The Moonspeaker:
Where Some Ideas Are Stranger Than Others...
Phylogenetic Trees are Cool (2025-10-27)
My first encounter with the method of mapping relationships between different species was in a class about dinosaurs. This was in the days when there was still considerable resistance to the idea of warm-blooded dinosaurs, or survival of dinosaurs in the form of birds. While I couldn't make head nor tail of the arguments for and against warm-bloodedness at first because of needing to learn more about the sorts of fossil evidence involved in it, the idea of smaller dinosaurs surviving to the present in much altered and evolved forms made sense. After all, if mammals made it out first by being small and gregarious, then by evolving fur and other means to survive cold and wet conditions, then it didn't seem so ridiculous for similarly small, gregarious dinosaurs to do the same. It's toughest to make it through large change sin climate, even temporary ones, for larger creatures. They don't have much wiggle room to go hungry, have less ease in moving to more promising places, and may not be able to live in groups large enough to get the benefits of a herd or troop. Well, I say all this now. Back then I found dinosaurs simply too cool to agree something as ridiculous as an asteroid strike wiped them all out completely in one shot. While obviously an asteroid strike is hardly trivial, if it was possible for one disaster to somehow neatly take out just one major type of animal or other organism from the world, well that just seemed too surgical. Plus, even then we had already learned about the extinction of the pleistocene megafauna, many of whose smaller sized cousin species made it through that alarming period. By no means all of course, a mass extinction is no party. Still, it probably really came down to me managing to hang onto the common perception of many kids that dinosaurs are awesome. Arguably the coolness of phylogenetic trees has a somewhat more adult basis, even if some of the most famous examples are apparently so in significant part because they are simple enough for tattoos and posters.
Phylogenetic trees aren't new exactly, although the most famous first example is drawn from Charles Darwin's notebooks, specifically one dated to 1837. The Digital Atlas of Ancient Life provides an excellent reproduction among the illustrations of its explanation of phylogenetics, which I am going to lean on heavily here. Practically speaking, a phylogenetic tree is quite similar to what we refer to as a family tree, in that it is meant to depict relationships between ancestors and descendants. As always, things are more complicated when we dig into the details. A phylogenetic tree represents hypotheses about evolutionary relationships between different types of organisms, whether they are alive or extinct. They are more obviously hypothetical and therefore contested than family trees, and the most reticent biologists are reluctant to refer to the organisms under study as species once they are identified wholly from the fossil record. The issue is not genetic relationship as such, but that the colloquial meaning of species can cause a great deal of confusion and unsupported expectations. The OED definition of a species doesn't reveal where the confusion can come in, stating "a group of living organisms consisting of similar individuals capable of exchanging genes or interbreeding." The trouble comes from an expectation very different looking organisms will inevitably be separate species and unable to exchange genes or interbreed. This expectation doesn't stand up to much scrutiny, as we have only to think about the extraordinary diversity of the domestic dog breeds, many of them maintained only by the type of forced breeding which among humans is firmly denounced as incest and liable to produce at best sickly offspring. More recently, recognition of the importance of symbiosis and its effects has added a further layer of complexity, although so far primarily on the genetic and microscopic rather than macroscopic level. In any case, unlike a human family tree, phylogenetic trees are meant to represent degrees of relationship, not literal lineal descent lines.
So, supposing you don't want to just look at these phylogenetic trees for their aesthetic qualities, how are they read? Well, these are analogous to trees, so they have branches extending away from a trunk or base. Therefore, the shorter and further from the base a branch is, the more distantly related it is to the group of organisms defining the base. The places where a new branch splits off is a node, and the node represents a common ancestor. According to the Digital Atlas of Life, "A phylogenetic tree is an illustration depicting the hypothesized degrees of evolutionary relationship amongst a selected set of taxa (singular = taxon). The taxa are typically species, but can also be higher-level Linnaean groupings like genera or families. Alternatively, some phylogenetic trees depict relationships among individuals within a species (e.g., from geographically isolated populations)." So don't be surprised on running into examples of phylogenetic trees tracing relationships between quite different groupings, but they can't mix levels. If the tree is meant to show relationships between species, all the names will be of species, if between genera, then genera names. The example reproduced above is a tree of phyla relationships, which roughly reflects shared body plans between all the organisms included in it. To begin with phyla were defined by body shape before anyone could study genetics. Nevertheless, the body shape based definition of a phylum does not have the same weakness as it would if used for defining species. Maybe a better way to refer to this is body type or body plan, which implies an examination of more than superficial similarities. (Taxonomy is all about arrangement and ranking. As serious biology students will be able to explain in their sleep, the taxonomic ranks from most inclusive to least are: Life > Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species)
While there are certainly people who find the idea of all life on Earth being literally related in a quite direct sort of way, especially via genetics, quite disturbing, I find it hard to share this perspective. On one hand, it is quite wonderful, wonderful in a truly ineffable sense. It is no wonder to me there are people so overwhelmed with delight at this, and at representations of it as to want to literally have it marked indelibly on their skin. On the other hand, yes, it is not wholly a pleasant thought when we are faced with species extinction, anthropogenic climate change, and less than pleasant or helpful other organisms in the world. Contrary to the views of a great many scientists and engineers, our ability to meddle with other organisms in the wildly complex network of life on Earth does not strike me as a powerful thing so much as a perversion of knowledge and failure to properly honour our kin. Indeed, such notions as humans supposedly being the epitome and ruler of life on Earth strikes me as an especially acute example of hubris.
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