Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)
Lars Nauheimer
A B C G , Lujing Cui D E , Charles Clarke A , Darren M. Crayn A B C D , Greg Bourke F and Katharina Nargar A B C D
+ Author Affiliations
- Author Affiliations
A Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, Qld 4878, Australia.
B Centre for Tropical Environmental Sustainability Science, James Cook University, McGregor Road, Smithfield, Qld 4878, Australia.
C Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, McGregor Road, Smithfield, Qld 4878, Australia.
D National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT 2601, Australia.
E School of Computer Science and Engineering, University of New South Wales, NSW 2052, Australia.
F Blue Mountains Botanic Garden, Bells Line of Road, Mount Tomah, NSW 2758, Australia.
G Corresponding author. Email: lars.nauheimer@jcu.edu.au
Australian Systematic Botany 32(3) 243-254 https://doi.org/10.1071/SB18057
Submitted: 11 September 2018 Accepted: 2 May 2019 Published: 12 June 2019
Abstract
Nepenthes is a genus of carnivorous plants consisting of ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships of most species because of the limited genetic divergence in previous studies. In the present study, we used a genome-skimming approach to infer phylogenetic relationships on the basis of 81 plastid genes and the highly repetitive rRNA (external transcribed spacer (ETS)–26S) for 39 accessions representing 34 species from eight sections. Maximum-likelihood analysis and Bayesian inference were performed separately for the nuclear and the plastid datasets. Divergence-time estimations were conducted on the basis of a relaxed molecular-clock model, using secondary calibration points. The phylogenetic analyses of the nuclear and plastid datasets yielded well resolved and supported phylogenies. Incongruences between the two datasets were detected, suggesting multiple hybridisation events or incomplete lineage sorting in the deeper and more recent evolutionary history of the genus. The inclusion of several known and suspected hybrids in the phylogenetic analysis provided insights into their parentage. Divergence-time estimations placed the crown diversification of Nepenthes in the early Miocene, c. 20 million years ago. This study showed that genome skimming provides well resolved nuclear and plastid phylogenies that provide valuable insights into the complex evolutionary relationships of Nepenthes.
Additional keywords: divergence time estimation, infrageneric classification, molecular systematics, Nepenthaceae.
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