Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae)

Xun Gong, Kuo Hsiang Hung, Yu Wei Ting, Tsai Wen Hsu, Lenka Malikova, Huyen Trang Tran, Chao-Li Huang, Shih Hui Liu, Tzen-Yuh Chiang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.

Original languageEnglish
Article numbere0183209
JournalPloS one
Volume12
Issue number8
DOIs
Publication statusPublished - 2017 Aug 1

Fingerprint

Liliaceae
Lilium
Gene Flow
Expressed Sequence Tags
gene flow
Phylogeny
Genes
Chloroplast DNA
phylogeny
expressed sequence tags
loci
Ribosomal Spacer DNA
chloroplast DNA
Genetic Recombination
Taxonomies
genetic recombination
ribosomal DNA
topology
Topology
genes

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Gong, X., Hung, K. H., Ting, Y. W., Hsu, T. W., Malikova, L., Tran, H. T., ... Chiang, T-Y. (2017). Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). PloS one, 12(8), [e0183209]. https://doi.org/10.1371/journal.pone.0183209
Gong, Xun ; Hung, Kuo Hsiang ; Ting, Yu Wei ; Hsu, Tsai Wen ; Malikova, Lenka ; Tran, Huyen Trang ; Huang, Chao-Li ; Liu, Shih Hui ; Chiang, Tzen-Yuh. / Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). In: PloS one. 2017 ; Vol. 12, No. 8.
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Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). / Gong, Xun; Hung, Kuo Hsiang; Ting, Yu Wei; Hsu, Tsai Wen; Malikova, Lenka; Tran, Huyen Trang; Huang, Chao-Li; Liu, Shih Hui; Chiang, Tzen-Yuh.

In: PloS one, Vol. 12, No. 8, e0183209, 01.08.2017.

Research output: Contribution to journalArticle

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AU - Tran, Huyen Trang

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Gong X, Hung KH, Ting YW, Hsu TW, Malikova L, Tran HT et al. Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). PloS one. 2017 Aug 1;12(8). e0183209. https://doi.org/10.1371/journal.pone.0183209