[논문]Phylogenetic relationships of Coreanomecon (Papaveraceae: Papaveroideae), an endemic genus in Korea, using DNA sequences

YUN, Narae; OH, Sang-Hun

doi:10.11110/kjpt.2018.48.4.289

Phylogenetic relationships of Coreanomecon (Papaveraceae: Papaveroideae), an endemic genus in Korea, using DNA sequences 원문보기

식물분류학회지 = Korean journal of plant taxonomy, v.48 no.4, 2018년, pp.289 - 300

YUN, Narae (Department of Biology, Daejeon University) , OH, Sang-Hun (Department of Biology, Daejeon University)

Abstract ▼ AI-Helper

Coreanomecon is a monotypic and endemic genus in Korea, distributed mainly in the southern regions. Coreanomecon is morphologically similar to Hylomecon by producing red latex, easily distinguished from Chelidonium, which produces yellow latex. Coreanomecon were merged into Hylomecon or Chelidonium depending on the authors. To understand the phylogenetic relationship of Coreanomecon, DNA sequences of chloroplast rbcL and matK and nuclear Internal Transcribed Spacer (ITS) regions were determined from the species of Papaveroideae (Papaveraceae) in Korea and analyzed with the Maximum Parsimony and Bayesian methods. Phylogenetic analyses of Papaveroideae suggest that Coreanomecon is sister to the clade of Chelidonium and Stylophorum in the ITS data and that it is sister to Hylomecon in the chloroplast (cpDNA) data. A constraining analysis using the Shimodaira-Hasegawa test (S-H test) suggested that the ITS data do not reject the sister relationship of Coreanomecon and Hylomecon. The S-H test also suggested that the cpDNA data is compatible with the placement of Coreanomecon as a sister to the clade of Chelidonium and Stylophorum. Although the conflicting phylogenetic results may stem from insufficient phylogenetic signals, they may also be associated with hybridization between Hylomecon and an ancestor of Stylophorum and Chelidonium. The results of this study suggest that Coreanomecon is a distinct lineage as an endemic genus, supporting the morphological data.

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문제 정의

We are grateful to Jung Won Youm, Yun Gyeong Choi, Dong-Hyuk Lee, and Chae Eun Lim for their help at various stages of this study. We thank the curator and other herbarium staff at KB who generously allowed us to obtain plant samples, as well as two anonymous reviewers for their critical reviews of the manuscript. This work was supported by a research grant, NIBR-201714101, from the National Institute of Biological Resources of Korea.

가설 설정

The resultant MP trees with the constrained relationships were evaluated with the original MP trees without the constraint. The objective of the constraint analysis was to test whether each data set does not reject the hypothesis that Coreanomecon is congeneric to Hylomecon or Chelidonium. For the SH test, 10,000 bootstrap replicates were re-sampled using the re-estimated log likelihood (RELL) method.

제안 방법

The Shimodaira-Hasegawa test did not reject the alternative topology. Enforcement of the sister relationship of Coreanomecon and Chelidonium (Fig. 4B), as suggested in the ITS data with the Korean taxa only (Fig. 1B), required three additional steps in the cpDNA data with Korean taxa only, and the alternative topology was compatible with the cpDNA data in the S-H test. However, eight additional steps were required to generate the sister relationship of Coreanomecon and Chelidonium in both cpDNA and ITS data with extended taxon samples, and this relationship was significantly rejected in the S-H test.
4) were tested using the Shimodaira-Hasegawa test. Enforcing a sister relationship of Coreanomecon and Hylomecon (Fig. 4A) in the ITS data, both for Korean taxa only and extended samples, required five additional steps (Table 3). The Shimodaira-Hasegawa test did not reject the alternative topology.
Gaps resulting from multiple alignments of indels were treated as missing data. Heuristic searches were used with 100 replicates of random sequence additions with tree bisection-reconnection branch swapping, with all of the best trees saved at each step (MulTrees). Bootstrap analyses (Felsenstein, 1985) of 1,000 pseudoreplicates were conducted with heuristic searches, a simple sequence addition in PAUP* to evaluate the support for each clade.
The first 4,000 trees (400,000 generations) were discarded as “burn-in,” and the remaining trees for which the log-likelihood values had reached a plateau were imported in PAUP* to calculate the posterior probability of each clade.
The objectives of the present study are (1) to infer the phylogenetic relationship of Coreanomecon, (2) to examine the implications of the molecular phylogeny on the evolution of the morphological characters of Coreanomecon, and (3) to assess the level of differentiation of the species and evaluate the resolution power of DNA barcodes to identify a species of Papaveroideae in Korea, with an emphasis on species of Papaver.

이론/모형

A specific phylogenetic hypothesis was tested using the Shimodaira-Hasegawa (1999; SH) test, as implemented in PAUP*. In this analysis, MP trees in extended ITS data in Analysis 2 were generated while constraining the topology using the heuristic search method described previously.
Bayesian phylogenetic analyses (BI) were performed with the program MrBayes version 3.2.5 (Huelsenbeck and Ronquist, 2001). A Markov chain Monte Carlo (MCMC) algorithm was employed for 2,000,000 generations, sampling trees every 100 generations, with four independent chains running simultaneously.
The objective of the constraint analysis was to test whether each data set does not reject the hypothesis that Coreanomecon is congeneric to Hylomecon or Chelidonium. For the SH test, 10,000 bootstrap replicates were re-sampled using the re-estimated log likelihood (RELL) method.
Dicentra and Corydalis were used as outgroups. Phylogenetic analyses were conducted using the maximum parsimony (MP) method in PAUP* (Swofford, 2002). All characters were treated as unordered and were weighted equally in the MP analyses.
Three phylogenetic hypotheses (Fig. 4) were tested using the Shimodaira-Hasegawa test. Enforcing a sister relationship of Coreanomecon and Hylomecon (Fig.
Table 3. Tree lengths in the MP analysis, log likelihood scores in the ML analysis, and the significance levels in the Shimodaira-Hasegawa (S-H) test for constrained topology. Differences in tree lengths and likelihood scores between the best and constrained trees for each data point are indicated in parenthesis.

성능/효과

Specific relationships within a triangle, not shown in this figure for brevity, were not constrained in the analysis. A. Coreanomecon is forced to be a sister to Hylomecon; B. Coreanomecon is made to be a sister to Chelidonium; C. Coreanomecon is enforced to be a sister to the clade of Stylophorum and Chelidonium.
Analysis 1 includes Korean taxa only to evaluate the level of molecular differentiation among the Korean taxa. All but one species of Papaveroideae distributed in Korea were included in this study, with a total therefore of seven species in four genera (Table 1). Papaver amurense, distributed in North Korea and in northeast China, including Inner Mongolia, was not included because samples were not available.
1B), required three additional steps in the cpDNA data with Korean taxa only, and the alternative topology was compatible with the cpDNA data in the S-H test. However, eight additional steps were required to generate the sister relationship of Coreanomecon and Chelidonium in both cpDNA and ITS data with extended taxon samples, and this relationship was significantly rejected in the S-H test. Placement of Coreanomecon as a sister to the clade of Chelidonium and Stylophorum (Fig.
The alignment of the combined data of the Korean taxa included 24 sequences with 2,030 sites, among which 367 were parsimoniously informative. In the extended data of cpDNA and ITS, which had more taxa of Papaveroideae for Analyses 2 and 3, the alignments include 1,358 and 753 sites, respectively, of which 167 (12.3%) and 359 (47.7%) were parsimoniously informative (Table 2).
The phylogenetic relationships among Macleaya, the Eomecon and Sanguinaria clade, and the Chelidonium/Coreanomecon clade were unresolved. Monophyly of these genera consisting of the tribe Chelidonieae was weakly supported (Bootstrap support of 64% and Bayesian post-probability of 0.6) (Fig. 2). Papaver was strongly supported as sister to the tribe Chelidonieae.
The cpDNA and ITS markers provided a high degree of species resolution and resolved all of the species of Papaveroideae in Korea, separately or in combination (Table 2). Adding more taxa (Figs.
1, 2). The nuclear data indicated that it is sister to the Stylophorum and Chelidonium clade (Fig. 3). The constraint analysis results suggest that the two different positions of Coreanomecon (Fig.
In this analysis, MP trees in extended ITS data in Analysis 2 were generated while constraining the topology using the heuristic search method described previously. Three constraints were tested: (1) forcing Coreanomecon and Hylomecon monophyletic, (2) Coreanomecon and Chelidonium monophyletic, and whether (3) Coreanomecon is a sister to the clade of Chelidonium and Stylophorum. The topology within the Papaver/Meconopsis and Eomecon/Glaucium clades was collapsed in the constraint, leaving no effect on the reconstruction of the MP tree in the given data set.

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