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Title: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

Author
item GARCIA, NICOLAS - University Of Florida
item Meerow, Alan
item FOLK, RYAN - University Of Florida
item CHAMALA, SRIKAR - University Of Florida
item GITZENDANNER, MATTHEW - University Of Florida
item OLIVEIRA, RENATA SOUZA DE - Universidad De Sao Paulo
item SOLTIS, DOUGLAS - University Of Florida
item SOLTIS, PAMELA - University Of Florida

Submitted to: Molecular Phylogenetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/6/2017
Publication Date: 4/16/2017
Citation: Garcia, N., Meerow, A.W., Folk, R.A., Chamala, S., Gitzendanner, M.A., Oliveira, R., Soltis, D.E., Soltis, P.S. 2017. Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Molecular Phylogenetics and Evolution.doi: 10.1016/j.ympev.2017.04.003.

Interpretive Summary: Using DNA sequences from the chloroplast and nucleus, a tree of life was inferred for the tribe Hippeastreae of the amaryllis family (Amaryllidaceae) using different statistical approaches. Conflicting results among the different genes support an hypothesis of early hybridization among lineages in the tribe. Strong discordance was confirmed in Hippeastrinae between the chloroplast and nuclear genomes, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and chloroplast signals, along a backbone that may also have been affected by retention of ancestral

Technical Abstract: Hybridization is currently considered to be a frequent and important force in plant evolution; 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 examined 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 next-generation sequencing, we obtained data for 18 nuclear loci and nearly complete plastid genome sequences for 35 ingroup taxa plus 5 outgroups. These data were analyzed with a variety of 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. Regarding relationships in Hippeastrinae, our results suggest the presence of two major nuclear lineages characterized by different chromosome numbers: 1) Tocantinia sp. and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, 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.