Demography europe, america and domestication

Question 1

What is the difference between kinship and ancestry?

Answer 1

kinship = family close in time, that you share much of your DNA with.
Ancestry = ancient genetic background

Question 2

The evolutionary history of modern humans is characterized by numerous migrations driven by, what? How do we identify migration patterns?

Answer 2

➢Environmental change
➢Population pressures
➢Cultural innovations

Human migration patterns can be studied by a large number of anthropological, archaeological and genetic methods

Question 3

When was the bronze age, Neolithic, Mesolithic and upper Paleolithic?

Answer 3

Holocene:
Bronze Age: 4.2 kya –2.8 kya (=2200 –800 BC)
Neolithic: 8 kya –4.2 kya
Mesolithic: 14 kya –8 kya

Pleistocene:
Upper Palaeolithic: 40 kya –14 kya: Many of the H. sapiens fossils from the upper paleolithic are not our direct ancestors, e.g. ust ishim, Oase1 and malta1.

Question 4

During the upper paleolithic in Europe, there were four prominent cultures, which and when?

Answer 4

Culture - Date
Aurignacian 40 – 28 kya: known for the “Lion-man” figurine (dated 40-35kya), evidence that humans arrived with culture, not developed on arrival. Also cave art.
Gravettian 33 –22 kya: known for Willendorf Venus, ca 24 kya.
Solutrean 22 -17 kya
Magdalenian 17 –14 kya: stone carvings.

Question 5

When were the first humans and last Neanderthals in Europe approximately?

Answer 5

• First modern humans in Europe ~45,000 years ago
• Last Neandertals ~38,000 years ago

–> definite overlap!

Question 6

How did the LGM likely affect European populations?

Answer 6

It is likely that some component of modern European ancestry can be traced back to one or more refugial populations around the time of the LGM (25-19 kya), likely in southern parts of Europe.

Question 7

During the Mesolithic we start to see dispersal in central Europe during the (B-A interstadial ~14 kya). How are the genetic profiles of Europe changing during this time?

Answer 7

At the start of the Mesolithic, we start to see a new genomic profile that starts to take hold: Villabruna cave - WHG which later mixes with the preexisting genetic profile of the Goyet cave- EHG + upper paleolithic. Some regions in the south retain the Goyet profile (Spain). Overall most central Europeans during the Mesolithic had mainly WHG ancestry.

Question 8

How did the genetic profiles in Europe change during the neolithic?

Answer 8

During the Neolithic (8 kya –4.2 kya), we see the first big wave of humans coming into Europe after the initial wave of modern humans into Europe during upper paleolithic. The Neolithic farmers coming in were mainly from Anatolia and spread gradually from southeast upwards = This was the neolithic revolution, which brought farming into Europe - changed the way of life drastically.

The Neolithic farmers did not just bring farming, they also brought their genetics. They came in and basically took over genetically, although some WHG ancestry was integrated. → Late Neolithic: genetic ancestry from Anatolian Neolithic farmers AND Western hunter-gatherers.

Question 9

What did the Neolithic revolution bring?

Answer 9

With the Neolithic revolution came farming –> settlements, pottery, domestication of animals (Sheep, goats, pigs, cows) + crops (lentils, flax, wheat, barley, peas etc.) and agriculture technology.

Question 10

What is the earliest evidence of large groups working together?

Answer 10

Göbekli Tepe: a monumental complex in south-east Turkey (part of Anatolia) dated to ca.12 000 -10 000 BP –> contribution of several hundred people, probably built by HG which already planted cops (Pre-pottery Neolithic).

Çatalhöyük: a proto city settlement dated to 9100 –7700 BP which could support 3000 –8000 inhabitants, which houses close to each other, doors on roof.

So the Neolithic revolution in Europe came much later than in Anatolia.

Question 11

After the big genetic turnover that came with the Anatolian farmers, there is a third big wave into Europe, when and which population?

Answer 11

During the late neolithic/early Bronze age, the Yamna-expansion occurred (the effect of which was unknown before archaeogenetics was applied!). The Yamna culture originated in the steppe of current day Ukraine and Russia, They were nomadic herders and brought the proto-indo-european language (hypothesized) and copper and bronze.

The Yamna expansion led to a third genetic turnover event, which is still present in European DNA today.

Question 12

The genetic ancestry of Europe has mainly been shaped by 3 components, which?

Answer 12

The genetic ancestry of Europe is shaped by the three big waves of people into europe, the WGH, the neolithic farmers and the Yamna. Different regions in europe have differeng ratios of descent from these three groups, but they are present in all populations.

Question 13

How does mobility affect genetic diversity in time and space?

Answer 13

When people get mobile, you get peaks of genetic diversity - bigger difference between populations. Low mobility = bigger difference through time, High mobility = bigger difference in space.

Question 14

After the Yamna expansion we start to see a lot of cultural shifts, which cultures were present during late neolithic-early and mid bronze age?

Answer 14

• The Corded Ware culture (c.3000 -2350 BC): Blend of Funnel Beaker (anatolian farmers) and Yamna cultural elements.
• The Bell Beaker phenomenon (c. 2900 –1800 BC): Pottery style that becomes “fashionable” from Iberia, spreads into Central Europe, then expanding through trade routes (British Isles, France, Iberian peninsula)
• The Unetice culture (c. 2300-1600 BC): Long-distance trade
• Urnfield culture (c. 1300BC –750BC) Going from burying the dead in graves to cremating them and putting their ashes in pits in the ground or funerary urns, NO aDNA :(

Question 15

When was the Iron age? Which cultures are represented here?

Answer 15

Iron Age: 800 BC –500 AD. In Europe, first came Hallstatt culture: Bringing the technology of iron: armament military weapons, equipment and jewelry also gold. Then came La Tène which developed out of the early Iron Age Hallstatt culture without any definite cultural break ca. 500 BC –100 BC –> Protoceltic/celtic-related, Famous for swords.

Question 16

What and when was the three waves of prehistoric expansions in Europe?

Answer 16

1. ca. 40 000 years ago: first modern humans (Palaeolithic)
2. ca. 7 500 years ago: Neolithic farmers, originating from Anatolia➢Settlements, pottery, domestication of crops and animals
3. ca. 4 500 years ago: Yamna, steppe pastoralists (early Bronze age)

Question 17

Briefly describe the global journey of humans out of Africa to all the continents, when and where?

Answer 17

1. Homo sapiens evolved in Africa ~300 000 ya
2. 70-50 000 kya - several waves of out of Africa migrations
3. Some populations migrated out into southern Asia, through Indonesia,, Philippines out into Australia ~50 000 ya.
4. migration into Europe 45-35 000 ya.
5. Migration to east Asia 45-35 000 ya
6. Asian populations moving northeast, entering the NA side of Beringia 20-15 000 ya.
7. Migrations out into NA and through the western route all the way down to south America 15-12 000 ya.

(8. Migration into Polynesian islands 2,500 kya.

Question 18

What genetic data provides solid support for the post-OoA migration patterns?

Answer 18

Mitochondrial Haplogroups provides solid support for the migration routes post OoA:

Africa: 5 haplogroups (L, L0-3)
Europe: 10 haplogroups (H, J, K, U, T. V, I, W, X, R)
Asia: 8 haplogroups (Z, G, C, D, B, F, Y, A)
Australia: haplogroups (Q, P, O, S)
America: 5 haplogroups (A, B, C, D, X2a) - all connecting to Eurasia through Beringia.

Y chromosome haplogroups have a very similar pattern.

Question 19

After entering North America, there are two possible routes of dispersal, which?

Answer 19

Either the ice free corridor (free after 14 kya) or the coastal route. Classical estimations imagine the ice free corridor, meaning that the peopling of the Americas happened after 14kya, but some older sites have been found in SA, e.g. monte Verde which is dated to about 14.6 ka. So we are not 100% sure.

Later on there is of course movement across the continents - lot of movement during the ice age.

Question 20

The timing of tuberculosis arrival in the Americas has been debated for a long time, what new evidence came and why is it strange?

Answer 20

New evidence found tuberculosis strains in remains dating back ~2000 years in America (southern Peru), which does not coincide with either the initial migration into America or with the arrival of Europeans (Columbus) ~500 years ago. But evidence points to that the strains they found were closely related to animal strains, specifically in seals, so it is possible that the strain that affected these individuals got is zoonotically from earing infected seal.

The strains that dominate in the Americas today are the European strains, In order to understand this better, we need more data on earlier strains in the Americas.

Question 21

Ethics are really important in aDNA research, why?

Answer 21

Especially with humans, it is really important to consider ethics when working with aDNA, many native groups have been oppressed but are of interest to research due to their long close ancestry. It is key to recognize and consult stakeholders before publishing data and checking that the language used is respectful. Publishing data open to all can be unethical, since the data could be used for malicious purposes relating to the descendants. Also collaborating with the affected tribes will provide a much more rich context and ensure good faith in science. Respecting the faith of the population is also key to collaboration, e.g. returning remains after the research is done if legislation says so (see the horribly handled case of the Kennewick man for reference). Also consulting local researchers should be done, as they have stake in the research too - also functions as a bridge between science and the specific group.

Bad handling/research that isn’t ethical can be detrimental, not only for future studies but it can also lead to underrepresentation of certain groups in clinical research that can affect peoples health. Ancestry studies can also help groups legally, so it is important that research remains a reliable resource for different groups.

Question 22

Why is it relevant to study domestication?

Answer 22

• Domestication is part of the foundation of civilization.
• Model of evolution - follow selection of traits over time. Opportunity to study evolutionary processes –model organisms
• What it is to be human: What colors, traits do we as humans like? a search for universals
• Proxy for human prehistoric societies –migration, socioeconomic change (mainly the Neolithization)

Question 23

What is domestication?

Answer 23

Domestication is a unique form of mutualism that develops between a human population and a target plant or animal population, and has strong selective advantages for both partners, but is usually more advantageous for humans.

Even through we often talk about “domestication events”, it is not an instantaneous event where a wild plant or animal is suddenly transformed into a domesticate -it is a cumulative process marked by changes on both sides of the mutualistic relationship, as both partner populations, over time, become increasingly interdependent. A very complex process, always a sliding scale.

Usually domestication involves some intent, and the power dynamics differ for different species. It is hard to set general thresholds for at what point something counts as domesticated, for example, if a wild relative is very genetically similar to a domesticate. Also, interactions between wild and domesticate also affect the “black and white”-ness of it.

Question 24

What is a domestic animal?

Answer 24

In its most developed form the domestic animal exhibits four principal characteristics:
1. Its breeding is under human control.
2. It provides a product or service useful to man (not always clear what historically)
3. It is tame.
4. It has been selected away from the wild type.

Question 25

What four main genetic processes are involved in the evolution of animals during domestication?

Answer 25

Four main genetic processes are involved in the evolution of animals during domestication; 1. Genetic drift: change in allele frequency due to random sampling. Bottleneck or founder effects increase the effect of genetic drift (effective population size) 2. Selection (directed): selection of traits that are "useful" for domestication, can lead to selection for traits that would be detrimental for the animal in the wild, which increases the dependency on humans. Usually phenotypes that can have multiple genetic origins – but could be single SNP. Pleiotropy and polygenicity make it hard to know what was selected for. 3. Inbreeding: Inbreeding leads to an overall reduction of genetic variability, and can lead to the accumulation of potentially harmful recessive alleles. If starting pop is small, this problem is bigger. Can also lead to traits going "too far" as with some dog breeds like pugs that has so short snouts that they have breathing problems - unethical. 4. Wild-domestic hybridization: Increases genetic diversity but also makes genetic studies harder. Often times we can infer geographic ancestry from morphology and genetics, which is helpful in trying to find domestication events. Genetic markers include e.g. mtDNA, Y-SNPs, autosomal SNPs and microsatellites and morphology like coat color, which is much easier to see. But genetic markers allows us to study this over time, which is mush harder on morphologic traits.

Question 26

What was the purpose of the Belyaev fox farm experiment? What was the result?

Answer 26

The goal of the Belyaev fox farm experiment was to try to find the "domestication gene" by only selecting for tameness/docility over generations. The did not find one, instead they found that the resulting foxes had many of the traits that are associated with domesticates overall: piebald ("fläckig") coat color, drooping ears, shorter, occasionally upturned tails and shortened snouts – typically domestic traits.

Question 27

Animal domestication: Where, when, how and why?

Answer 27

The when and why is easier to elucidate, one can use genetics: The more variation you have, the closer you are in both space and time to where it started. The how and why is way more tricky: For example, some species that have been domesticated are big and aggressive in the wild, how the heck did we domesticate them? The why we can only speculate, we can see the benefits and infer from climate and overall conditions how they might have been useful.

Question 28

There are several domestication centers that have been found throughout time, give one example.

Answer 28

One major domestication center was in the middle east/Anatolia ~10-11 kya, with domestication of pigs, cattle, sheep and goats happening. During the neolithic expansion into Europe we see and can follow how domesticated animals spread.

Question 29

What was the aim of the pig domestication project and what was the results?

Answer 29

The aim of the pig domestication project was to study the spatiotemporal origins of Eurasian pigs, by morphometric data like teeth and coat color, genetic variation ion ancient populations and compare the results with archaeological data. They found that there had been three populations of pigs that made up the pre-neolithic variation (13-7,5 kya), European wild boar, Italy and Near east pigs. During the Pre neolithic, there is not trace of near east ancestry in Europe. Then with the neolithic, there is clear trace of introduction of near east pigs in Europe (7,5-5,9 kya), which was very genetically similar to wild pops, but interacted with European wild boars. Then came a turnover event around 5.9-2,7 kya, where the signal from near east pig disappear, probably though slaughter and then replaced by European domesticated pigs. After, 2,7 kya - 500 ya there was a second turnover where European pigs were replacing the near east pigs in the near east.

Question 30

How can coat colors be useful in studying domestication?

Answer 30

Most coat colors in the wild provide camouflage, but humans like sharp colors like black/white/solid (as seen in rock art, historical documents etc.), so if we can find the gene that produces all over black color in pigs for example, we can use that to track/infer domestication. So, sharp colors can be used as a domestication indicator. Same can also be used in plants, grapes for example - there are two mutations that are present in all 55 white grape varieties, which suggests one single domestication event. Also rice was originally red, migration patterns in Asia using rice color can be followed. We can also use colors to trace trade patterns, if one color variety is only present in one place, we can follow where it ended up to infer trade and migration routes. Oftentimes sharp colors are not great for the organism, especially white which is terrible camouflage (unless in the arctic) and is ass. with blindness, but humans work hard to retain this - working against natural selection because of beauty. --> Though we are a product of evolution, we select for, and create, things evolution abhors.

Question 31

Why are dogs and dog domestication so special?

Answer 31

Dogs are unique among all domestic animals in that it was the first to be domesticated. The first unambiguous domestic dogs precede the appearance of settled agriculture in the archeological record by several thousand years. The dog was the first but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere - very debated, studied and a lot of interest!

Question 32

It is hard to imagine that all modern dog breeds are descendants of gray wolves. When do we think dog domestication started?

Answer 32

The consensus is that dog domestication started ~18kya but it is debated, might be even earlier? There is evidence of "dog-like" finds in the Belgium, Siberia and czech republic dated to ~36-32 kya, but they are not dogs per se, could be extinct wolf. But dogs were definitely domesticated before agriculture - 12kya burial of dog and human, with persons hand arranged on dogs shoulder = prehistoric pet evidence.

Question 33

Why have we not yet solved the question of when and where dog domestication took place?

Answer 33

Genetic finds looking at both ancient and modern dogs and wolves are consistent with a scenario in which all dogs derive from a single ancient, now-extinct wolf population, or possibly multiple closely related wolf populations. We still have not found the source population, which makes it impossible to see overall ancestry. Modern wolfs have undergone major bottlenecks, not useful. Also domesticated dogs don't seem to follow human migration patterns, which makes it a bad proxy. Evidence show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analyzed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. Two scenarios: (1) independent domestication of the eastern and western progenitors that later merged in the west or (2) single domestication of the eastern progenitor, followed by admixture from western wolves as dogs arrived into southwestern Eurasia. Solution: find and analyze more wolf remains that predates dog domestication.