Hybridization between rainbow and cutthroat is primarily a problem in areas where rainbow have been introduced to formerly all-cutthroat habitat. This, of course, includes most of the Rocky Mountain west. In areas where cutthroat and rainbow evolved and existed sympatrically for millenia, the incidence of hybridization in much lower or, in some cases, nonexistent.
Essentially, where rainbow and cutthroat coexisted, reproductive isolation provided a pretty effective bar to hybridization. This is true of the coastal cutthroat (Oncorhynchus clarki clarki) and the coastal rainbow/steelhead (O. mykiss irideus) as well as the westslope cutthroat (O. clarki lewisi) and the redband rainbow/steelhead (O. mykiss gairdneri).
When non-native rainbow were introduced where native cutthroat populations had not developed such strategies, the result was massive hybridization and the gradual domination of the rainbow strain. If your question is really "If cutthroat and rainbow are close enough genetically to produce fertile offspring, why are they considered to be different species?", you'll have to take that up with the taxonomists and geneticists. Apparently not all differing species have diverged enough to lose the ability to produce fertile hybrid offspring.
Preston's reply to your specific question was spot-on. Here is some more information on species and speciation.
What is a species?? A central problem in biology and not always subject to a straight answer (or consistent answer). One reasonably accepted view of a species is a group of populations that could share genes and therefore have a joint evolutionary future. Two populations would be separate species if their populations cannot share genes (at least to any great extent) and they have separate evolutionary futures.
Speciation is a process in which a group of interbreeding (or potentially interbreeding populations) develop isolating mechanisms that block gene exchange. Some of these blocking mechanisms occur before mating: different breeding locations, different breeding times, different breeding behaviors/signals, different breeding parts. Others are post-mating barriers: incompatible egg/sperm, hybrid sterility or reduced fertility/survival (viability) by hybrids. The evolution of these isolating mechanisms is generally not instantaneous; small differences become magnified over time.
For example, when you see various subspecies of a fish species (westslope. vs. coastal, vs. Lahontan vs Crescent lake cutts), you are seeing isolated populations that are evolving independently in response to selection pressures in their local environments. If these local adaptations impact reproduction, you may see the beginning of reproductive (=evolutionary) isolation. Carried far enough, these could become separate species. This is especially true if hybrids are at an evolutionary disadvantage; any trait that prevents breeding by the two forms will spread rapidly because those that don't are wasting their reproductive opportunity - mating isolation.
There are several well-documented cases of stable hybrid zones at the area where two species meet. Hybrids occur, but the genes of one species do not penetrate farther into the population of the other species. Most of the hybrids are either first or second generation only. Often in these hybrid zones, mating isolation mechanisms are stronger (but still imperfect in preventing the appearance of hybrids) than in populations that are farther from the hybrid zone; trading gametes with wrong individual is a real disadvantage in the first case and doesn't occur in the second.
But if the physical barriers that isolate two populations break down / are removed, the local differences between the two populations could be swamped by reproduction between the two forms. What were two subspecies becomes one. Along the east coast, the black duck is apparently being swamped by mallards.
So what factors are used when deciding if two populations belong to one species or separate species? Classically, the deciding factor was morphology. If the two populations look very different, then they are different species. This is not always reliable as individuals in two populations could look very different, but they could still be capable of breeding (think of crossing a beagle with a great dane - possible, but challenging…). In other cases, two species can look alike, but still be isolated by the other factors; these are cryptic species. [The resident and transient killer whales should probably be classified as separate species IMO.] One pretty solid test is to see if individuals from two populations/species reproduce when they have an opportunity in the wild and if they do reproduce how viable (survival + reproductive potential) are their offspring. More recently, scientists have used genetic analysis to test if there is significant gene flow from one population/species to another. There was a thread on coyote / wolf breeding that I contributed to in which I pointed out that while there were examples of coyote / wolf hybrids, there did not appear to be much gene exchange.
Some species decisions are easy. X and Y are different species; steelhead do not reproduce with Chinook. Other decisions are also easy. X1 and X2 are found in different areas (Great Lake vs. Skagit), but if they could be brought together naturally (world's greatest geological cataclysm….) they would freely reproduce. Then, there are the hard calls, where you are making predictions about the future. For example, the prevailing prediction is that rainbow trout are a different species than coastal cutthroat, even though they do reproduce. But coastal cutthroat and westslope cutts are the same species. To really see how complex it can be, Google ring species……..
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