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dc.contributor.author García, Nicolás
dc.contributor.author Folk, Ryan A.
dc.contributor.author Meerow, Alan W.
dc.contributor.author Chamala, Srikar
dc.contributor.author Gitzendanner, Matthew A.
dc.contributor.author Oliveira, Renata S. de
dc.contributor.author Soltis, Douglas E.
dc.contributor.author Soltis, Pamela S.
dc.coverage.spatial South America
dc.date.accessioned 2017-04-11T14:34:59Z
dc.date.available 2017-04-11T14:34:59Z
dc.date.issued 2017-04-06
dc.identifier doi:10.5061/dryad.kg686
dc.identifier.citation García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RSd, Soltis DE, Soltis PS (2017) Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Molecular Phylogenetics and Evolution 111: 231–247.
dc.identifier.issn 1055-7903
dc.identifier.uri http://hdl.handle.net/10255/dryad.143032
dc.description Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
dc.relation.haspart doi:10.5061/dryad.kg686/1
dc.relation.haspart doi:10.5061/dryad.kg686/2
dc.relation.haspart doi:10.5061/dryad.kg686/3
dc.relation.haspart doi:10.5061/dryad.kg686/4
dc.relation.haspart doi:10.5061/dryad.kg686/5
dc.relation.haspart doi:10.5061/dryad.kg686/6
dc.relation.haspart doi:10.5061/dryad.kg686/7
dc.relation.haspart doi:10.5061/dryad.kg686/8
dc.relation.haspart doi:10.5061/dryad.kg686/9
dc.relation.haspart doi:10.5061/dryad.kg686/10
dc.relation.haspart doi:10.5061/dryad.kg686/11
dc.relation.haspart doi:10.5061/dryad.kg686/12
dc.relation.haspart doi:10.5061/dryad.kg686/13
dc.relation.isreferencedby doi:10.1016/j.ympev.2017.04.003
dc.subject hybridization
dc.subject coalescence
dc.subject species tree
dc.subject target enrichment
dc.subject cytonuclear discordance
dc.title Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
dc.type Article
dc.contributor.correspondingAuthor García, Nicolás
prism.publicationName Molecular Phylogenetics and Evolution
dryad.fundingEntity DEB-1310839@National Science Foundation (United States)
dryad.dansTransferDate 2018-05-31T21:25:17.957+0000
dryad.dansEditIRI https://easy.dans.knaw.nl/sword2/container/100f48df-0ec2-4309-ae52-816be4f36d1e
dryad.dansTransferFailed 2018-05-17T10:55:39.171+0000
dryad.dansArchiveDate 2018-05-31T23:03:15.698+0000

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Title bait-120-60-selection
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Description Sequences used to design MYbaits kit.
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Title Curated alignments and gene trees
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Description Includes alignments and partition files, RAxML bootstrap and best tree files for curated nuclear loci.
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Title aTRAM alignments and gene trees
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Description Includes raw alignments for 48 nuclear loci obtained through aTRAM assembly. Also edited alignments and RAxML output files for 39 nuclear loci.
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Title Concatenated alignments and trees
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Description Includes alignments and trees for concatenated analyses of 39 aTRAM nuclear loci, 15 curated nuclear loci (including and excluding noncoding regions), and curated nuclear plus plastid regions.
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Title Networks
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Description Includes tree and nexus files used to compute neighbor-net and hybridization networks.
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Title ASTRAL
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Description Includes output files from ASTRAL-II analyses of 12 curated nuclear loci and 39 aTRAM nuclear loci.
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Title BUCKy
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Description Includes alignments used in BUCKy and output files for analyses with two different alpha values (1, INFINITY).
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Title *BEAST
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Description Includes xml, log, and species tree files for all runs performed for each analysis.
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Title JML
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Description Includes control and output files for JML analyses of 12 curated nuclear loci and plastid coding sequences. Also collection of *BEAST species trees used in analyses.
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Title Coalescent simulations
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Description Includes simulated gene trees under three branch length scaling factors from ASTRAL species trees inferred from 12 curated loci and 39 aTRAM loci.
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Title run_cut_trim_blat.qsub
Downloaded 4 times
Description Submission script to run Cutadapt, Sickle, Blat, and python script to pull out blat hits.
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Title get_reads_w_blat_hit_pe
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Description Python script
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Title Reference sequences
Downloaded 9 times
Description Transcriptomic reference sequences for 48 nuclear loci.
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