Phylogeny of Campanuloideae (Campanulaceae) with Emphasis on the Utility of Nuclear Pentatricopeptide Repeat (PPR) Genes

Abstract

BackgroundThe Campanuloideae (Campanulaceae) are a highly diverse clade of angiosperms found mostly in the Northern Hemisphere, with the highest diversity in temperate areas of the Old World. Chloroplast markers have greatly improved our understanding of this clade but many relationships remain unclear primarily due to low levels of molecular evolution and recent and rapid divergence. Furthermore, focusing solely on maternally inherited markers such as those from the chloroplast genome may obscure processes such as hybridization. In this study we explore the phylogenetic utility of two low-copy nuclear loci from the pentatricopeptide repeat gene family (PPR). Rapidly evolving nuclear loci may provide increased phylogenetic resolution in clades containing recently diverged or closely related taxa. We present results based on both chloroplast and low-copy nuclear loci and discuss the utility of such markers to resolve evolutionary relationships and infer hybridization events within the Campanuloideae clade.ResultsThe inclusion of low-copy nuclear genes into the analyses provides increased phylogenetic resolution in two species-rich clades containing recently diverged taxa. We also obtain support for the placement of two early diverging lineages (Jasione and Musschia-Gadellia clades) that have previously been unresolved. Furthermore, phylogenetic analyses of PPR loci revealed potential hybridization events for a number of taxa (e.g., Campanula pelviformis and Legousia species). These loci offer greater overall topological support than obtained with plastid DNA alone.ConclusionThis study represents the first inclusion of low-copy nuclear genes for phylogenetic reconstruction in Campanuloideae. The two PPR loci were easy to sequence, required no cloning, and the sequence alignments were straightforward across the entire Campanuloideae clade. Although potentially complicated by incomplete lineage sorting, these markers proved useful for understanding the processes of reticulate evolution and resolving relationships at a wide range of phylogenetic levels. Our results stress the importance of including multiple, independent loci in phylogenetic analyses.

Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia

“…Recent studies conducted within the Campanulaceae family have made significant progresses toward a robust phylogenetic hypothesis of the group (Crowl et al., ; 2016). These authors concluded that previous studies including ITS have shown significant limitation in resolving species level relationships and providing accurate information on the placement of several genera (e.g., Jasione and Musschia ).…”

“…Six chloroplast (cpDNA) regions were amplified: atpB , matK , petD , rbcL , trnL‐F (Crowl et al., ) and psbA‐trnH (Kress, Wurdack, Zimmer, Weigt, & Janzen, ); and one nuclear region (ITS) with the primers of Douzery et al. ().…”

“…Several Cyphia P.J. Bergius species were used as out‐group, such as C. elata Harv., C. comptonii Bond, C. decora Thulin, C. rogersii S. Moore, and C. tysonii E. Phillips (Crowl et al., ). The obtained tree topology for each marker was then compared in order to detect discrepancies.…”

The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

“…Phylogenies were inferred using maximum likelihood (ML) and Bayesian inference as implemented in RAxML 8.0 (Stamatakis, ) and B east 2.1.3 (Bouckaert et al ., ). Four calibration points were used to estimate divergence times: the fossil seed of † Campanula paleopyramidalis as a minimum age constraint of 16 Myr for the most recent common ancestor of C. pyramidalis and C. carpatica (Cellinese et al ., ; Crowl et al ., ); a geological maximum age constraint of 29.8 Myr, which corresponds to the age of the Kure atoll, the oldest emerged island of the Hawaiian Ridge (Clague, ), for the crown group of the endemic Hawaiian clade, encompassing c . 125 spp.…”

Campanula aureliana (Campanulaceae), a new species from Albania

“…The annual and perennial Campanula taxa grow in various habitats, such as meadows, grasslands, garrigues, woodlands, and mainly in rupestrian stands (Kovačić 2004;Roquet et al 2008). The high variability of the morphological traits provided numerous classification proposals (De Candolle 1830;Boissier 1875;Gadella 1966a, b;Contandriopoulos 1984;Kolakovsky 1994), but none of them reflect the phylogenetic relationships recently obtained with molecular data, which showed that Campanula and many closely related genera are not monophyletic (Eddie et al 2003;Park et al 2006;Roquet et al 2008Roquet et al , 2009Borsch et al 2009;Cellinese et al 2009;Haberle et al 2009;Mansion et al 2012;Crowl et al 2014). Nevertheless, molecular data identified several wellsupported monophyletic groups within Campanula, e.g., the garganica clade (Park et al 2006;Frajman and Schneeweiss 2009;Bogdanović et al 2014a, b), the fragilis clade, the pyramidalis clade (Lakušić et al 2013), and closely related lineages, e.g., Phyteuma ).…”