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The goal of phylogenetic trees is to track the organisms we know of through their place in evolution.

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And if you are one of the first thousand people to click the link in the description you can get a two-month free trial of Skillshare’s Premium Membership. There are so, so, so many microbes in the world.

This far into our journey, it’s kind of astonishing to think that for all of the exciting and odd creatures we’ve watched, we’ve only kinda dipped into the shallows of the microcosmos. And like, have you ever sat back and been overwhelmed by the enormity of this minuscule world? Of just how many organisms are out there, both known and unknown, whose lives have been sustaining ecosystems and changing climates and doing just so much stuff for eons and eons as this diverse, invisible mass?

Scientists have been parsing through this overwhelming world for a few centuries now, identifying the specifics of how individual organisms live and connecting them to the bigger picture of how our world works. But what we especially love to do with the natural world is categorize, and perhaps the most familiar image of the categories we’ve created is the phylogenetic tree. The goal of phylogenetic trees is to track the organisms we know of through their place in evolution.

Take, for example, these various corkscrew-shaped bacteria, members of the Spirochaetes phylum. This phylogenetic tree is from the 90s and has been updated with more data, but we’ll use it just for now because it's relatively simple and that’s useful for explaining how the trees themselves work. The ends of these trees are the various spirochetes that scientists have been able to study, and if you move to the left, you can see their branches coming to an unnamed ancestor shared with other similar spirochetes.

These ancestors then branch back and connect with each other in various structures, creating that oh-so-familiar tree-like structure. And at the bottom is E. Coli, which functions here as an outgroup, a useful reference as something not immediately part of the Spirochete phylum.

We use these diagrams along with the words “kingdom” and “phylum” to categorize everything from the tiniest microbe to the largest whale, but it’s important to remember that these trees are our interpretation of what we’ve seen. Nature didn’t set out to create kingdoms and phylums, those are categories we created to help us make sense of the natural world. It takes a lot of complex work to simplify nature in this way, and the process behind creating these evolutionary trees has itself been an evolving one.

In the days of Darwin, evolution was connected to the things we could see, and when it comes to macroscopic animals, the things we see, like anatomy and fossils, are very useful. Microbes though, are a bit tougher. When we first began observing them, we tried to understand them with words we already knew, which led to confusion over whether they should be considered tiny plants or tiny animals.

But with time and more observations, scientists began to divide these organisms, and really all of life, into two overarching categories: bacteria and eukaryotes. This dichotomy would be most obvious in the microcosmos, but these divisions were still just a container that hid a confusing array of connections. Bacteria, for example, might be grouped together according to all sorts of factors, like their ability to form colonies or the danger they posed to humans.

But it hadn’t always been clear that the commonality of these traits necessary links in anyway to how they evolve. We’ve seen this again and again in our journey through the microcosmos: in the amoebas and euglenoids and so many other organisms whose evolutionary connections seem straightforward based on their morphology. And then, inevitably, we bring out the source of so many plot twists.

We’re talking about molecular phylogeny and the host of techniques it encompasses to reveal genetic connections that our eyes cannot see. But molecular phylogeny doesn’t just show us a whole bunch of things we got wrong. It’s helped reveal new categories and relationships within the microcosmos.

The seminal work behind these techniques was published by Carl Woese and George Fox in 1977, and it was rooted in a straightforward but powerful notion, that the sequences of molecules inside microbes could help us make connections that their morphology could not. This wasn’t a new idea: scientists had been linking amino acid sequences between animals. But the real challenge lay in figuring out what molecular sequence would actually be best to accomplish this goal in microbes.

We needed something universal enough to connect all organisms, but also simple enough to compare using the sequencing methods available at the time. So Woese suggested an organelle that you might not think of all that often: the ribosome. Across all living cells, ribosomes are the protein factory, taking in RNA and translating it into the molecules that make our bodies and all life work.

And the ribosome itself has an interesting structure, made up of both protein and RNA. Woese and Fox picked out a particular subset of that ribosomal RNA, compared the sequence different organisms used to construct that segment, and then built a phylogenetic tree out of the similarities and differences in that sequence. Their results did more than just create a tree though, it revealed a whole new subset of life that lay outside what we had assumed to be the binary divide between bacteria and eukaryotes.

They had uncovered the archaea, a type of prokaryote that had been assumed, up to that point, to be a strange type of extremophile bacteria. But thanks to archea’s ribosomal RNA and additional understanding of their morphology,. Woese and Fox realized that they were separate from bacteria.

An entire new domain of life. Molecular phylogenetic techniques have gone on to shift our understanding of microbes, raising questions and providing insights into how everything from sex to eating have evolved. But there are still many other methods of evolution that may not be captured by these techniques, including of course endo symbiogenesis and horizontal gene transfer.

Everybody’s two favorite non-linear methods of evolution. Establishing these phylogenetic trees, for all that it has helped us simplify nature, also emphasizes just how many complexities we cannot easily illustrate. Connecting organisms through their evolutionary relationships helps us establish a history of nature and map out the microbial world as it exists today.

That map will likely never be complete, but the work that goes into it helps us navigate through time and space and through invisible lives, long gone, to see how our world today is connected to the microcosmos of the past. Thank you for coming on this journey with us as we explore the unseen world that surrounds us. A lot of us are working at home right now, and for many people, it’s the first time they’re experiencing the work from home lifestyle.

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This is the last episode of Season 2 of Journey to the Microcosmos. We’re gonna take a couple of weeks off, but then we will be back on August 10 with a new episode. If you want to see more from our Master of Microscopes James, check out Jam & Germs on Instagram.

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