02347nas a2200217 4500008004100000245008300041210006900124490001000193520169700203653002801900653001201928653002401940653002101964100001901985700001302004700001202017700001902029700001702048700001602065856004802081 2020 eng d00aConflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)0 aConflicting phylogenetic signals in plastomes of the tribe Laure0 v101553 a

Background. Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict.
Results. We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node.
Conclusions. Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.

10aIntra-plastome conflict10aLaureae10aPhylogenetic signal10aTree discordance1 aXiao, Tian-Wen1 aXu, Yong1 aJin, Lu1 aLiu, Tong-Jian1 aYan, Hai-Fei1 aGe, Xue-Jun uhttps://lauraceae.myspecies.info/node/20416