Of course, there were a few major factors that blocked or slowed gene flow over the past few millennia.
The Atlantic and Pacific oceans were important barriers. There was very little contact between the peoples of the Old and New Worlds before Columbus. Australia was much easier to reach from Indonesia or New Guinea than the Americas were. There were definitely visiting sailors from Indonesia fishing for sea cucumbers along the north coast of Australia beginning around 1720. There must have been other early contacts, but the amount of gene flow was not large, judging from what we know of Y-chromosome and mtDNA variants in Australian Aborigines.8 The north coast did not attract settlers from Indonesia or Southeast Asia, probably because that coast was un-suited to their forms of agriculture. Moreover, new alleles that were adaptive in the context of agriculture may not have had an advantage in Australia: Even if some were introduced, they may not have spread widely.
Deserts mattered. There was plenty of gene flow between North Africa and the other lands surrounding the Mediterranean, particularly after the development of sailing ships, but the Sahara certainly interfered with movement to and from sub-Saharan Africa. The block wasn't absolute. The Sahara was a much friendlier environment in the early Neolithic than it is today. Later, the domestication of the camel favored trans-Saharan trade, while the European and Arab slave trade eventually brought African alleles to other parts of the world.
Still, we know that the amount of gene flow into sub-Saharan Africa was limited in the past, since several local mutations that cause lactose tolerance became common among the cattle-raising peoples in the Sudan and Ethiopia, even though the European version is considerably older. If there had been much gene flow into sub-Saharan Africa back then, the European mutation would most likely have dominated. In fact, if even one person carrying that European allele had successfully settled in the Sudan back in the Bronze Age, he would have had a fair chance of introducing it, as a kind of genetic Johnny Ap-pleseed.The Sahara Desert made such contacts rare, but it may also be that tropical diseases such as malaria and yellow fever interfered, just as they later interfered with European colonization attempts. The local sub-Saharan Africans had enough resistance to those diseases to get by, but outsiders generally did not.
Most mountain ranges affect gene flow but aren't impassable enough to substantially block it. The Himalayas, however, are an exception. Judging from the limited information we have today, it seems that India shares a fair number of favored new alleles with Europe and the Middle East, but has mixed far less with China. Since the Himalayas are the tallest mountains on earth, backed by the Tibetan Plateau, it's possible to believe that they greatly reduced gene flow between India and China, and ultimately between east and west Eurasia.
Other people getting in the way must have been one of the most powerful forces slowing gene flow. Many alleles that helped people adjust to agriculture probably came into existence in the Middle East, since agriculture began there. When we consider the ways in which those alleles could have reached western Europe, where agriculture developed later, it's worth remembering that it only takes a few months to walk that entire distance. If that happened often, you'd expect genes to have spread far more rapidly than they actually did. The problem is that would-be long-distance travelers quickly encountered other groups that spoke a different language and had uncongenial customs. Some were enemies, and all were suspicious of strangers. Passing through other groups was very difficult, so long-distance land travel was almost impossible.
In The Third Chimpanzee, Jared Diamond describes this pattern in highland New Guinea, one of the last places in the world to make contact with outsiders. He wrote, "When I was living among Elopi tribespeople in west New Guinea and wanted to cross the territory of the neighboring Fayu tribe in order to reach a nearby mountain, the Elopis explained to me matter-of-factly that the Fayus would kill me if I tried. From a New Guinea perspective, it seemed so perfectly natural and self-explanatory. Of course the Fayus will kill any trespasser: you surely don't think they're so stupid that they'd admit strangers to their ter ritory? Strangers would just hunt their game animals, molest their women, introduce diseases, and reconnoiter the terrain in order to stage a raid later."9 Before outside contact, New Guinea highlanders spent their entire lives within a few miles of their villages, and as far as we know, none had ever seen the sea, which was just 100 miles away. It seems likely the whole world was like this in prehistory.
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