skip to main content

Title: Are Palmer’s Elm-Leaf Goldenrod and the Smooth Elm-Leaf Goldenrod Real? The Angiosperms353 Kit Provides Within-Species Signal in Solidago ulmifolia s. 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 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.  more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Systematic Botany
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    We assessed the status of two New Zealand endemic morphodemes in the genus Sticta, currently treated as two separate taxa, Sticta filix and Sticta lacera. Both are green-algal lichens with a distinct stipe that grow in forested habitats and are suitable indicators of the indigenous vegetation health in forest ecosystems in New Zealand. They exhibit different morphologies and substrate ecologies: S. filix forms rather robust thalli, often on exposed trunks of phorophytes, with erect stems distinctly emerging from the substrate, whereas S. lacera is a more delicate lichen growing near the base of trees, usually among bryophyte mats or sheltered in the exposed portions of the phorophyte root-plate, with a prostrate, branched, stolon-like stem barely emerging from the substrate. Throughout their range, both taxa grow sympatrically and often in close proximity (syntopically). Despite the differences, ITS barcoding does not support the two morphodemes as separate species. In this study we assessed two possible explanations: (1) S. filix and S. lacera are discrete phenotypes of a single species, caused by developmental switching triggered by a discrete environmental variable, the propagules developing either on bare substrate or between bryophytes; and (2) the two morphodemes represent separate lineages, but ITS does not provide sufficient resolution to reflect this. We performed a quantitative analysis of morphological and ecological parameters, based on vouchered herbarium collections and field observations on iNaturalist NZ (, to assess the level of discreteness of the growth forms and to test for a correlation with the presence of a bryophyte mat. We further took advantage of an existing molecular data set from a target capture approach, comprised of 205 protein markers. This data set was used to establish a framework of percentage identities between pairs of the same and of different species among lobarioid Peltigeraceae and then to test whether the S. filix/lacera pairing fell closer to a within-species or a between-species pairing. The morphometric analysis of herbarium material resolved S. filix and S. lacera as two discrete morphs with little overlap, supported by numerous observations on iNaturalist NZ. However, whereas herbarium material suggested a significant association of the lacera morph with bryophyte mats, no such pattern was evident from field images on iNaturalist NZ, in which both morphs frequently associated with bryophyte mats. This highlights the limitations of herbarium material to correctly assess substrate ecology, whereas iNaturalist NZ postings had issues with correct identifications, given that especially S. lacera is easily confused with Pseudocyphellaria multifida. Based on the target capture data, the percentage identity of the S. filix/lacera pairing (99.43%) was significantly higher than that of all 12 between-species pairings (93.20–98.01%); it was at the same time lower than that of all within-species pairings (99.63–99.99%) but significantly so only in comparison with five out of the eight within-species pairings. The target capture approach is thus inconclusive, but the combination of all data suggests that S. filix and S. lacera are not discrete morphodemes of a single species but represent two separate lineages which emerged recently and hence cannot be resolved using the ITS barcoding marker or even a deeper phylogenomic approach based on protein-coding markers. We propose transplantation experiments and the application of RADseq to further assess this situation.

    more » « less
  2. Premise

    The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associatedDNAsequencing (ddRADseq) protocol usingDNAs from four genera extracted from both silica‐dried and herbarium tissue.


    DNAs fromDraba,Boechera,Solidago, andIlexwere processed with a ddRADseq protocol. The effects ofDNAdegradation, taxon, and specimen age were assessed.


    Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples.


    These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.

    more » « less
  3. A review of the species Cryptantha maritima (Boraginaceae) supports the continued recognition of the three varieties, these differing in corolla size, ovule and nutlet number, and calyx vestiture. Mapping of these taxa from verified specimens demonstrates some geographic trends, but also some overlap in ranges. In the process of our study, we discovered a new taxonomic entity. Cryptantha maritima var. vizcainensis is described as new. This variety is restricted to the Vizcaíno Desert of Baja California Sur, Mexico and should be considered rare, as it is known to date from only eleven collections. It differs from the other three varieties of the species in having a canescent, appressed-strigose stem vestiture lacking spreading trichomes, in having a relatively large corolla, and in having a fruit derived from two 1-ovuled ovary lobes, developing into two heteromorphic nutlets. We also discovered that the species Cryptantha pondii, previously treated as a synonym of C. patula, should be resurrected as a distinct taxon. Cryptantha pondii is restricted to the western Vizcaíno Desert and to Natividad Island of Baja California Sur. It is morphologically distinctive in having bracteate flowers, relatively large corollas, and four smooth nutlets heteromorphic by size. It is to date known from only three collections and should be considered extremely rare. We also reviewed the morphological and phylogenetic status of Johnstonella echinosepala. This taxon shows similarities to Cryptantha maritima and also exhibits some morphological discontinuity between Pacific and Gulf populations in Baja California Sur. Evidence from both morphological and phylogenetic studies supports the transfer of this species from the genus Johnstonella back to the genus Cryptantha. Finally, we propose that both C. pondii and C. echinosepala are likely close relatives of C. maritima, all of the “Maritimae clade,” a group distantly related to the main core of the genus Cryptantha. This study confirms the great importance of studying herbarium specimens in taxonomic research. 
    more » « less
  4. Abstract

    Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned data set, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after the removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.]

    more » « less
  5. null (Ed.)
    PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)—typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens. 
    more » « less