Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)

Abstract

Premise of the study: The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010.

Methods: Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species.

Results: Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species.

Discussion: These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.

Keywords: Solidago; genotyping by sequencing; herbarium specimens; next-generation sampling; species delimitation.

Fig. 1.

Effect of Solidago specimen age on data quantity/quality. (A) Relationship between specimen age and the number of quality reads obtained for the 95 analyzed samples (r² = 0.27, P = 6.8 × 10⁻⁸). (B) Relationship between specimen age and the percentage of the 8470 unfiltered SNPs missing for the 95 analyzed samples (r² = 0.22, P = 9.2 × 10⁻⁷).

Fig. 2.

Multidimensional clustering (PCO-MC) of GBS data for three Solidago subsections. (A) Graphical representation of the five most highly ranked, statistically significant clusters recovered for subsection Junceae. The rank of each cluster by stability (see Methods) and this value (in parentheses) appear at the bottom right of each cluster. Locality information for each specimen refers to the collection locality in Appendix 1. (B) Results for subsection Triplinerviae. (C) Results for subsection Squarrosae. (D) Range maps for select species (scale bars = 100 km).