PREMISE: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS: Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION: The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

Berlin Center for Genomics in Biodiversity Research Berlin Germany

Botanic Institute of Barcelona Pg del Migdia s n ES 08038 Barcelona Spain

Botanischer Garten und Botanisches Museum Berlin Freie Universität Berlin Königin Luise Str 6 8 14195 Berlin Germany

Center for Biodiversity University of Memphis Memphis Tennessee 38152 USA

Data Science Lab Office of the Chief Information Officer Smithsonian Institution Washington D C 20013 7012 USA

Department of Biological Sciences University of Memphis Memphis Tennessee 38152 USA

Department of Botany Faculty of Science Charles University Benátská 2 CZ 12800 Prague Czech Republic

Department of Botany National Museum of Natural History Smithsonian Institution Washington D C 20013 7012 USA

Department of Plant Biology Ecology and Evolution Oklahoma State University Stillwater Oklahoma 74078 USA

Freie Universität Berlin Evolutionary Biology Berlin Germany

Institute of Botany The Czech Academy of Sciences Zámek 1 CZ 25243 Průhonice Czech Republic

Leibniz Institute of Freshwater Ecology and Inland Fisheries Berlin Germany

Plant Science and Biodiversity Centre Slovak Academy of Sciences SK 84523 Bratislava Slovakia

Zobrazit více v PubMed

Abadi, S. , Azouri D., Pupko T., and Mayrose I.. 2019. Model selection may not be a mandatory step for phylogeny reconstruction. Nature Communications 10(1): 934. PubMed PMC

Adams, R. H. , and Castoe T. A.. 2019. Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error. Molecular Phylogenetics and Evolution 134: 164–171. PubMed

Bakker, F. T. , Lei D., Yu J., Mohammadin S., Wei Z., van de Kerke S., Gravendeel B., et al. 2016. Herbarium genomics: Plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline. Biological Journal of the Linnean Society 117(1): 33–43.

Baldwin, B. G. , and Sanderson M. J.. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences USA 95(16): 9402–9406. PubMed PMC

Barker, M. S. , Li Z., Kidder T. I., Reardon C. R., Lai Z., Oliveira L. O., Scascitelli M., et al. 2016. Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae. American Journal of Botany 103(7): 1203–1211. PubMed

Barreda, V. D. , Palazzesi L., Tellería M. C., Olivero E. B., Raine J. I., and Forest F.. 2015. Early evolution of the angiosperm clade Asteraceae in the Cretaceous of Antarctica. Proceedings of the National Academy of Sciences USA 112(35): 10989–10994. PubMed PMC

Bayzid, M. S. , and Warnow T.. 2013. Naive binning improves phylogenomic analyses. Bioinformatics 29(18): 2277–2284. PubMed

Bergsten, J. 2005. A review of long‐branch attraction. Cladistics 21(2): 163–193. PubMed

Blanc, G. , and Wolfe K. H.. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16(7): 1667–1678. PubMed PMC

Bogarín, D. , Pérez‐Escobar O. A., Groenenberg D., Holland S. D., Karremans A. P., Lemmon E. M., Lemmon A. R., et al. 2018. Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Molecular Phylogenetics and Evolution 129: 27–47. PubMed

Bolger, A. M. , Lohse M., and Usadel B.. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30(15): 2114–2120. PubMed PMC

Borowiec, M. L. 2016. AMAS: A fast tool for alignment manipulation and computing of summary statistics. PeerJ 4: e1660. PubMed PMC

Buddenhagen, C. , Lemmon A. R., Lemmon E. M., Bruhl J., Cappa J., Clement W. L., Donoghue M., et al. 2016. Anchored phylogenomics of angiosperms I: Assessing the robustness of phylogenetic estimates. bioRxiv: 086298.

Bürkner, P.‐C. 2017. brms: An R package for Bayesian multilevel models using Stan. Journal of Statistical Software 80(1): 1–28.

Capella‐Gutiérrez, S. , Silla‐Martínez J. M., and Gabaldón T.. 2009. trimAl: A tool for automated alignment trimming in large‐scale phylogenetic analyses. Bioinformatics 25(15): 1972–1973. PubMed PMC

Carlsen, M. M. , Fér T., Schmickl R., Leong‐Skornickova J., Newman M., and Kress W. J.. 2018. Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data. Molecular Phylogenetics and Evolution 128: 55–68. PubMed

Chau, J. H. , O'Leary N., Sun W.‐B., and Olmstead R. G.. 2017. Phylogenetic relationships in tribe Buddlejeae (Scrophulariaceae) based on multiple nuclear and plastid markers. Botanical Journal of the Linnean Society 184(2): 137–166.

Chifman, J. , and Kubatko L. S.. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30(23): 3317–3324. PubMed PMC

Chou, J. , Gupta A., Yaduvanshi S., Davidson R., Nute M., Mirarab S., and Warnow T.. 2015. A comparative study of SVD quartets and other coalescent‐based species tree estimation methods. BMC Genomics 16: S2. PubMed PMC

Collet, G. 2012. MstatX. Website: https://github.com/gcollet/MstatX/ [accessed 20 June 2017].

Constantinides, B. , and Robertson D. L.. 2017. Kindel: indel‐aware consensus for nucleotide sequence alignments. The Journal of Open Source Software 2(15): 282.

Couvreur, T. L. P. , Helmstetter A. J., Koenen E. J. M., Bethune K., Brandão R. D., Little S. A., Sauquet H., et al. 2019. Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes. Frontiers in Plant Science 9: 1941. PubMed PMC

Criscuolo, A. , and Gribaldo S.. 2010. BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology 10(1): 210. PubMed PMC

Crowl, A. A. , Myers C., and Cellinese N.. 2017. Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade. Evolution 71(4): 913–922. PubMed PMC

de La Harpe, M. , Hess J., Loiseau O., Salamin N., Lexer C., and Paris M.. 2019. A dedicated target capture approach reveals variable genetic markers across micro‐ and macro‐evolutionary time scales in palms. Molecular Ecology Resources 19(1): 221–234. PubMed

de Oliveira Martins, L. , and Posada D.. 2017. Species tree estimation from genome‐wide data with guenomu. Methods in Molecular Biology 1525: 461–478. PubMed

Diazgranados, M. , and Barber J. C.. 2017. Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): A remarkable example of recent rapid radiation in sky islands. PeerJ 5: e2968. PubMed PMC

Du, P. , Hahn M. W., and Nakhleh L.. 2019a. Species tree inference under the multispecies coalescent on data with paralogs is accurate. bioRxiv 498378 [Preprint]. 23 January 2019 [cited 7 June 2019]. Available from: 10.1101/498378. DOI

Du, P. , Ogilvie H. A., and Nakhleh L.. 2019b. Unifying gene duplication, loss, and coalescence on phylogenetic networks In Cai Z., Skums P., and Li M. [eds.], Bioinformatics research and applications. International Symposium on Bioinformatics Research and Applications 2019. Lecture Notes in Computer Science, vol. 11490 Springer, Cham, Switzerland.

Edwards, S. V. 2016. Phylogenomic subsampling: A brief review. Zoologica Scripta 45(S1): 63–74.

Edwards, S. V. , Xi Z., Janke A., Faircloth B. C., McCormack J. E., Glenn T. C., Zhong B., et al. 2016. Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. Molecular Phylogenetics and Evolution 94(Pt A): 447–462. PubMed

Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27(4): 401–410.

Fér, T. , and Schmickl R. E.. 2018. HybPhyloMaker: Target enrichment data analysis from raw reads to species trees. Evolutionary Bioinformatics Online 14: 10.1177/1176934317742613. PubMed DOI PMC

Folk, R. A. , Mandel J. R., and Freudenstein J. V.. 2015. A protocol for targeted enrichment of intron‐containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). Applications in Plant Sciences 3(8): 1500039. PubMed PMC

Fu, Z.‐X. , Jiao B.‐H., Nie B., Zhang G.‐J., and Gao T.‐G.. 2016. A comprehensive generic‐level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae. Journal of Systematics and Evolution 54(4): 416–437.

Funk, V. A. , Anderberg A., Baldwin B. G., Bayer R. J., Bonifacino J. M., Breitwieser I., Brouillet L., et al. 2009. Compositae metatrees: The next generation In Funk V. A., Susanna A., Stuessy T., and Bayer R. [eds.], Systematics, evolution, and biogeography of Compositae, 747–777. IAPT, Vienna, Austria.

Garcia, S. , Leitch I. J., Anadon‐Rosell A., Canela M. A., Galvez F., Garnatje T., Gras A., et al. 2014. Recent updates and developments to plant genome size databases. Nucleic Acids Research 42(Database issue): D1159–D1166. PubMed PMC

Gardner, E. M. , Johnson M. G., Ragone D., Wickett N. J., and Zerega N. J. C.. 2016. Low‐coverage, whole‐genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery. Applications in Plant Sciences 4(7): 1600017. PubMed PMC

Garnatje, T. , Canela M. Á., Garcia S., Hidalgo O., Pellicer J., Sánchez‐Jiménez I., Siljak‐Yakovlev S., et al. 2011. GSAD: A genome size in the Asteraceae database. Cytometry Part A 79A(6): 401–404. PubMed

Gatesy, J. , Sloan D. B., Warren J. M., Baker R. H., Simmons M. P., and Springer M. S.. 2019. Partitioned coalescence support reveals biases in species‐tree methods and detects gene trees that determine phylogenomic conflicts. Molecular Phylogenetics and Evolution 139: 106539. PubMed

Gerth, M. 2019. Why we should not abandon model selection in phylogeny reconstruction. Website: https://www.michaelgerth.net/news--blog/why-we-should-not-abandon-model-selection-in-phylogeny-reconstruction [accessed June 2019].

Hart, M. L. , Forrest L. L., Nicholls J. A., and Kidner C. A.. 2016. Retrieval of hundreds of nuclear loci from herbarium specimens. Taxon 65(5): 1081–1092.

Harvey, M. G. , Smith B. T., Glenn T. C., Faircloth B. C., and Brumfield R. T.. 2016. Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Systematic Biology 65(5): 910–924. PubMed

Heled, J. , and Drummond A. J.. 2010. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution 27(3): 570–580. PubMed PMC

Hellmuth, M. , Wieseke N., Lechner M., Lenhof H.‐P., Middendorf M., and Stadler P. F.. 2015. Phylogenomics with paralogs. Proceedings of the National Academy of Sciences USA 112(7): 2058–2063. PubMed PMC

Herrando‐Moraira, S. , Calleja J., Carnicero P., Fujikawa K., Galbany‐Casals M., Garcia‐Jacas N., Im H., et al. 2018. Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae). Molecular Phylogenetics and Evolution 128: 69–87. PubMed

Herrando‐Moraira, S. , Antonio Calleja J., Galbany‐Casals M., Garcia‐Jacas N., Liu J. Q., Lopez‐Alvarado J., Lopez‐Pujol J., et al. 2019. Nuclear and plastid DNA phylogeny of tribe Cardueae (Compositae) with Hyb‐Seq data: A new subtribal classification and a temporal diversification framework. Molecular Phylogenetics and Evolution 137: 313–332. PubMed

Heyduk, K. , Trapnell D. W., Barrett C. F., and Leebens‐Mack J.. 2015. Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture. Biological Journal of the Linnean Society 117(1): 106–120.

Huang, C.‐H. , Zhang C., Liu M., Hu Y., Gao T., Qi J., and Ma H.. 2016. Multiple polyploidization events across Asteraceae with two nested events in the early history revealed by nuclear phylogenomics. Molecular Biology and Evolution 33(11): 2820–2835. PubMed PMC

Hulsen, T. , de Vlieg J., and Alkema W.. 2008. BioVenn: A web application for the comparison and visualization of biological lists using area‐proportional Venn diagrams. BMC Genomics 9: 488. PubMed PMC

Huson, D. H. , and Bryant D.. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254–267. PubMed

Jiao, Y. , Wickett N. J., Ayyampalayam S., Chanderbali A. S., Landherr L., Ralph P. E., Tomsho L. P., et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97–100. PubMed

Johnson, M. G. , Gardner E. M., Liu Y., Medina R., Goffinet B., Shaw A. J., Zerega N. J. C., et al. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7): 1600016. PubMed PMC

Johnson, M. G. , Pokorny L., Dodsworth S., Botigue L. R., Cowan R. S., Devault A., Eiserhardt W. L., et al. 2019. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k‐medoids clustering. Systematic Biology 68: 594–606. PubMed PMC

Jones, K. E. , Fér T., Schmickl R. E., Dikow R. B., Funk V. A., Herrando‐Moraira S., Johnston P. R., et al. 2019. Data from: An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Dryad Digital Repository. 10.5061/dryad.60vb576 PubMed DOI PMC

Kadlec, M. , Bellstedt D. U., Le Maitre N. C., and Pirie M. D.. 2017. Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”? PeerJ 5: e3569. PubMed PMC

Kainer, D. , and Lanfear R.. 2015. The effects of partitioning on phylogenetic inference. Molecular Biology and Evolution 32(6): 1611–1627. PubMed

Kates, H. R. , Johnson M. G., Gardner E. M., Zerega N. J. C., and Wickett N. J.. 2018. Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus . American Journal of Botany 105(3): 404–416. PubMed

Katoh, K. , and Standley D. M.. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30(4): 772–780. PubMed PMC

Kent, W. J. 2002. BLAT—the BLAST‐like alignment tool. Genome Research 12(4): 656–664. PubMed PMC

Kilian, N. , Gemeinholzer B., and Lack W.. 2009. Tribe Cichorieae In Funk V. A., Susanna A., Stuessy T., and Bayer R. [eds.], Systematics, evolution, and biogeography of the Compositae, 343–383. IAPT, Vienna, Austria.

Kilian, N. , Hand R., and von Raab‐Straube E.. 2009+ (continuously updated). Cichorieae Systematics Portal. Website: http://cichorieae.e-taxonomy.net/portal/ [accessed September 2018].

Kilian, N. , Sennikov A., Wang Z.‐H., Gemeinholzer B., and Zhang J.‐W.. 2017. Sub‐Paratethyan origin and Middle to Late Miocene principal diversification of the Lactucinae (Compositae: Cichorieae) inferred from molecular phylogenetics, divergence‐dating and biogeographic analysis. Taxon 66(3): 675–703.

Knope, M. L. , Morden C. W., Funk V. A., and Fukami T.. 2012. Area and the rapid radiation of Hawaiian Bidens (Asteraceae). Journal of Biogeography 39(7): 1206–1216.

Kozlov, A. M. , Darriba D., Flouri T., Morel B., and Stamatakis A.. 2019. RAxML‐NG: A fast, scalable, and user‐friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 10.1093/bioinformatics/btz305. PubMed DOI PMC

Kubatko, L. S. , and Degnan J. H.. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56(1): 17–24. PubMed

Lanfear, R. , Calcott B., Kainer D., Mayer C., and Stamatakis A.. 2014. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology 14(1): 82. PubMed PMC

Lanfear, R. , Frandsen P. B., Wright A. M., Senfeld T., and Calcott B.. 2016. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34(3): 772–773. PubMed

Liu, L. , and Yu L.. 2011. Estimating species trees from unrooted gene trees. Systematic Biology 60(5): 661–667. PubMed

Liu, Y. , Johnson M. G., Cox C. J., Medina R., Devos N., Vanderpoorten A., Hedenäs L., et al. 2019. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications 10(1): 1485. PubMed PMC

Mai, U. , and Mirarab S.. 2018. TreeShrink: Fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics 19(Suppl 5): 272. PubMed PMC

Mandel, J. R. , Dikow R. B., Funk V. A., Masalia R. R., Staton S. E., Kozik A., Michelmore R. W., et al. 2014. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. Applications in Plant Sciences 2(2): 1300085. PubMed PMC

Mandel, J. R. , Dikow R. B., and Funk V. A.. 2015. Using phylogenomics to resolve mega‐families: An example from Compositae. Journal of Systematics and Evolution 53(5): 391–402.

Mandel, J. R. , Barker M. S., Bayer R. J., Dikow R. B., Gao T.‐G., Jones K. E., Keeley S., et al. 2017. The Compositae Tree of Life in the age of phylogenomics. Journal of Systematics and Evolution 55(4): 405–410.

Mandel, J. R. , Dikow R. B., Siniscalchi C. M., Thapa R., Watson L. E., and Funk V. A.. 2019. A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proceedings of the National Academy of Sciences USA 116(28): 14083–14088. PubMed PMC

Mirarab, S. , and Warnow T.. 2015. ASTRAL‐II: Coalescent‐based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31(12): i44–i52. PubMed PMC

Mirarab, S. , Reaz R., Bayzid M. S., Zimmermann T., Swenson M. S., and Warnow T.. 2014. ASTRAL: Genome‐scale coalescent‐based species tree estimation. Bioinformatics 30(17): i541–i548. PubMed PMC

Mitchell, N. , Lewis P. O., Lemmon E. M., Lemmon A. R., and Holsinger K. E.. 2017. Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. American Journal of Botany 104(1): 102–115. PubMed

Molloy, E. K. , and Warnow T.. 2019. Statistically consistent divide‐and‐conquer pipelines for phylogeny estimation using NJMerge. bioRxiv 469130 [Preprint]. 7 February 2019 [cited 14 June 2019]. Available from 10.1101/469130. PubMed DOI PMC

Moore, A. J. , Vos J. M., Hancock L. P., Goolsby E., and Edwards E. J.. 2018. Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales). Systematic Biology 67(3): 367–383. PubMed

Murphy, B. , Forest F., Barraclough T., Rosindell J., Bellot S., Cowan R., Golos M., et al. 2019. A phylogenomic analysis of Nepenthes (Nepenthaceae). bioRxiv 680488 [Preprint]. 24 June 2019 [cited 8 September 2019]. Available from: 10.1101/680488. PubMed DOI

Nicholls, J. A. , Pennington R. T., Koenen E. J., Hughes C. E., Hearn J., Bunnefeld L., Dexter K. G., et al. 2015. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science 6: 710. PubMed PMC

Panero, J. L. , and Crozier B. S.. 2016. Macroevolutionary dynamics in the early diversification of Asteraceae. Molecular Phylogenetics and Evolution 99: 116–132. 10.1016/j.ympev.2016.03.007. PubMed DOI

Paradis, E. , and Schliep K.. 2019. ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35(3): 526–528. PubMed

Paradis, E. , Claude J., and Strimmer K.. 2004. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20: 289–290. PubMed

Parks, S. L. , and Goldman N.. 2014. Maximum likelihood inference of small trees in the presence of long branches. Systematic Biology 63(5): 798–811. PubMed PMC

Pelser, P. B. , Kennedy A. H., Tepe E. J., Shidler J. B., Nordenstam B., Kadereit J. W., and Watson L. E.. 2010. Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies. American Journal of Botany 97(5): 856–873. PubMed

Pisani, D. 2004. Identifying and removing fast‐evolving sites using compatibility analysis: An example from the Arthropoda. Systematic Biology 53(6): 978–989. PubMed

Pouchon, C. , Fernández A., Nassar J. T., Boyer F., Aubert S., Lavergne S., and Maváruz J.. 2018. Phylogenomic analysis of the explosive adaptive radiation of the Espeletia complex (Asteraceae) in the Tropical Andes. Systematic Biology 67(6): 1041–1060. PubMed

Qu, X.‐J. , Jin J.‐J., Chaw S.‐M., Li D.‐Z., and Yi T.‐S.. 2017. Multiple measures could alleviate long‐branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae). Scientific Reports 7: 41005. PubMed PMC

R Core Team . 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing; Vienna, Austria.

Roch, S. , and Steel M.. 2015. Likelihood‐based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theoretical Population Biology 100: 56–62. PubMed

Ruprecht, C. , Lohaus R., Vanneste K., Mutwil M., Nikoloski Z., Van de Peer Y., and Persson S.. 2017. Revisiting ancestral polyploidy in plants. Science Advances 3(7): e1603195. PubMed PMC

Sanderson, M. J. , Wojciechowski M. F., Hu J. M., Khan T. S., and Brady S. G.. 2000. Error, bias, and long‐branch attraction in data for two chloroplast photosystem genes in seed plants. Molecular Biology and Evolution 17(5): 782–797. PubMed

Schmickl, R. , Liston A., Zeisek V., Oberlander K., Weitemier K., Straub S. C., Cronn R. C., et al. 2015. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: The pipeline and its application in southern African Oxalis (Oxalidaceae). Molecular Ecology Resources 16(5): 1124–1135. PubMed

Shen, X.‐X. , Hittinger C. T., and Rokas A.. 2017. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecology & Evolution 1: 0126. PubMed PMC

Simon, S. , Narechania A., Desalle R., and Hadrys H.. 2012. Insect phylogenomics: Exploring the source of incongruence using new transcriptomic data. Genome Biology and Evolution 4(12): 1295–1309. PubMed PMC

Slovák, M. , Kučera J., Marhold K., and Zozomová‐Lihová J.. 2012. The morphological and genetic variation in the polymorphic species Picris hieracioides (Compositae, Lactuceae) in Europe strongly contrasts with traditional taxonomical concepts. Systematic Botany 37(1): 258–278.

Slovák, M. , Kučera J., Záveská E., and Vd'ačný P.. 2014. Dealing with discordant genetic signal caused by hybridisation, incomplete lineage sorting and paucity of primary nucleotide homologies: A case study of closely related members of the genus Picris subsection Hieracioides (Compositae). PLoS ONE 9(9): e104929. PubMed PMC

Slovák, M. , Kučera J., Lack H. W., Ziffer‐Berger J., Melicharkova A., Záveska E., and Vd'acný P.. 2018. Diversification dynamics and transoceanic Eurasian‐Australian disjunction in the genus Picris (Compositae) induced by the interplay of shifts in intrinsic/extrinsic traits and paleoclimatic oscillations. Molecular Phylogenetics and Evolution 119: 182–195. PubMed

Smith, S. A. , Moore M. J., Brown J. W., and Yang Y.. 2015. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology 15: 150. PubMed PMC

Sousa, F. , Bertrand Y. J. K., Doyle J. J., Oxelman B., and Pfeil B. E.. 2017. Using genomic location and coalescent simulation to investigate gene tree discordance in Medicago L. Systematic Biology 66(6): 934–949. PubMed

Staats, M. , Erkens R. H. J., van de Vossenberg B., Wieringa J. J., Kraaijeveld K., Stielow B., Geml J., et al. 2013. Genomic treasure troves: Complete genome sequencing of herbarium and insect museum specimens. PLoS ONE 8(7): e69189. PubMed PMC

Stamatakis, A. 2006. RAxML‐VI‐HPC: Maximum likelihood‐based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21): 2688–2690. PubMed

Stamatakis, A. 2014. RAxML version 8: A tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics 30: 1312–1313. PubMed PMC

Stephens, J. D. , Rogers W. L., Heyduk K., Cruse‐Sanders J. M., Determann R. O., Glenn T. C., and Malmberg R. L.. 2015. Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment. Molecular Phylogenetics and Evolution 85: 76–87. PubMed

Štorchová, H. , Hrdličková R., Chrtek J., Tetera M., Fitze D., and Fehrer J.. 2000. An improved method of DNA isolation from plants collected in the field and conserved in saturated NaCl/CTAB solution. Taxon 49(1): 79–84.

Straub, S. C. , Moore M. J., Soltis P. S., Soltis D. E., Liston A., and Livshultz T.. 2014. Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long‐branch attraction, and model selection in crown clade Apocynaceae. Molecular Phylogenetics and Evolution 80: 169–185. PubMed

Talavera, G. , and Castresana J.. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56(4): 564–577. PubMed

Tiley, G. P. , Ané C., and Burleigh J. G.. 2016. Evaluating and characterizing ancient whole‐genome duplications in plants with gene count data. Genome Biology and Evolution 8(4): 1023–1037. PubMed PMC

Tremetsberger, K. , Gemeinholzer B., Zetzsche H., Blackmore S., Kilian N., and Talavera S.. 2012. Divergence time estimation in Cichorieae (Asteraceae) using a fossil‐calibrated relaxed molecular clock. Organisms Diversity & Evolution 13: 1–13.

Uribe‐Convers, S. , Settles M. L., and Tank D. C.. 2016. A phylogenomic approach based on PCR target enrichment and high throughput sequencing: Resolving the diversity within the South American species of Bartsia L. (Orobanchaceae). PLoS ONE 11(2): e0148203. PubMed PMC

Vallès, J. , Canela M. Á., Garcia S., Hidalgo O., Pellicer J., Sánchez‐Jiménez I., Siljak‐Yakovlev S., et al. 2013. Genome size variation and evolution in the family Asteraceae. Caryologia 66(3): 221–235.

Vanneste, K. , Baele G., Maere S., and Van de Peer Y.. 2014. Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous‐Paleogene boundary. Genome Research 24(8): 1334–1347. PubMed PMC

Vatanparast, M. , Powell A., Doyle J. J., and Egan A. N.. 2018. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. Applications in Plant Sciences 6(3): e1036. PubMed PMC

Villaverde, T. , Pokorny L., Olsson S., Rincón‐Barrado M., Johnson M. G., Gardner E. M., Wickett N. J., et al. 2018. Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above. New Phytologist 220(2): 636–650. PubMed

Walker, J. F. , Brown J. W., and Smith S. A.. 2018. Analyzing contentious relationships and outlier genes in phylogenomics. Systematic Biology 67(5): 916–924. PubMed

Wang, N. , Yang Y., Moore M. J., Brockington S. F., Walker J. F., Brown J. W., Liang B., et al. 2019. Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments. Molecular Biology and Evolution 36: 112–126. PubMed

Wanke, S. , Granados Mendoza C., Müller S., Paizanni Guillén A., Neinhuis C., Lemmon A. R., Lemmon E. M., et al. 2017. Recalcitrant deep and shallow nodes in Aristolochia (Aristolochiaceae) illuminated using anchored hybrid enrichment. Molecular Phylogenetics and Evolution 117: 111–123. PubMed

Warnow, T. 2015. Concatenation analyses in the presence of incomplete lineage sorting. PLoS Currents 7: 10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7. PubMed DOI PMC

Weitemier, K. , Straub S. C. K., Cronn R. C., Fishbein M., Schmickl R., McDonnell A., and Liston A.. 2014. Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Sciences 2(9): 1400042. PubMed PMC

Wolf, P. G. , Robison T. A., Johnson M. G., Sundue M. A., Testo W. L., and Rothfels C. J.. 2018. Target sequence capture of nuclear‐encoded genes for phylogenetic analysis in ferns. Applications in Plant Sciences 6(5): e01148. PubMed PMC

Wood, T. E. , Takebayashi N., Barker M. S., Mayrose I., Greenspoon P. B., and Rieseberg L. H.. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences USA 106(33): 13875–13879. PubMed PMC

Wu, M. , Chatterji S., and Eisen J. A.. 2012. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7(1): e30288. PubMed PMC

Xi, Z. , Ruhfel B. R., Schaefer H., Amorim A. M., Sugumaran M., and Wurdack K. J.. 2012. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences USA 109(43): 17519–17524. PubMed PMC

Xu, H. , Luo X., Qian J., Pang X., Song J., Qian G., Chen J., et al. 2012. FastUniq: A fast de novo duplicates removal tool for paired short reads. PLoS ONE 7(12): e52249. PubMed PMC

Zhang, C. , Rabiee M., Sayyari E., and Mirarab S.. 2018. ASTRAL‐III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 8(19): 153. PubMed PMC

How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

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10.5061/dryad.60vb576