TY  - JOUR
A1  - Shah, Toral
A1  - Schneider, Julio V.
A1  - Zizka, Georg
A1  - Maurin, Olivier
A1  - Baker, William
A1  - Forest, Félix
A1  - Brewer, Grace E.
A1  - Savolainen, Vincent
A1  - Darbyshire, Iain
A1  - Larridon, Isabel
T1  - Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits
T2  - American journal of botany
N2  - Premise: Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships.
Methods: We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support.
Results: For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree.
Conclusions: The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
KW  - coalescence
KW  - custom
KW  - maximum likelihood
KW  - missing data
KW  - phylogenetic informativeness
KW  - probe kit
KW  - universal
Y1  - 2021
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/63923
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-639235
SN  - 1537-2197
N1  - Data Availability
Raw sequence data for the Ochnaceae-specific probe kit are available from GenBank SRA under the Bioproject number PRJNA602196: http://www.ncbi.nlm.nih.gov/bioproject/602196 (Schneider et al., 2020). Raw sequence data for the universal Angiosperms353 probe kit are available from European Nucleotide Archive under the umbrella project number PRJEB35285: https://www.ebi.ac.uk/ena/browser/view/PRJEB35285. Voucher information for all samples used are listed in Appendix 1. All the sequence alignments, gene trees and species trees for both probe kits and the combined dataset are available from the Dryad Digital Repository at https://doi.org/10.5061/dryad.2547d7wsz.
N1  - This work was funded by grants from the Calleva Foundation and the Sackler Trust to the Plant and Fungal Tree of Life Project (PAFTOL) at the Royal Botanic Gardens, Kew, and from the Deutsche Forschungsgemeinschaft to G.Z. (ZI 557/14-1).
VL  - 108
IS  - 7
SP  - 1201
EP  - 1216
PB  - Wiley
CY  - Hoboken, NJ
ER  -