4.3 Practical considerations of using Angiosperms353 in conservation genetics
Our results exemplify the potential of using target capture sequencing with the universal bait panel Angiosperms353 for population genetic studies (Slimp et al., 2021), offering high data quality and valuable cost efficiency for population-level analyses. Angiosperms353 target capture has broad applications for conservation genetics, effectively capturing intraspecific variation within populations and supporting conservation genomics for rare or threatened taxa. The ability to integrate herbarium samples makes it particularly suited for conservation genetics (Slimp et al., 2021). Although Phang et al. (2023) found that population structure analysis using Angiosperms353 yielded limited resolution within species, our results demonstrate a higher resolution, likely because we did not combine multiple species when calling SNPs.
Based on SNPs data extracted from intronic regions, we developed specific recommendations: 1) inspecting samples with low target sequence recovery, as generated in HybPiper, which could serve as indicators to assess subsequent SNPs recovery and/or errors in population genetic structure results (Yi & Latch, 2022), although the levels of missing data are expected to be lower than in other approaches such as RADseq (Slimp et al., 2021); 2) prioritization of intronic SNPs for population genetics due to their higher mutation rate, although this could vary in other species; 3) exclusion of paralog genes (Bryc et al., 2013), and 4) removing highly heterozygous SNPs (HO > 0.5) to enhance data accuracy in polyploid species.