Just to give a few quick examples;
Australia was dominated by marsupials until only very recently in geologic time, and the general idea of why they flourish there but are rare or absent across the rest of the planet is that they were able to colonize Australia via migrating across Antarctica (warm at this time period) from South America. However, Australia was not directly connected by land, and the ‘placental’ mammals were also present in the same region at the same time period. Thus the suggestion is that the marsupials just happened to exploit an opportunity at a very brief window of time. Such a brief window suggests, at least to me, that the total founding member count cannot of have been very high. Not million of individuals, and even hundreds feels generous.
Monkeys reached South America from Africa by ‘rafting’. Not as in, building a physical raft, but being blown across in storms in either large trees, mats of vegetation, or chunks of landmass that were dislodged. For the monkeys to have bred they would have had to be closely related species (so a baboon and a chimpanzee wouldn’t be able to start a founding population even if both were blown over there), and given the sheer amount of distance and how closely groups would have to have arrived to meet and breed, this also seems like it only happened once. I don’t imagine you could fit hundreds of monkeys on even a large tree.
Lastly, all the species of true crocodiles in the Americas are not only descended from african crocodiles, either blown in or having swum the enormous amount of distance, but genetics seem to suggest that all, at some point in relatively recent history, were descended from the same female individual. Whether a single pregnant female made the journey and led to various descendance through inbreeding, or several crocodiles were blown over but only one female survived, the result is the same.
In all cases it seems that enormous variety has arisen from very small pockets of closely related animals. How have these animals ‘beaten’ the issues that arise from inbreeding?
In: Biology
One important thing to know is that the starting population may have had a lot of genetic diversity. Humans actually do *not* have very much genetic diversity compared to many other species, so a lot of our assumptions of how bad inbreeding is are overestimates when applied to other species.
That said, inbreeding can and does lead to problems, and the animals we see now are the species who managed to survive this. Plenty did not. I have seen some speculation that woolly mammoths isolated on islands in prehistoric times died out due to inbreeding. [Relevant xkcd](https://xkcd.com/1827/)
Inbreeding in and of itself does not make problems out of nothing. A lot of the problems associated with inbreeding come from specific recessive traits. You have one copy of every gene that came from your mother, and another copy that came from your father. Recessive traits are if you have one copy of the recessive allele (allele = version of a gene, when people talk about genes colloquially usually they mean allele) and one copy of a different allele, you have no issues, but if you have two copies of the recessive allele, you do have issues. If the founding population has the recessive allele, it constitutes a higher proportion of the population and thus there will be more individuals who have two recessive copies and thus have the inbreeding-related disease. Enzyme deficiencies are a really common example of this, where there’s a mutant version of a gene for producing a particular enzyme that either does not work, or produces only very little. But if you have one fully functional copy, that one copy is able to make more than enough of the enzyme so you have no issues at all. The problems only arise if both copies of the gene are nonfunctional.
If, by chance, the founder population does not have any of these mutations, then the descendants aren’t going to have that many issues.
You talk about inbreeding like it’s always bad. That’s not exactly how things work. Inbreeding can distill undesirable traits, but it can also distill useful ones.
If you raft 50 monkeys to SA from Africa, they might develop some defect and die out in 10 generations. Oh well. The next raft might develop other traits that are really well suited to living in SA, and those are the survivors.
Random mutation sets a more stable variation as the community grows and 500 years later you have a genetically stable species in an ecologic niche.
That doesn’t mean it works 100% of the time, nothing in nature is 100%. All you see is the cases where bad things didn’t happen, what’s generally called “survivor bias”. Even if the survivor case is only 1% likely, in enough tries it will happen and the 99 dead species will hardly be a blip in the fossil record.
There’s a really fun book called Tears of the Cheetah that you may really like, because at some points it talks about “bottle-neck” events where a population got decimated and bounced back. Part of the reason a population seems fine is that any severe recessive genes that would kill an animal would not get passed down because the animal would die young. But also there are huge downsides to the inbreeding; a lot of these populations are vulnerable to new diseases. Without genetic variety, if the new disease can get one of the species it can often wipe out a huge swath of the population before they adapt
The major problems with inbreeding is that inbreeding has a higher chance of genetic defects or diseases popping up, and if those inbred animals survive to breed, or inbreed, the traits can get passed along or get worse with each generation.
However, this both implies that the animals had a serious risk of defects in their genome to begin with, and that the inbred individuals with defects survived. Animals with serious defects that disable them to some extent usually die long before they can really spread their genes into the world. Basically even if they are all severely inbred, you can still get to a large population if enough healthy individuals are born that survive, and most of the animals born with serious defects do not. If the initial few animals that arrived were very distinct and not related, even better chances.
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