Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1111/1755-0998.13523
Licence creative commons licence
Title (Primary) Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations
Author Yardeni, G.; Viruel, J.; Paris, M.; Hess, J.; Groot Crego, C.; de La Harpe, M.; Rivera, N.; Barfuss, M.H.J.; Till, W.; Guzmán-Jacob, V.; Krömer, T.; Lexer, C.; Paun, O.; Leroy, T.
Journal Molecular Ecology Resources
Year 2022
Department BOOEK
Volume 22
Issue 3
Page From 927
Page To 945
Language englisch
Topic T5 Future Landscapes
Data and Software links
Keywords Bromeliaceae; phylogenomics; plant radiation; population structure; target capture; Tillandsia
Abstract Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
Persistent UFZ Identifier
Yardeni, G., Viruel, J., Paris, M., Hess, J., Groot Crego, C., de La Harpe, M., Rivera, N., Barfuss, M.H.J., Till, W., Guzmán-Jacob, V., Krömer, T., Lexer, C., Paun, O., Leroy, T. (2022):
Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations
Mol. Ecol. Resour. 22 (3), 927 - 945