On the potential of Angiosperms353 for population genomic studies

Abstract

The estimation of demographic parameters in natural populations is a critical tool for species delimitation (Duminil and Di Michele, 2009), biogeography studies (Overcast et al., 2019), and monitoring of populations and species in a dynamically changing environment (Allendorf et al., 2010). The feasibility of estimating demographic parameters (including heterozygosity, effective population size, and levels of introgression) in non-model taxa relies on retrieving homologous markers that allow detection of sufficient variation across the genome, while remaining cost-effective for the analysis of hundreds of individuals. In plants, population genomic studies could benefit from markers that enable the further unlocking of herbarium specimens for botanical research, paralleling the impact of herbarium specimens in phylogenomics (e.g., Shee et al., 2020), microbiome research (e.g., Heberling and Burke, 2019), and studies of the effects of climate change on plant populations (e.g., Miller-Rushing et al., 2009). Traditional Sanger sequencing of PCR amplicons often employs universal primer sequences, but the genes targeted (e.g., the plastid markers matK and rbcL, or the nuclear ribosomal ITS) do not

Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

“…Despite its promise, target capture-based phylogenetics also faces several challenges. Although the genes targeted are putatively low-or single-copy, it is difficult to avoid paralogy, particularly in polyploid plants (Morales-Briones et al, 2018;Jones et al, 2019;Stubbs et al, 2020;Siniscalchi et al, 2021). The inclusion of paralogs can increase conflicting phylogenetic signal among genes.…”

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

“…In fact, genetic markers obtained from both data sets provided sufficient information to infer species but no geographic structure, suggesting that Tillandsia could be characterized by high gene dispersal among populations. Considering that the Angiosperms353 kit has shown potential to provide within-species signal, as recently demonstrated by Beck et al (2021) on Solidago ulmifolia, and to estimate demographic parameters from herbarium specimen (Slimp et al, 2021), we would expect the taxon-specific set to accurately reveal a geographical genetic structure. However, the present study is generally based on small sample sizes per species (n = 4-8), mostly sampled within a limited geographic range, limiting our ability to draw robust conclusions on the levels of intraspecific population structure.…”

Neotropical niche evolution of Otoba trees in the context of global biogeography of the nutmeg family

“…The Angiosperms353 probeset is a toolkit that plant systematists are using to successfully resolve relationships across taxonomic groups and phylogenetic depth (Johnson et al, 2019; Slimp et al, 2021). While we were able to infer relationships in Otoba using Angiosperms353 loci, low variation and inconsistent capture contributed to low support values.…”