Botanical Time Travel — Reconstructing extinct worlds using herbarium specimens

Collected 400 years ago: Caspar Bauhin was the first botany professor in Basel and collected thousands of plants of which many are regionally extinct today.

“So how long are you guys keeping this junk?,” a good friend of mine asked, when I showed him a random herbarium specimen a few years ago. Basel has one of the world’s oldest herbarium collections. Still, the uninitiated may be unimpressed with the few, damaged leaves with tiny buds, and an unassuming label stating that a twig was collected, say, some 42 years earlier, from a 60 cm thick tree, 3 km NW of a village in Borneo. But that tree could have been one of the last of its kind, of a forest now long transformed into a palm oil plantation. And that twig’s DNA might reveal how that particular species evolved during millions of years and how the world is changing.

As curator of the Basel Herbarium and senior scientist at the University of Basel, I look after 700 000 herbarium specimens, which record the history of plants over more than 400 years. These preserved plants are not only beautiful — they are also an extremely important resource for research. We use the herbaria to understand how plant diversity changes, and how human activity and natural processes drive these changes. Large parts of the Basel Herbarium have already been digitized and are publicly available.

Me at the Basel Herbarium. The collection dates back to the 16th century and contains more than 700 000 herbarium specimens. I’m holding a rare “Herbarium Vivum”, a bound herbarium from the mid seventeenth century. Photo: © BaslerZeitung / Mischa Hauswirth

There can be no doubt that the world of wild plants today is very different from that 150 years ago. The Basel region is just one example where a world-wide problem plays out on a local scale. We know as much from our Herbarium, which includes the oldest scientific plant collection of Switzerland.

It was started by Caspar Bauhin in the late 16th century. Bauhin exchanged herbarium specimens of crop plants like his contemporaries, but — and this was mostly new — also carefully collected wild plants in our region, amassing thousands of specimens. A first survey in the 1980s revealed massive local extinction of dozens of species, especially of plants adapted to nutrient-poor areas such as dry meadows and swamps.

Extinct in Basel: Specimens of the so-called “Kleine Mäuseschwanz” (Myosurus minimus) in a voucher from 1849.

Witnessing extinction

In fact, it was the first-hand experience of extinction that brought me to what I am doing today. Some 15 years ago, I was on a hunt through Cameroon to gather species of yellow-flowering begonias for DNA sequencing. I visited several sites where herbarium labels indicated that other researchers had collected the plants in past decades. Multiple times, however, I would arrive at a site only to find a radically changed landscape — I was looking for rainforest species, but ended up standing in a city. It was then that I realized just how massive the scale of destruction or land-use change has been over the past 30 or 50 or 100 years.

Reconstructing the extinct world

At the time, it was still impossible to get DNA sequences from herbarium specimens. In dried plants there is very little DNA left, and it degrades to small fragments. That’s why I went to Cameroon in the first place, to collect the actual leaves.

Luckily, nowadays, special labs and new methods allow us to sequence whole genomes of herbarium specimens. In the trial-phase of a current project in collaboration with the Paleogenetics Group at the University of Zürich, we successfully sequenced ancient DNA. But because the scientific field of herbarium genomics is highly competitive, we cannot yet reveal what we did exactly — so stay tuned for updates in the coming two years! Suffice it to say that the results will allow us to find the specific genes that changed between the time of collection and now: Evolution caught in the act!

February 2019. Me in the Ancient DNA lab of Prof. Schünemann, University of Zurich. The full protective suit, including double face mask and triple gloves are necessary to avoid DNA contamination. For the same reason, the inner rooms have increasing air pressure to avoid contaminated air flowing in. Photo: Gülfirde Akgül

Completing the evolutionary tree of life

Now that we can use herbarium specimens to sequence DNA, rather than field-preserved DNA, it is logistically much easier to infer large phylogenies. These evolutionary trees are the basic tool to study how life diversified. We use them to reconstruct how evolution happened in deep time, over hundreds of thousand to millions of years. They even hold clues to extinct species, because extinction leaves a characteristic signature in the branching pattern.

While some extinction may be natural, the profound changes we see nowadays are not. Are they driven by land use change or climate change? We don`t yet know.

The future

And now what? We keep collecting relevant plants, not just for our own research, but also to enable the research of future scientists. I sometimes imagine myself explaining to Bauhin and all the other classic botanists how we use their specimens for botanical time traveling. I then marvel at how far we have advanced, and how valuable it was to simply press, dry and annotate a plant. I hope that in some centuries, other botanists will travel to our time too.

July 2019. I’m preparing a specimen of Gentiana bavarica, on the slopes of the Weissmies in Switzerland at 3150m, during a collection expedition of the Basel Botanical Society. How will these super specialized plants respond to melting glaciers? Herbaria collections are the foundation of addressing such questions.

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