A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set
- Maurin, Olivier1
- Anest, Artemis2
- Bellot, Sidonie1
- Biffin, Edward3
- Brewer, Grace1
- Charles-Dominique, Tristan4
- Dodsworth, Steven5
- Epitawalage, Niroshini1
- Gallego, Berta1
- Giaretta, Augusto6
- Goldenberg, Renato7
- Gonçalves, Deise J.P.8
- Graham, Shirley9
- Hoch, Peter9
- Mazine, Fiorella10
- Low, Yee Wen11
- McGinnie, Catherine1
- Michelangeli, Fabián A.12
- Morris, Sarah1
- Penneys, Darin S.13
- Pérez Escobar, Oscar Alejandro1
- Pillon, Yohan14
- Pokorny, Lisa15
- Shimizu, Gustavo16
- Staggemeier, Vanessa G.17
- Thornhil, Andrew18
- Tomlinson, Kyle W.2
- Turner, Ian19
- Vasconcelos, Thais20
- Wilson, Peter G.21
- Zuntini, Alexandre R.1
- Baker, William J.1
- Forest, Félix1
- Lucas, Eve1
- 1. Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
- 2. Xishuangbanna Tropical Botanical Garden (XTBG), Yunnan, China.
- 3. School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia 5005, Australia
- 4. Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, 75005 Paris, France
- 5. School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom.
- 6. Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS - Brazil.
- 7. Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.
- 8. Department of Ecology and Evolutionary Biology University of Michigan, United States of America.
- 9. Missouri Botanical Garden, St. Louis, MO 63110, United States of America
- 10. Departamento de Ciências Ambientais, Universidade Federal de São Carlos, 18052780 Sorocaba, SP, Brazil.
- 11. Singapore Botanic Garden, NParks, 1 Cluny Road, Singapore 259569
- 12. Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, United States of America
- 13. Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC 28403, United States of America.
- 14. Institut de recherche pour le développement (IRD), Campus international de Baillarguet, 34398 Montpellier, France.
- 15. Centre for Plant Biotechnology and Genomics (CBGP UPM – INIA), Autopista M-40, Km 38, 28223 Pozuelo de Alarcón (Madrid), Spain.
- 16. Department of Plant Biology, University of Campinas, 13083‐970 Campinas, São Paulo, Brazil
- 17. Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, 59078-970, Natal, RN, Brazil.
- 18. Centre for Australian National Biodiversity Research, National Research Collections, Black Mountain, CSIRO, Canberra, ACT 2601, Australia.
- 19. Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom.
- 20. Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, United States of America.
- 21. Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
Description
The premise of this study is to further advance the understanding of the species-rich, economically and ecologically important Myrtales, an angiosperm order in the rosid clade comprising nine families, approximately 400 genera and almost 14000 species occurring on all continents (except Antarctica). The potential of High Throughput Sequencing (HTS) and target enrichment with the Angiosperms353 probe kit is evaluated on a sample of 485 species in 305 genera (76% of all genera in the order). Results provide technical considerations for processing HTS data and the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks such as the relationship of the early diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. HTS and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to enable selection of genes and gene trees that account for incomplete lineage sorting and hybridisation events.