From Darwin to DNA - redrawing the tree of life
Edward Hitchcock’s Tree of Life, 1840. Via Wikipedia, Public Domain.
Flip open any biology textbook and you’ll probably see a typical ‘tree of life’ – a family tree-like diagram showing the relationships between species as they’ve evolved and diverged from a common ancestor.
Darwin’s 1837 Tree of Life sketch. Via Wikipedia, public domain
Perhaps the most famous example is from Charles Darwin himself, whose first sketched out a small spidery tree explaining the evolutionary relationships between species back in 1837, labelled with the immortal words “I think…”
Scientists have been drawing and re-drawing the tree of life for hundreds of years, based on observed similarities and differences between species.
Advances in DNA sequencing now allow us to analyse genetic relationships between species, refining these trees with ever greater depth and accuracy, and adding in more and more branches and a trunk that stretches all the way back to the beginning of life on earth, some 4 billion-or-so years ago.
But rather than making things clearer, all this information has turned Darwin’s simple tree into a thorny, tangled thicket, and raises questions about what it even means to be a species.
So how did we get here? To find out, we need to take a trip back to the 18th century, to meet Carl Linnaeus – the father of taxonomy.
Born in 1707, Carl Linnaeus was a Swedish botanist, zoologist and physician who was obsessed with collecting, identifying, naming, and classifying organisms into different species. He had a particular love for plants – the more exotic the better.
Rather than taking to the ocean waves himself to indulge this passion - his furthest expedition was to Lapland and he never left Sweden after the age of 30 – Linnaeus sent his students to travel abroad and collect specimens to send back to him.
He dubbed these botanical adventurers his ‘apostles’ – which fitted well with his apparently high opinion of himself as the self-styled ‘prince of botany’. As it turns out, ‘martyrs’ might have been a better name for his unlucky crew, as seven of them died during their travels.
Thanks to this army of apostles, word soon started to spread about their plant-loving professor and his interest in collection and classification. Thousands of specimens started flooding in from across the globe, causing Linnaeus to complain that he was working night and day ‘hatching new species’ like a hen hatching her eggs.
Struggling with the information overload, he had to come up with a way of organising all these species in a way that made sense and captured the relationships between them. But rather than a tree, the first attempt at cataloguing life was a table.
Linnaeus’ Systema Naturea, published in 1753, consisted of three tables, one for animals, one for plants and one for minerals. He then used columns and rows to group similar organisms. As he and his apostles gathered more and more specimens, the tables had to be expanded, redrawn and republished.
Some species were also reclassified as Linnaeus learned more about them. For example, whales and manatee were classified as fish in the first edition but later moved to the mammal section.
By the twelfth edition, published in 1770 just eight years before Linnaeus’ death, the Systema Naturea contained around 13,000 species – an impressive attempt at describing the logic of life. As he so modestly put it, "God created, Linnaeus organized."
Although Charles Darwin is often credited with drawing the first tree of life with his 1830s sketch, the honour should really go to French nobleman, schoolteacher and priest Augustin Augier.
His Arbre botanique, published in 1801 represents the relationships of plants in the shape of a literal as well as metaphorical tree, demonstrating the beauty and perfect order of divine creation, as Augier saw it.
A few years later in 1809, his compatriot, the zoologist Jean-Baptiste Lamarck, drew the first family tree of animals. But it was Darwin who really cemented the idea of the tree of life as a way of describing the evolutionary relationships between species and how one might evolve from another.
In Origin of Species he writes:
“The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. ....
The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups.”
However, Darwin’s tree of life didn’t contain any actual existing species, just theoretical relatives. He left it to others to try and draw up family trees capturing the relationships between real life organisms, which we now refer to as phylogenetic trees.
Ernst Haeckel’s Tree of Life, 1879. Via Wikipedia, public domain
Ernst Haeckel, a German zoologist and accomplished artist, drew one of the most famous examples – a mighty oak with simple organisms like bacteria at the bottom of the tree and humans at the top. He even labelled his diagram ‘Pedigree of Man’, because of course men are the pinnacle of evolution…
Although he was a big fan of Darwin, Haeckel’s tree of life didn’t exactly follow Darwinian principles. For a start, he included living species as internal branches of the tree, when those should only be extinct ancestors with living relatives out on the twiggy tips.
Other scientists of the time did produce phylogenetic trees that fitted Darwin’s principles better. But perhaps because of their comparative lack of artistic prowess, they are often overlooked – as so often in science, having good PR does help.
Scientists continued drawing and re-drawing the tree of life and sections within it, basing them on hypothesised evolutionary relationships inferred from the shared characteristics they could see between species.
For Darwin, this was a vindication of his ideas and in 1857, he sent a letter to his fellow evolutionist Thomas Huxley in which he writes:
“The time will come I believe, though I shall not live to see it, when we shall have very fairly true genealogical trees of each great kingdom of nature.”
As the science of genetics emerged throughout the 20th century, gathering pace with the invention of DNA sequencing in the late 1970s and exponentially exploding with the advent of computer-based analysis or bioinformatics in the 1990s, it started to look like Darwin’s prediction was coming true.
Scientists can now compare DNA sequences across thousands of species to see how they’re related and calculate the evolutionary distance between them. And the increasing ability to sequence and analyse DNA from ancient specimens is opening a genetic window into the past.
But with all this progress comes a new problem: what exactly is a species anyway?
Biologists have been grappling with the question ’what is a species?’ for centuries. For Linnaeus, who believed that God created all species and that they were fixed, different species could be teased apart by looking for distinctive physical characteristics – although even he struggled with drawing the line in some cases, asking:
“Is the plant Thalictrum lucidum sufficiently distinct from Thalictrum flavum? It seems to me a daughter of time.”
In 1856, Darwin wrote to his closest friend Joseph Hooker, saying:
"It is really laughable to see what different ideas are prominent in various naturalists' minds when they speak of 'species'; in some, resemblance is everything and descent of little weight - in some, resemblance seems to go for nothing, and Creation the reigning idea - in some, descent is the key — in some, sterility an unfailing test, with others it is not worth a farthing. It all comes, I believe, from trying to define the undefinable."
As an attempt to nail down some definitions, there have been a number of ideas put forward as to what makes a species a species. One of them – the biological species concept - suggests that organisms are the same species if they can interbreed and produce fertile offspring, and different species if they can’t.
But lions and tigers - which are separated by geography, genetics and 3 million or more years of evolution – can interbreed to produce ligers, which are fertile 50% of the time. And then there are ‘cryptic species’ – organisms that look for all the world as if they’re the same species but can’t or don’t actually get down to it and breed with each other.
All the living things on earth right now are caught in the act of evolution – and evolution is messy. It isn’t a directed process, neatly creating precise species boundaries according to some celestial taxonomy. There’s a fair bit of fuzziness around the edges – a biological grey zone where defining two animals as different or the same species, such as tigers and lions, is difficult, even if they appear to be physically distinct.
In 2016, French researcher Camille Roux and his team attempted to shed some light on this grey zone, comparing the genomes of 61 pairs of animal populations with varying levels of difference between them, from very simple organisms like molluscs and worms to mice, hares and monkeys. Some were classified as distinct species according to conventional taxonomy, while others were classed as sub-species.
They found that regardless of the animal or where they lived, there was around 0.5% and 2% of difference in the genomes of each pair. While this isn’t a hard and fast rule - less than 0.5% difference and you’re the same species, more than 2% difference and you’re different – the study helps to set some parameters on the biological species concept.
Now biologists can peer into the genomes of anything that they can throw through a DNA sequencer, the tree of life has gone through a dramatic phase of vibrant, vigorous growth.
Some of the new additions are previously unknown species that have been discovered for the very first time. Others are examples of what’s known as the Lazarus effect, where a species that was thought to be extinct is found very much alive and well.
For example, the missing presumed extinct rock rat and an entirely new species of rabbit turned up being sold as food in a village market in Laos. However, many others have been created by splitting one existing species into two or even more – something known as ‘taxonomic inflation’.
Hundreds of new species of mammal have been ‘discovered’ (or at least labelled) since 1993, including the reclassification of African elephants into two species, while the neotropical skipper butterfly has been regrouped into ten.
This is particularly important for very small organisms that might not have a lot of physical characteristics for taxonomists to go on. My favourite are placozoa - tiny sea creatures that are little more than a ball of cells. Their lack of distinguishing features has meant that they’ve spent the past century lumped into a single species, Trichoplax adhaerens.
But when a team of German researchers compared the genomes of plazocoa around the world, they found one population that was so different that there was no option but to classify it as an entirely new species – even though it looks exactly the same as all the rest.
Because these animals were found in the Ho Chung River in Hong Kong, they were named Hoilungia hongkongensis, which translates as Hong Kong Sea Dragon. And just like the shape-shifting mythological Chinese dragon king, placozoans can easily change their shape too.
Instead of the majestic oak envisioned by Haeckel and his ilk in the 1800s, the tree of life now resembles a bizarre and somewhat unruly bush, constantly growing as more genetic data come to light.
Projects like the Darwin Tree of Life and Earth Biogenome, aiming to sequence all life on earth, are only adding to it. And rather than being at the top of the tree, humans are lost somewhere in the thicket – just a tiny twig amongst the exuberant diversity of life on earth.
References and further reading:
Life and works of Augustin Augier de Favas (1758–1825), author of “Arbre botanique” (1801)
The Grey Zone: Napoleon Dynamite and what makes a species PLoS Blogs
Taxonomic inflation: its influence on macroecology and conservation
lNick J.B.Isaac1JamesMallet2Georgina M.Mace1 Trends in Ecology & Evolution
