Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
A peer-reviewed article of this Preprint also exists.
Author and article information
Abstract
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for “one size fits all” universal markers, we should improve and make more accessible the tools necessary for developing “made to measure” ones.
Cite this as
2017. Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”? PeerJ Preprints 5:e2763v3 https://doi.org/10.7287/peerj.preprints.2763v3note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a preprint of a paper currently in review. It differs from the previous version in various revisions made in response to peer review, most notably in further documentation of the previously provided scripts and changes to the selection and presentation of phylogenetic trees in Fig. 6.
Sections
Supplemental Information
Supplementary data 1: Exons sequences corresponding to the 134 markers selected for the empirical study and the complete pools of marker selected using each of the methods compared (fasta format)
Summary table of markers
Supplementary data 3 - Table documenting markers as represented in Supplementary data 1-4.
Gene trees from empirical data
Supplementary data 4 - Gene trees inferred under RAxML
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Malvina Kadlec conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables.
Dirk U Bellstedt contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Nicholas C Le Maitre contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Michael D Pirie conceived and designed the experiments, wrote the paper.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
We thank Cape Nature and South Africa National Parks for assistance with permits (Cape Nature: 0028-AAA008-00134; South Africa National Parks: CRC-2009/007-2014)
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Sequence alignments are available in a supplemental file. Raw sequence reads are available from NCBI: PRJNA388814, https://www.ncbi.nlm.nih.gov/bioproject/388814
Data Deposition
The following information was supplied regarding data availability:
GitHub
9765d11
https://github.com/MaKadlec/Select-Markers/tree/AllMarkers
GitHub
31409eb
https://github.com/MaKadlec/Select-Markers/tree/BestMarkers.py
Funding
The authors acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG; PI1169/1-1 to MDP); South African National Research Foundation (NRF; DUB and MDP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
