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.