A biological, ‘Lineal’ system is one made to reflect evolutionary ancestry.
A biological, ‘Linnaean’ system is one made to reflect hierarchical created kinds.
The irony/etymology of the strikingly similar names is coincidental and the wonder is that the system, still (after 250 years) holds dual functionality as baraminology and the phylocode have both (for very different reasons) failed to take off or replace it.
The term, ‘tree’ is of course, a representation of how life was/is, and merely tries to compare and conjure up an image and show, relationally, how one real, live realm is visualised on paper or as a computer programme or simulation. Other terms put forward, include bush, shrub, forest, hedgerow, weed system and (Darwin’s suggestion, not mine), Coral.
My own offer is a, ‘sponge’. This eliminates all the free or empty space/gaps of non-life and other events, and brings all life together, with mere walls separating them, with gaps only where there are life gaps, like extinction/the end of a lineage. Food for thought, perhaps. Sometimes a visualisation has to be different, even complex, in order to capture clarity, just as some simple visually similar representations may confuse when looking deeper. And such is the case here.
A phylogeny, (or a phylogenetic tree) as Wikipedia nicely puts it, is a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the 'end', or the present/ongoing, in an evolutionary lineage.
Like many representations, allegories or examples in life, this system is also limited, has its boundaries and only tells one part of a story. It skips thousands of generations and has convenient, unnatural, selective stages (clade nodes), omitting other less interesting ones and has forever, in-between nodes to be discovered or included. There is no direct, ‘individual’ lineage shown in a phylogeny. It assumes multiple generations between stages. This can cover a multitude of, ‘sins’ literally – as genealogies now show!). Let me explain.
There are phylogeny comparables out there. Imagine trying to build a human/family genealogy tree (micro phylogeny), with the typical tree based methodology used. This would seem a good, logical method and based on ancestry.
But it is not always as we think. The pretty structure (and the genetics) gets messed up in many ways. When someone adopts a child, has a sex change, marries someone of the same sex or a relative, has a child-producing affair, uses a sperm or egg bank, is artificially enabled to reproduce, is a bigamist, step/half sibling, rapes or gets raped, is a sperm/egg donor or reproduces with a different ape species.
Those pretty trees, as followed (for example by own Latter Day Saint friends) showing happy families - brothers, sisters, parents, grandparents, uncles, aunties etc. are often wrong in many ways. Try building a tree with some of these inconvenient factors (just mentioned) and see how challenging it is. The question is, do we intend to show history or genetic ancestry or happy families or all of these?
The fact that this is so much more difficult to lay out on paper or a computer, is because we only started with, or looked at, part of the story, which is not necessarily compatible with our limited/false selection of pretty, natural, undiluted ancestry tree.
It depends what you want from it. If we want a fuller, more complete, detailed understanding of evolution, then the current clade, hierarchical or phylogeny based methods won’t cut it. They either need to accommodate much more and varied information or numerous data diagrams/dendrograms need compiling and linked or overlaid. Think about digital maps with optional/selectable layers of terrain, sub-terrain, populations, crime stats, roads, views over time etc.) to give a greater understanding and perspective. With evolution, we have only scraped the surface.
The problems are, 1.) the technology to build/incorporate all this data and bring it together, plus 2.) the very limited information we have, both of the past (especially, but not exclusively very early life) and current (e.g. we simply can’t really track (or indeed recognise) interbreeding of populations or across genera or between species most of the time, in 99.999% of cases, so we have too little information and the research needed to even begin to monitor this is too little, too late, aside from the costs/staff needed. By way of example, imagine trying to compile history or a genealogy, if most of the records are destroyed or don’t exist, using what, if anything, is left.
So, we can’t even track our true/near ancestry under our noses, (e.g. because secret, ‘things’ sometimes go on under someone else’s bed sheets) for some of the reasons listed. This throws things off track or muddies the bloodline and gene pools. So how much worse and inaccurate is it, when we are working at a hugely zoomed out level (of species with thousands or more of missed generations between), and many unknown or extinct or taxa of indeterminate lineage.
Fortunately, we have tools now, which can help us link the present to the past, making it less important to know who or what slept with who or what, because we can slice though the secrets of the bedroom and remove time-based CCTV. DNA, genetics and decoding species genomes does all of this. Paternity tests using a simple swab or blood sample. Using microscopes and computers that can transfer millions of bits of biological data related to a species or individual, for computer analysis or comparison. This can reveal solid evidence of inheritance. It trumps any testimony, denial, good character or alibi by placing you/it, microscopically at the scene. Guilty. Genes don’t lie, even though they may be incomplete and not tell the whole story. Ask me no questions and I’ll tell you no lies.
So, even if we sub-divide subspecies (like domestic dogs) into breeds on the tree (which hybridises phylogeny and genealogy) or we include ring species or add cross pollinators or occasional ancestral population meetups (like Motty the elephant) due to natural or un-natural events, or even if we breed with other apes, it doesn’t really change the bigger macro picture, as these are micro events by comparison. Whether some, ‘butterfly’ effect could change things, (or a huge genetic fertility mix across class, phylum or kingdom), I don’t know, but the HGT dog’s dinner, in effect, already does this.
At Phylogeny Explorer Project HQ, we are building an, ‘accurate a representation of the phylogeny of life’ as we can, in as far as we can determine it. The team is brimming with ideas to add value and added information to anything else already out there (and here is one example, which attempts to reflect how populations can or have or do remain inter-fertile and attempt to define the limits of speciation in populations, which can have multiple new applications), but we really need your support to get there, by volunteering or donating, both/either of which can be found on this Website.