Genomics at the Origins of Agriculture

Genomics at the Origins of Agriculture, Part One

The causes and consequences of the Neolithic revolution represent a fundamental problem for anthropological inquiry. Traditional archeological evidence, ethnobotanical remains, artifacts, and settlement patterns have been used to infer the transition from foraging to primary food production. Recent advances in genomics (the study of the sequence, structure, and function of the genome) has enhanced our understanding of the process of plant and animal domestication, revealed the impact that adaptation to agriculture has had on human biology, and provided clues to the pathogens and parasites thought to have emerged during the Neolithic. Genomic analysis provides insights into the complexity of the process of domestication that may not be apparent from the physical remains of bones and seeds, and allows us to measure the impact that the shift to primary food production had on the human genome. Questions related to the location and the process of domestication can be answered more fully by analyzing the genomes of the plants and animals brought under human control. The spread of the agriculture package (plants, animals, and technology) by cultural diffusion or demic expansion can also be investigated through this approach. Whether dissemination by farmers or the diffusion of farming knowledge and technology was the source of the Neolithic expansion, this process should be revealed by the patterh of genetic and linguistic diversity and language found from centers of agricultural Neolithic development. In addition, a number of pathogens that were previously thought to have been transmitted from domesticated species to human now appear to have been present in foragers long before the agricultural revolution took place. Furthermore, we now have evidence that humans were the source of the transmission of some parasites to domesticated animals. For all of these reasons, data from genomic studies are providing a more complete understanding of the origins of agriculture, a critical hallmark in human evolution.

Genomics at the Origins of Agriculture, Part Two

Agricultural expansion was such a momentous event that cultural or genetic evidence of its impact should be apparent. Abundant evidence indicates that agriculture was introduced into Europe at least 9,000 years ago. The primary issue remains whether agriculture spread by contact or by farmers moving into Europe. If agriculture was brought by farmers moving into foragers’ territory, then genetic evidence should be apparent in the genes of modern Europeans. If foragers were displaced, then European genetic profiles should reflect the source population from the Near East. If there was interbreeding with the foragers who had a distinct genetic profile, then the genes of the Europeans descendants should reflect this admixture, with a clinal distribution of traits radiating from the Near East. These scenarios have been the focus of decades of debates between anthropologists and geneticists. In addition, genomic studies have been applied to pathogens in order to explore the link between agriculture and infectious disease.

The most interesting of these is the second in my opinion, with a detailed section about diseases intoduced due to agriculture and domestication. It seems we can blame cows for TB. One thing I spotted was that malaria as a common human illness is dated to 6,00o BP, but the skeletons at Catal Hoyuk show anaemias associated with it, although I’m not sure at what date. Another interesting snippet was that you need a population of about 300,000 to maintain an endemic disease like measles.  You learn something everyday. Although worthy of mention is a quote from the Ramayana in the first one..

In the Golden Age, agriculture
was abomination. In the Silver
Age, impiety appeared in the
form of the agriculture. In the
Golden Age, people lived on
fruits and roots that were obtained
without any labour. For
the existence of sin in the form
of cultivation, the lifespan of
people became shortened

Which seems to be a pretty accurate description of what happened. It really makes you wonder why we swapped to agriculture when you read this..

Harlan demonstrated that in three weeks a family could hand strip enough wild einkorn grain to last them a year

The only real reason I can think of to abandon this kind of lifestyle is population pressure. I’ll have to look up the climate in the Euphrates/Zagros area about 12,000 to 11,000 years ago to get a better picture.

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Basenji origin and migration

Basenji origin and migration; through the African threshold

A pdf link that won’t let me copy out any text or images unfortunately. It describes the African Basenji’s path down into Africa, and has some nice rock art images of the dogs. Followed by…

Basenji Origin and Migration: Into the Heart of Africa

Enset culture and its history in highland Ethiopia

Enset culture and its history in highland Ethiopia

Cultural and linguistic evidence concerning the origin and distribution of enset culture seem to point generally in the same direction. Enset was part of a widespread and ancient system of cultivation of vegetative crops formerly distributed much more widely through the Ethiopian highlands. The main cultivators of enset were Omotic-speakers, though it was probably adopted early by some groups of Cushitic-speakers. However, when the Ethio-Semites entered Ethiopia bringing seed agriculture and the plough, enset and other root crops such as yams (Dioscorea spp.) and the Labiates (Coleus spp.) were pushed into residual cultivation, except where the terrain was so highly dissected that ploughing was effectively impossible. In this situation, notably in the southwest, the Gurage Semitic-speakers adopted enset and it became central to their production system, permitting the expansion of population to levels such that no other crop would support comparable densities in similar terrain.

Having just blasted through some of  Blench’s work I can tell you that Cushitic speaking languages essentially date to the Neolithic as they have root words for sheep and goat, that wouldn’t have arrived until at least 7,000 BP in that area, and probably a lot later. This would suggest a later domestication date for enset, sometime around 5,000 BP.

Pastoral rock art in the Horn of Africa; making sense of udder chaos

Pastoral rock art in the Horn of Africa; making sense of udder chaos

Seriously, this is the papers title. Unable to cut and paste any, I’ll copy out a few snippets:

Pastoral rock art appears to be a comparatively recent phenomenon in the Horn, spanning only the last four to five thousand years.

The only evidence for cultigens is from Lalibela cave near lake Tana in north central Ethiopia where Dombrowski recovered barley chickpea and legumes from levels dating to no earlier than 2,500 BP.

The archaeological evidence for cattle is largely restricted to dental fragments  from Gobedra and Lalibela in the Ethiopian highlands, lake besaka in the Southern Afar rift, Laga Oda on the Somali plateau near Harar and Gogoshiis Qabe shelter ar Buur Heybe, southern Somalia. None of these faunal remains date to earlier tha 3,500 bp. Clay figurines from the site of Hawlti show that Pre-Axumites were still breeding humpless cattle as late as the first to second century AD. The earliest evidence of a humped Zebu cow is in the form of a small figurine from the 2nd century AD early Axumite site of Zeban Kutur.

It has some info on the rock art in Somalia and Ethiopia, it’s from 1987, but as far as I know no earlier dates have been found in Ethiopia for domesticates. However, some dates fo finger millet and sorghum are older in the Arabian peninsula and India, becoming staples by 2000 BC.

Dates for ovicaprines and other domesticates in Africa

Sheep and goats are not native to Africa, and are introduce into Africa at with the appearance of farming. Just a brief entry so I can find the info again. From Archaeology, language, and the African past, By R. Blench.

Sahara                       Air Massif      Adrar Bous                  5000 BC
Sahara                       Niger               Arlit                                 4300 BC
East Africa               Sudan          Esh Shaheinab                 3,200 BC
West Africa             Mali               Winde Koriji West         2,200 BC
West Africa             Mali               Kolima Sud                      1,400 BC
West Africa             Nigeria         Gajiganna                         1,520BC
Horn Africa            Ethiopia       Lake Besaka                     1,500 BC
East Africa              Kenya            Ga Ji  4                              2,000 BC
East Africa              Kenya            Ngamuriak                      1000 BC
Southern Africa    Namibia       Falls rockshelter            190 BC
Southern Africa    SA                  Ma38                                   200 AD       

And another PDF  with some info on it that includes dates for chickens, horses, etc, for reference.

The history and spread of donkeys in Africa

The history and spread of donkeys in Africa

The domestication and historical development of the donkey are traced through archaeological and linguistic associations. The donkey is indigenous to the African continent and its wild progenitor is usually considered to be the Nubian wild ass. Historically, a chain of races of wild ass spread from the Atlas Mountains to the Red Sea and probably as far south as the border of present-day northern Kenya. The wild ass may well have been domesticated several times, given the semi-feral production systems under which it was managed until recently. Records of domestic asses begin in Egypt in the fourth millennium BC. The extent to which the wild ass penetrated the interior of Africa is unknown. Faunal remains and rock art representations are extremely rare, which is somewhat at odds with the widespread distribution and economic importance of the donkey in Africa today. This apparent contradiction can probably be explained by the fact that donkeys have been of most importance to poor households and have consequently had low prestige. The spread of the donkey across Africa was linked with the proliferation of long distance caravans. It is argued that greater attention to the nearly extinct wild ass and to traditional management systems could be helpful in the future development of the donkey in Africa.

In brief – donkeys domesticated probably in the Egypt/Nubia area at the beginning of the neolithic in Africa about 6,500 years ago. Their expansion also seems to mark the expansion of sorghum as a crop, so assuming a similar date for both domestications seems reasonable. I can tell you from memory the oldest donkey remains in Syria/Iraq are about 4,800 years old, similar for sorghum. I have another item around here somewhere on this subject. The conclusion is…

The donkey is certainly derived from the African wild ass, although it may have been domesticated several times in regions of its former range no longer represented by its present-day distribution. This appears to be confirmed by studies of terms for donkey in various African language families. Egypt remains the most likely centre for its early development for agricultural work, although without further archaeology outside the Nile Valley this is uncertain.

Early Holocene cultivation before domestication in northern Syria

Early Holocene cultivation before domestication in northern Syria

Abstract Charred plant remains from the sites of Tell Qaramel, Jerf el Ahmar, Dja’de and Tell ‘Abr situated in northern Syria and dated to the tenth and ninth millennia cal B.C. demonstrate that a wide variety of wild pulses, cereals, fruits and nuts was exploited. Five lines of evidence suggest that cultivation was practised at three of the sites. (1) Wild einkorn, wild rye and lentils occur outside their natural habitats. (2) The founder crops barley, emmer and single-grained einkorn appear at different times. (3) An assemblage of weeds of cultivation was identified. (4) There is a gradual decrease in gathered plants such as small seeded grasses and Polygonum/Rumex. (5) Barley grains increase in breadth and thickness. Morphological domestication did not become established, perhaps because seed stock was regularly collected from wild stands. Charred rodent droppings indicate large-scale grain storage.

I shall have a go at reading this one when my kids are at school tomorrow. So far, I have picked out-

A good sign of pre-domestic cultivation is the presence of wild cereals outside their natural habitats. The sites of Jerf el Ahmar, Cheik Hassan, Mureybet and Abu Hureyra are almost 200 km south of current-day wild rye habitats and between 100 and 150 km south of wild einkorn habitats.

-as interesting. Which makes it even more baffling that rye was being grown at Abu Hureyra about 13k ago, and suggests that a more northerly Euphrates based group started growing it first. However, this will have to wait until tomorrow as dinner has to be put on the table right now.

The oldest known grape wine, from Iran

So far, the oldest known evidence of grape wine is about 7,000 years old, from a Neolithic settlement in Iran’s Zagros mountains, Hajji Firuz Tepe. Link, byMark Berkowitz.

A  7,000 years old potsherd  came from one of six two-and-one-half-gallon jars came from the kitchen area of a mud-brick building in Hajji Firuz Tepe, a Neolithic village in Iran’s northern Zagros Mountains. A team from the University of Pennsylvania Museum found calcium salt from tartaric acid, which occurs naturally in large amounts only in grapes. Resin from the terebinth tree was also present, presumably used as a preservative, indicating that the wine was deliberately made and did not result from the unintentional fermentation of grape juice. It also suggests that the wine makers weren’t beginners, as adding preservative is something that will take time to figure out

Analysis of the Hajji Firuz Tepe sherd comes in the wake of two other recent discoveries of early wine-making in this region where grapes grow in the wild. Residue from a jar from Godin Tepe, in the nearby middle Zagros Mountains, was dated to 5,100 years ago, until now the earliest evidence of wine-making. Grape presses dating to the late third millennium B.C. have been found at Titris Höyük in southeastern Turkey.

I wonder… would drinking alcohol have been a survival advantage? The liquid would be sterile. Historically even children drank  ‘small beer’ ( a very weak beer) in England because it was safer.

Domestication of the donkey: Timing, processes, and indicator

Abydos donkeys in brick tombs.

Domestication of the donkey: Timing, processes, and indicator

Domestication of the donkey from the African wild ass transformed ancient transport systems in Africa and Asia and the organization of early cities and pastoral societies. Genetic research suggests an African origin for the donkey, but pinpointing the timing and location of domestication has been challenging because donkeys are uncommon in the archaeological record and markers for early phases of animal domestication are hard to determine.We present previously undescribed evidence for the earliest transport use of the donkey and new paleopathological indicators for early phases of donkey domestication. Findings are based on skeletal data from 10 ~5,000-year-old ass skeletons recently discovered entombed in an early pharaonic mortuary complex at Abydos, Middle Egypt, and a concurrent study of 53 modern donkey and African wild ass skeletons. Morphometric studies showed that Abydos metacarpals were similar in overall proportions to those of wild ass, but individual measurements varied. Midshaft breadths resembled wild ass, but midshaft depths and distal breadths were ntermediate between wild ass and domestic donkey. Despite this, all of the Abydos skeletons exhibited a range of osteopathologies consistent with load carrying. Morphological similarities to wild ass show that, despite their use as beasts of burden, donkeys were still undergoing considerable phenotypic change during the early Dynastic period in Egypt. This pattern is consistent with recent studies of other domestic animals that suggest that the process of domestication is slower and less linear than previously thought.

As the paper says at one point:

In the 1980s zooarchaeologists working in southwestern Asia found bones attributable to donkey from sites in Syria, Iran, and Iraq dating to ca. 2800–2500 B.C.

the oldest date at 4,800 BP is from the Iranian highlands. So logically the domestiction of the ass in Africa would date to a substantial amount before 2,800 BC, and given the rate of expansion of camels and other livestock I’d say 6,000 years would be more realistic.

The Romanian Mesolithic and the transition to farming. A case study: the Iron Gates

The Romanian Mesolithic and the transition to farming. A case study: the Iron Gates

The transition from foraging to agriculture in the last few decades has become a subject increasingly studied in academia. More complex research involving a large number of disciplines has made possible a substantial reevaluation of older concepts, but has also raised new questions and controversies. With the growing body of data from different regions of the world, it has become apparent that agriculture developed independently in more areas than was previously thought, and that the process of its geographic diffusion was much more complex than initially envisioned. The important role played by pre-Neolithic populations has come to be accepted by a growing number of archaeologists. The social and ideological implications associated with the adoption of agriculture have become more relevant, involving an association of causal factors with aspects other than economics. Regardless, questions such as why agriculture and how did it spread remain unanswered to a large degree. Most unfortunate, the body of knowledge related to the spread of agriculture in Europe
was constrained by a relative neglect of the Mesolithic period. This situation persists in many parts of the continent. Most of the data and studies come from the northern lands of Europe where many Mesolithic sites were discovered. On the other hand, the scarcity of sites in south and southeastern Europe focused most of the research on one of the richest Mesolithic archaeological locations on the continent: the Danube “Iron Gates” canyon.

A pdf with  plenty of information on the arrival of the Neolithic into Europe. It’s suggesting independent domestication of pigs in various European locations, but I don’t think it means pristine domestication, probably later ones by people already farming.

Anyone curious after reading it, Neolithic farmers made a substantial genetic ontribution to Southern Europe, but not much to Northern Europe; overall it’s about 20% (if memory serves). The ‘wave of advance’ theory of the Neolithic seems partially true, but only in Southern Europe. The paper concludes:

Besides pottery, there is no evidence for other developments associated with a food production economy. Of an extreme importance is a future pottery petrographic and chemical analysis by the excavated levels at least for Icoana and Schela Cladovei, in order to determine the earliest level with Starčevo ceramics at each site. Although all Mesolithic sites in the canyon proper are presently under water, it is not excluded that more sites may still exist on the islands of Ostrovul Banului and Ostrovul Corbului. The stratigraphy of the sites on both banks of the Danube need to be clarified and re-interpreted.

Claims for the practice of agriculture during the Mesolithic do not stand up to scrutiny, and in the archaeological strata associated with the appearance of Starčevo Neolithic in the area, agricultural implements are almost absent. There is also no evidence of domestic animals besides dog. It has been shown (A. Dinu et alii , this volume) that during Late Mesolithic no local domestication of European wild pig took place along the Lower Danube frontier between Starčevo Neolithic and the local Mesolithic cultures. It is not clear at this point when Starčevo domestic Asia Minor pigs showed up at Iron Gates, but it is more probable that it happened after 5500 BC.  Subsequently, if a replacement of the Starčevo Asia Minor domestic pigs took place in the following centuries, it is clear that Mesolithic Iron Gates played no role in wild pigs domestication North of the Danube.

As shown by the radiocarbon dates, contact between the Mesolithic and the Early Neolithic groups was chronologically possible. Still, there are no clear signs of influences in between these groups (economic exchanges, ideology religion etc.).

There is stll to be clarified the problem of the Mesolthic communities disapperance and the origins and way of penetration of the Early Neolithic.

Seeming to put the dampers on the idea of Mesolithic agriculture in Europe. However, 8,000 year old pots in Hungary and Switzerland show the remains of milk products in them , which essentially proves dairying was going on at the time then. It’s looking like the domestication of goats and sheep go back a very long time (12,000 years or more), probably somewhat longer than domesticated cattle. Another ‘however’ is that pottery appears after farming, and about 5,500 BC towns with metallurgy are found in the Balkans, so I find it hard to think that farming wasn’t in this area by then.