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Research Project: Genetic Characterization, Genetic Improvement, and Best Horticultural Management Practices for Subtropical/Tropical Ornamental Germplasm

Location: Subtropical Horticulture Research

Title: Exploration of reticulate evolution in Amaryllidaceae tribe Hippeastreae (Asparagales) using sequence capture and NGS of low-copy nuclear markers

Author
item Garcia, Nicolas - University Of Florida
item Meerow, Alan
item Chamala, Srikar - University Of Florida
item Gitzendanner, Matthew - University Of Florida
item Oliveira, Ranta Souza De - Universidade Nacional De Sao Paulo
item Soltis, Douglas - University Of Florida
item Folk, Ryan - University Of Florida
item Soltis, Pamela - University Of Florida

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/21/2016
Publication Date: 8/2/2016
Citation: Garcia, N., Meerow, A.W., Chamala, S., Gitzendanner, M., Oliveira, R., Soltis, D., Folk, R., Soltis, P. 2016. Exploration of reticulate evolution in Amaryllidaceae tribe Hippeastreae (Asparagales) using sequence capture and NGS of low-copy nuclear markers. Meeting Abstract.

Interpretive Summary: Interpretive Abstract Amaryllidaceae tribe Hippeastreae constitute a horticulturally valuable group of approximately 180 species of American flower bulbs, characterized by various numbers of chromosomes. A recent hypothesis based on nuclear ribosomal DNA and chloroplast sequence data states that Hippeastreae experienced ancient diploid hybridization(s) that preceded the radiation of the major subclade, Hippeastrinae. Target-enriched DNA libraries were sequenced on the Illumina MiSeq platform for 35 taxa (representing only diploid taxa) plus five outgroups. Gene trees and coalescent-based species trees were estimated using 18 nuclear loci. Species tree and concordance analyses suggest two major clades within Hippeastrinae, one characterized by 2n = 22 (Tocantinia, Hippeastrum) and another by 2n = 12, 14, and 18 (Eithea, Habranthus, Rhodophiala, Zephyranthes). Whole chloroplast genome (cpDNA) sequences were extracted from Illumina reads and we analyzed an edited alignment of ca. 130,000 bp (after removing one Inverted Repeat and problematic regions) with 2% missing data. A strongly supported cpDNA tree was obtained, albeit widely conflicting with the nuclear species tree regarding relationships in Hippeastrinae. Network analyses were performed to summarize conflicts among nuclear loci and between nuclear and cpDNA data. The source of incongruence was explored with JML (posterior predictive approach) and coalescent simulations. The resulting phylogenetic framework will serve as a basis for understanding patterns of character evolution in Hippeastreae and for reclassification of the tribe at the generic level.

Technical Abstract: Technical Abstract Amaryllidaceae tribe Hippeastreae constitute a horticulturally valuable group of approximately 180 species of American petaloid monocots, characterized by dysploidy and polyploidy. A recent hypothesis based on ITS and chloroplast sequence data states that Hippeastreae experienced ancient diploid hybridization(s) that preceded the radiation of the major subclade, Hippeastrinae. Target-enriched DNA libraries were sequenced on the Illumina MiSeq platform for 35 ingroup taxa (representing only diploid taxa) plus five outgroups. Gene trees and coalescent-based species trees were estimated using 18 nuclear loci. Species tree and concordance analyses suggest two major clades within Hippeastrinae, one characterized by 2n = 22 (Tocantinia, Hippeastrum) and another by 2n = 12, 14, and 18 (Eithea, Habranthus, Rhodophiala, Zephyranthes). Whole chloroplast genome (cpDNA) sequences were extracted from Illumina reads and we analyzed an edited alignment of ca. 130,000 bp (after removing one Inverted Repeat and problematic regions) with 2% missing data. A strongly supported cpDNA tree was obtained, albeit widely conflicting with the nuclear species tree regarding relationships in Hippeastrinae. Network analyses were performed to summarize conflicts among nuclear loci and between nuclear and cpDNA data. The source of incongruence was explored with JML (posterior predictive approach) and coalescent simulations. The resulting phylogenetic framework will serve as a basis for understanding patterns of character evolution in Hippeastreae and for reclassification of the tribe at the generic level.