title: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae).
abstract: 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.
authors.affiliation: Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Av. Santa Rosa 11315, La Pintana, Santiago, Chile; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. Electronic address: nicogarciab@gmail.com.
authors.forename: Nicolás
authors.initials: N
authors.lastname: García
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. Electronic address: ryanfolk@ufl.edu.
authors.forename: Ryan A
authors.initials: RA
authors.lastname: Folk
authors.affiliation: USDA-ARS-SHRS-National Germplasm Repository, 13601 Old Cutler Road, Miami, FL 33158, USA. Electronic address: Alan.Meerow@ars.usda.gov.
authors.forename: Alan W
authors.initials: AW
authors.lastname: Meerow
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA. Electronic address: srikarchamala@gmail.com.
authors.forename: Srikar
authors.initials: S
authors.lastname: Chamala
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA. Electronic address: magitz@ufl.edu.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Gitzendanner
authors.affiliation: GaTE Laboratory, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, IBUSP, Rua do Matão 277, CEP: 05508-090 São Paulo, SP, Brazil. Electronic address: rsolive1@gmail.com.
authors.forename: Renata Souza de
authors.initials: RS
authors.lastname: Oliveira
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: dsoltis@ufl.edu.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: psoltis@flmnh.ufl.edu.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
mesh_terms: D000070378:Amaryllidaceae / Q000033:anatomy & histology* / Q000145:classification*; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D003198:Computer Simulation; D004171:Diploidy; D056426:Genetic Loci; D006801:Humans; D006824:Hybridization, Genetic; D016013:Likelihood Functions; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
keywords: Coalescence; Cytonuclear discordance; Hybridization; Species tree; Target-enrichment