I may address the areas I only briefly mention another time.
Many representations in life, be it an example, a parable, a chart or a system or classification are like Plato’s cave analogy and don’t or can’t fully or accurately represent reality or the thing it purports to reveal.
A colourful pretty spreadsheet chart bears little resemblance to a bank vault or cheese shop, but it portrays what needs to be done or how well things are in the associated business, in a way that people can visually relate to. Without further examples, clades and the phylogenetic tree of life are only visual, 'representations' and don’t show the full story and cannot cater for everything that goes on. For a start, most points (like clade nodes and lines) are arbitrary. We select elements that are convenient to us or that have (in our view) some major significance. In reality, evolution is a pretty fluid spectrum of events with no such increments or stepping stones. But such is life, that we have to make sacrifices in order to help us understand and comprehend reality.
There are so many factors which contribute to evolution, and on top of all the ones we try to follow and accommodate and factor in, there are quasi-factors which may or may not be a part of evolution and may or may not be represented (for whatever reason) in structures and dendrograms, showing evolution. For example:
· Horizontal gene transfer
· Inter planetary/stellar origins or movement or interaction
· Viral independence or mutation/evolution to a lifeform
· Genetic engineering or re-introducing extinct species or introducing new lifeforms in the laboratory
· Cross species or genus (or higher) interbreeding
In the extended Linnaean hierarchical taxonomy structure, plants, (in the same domain as animals) are differently laid out/classified. This shows how, when the roots of the tree of life start to disperse, evolution and mechanisms can take on different scales and we have to represent this differently.
Apart from the above examples, I want to mention another potential anomaly on the tree of life as food for thought as well as a point of interest, perhaps new to many readers.
The Portuguese man o’ war is one strange beast... or beasts. Is it one or more?
It looks and acts like a jellyfish, though jellyfish is not a monophyletic clade. It is also venomous. It is up to 200 feet from end to end stretched out, so possibly the longest animal ever recorded. The (aka) man-of-war is one of only two species in a sole extant genus in an otherwise empty family, along with the bluebottle. But the species itself is comprised of many organisms. So why is it classed as one organism with a binomial name? It isn’t made up of ‘other’ organism species. It is made up of organisms of the, 'same' species as itself. So why isn’t it a colony? Well each individual organism (whilst the same species) has a different role, e.g. to reproduce, eat or sting – as ants (for example) often have different roles. But in the man o’ war’s case, they cannot survive independently after the pre-pubescent polyp stage, and need to come together and physiologically unite and work together, symbiotically. So, we have many individual organisms (of the same species), which are born and are legitimate and genetic individuals, which (in taxonomy/phylogeny) don’t count as individual species, but are. And they are only classified as a colonial part of a whole (which has the same species name as all those who make it the whole) and so we have a colony which is classed as a single organism. It's like reproducing and delivering different body parts in pre-pubescent form and then uniting to a whole organism when the next stage develops. If you thought the theological trinity was hard to grasp, work this biological duality out! This (Hydrazoans) is not an area I am well versed in and anyone who is, is welcome to explain, comment, correct or add to this.
If you find this or similar or related stuff interesting, want to know more or would be interested in helping with the project, get in touch or go to the volunteer header section for more details. You may like to be part of the teams entering data, building the database/dendrogram/tree or a variety of other, including non-biology, roles available.