| Abstract Detail
Phylogenomics Shah, Toral [1], Schneider, Julio [2], Zizka, Georg [3], Maurin, Olivier [4], Baker, William J. [5], Forest, Félix [5], Brewer, Grace E. [4], Savolainen, Vincent [6], Darbyshire, Iain [4], Larridon, Isabel [7]. How well does an angiosperm-wide vs. a family-specific targeted sequencing probe kit unravel relationships in the pantropical Ochnaceae. PREMISE: High-throughput sequencing is becoming the norm for reconstructing phylogenetic relationships in angiosperms. Although both universal and family-specific targeted sequencing probe kits are becoming more widely available, few studies have explored the benefits and drawbacks of using a universal versus a more specific kit in unravelling relationships between genera in a plant family. In this study, we explore the capability of two probe kits in resolving current taxonomic uncertainties within the pantropical Ochnaceae family.
METHODS: We sampled 25 Ochnaceae genera and used targeted sequencing with two probe kits, the angiosperm-wide Angiosperms353 kit and a family-specific Ochnaceae kit. We used both a maximum likelihood and coalescence-based approach to infer evolutionary relationships in the family. We explored phylogenetic informativeness and impact of missing data on the resolution and support of tree inference.
KEY RESULTS: The maximum likelihood approach provided more consistent topologies than the coalescence-based approach. The Angiosperms353 probe kit resulted in more variation in relationships, with poorer support and less gene tree agreement. However, the results improved significantly after filtering sites of missing data at threshold of 70%. The Ochnaceae-specific kit resolved consistent topologies with both approaches and no major improvements after data filtering were obtained.
CONCLUSIONS: Both probe kits unravelled relationships between Ochnaceae genera with moderate to high confidence, but the angiosperm-wide probe kit was more subject to effects of missing data and the phylogenetic inference approach used than the Ochnaceae-specific kit. Our analyses found that Ochna is likely sister to a group of taxa rather than a single genus. Both Sauvagesia and Campylospermum in their current circumscription are polyphyletic and in need of revision. Finally, the subfamilies Medusagynoideae and Quiinoideae form a clade sister to the rest of Ochnaceae.
1 - Royal Botanic Gardens, Kew, The Herbarium, Royal Botanic Gardens, Kew. Richmond. Surrey., The Herbarium, Royal Botanic Gardens, Kew. Richmond. Surrey., London, SRY, TW9 3AE, United Kingdom
2 - Botany & Molecular Evolution, Senckenbergananlage 25, Frankfurt, HE, 60325, Germany
3 - Botany And Molecular Evolution, Senckenberganlage 25, Frankfurt/Main, 60325, Germany
4 - Royal Botanic Gardens, Kew, Royal Botanic Gardens, Kew. Richmond. Surrey., London, Surrey, TW9 3AE, United Kingdom
5 - Royal Botanic Gardens, Kew, Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
6 - Imperial College, London, United Kingdom
7 - Royal Botanic Gardens Kew, Royal Botanic Gardens Kew, Royal Botanic Gardens Kew, Richmond, TW9 3AE, United Kingdom
Keywords:
Ochnaceae
missing data
probe kit
Targeted sequencing
phylogenetic informativeness
Coalescence.
Presentation Type: Oral Paper
Session: PHYL1, Phylogenomics I
Location: Virtual/Virtual
Date: Monday, July 27th, 2020
Time: 2:00 PM
Number: PHYL1007
Abstract ID:283
Candidate for Awards:None |
