Molecular identification of plants : from sequence to species

Abstract

Names are the carriers of knowledge. Without names, much of science would be meaningless. Names give us insight into the diseases that affect our health; the objects that sustain our economies; the celestial bodies that travel in the Universe. Names solve ambiguity.In botany, the name of a plant may provide the first clues as to its characteristics, also called traits. Is it edible, or poisonous? Beautiful, or ugly? While some traits are relative (edible by whom, ugly to whom?), others are absolute: thorny, succulent, epiphytic. Some are obvious, others elusive. From morphological descriptions and DNA sequences to historical accounts and traditional uses, they are all linked by the name.Until recently, the reliable identification of plants was the task of a select few: the taxonomists. Today, this is less so. The molecular identification of plants through DNA barcodes has been shown to perform just as well, and in fact often better, than taxonomists for many taxa, particularly when specimens lack reproductive structures. Other techniques, such as image recognition through machine learning and the spectrophotometric signature of leaves, can yield similar results. Does this mean the demise of taxonomists is on the horizon?Not at all. I believe it is very much the opposite: in the current environmental crisis, the need to document and protect the world’s biodiversity has never been more acute. At the same time, some 20% of all plant species have not yet been scientifically described, and many of them may disappear even before we have identified and characterized them. The work of taxonomists remains therefore critical, but as molecular identification of species is underway and set to become routine across the private and public sectors, expert time can now be reallocated from bulk identifications to the training of students, build-up of physical and digital reference collections, and further development of identification methods. Technologies are here to help – not replace – taxonomy, by complementing the human strengths and compensating for some of our human weaknesses: an insufficient memory, a biased brain, and lack of time.This book is for you who are curious about how plants can be identified using DNA: the most powerful source of information to link a plant to a name. This may sound trivial, but it is not. But don’t despair in advance: it is doable, mostly fun, and always rewarding. You just need to learn how.Here, you will not only learn how various types of materials containing plant fragments can be identified to species in the lab and how to execute sophisticated computer analyses, but also gain a deeper understanding of the complexities and challenges faced by taxonomy in general, and plant identification in particular, including the lack of comprehensive reference databases. Enforcing strict species concepts onto nature’s inherent fluidity doesn’t always work, and despite all recent advances in this field it still happens that some plant samples cannot be confidently named. Yet, if this ever happens to you, this initially frustrating insight can also be scientifically revealing, and help you design further experiments.The applications of molecular identification are far more numerous and trans-disciplinary than most people would imagine. Several chapters take a deep dive at applications in fields as seemingly disparate as palaeobotany and healthcare, but as I argued at the start of this text, they are all unified by a common denominator: the name, the information-carrier.