Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the Eastern Mediterranean

At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid-Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin

Mass Taxon-Sampling as a Strategy towards Illuminating the Natural History of Campanula (Campanuloideae)

Speciose clades usually harbor species with a broad spectrum of adaptive strategies and complex distribution patterns, and thus constitute ideal systems to disentangle biotic and abiotic causes underlying species diversification. The delimitation of such study systems to test evolutionary hypotheses is difficult because they often rely on artificial genus concepts as starting points. One of the most prominent examples is the bellflower genus Campanula with some 420 species, but up to 600 species when including all lineages to which Campanula is paraphyletic. We generated a large alignment of petD group II intron sequences to include more than 70% of described species as a reference. By comparison with partial data sets we could then assess the impact of selective taxon sampling strategies on phylogenetic reconstruction and subsequent evolutionary conclusions

Data from: Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the eastern Mediterranean

At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid-Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin

Campanuloideae_Roucela_atpB_matK_petD_rbcL_Spacer_AT11_AT70

FASTA alignment file of all Campanuloideae taxa (including Roucela species) included in the study. Alignment contains atpB, matK, petD, rbcL, atpB-rbcL spacer region, AT11, and AT70 sequences

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

<div><p>Background</p><p>The 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.</p><p>Results</p><p>The 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 (<i>Jasione</i> and <i>Musschia</i>-<i>Gadellia</i> clades) that have previously been unresolved. Furthermore, phylogenetic analyses of PPR loci revealed potential hybridization events for a number of taxa (e.g., <i>Campanula pelviformis</i> and <i>Legousia</i> species). These loci offer greater overall topological support than obtained with plastid DNA alone.</p><p>Conclusion</p><p>This 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.</p></div

Combined Plastid and PPR Phylogeny.

<p>Best tree from maximum likelihood analysis of combined plastid-PPR dataset: <i>atpB</i>, <i>matK</i>, <i>petD</i>, <i>rbcL</i>, <i>trnL</i>-<i>F</i>, <i>PPR11</i>, and <i>PPR70</i>. Numbers above branches are bootstrap values >50%. Numbers below branches indicate posterior probabilities >.70 from Bayesian analysis. Letters refer to nodes and clades discussed in the text. Nodes for which bootstrap values are increased compared to the plastid-only analysis are highlighted in blue.</p

Chloroplast and Nuclear Loci Used in this Study.

<p>Chloroplast and Nuclear Loci Used in this Study.</p

Divergence Time Estimates for Combined Plastid and PPR Tree.

<p>Chronogram from BEAST analysis of the combined plastid-PPR dataset. Scale bar is in millions of years before present. Green star indicates placement of fossil constraint. Green diamonds indicate age constraints obtained from a previous study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094199#pone.0094199-Bell1" target="_blank">[53]</a>. Numbers above branches indicate mean age estimates for clades (in millions of years). Error bars around nodes correspond to 95% highest posterior distributions of divergence times for clades discussed in the text.</p

Comparison of Support for Plastid-only Tree and Combined Plastid-PPR Tree.

<p>Maximum-likelihood trees from the plastid dataset (a) and the combined plastid-PPR dataset (b) with taxon names removed. Branches are shaded relative to BS support with darker branches indicating higher support. Letters correspond to clade/node names in text and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094199#pone-0094199-g001" target="_blank">Figure 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094199#pone-0094199-g003" target="_blank">Figure 3</a>. Support for many clades is increased with the inclusion of PPR loci while other areas of the tree remain poorly supported.</p

Plastid Phylogeny.

<p>Best tree from maximum likelihood analysis of combined plastid dataset: <i>atpB</i>, <i>matK</i>, <i>petD</i>, <i>rbcL</i>, and <i>trnL</i>-<i>F</i>. Numbers above branches are bootstrap values >50%. Numbers below branches indicate posterior probabilities >.70 from Bayesian analysis. Letters A-K refer to nodes and clades discussed in the text.</p