Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)

Nauheimer, Lars, Cui, Lujing, Clarke, Charles, Crayn, Darren M., Bourke, Greg, and Nargar, Katharina (2019) Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales). Australian Systematic Botany, 32. pp. 243-254.

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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.

Item ID: 60520
Item Type: Article (Research - C1)
ISSN: 1446-5701
Keywords: divergence time estimation, infrageneric classification, molecular systematics, Nepenthaceae.
Copyright Information: © CSIRO 2019
Funders: Australian Pacific Science Foundation, Commonwealth Scientific and Industrial Research Organisation (CSIRO)
Projects and Grants: APSF 16/04
Date Deposited: 08 Oct 2019 03:03
FoR Codes: 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis @ 40%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 20%
06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060310 Plant Systematics and Taxonomy @ 40%
SEO Codes: 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960803 Documentation of Undescribed Flora and Fauna @ 40%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 60%
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