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Twenty-one

Molecular Ecology

Mapping the genes of the planet…

Molecular Ecology

Mapping the genes of the planet

When scientists announced that they had mapped the human genome, the world held its breath in amazement. It was an epic achievement which promised significant breakthroughs in healthcare and the dawn of a new science. But nowadays “molecular ecologists” can map the DNA of the environment – and have their sights set on sequencing all life on Earth...

Whether he is sequencing the DNA of insect soup or pandas’ excrement, or trying to establish whether sheep affect the sexual reproduction of very rare flowers, Professor Pete Hollingsworth is a man on a mission.

As the Director of Science at the Royal Botanic Garden Edinburgh (RBGE), Hollingsworth is in charge of a team of 100 researchers, and his specialist subject is a science called molecular ecology, using the power of genetics to understand the natural world.

Molecular ecology sounds very fancy, but Hollingsworth explains that the blueprint of life is “beautifully simple,” because our DNA (genetic code) is built from four basic components (ATGC) – like all other life forms on Earth. According to Hollingsworth, molecular ecology provides a universal tool to understand the vast complexity of life on the planet, aiding conservation by identifying species and varieties within them, and the interconnectedness of different species; as well as their history, ecology and evolution.

By looking at genetic differences amongst individuals, populations or species, it is possible to gain powerful insights into the workings of the natural world. For example, DNA testing reveals that the massive economic impacts caused by the invasive Japanese knotweed are due to a single female plant that has spread throughout the country without sex or variation – all individuals are genetically identical. Understanding this is important for predicting the further spread of the species, as well as designing ways to control it. At a larger scale, greater genetic similarity than expected amongst a highly diverse group of tropical tree species provides evidence that the tree diversity of the Amazon may be younger in evolutionary terms than expected – with clear evidence for recent evolution of many new species over the last few million years.

The ultimate aim of molecular ecology is to understand life on Earth, and to protect endangered species and the biodiversity of life on the planet. But where do you start? According to Hollingsworth, this involves making decisions on “what is most important and also what is fundable.” Some iconic species, such as the panda, are more popular than others – and Hollingsworth’s group has recently received funding to sequence the excrement from pandas to see exactly which species of bamboo they are eating. Despite the simple fact that pandas eat bamboo, more than 60 different bamboo species are reported in their diet, and telling bamboo species apart is hard enough in the field – let alone when they have been digested by a panda.

However, despite the obvious appeal of visibly charismatic species, many of the smaller species play critically important ecological roles, and understanding the biology of species such as lichens and mosses can be equally important, says Hollingsworth.

In addition, you never know what you may find or how valuable any one project may turn out to be. Hollingsworth cites the “weirdly important” example of begonias and Sir Isaac Bayley Balfour – former Regius Keeper of the RBGE. In 1880, Bayley Balfour brought back a single begonia plant to Scotland from an island off the coast of Yemen. Recent DNA testing reveals that this sole plant is now involved in the parentage of all the winter flowering Begonia hybrid cultivars – driving an industry worth millions of pounds every year.

Sometimes, certain species can arouse more public passion than others. For example, in the UK, the plight of bluebells is a classic, well-publicised conservation issue. Bluebells regularly top the polls in votes for the public’s favourite flower, and there is concern that they are threatened with extinction, due to hybridisation with the introduced and invasive Spanish bluebell. Genetic studies are being used to quantify the scale of that threat – by measuring the degree to which our native bluebells are being ‘invaded’ by the Spanish bluebell’s genes.

The case of the rare Irish Lady’s Tresses orchid is another mystery which has been investigated using new molecular ecology techniques. Outwith North America, this orchid is found in only a few remote coastal locations in Scotland and Ireland. Despite exhaustive searching, no trace of seed was found in this species, leading to the idea that its European populations have abandoned sex, and reproduce entirely via vegetative spread. The alternative possibility was that sex and seed production happens – but just very rarely and sporadically. Understanding this was important for determining management plans. Irish Lady’s Tresses occur in heavily grazed sites and if grazing sheep consume the flowers (which grow only a few centimetres high), they will “bite their sexual organs off” (as Hollingsworth remarked in a newspaper article some time ago), limiting seed production. By looking at the plant’s DNA, research showed that each plant is genetically different – demonstrating that they must have been produced from seed and sexual reproduction, and ruling out vegetative spread. This simple observation highlighted the importance of grazing controls to promote flowering, to maximise the chance of the rare but important production of seed for enabling these populations to persist.

Rapid advances

Molecular ecology has changed out of all recognition since Hollingsworth first got involved as a graduate student, “counting chromosomes” in the Botany Department of the University of Leicester in the early 1990s. With a degree in fish ecology, he then began his PhD in the new science, using the same very basic equipment researchers had been using since the pioneering days of the 1950s. Since the 1990s, there has been a “transformation” in technology, and jobs that used to take years can now be completed in seconds, making it possible to do things researchers could never have dreamed of before by automating many of the processes involved.

Says Hollingsworth: “The last five years have also seen totally new platforms come into play, allowing for orders-of-magnitude changes in data generation and information processing. The challenge now is not how to gather the data, but how to manage and analyse the data.”

Hollingsworth also explains that the technology is also much more accessible, as well as highly scalable: “In the past, molecular ecologists were like master craftsmen, whereas today the machines are more automated.”

The barcode of life

In recent years, Hollingsworth has played a key role in the identification and discovery of plants, by Chairing the Scientific Steering Committee of the International Barcode of Life project. Involving thousands of researchers around the world, the project takes advantage of the latest DNA sequencing methods to establish the unique genetic signature of various species and determine the minimum data required to tell species apart. The taxonomic challenge (identifying species and where they are found) is immense – a total of about two million species have been described out of an estimated 10 million on earth. In land plants alone, there are an estimated 400,000 species, and 20% of them are threatened with extinction. About 70,000 still await description. The paper setting the standard DNA barcoding approach for plants was led by the Royal Botanic Garden Edinburgh and adopted internationally. Key to the success of the project was standardisation, so that scientists around the world would use the same barcodes and, as a result, researchers have been able to discover several unknown and endangered species. One example of this is the DNA barcoding discovery of the moss relative – the Viking prongwort (Herbertus norenus) – known only from Shetland and Norway. The same study revealed that a closely related species, the northern prongwort (Herbertus borealis), is known to grow on only one mountain – Beinn Eighe in the Scottish Highlands.

“Genetics gives us insights into problems,” says Hollingsworth, “and molecular ecology is part of the biodiversity toolkit – a giant magnifying glass to study the natural world in incredible detail.”

Conservation is an obvious use for the toolkit, but molecular ecology is also reaching into other areas, including criminal investigation, wildlife forensics and consumer protection – for example, testing the ingredients of herbal medicine or analysing ivory and hardwoods to identify where they have come from. Barcoding yew trees has also provided a framework to discover new species, which may, in turn, help identify new types of taxol, a plant extract used in anti-cancer drugs. And the benefits could have an impact on all sorts of species – studies in North America showed that about 30% of tested fish in markets and restaurants are not the fish we think they are.

“This is really exciting and empowering. This application of molecular ecology enables us to identify the previously unidentifiable and, hence, regulate the previously unregulatable,” Hollingsworth adds.

Environmental DNA

One of the most exciting areas in molecular ecology is what is called “environmental DNA”. Hollingsworth explains that every organism sheds small amounts of its DNA in the course of the day, and much of this ends up in the wider environment. For instance, when you analyse the DNA dissolved in water (e.g., in a mountain lochan), you can find traces of everything living above and around it, washed down in rivers and streams. This means you can identify invasive species and other wildlife, by “DNA sequencing the environment.”

Molecular ecologists have also gathered insects in the jungle, and put the whole catch in a blender to make “insect soup.” Instead of going around with a butterfly net, catching insects at random, they can place traps in different locations and analyse the contents to discern spatial variations and profile each location – identifying all the local insects as well as what they are eating. “These are industrial- scale samples of complex ecological systems,” says Hollingsworth. “Technology is enabling us to sequence more individuals and more genes than ever before.”

Molecular ecology is transforming our view of the planet by providing a toolkit that “measures” its biodiversity, going back thousands of years. DNA sequencing ancient sediments and soils also enables high-resolution reconstruction of past species assemblages, enhancing our understanding of how species have responded to past environmental change. And Hollingsworth believes that one big challenge facing the science today is how to understand the links with history – to make it easier to predict what future changes will look like.

 

Global gardens

The RBGE is not just a pretty park where people come to see exotic trees and flowers, but a hot-bed of advanced scientific research with a diverse collection of three million preserved plants, gathered from locations all over the world since 1697, and a living collection of 13,500 plant species. The early researchers were also very interested in the practical aspects of plants, particularly their medicinal value, and Hollingsworth and his team have inherited this scientific tradition, aware they must demonstrate impact as well as carry on the basic conservation. You never know when a particular plant may turn out to be useful, and DNA sequencing now makes it possible to analyse samples preserved in the archives for hundreds of years.

The RBGE has various priorities, including conservation projects in Scotland and overseas, but its collection of preserved species is one of its most valuable assets and gives it a distinct “market niche.”

“With new advances in technology – we now call this our genomic treasure trove,” says Hollingsworth.

Researchers also get involved in large-scale international projects, such as using satellite technology to assess the success of massive reforestation programmes in China, and monitoring the spread and establishment of rubber plantations to assess the extent of risks to sustainable production where plantations are established in sub-optimal environments. Another major project is in Nepal, working in collaboration with Nepalese botanists to understand and characterise the plant resources of the country’s extremely diverse flora.

 

 

 

 

 

"Molecular Ecology". Science Scotland (Issue Twenty-one)
Printed from http://www.sciencescotland.org/feature.php?id=330 on 18/10/17 02:51:35 AM

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