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

Targeted sequencing using Angiosperms353 has emerged as a low-cost tool for phylogenetics, with early results spanning scales from all flowering plants to within genera. The use of universal markers at narrower scales- within populations- would eliminate the need for specific marker development while retaining the benefits of full-gene sequences. However, it is unclear whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters. Using herbarium specimens from a 50-year-old floristic survey of Guadalupe Mountains National Park, we sequenced 95 samples from 24 species using Angiosperms353. We adapted a data workflow to process targeted sequencing data that calls variants within each species and prepares data for population genetic analysis. We calculated genetic diversity using standard metrics (e.g. heterozygosity, Tajima's D). Angiosperms353 gene recovery was associated with genomic library concentration, with limited phylogenetic bias. We identified over 1000 segregating variants with zero missing data within 22 of 24 species. A subset of these variants, which were filtered to remove linked SNPs, revealed high heterozygosity in many species. Tajima's D calculated within each species indicated a moderate number of markers potentially under selection and identified evidence of population bottlenecks in some species. Despite sequencing few individuals per species, the Angiosperms353 markers contained sufficient variation calculate demographic parameters. Larger sampling within species will allow for estimating gene flow and population dynamics in any angiosperm. Our study will benefit conservation genetics, where Angiosperms353 provides universal repeatable markers, low missing data, and haplotype information.

The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia. Solidago ulmifolia var. palmeri’s status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the “Angiosperms353” probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla) was also assessed. Both morphological and phylogenic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species.

No abstract

Abstract— The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia. Solidago ulmifolia var. palmeri’s status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the “Angiosperms353” probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla) was also assessed. Both morphological and phylogenetic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species.