Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)

Abstract

As one of the largest genera of Lamiaceae and of great medicinal importance, Isodon is also phylogenetically and taxonomically recalcitrant largely ascribed to its recent rapid radiation in the Hengduan Mountains. Previous molecular phylogenetic studies using limited loci have only successfully resolved the backbone topology of the genus, but the interspecific relationships suffered from low resolution, especially within the largest clade (Clade IV) which comprises over 80% species. In this study, we attempted to further elucidate the phylogenetic relationships within Isodon especially Clade IV using plastome sequences with a broad taxon sampling of ca. 80% species of the genus. To reduce systematic errors, twelve different plastome data sets (coding and non-coding regions with ambiguously aligned regions and saturated loci removed or not) were employed to reconstruct phylogeny using maximum likelihood and Bayesian inference. Our results revealed largely congruent topologies of the 12 data sets and recovered major lineages of Isodon consistent with previous studies, but several incongruences are also found among these data sets and among single plastid loci. Most of the shallow nodes within Clade IV were resolved with high support but extremely short branch lengths in plastid trees, and showed tremendous conflicts with the nrDNA tree, morphology and geographic distribution. These incongruences may largely result from stochasticity (due to insufficient phylogenetic signal) and hybridization and plastid capture. Therefore, the uniparental-inherited plastome sequences are insufficient to disentangle relationships within a genus which has undergone recent rapid diversification. Our findings highlight a need for additional data from nuclear genome to resolve the relationships within Clade IV and more focused studies to assess the influences of multiple processes in the evolutionary history of Isodon. Nevertheless, the morphology of the shape and surface sculpture/indumentum of nutlets is of systematic importance that they can distinguish the four major clades of Isodon.

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

“…39 within Isodon are non-monophyletic and that instead, the genus can be divided into four clades (Clade I−Clade IV). However, in previous studies, resolving the phylogenetic relationships within the largest group, Clade IV, has been difficult (42,44). By Beyond the recent rapid radiation of Isodon, our results also suggest a correlated evolution between shrubby growth form and dry valley habitat (H1; SI Appendix, Figs.…”

“…Previous phylogenetic studies using several molecular markers and plastome sequences consistently recovered four well-supported clades (Clade I−Clade IV) within Isodon , but the phylogenetic relationships within Clade IV, which comprises ca. 80% species of the genus, were poorly resolved (42, 44). Compared with previous analyses, both the ML tree and the coalescent tree retrieved in present study had greater resolution, with most nodes receiving maximal support (Fig.…”

“…39 within Isodon are non-monophyletic and that instead, the genus can be divided into four clades (Clade I−Clade IV). However, in previous studies, resolving the phylogenetic relationships within the largest group, Clade IV, has been difficult (42, 44). By utilizing 7,204 orthologs, we are able to resolve four strongly supported clades (Clade IVa−Clade IVd) within Clade IV (Fig.…”

“…The combination of low dispersal ability, short distances of overall gene flow, and the strong environmental heterogeneity in southwest China could be what drove the rapid diversification of Isodon in dry valleys subsequently, i.e., a signature of geographic speciation (55). The diaspores of Isodon are nutlets, which are mostly of a small size and a smooth and glabrous surface (44). For species inhabiting seasonally dry habitats, dispersal appears to occur without specialized adaptations.…”

Home at last: Molecular phylogenetic analyses support subsuming Metastachydium within Phlomoides (Lamiaceae)

“…ex Benth.) Spach (Chen & al., 2022b). In general, the incongruities between plastid and nuclear DNA markers within Lamiaceae have been explained by incomplete lineage sorting (ILS) and/or hybridization (Albaladejo & al., 2005; Drew & Sytsma, 2013; Drew & al., 2014; Deng & al., 2015; Walker & al., 2015; Hu & al., 2018; F. Zhao & al., 2021b; Chen & al., 2022b).…”