A new era for natural history collections: the impact of digitisation and phylogenetics on analysis of biodiversity data

Brent D. Mishler
University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA 94720-2465, USA
Email: BMishler@calmail.berkeley.edu

Abstract of keynote address at the Australasian Systematic Botany Society Conference 2012, 23-28 September, 2012, in Perth, Western Australia

Digitisation is rapidly making specimen data available to the public, via increasingly advanced bioinformatics. Inexpensive DNA sequencing and rapid advances in computational methods for both tree building and tree using have eclipsed previous limits on the scope of phylogenetic investigations and phylogenetic systematics. Natural history collections are the nexus where it all comes together; specimens and their associated meta data are the ground truth for all biodiversity studies. Specimens are essential DNA vouchers, fundamental phylogenetic, geographic, evolutionary and ecological data points, sole resolvers of taxonomic issues, and primary evidence for global change and other human-caused modifications of the environment. I will present examples of new uses for specimen data, drawing mainly from two places with an advanced state of herbarium digitisation, Australia and California, but also from other efforts around the world. The many uses of collection databases include important practical applications, taking advantage of temporal aspects of collection data, such as: 1) climate change modelling; 2) spatial ecology/mapping historical habitats and landscapes; 3) tracking the introduction of pathogens and invasive species; and 4) phenology estimates through time, as well as scientific applications, such as: 1) identification of under-collected areas (targeted exploration) and other collection biases; 2) production of floras and identification tools; 3) discovery of previously undescribed taxa; 4) reconstructing assembly of communities; 5) biogeography and diversification studies; and 6) assessing biodiversity and endemism using new phylogenetic approaches.