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Defining biodiversity genomics

Astronomy, mathematics, physics, chemistry, biology. The sciences have unfolded over time as we noticed what was around us, built concepts to describe and tools to observe and measure, and gained a better grasp of the realities of the Universe.

Many say now is the century of biology, the study of life. Genomics is therefore “front-and-centre”, as DNA, is the software of life.

From staring at stars, we are now staring at DNA. We can’t use our eyes, like we do in star gazing, but just as telescopes show us the far reaches of the Universe, DNA sequencing machines are reading out our genomes at an astonishing pace.

Since the start of the era of genomics in 1995, marked by the sequencing of the first complete genome of a free-living bacterium, genomics has spawned numerous subfields. These include ecological, evolutionary, comparative, and environmental genomics, to name a few.

Now it is time for a merger between the millennia old study of the diversity of life, or biodiversity, and genomics – to create “biodiversity genomics”.

DNA is the blueprint of an organism. It not only uniquely identifies as individual, but places it within context in the ‘Tree of Life’, from nearest kin, to population group, up through species and the chain of evolution that links all life through a common, first ancestor.

DNA research is percolating into traditional studies of biodiversity where it is primarily being used to classify and identify organisms and track the movement and histories of individuals, kinship grows, populations, species, and communities (especially when they are microscopic and DNA offers the only way to easily characterize their masses and complexities).

Our need to understand the natural world has never been so pressing.

Likewise, the leaders of the vast genome factories are realizing the importance of looking at genomes in an organismal context, right up to how gene interaction works in complex communities.

The first camera was laborious and took minutes to get one, costly photograph. Today we all carry smart phones and snap pictures of anything that catches our fancy.

The same evolution is happening in genomics, and the technology is starting to be fast enough and the cost low enough to start thinking about tackling biodiversity – because it is large.

Gathering samples in biodiversity studies that are suitable for DNA analysis is still a key bottleneck in the growth of this field – but things are changing. Eco-genomic sensors are being developed that can take real-time samples, for example, in the ocean, and genomics experts are travelling to remote parts of the global with DNA sequencers in their backpacks to study the emergence of deadly viruses in real-time.

The de facto sequencing of the Planetary Genome has long been in progress. We are sequencing the Earth, from millions of human genomes down to microbes. There are more than fifty megasequencing projects with hundreds to millions of genomes in the pipeline.

In 2014, the Smithsonian launched a visionary project to catalyze the process and safe-keep suitable samples for the future. The ambitious Global Genomes Initiative (GGI) is working to save biological samples to support the sequencing of at least one representative of the entire tree.

So what is biodiversity genomics? What could this field be once biodiversity and genomics truly marry up?

The phrase “biodiversity genomics” is young, but two key players have self-identified themselves to help catalyze the field.

The University of Guelph’s Center for Biodiversity Genomics (CBG) resides within the Biodiversity Institute of Ontario, and is the culmination of efforts by Paul Hebert to pioneer the global DNA barcoding movement. The mission of the CBG is to “advance species discovery and identification through the analysis of short, standardized gene regions known as DNA barcodes”.

The Smithsonian has wrapped the GGI and related initiatives into an Institute for Biodiversity Genomics, which will “focus its research on characterizing and interpreting these genomes in order to gain a greater understanding of the natural world and the complex interconnectedness of its species and ecosystems”.

“Biodiversity genomics” is also being championed by the Genomic Standards Consortium, who have brought together over thirty groups working in diverse areas of biodiversity, informatics, taxonomy, and genomics to help integrate concepts, people, and data.

All of these activities, and thousands more, herald the dawn of a new extension of the way genomics is applied to real-world questions (and problems) and the acceptance of an immensely powerful new tool within the venerable field of biodiversity.

A key pinch point in this process is the integration of biodiversity and molecular (DNA) databases – a significant challenge but critical goal. Ideally, efforts to unify and raise the profile of the biodiversity informatics community will eventually link together with the rich and growing field of bioinformatics.

So, the definition of the term “biodiversity genomics” must be broad enough to cast a wide net.  It must include a wide range of activities and groups and scientific questions.

The term is obviously still aspirational so it is clear that the definition should reflect the possibilities of the future.

It is crucial today to point out where we should head.

Thus, biodiversity genomics can be defined as the use of DNA, as part of a larger framework of integrated data, to answer questions about the diversity and processes that govern the patterns of life on the planet, and how they change. 

Our need to understand the natural world has never been so pressing.

The great Harvard naturalist, Edward O. Wilson, has encapsulated the challenges ahead in his new book Half-Earth: Our Planet’s Fight for Life. He suggests we put aside half of the earth for biodiversity for humanity to have a chance. We are actively reshaping the Planetary Genome to meet human requirements, although this is short-sighted and potentially disastrous. Species extinctions are pushing us into a sixth mass extinction at the same time that synthetic genomics and gene-editing is taking off. We are pruning the Tree of Life while we are gaining the profound ability to add to it.

Featured image credit: Night stars, by Pexels. CC0 Public Domain via Pixabay.

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