Abstract
High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.
| Original language | English |
|---|---|
| Pages (from-to) | 1000-1019 |
| Number of pages | 20 |
| Journal | Molecular Ecology Resources |
| Volume | 18 |
| Issue number | 5 |
| DOIs | |
| State | Published - Sep 2018 |
Bibliographical note
Funding Information:We thank Ivy Wan and Shaobin Hou for assistance with sequencing that was conducted at the Advanced Studies in Genomics, Proteomics and Bioinformatics core facility at the University of Hawai’i at Mµanoa, Boyd Mori for statistical assistance, Nicole Yoneishi and Jaymie Masuda for laboratory work and Edward Braun, Brant Fair-cloth and three anonymous reviewers for their insightful comments on this manuscript. We thank Bishnu Bhandari, Kemo Badji, J. Caballero, Salley Cowen, Elaida Fiegalan, M. Aftab Hossain, Chia-Lung Huang, H.Y. Huang, David Haymer, Will Haines, Y.F. Hsu, Akito Kawahara, Sada Lal, Yuchi Lin, R. Messing, Aiko Ota, Sylvain Oue-drago, Rudolph Putoa, N. Pierce, J. Quintana, Eric Rodriguez, T. Stark, Ema Tora Vueti, Misael Valladares, L.H. Want, James Walker, Koon Hui Wang, Tianlin Xian and US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) technicians for collecting specimens. Funding for this project was provided by USDA Agricultural Research Service (ARS) and USDA-APHIS Farm Bill Section 10007 projects “Diagnostic Resources to Support Fruit Fly Exclusion and Eradication, 2012–2014” and “Genomic approaches to fruit fly exclusion and pathway analysis, 2015–2016” to USDA-APHIS, USDA-ARS and UH Manoa [projects 3.0251.02 and 3.01251.03 (FY 2014), 3.0256.01 and 3.0256.02 (FY 2015), and 3.0392.02 and 3.0392.03 (FY 2016)]. Figures were created using R (R Core Team 2016), INKSCAPE version 0.91 (The Inkscape Team 2017) and GRAPHLAN version 0.9.7 (Asnicar et al., 2015). USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.
Funding Information:
We thank Ivy Wan and Shaobin Hou for assistance with sequencing that was conducted at the Advanced Studies in Genomics, Proteomics and Bioinformatics core facility at the University of Hawai'i at Mānoa, Boyd Mori for statistical assistance, Nicole Yoneishi and Jaymie Masuda for laboratory work and Edward Braun, Brant Faircloth and three anonymous reviewers for their insightful comments on this manuscript. We thank Bishnu Bhandari, Kemo Badji, J. Caballero, Salley Cowen, Elaida Fiegalan, M. Aftab Hossain, Chia-Lung Huang, H.Y. Huang, David Haymer, Will Haines, Y.F. Hsu, Akito Kawahara, Sada Lal, Yuchi Lin, R. Messing, Aiko Ota, Sylvain Ouedrago, Rudolph Putoa, N. Pierce, J. Quintana, Eric Rodriguez, T. Stark, Ema Tora Vueti, Misael Valladares, L.H. Want, James Walker, Koon Hui Wang, Tianlin Xian and US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) technicians for collecting specimens. Funding for this project was provided by USDA Agricultural Research Service (ARS) and USDA-APHIS Farm Bill Section 10007 projects “Diagnostic Resources to Support Fruit Fly Exclusion and Eradication, 2012–2014” and “Genomic approaches to fruit fly exclusion and pathway analysis, 2015–2016” to USDA-APHIS, USDA-ARS and UH Mānoa [projects 3.0251.02 and 3.01251.03 (FY 2014), 3.0256.01 and 3.0256.02 (FY 2015), and 3.0392.02 and 3.0392.03 (FY 2016)]. Figures were created using r (R Core Team), inkscape version 0.91 (The Inkscape Team) and graphlan version 0.9.7 (Asnicar et al.,). USDA is an equal opportunity employer. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.
Publisher Copyright:
Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
Keywords
- Bactrocera
- Tephritidae
- high-throughput sequencing
- phylogenetics
- systematics
ASJC Scopus subject areas
- Biotechnology
- Ecology, Evolution, Behavior and Systematics
- Genetics