Phylogeny of Campanuloideae (Campanulaceae) with emphasis on the utility of nuclear pentatricopeptide repeat (PPR) genes.
BACKGROUND
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.


RESULTS
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 (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.


CONCLUSIONS
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.
Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America; Department of Biology, University of Florida, Gainesville, Florida, United States of America.
Andrew A
AA
Crowl
Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America.
Evgeny
E
Mavrodiev
Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany.
Guilhem
G
Mansion
Biology Department, Pacific Lutheran University, Tacoma, Washington, United States of America.
Rosemarie
R
Haberle
Museo Regionale di Scienze Naturali, Torino, Italy.
Annalaura
A
Pistarino
Department of Biology, University of Patras, Patras, Greece.
Georgia
G
Kamari
Department of Biology, University of Patras, Patras, Greece.
Dimitrios
D
Phitos
Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany.
Thomas
T
Borsch
Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America.
Nico
N
Cellinese
D029422:Campanulaceae / Q000145:classification* / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage; D017343:Genes, Plant; D005819:Genetic Markers; D014644:Genetic Variation; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
D018742:DNA, Chloroplast; D018744:DNA, Plant; D005819:Genetic Markers; D010940:Plant Proteins