The Reality of Domestication - Archaeological Science Ep 6

Where would we be without domesticated plants and animals? The advent of domestication and the development of agriculture were such pivotal moments in the human story. They helped sustain larger populations, allowed people to live in sedentary settlements, and paved the way for the rise of the world's first civilizations. But, what exactly is domestication, and how does a plant or animal go from being wild to domesticated? I'm Madam Archaeologist, your go-to informant on everything archaeology, and in this episode, I'll show you how both modern and ancient DNA from animals and plants are changing our perception of domestication and how it took place. I know this topic is a bit different from other ones that I've discussed on my channel, since archaeology is essentially the study of people in the past, but since domestication is a process initiated by humans, and its impact on human history has been tremendous, I thought it would be interesting to discuss how DNA has revolutionized our understanding of it. Let's begin by asking, what is domestication? A simple definition would be that it's a mutualistic relationship between people and plants or people and animals, whereby humans interfere in their reproductive practices, usually by isolating a population, and these interferences result in genotypic and thus phenotypic changes. Why do we call this a mutualistic relationship? Because the relationship benefits both humans and the domesticated plants or animals. These domesticated species benefit us in some way, such as helping us sustain larger populations, for example, and in turn, we help those domesticated animals or plants survive. When we domesticate a species of animal or plant, we eventually see differences in the domesticates and their wild counterparts. Here you can see the difference between domesticated maize and wild teosinte. Teosinte plants have more branches, and they're longer in comparison to maize. Also, teosinte plants can have hundreds of ears, but only a few kernels, whereas maize plants have one or two ears, but with lots of kernels, amongst other differences. Here's a domesticated goat on the left versus a wild one on the right. One obvious physical difference between them is that the wild goat has horns that arch backwards, making this really nice curve, while the domestic goat's horns are in this twisted shape. Another physical difference can be seen in the ears. And another thing that can change too in animals is behavior, but beneath all these external or observable changes are genetic changes, changes in the genes of these plants and animals. Our genes affect our phenotype, or what we look like. So, for example, a change in the gene TGA1 is associated with kernels becoming exposed in domesticated maize. I'll note that these genes are an active field of research within archaeogenetics, so our depth of knowledge varies between species. In general, more research on domestication genes in general has been done on plants than on animals. When we look at plants and animals living today, it's often easy to spot a domesticated population from a wild one. But you're probably wondering, how do we distinguish wild from domesticated archaeologically? For animals, archaeologists can usually identify domesticated animals by their bones and teeth. These are usually smaller in domesticates compared to their wild counterparts. Here we've got the leg bones of cows versus wild aurochs. The aurochs' bones are quite a bit larger. As for plants, archaeologists typically look for signs of something we call the domestication syndrome, which simply refers to the traits observed in a domesticated population. One trait is seed size, since we often find seeds. The seeds of domesticated plants tend to be larger than their wild counterparts. Here we can see a variety of seeds, with the seeds of domesticated plants on the right and the seeds of the wild progenitors on the left. On the top we have pistachio, then coffee, then soybean, then barley, then North American wild rice, and finally sorghum. Finding tools associated with agriculture are also signs that people were cultivating plants at a site. Traditionally, domestication has been seen as an event, where a plant or an animal is domesticated in a core region and their presence in other regions have been ascribed to people migrating and bringing these plants and animals with them after they've been fully domesticated. So when we say, for example, that maize was domesticated in lowland Mexico, we're implying that the main domestication event took place there and that maize that's been found in other regions represents the movement of fully domesticated maize out of lowland Mexico. But, when we look at the DNA evidence, we see that the reality of domestication is much more complex. It's not an event that takes place in a specific location, it's an ongoing process. I'll show you how. West Eurasian pigs are a very interesting case study. It looks like people started domesticating them from the wild boar Sucrofa in the Middle East around 10,500 years ago. Keep in mind that the term pig implies domesticated, while boar is the wild counterpart. Now, just like us humans, animals carry haplogroups. Mitochondrial haplogroups trace direct maternal lines and Y-chromosomal haplogroups direct paternal lines. Those early domesticated pigs from the Middle East were found to carry a mitochondrial haplogroup that's been named ARM1T, and after they migrated into western Anatolia, they acquired the haplogroup Y1, probably from mixing with local boars there. After their arrival in Europe about 8,500 years ago, the pigs acquired yet more haplogroups from local boars, and this resulted in a mitochondrial turnover in pigs, meaning that the mitochondrial DNA of wild boars replaced that of domesticated pigs. One question that arose from this was, was this turnover caused by introgression from wild boars, meaning that the domesticates mixed with their wild counterparts and so acquired genes from the wild boar population, or did the farmers from the Middle East that migrated into Europe domesticate the local boars in Europe? Nuclear DNA, that is, looking at the entire genomes of pigs and boars rather than just their haplogroups, supports the former scenario. Those pigs that moved with people from the Near East into Europe mixed with wild European boars. And hear this, it's not just that pigs and boars mixed in continental Europe. There was a near-complete nuclear genomic turnover in pigs as well. The interbreeding was so strong in just three or so millennia, European pigs lost more than 50% of their Middle Eastern ancestry, and today they retain only up to 4% of that ancestry. This completely changes our understanding of domestication. Strict reproductive isolation was not maintained, obviously. Interbreeding between domesticated pigs and wild boars was actually quite common, and we can't say that pigs fit the generalized model of a species becoming domesticated in a region and then dispersing as a homogeneous, fully domesticated species. Rather, people were interacting with pigs and boars in different ways in different regions over time. If we look at this graph here from the 2019 paper that these DNA results were published in, we can see these changes over time. On the top left, we see a map of Western Eurasia with three colors. These colors represent mitochondrial haplogroups of wild boars. East Asian haplogroups are represented by blue, the Middle Eastern haplogroups are in yellow, and European haplogroups are in red. Those purple parts represent another haplogroup, whitetoon. The black dots represent the locations where modern and ancient boar DNA samples came from. The other boxes show the distribution of these haplogroups amongst domesticated pig samples over time. You can see the European haplogroups increasing. In more recent times, European pigs have a mix with East Asian ones to varying degrees in different regions as well. You can see that represented by blue in the pie charts in the bottom right. Moving on to plants. I'm going to talk about maize, aka corn. Does DNA paint a similar picture here? Before we dive into the modern and ancient DNA evidence, I'll note that plant DNA is a bit different from animal DNA, but there are many similarities as well. Animals have the same type of cells as us humans. We call them animal cells. DNA is packed into units called chromosomes that are found in the nucleus of the cell, and it's also found in the cell's mitochondria. But not all animals have the same number of chromosomes. For example, we have 46 chromosomes, dogs have 78 chromosomes, cats 38, pigs 38 as well, and so on. Now, plants have plant cells, and plant DNA can be found in three organelles. Like us, DNA is found in the nucleus and in the mitochondria, but it's also found in the chloroplast, an organelle that animal cells don't have. Plant DNA, though, is similar to human and animal DNA because all are made up of the same four nitrogenous bases that pair together, adenine with thymine and guanine with cytosine. And the nuclear DNA in plants is also packed into chromosomes. The focus of DNA research on plants differs a bit from animals because it's been mainly on looking at domestication genes. For example, as noted before, a change in the gene TGA1 causes exposed kernels in corn. Nevertheless, this research on plant DNA, both ancient and modern, is also showing us how complex the domestication process actually is. Maize was domesticated in lowland Mexico from Teosinte, specifically a type known as wild balsas Teosinte, and the process appears to have started around 9,000 years ago. Archaeological evidence shows that by about 7,500 years ago, maize had reached Central America, by about 6,500 years ago it had spread into South America, and by about 4,000 years ago to the southwestern United States and Colorado Plateau. But did maize spread out of its core region fully domesticated? As we saw with pigs, domestication wasn't an event, it was a process. Can we say the same thing for maize? When people domesticate a species, mutations occur in specific genes that result in alleles. Now, it takes time for those new alleles to become fixed in a population. By fixed, we mean that those alleles are carried by the entire population. The alleles that are associated with the domesticated species are called the derived alleles. Interestingly, DNA studies on a 5,310-year-old cob found in Mexico's Tehuacan Valley showed that it did not carry all the derived alleles. Some of the genes were still in the ancestral Teosinte state. Some important alleles, like the one in the gene TGA1 associated with exposed edible kernels, were present, but not all of the genes associated with the domestication syndrome were. So, it looks like maize did not spread out of its core region after becoming fully domesticated, because this cob was only partially domesticated. And it gets even more interesting. Today, alleles associated with the domestication syndrome are fixed in different land races found across the Americas. However, maize was also only partially domesticated when it reached South America by about 6,500 years ago. The fact that alleles associated with the domestication syndrome are fixed in maize populations today means that humans were strongly selecting for these traits simultaneously in different regions. These interactions between humans and maize, however, were varied. For example, we have evidence that maize in highland Mexico was mixed with a species of wild Teosinte known as Zia maize subspecies Mexicana. So, just like pigs, the domestication of maize was not an event, but rather a long-term process. This graph explains the situation well. On the top, we have the traditional view of maize domestication, where maize acquired all its domestic traits in the core region of lowland Mexico, and then spread out and gave rise to diverse land races. On the bottom, we have the new picture gleaned from ancient DNA, whereby maize spread out in a semi-domesticated state, and these semi-domesticated subgroups then acquired all the domestication traits and gave rise to the diverse land races we see today. When we assess what DNA has revealed about the reality of domestication, can we still say that pigs were domesticated in the Middle East and that maize was domesticated in lowland Mexico? I think this is an important question, because DNA has shown us that domestication isn't an event, it's a process. So what's safe is to say then, considering all the DNA evidence we've gathered so far, is that the domestication of pigs and maize started in the Middle East and lowland Mexico, respectively. Those are the regions where interactions between people and boars, or people and teosinta began, and then these interactions continued as people moved their pigs into Europe, and when people brought their maize crops to different parts of the Americas. I hope you learned something interesting here, I know the theme is a bit different from my other episode since the focus was on animal and plant DNA and not on human DNA, but domestication is extremely relevant to archaeology not only because it's a process involving humans, but also because it played such an important part in the human story, allowing us to shift from hunting and gathering ways of life to living in sedentary settlements. And I want to mention that domestication is an active field of research within archaeogenetics, there's lots of interesting work that's been done, and there's lots that still needs to be done. And ancient DNA is certainly revolutionizing the way we see the domestication process. Don't forget to give this video a like and subscribe for more cool content by your go-to informant on everything archaeology, Madam Archaeologist.