitry A. German, Ihsan A. Al-Shehbaz, Klaus Mummenhoff, Bengt Oxelman Phylogenetic perspectives on diversification and character evolution in the species-rich genus Erysimum (Erysimeae; Brassicaceae) based on a densely sampled ITS approach, Botanical Journal of the Linnean Society 175, no.44 (Jul 2014): 497–522.https://doi.org/10.1111/boj.12184SIMON JOLY JML: testing hybridization from species trees, Molecular Ecology Resources 12, no.11 (Sep 2011): 179–184.https://doi.org/10.1111/j.1755-0998.2011.03065.xPhilippa C Griffin, Charles Robin, Ary A Hoffmann A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses, BMC Biology 9, no.11 (Mar 2011).https://doi.org/10.1186/1741-7007-9-19Related articlesA Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting.17 Jul 2015The American Naturalist
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