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

Abstract

Target capture emerged as an important tool for phylogenetics and population genetics in non-model 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 1,776 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, e.g. 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.

Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae)

“…(2021), and Yardeni & al. (2022) for Bromeliaceae. Nevertheless, this study demonstrates that even 125 universal target‐loci can be very effective in solving relationships when compared to Sanger sequencing of a few loci.…”

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).…”

Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics

“…This resource will facilitate systematic work in the family and is also expected to be useful in population and conservation genomic studies. The incorporation of the Angiosperms353 loci along with custom marker genes is becoming more common (Yardeni et al, 2019;Jantzen et al, 2020;Christe et al, 2021;Ogutcen et al, 2021), and will allow collaboration between research teams and foster data sharing across studies. Comparative analyses of the custom sets and the Angiosperms353 set will naturally follow (e.g., see Larridon et al, 2020;Shah et al, 2021).…”

“…For example, Ufimov et al (2021) found a similar amount of parsimony informative sites using the Angiosperms353 probe set and a custom probe set in their study of Rosaceae subtribe Malinae. They also showed that the custom probes allowed for improved locus recovery rates across samples and lower levels of gene tree discordance (but see Yardeni et al, 2019). Siniscalchi et al (2021) compared their lineage-specific Compositae1061 probes with the Angiosperms353 probes in eight members of the sunflower family.…”