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A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae
Kangshan Mao1, Markus Ruhsam2, Yazhen Ma1
1Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China.
Annals of Botany
|August 21, 2018
Summary
This study used transcriptome data to resolve conifer evolutionary relationships, finding strong support for the (Hesperocyparis-Callitropsis-Xanthocyparis, (Juniperus, Cupressus)) clade. Rapid divergence and incomplete lineage sorting explain previous phylogenetic conflicts.
Area of Science:
- Botany
- Evolutionary Biology
- Genomics
Background:
- Conifer phylogeny, particularly within the Cupressoideae subfamily, has been challenging to resolve due to rapid evolutionary divergence and reticulate evolution.
- Previous studies using limited nucleotide data struggled to clarify the relationships between Juniperus, Cupressus, and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) clade.
Purpose of the Study:
- To resolve long-standing phylogenetic controversies within the Cupressoideae subfamily of conifers.
- To investigate the evolutionary relationships between Juniperus, Cupressus, and the HCX clade using large-scale transcriptome data.
Main Methods:
- Transcriptome sequencing of 20 Cupressoideae species.
- Extraction and phylogenetic analysis of single-copy nuclear (SCN) genes using MarkerMiner.
- Phylogenetic reconstruction using concatenated data, species trees, and phylogenetic networks.
- Examination of alternative backbone topologies for biogeographic and dating analyses.
Main Results:
- Phylogenetic analyses of 73 SCN genes strongly supported the relationship (HCX, (Juniperus, Cupressus)).
- Molecular dating estimated the most recent common ancestor of these lineages at approximately 60 million years ago, with Juniperus and Cupressus diverging around 56 Mya.
- Ancestral area reconstructions indicated an Asian origin for the clade, followed by dispersal to North America, Europe, and Africa.
Conclusions:
- The study resolves a major phylogenetic controversy in Cupressoideae using SCN genes.
- Rapid evolutionary divergence and incomplete lineage sorting are identified as causes of conflicting phylogenetic inferences.
- Updated phylogenetic backbone improves biogeographic history reconstruction for Cupressoideae.
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