Charles’ tree

February 12, 2019
by Dr. Marianna Ricci, DVM - Medical + Science Writer and Communicator

London, 1837– A young man is home from the voyage on the Beagle brig, a 5 years trip around the world that will determine his entire career. The desk is full of notes and specimens collected during the expedition and the naturalist feels that animal and plants may change over time.

Charles grabs his red leather notebook and writes “I think” at the top of page 36. He knows he’s a terrible artist but starts doodling while brainstorming about his theory and sketches an irregularly branched tree - species evolving along branches, some branches far more branched and others with dead ends.

That’s probably how Charles Darwin gave an evolutionary twist to the old image of the Tree of Life, the only illustration in the Origin of Species.

“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.” - Charles Darwin, The Origin of Species 1859.

Darwin’s tree of life or phylogenetic tree is a branching diagram showing the evolutionary relationships among species that continue to be useful in Science.

But Darwin himself had second thoughts and felt that the image was powerful, still too simplistic.

And damn, he was right.

 “The tree of life should perhaps be called the coral of life, base of branches dead; so that passages cannot be seen. — this again offers contradiction to constant succession of germs in progress 
no only makes it excessively complicated.” - Charles Darwin, notebook B 1837 (pagg 25-26).

Reality (and phylogenetic tree) is even more complicated than Darwin may have envisioned and new discoveries are now heavily transforming - and questioning - Charles’ tree.

Darwin was half-right
(and natural selection still applies)

Much has changed since Darwin sketched out his tree in 1837.
He couldn’t imagine how advanced technologies (such as genome sequencing and bioinformatics) allow modern scientists to revise his theory.

Indeed, the concept of phylogenetic trees is going through a huge revision and constantly changing, but is still useful as framework to understand the natural selection and the evolution of species. Plus, phylogenetic trees continue to have practical applications, such as targeting closely related species to search for shared features of interest (e.g. sensitivity to a drug).

That said, the latest science is changing our understanding of evolution and species connections.

The third branch and the web of life 

In the 1970s, the microbiologist Carl R. Woese discovered the Archaea: they look like - and had been mistaken for - bacteria but are drastically unlike bacteria from a genetic point of view. Archaea constituted a “third kingdom” because they didn’t fit within the existing two kingdoms of living creatures (Bacteria and Eukarya). So, Darwin’s tree was missing a major limb arising from the trunk.

Furthermore, in the last few decades genetic tests revealed that different species can crossbreed: genes are not simply passed down a single branch but also between branches and from a creature into another. With horizontal gene transfer we discovered another significant form of variation (different from mutation).

It has also revealed that natura non facit saltus (nature can make leaps) and chunk of genetic material can appear quite suddenly in an individual or population. Therefore, a more realistic Tree of Life would be a Web of Life, a messier thicket where species on distant branches are not necessarily different.

We now understand that very different species can be linked and even composite. Think about the microbes living in your intestines (microbiome) or mitochondria, the descendants of bacteria that at some point entered our cells. About 8% of our genome is viral DNA, acquired through infection over the last million years (some still functioning and affecting our health as genes), and we seem to share some genes with other species. We’re barely at the beginning of this research but speculation is that without this genetic mix-and-match, evolution would have looked different.

"Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. […] I have called this principle […] by the term of Natural Selection"
- Charles Darwin, The Origin of Species 1859.

New discoveries may have caused criticism about the standard phylogenetic tree model in the scientific community, but that simple and powerful intuition has generated a vast body of understanding, knowledge and awareness.

Charles’ tree embodies the concept of natural selection and the fact that we are connected to every living organism (past and present) – a realisation that should also force us to consider extinction of species and our role in it.

Happy 210^th birthday, Charles.