In a timeline with minimal European intervention in the Americas, what happens to the Natives?

There is no doubt that many factors worked synergistically to decimate the Native American populations, and make subsequent penetration by Europeans much easier in all of the new world. Even if the death rates from diseases are ameliorated, there will still be significant disruption of existing native societies. Furthermore those tribes in contact with the fringe settlers will see the impacts of trade, such as the inter-tribal fighting over access to fur animals, cause further disruptions. While the firearms of the early settlement period were not a significant advantage over bows and arrows, this changed rapidly. In order to have a chance at resisting European incursion, which will happen sooner or later, the native societies need to go from stone age to having some industrial capability almost overnight, which is not realistic.

The "Khyber gunsmiths" could come about because they had favorable terrain and were distant from centers of European occupation, and lived in areas not really desirable for exploitation. In Africa, away from the coast and even on the coast, the hostility of the environment worked to limit penetration for centuries. In the Americas, with some exceptions, the natives had few allies in the environment with disease or geography to prevent eventual occupation by Europeans.Where they had those allies, various mountainous regions or Amazonia, Florida swamps, Arctic areas, the conditions for the development of political and technological structures to form centers of resistance weren't there.

Looking at North America as an example, the resources there - fertile land, timber, minerals, etc were simply so attractive that sooner or later they would be irresistible. Native polities politically and militarily strong enough to resist this were ASB IMHO. The only thing that would slow this would be conditions in Europe that would lower the drive to colonize emigrate. Had Europe had a round of an epidemic in the 17th/18th century that depopulated it as badly as the Black Death (perhaps 1/3), this would reduced land hunger and also resources for colonization for some time.
So you think that not even the introduction of domesticated animals (such as horse, cow, yak, water buffalo, goat, alpaca, lama, bactrian camel and if the alpacas failed to take off in the Southwest, then sheep) would prevent the total conquest of North America?
 
Virgin Soil is debated to death here.
I'll just pick up the ball and kick it around a little:
So there is no large-scale conquest of the Americas, instead, rather limited contact, like with Siberia's natives, or Africa's. (This is plausible enough imho, as I've argued many times, but let's just assume it as a given, regardless of its plausibility.)
Before we discuss the question of preventing total conquest, let's focus on what's a lot more fascinating: how native American groups could evolve post-contact.

Native Americans don't just get germs. They get all sorts of domesticated animals, too, and a number of new crops and tools, and a crazy amount of ideas and cultural concepts they won't necessarily copy, but which will influence them nonetheless. (Ironworking, on the other hand, is something I don't expect them to copy until a lot of other things have changed internally, and the same applies to firearms.)

Let's map out how this alt-contact takes off.
Vinland is overdone, I want something else.
I'll go with Castile-Aragon not uniting and not funding Columbus. Instead, the Portuguese arrive in Brasil at some date in the early 16th century, and the English arrive in Newfoundland around the same time or maybe a bit later.

Would the Portuguese behave in Brasil the same way they did in Africa? To some extent, yes (acquiring wood and slaves, building forts / feitorias, erecting crosses and generally going about hypocritically pretending to spread Christianity). But the differences would also be marked (much fewer ships calling there because it's not en route to India; less complex chiefdoms providing fewer opportunities for instrumentalisation of local rulers). Either way, over time, some development similar to the establishment of the Kingdom of Congo is likely to start from the Brasilian coasts and eat its way upriver. Domesticated animals are probably less important here, but a number of African crops could be adopted.

What would the English do on the Atlantic coast? They'd want to monopolise fishing and whaling grounds, acquire furs... what else? They'd mostly deal with Algonquin-speaking groups. The coagulation into confederacies is sped up, but not as much as IOTL. What did native tribes adopt IOTL here?

Native history as we know it would be utterly butterflied. It would certainly take a lot longer before horses arrive in the prairies.

Many have argued to the Triple Alliance was bound for downfall anyway - I'm not so sure. Even if it is, Mexico remains a centre of innovation and centralization. When would the Maya encounter the first European ships, and how fast would they copy blue water sailing technology?

How much bigger does Tawantinsuyu grow?
 
Jones is an epidemologist (well, he's a historian of medicine now, but you get the point). Indeed, the supposed mortality rates of 90%-95% would sound insane to an epidemologist more than to any anthropologist. To quote him in Beyond Germs:
When I first encountered the literature on the Columbian Encounter as a medical student, I was startled by the ubiquitous—and impossible—assertions of “no immunity.” Reading more, I found the work by scholars who emphasized contingency, as well as work in medical anthropology about social suffering and embodiment. When I returned to the medical literature on race, genetics, and immunology, I found more reasons to be skeptical of the simplistic claims made by Diamond and so many others.​

Diamond is an ornithologist. There are very good reasons to be sceptical of whatever he says. He has interesting overarching theories but whenever he writes about something I know anything about, all the details he bases his theories on are wrong. But Diamonds claims and research standard is by no means representative of the field, and he should not be assumed to be representative of it.

The thing is, virgin soil epidemics are not a theory. They are an observed, well-recorded phenomenon through modern history. For example, we have very good records of epidemics in late-contacted Pacific populations. Dysentery in Fijii in 1802-1803 killed over 20 % of the population. A Measles virgin soil epidemic in Alaska in 1900 spread from village to village with mortality rates between 25 and 50 % of the population. A study of contact-related epidemics in Amazonia looked at 117 epidemics between 1875 and 2008, found mortality rates ranging from 1 to 97 %. Seven epidemics had a mortality of 80 % or above. (They also found mortality dropping with the number of years since contact). The average virgin soil epidemic seem to have a mortality of about 20-25 % outside the Americas. Smallpox a bit higher. These are not disputed theories. There is a wealth of recorded facts.

Now you may ask how we get to a mortality of 95 % and above among native Americans, when only about 1 in 25 of the recent contact epidemics have mortalities above 80 % ? Well, all those epidemics were single-disease epidemics. The native americans were subjected to smallpox, measles, diphtheria, typhus, croup, leprosy, influenza, bubonic plague, yellow fever, Lyme disease, Q-fever, dengue, various parasitic diseases, malaria, salmonella (cocoliztli), paratyphus, chickenpox, scarlet fever, whopping cough, etc, etc at the same time or in sucession. And surviving one did not actually indicate that you had any better chance of surviving the next. Often the opposite. Some of the diseases such as measles had immunosuppressant effects and made you more susceptible to other diseases. If you survived.

Additionally, there is a cumulative effect where a large number of people in a society falling ill means there is no one to nurse or feed the sick. Or bury the dead. (Diphtheria virgin soil in Hawaii 1804 "Not enough alive to bury the dead").

See, sometimes when a scientist wants to make a name for him or herself, they try to overturn something established that they feel iffy about. Sometimes that leads to an established paradigm being overturned and science advancing. But mostly it leads to some headlines and later research buring the new notion. As a somewhat relevant example, Cocoliztli was an old world disease that devastated Mexico from the 1500s. It was a fairly classic case of virgin soil from Europe, with contemporary physicians reporting on its selectivity for native Americans with Europeans left untouched, and Africans somewhere in between. Someone published some badly supported theory that it was an American indigenous disease, and had it taken seriously until the genes of the disease got sequenced.

Trying to overturn the idea of virgin soil epidemics... it would take a fantastic amount of results to overturn practically every physicians records from the age of exploration and quite a few from then until now. Now there is a discussion going about how much of a role genetics had in the devastation of the Americas, but they got an uphill battle too, because there are a lot of records.
 
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Leaving aside the virgin soil controversy (nobody is going to convince/convert others here), and also using handwavium to prevent the Europeans from advancing much beyond coastal enclaves what now. Enclaves will not be strictly coastal, when you have navigable rivers (like the Hudson), you'll get settlements at the head of navigation (like OTL Albany) to use the river for transport to/from)

Like OTL there will be conflict among the tribes for access to resources (furs for example) that the traders want in order to get thing like firearms/powder, metal items/tools, blankets etc. The tribes getting the most "goodies" from the Europeans especially iron weapons/tools and muskets, will proceed to use them to exercise power over tribes without them (happened OTL in North America and Africa). This means some level of consolidation near the trading sites/settlements giving rise to confederations or other larger polities, the further you go from European influence the less there is.

As far as crops and domestic animals go, some European crops will be adopted, although there will be a learning curve to make them work. Others not, simply because without a plow and a horse/mule (and the harness to utilize the horse) tilling the soil for these crops is not useful in terms of yield. Similarly some animals may be adopted - horses are less useful than one might think for the wild forests of Eastern North America for many uses. When the factors are right, wide adoption will be rapid, think horses for the Plains tribes and sheep for the Navajo as examples. Technology is the bog problem. All of the native societies are pre-literate, and stone age technology. They can't make gunpowder, so they are very dependent on the Europeans for this, and can't fix broken iron tools/weapons. Even those societies which are fixed farmers operate on a very low level, and many are migratory or semi-migratory. All of this mitigates against rapid adoption of the basic technology, not the products which they can use rather quickly.

It is much easier for permanent trading sites to develop local infrastructure than to be dependent on importing everything in North America. This is unlike Africa where the environment is much more hostile. So you will have people farming to provide food other than what you get from hunting or foraging, growing both native crops and imported ones. Dairying, hogs etc. You'll need an infrastructure, such as blacksmithing, to deal with horse needs, ironwork for local use, making trading goods etc. You'll have women, either native women or some from Europe and then children so these trading posts will tend to be oil spots that spread out, even if slowly and a little bit at a time. Nearby forest will be cleared for the timber and to create farm/pastureland. A self sustaining trading center is much more profitable than one highly dependent on importing everything, especially when there are resources to produce much of what you need locally.

In order to resist Europeanization of this sort, the natives need to develop political structures that go beyond temporary alliances (think Tecumseh) or limited confederations. They need to learn and adopt the basic technology, and then build the physical infrastructure to produce it. All of this would require major changes in their societal structures and lifestyle that took many many centuries to do in the old world. At the same time the natives are trying to master making gunpowder and somehow making firearms from scratch, technological progress is proceeding and accelerating in Europe. IMHO the scenario might mean a fragmented North America with several powers having significant areas, and some native polities that survive as independent or semi-independent, but a North America limited to a few European enclaves and ruled by purely native polities outside of that is pretty ASB, evern with essentially zero excess mortality due to new diseases.
 
Leaving aside the virgin soil controversy (nobody is going to convince/convert others here), and also using handwavium to prevent the Europeans from advancing much beyond coastal enclaves what now. Enclaves will not be strictly coastal, when you have navigable rivers (like the Hudson), you'll get settlements at the head of navigation (like OTL Albany) to use the river for transport to/from)

Like OTL there will be conflict among the tribes for access to resources (furs for example) that the traders want in order to get thing like firearms/powder, metal items/tools, blankets etc. The tribes getting the most "goodies" from the Europeans especially iron weapons/tools and muskets, will proceed to use them to exercise power over tribes without them (happened OTL in North America and Africa). This means some level of consolidation near the trading sites/settlements giving rise to confederations or other larger polities, the further you go from European influence the less there is.

As far as crops and domestic animals go, some European crops will be adopted, although there will be a learning curve to make them work. Others not, simply because without a plow and a horse/mule (and the harness to utilize the horse) tilling the soil for these crops is not useful in terms of yield. Similarly some animals may be adopted - horses are less useful than one might think for the wild forests of Eastern North America for many uses. When the factors are right, wide adoption will be rapid, think horses for the Plains tribes and sheep for the Navajo as examples. Technology is the bog problem. All of the native societies are pre-literate, and stone age technology. They can't make gunpowder, so they are very dependent on the Europeans for this, and can't fix broken iron tools/weapons. Even those societies which are fixed farmers operate on a very low level, and many are migratory or semi-migratory. All of this mitigates against rapid adoption of the basic technology, not the products which they can use rather quickly.

It is much easier for permanent trading sites to develop local infrastructure than to be dependent on importing everything in North America. This is unlike Africa where the environment is much more hostile. So you will have people farming to provide food other than what you get from hunting or foraging, growing both native crops and imported ones. Dairying, hogs etc. You'll need an infrastructure, such as blacksmithing, to deal with horse needs, ironwork for local use, making trading goods etc. You'll have women, either native women or some from Europe and then children so these trading posts will tend to be oil spots that spread out, even if slowly and a little bit at a time. Nearby forest will be cleared for the timber and to create farm/pastureland. A self sustaining trading center is much more profitable than one highly dependent on importing everything, especially when there are resources to produce much of what you need locally.

In order to resist Europeanization of this sort, the natives need to develop political structures that go beyond temporary alliances (think Tecumseh) or limited confederations. They need to learn and adopt the basic technology, and then build the physical infrastructure to produce it. All of this would require major changes in their societal structures and lifestyle that took many many centuries to do in the old world. At the same time the natives are trying to master making gunpowder and somehow making firearms from scratch, technological progress is proceeding and accelerating in Europe. IMHO the scenario might mean a fragmented North America with several powers having significant areas, and some native polities that survive as independent or semi-independent, but a North America limited to a few European enclaves and ruled by purely native polities outside of that is pretty ASB, evern with essentially zero excess mortality due to new diseases.
I don't disagree with you: if the horses, wool bearing animals (llamas & alpacas as well as sheep & goats), cows, water buffalo & yaks are introduced in 1500+ it's already too late for the surplus induced technology to spread.
Really these animals need to be introduced early: potatoes & quinoa introduced in say Northern Oregon/Plateau/Haida island, then the alpacas & llamas taken to suitable terrain (maybe Colorado)... the potatoes especially should accelerate the spread of agriculture. Then introduce plough bearing animals (cows, yaks, waterbuffalo) then the Bactrian camel, then the horse...
It's hard for such a transfer of livestock to be anything but deliberate
 
If European diseases such as smallpox, tuberculosis, and measles are introduced, and they will be, you will still see a massive die-off of Native Americans. It may be slower and perhaps not quite as bad as OTL but still will be a huge percentage of the population. Trade routes and movement of more migratory natives were quite extensive, and there is ample evidence that the wave front of European diseases progressed well ahead of any meaningful European presence. First explorers, traders, or trappers would often find evidence of populations reduced or eliminated by disease when they arrived at some new location. The other problem with these massive die-offs was the tremendous disruptions in societies. Cultures, governing systems, and "corporate knowledge" (like how to make a bow) may vanish as the holders of such knowledge die before passing on skills and also the young who survive may starve if they cannot fend for themselves.

Obviously, absent waves of colonists the natives at a distance from enclaves can reorganize, but it will be slow and knows how viable they will be.
After the population reaches a low point, some of the pre-Columbian Empires may start to recover without the forced labor and slavery under the Spanish. This could quickly become dystopian if a surviving Mexica Empire manages to trade its way into possession of muskets, cannons, and gunpowder weaponry.

The Aztec priesthood may interpret the diseases as a punishment from god and decide that more prisoners of war or slaves need to be sacrificed in order to appease Quetzalcoatl and Huitzilopochtli. It would be interesting to see how religions in the Americas develop without being wiped out or mixed with Christianity as OTL.
 
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