Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Abstract

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.

Data Types and the Phylogeny of Neoaves

“…The tight linkage between coding and non-coding in the Prum dataset makes this study an excellent complement to Reddy et al [13], which compared trees estimated using unlinked coding and non-coding data. When the evidence for data type effects in this study is combined with the results of Reddy et al [13] and Jarvis et al [11] they provide strong evidence that the important variable is the data types and not any idiosyncratic features of specific genomic regions in each study, Data type effects have been described in a number of studies, though the nature of the effects range from those that are quite subtle [49,53] to much stronger effects [11,13,[18][19][20][21][22][23]. Some reported examples of data type effects reflect analyses of the same coding regions as nucleotides and after translation to amino acids [18,[54][55][56].…”

“…However, Reddy et al [13] analyzed a slightly larger number of species than Prum et al [12] and they recovered a tree with similarities to the primary Jarvis et al [11] tree (which they called the "TENT"). This suggests that differences are due to data type effects.The use of large-scale ("phylogenomic") datasets to examine relationships among organisms has revealed cases where analyses of different data types (e.g., coding versus non-coding data) yield different tree topologies [11,13,[18][19][20][21][22][23]. Some data type effects are strong enough that the tree topology based on one data type can be rejected in analyses using the other data type.…”

Data Types and the Phylogeny of Neoaves

“…Data type effects have been described in a number of studies, though the nature of the effects range from those that are quite subtle [49,53] to much stronger effects [11,13,[18][19][20][21][22][23]. Some reported examples of data type effects reflect analyses of the same coding regions as nucleotides and after translation to amino acids [18,[54][55][56].…”

“…This suggests that differences are due to data type effects. The use of large-scale ("phylogenomic") datasets to examine relationships among organisms has revealed cases where analyses of different data types (e.g., coding versus non-coding data) yield different tree topologies [11,13,[18][19][20][21][22][23]. Some data type effects are strong enough that the tree topology based on one data type can be rejected in analyses using the other data type.…”

Complete plastid genome sequence of Neolitsea aciculata (Laurales: Lauraceae), an evergreen broad-leaved tree endemic to East Asia

“…To date, only two Neolitsea plastid genomes (plastomes) have been sequenced. A study on the woody plants, N. pallens (D. Don) Momiyama and H. Hara and N. sericea (Blume) Koidz., has provided powerful phylogenetic utilities, regarding the Litsea complex in particular (Xiao et al 2020 ). However, given their high species diversity, such deficiency in the plastome sequence resources on the genus level is a hindrance to improving our understanding of the woody plant-related evolutionary processes in tropical and subtropical forests.…”