Most people know that sexual reproduction creates offspring that are genetically distinct from both of the their parents. That's true, but the genetic scrambling that occurs is more significant than is sometimes reported. Let's start by looking at chromosomes.
Like every other animal (or plant or pretty much any other organism), your genetic endowment is carried in chunks of DNA called chromosomes. You have 23 of these chunks, which are rather like volumes in a set of encyclopedias. More completely, you have 23 pairs of these volumes; one set was contributed by your mother and the other by your father. Each of your parents had a complete set, also consisting of a set from Mom and a set from Dad. When your mother made the egg that became the zygote that became you, she provided you with one copy of each volume in the set, and she chose those copies randomly. For example, she may have chosen her dad's copy of chromosome 1, but her mom's copy of chromosome 2. Just by virtue of this random picking process, she made an egg with a shuffled version of her own genetic cards. Dad did the same when he made his sperm, and so your genetic complement is an amalgamation of your parents' genomes which were amalgamations of your grandparents' genomes, and so on.
But before the random picking process occurred in the steps leading up to the final egg/sperm, something remarkable happened to further shuffle the genetic deck. For each chromosome, the different copies lined up with each other and exchanged contents. In other words, a new chromosome 1 was made that was an amalgamation of the maternal chromosome 1 and the paternal chromosome 1. The two new versions were chromosomes unlike any in your mom or dad; they were new creations, clearly designed to maximize the diversity in your genetic inheritance. This process, which is illustrated in the diagram below, is called crossing over.
The figure shows two instances of crossing over, creating the amalgamations that are part white, part black. In the real process, crossing over can occur at multiple sites along the chromosome, so that the resulting amalgamations are black-white-black-white and so on.
What this means is that you received, from each of your parents, a set of chromosomes that included at least some which were shuffled versions of their own chromosomes. And more importantly, this means that the units of genetic material that you received were much bigger than individual genes (which can barely be visibly represented on a diagram like the one above) but typically smaller than an entire chromosome. It's as if you were given a set of encyclopedias in which individual volumes had chapters from one version of that volume and chapters from another. Individual genes would be merely pages. The basic lesson here is that you received your genes from your parents in chunks, like chapters, and not one by one, like pages.
What does this have to do with hitchhiking? Well, suppose that in one of those chapters, meaning in one section of one chromosome, there appeared a beneficial mutation of some kind, and suppose that this mutation conferred an advantage on every individual who carried it. Over a relatively short time (evolutionarily speaking), that chapter could become a lot more common in the population. It may even become so common that it's the norm, in which case it would be considered to be fixed in the population. (The process is then called fixation.) Notice, importantly, that we said the chapter will become fixed. Why not just the gene? Because the pieces of DNA that are passed down in each generation are a lot bigger than that, as we just saw.
The basic message, then, is this: when an organism inherits some new and beneficial gene, it inherits everything in the vicinity of that gene as well. If that new and beneficial gene becomes fixed in the population, then everything in the vicinity will be fixed as well. The result is that when a strong selection process acts, and drives a new gene to fixation in a relatively short time, it leaves a mark on the genome: one chapter in the set of encyclopedias will be oddly the same in everyone. That chapter will display a lot less genetic diversity than other chapters. That's the signature of recent positive selection, resulting from a so-called selective sweep. And it results in the fixation of a lot of stuff, most of which is just along for the ride by virtue of being located in the same chapter as the beneficial gene. All that other stuff got there by hitchhiking.
Image credit: Wikipedia. Image is from T.H. Morgan, A Critique of the theory of evolution (1916).
