The tree of life on this planet undergoes extensive and regular pruning. Understanding how this process occurs is essential to creating a constructed world with a plausible biosphere. The art of creating a biosphere, like the art of creating a detailed family languages, is distinguished by the fact that you can do as much or as little as you like, and still captivate a casual reader—but you will still have a rotten taste in your mouth if you skimp on constructing a plausible history.
Natural selection, as you most likely know, is the process whereby certain variations of a pattern become more dominant among a population because they are better at surviving or proliferating, and crowd out less-capable varieties. Most commonly, this pattern is discussed as being an entire genome (the set of all genes in an organism), but it can also refer to alleles, genes, or learned behaviours passed from parent to child. (An allele, for those unfamiliar, is a variation on a gene, such as albinism or blood type. A gene itself is a blueprint for a molecular machine, and can be thought of as part of a computer program.)
Artificial selection also exists. This is when organisms are refined by the conscious efforts of intelligent organisms who desire to emphasise certain traits in those they have control over. A key form of this is called domestication, and has been widely used by humans for millennia, most productively in agriculture.
Typically the environment in which natural selection occurs consists of the physical challenges of the area around it, and interactions with other members thereof. These can include predatory, mutualistic, and commensal (to the benefit of one group, with no effect on the other) relationships. One must also consider the niche which an organism occupies within its environment: a tree-dwelling creature will experience different pressures from a burrowing one, as will a hummingbird from a woodpecker. An organism's niche is primarily a question of how it occupies its environment, and which other organisms interact with it as a result of that behaviour.
Life is not static. Organisms do not merely adjust to fit an environment once and then settle there; over the course of generations, an eternal arms race between ever-changing threats and opportunities emerges. Although we comprise the best-known example of organisms that have dramatically altered the Earth's environment, humans have been, at best, only the second most destructive group; the planet's atmosphere once almost completely lacked free oxygen, making many fundamental parts of atmospheric chemistry radically different, and dramatically changing what was available to the fundamental metabolic pathways organisms use. The development of cyanobacteria and primitive plant life, which converted carbon dioxide into free oxygen, made it possible for other, enterprising bacteria to access the energy held in oxygen-oxygen bonds as a source of fuel. Consequentially, the Archaeans, one of the most ancient and (then) prolific forms of life on this planet, were set on the track toward relegation as extremophiles, eking out meagre existences in environments where more oxygen-hungry life cannot tread. The trimming of the tree of life was so drastic that this period of history, which took many millions of years, is sometimes called the Oxygen Catastrophe.
Changes like these have supported evolution's march into higher and more complex forms, but as far as we know, abiogenesis couldn't have occurred on Earth today without some very special circumstances. The building blocks of the first cells, which many scientists believe consisted primarily of RNA, simple peptides, and lipids, would have required an environment similar to the interior of a living cell in which to combine, or at least a plausible route to getting there. Exactly what these circumstances are is highly debated, however, and numerous theories about the ultimate origin of life persist.
It is the sum of these environmental changes that gives rise to the distinctness of a clade (a branch on the tree of life). Each organism is the latest chapter in an endless chronicle that describes the challenges its parents and ancestors faced, right back to the beginning of life on this planet. When designing an organism, it is important to consider not only what its ancestors looked like, but why they look that way. Without this, or some very careful planning, multiple such creations may tend to develop inconsistencies and conflicting niches when put into an ecosystem together. (Which, of course, does happen in real life, too, but not many people want to be told that their favourite animals or plants would eat each other to death inside of a year.)
Throughout this post thus far, the term species has been avoided entirely. This is because the concept of a species is fuzzy. Right now we use a number of different criteria to describe when two populations split off into separate species—that they stop reproducing with each other is the primary concern. This may be caused by something as harmless as physical separation, a mutation that causes one sub-group to be nocturnal (so that they're never around at the right time), or the more widely-recognized physical and genetic incompatibilities that interfere with reproduction directly—although genetic incompatibilities rarely accumulate on their own so rapidly that the species splits; they generally must have some form of isolation as well, to prevent cross-pollination of the new changes. Many people know only about the "if it can't mate, it isn't the same species" idea, which is a little simplistic, and frequently violated.
But the truth is that "species" is just a label of convenience, created by early taxonomists before evolution was well-understood, to help them label their world. (After all, it's just a Latin word that means "kind.") All organisms are merely different arrangements of nucleotides, operating in conjunction with the machinery those nucleotides are responsible for creating and maintaining. All we can really say is where one cell ends and the next begins—and even when that happens, exactly, is a bit muddy.
Historically, we've used terms like subspecies, race, breed, and variety to describe these minute differences, but in truth there's no cut-off. If the distance between two organisms can be measured as the difference in DNA sequence, then that can be extended, through history, from a mother and daughter all the way up to a human and a chimpanzee, or a human and a mouse, or a human and a bacterium, all continuously, and all without ever having to traverse a sudden skip in relatedness that we can point to and say 'Aha! A speciation event!' (Well, this is not entirely true. Some speciation events are caused by major changes like the merging/splitting of a chromosome, or horizontal gene transfer—but these can happen without breaking species, too.) Such is surely the greatest advantage of having millions of years to do much of anything.
With that out of the way, let's talk about adaptations, alternative biochemistry, and the origin of intelligence.
Click here to read part 2.