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To further complicate the picture, certain types of animals tend not to get fossilized -- terrestrial animals, small animals, fragile animals, and forest-dwellers are worst.
And finally, fossils from very early times just don't survive the passage of eons very well, what with all the folding, crushing, and melting that goes on.
The term "transitional fossil" is used at least two different ways on talk.origins, often leading to muddled and stalemated arguments.
I call these two meanings the "general lineage" and the "species-to-species transition": This is a sequence of similar genera or families, linking an older group to a very different younger group.
It's a very fine-grained sequence documenting the actual speciation event, usually covering less than a million years.
These species-to-species transitions are unmistakable when they are found.
Throughout successive strata you see the population averages of teeth, feet, vertebrae, etc., changing from what is typical of the first species to what is typical of the next species.
Sometimes, these sequences occur only in a limited geographic area (the place where the speciation actually occurred), with analyses from any other area showing an apparently "sudden" change.
There are now several known cases of species-to-species transitions that resulted in the first members of new higher taxa. Ideally, of course, we would like to know each lineage right down to the species level, and have detailed species-to-species transitions linking every species in the lineage.
However, they are assumed to be closely related to the actual ancestor, since they have intermediate morphology compared to the next-oldest and next-youngest "links".
The major point of these general lineages is that animals with intermediate morphology existed at the appropriate times, and thus that the transitions from the proposed ancestors are fully plausible.
The first and most major reason for gaps is "stratigraphic discontinuities", meaning that fossil-bearing strata are not at all continuous.
There are often large time breaks from one stratum to the next, and there are even some times for which no fossil strata have been found.