Specimen database

Taxonomy

Hierarchical searches

Our database may be searched not only by genus, species or variety but also by higher taxa or clades.  Such “hierarchical searches” retrieve all the “child” or “lower” taxa within the particular higher taxon searched.  This capability enables very powerful searches (for example, “all specimens of Fabaceae from Pima County”).  Our search engine enables you to search by any node within the vascular plant phylogeny: both traditional Linnaean ranked taxa such as Brassicaceae and Brassicales, as well as non-Linnaean clades such as “Eudicot”, “Rosid” or “Asterid”.  Our search engine uses the same phylogenetic framework as GenBank (NCBI taxonomy; see “Sources“, below).

Sources

Our specimen database currently derives its phylogenetic backbone (above the level of genus) from the NCBI Taxonomy Database.  This is the same phylogenetic structure which underlies GenBank. As stated on the NCBI website (How to reference the NCBI taxonomy database):

The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow  a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts.

For more information on sources of plant names and phylogenies within the NCBI database, see NCBI Taxonomy Reources: Plants.

Current vs. accepted families, or “Whatever happened to Sterculiaceae???”

For each specimen, we report the original family of determination, as displayed on the original label or later annotation slip.  For family-level classifications no longer supported by recent systematic research we report both the original family of determination, as well as the newer, “accepted” family (according to NCBI taxonomy).

For example, Sterculiaceae is now included within a broader Malvaceae. To see how we display such information, click on the following specimen of Ayenia microphylla.