Green ham and eggs: sequencing every species on Earth

What's the point, exactly?

From 1831 to 1836, Charles Darwin sailed around the world aboard the Beagle, collecting and cataloging more than a thousand species. From tortoises in the Galapagos to corals in the Cocos, Darwin’s wide-ranging interactions with the natural world helped him formulate his theories of evolution. His book, On the Origin of Species, birthed evolutionary biology, intertwining the fields of genetics, ecology, and paleontology in its aim to explain the diversity of life on Earth. Today, over 160 years later, the naturalist is reborn in the Darwin Tree of Life Project, which seeks to sequence the genomes of all species in the British Isles.

Darwin was an astute observer. His insight into how the depth of a finch’s beak impacted its ability to feed during times of drought and subsequently produce offspring was a key of his evolutionary theory. He may have observed dozens of anatomical and behavioral phenotypes from the thousands of animals that crossed his path but he knew nothing of DNA.

Darwin’s favorite feathered friends, ScienceDirect

Each species is a product of its genetic code. Differences in the order of billions of nucleotide bases determine an organism’s color, size, lifespan, scent, phosphorescence, and millions of other phenotypes. These genotypes (G) interact with countless environments (E) to form the amazing variety of traits we see today. As an aside, while each animal has its own unique genotype, Tree of Life is starting by sequencing one to a few organisms from each species. This is because you’re much more closely related to someone from Uzbekistan than you are to a giraffe or chimpanzee and collecting DNA from all the Earth’s organisms is probably impossible. Think of it more like a Noah’s Ark project to sequence one representative sample from each animal.

When everyone plays nice with the scientists, Cobble Hill Puzzles

Why undertake this extensive cataloging of the planet? There are obvious benefits to advancing conservation efforts and protecting biodiversity. However, I think the larger impact will be in the applications of this data. This is because what you measure you can understand, and what you understand you can use.

Already, Tree of Life scientists have sequenced the genomes of Pyrochroa serraticornis (beetle), Melanotus villosus (beetle), and the beautiful Calvia quattuordecimguttata (also beetle). Evidently they should’ve called Darwin’s boat HMS Beetle. All told, the British Isles are predicted to contain seventy thousand plant, fungi, and animal species (and 4000 species of beetle). This seventy thousand is about 0.8% of the estimated 8.7 million species worldwide, of which 86% are thought to be undescribed. The Tree of Life project is part of a broader initiative, the Earth Biogenome Project (EBP), whose ambitious goal is to sequence all species on Earth within 10 years. The EBP is probably just passing the 0.5% threshold now, which may be a little off track for its 10 year timeline unless we see big rises in the efficiency and affordability of sequencing technology. It’s that or we lop a few million species off the to-do list.

First, maybe we need to take a step back and explain what a species is. The definition is more complicated than it initially sounds. A species is a group of organisms capable of interbreeding and producing fertile offspring. Donkeys and horses can breed to produce mules but these hybrid children are infertile, making their parents separate species. A lineage of animals may speciate (separate into two species) due to geographic isolation, like seeds washing up on a new island, ecological isolation, like bats eating different kinds of fruit, or behavioral isolation, like birds singing distinctive mating calls. These forms of isolation allow mutation, along with natural selection for or against these mutations, and genetic drift (random changes of gene proportions in a population) to drive genetic change that eventually renders the population unable to mate with non-species peers. Male and female anglerfish, two animals from the same species, look drastically different.

Females are up to a million times heavier, Natural History Museum

Conversely, Tawny-bellied and Pearly-bellied cappuccino finches, two animals from different species, look exactly the same. Females from these species are indistinguishable and it's thought that there is just a 0.03% difference in their DNA. (No definitive word from the Tree of Life team yet. They’re still at work on the beetles).

They look pretty different to me, Cornell Lab

Jokes aside, you may walk by an undescribed species every day. Why does cataloging these differences in species matter to us when it doesn’t seem to matter to the natural world?

Because diversity is power. The world’s biodiversity may seem insignificant when you’re speaking about two species that look and behave almost exactly alike but these minute differences are critical to the planet’s resilience in response to change. The world is in a constant state of flux (ΔE). Some genotypes may respond well to these environmental changes while most do not. Only by having a wide range of genotypes (G) can life ensure that it persists. A low level of mutation for a species is like keeping tire chains in your car. Most of the time, the extra weight slows you down and decreases your gas mileage, just as most mutations have little or negative effect. But, when the environment changes, like a foot of snow falling overnight, the individuals with mutations suited to the new conditions are able to survive and pass on their genes.

As we’re seeing, our environment is becoming ever more volatile. Measuring and understanding the world’s DNA gives us an almost endless toolbox to pull from in our efforts to treat disease, feed ourselves, produce products, and in the long run, survive.

As we experienced with COVID, deadly pathogens can arise at any time. Certain species have evolved remarkable responses to these diseases that we can co-opt for saving human life. For example, penicillin, one of the first revolutionary antibiotics, was adopted from the fungi Penicillium. By sequencing the genome of it and its peers, we can not only identify genes that produce novel antibiotics but use our understanding of genetic engineering to modify these genes and the proteins they produce to be evermore effective in treating disease.

Similarly, sequencing crops from drought plagued regions like the Sahel or central Asia allows us to identify the core genetics that help these species survive in such hostile climates. As climate change worsens, breeding drought, heat, and salinity resistant genes into our cash crops will be critical to ensuring the world is properly fed. By recording the genetic code of various species, we can virtually preserve these sequences for later generations, who may develop tools to truly bring animals back from the dead (see my article on dire wolves and de-extinction here).

Lastly, the world of synthetic biology, or designing and building biological systems, is still in its infancy. Already, companies are exploring editing bacteria to produce biofuels, digest plastic, or synthesise nitrogen for fertilizer. One of the first success stories involved the gene GFP, or green fluorescent protein, which was taken from the humble jellyfish Aequorea victoria and is now widely deployed across the science world as a genomic tool to color cells.

GFP fluorescent pigs, Newcastillian News

The Darwin Tree of Life and Earth Biogenome Project are assembling a biological toolbox that will become increasingly important as species continue to go extinct and environments fluctuate ever more violently. There are probably thousands of penicillin, GFP, or drought-resistant gene equivalents that we have yet to discover and which will become useful and commonplace after their identification and implementation.

Further Reading:

• How the world’s species count was estimated. Granted this is an old article but the best I could find.

• For those of you who want to learn more about cappuccino finches. (Probably the most anyone has read about birds in a while).

• A personal history of GFP from S James Remington, one of the scientists who engineered the gene for scientific use.