Plastomes of nine hornbeams and phylogenetic implications

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.

Plastomes of Betulaceae and phylogenetic implications

“…Except for the Ostrya / Carpinus clade, three other genera, Betula , Ostryopsis , and Corylus , also show multiple incongruencies with respect to interspecific relationships between the two phylogenetic trees. A recent phylogenetic study of Carpinus , including more species than our study, also found such extensive incongruence between the two kinds of trees (Li et al, ).…”

Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics

“…Considerable phylogenetic incongruence can exist among the genes of the plastid genome, which necessitates customized phylogenetic analyses in plastid phylogenomic studies. Incongruent phylogenetic signal among the genes of the plastome has been reported from an increasing number of investigations [23][24][25][26]. Such incongruence can have a considerable impact on phylogeny reconstructions and may even lead to cases where relationships among divergent lineages are driven by only a handful of genes [27].…”

Involucre fossils of Carpinus, a northern temperate element, from the Miocene of China and the evolution of its species diversity in East Asia

“…However, understanding how temperate woody plant groups has accumulated diversity requires specific tests: time-calibrated molecular phylogenetic study and paleobotanical study. In recent years, many molecular phylogenetic studies on temperate woody plants have suggested that most of them originated in the Paleogene and diversified at different times throughout the Paleogene or Neogene ( Chin et al., 2014 , Forest et al., 2005 , Grimm and Renner, 2013 , Hinsinger et al., 2013 , Li et al., 2018 , Naciri et al., 2019 , Renner et al., 2008 , Yang et al., 2019a , Yang et al., 2019b ). Compared to molecular phylogenetic studies, paleobotanical studies provide more direct evidence of the evolutionary history of plants in East Asia; however, few paleobotanical studies have been conducted on the temperate woody plants.…”