Let's divide the 16 food sources listed above into three buckets:

1. Pre-Agriculture Food Sources: Meat & Fish, Vegetables, Fruits, Nuts & Seeds, Herb & Spices would belong to Pre-Agriculture era when 'hunter-gatherer' lifestyle or 'forest dweller' lifestyle was the norm.
2. Agriculture Food Sources: With the domestication of both plants and animals, farmlands and villages came into being. Later, cities developed. Food sources expanded to include Grains, Beans & Legumes, Milk & Eggs. In addition, SOS extracts came into being: Salt, Oil, Sugar.
3. Industrial Food Sources: Processed Foods and Supplements have been developed in the last 150 years. The term Supplements is unambiguous but the term Processed Foods is difficult to define. At a high level, Processed Foods include refined grains, refined sugars and packaged foods.

Note: The list of 16 food sources is not a comprehensive list of all foods in Pre-Agiculture, Agriculture and modern food systems. Over the ages, we have consumed many foods that do not belong to any of the 16 food sources listed above. Examples include fungii (mushrooms), algae (sea vegetables like nori and kelp), bacteria (in fermented foods), insects and rocks (via rock salt)! The 16 food sources have been chosen to simplify the big picture of diets and fasts chalked out in these articles: Part 1 and Part 2.

Over the last 10,000+ years, humans have engaged in 'selective breeding' (also known as 'artificial selection') to convert animals into various shapes and sizes, with qualities that are deemed beneficial to us! Zooarchaeology is the branch of science that studies domestication of animals.

Agriculture introduced domestication of animals for farming and transport; we also started raising animals for milk and meat.

Some intriguing questions: Where do cows, pigs, dogs and cats come from? What are their origins? Who are their ancestors? How many years did it take us to make cattle as they are today, endowed with qualities that humans deem useful. For example, an ox is a physically strong, relatively docile, castrated male cattle that helps us plough lands. A female cow today has large udders to produce milk for humans.

1. Cows: Said to be domesticated aurochs (Wikipedia), a ferocious wild animal whose herds were last seen around 1620s in Europe. For details, see History of Domestication of Cows and Cattle Domestication: from Aurochs to Cow. Over time, we have started breeding cows that produce far more milk than their ancestors; such cows have large-sized udders.
2. Other Animals: Geography of Livestock (13 mins, YouTube) explains the origins of dogs, cows, pigs, horses, and so on. For example, pigs were developed from wild boars, and dogs were developed from wolves.

Juliet Clutton-Brock (1933 - 2015), an expert in zooarchaeology, has written these interesting books:

1. Natural History of Domesticated Mammals: 1st Edition (1988) — 2nd Edition (1999, with color pics).
2. Animals as Domesticates (200 pages, 2012).

One of the earliest books on the subject of 'selective breeding' ('artificial selection') is by Charles Darwin: The Variation of Animals and Plants under Domestication (1868).

Agriculture introduced a steady supply of new plant-based food sources like Grains and Beans. These two food sources were not commonplace in pre-Agriculture days. In addition, through selective breeding, we started producing new varities of Grains and Beans with shapes and sizes very different from their ancestors. The Pedigree of Grains is a nice article with images that explains grain families and how modern grains were derived from ancient grains! For example, neither wheat nor corn (maize) are found in the wild. Both were created by humans through selective breeding.

1. Wheat: Wheat Domestication presents an overview of wheat history. About 11,000 years ago, we cultivated wheat from its ancestor: emmer. Luckily, emmer is still found today! Now emmer itself was derived from another ancient grain called 'einkorn' which is also found today.

2. Corn: Tracking the Ancestry of Corn Back 9,000 Years (NY Times, 2010) explains that corn (maize) was cultivated from its ancestor: a wild grass called 'teosinte', which does not look like corn at all! Teosinte is still found today — it is grown for fodder.

This article has a beautiful infographic tracing the history of wheat, barley, rice, millets and sorghum in Asia, Europe and Africa.

Ancient Grains is a gorgeous 4-min video! It's actually an ad by a bakery that encourages us to consume 'ancient grains' like einkorn, emmer, khorasan, ancient spelt, ancient rye, and so on.

Agriculture resulted in selective breeding (artificial selection) of fruits and vegetables too, both of which were part of our diet in pre-Agriculture times as well. However, through selective breeding, we started producing new varities of fruits and vegetables with shapes and sizes very different from their ancestors. Almost all Vegetables and Fruits found in the market today are the result of hundreds and thousands years of selective breeding. Most of these are not found in the wild. Let's look at two fascinating examples.

1. Brassica Oleracea: The wild mustard plant which has been selectively bred into over a dozen different vegetables: cabbage, cauliflower, kale, broccoli, kohlrabi, brussels sprouts, gai lan, and so on! All of these seemingly different vegetables are actually one species! For details, see this article at the blog "Botanist in the Kitchen" and Wikipedia article.
2. Citrus Fruits: Most citrus fruits sold in th market are hybrids developed by humans.

      Pomelo + Mandarin → Sweet Orange
      Sweet Orange + Pomelo → Grapefruit
      Grapefruit + Mandarin → Tangelo
      … and so on.

   This video is a peek into the fascinating history of citrus fruits. Some of the citrus fruits can be traced back to a few thousand years. [Maybe some developed accidentally in nature? Not sure: online articles suggest that oranges (both sweet and sour) were developed by humans a few thousand years ago by combining pomelo + mandarin; they are not found in the wild.]

   Details: The Citrus Family Tree (National Geographic, 2017) — The Citrus Family — Citrus (Wikipedia) — Orange at Purdue Univ.

3. Other Fruits & Vegetables: An interesting article: Here's what 9,000 years of breeding has done to corn, peaches, and other crops (2016). Some cute sketches are found here: The Great-Grandparents of our Fruits and Vegetables.

I have come across two food systems that are inspired by how pre-Agriculture communities lived. One is the Paleo food system that emphasizes Meat and Fish: see Diets with Meat. The other is a raw foods system in India that emphasizes Vegetables and Fruits (no Meat, no Fish, No Milk, No Eggs). See New Diet System (NDS) by Shri BV Chouhan. In both cases, we must remember that the actual foods that our ancestors consumed were very different from the foods that we get in the market today. Also, our food preparation techniques are different. And we don't spend time in forests any more; most of us live in cities. So we don't walk barefoot on natural soil, we don't dip in rivers, we don't climb trees. Many of us don't spend enough time in the sun. In fact, many of us live in high latitudes, far away from the equator. How does all this affect nutrition? Let's look at some specific examples.

Magnesium is found in plant foods. But magnesium (and other minerals) get absorbed transdermally (through the skin) as well! We can get additional magnesium naturally by swimming in the ocean, walking barefoot on sandy beaches and taking dips in mineral-rich hot springs. In the modern world, we may also buy epsom salt (magnesium sulfate) and soak some parts of our body (typically our feet and legs) in a mixture of epsom salt and warm water.

Vitamin D: When the angle of the sun is less than 35 degrees, our skin does not produce any Vitamin D even when exposed to sunlight. Such low angles are found in northern latitudes. This video explains.

Even in latitudes near the equator, people don't get enough Vitamin D these days because we simply don't spend enough time in the sun! Here is a paper from 2009: Global Vitamin D Status and Determinants of Hypovitaminosis D, published in Osteoporosis International — this research paper has over 1300 citations according to Google Scholar. If interested in Indian sub-continent numbers, please jump to the section titled "Asia" — some alarming numbers await you.

The best guidelines for Vitamin D intake through a combination of sun exposure and supplements are by Dr Greger: Optimum Nutrition Recommendations (2011, updated in 2016).

Vitamin B12: At offset 2:02 in this video, Dr Greger explains

We likely used to get all the B12 we needed drinking out of mountain streams or well water, but now we chlorinate our water supply to kill off any bacteria. So, we don't get a lot of B12 in our water anymore; we don't get a lot of cholera either! So, that's a good thing.

But in our sanitized modern world, studies continue to show that those eating plant-based diets are simply not getting enough vitamin B12. Is this really a problem? Let me review the medical literature on B12 deficiency just over the last year.

Dr Greger than goes on to explain that a large percentage of vegans develop B12 deficiencies if they don't take Vitamin B12 supplement or consume B12 fortified foods.

Fiber: Dr Erica Sonnenburg and Dr Justin Sonnburg lead the Sonnenburg Lab at Stanford whose objective is research in gut microbiota. In this talk: Understanding The Microbiome (60-min presentation, 30-min Q&A), Dr Sonnenburg explains that contemporary primitive communities and ancient Paleolithic communities had a rich and diverse gut microbiome (populated with many different species of bacteria) and that this diversity is related to the amount of fiber they consumed! Specifically, at offset 1:04:09 in the talk, Dr Sonnenburg explains that contemporary primitive communities and ancient Paleolithic communities consumed an extraordinarily large amounts of fiber! Below is an excerpt from Dr Sonnenberg's talk (from offset 1:04:09):

Part of why we started that center for human studies is that we wanna ask these questions, "Does any dietary fiber help? Is it lots of any one type or does it have to be a diversity of different types of dietary fiber?" We don't know the answers to those questions.

What we think is if we look at these traditional populations, their diet is pretty simple: they are only eating only 5 or 6 kinds of foods. But if you look at the composition of the foods they are eating, the carbohyderates in there are incredibly complex! So we think that diverse amount of dietary fiber is good. So that would be from plants, fruits, vegetables, whole grains, legumes, whatever.

So these populations don't eat things like legumes and whole grains because those are a product of agriculture. But i think that part of the problem with this Paleolithic diets that people are interested is that we don't have access to the food that our paleolithic ancestors ate because we domesticated all the plants to make them less fibrous and higher in sugar.

So that tuber I showed you [in an earlier slide showcasing foods eaten by a contemporary primitive community], there is no Whole Foods [name of a grocery chain in USA] that you can go and find something like that. That food does not exist.

So how do you get a high fiber diet with the foods that we have [in contemporary western world]? Legumes and grains are great because they have a lot of fiber. So it's an easy way to eat a lot of fiber in a small amount of food.

We're running a study right now where we are telling people to increase dietary fiber as much as they possibly can. We don't give them an upper limit. We wanna see what's possible in kind-of a western culture.

These people at best can get to 80 grams of fiber per day. They said that it's incredibly difficult because there are no convenience foods really. I mean, you can eat like raw fruits and vegetables but you knjow, they are eating a lot of beans and stuff. The other thing they said is that it's incredibly hard to eat a lot of dietary fiber because they are so full. If you get to like 50 grams of dietary fiber, that's a lot of plants; you become so full that you can't eat any more.

And so, my husband and I joke that, "Oh, if we write another book, it should be the '1-rule Diet'" because we tell these people, just get as much dietary fiber as you can. What we find that is that their amount of saturated fats go down, their amount of sugar that they eat go down, their total clories go down. We haven't told them to do any of that. Just to eat that amount of fiber, you just don't have room for other types of food.

What did I learn from the above excerpt? (A) Ancient plant foods had much more fiber than contemporary plant foods produced via agriculture (through artificial selection, we have converged to modern fruit and vegetables with less fiber). (B) Eating a lot of fiber is considered critical for our gut microbiome, and our overall health. (C) In the modern world, how may we consume that much fiber? By eating beans and grains, both of which were introduced in a big way into human diet via agriculture.

For further information, browse through videos referenced here: Microbiome and Fiber.

How should we mimic the ancients? By making prudent choices! A guideline that I have developed for myself: when we adopt an ancient lifestyle in modern times, we must also take advantage of modern scientific knowledge (whatever we know so far) and make a judgment call: how may I combine guidelines from ancient traditions with the reality of the modern world, as explained by scientific studies?