How relevant is new genetic diversity for plant/animal populations badly bottlenecked several centuries ago?

Question

Scenario: A major ecological disaster occurred five hundred years ago, in which large numbers of species (including almost all wild fauna) went extinct. Assume that the environment both before and after is modern-Earth equivalent; effects not discussed here mitigated the major effects on temperature, environmental composition, etc. Humans survived, although not in vast numbers, and in doing so preserved a number of highly productive and easy to grow crops along with some domesticated animal species. A few clever biologists also managed to preserve some really ecological critical wild species, like some relatively flexible pollinators. However, all of the non-human populations suffered some fairly extreme bottlenecks, in some cases probably down to the equivalent of a couple of seed packets. Humans only had a couple of months of warning to prepare, and not all species would have been preserved by people with a strong understanding of either theoretical or practical genetics (e.g. animal breeding). Unlike most of the other genetic bottleneck scenarios I've seen here, this one explicitly does not have a maximally diverse population during the bottleneck, which presumably would make the effects worse.

Five hundred years later, what kinds of problem (if any) is that lack of diversity going to cause, and how valuable would it be to have someone show up with new viable samples from the original populations? Does having a hundred new samples make a meaningful difference over just one? It will presumably vary by species, but I don't know what factors would make a difference one way or another.

With regard to what "valuable" means: I'm trying to figure out how excited a biologist who works in species maintenance and restoration would be to find these new samples. I am, unfortunately, not enough of a biologist to even guess at the correct criteria to use to evaluate this question. I'll happily revise the question if someone has suggestions for more precise criteria.

We can assume that the humans have been doing responsible husbandry for all of the domesticated species since the disaster, and that they started doing at least some preservation efforts for the wild species several decades after the disaster. A few species would probably have been lost to disease along the way due to common vulnerability; would we still be worrying about that, five hundred years on?

Answer 1

Species with little genetic diversity have two problems:

1. Inbreeding. If you start from a very small founder population, and they are all interbreeding with each other, then any recessive genetic traits will show up far more often than they would in a large, out-breeding population. An example is a Hutterite religious community, which was founded by about 100 people and who prefer to marry within their own religious sect. One woman of those original 100 had the genes for a hereditary form of deafness. A large proportion of the modern population (13% IIRC) are deaf, because they can all trace their ancestry back to her. And of course, deafness is not a life threatening condition. The recessives could just as easily be something that kills in childhood, infancy or in the womb. Reduced fertility is another consequence of inbreeding.
2. Lack of disease resistance. If you have reduced diversity you also have a reduced pool of different genetic resistance to diseases. Effectively, you are growing or breeding a monoculture. If a disease hits, it can be much more devastating than when there is a varied population with lots of different types of resistance. For instance, blood group B is said to confer resistance to the bubonic plague and blood group O to be especially susceptible to cholera.

Expanding the gene pool will get your biologist excited because it can solve the above problems. Also, different varieties of plant and animal will be better suited to different climates and micro-climates. Sheep suitable for wet, Welsh hillsides will not be happy in dry, Middle Eastern terrain. Potato varieties which like dry, well-aerated soil will not be happy in soggy, clay soil. If you have new varieties, suddenly you have more options as to where you can get decent yields from your crops, and you can cross-breed to create new combinations of features.

Answer 2

Nature is fairly brilliant in recovering from natural disasters. More than once the majority of (fauna) species have gone extinct due to disasters, yet many plants and micro-organisms such as bacteria or algae have survived all these for billions of years with little to stop them. So have many fish, sharks, octopus, crocodiles and insects like ants.

As your assumption is that (some) humans have survived for 500 years, you must have preserved a sufficient amount of plants to produce oxygen and food for them and their preserved live stock. Even if some species of plants die out due to lack of pollinators, vegetation has other means to survive, as long as some sunlight can still reach the surface to provide them with energy for photo-snythesis. If many species of plants die out, others will take their place. Sun-light is just too valuable an energy source to not use the whole planet's surface, whether on land or in the sea. This will of course change the flora, if the whole surface is wiped of plants, only algae or lichen - algae-fungi symbionts - will gradually reclaim the planetary surface, while algae will likely recover more quickly in the sea. If survival conditions become too extreme for almost any form of this life, there are always archae-bacteria which had millions of years of adapting to extreme conditions ahead of any other life-form. If the surface becomes unhabitable enough to allow no other life than archae-bacteria, you do not have to worry about reintroducing any current species of plant or animal, none would be able to survive.

As soon as species die out, others will try to evolve in order to fill the niche which is left behind. 500 years means more than billions of generations for bacteria, fungi and algae, chance enough to evolve and adapt. Insects can have hundreds of generations and you only need 1 surviving 'wild' ant, bee or wasp queen to refound their populations, if they still have food sources available. Ants being adaptive, omnivorous and able to survive even nuclear disaster, would be most likely to survive your events and feast and replenish the cadavers of the dying wildlife, grow fungi, when they run out of other foodstuff or even take over pollination from bees, if the need arises to get their food from the flowering plants when running out of alternative food sources. If you preserve them during the main impact of the disaster, you can reintroduce them into the left over eco-system very soon afterwards without having to wait for 500 years.

Larger animals and long-lived plants like trees have it harder, as they have very few generations in such an evolutionary short time span. Some trees might actually still stand from before the disaster, unless they were directly affected and reintroducing their pollinators would make a difference for them in case their species rely on pollinators. Reintroducing predators without sustainable amounts of their prey will be useless. Reintroducing plant digesting animals without a flora comparable to our current one for which their digestive system is evolved will be so too.

The main challenge is not to reintroduce species based on a few preserved seeds or recovered individuals, but to keep enough bio-diversity in your preserved species to keep them alive, healthy and genetically flexible enough to be able to adapt to new situations. Lack of a large enough genetic pool for quick adaptation of reintroduction might actually be the greatest challenge of your programme to reintroduce extinct species, as it is a major problem for zoos today when breeding species at the verge of extinction in order to preserve their survival.

Answer 3

For plants in particular, low genetic diversity isn't a problem per se, but it can lead to problems if a disease or blight that takes hold. Many agricultural products have only a few templates that are used the world over, which normally is perfectly fine... until it isn't. Consider the fate of the Gros Michel banana, which was devastated by blight. In that case it wasn't such a big deal because a) there were other, resistant banana cultivars with which to continue production, and b) bananas aren't really critical to life as we know it, but if it had been a staple crop, famine and/or ecological collapse (at least regionally) could've been on the table.

(As an aside: ecological collapse wouldn't be a consequence of this sort of problem in the modern world, because wild ecosystems don't have the same lack of diversity that agriculture does. But in your world, the wilderness also lacks diversity, so the problem can potentially be much larger.)

If you're looking for a scenario where it's vital to find a particular seed sample, you could have something like this: Crop A, on which the country's/continent's/world's economy and food supply rely, is at risk from Disease B. No known strain of Crop A is resistant to Disease B and disaster seems imminent. However, according to old records, there is a strain or related species C that could be used to replace/hybridize/genetically engineer A to end the threat. All they have to do is locate it. If you want the stakes to be lower, replace the staple with a luxury: maybe the world's only supply of roses is at stake, and fame and fortune await anyone who can save them.