Digitization workflows for flat sheets and packets of plants, algae, and fungi.

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation's (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7-36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged.

Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography.

Climatic changes and tectonic events in the Cenozoic have greatly influenced the evolution and geographic distribution of the temperate flora. Such consequences should be most evident in plant groups that are ancient, widespread, and diverse. As one of the most widespread genera of trees, Pinus provides a good model for investigating the history of species diversification and biogeographic disjunction in the Northern Hemisphere. In this study, we reconstructed the phylogeny and investigated the evolutionary and biogeographic history of sect. Quinquefoliae (Pinus), a species-rich lineage disjunctly distributed in Asia, Europe and North America, based on complete taxon sampling and by using nine DNA fragments from chloroplast (cp), mitochondrial (mt) and nuclear genomes. The monophyly of the three subsections, Krempfianae, Gerardianae, and Strobus, is well-supported by cpDNA and nuclear gene phylogenies. However, neither subsect. Gerardianae nor subsect. Strobus forms a monophyletic group in the mtDNA phylogeny, in which sect. Quinquefoliae was divided into two major clades, one consisting of the North American and northeastern Asian species as well as the European P. peuce of subsect. Strobus, and the other comprising the remaining Eurasian species belonging to three subsections. The significant topological incongruence among the gene trees, in conjunction with divergence time estimation and ancestral area reconstruction, indicates that both ancient and relatively recent introgressive hybridization events occurred in the evolution of sect. Quinquefoliae, particularly in northeastern Asia and northwestern North America. In addition, the phylogenetic analysis suggests that the species of subsect. Strobus from subtropical eastern Asia and neighboring areas may have a single origin, although species non-monophyly is very widespread in the nuclear gene trees. Moreover, our study seems to support a Tethyan origin of sect. Quinquefoliae given the distributions and phylogenetic positions of subsects. Krempfianae and Gerardianae, and also highlights the importance of active mountain buildings and climatic changes during the Late Neogene in shaping the species diversity and geographic distribution of Pinus.

Geographic origins and patterns of radiation of Mertensia (Boraginaceae).

PREMISE OF THE STUDY: Numerous molecular phylogenetic studies have used new biogeographic tools to explain species distributions. However, questions remain about origins, timing, direction of movement, and relationships between range expansion and diversification. We investigated geographic origins and temporal and spatial diversification of Mertensia, giving particular attention to divergence between Asian and North American lineages and radiation of western North American clades. METHODS: Divergence time estimation and biogeographic analyses were based on phylogeny reconstruction inferred from nuclear ribosomal ITS and 12 plastid DNA sequence regions and a broad sampling of Mertensia, Boraginaceae, and core eudicots. KEY RESULTS: Mertensia split from Asperugo in the late Oligocene to mid Miocene (26.83-12.22 million years ago [Ma]), followed by the first divergence in the crown group in the late Miocene (10.36-5.19 Ma). The ancestral area is inferred to have been Asia or a widespread distribution across Asia, Beringia, and circumboreal locales. Initial range expansion of North American Mertensia occurred in Beringia and the Pacific Northwest (7.70-4.22 Ma), followed by diversification of three clades (Pacific Northwest, southern Rocky Mountains, central Rocky Mountains). CONCLUSIONS: The crown divergence of extant Mertensia coincides with the onset of extreme cooling and fragmentation of a once extensive mixed mesophytic forest that was subsequently replaced by a boreal coniferous forest. Early diversification likely occurred when Beringia was connected and available for floristic exchange. The north-south orientation of the Rocky Mountain Range and Pleistocene glacial-interglacial cycles appear to have been important in the North American diversification of Mertensia.