Abstract
Poor phylogenetic resolution and inconsistency of gene trees are major complications when attempting to construct trees of life for various groups of organisms. In this study, we addressed these issues in analyses of the genus Carpinus (hornbeams) of the Betulaceae. We assembled and annotated the chloroplast (cp) genomes (plastomes) of nine hornbeams representing main clades previously distinguished in this genus. All nine plastomes are highly conserved, with four regions, and about 158–160 kb long, including 121–123 genes. Phylogenetic analyses of whole plastome sequences, noncoding sequences, and the well‐aligned coding genes resulted in high resolution of the sampled species in contrast to the failure based on a few cpDNA markers. Phylogenetic relationships in a few clades based only on the coding genes are slightly inconsistent with those based on the noncoding and total plastome datasets. Moreover, these plastome trees are highly incongruent with those based on bi‐parentally inherited internal transcribed spacer (ITS) sequence variations. Such high inconsistencies suggest widespread occurrence of incomplete lineage sorting and hybrid introgression during diversification of these hornbeams.
Highlights
Poor phylogenetic resolution and inconsistency of gene trees are major complications when attempting to construct trees of life for various groups of organisms, as illustrated by numerous authors (e.g., Mallet, Besansky, & Hahn, 2016; Ren, Conti, & Salamin, 2015; Xu, Wu, Gao, & Zhang, 2012; Zeng et al, 2017; Zhang & Li, 2011). We addressed these issues in analyses of the genus Carpinus L., subfamily Coryloideae, of the Betulaceae
We found that the nine Carpinus plastomes have highly conserved features (Figures 1 & 2), including a typical quadripartite structure consisting of a pair of inverted repeats (IRs; 52,117–55,134 bp) separated by large single copy (LSC; 84,605–84,966 bp) and small single copy (SSC; 17,167–18,825 bp) regions (Table 1)
In the internal transcribed spacer (ITS) tree, C. betulus, C. tientaiensis, C. putoensis, and C. tschonoskii clustered as one clade, while C. caroliniana grouped with C. viminea, but with low support in both analyses
Summary
Poor phylogenetic resolution and inconsistency of gene trees are major complications when attempting to construct trees of life for various groups of organisms, as illustrated by numerous authors (e.g., Mallet, Besansky, & Hahn, 2016; Ren, Conti, & Salamin, 2015; Xu, Wu, Gao, & Zhang, 2012; Zeng et al, 2017; Zhang & Li, 2011). With the development of high-throughput sequencing technology, it is becoming much cheaper and easier to sequence whole plastomes of plants (Hu et al, 2016; Zhang & Li, 2011) and increase the resolution of previously ambiguous phylogenetic relationships based on several cpDNA markers (Hu et al, 2016; Jansen et al, 2007). Zeng et al (2017) used whole plastome sequences and coding genes to construct phylogenetic trees of Rehmannia, both of which indicated four nearly identical clades and had high levels of phylogenetic resolution. The noncoding regions in a plastome usually have higher variation rates than the coding genes (Hu et al, 2016; Zhang & Li, 2011) It is not known whether phylogenetic trees based on noncoding sequences and coding genes of plastomes of the genus Carpinus would be consistent. Does use of the three plastomic datasets covering more informative sites provide greater phylogenetic resolution of the sampled clades than use of a few cpDNA markers? Are phylogenies based on the three datasets consistent? Are phylogenies based on plastome datasets consistent with those based on nuclear ITS sequences?
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