Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations

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.

New plastome structural rearrangements discovered in core Tillandsioideae (Bromeliaceae) support recently adopted taxonomy

“…Our results are in general consistent with the phylogenetic relationships recovered by previous studies using plastid data ( Barfuss et al, 2016 ; Machado et al, 2020 ; Loiseau et al, 2021 ), albeit in discordance with the phylogenetic relationships retrieved by Loiseau et al (2021) based on nuclear data, where subtribe Cipuropsidinae (tribe Vrieseeae) is recovered as sister to tribe Tillandsieae (vs. sister to subtribe Vrieseinae), and Werauhia is retrieved as sister to the remaining genera of subtribe Cipuropsidinae (vs. sister to Lutheria ). Genus level phylogenetic relationships obtained by Yardeni et al (2022) from the analysis of their nuclear dataset are mostly in agreement with our results, except for the position of Racinaea which is recovered nested within Tillandsia by these authors. Despite the differences in taxon samplings across studies, the consistently retrieved strongly supported phylogenetic discordance between plastid and nuclear data sources suggest that evolutionary processes, such as hybridization or lineage sorting, could have shaped the evolution of the core Tillandsioideae.…”

“…Then, Loiseau et al (2021) expanded the plastid genomic dataset of Machado et al (2020) , by mining additional nuclear and mitochondrial loci for an increased taxon sampling. Lastly, Yardeni et al (2022) explored the utility of two nuclear target capture kits to resolve phylogenetic relationships in Bromeliaceae, including 56 species of the subfamily Tillandsioideae.…”

“…Bromeliaceae are known for their low substitution rates compared to other Poales ( Smith and Donoghue, 2008 ). Therefore, phylogenetic resolution and support in core Tillandsioideae could benefit from the inclusion of NGS based data, as demonstrated by the studies of Machado et al (2020) ; Loiseau et al (2021) , and Yardeni et al (2022) . To our knowledge, no study has explored plastome diversity and evolution on a representative taxon sampling of the core Tillandsioideae, since full plastome sequences are only available for three (i.e., Guzmania , Tillandsia , and Vriesea ) of the 22 currently recognized genera of the entire subfamily.…”

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

“…On the other hand, bioinformatic analyses took longer due to the iterative refinement, and only a portion of captured sequence data was ultimately used for phylogenomic or population genomic analyses in each focal group (see Tables S1–S3 ). Higher costs per used sequence could be compensated by enriching DNA of up to six individuals in a single hybridization reaction, a strategy that has been used successfully in other studies (e.g., de La Harpe et al, 2018 ; Yardeni et al, 2022 ). To further reduce costs, future target enrichment experiments in Dalbergia could be focused on genomic regions targeted by the 6190 sequences of the Dalbergia2396 probe set.…”

“…However, several comparisons revealed that microevolutionary relationships are often better resolved when targeting more loci using taxon‐specific probe sets (e.g., Shah et al, 2021 ; Siniscalchi et al, 2021 ; Ufimov et al, 2021 ). The development of taxon‐specific probe sets therefore remains valuable for detailed phylogenetic and population genetic analyses (Yardeni et al, 2022 ).…”