Is Palmer’s elm leaf goldenrod real? The Angiosperms353 kit provides within-species signal inSolidago ulmifolias.l

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 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.

Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales inCastilleja

“…From our analyses of gene tree conflict, it seems clear that insufficient time has passed for tree‐based methods to adequately account for variation at this level, which is consistent with recent work that describes the relationship between gene tree conflict and rapid morphological evolution (Parins‐Fukuchi et al, 2021). Given that the Angiosperms353 loci are a relatively new tool that was designed primarily for phylogenetics, the utility of these gene regions for population‐level analysis is a promising but still developing area of study (Beck et al, 2021 [Preprint]; Slimp et al, 2021). However, as is the case for using these loci for phylogenetics, using Angiosperms353 to explore species‐level and population‐level questions facilitates reproducibility and compatibility with future work.…”

Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family

“…Johnson et al (2019) showed an average recovery of ~283 loci per species for the Angiosperms353 probe set, and at least 100 loci for over 600 angiosperm species, but this can be increased further using the pipeline recently described by McLay et al (2021). It has been successfully implemented with low-quality material such as herbarium specimens (Brewer et al, 2019;Shee et al, 2020) and performed well for resolving shallow-level relationships (e.g., radiations [Larridon et al, 2020;Shee et al, 2020] and even at the intraspecific level [Van Andel et al, 2020;Beck et al, 2021;Slimp et al, 2021]). A few studies have compared the performance of Angiosperms353 with other taxon-specific probe sets (e.g., in Cyperus L. [Larridon et al, 2020], in the subtribe Malinae of the Rosaceae [Ufimov et al, 2021], and in the Ochnaceae [Shah et al, 2021]), but only Larridon et al (2020) directly tested the mergeability of different data sets.…”

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, 2020), 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 intra-specific population structure.…”

“…Its utility at microevolutionary levels is yet to be fully realized, although several works established its suitability to deliver informative signals at a lower taxonomic level (Beck et al, 2021) and in acquiring population genomics parameters (Slimp, Williams, Hale, & Johnson, 2020). The use of highly-conserved markers in a universal kit may, however, limit resolution power.…”