Tag Archives: domestication

Animal domestication is older than previously thought

NY times article

Like this surprises me much, I’ve said before that it was older than claimed. At least this map agrees with my points of domestication (I did something similar a few months ago). I’ve always maintained Southern Turkey was the origin point of the Western Neolithic revolution.

The invention of agriculture was a pivotal event in human history, but archaeologists studying its origins may have made a simple error in dating the domestication of animals like sheep and goats. The signal of the process, they believed, was the first appearance in the archaeological record of smaller boned animals. But in fact this reflects just a switch to culling females, which are smaller than males, concludes Melinda Zeder, an archaeologist at the Smithsonian Institution.

Using a different criterion, that of when herds first show signs of human management, Dr. Zeder finds that goats and sheep were first domesticated about 11,000 years ago, much earlier than previously thought, with pigs and cattle following shortly afterwards. The map, from her article in the August 11 issue of the Proceedings of the National Academy of Sciences, shows the regions and dates where the four species were first domesticated. Other dates, color-coded as to species, show where domesticated animals first appear elsewhere in the Fertile Crescent.

The earlier dates mean that animals were domesticated at much the same time as crop plants, and bear on the issue of how this ensemble of new agricultural species – the farming package known as the Neolithic revolution – spread from the Near East to Europe.

Some experts say the technology spread by cultural diffusion, others that the first farmers themselves moved into Europe, bringing their new technology with them and displacing the resident hunter gatherers.

Dr. Zeder concludes that both processes were involved. A test case is the island of Cyprus, where the four domesticated species of livestock appear as early as 10,500 years ago, replacing native fauna such as pygmy elephants and pygmy hippopotamuses (large animals often get downsized in island settings).

Since Cyprus lies 60 kilometers off the Turkish coast, the suite of agricultural species must have been brought there on boats by the new farmers. That establishes one episode of colonization, and Dr. Zeder sees evidence for several others. The second map shows, in red circles, the dates when farming colonists’ enclaves were set up around the Mediterranean.

Dr. Zeder believes that in France and Spain the indigenous hunter gatherers adopted the new farming technology by cultural diffusion (shown as green dots). The farmers themselves settled the regions that are now Turkey and the Balkans (red dots) but in surrounding areas they integrated with indigenous peoples (blue dots).

Dr. Zeder says her evidence indicates that several waves of settlers spread the new farming technology through the Mediterranean. It’s yet not known what drove the expansion, or what the relationship was between the colonists and the native inhabitants. Studies of ancient DNA, she said, may help test her thesis that farming spread through a mix of colonization and cultural diffusion.

The logic that is used to observe the livestock arriving in Cyprus is similar to my dating of agriculture arriving at Francthi cave; essentially multiple crop plants make a simulaneous appearance in Francthi cave about 11,000 years ago (500 years before cereals are seen).

A nicely dated map/timeline of the expansion of farming (well, it’s a bit out, as Francthi in Greece was 11,000 BP)

I’m feeling moderately smug now. Told ‘em so.

DNA and the domestication of cattle.

African, Asian and European cattle.

Archaeological evidence suggests that cattle were first domesticated In Turkey, in the Catal Hoyuk area, from about 10,000 years ago. DNA suggests that there was a second domestication, with archaeological evidence dating that to about 7,000 years ago (pre-Harappan in Pakistan). As yet, no DNA evidence for an independent African domestication, just hybridisation. It also suggests European cattle contain some wild auroch DNA.

Mitochondrial genomes of extinct aurochs survive in domestic cattle

Archaeological and genetic evidence suggest that modern cattle might result from two domestication events of aurochs (Bos primigenius) in southwest Asia, which gave rise to taurine (Bos taurus) and zebuine (Bos indicus) cattle, respectively [1, 2, 3]. However, independent domestication in Africa [4, 5] and East Asia [6] has also been postulated and ancient DNA data raise the possibility of local introgression from wild aurochs [7, 8, 9]. Here, we show by sequencing entire mitochondrial genomes from modern cattle that extinct wild aurochsen from Europe occasionally transmitted their mitochondrial DNA (mtDNA) to domesticated taurine breeds. However, the vast majority of mtDNAs belong either to haplogroup I (B. indicus) or T (B. taurus). The sequence divergence within haplogroup T is extremely low (eight-fold less than in the human mtDNA phylogeny [10]), indicating a narrow bottleneck in the recent evolutionary history of B. taurus. MtDNAs of haplotype T fall into subclades whose ages support a single Neolithic domestication event for B. taurusin the Near East, 9–11 thousand years ago (kya).

An Unusual Pattern of Ancient Mitochondrial DNA Haplogroups in Northern African Cattle,

Which is too fiddly to reproduce here.

Microsatellite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos taurus and Bos indicus)

D. E. MacHugh, M. D. Shriver, R. T. Loftus, P. Cunningham and D. G. Bradley
Department of Genetics, Trinity College, Dublin 2, Ireland

Genetic variation at 20 microsatellite loci was surveyed to determine the evolutionary relationships and molecular biogeography of 20 different cattle populations from Africa, Europe and Asia. Phylogenetic reconstruction and multivariate analysis highlighted a marked distinction between humpless (taurine) and humped (zebu) cattle, providing strong support for a separate origin for domesticated zebu cattle. A molecular clock calculation using bison (Bison sp.) as an outgroup gave an estimated divergence time between the two subspecies of 610,000-850,000 years. Substantial differences in the distribution of alleles at 10 of these loci were observed between zebu and taurine cattle. These markers subsequently proved very useful for investigations of gene flow and admixture in African populations. When these data were considered in conjunction with previous mitochondrial and Y chromosomal studies, a distinctive male-mediated pattern of zebu genetic introgression was revealed. The introgression of zebu-specific alleles in African cattle afforded a high resolution perspective on the hybrid nature of African cattle populations and also suggested that certain West African populations of valuable disease-tolerant taurine cattle are under threat of genetic absorption by migrating zebu herds.
Evidence for two independent domestications of cattle.


R T Loftus, D E MacHugh, D G Bradley, P M Sharp, and P Cunningham
Department of Genetics, Trinity College, Dublin, Ireland.
 
AbstractThe origin and taxonomic status of domesticated cattle are controversial. Zebu and taurine breeds are differentiated primarily by the presence or absence of a hump and have been recognized as separate species (Bos indicus and Bos taurus). However, the most widely held view is that both types of cattle derive from a single domestication event 8000-10,000 years ago. We have examined mtDNA sequences from representatives of six European (taurine) breeds, three Indian (zebu) breeds, and four African (three zebu, one taurine) breeds. Similar levels of average sequence divergence were observed among animals within each of the major continental groups: 0.41% (European), 0.38% (African), and 0.42% (Indian). However, the sequences fell into two very distinct geographic lineages that do not correspond with the taurine-zebu dichotomy: all European and African breeds are in one lineage, and all Indian breeds are in the other. There was little indication of breed clustering within either lineage. Application of a molecular clock suggests that the two major mtDNA clades diverged at least 200,000, and possibly as much as 1 million, years ago. This relatively large divergence is interpreted most simply as evidence for two separate domestication events, presumably of different subspecies of the aurochs, Bos primigenius. The clustering of all African zebu mtDNA sequences within the taurine lineage is attributed to ancestral crossbreeding with the earlier B. taurus inhabitants of the continent.

 

Mitochondrial diversity and the origins of African and European cattle
Daniel G. Bradley, David E. MacHugh, Patrick Cunningham, and Ronan T. Loftus 

The nature of domestic cattle origins in Africa are unclear as archaeological data are relatively sparse. The earliest domesticates were humpless, or Bos taurus, in morphology and may have shared a common origin with the ancestors of European cattle in the Near East. Alternatively, local strains of the wild ox, the aurochs, may have been adopted by peoples in either continent either before or after cultural influence from the Levant. This study examines mitochondrial DNA displacement loop sequence variation in 90 extant bovines drawn from Africa, Europe, and India. Phylogeny estimation and analysis of molecular variance verify that sequences cluster significantly into continental groups. The Indian Bos indicus samples are most markedly distinct from the others, which is indicative of a B. taurus nature for both European and African ancestors. When a calibration of sequence divergence is performed using comparisons with bison sequences and an estimate of 1 Myr since the Bison/Bos Leptobos common ancestor, estimates of 117-275,000 B.P. and 22-26,000 B.P. are obtained for the separation between Indians and others and between African and European ancestors, respectively. As cattle domestication is thought to have occurred approximately 10,000 B.P., these estimates suggest the domestication of genetically discrete aurochsen strains as the origins of each continental population. Additionally, patterns of variation that are indicative of population expansions (probably associated with the domestication process) are discernible in Africa and Europe. Notably, the genetic signatures of these expansions are clearly younger than the corresponding signature of African/European divergence.
Extensive MHC class II DRB3 diversity in African and European cattle

Sofia Mikko1 and Leif Anderson1

 Genetic deversity at the highly polymorphic BoLA-DRB3 locus was investigated by DNA sequence analyses of 18 African cattle from two breeds representing the two subspecies of cattle, Bos primigenius indicus and Bos primigenius taurus. Yhe polymorphism was compared with that found in a sample ofd 32 European cattle from four breeds, all classified as B. p. taurus. Particularly extensive genetic diversity was found among African cattle, in which as many as 18 alleles were recognized in this small random sample of animals from two breeds. The observed similarity in allele frequency distribution between the two African populations, N’Dama and Zebu cattle, is consistent with the recent recognition of gene flow between B. p. indicus and B. P taurus cattle in Africa. A total of 30 DRB3 alleles were documented and as many as 26 of these were classified as major allelic types showing at least five amino acid substitutions compared with other major types. The observation of extensive genetic diversity at MHC loci in cattle, as well as in other farm animals, provides a compelling argument against matin-type preferences as a primary cause in maintaining major histocompatibility complex diversity, since the reproduction of these animals has been controlled by humans for many generations.
The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been given the accession numbers X87641-X87670

An Unusual Pattern of Ancient Mitochondrial DNA Haplogroups in Northern African Cattle

Comparative DNA studies of the control region for mitochondrial DNA (mtDNA) have revealed surprising complexity in the evolutionary history of Old and New World livestock species (Bruford et al. 2003). For the greater Mediterranean area, these analyses have shown that the mitochondrial control region haplotypes for modern cattle (i.e., Bos taurus) belong to one of 4 sequence clusters or haplogroups (Fig. 1). Most (94%) modern cattle populations from Northern Africa carry haplogroup T1, which is rarely found outside of Africa (6% in the Near East and absent elsewhere). In contrast, modern populations from mainland Europe carry 2 very similar haplogroups, T and T3 (94%), which decrease in the Middle East (65%-74%) and almost completely disappear in Africa (6%). Haplogroup T2 makes up the remainder of this mtDNA diversity and is present at 6% in Europe and 21%-27% in the Near East, but is absent from Africa. These haplogroup distributions have been interpreted as indicating a Near East origin for European B. taurus and the  independent domestication of cattle in Africa (Bradley et al. 1996, Troy et al. 2001, Hanotte et al. 2002).

In this note, we report on the analysis of an ancient mtDNA (control region) sequence as
obtained from a bovine skeletal sample from an early, first millennium, archaeological site near the community of Adi Nefas, Eritrea in Northeastern Africa (900 yr before the present; YBP; Schmidt and Curtis 2001) (Fig. 1). This newly acquired ancient DNA sequence is combined with data for the same mitochondrial control region as determined for 4 specimens from Mali, Northwestern Africa (ca. 900-2200 YBR; Edwards et al. 2004). In concert with the modern mtDNA data, these 5 ancient DNA sequences raise the  possibility that the mtDNA gene pool for Northern African cattle was more diverse ca. 900-2000 yr ago.

MATERIALS AND METHODS
The original source of the ancient DNA from Eritrea consisted of a bone section (2 g) that was obtained from a larger piece of fragmented bone. Multiple DNA extractions, amplifications, cloning, and sequencing were performed according to established procedures for ancient DNA (Mulligan 2005). The DNA amplifications and sequencing
relied on the primer pair, AN1 (5′-ACGCGGCAT GGTAATTAAGC-3′) and AN2 (5′-GCCCCAT
GCATATAAGCAAG-3′), for an internal segment of the mitochondrial control region (see below).

Throughout this study, rigorous safeguards were routinely employed to ensure the authenticity of the final sequence, e.g., the DNA extractions and amplifications were conducted in a separate laboratory and building with positive air pressure and HEPA air filtration where no previous bovid material, either contemporary or ancient, had ever been
analyzed. In general, hot arid climates result in poorer organic preservation than colder climates (Edwards et al. 2004). Thus, the fact that this specimen was associated with a cool highland environment may have facilitated the successful DNA extraction.

RESULTS AND DISCUSSION
The new ancient DNA sequence from Adi Nefas, Eritrea was 116 base pairs in length
(GenBank accession no.: AY524815), corresponding to positions 16,042-16,157 of the bovine mtDNA genome (Anderson et al. 1982). This mtDNA sequence is identical to a known control region haplotype for B. taurus (L27727; Loftus et al. 1994). Thus, as a representative of L27727, this ancient DNA sequence belongs to the combined haplogroup T/T3, which is common in modern cattle populations from Europe and the Near East, but rare in those from Northern Africa (Fig. 1). Furthermore, as characteristic of B. taurus, it corroborates the initial morphological identification Fig.

The previously reported ancient mtDNA sequences for the 4 Mali individuals consist of 1
T/T3 and 3 T1 haplotypes (Edwards et al. 2004). Combining the new Eritrean sequence with these 4 Mali orthologues resulted in an ancient mtDNA sample for Northern Africa of 2 T/T3 and 3 T1 haplotypes (Fig. 1). Assuming that these 5 represent a valid random sample (which admittedly is unlikely), a standard binomial test reveals that the probability  of drawing by chance 2 or more T/T3 sequences out of five, given the contemporary haplogroup frequencies for Northern African cattle (Fig. 1), is only 3.5%. Minimally, this result highlights the fact that this set of 5 ancient DNA sequences appears􀂨unusual􀂩, because of the greater frequency of the rare T/T3 haplogroups compared to modern populations of Northern African cattle.

In conclusion, our results raise the possibility that the mtDNA gene pool for Northern African cattle ca. 900-2000 yr ago was more polymorphic in terms of the frequencies of the T1 and T/T3 haplogroups that currently predominate in African and European populations, respectively. This older polymorphism in Northern African cattle may reflect a transition from an even more-diverse ancestral gene pool (as characteristic of its Near East progenitor) and/or the later secondary introduction of T/T3 haplotypes into this region by the immigration of European cattle (Hanotte et al. 2002, Bruford et al. 2003). Concomitantly, selective pressures from domestication and breeding efforts and/or genetic drift may have then led to the final homogenization of this older polymorphism into the current situation of essentially only the T1 haplogroup occurring in Northern Africa. These possibilities reemphasize the fact that both ancient and modern DNA data are of value in the ultimate resolution of the complex history of African cattle
(Edwards et al. 2004).

Early history of European domestic cattle as revealed by ancient DNA

We present an extensive ancient DNA analysis of mainly Neolithic cattle bones sampled from archaeological sites along the route of Neolithic expansion, from Turkey to North-Central Europe and Britain. We place this first reasonable population sample of Neolithic cattle mitochondrial DNA sequence diversity in context to illustrate the continuity of haplotype variation patterns from the first European domestic cattle to the present. Interestingly, the dominant Central European pattern, a starburst phylogeny around the modal sequence, T3, has a Neolithic origin, and the reduced diversity within this cluster in the ancient samples accords with their shorter history of post-domestic accumulation of mutation.

Genetics and Domestic Cattle Origins

Genetics has the potential to provide a novel layer of information pertaining to the origins and relationships of domestic cattle. While it is important not to overstate the power of archeological inference from genetic data, some previously widespread conjectures are inevitably contradicted with the addition of new information. Conjectures regarding domesticated cattle that fall into this category include a single domestication event with the  development of Bos indicus breeds from earlier Bos taurus domesticates; the domestication of a third type of cattle in Africa having an intermediate morphology between the two taxa; and the special status of the Jersey breed as a European type with some exotic influences. In reality, a wideranging survey of the genetic variation of modern cattle reveals that they all derive from either zebu or taurine progenitors or are hybrids of the two. The quantitative divergence between Bos indicus and Bos taurus strongly supports a predomestic separation; that between African and European taurines also suggests genetic input from native aurochsen populations on each continent. Patterns of genetic variants assayed from paternally, maternally, and biparentally inherited genetic systems reveal that extensive hybridization of the two subspecies is part of the ancestry of Northern Indian, peripheral European, and almost all African cattle breeds. In Africa, which is the most extensive hybrid zone, the sexual asymmetry of the process of zebu introgression into native taurine breeds is strikingly evident.

Figure 1. This map shows approximate distributions for the various types of domesticated cattle found in Asia, Africa, and Europe. Also shown are distributions for the closely related Bibos species, banteng and gaur. This diagram is modified from Payne6 and Epstein and Mason.5

Domesticated animals across the Sahara, North Africa and Nile.

There are claims that the Africans domesticated cattle first, which seems unlikely as the DNA from African cattle is pretty much restricted to sub Saharan Africa, with minority contribution in Northern Africa and a little in Portugal , whereas it would have been all over the place if it had been first. Interesting bits in bold. I’ve added this item because the appearance of the sheep and goats helps to trace the arrival of the Neolithic revolution into Africa.

Taken from ‘The antiquity of man’.

Extracts from:

Are the early Holocene cattle in the Eastern Sahara domestic or wild?
Fred Wendorf & Romuald Schild (Evolutionary Anthropology 3(4), 1994)

In the early Holocene, the Eastern Sahara had more rainfall, probably between 100 and 200 mm per year in its Egyptian area The rain probably fell during the summer. This inference is drawn from the fact that the plant remains in the early Holocene archeological sites are the same as those growing today several hundred kilometers to the south, on the northern margin of the Sahel and the adjacent Sahara, which are in a summer rain-fall regime. The quantity of rainfall was sufficient for seasonal pools or playas to form in large depressions. There may also have been permanent water about 250 km farther south at Sehima, and there certainly were permanent lakes near Merga in northern Sudan about 500 km south of the Egyptian border. Nevertheless, the Eastern Sahara was, at best, a marginal and highly unstable environment with frequent droughts and episodes of hyper-aridity. The Eastern Sahara in Egypt was not an environment that could have supported wild cattle nor one where the earliest domestication of cattle would have been like likely to occur. Cattle need to drink every day or at least every other day and there was no permanent water anywhere in the area.

Early Neolithic

Radiocarbon dates indicate that the early Holocene rains began sometime before 10,000 B.P., perhaps as early as 11,000 or 12,000 B.P. However, there is no evidence of human presence before 9,500 B.P. except for a radiocarbon date of around 10,000 years ago from a hearth west of Dakhla. The earliest sites with large bovid remains are imbedded in playa sediments that overlay several meters of still older Holocene playa deposits.

All of these sites contain well-made, bladelet-based lithic assemblages. Straight-backed pointed bladelets, perforators, and large endscrapers made on reused Middle Paleolithic artifacts are the characteristic tools. A few grinding stones and rare sherds of pottery also occur. The pottery is well made; the pieces are decorated over their entire exterior surfaces with deep impressions formed with a comb or wand in what is sometimes referred to as the Early Khartoum style.

These assemblages have been classified as the El Adam type of the Early Neolithic. Several radiocarbon dates place the complex between 9,500 and 8,900 B.P. There is no evidence that there were wells during this period. It is assumed, then, that these sites represent occupations that took place after the summer rains and before the driest time of the year when surface water was no anger available. Three of these sites, E-77-7, E-79-8, and E-80-4, all having only El Adam archeology and all located between km and 250 km west of Abu Simbel, have yielded, through excavation, more than 20 bones and teeth of large bovids that have been identified as Bos. These occurred along with several hundred bones of gazelle (Gazella dorcas and G. dama) and hare (Lepus capensis); a few bones of jackal (Canis aureus), turtle (Testudo sp.); and birds (Otis tarda and Anas querquedula); the large shell of a bivalve (Aspatharia rubens), probably of Nilotic origin; and various snail shells (Bulinus truncatus and Zoorecus insularis).

After a period of aridity around 8,800 years ago, when the desert may have been abandoned, the area was re-occupied by groups with a lithic tool-kit that emphasized elongated scalene triangles. The grinding stones, scrapers, and rare pieces of pottery that are present characterize the El Ghorab type of Early Neolithic and have been dated between 8,600 and 8,200 B.P. Oval slab-lined houses occur during this phase. all of them located in the lower pans of natural drainage basins. However, there are no known wells, suggesting that the desert still was not occupied during the driest part of the year. Faunal remains are poorly preserved in these sites and. indeed, only one bone of a large bovid was recovered from the four sites with fauna. in these sites the Dorcas gazelle is the most numerous, followed by hare, together with single bones of wild cat (Felis silvestris), porcupine (Hystrix cristata), desert hedge-hog (Paraechinus aethiopicus) an amphibian, and a bird.

Another brief period of aridity between 8.200 and 8,100 B.P. coincides with the end of the El Ghorab type of Early Neolithic in the desert. With the return of greater rainfall between about 8,0100 B.P., a new variety of Early Neolithic, the El Nabta type, appeared in the area. El Nabta. sites are often larger than the previous Early Neolithic sites and usually have several large, deep wells, some with adjacent shallow basins that might have been used to water stock. A variety of lithic and bone tools occur in these sites, including stemmed points with pointed and retouched bases, perforators, burins, scrapers. notched pieces, bone points, and scalene triangles measuring about one centimeter. Grinding stones and sherds of pottery are more numerous than in the earlier sites, but still are not abundant. Their deeply impressed designs are similar to those on objects recovered from sites of the El Adam and El Ghorab types of Early Neolithic. Occasional pieces have “dotted wavy line” decoration.

Radiocarbon dates place the El Nabta sites between 8,100 and 7,900 B.P. One of these, E-75-6, is much larger than the others and consists of a series of shallow, oval hut floors at–ranged in two, possibly three, parallel lines. Beside each house was one or more bell-shaped storage pits; nearby were several deep (2.5 m) and shallow (1.5 m) water-wells. This site, located near the bottom of a large basin, was flooded by the summer rains. The houses were repeatedly used, probably during harvests in fall and winter Several thousand remains of edible plants have been recovered from these house floors. They include seeds, fruits, and tubers representing 44 different kinds of plants, including sorghum and millets. All of the plants are morphologically wild, but chemical analysis by infrared spectroscopy of the lipids in the sorghum indicates that this plant may have been cultivated. Of the four El Nabta sites that have yielded fauna, two contained bones of a large bovid identified as Bos. The faunal samples from the other two sites are very small.

Middle Neolithic

Another brief period of aridity separated the El Nabta Early Neolithic from the succeeding Middle Neolithic, which is marked by the much greater abundance of pottery. In addition, each piece of pottery is decorated over its entire exterior surface with closely packed comb- or paddle-impressed designs. Some of the pots are large, and analysis of the clays indicates that they were made locally. There were also some changes in lithic tools. More of them were made of local rocks, but there was sufficient continuity in lithic typology to suggest that the preceding Nabta population was also involved.

Radiocarbon dates indicated an age for the Middle Neolithic between 7,700 and 6,500 B.P. The sites from the early part of this period range from one-or-two house homesteads in some of the smaller playas to multi-house villages in the larger basins. There is also one very large settlement along the beach line of the largest playa in the area, as well as, small camps on the sandsheets and the plateaus beyond the basins. This variation in site size has been interpreted as reflecting a seasonally responsive settlement system in which the population dispersed into small villages in the lower pans of the basins during most of the year, particularly the dry season, then, during the wet season, aggregated into a large community along the edge of the high-water stand of the largest playa.

Various house types are represented in the villages: some are circular and semi-subterranean (30 to 40 cm deep), some slab-lined, and others appear to have had walls of sticks and clay (wattle and daub). All of the sites have large, deep walk-in wells and storage pits. Except for the small camps, most of the sites appear to have been reused many times, with new house floors placed on top of the silt deposited during the preceding flood.

Excavations at five Middle Neolithic sites have yielded more than 50 bones from large bovids. Most of these bones came from the large “aggregation” site (E-75-8) at the margin of the largest playa in the area and from the early Middle Neolithic site E-77-l, dated before 7,000 B.P., which is located on a dune adjacent to another large playa. Each of the other three Middle Neolithic sites yielded only one to three large bovid bones.

Around 7,000 B.P., the remains of small livestock (sheep or goats) appear in several Middle Neolithic sites at Nabta. Because there are no progenitors for sheep or goats in Africa, these caprovines were almost certainly introduced from southwest Asia.

The faunal remains in many of these sites are extensive, including not only the same species recovered from the Early Neolithic sites, but also lizards (Lacertilia sp.) ground squirrel (Euxerus erythropus), field rat (Aricanthis nioloticus), hyena (Hyaena hyaena), and sand fox (Vulpes rueppelii). One bone is from either orstx (Oryx dammah) or addax (Addax nasosulcatus), The most nurmerous remains are those of hare and the Dorcas gazelle. Nevertheless, the paucity of the fauna and the absence, except for cattle and small livestock, of animals that require permanent water suggests a rather poor environment, most likely comparable to the northernmost Sahel today with about 200 mm of rain or less annually.

The Middle Neolithic was brought to an end by another major but brief period of aridity slightly before 6,500 B.P., when the water table fell several meters and the floors of many basins were deflated and reshaped, The area probably was abandoned at this time.

Late Neolithic

With the increase in rainfall that began around 6,500 years ago. human groups again appeared in the area, but this time with ceramic and lithic traditions that differed from those of the preceding Middle Neolithic. This new complex, identified as Late Neolithic, is distinguished by pottery that is polished and sometimes smudged on the interiors. This pottery resembles that found in the slightly later (about 5,400 or, possibly, 6,300 B.P.) Baderian sites in the Nile Valley of Upper Egypt. [12, 13] It seems likely that an as yet undiscovered early pre-Badarian Neolithic was present in that area and either stimulated or was the source of the Late Neolithic pottery in the Sahara. It is unlikely, however, that this hypothetical early Nilotic Neolithic will date much earlier than 6,500 B.P. There are terminal Paleolithic sites along the Nile that are dated to around 7,000 B.P. and it is highly improbable that two such different life-ways could co-exist exist for long in the closely constrained environment of the Nile Valley.

Late Neolithic sites in the Egyptian Sahara consist mostly of numerous hearths representing many separate episodes of occupation. The hearths are long and oval, dug slightly into the surface of the ground, and filled with charcoal and fire-cracked rocks. No houses are known. Most of the sites are dry-season camps located in the lower parts of basins that were flooded by the seasonal rains. Many of the sites are associated with several large, deep wells.

Many of the Late Neolithic tools are made on “side-blow flakes” that have been retouched into denticulates and notched pieces There are also a few bifacial arrowheads, often with tapering stems, or, rarely with concave bases similar to those found in the Fayum Neolithic where they date between 6,400 and 5,7OO years ago.The end of the Late Neolithic in the Eastern Sahara is not well established.The period may have tasted until around 5,300 B.P. when this part of the Sahara was abandoned.

Due to poor preservation faunal re-mains in Late Neolithic sites are not as abundant as those from the Middle Neolithic. However, the Late and Middle Neolithic samples generally include the same animals suggesting that the environment was also generally similar during these periods. Although large bovids are also present in three Late Nealithic sites, and more frequently than in the faunal assemblages of the preceding period, they still are a minor component of the sample.

The Late Neolithic Nabta is marked by interesting signs of increased social complexity, including several alignments of updght slabs (2 x 3 m) imbedded in, and sometimes almost covered by, the playa sediments. Circles of smaller uptight stabs may calendrical devices. Stone-covered tumuli are also present; two of the smaller ones contain cow burials, one in a prepared and sealed pit. none of the more than 30 large tumuli thus far located, which are by large, roughly shaped blocks of stone, has been excavated.

Even the earliest of these early Holocene Eastern Sahara sites have been attributed to cattle pastoralists. It is presumed that these Early Neolithic groups came into the desert from an as yet unidentified area where wild cattle were present and the initial steps toward their domestication been taken.

This area may have been the Nile Valley between the First and Second Cataracts, where wild cattle were present. Moreover, lithic industries were closely similar to those in the earliest Saharan sites. It has been suggested that cattle may have facilitated human use of the Sahara by providing a mobile, dependable, and renewable source of food in the font of milk and blood. The use of cattle as a renewable resource rather than for meat is seen as a possible explanation for the paucity of cattle remains in most of the Saharan sites. Such use in a desert, where other foods were so limited, may have initiated the modern East African pattern of cattle pastonlism in which cattle are important as a symbol of prestige, are primarily used for milk and blood, and rarely are killed for meat.

It is assumed, because of the apparrent absence of wells at the earliest sites, that the first pastoralists used the desert only after the summer rains, when water was still present in the larger drainage basins. After 8,000 years ago, when large, deep wells were dug, the pastoralists probably resided in the desert year-round.

Evidence from other parts of North Africa

The antiquity of the known domestic cattle elsewhere in North Africa does not offer much encouragement with regard to the presence of early domestic cattle in the Eastern Sahara. Gautier recently summarized the available data, noting that domestic cattle were present in coastal Mauritania and Mali around 4,200 years ago and at Capeletti in the mountains of northern Algeria about 6,500 years ago. At about that same time, they may have been present in the Coastal Neolithic of the Maghreb. Farther south in the Central Sahara, domestic cattle were present at Meniet and Erg d’Admco, both of which date around 5,400 years ago, and at Adrar Rous, where a complete skeleton of a domestic cow is dated 5,760 +/- 500 years B.P ].

Domestic cattle have been found in western Libya at Ti-n-torha North and Uan Muhuggiag, where the lowest level with domestic cattle and small livestock (sheep and goats) dated at 7,438 t 1,200 B.P. At Uan Muhuggiag, there is also a skull of a domestic cow dated 5,950 +/- 120 years. In northern Chad at Gabrong and in the Serir Tibesti, cattle and small livestock were certainly present by 6,000 B.P. and may have been there as early as 7,500 B.P. We are skeptical, however, about the presence of livestock at Uan Muhuggiag and the Serir Tibesti before 7,OO0 B.P., when small livestock first appear in the Eastern Sahara, if we must assume that these animals reached the central Sahara by way of Egypt and the Nile Valley. This also casts doubt on the 7,500 B.P. dates for cattle in these sites.

The earliest domestic cattle in the lower Nile Valley have been found at Merimda, in levels that have several radiocarbon dates ranging between 6,000 and 5,400 B.P. and in the Fayum Neolithic, which dates from 6,400 to 5, 400 B.P. These sites also have domes-tic pigs and either sheep or goats. In Upper Egypt, the earliest confirmed domestic cattle are in the Predynastic site of El Khattara, dated at 5,300 B.P. However, domestic cattle were almost certainly present in the earliest Badarian Neolithic, which dates before 5,400 B.P. and possibly were there as early as 6,300 B.P. Farther south, in Sudan near Khartoum, the first do-mestic cattle and small livestock oc-curred together in the Khartoum Neolithic, which began around 6,000 B.P.

It is probably significant that none of the early Holocene faunal assemblages in the Nile Valley from the Fayum south to Khartoum that date between 9,000 and 7,000 H.P contains the remains of cattle that have been identified as domestic It is this ab-sence of any evidence of recognizable incipient cattle domestication in the Nile Valley or elsewhere in North Africa that cautions us to consider carefully the evidence of early domestic cattle in the Eastern Sahara.

Other opinions

Numerous scholars, including Clutton-Brock, Robertshaw, Muzolini, and Smith, have debated about whether the large bovids are cattle or buffalo and stated that if they are cattle, they probably were wild.

It has also been suggested, because the large bovid bones are so rare, that the Bos were possibly intrusive and not associated with the dated occupations where they occurred That argument is not convincing The occupations at many of the sites with large bovids were limited to only one type of Early Neolithic. Moreover, the bovids were recovered from excavations at 15 Neo-lithic sites dating before 6,500 years ago and, in fact, were found at every site that yielded more than 41 speci-mens of identifiable faunal remains. Unfortunately, it is not possible to date these large bovid hones directly. Several attempts have been made and each was unsuccessful. Apparently. collagen is not preserved in bones found in hyper-arid environments. It should also be noted that the large bovid hones are not fossilized, and thus are not geological intrusions. Also, there are no large bovids living in the Eastern Sahara today nor have there been for several thousands of years.

It has been suggested that the faunal samples from the archeological sites do not reflect the range of animals that existed in that environment. However, Gautier has identified a long list of animals from these sites and, except for gazelles and hares, none is common. Beyond that, all are small and desert-adjusted. These faunal samples probably reflect the expected range of animals living in the desert at that time.

Smith made the most detailed criticism of Gautier’s hypothesis about domestic cattle, basing his objections on two major points. The first is environmental. He noted that Churcher identified wild cattle, African buffalo, hartebeests zebras, and gazelles from an “Early Neolithic” context at Dakhleh Oasis, 300 km north of Bir Kiseiba. If this is a true Early Neolithic faunal assemblage, however, the area would have required a much wetter environment than is indicated by the geological evidence. In fact, this Dakhleh assemblage in-cludes species that require much more moisture than do the species that were in the Nile Valley at this time. This suggests that the environment at Dakhleh was richer and more hospitable than that along the Nile, which is highly unlikely, to say the least. Also, Equus, even in the Late Paleolithic, seems to have been confined to the Red Sea Hills and the east bank of the Nile. [39] The Dakhleh fauna closely resembles that found with lacustrine deposits in the Eastern Sahara and dating to the Last Inter-glacial, while they are associated with Middle Paleolithic artifacts. It seems likely that this Dakhleh fauna was de-rived born deposits of the Middle Pa-leolithic and was somehow mixed with Neolithic artifacts. Churcher (personal communication) accepts this as a possible explanation.

Smith also noted that the Eastern Sahara faunal assemblages do not include the addax, which is still found today in the Central Sahara, or the onyx, giraffe, rhinoceros, or elephant he would expect to see in even the driest environments. There are, of course, two bones of either addax or onyx in the collections. Also, giraffes survived until recently in areas of the Gilf Kebir where there was water. There is, however, no evidence of giraffe on the plains of the Eastern Sahara after the lakes of the Last Interglacial became dry between 70,000 and 65,000 years ago. Occasional elephant teeth and a partial skull have been found in the Neolithic sites, but the elephant skull is more mineralized than are the bones of other fauna recovered from the same site. That skull, as well as the elephant teeth found in other sites, are regarded as Middle Paleolithic or earlier fossils collected by Neolithic people. In our view, the Eastern Sahara was simply too dry for these larger mam-mals, all of which, except the elephant, require nearby water. (The elephant is known to range consider-able distances away from water)

Smith’s other argument is osteological. He noted that Gautier was very cautious in his identifications, using circumstantial evidence to establish the identity of species. Smith observed that large bovid remains from the Eastern Sahara are within the size range of wild cattle in both Europe and North Africa, but that some are larger than known do-mestic cattle. He suggested that these large bovids could just as well be African buffalo (Syncerus caffer) or giant buffalo (Pelorovis antiquus). Both possibilities, however, can be rejected on osteometric and morphological grounds. The entire collection was carefully re-examined to resolve this particular question and the initial identification of the hones as those of Bus was confirmed.

It seems possible that we have not been adequately clear in our discus-sion of the sedimentary and other geological data that support the argument that there was no permanent water in this part of the Sahara. Perhaps, also, our critics’ personal experience in the Sahara has been limited to its more tropical and luxurious areas where permanent lakes existed in the Early Holocene. If so, this may have left them with a dis-torted view of the environment in the Eastern Sahara, where there are nu-merous deflated basins. In the center of many of these basins are extensive remnants of typical playa clays, which grade to silts and sands toward their margins. Diatomites, freshwater limestones, and other organogenic evidence of permanent water do not occur. There are no aquatic species of invertebrates and none of the fauna except large bovids requires permanent water. It is for these reasons that we reject the hypothesis that cattle were an integral part of the natural, wild fauna of the Eastern Sahara in the early Holocene. In this area under these conditions, cattle had to have been under human control, and thus at least incipiently domestic. The cattle had to have been moved from one grazing area and water hole to another and then, when the drainage basins became dry returned to a place with permanent water.

Wild cattle were numerous in the Nile Valley at this time. It might be hypothesized that after the summer rains the cattle ranged westward on their own to graze and the new grass then returned to the valley before the dry season. Although it is possible that this could have happened at Nabta, which is only 100 km from the Nile, it is extremely unlikely to have occurred at Bir Kiseiba, about 250 km west of the Nile. Also, this hypothesis makes little ecological sense. If large cattle went far out into the desert, why didn’t medium-size animals do the same? This is a particularly important question with regard to the hartebeest, which is also common in the Nile Valley and is better adapted to aridity than are cattle.

We have also considered the possibility that the cattle bones are remnants of food brought to the desert from the Nile Valley by groups of hunters. However, this is unlikely, for almost all of the bones recovered are lower limb elements, which have little or no meat and frequently are discarded at killing and butchery sites.

Conclusion

How can we accommodate the conflicting evidence regarding cattle pastoralists during the early Holocene in the Eastern Sahara? In particular, how can we propose that the first steps toward cattle domestication began in the Nile Valley, perhaps during the Late Pleistocene, when there is so little faunal evidence to support that hypothesis? The answer may lie in the identification of the cattle remains found in the Late Paleolithic sites in Sudanese and Egyptian Nubia. It has been suggested that it would be very difficult to separate the bones of the incipiently domestic cattle from those of wild cattle. When the first cattle were discovered in the Eastern Sahara, Gautier rechecked the Bos remains that had been found in all of the Late Paleolithic Nilotic sites. He gave particular attention to those from the Qadan site at Tushka, dated 14, 500 B.P., where cattle skulls were used as head markers for several human burials, and those from the Ark-inian site with a 14C date around 10,500 B.P. The Arkinian site was of special interest because the little lithic assemblage from there closely resembles the assemblages from the earliest El Nabta type Neolithic in the Eastern Sahara. Gautier found that the cattle in both the Qadan and Arkinian sites fell in two size groups one of which he considered to be males, the other females both groups were identified as being wild Bos primigenius.

Recently, however, work in a killing and butchery site near Esna, Egypt, dated 19,100 B.P., yielded the remains of six very large Bos, much larger than any other previously recovered in the Nile Valley. Indeed, these Bos are even larger than those from much older Middle Paleolithic sites. On the basis of this discovery, Gautier has suggested that Bos primigenius bulls in the Nile Valley may well have been much larger than was previously believed, and that the larger Bos from the Qadan and Arkinian sites were female wild Bos. If so, the smaller animals in those assemblages may have been these ones that were in an early stage of domestication. Morphologically, the Eastern Sahara cattle would then be well within the range of these incipiently domestic cattle. The additional work planned at the Esna butchery site may clarify this hypothesis.

By employing the method of “strong inferences,” which involves formulating alternative hypotheses, testing them to exclude one or more, arid adopting those that remain, we have concluded that domestic cattle probably were present in the Eastern Sahara as early as 9,000 years ago and, perhaps earlier. At the same time, we recognize that there is no such thing as proof and that science advances only by disproofs. Future evidence may suggest a better hypothesis or indeed, this controversy may be conclusively resolved if DNA testing now under way determines that the Bos remains found in African and Southwest Asian archeological sites belong to the same closely related gene pool or that they represent two populations that have been separated for many thousands of years. Until then, Gautier’s hypothesis of domestic cattle in the Eastern Sahara during the Early Holocene remains reasonable, if insecure

I have to say I disagree with them, on two grounds. DNA distribution of African cattle is pretty limited, and the main basis for their case four is that very big cattle bones have been found at another site. If cattle bones from the area generally showed that the wild cattle were big, but one group found near humans were small, I’d  buy it. This could easily be the remains of an extinct subspecies, or they were just selecting the biggest bulls they could find for some ritual purpose. And why were the cattle that came before smaller? the linguistic arguments (on original) were pretty thin too.

Case for the early domestication of African cattle… pretty thin, but not impossible. Maybe they could compare their DNA diversity to the other two kind to compare them!

The domestication of sheep,

An Anatolian wild sheep. Looks a lot like a goat.

Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events

Archaeological data suggest two different areas with independent sheep domestication events in Turkey: the upper Euphrates valley in eastern Turkey, where the most important reference is the Nevali Cori settlement, considered the oldest domestication site in the Near East and Central Anatolia (particularly, the Catal höyük and Asikli höyük sites.

 Archaeological data from Early Neolithic human settlements distant from one another throughout the Near East support the occurrence of independent domestication events in this area. The first region of importance, with the oldest human settlements in the Near East (Nevali Cori and Çayönü Tepesi), is dated about 8500 BC and located in the upper Euphrates valley in eastern Turkey, near the northern arc of the so-called Fertile Crescent . The Zagros region of modern day Iran and Iraq is also recognized as a primary centre of sheep domestication . In central Anatolia, the Asikli Höyük and Çatalhöyük sites have also revealed morphologically domestic caprines . Finally, the Southern Levant region of southern Syria, western Jordan and Israel has also been suggested as a centre of sheep domestication. Actually, the first two regions, the upper Euphrates valley and Zagros were proposed by  as the origin of two out of the three goat lineages, presumably rising from independent domestications.

On the basis of all this, the multiple sheep maternal lineages revealed in our study suggest that the process of sheep domestication was more complex than previously thought. Estimated divergence time, long before domestication dating (around 8000 BC), suggests that at least three independent domestication events were involved in the origin of modern domestic sheep.

So it seems sheep were domesticated in multiple locations.

The domestication of the goat, another first from Neolithic Turkey.

Science News,  Oct 14, 2006  by B. Bower

Present-day domestic goats may look humble, but they harbor more genetic diversity than any other livestock species. In fact, analyses of goats’ mitochondrial DNA have shown that these animals evolved through five distinct maternal lines that spread from the Near East and central Asia across Europe.

A new study indicates that goats representing the earliest two of the five genetic lines inhabited the same location in southwestern Europe by about 7,000 years ago, only 3,000 years after the initial domestication of the animals in the Near East.

This ancient genetic diversity in a region far from the goat strains’ origins reflects the long-distance transport of goats from the Near East by European pioneers soon after the origins of animal domestication, farming, and village life, say geneticist Pierre Taberlet of Joseph Fourier University in Grenoble, France, and his colleagues in an upcoming Proceedings of the National Academy of Sciences.

Today’s other three genetic lines arose later in parts of central Asia, Taberlet’s group proposes.

The scientists analyzed mitochondrial DNA retrieved from 19 goat bones found at an ancient farming site in southern France. Other researchers had excavated these fossils about 20 years ago in soil that contained the remains of more than 5,000 animals, including pigs, cattle, and sheep.

New radiocarbon measurements of five goat bones placed them at between 7,300 and 6,900 years old.

By extracting and analyzing genetic material from several goat bones, two independent laboratories confirmed that the sequences that Taberlet’s group examined were uncontaminated, ancient DNA.

Comparisons of the ancient goat mitochondrial DNA with sequences of modern goat DNA revealed that the two Near Eastern lineages had inhabited the prehistoric French site at the same time.

Taberlet and his colleagues suspect that early farmers transported each line of goats into Europe along a separate westward route, one inland and the other running along the Mediterranean Sea.

A preference for moving goats long distances in ancient times makes sense (SN: 5/12/01, p. 294). Goats are the hardiest livestock species. They’re easy to transport by land or boat, and they willingly follow people.

The new data convincingly show the domestication of two ancient goat lineages at the same time somewhere in the Fertile Crescent region, remarks archaeobiologist Melinda A. Zeder of the Smithsonian Institution’s National Museum of Natural History in Washington, D.C.

Genetic studies of modern domestic sheep have revealed a pattern similar to that of goats, with three to four ancient lineages, Zeder notes. “This suggests that both sheep and goats moved together, as they do today, in mixed herds as they diffused out of the Near East,” she says.

Also..

Archaeological data suggest two distinct places of domestication: the Euphrates river valley at Nevali Çori, Turkey (11,000 bp), and the Zagros Mountains of Iran at Ganj Dareh (10,000). Other possible sites of domestication include the Indus Basin in Pakistan at (Mehrgarh, 9,000 bp) and perhaps central Anatolia and the southern Levant.

And, a DNA study on goats.

Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas

Helena Fernández*, Sandrine Hughes,,, Jean-Denis Vigne¶, Daniel Helmer||, Greg Hodgins**, Christian Miquel*, Catherine Hänni,, Gordon Luikart*,, and Pierre Taberlet*,

Goats were among the first farm animals domesticated, 10,500 years ago, contributing to the rise of the “Neolithic revolution.” Previous genetic studies have revealed that contemporary domestic goats (Capra hircus) show far weaker intercontinental population structuring than other livestock species, suggesting that goats have been transported more extensively. However, the timing of these extensive movements in goats remains unknown. To address this question, we analyzed mtDNA sequences from 19 ancient goat bones (7,300–6,900 years old) from one of the earliest Neolithic sites in southwestern Europe. Phylogenetic analysis revealed that two highly divergent goat lineages coexisted in each of the two Early Neolithic layers of this site. This finding indicates that high mtDNA diversity was already present >7,000 years ago in European goats, far from their areas of initial domestication in the Near East. These results argue for substantial gene flow among goat populations dating back to the early neolithisation of Europe and for a dual domestication scenario in the Near East, with two independent but essentially contemporary origins (of both A and C domestic lineages) and several more remote and/or later origins.

The domestication of emmer wheat.

The domestication of emmer wheat (Triticum turgidum spp. dicoccoides, genomes BBAA) was one of the key events during the emergence of agriculture in southwestern Asia, and was a prerequisite for the evolution of durum and common wheat. Single- and multilocus genotypes based on restriction fragment length polymorphism at 131 loci were analyzed to describe the structure of populations of wild and domesticated emmer and to generate a picture of emmer domestication and its subsequent diffusion across Asia, Europe and Africa. Wild emmer consists of two populations, southern and northern, each further subdivided. Domesticated emmer mirrors the geographic subdivision of wild emmer into the northern and southern populations and also shows an additional structure in both regions. Gene flow between wild and domesticated emmer occurred across the entire area of wild emmer distribution. Emmer was likely domesticated in the Diyarbakir region in southeastern Turkey, which was followed by subsequent hybridization and introgression from wild to domesticated emmer in southern Levant. A less likely scenario is that emmer was domesticated independently in the Diyarbakir region and southern Levant, and the Levantine genepool was absorbed into the genepool of domesticated emmer diffusing from southeastern Turkey. Durum wheat is closely related to domesticated emmer in the eastern Mediterranean and likely originated there.
So, another Turkish origin for a neolithic founder crop. So far, the only non-Turkish wild progenitor crop seems to be barley (Israel/Jordan). I’m starting to doubt that ‘it all began in the Levant’. I’m thinking, mmm, you know, the evidence is way better for Turkey. Specifically, the Cayonu/Taurus mountains area in South East Turkey. This would make the nearest known neolithic settlement to the area of Emmer domestication Cayonu Tepesi.

The double domestication of barley.

According to this recent DNA study of barley, it was domesticated twice, once in Jordan/Israel, and once somewhere East of the Zagros mountains in Iran. The earliest known domestication of barley is about 4,000 years later than that of emmer wheat, and seems to have been a crop domesticated during the Neolithic farmers expansion, not before it.

Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent
December 21, 2006.
 
Cereal agriculture originated with the domestication of barley and early forms of wheat in the Fertile Crescent. There has long been speculation that barley was domesticated more than once. We use differences in haplotype frequency among geographic regions at multiple loci to infer at least two domestications of barley; one within the Fertile Crescent and a second 1,500–3,000 km farther east. The Fertile Crescent domestication contributed the majority of diversity in European and American cultivars, whereas the second domestication contributed most of the diversity in barley from Central Asia to the Far 

The domestication of barley is fundamental to understanding the origins and early diffusion of agrarian culture. Barley, as one of the earliest and most important crops in Neolithic agriculture (1), sits at the nexus of what many regard as the most fundamental technological transformation in human history. The oldest archaeological remains of domesticated barley and early forms of wheat are found in human Neolithic sites in the Fertile Crescent such as Abu Hureyra and Jericho (Fig. 1) and are dated to ≈8500 calibrated years BC


 Fig. 1.

The geographic distribution of sampled wild barley accessions and the locations of the human Neolithic sites mentioned in the text that contain early evidence of domesticated barley. The 25 wild barley accessions where all 18 loci were sequenced are indicated by filled circles. An additional 20 accessions (see Materials and Methods) were sequenced at four loci and are indicated by asterisks. Samples with majority assignment to the eastern cluster are shown in red, and samples with majority assignment to western cluster are shown in blue. The Neolithic sites indicated include Jericho (Palestine), Abu Hureyra (Syria), Jarmo (Iraq), Ali Kosh (Iran), Jeitun (Turkmenistan), and Mehrgarh (Pakistan).

For 2,000 years or more, barley along with einkorn and emmer wheat were the primary cereal crops (1). Unlike wheat and other Fertile Crescent founder crops, the natural range of wild barley, the progenitor of cultivated barley, extends east into Central Asia to present day Kyrgyzstan, Afghanistan, and western Pakistan (1). Barley has been continuously cultivated for >8,000 years in southern Central Asia, east of the Fertile Crescent, but it has never been clear whether barley was domesticated locally or imported along with other founder crops from the Fertile Crescent (5).

Domestication of food plants involved not only profound modifications of human societies but also genetic changes in wild plants as cultivated forms were selected. Perhaps the most essential domestication trait in barley, the presence of nonbrittle ears of grain, is controlled by two distinct genetic loci (6–9). In domesticated barley (with nonbrittle ears), grains remain attached to the upright stems where they can be readily harvested. The locus responsible for nonbrittle ears differs among landraces from eastern and western Asia, suggesting independent origins (10) and fueling decades of discussion among archaeologists and biologists as to the number of domestications of barley (5, 11–13). Zohary (13) identifies two types of genetic evidence likely to be informative as to the number and/or locations of domestication.

First, the specific allelic composition of domesticates is the result of subsampling populations of the wild progenitor (13). If the wild progenitor has marked differences in allele frequencies among geographic regions, i.e., when there is geographically based genetic differentiation, allelic composition is especially likely to be informative as to the number and locations of origin of domesticates. Allelic composition in barley could be very informative because in wild barley roughly half of sequenced loci exhibit significant differentiation among the eastern and western portion of the species range (14–18). Differences in allele frequencies among eastern and western landrace barleys have also been reported (14, 19, 20). For example, at three of four esterase loci examined by Kahler and Allard (20), Central Asian and Far East landraces had alleles at ≈20% or greater frequency, which were found at much lower frequencies in European landraces and in wild barley from Israel and Turkey. Although there has been criticism of the methods used (21), neighbor-joining clustering based on distance among amplified fragment length polymorphism genotypes lead Badr et al. (14) to conclude that cultivated barley had a single origin.

Zohary (13) also argues that independent domestications are likely to select for nonallelic mutations that govern the principal domestication-related traits (e.g., nonbrittle ears in cereals and the loss of germination inhibition). Distinct genetic loci governing the same domestication-related trait but found in different portions of the geographic range of a crop constitute strong evidence for multiple independent domestications (13). The genetic determination of three of the primary domestication-related traits in barley has been analyzed: (i) nonbrittle ears (22); (ii) “kernel row type,” which controls whether two or six rows of grains are produced (23–26); and (iii) the presence or absence of hulls around the grain (27, 28). Although the two genetic loci for nonbrittle ears are very closely linked (22, 29), haplotype data from a flanking marker is consistent with the earlier finding of Takahashi (6, 10) that different loci predominant in eastern and western cultivars (26, 30). The kernel row-type trait is also controlled by two separate genetic loci (24). The presence of hull-less grains is controlled by a single locus and appears to have had a single origin in domesticated barley, apparently somewhere east of the Fertile Crescent (27).

Wild barley offers an exceptional opportunity to detect multiple domestications because it has relatively high levels of nucleotide sequence diversity (15, 31, 32) and, more importantly, because loci sampled from different geographic regions often show marked differences in haplotype frequency (18). Ten of the 18 loci sampled by Morrell et al. (17, 18) show significant (P ≤ 0.05) geographic differentiation based on the nearest neighbor test (33) (Table 1). The most extreme geographic differentiation observed in wild barley is 2.2% per-site divergence among the major haplotypes from the Adh3 locus (15, 17); Dhn4 and G3pdh show similar per-site divergence among the major haplotypes in the eastern and western portions of the species range (17, 18).

Table 1.

Results of the nearest neighbor test (10,000 replicates) for geographic structure, Snn, at 18 wild barley loci

Locus Snn P value
Adh1 0.506 0.3061
Adh2 0.553 0.2082
Adh3 0.743 0.0070
α-amy1 0.505 0.1588
Cbf3 0.756 0.0007
Dhn1 0.576 0.1883
Dhn4 0.735 0.0032
Dhn5 0.625 0.0720
Dhn7 0.721 0.0107
Dhn9 0.725 0.0001
Faldh 0.733 0.0039
G3pdh 0.721 0.0051
ORF1 0.741 0.0000
5′Pepc 0.440 0.8258
Pepc 0.465 0.5735
Stk 0.673 0.0268
Vrn1 0.472 0.5104
Waxy 0.658 0.0447
The sample is divided among eastern and western clusters based on assignment testing.
Proc Natl Acad Sci U S A. 2007 February 27; 104(9): 3289–3294.
Published online 2007 February 21. doi: 10.1073/pnas.0611377104.

 

 

 

 Geographic patterns of genetic differentiation are associated with the major topographic feature within the range of wild barley, namely the Zagros Mountains (Fig. 1), that trend northwest to southeast and roughly bisect the range of the species. The Zagros also delineate the eastern edge of the Fertile Crescent; thus, the most dramatic differences in haplotype composition in wild barley occur between the Fertile Crescent and the portion of the range east of the Zagros (17). Differences in haplotype frequencies among regions also suggest that human activity, including transportation of cultivated barley among regions, has not homogenized genetic diversity across the range of the wild progenitor.

We have resequenced seven loci that show significant geographic structure in wild barley (Table 2) (18) in a sample of 32 cultivated barleys, the majority of which are landraces used in traditional agriculture [Fig. 2; see also supporting information (SI) Table 3]. The data set includes 196 SNPs from cultivated barley. The correspondence of haplotypes observed in cultivated and wild barleys can be used to estimate the probability that a landrace is derived from one or more portions of the range of the progenitor. Thus, we ask whether the haplotypic composition of landraces is concordant with that of wild barley from the same region.

Table 2.

Seven loci sequenced in both wild and cultivated barley

Locus Aligned length, bp Parsimony-informative SNPs
Cbf3 1,515 23
Dhn4 1,074 31
Dhn9 1,013 12
Faldh 1,094 17
G3pdh 2,011 45
ORF1 1,533 23
Stk 1,057 20
Averages 1,328.1 23.71
The aligned length and number of observed parsimony-informative SNPs (SNP observed at least twice) in wild samples are reported for each locus.
Proc Natl Acad Sci U S A. 2007 February 27; 104(9): 3289–3294.
Published online 2007 February 21. doi: 10.1073/pnas.0611377104.

 

 

 

 Fig. 2.
The geographic distribution of sampled barley landraces. The estimated probabilities of eastern and western wild barley origin for each sample are shown in red and blue, respectively. A landrace sample from Peru is not depicted. 

To identify geographic discontinuities in genetic diversity in wild barley, we used resequencing data from 18 loci and 25 accessions that included a total of 684 SNPs (Fig. 1 and Table 1). A genetic assignment algorithm (34) was applied to the data with K = 2–4 clusters, without using prior information on geographic origin. The model-based algorithm identifies up to K clusters (where K may be unknown), each of which is characterized by distinct allele frequencies at each locus. With K = 2 clusters, the sample is split between the eastern and western portions of the species range, with the transition between predominantly eastern and western assignment occurring among accessions from the northern Zagros Mountains. However, samples from the northeastern extreme of the range cluster partially with western samples. With K = 3 or 4, northeastern samples are differentiated from both western and other eastern samples. This observation is consistent with haplotype composition; northeastern samples carry many private alleles, or haplotype segments, not sampled elsewhere.

Comparison of the percentage of alleles shared among samples to great circle geographic distance also reflects a change in allelic composition between the eastern and western clusters. In SI Fig. 4A, samples are compared both within and between eastern and western clusters. A group of highly differentiated pairs of samples occurs at ≈1,100 km, between accessions from the Mediterranean coast and the Zagros region, reflecting a change in allelic composition (Fig. 1 and SI Fig. 4A). A very similar pattern is also evident in wild barley based on the seven loci also sequenced in barley landraces (SI Fig. 4B) (discussed below).

For STRUCTURE analysis, the data must be treated as unique alleles. Each of the loci was broken into alleles (haplotype segments) based on direct evidence of recombination (see Materials and Methods). Among the 61 haplotype segments from the 18 loci, there are 329 total alleles, 182 of which are private to either eastern of western wild barley. Of these alleles, 40 occur at a frequency of ≥22% within one of the two partitions of the sample. Eighteen of these alleles are private to the eastern cluster, and 22 are private to the western. If the species-wide frequency of an allele is ≥22%, there is >95% probability that the allele would be sampled in accessions from both the eastern and western cluster.

Levels of nucleotide sequence diversity among the eastern and western cluster are similar, with average θπ for all sites over all 18 loci of 0.00579 for eastern wild barley and 0.00597 for western wild barley.

Taken together, these results suggest that the clusters of wild samples identified in STRUCTURE analysis result from long-standing differences in allelic composition in populations east and west of the Zagros Mountains rather than recent demographic events (e.g., a bottleneck associated with recent founding of eastern populations).

Given that the primary geographic structure in wild barley differentiates western wild barley (from the Fertile Crescent) from eastern wild barley (from the Zagros and further east) we used STRUCTURE to estimate the probability of assignment for each cultivated barley accession to either of these two regions. We found that landrace accessions from east or west of the Zagros have very different probabilities of assignment to the western wild barley cluster (from the Fertile Crescent region). The median probability of assignment for western landraces is 99.4%, with a range of 62.2–99.8% (Fig. 2 and SI Fig. 5). Eastern landraces have a median probability of assignment to the western cluster of only 33.6%, with a range from 0.2% to 78.8%. Three-quarters of eastern landraces have <50% assignment to the western wild barley cluster. Accessions from the Zagros Mountains and Caspian Sea region show the lowest probability of origin in the Fertile Crescent (Fig. 2 and SI Fig. 5). Changes in specification of the data model in STRUCTURE (see Materials and Methods) do not change the primary assignment of individual landrace accessions but do result in less discreet clustering.

As was the case in wild barley, comparison of the percentage of shared alleles with geographic distance within versus between eastern and western landraces indicate differentiation among geographic regions (SI Fig. 6).

At six of the seven loci sequenced in the landrace samples (all but Dhn4), haplotypes that were found exclusively in eastern wild samples also were found to be present in eastern landraces (see SI Fig. 7). The haplotypes include 10 SNPs found only in eastern wild barley and eastern landraces.

These lines of evidence strongly suggest an independent domestication of barley outside the Fertile Crescent. All landrace accessions from east of the Zagros, across Asia to North Korea, have substantial identity to eastern wild barleys (Fig. 2 and SI Fig. 5), with assignment probabilities suggesting a mix of eastern and western origin. These data suggest that eastern landraces have been subject to admixture from imported, western landraces. Archaeological evidence indicates extensive introduction of other Fertile Crescent founder crops into central and southern Asia; for example, einkorn wheat was introduced by ≈6,000 B.C. (4, 5, 11). Thus, it would be surprising if western barley landraces had not been imported along with other domesticates. Introgression with western domesticated barley is likely to have been ongoing; Ordon et al. (19) report high levels of similarity between Japanese barley bred for malting quality and European cultivars.

Which geographic regions have contributed to modern cultivars? To address this question we considered 10 modern cultivars and three barley genetic stocks from North America and Europe. The cultivars have a median 89.7% probability of assignment to the western wild cluster, consistent with the introduction of barley into Europe and ultimately North America from the Fertile Crescent region (Fig. 3) (35). However, two U.S. cultivars and one line of the genetic stocks have <50% probability of assignment to the western cluster, probably because modern barley breeding programs have introduced genetic material from eastern wild barley in the quest to exploit novel germplasm (36). More generally, assignment tests indicate that wild barley from the Fertile Crescent contributed the majority of genetic diversity in present-day European and American cultivars, whereas wild barley from Central Asia contributed half or more of the genetic diversity in barley cultivated from Central Asia to the Far East.

 Fig. 3.
Assignment of cultivated barley samples and barley genetic stocks relative to the eastern and western wild barley clusters. Each column represents a single individual, with the probability of assignment to eastern wild barley shown in red and the probability (more …)

Where could a second barley domestication have occurred? The relatively broad, species-wide sample mesh in the present study suggests an origin of eastern landraces in the western foothills of the Zagros or points farther east. Much of the region immediately east of the Zagros is a high-elevation plateau, where both wild barley populations (4) and known human Neolithic sites are relatively rare (5). However, the locations of early Neolithic agropastoral settlements suggest three general regions in which the secondary domestication could have taken place. In the foothills of the Zagros, at such sites as Ali Kosh and Jarmo (Fig. 1), domesticated barley is dated to ≈7,000–8,000 cal. B.C. Domesticated barley is found at the Indus Valley site of Mehrgarh (in present day Pakistan) from ≈7,000 cal. B.C. Finally, in the piedmont zone between the Kopet Dag mountain range and Kara Kum Desert (east of the Caspian Sea in present day Turkmenistan), cultivated barley was present by ≈6,000 cal. B.C. (see ref. 37). Both naked and hulled six-row barleys were cultivated at Mehrgarh and by the Jeitun culture (in the Caspian Sea region) (5). Mehrgarh lies near the eastern edge of the range of wild barley (1); thus, it is possible that barley found at Mehrgarh was domesticated locally. At Jeitun in southern Turkmenistan (the type site of the Jeitun Culture on the Kopet Dag piedmont), domesticated forms of (probably six-row) barley and einkorn wheat (Triticum monococcum) were being cultivated, and domesticated goats and sheep were being herded, by 6,000 cal. B.C., indicating the presence of a well developed agrarian society (5, 37).

Sample size in the present study limits our ability to compare haplotype composition in various portions of the eastern range of wild barley with that of eastern landraces. However, among the haplotype segments (from six loci) most indicative of eastern origin, i.e., those shared by eastern landraces and eastern wild barley but not sampled in western wild barleys, all but one were found in wild barleys from east of the Caspian Sea, and five segments were exclusive to that region; only one of the 11 segments was sampled only in the western Zagros. Based on a combination of archaeological and genetic data, the most likely location for a second origin of barley is ≈1,500–3,000 km east of sites in the Fertile Crescent where western barley is most likely to have been domesticated.

Evidence for two domestications must be weighed against the alternative, a single domestication in the Fertile Crescent followed by extensive introgression (14). Introgression from Central Asian wild barley into landraces imported from the Fertile Crescent would be necessary because wild barley samples from the Fertile Crescent do not carry all of the haplotype diversity found in eastern landraces. Expanding agrarian cultures could have imported landraces from the Fertile Crescent to Central Asia (5), where introgression with wild barley occurred (14).

There are two principal problems with this scenario (a single domestication followed by introgression). First, in what was perhaps 2,000 or more years before agrarian culture expanded into Central Asia, cultivated barley was subject to human selection for agronomically desirable polygenic traits, such as seed size and loss of seed dormancy (12, 38). After hybridization between wild and landrace barley, repeated back-crossing to the recurrent parent (imported landraces) would be necessary to recover agronomically important traits, diminishing the potential genetic contribution of the donor parent (eastern wild barley). The second issue is that a single domestication cannot explain the two independent origins of the domestication-related traits, nonbrittle ears and kernel row type. As Zohary (13) points out, the fixation of independent mutations at nonallelic, nonbrittle ear loci in cultivated barley is strongly suggestive of at least two domestications. With the addition of multilocus haplotype data demonstrating a strong geographic discontinuity in the probable wild founder populations of barley landraces, both of Zohary’s criteria for identifying multiple domestications are satisfied.

Modern analytical methods, combined with high-throughput DNA sequencing at multiple informative loci permit a clearer view of historical events associated with domestication of a major founder crop and reveal at least two initial domestications at the dawn of agriculture. Because both wild and domesticated barleys maintain high levels of informative nucleotide sequence diversity (31), it is probable that more intensive sampling from an appropriate geographic mesh can provide a finer scale view of the history of domestication.
 

References and Data Collection. Seeds of wild and cultivated barley landraces and cultivars were obtained from the U.S. Department of Agriculture, Agricultural Research Service, National Small Grains Collection (Aberdeen, ID). Sampled wild barleys were included in previous studies (e.g., refs. 16, 31, and 39). Seeds for U.S. and Canadian cultivated barleys and genetic stocks were provided by the laboratories of Timothy Close (University of California, Riverside) or Patrick Hayes (University of Oregon, Eugene). Sampled accessions were drawn from across the natural geographic and cultivated range of the species, with a special emphasis on landrace barleys from regions that archaeological evidence suggests were early sites for barley cultivation (see SI Table 3). Leaf material from individual plants was harvested, and DNA was extracted by using DNAzol ES (Molecular Research Center, Cincinnati, OH) according to the instructions of the manufacturer.

Seven loci (Table 1) were completely resequenced in a panel of 32 cultivated barleys (SI Table 3). Nineteen of the accessions are listed by the U.S. Department of Agriculture GRIN (The Germplasm Resources Information Network) database as landraces. Sampled landraces are primarily from western and central Asia, with one sample each from Africa, Europe, and South America (see SI Table 3 for the country and geographic locality of origin of each accession). The balance of the sample includes 10 modern cultivars and three North American genetic stocks. The modern cultivars include one each from Scotland and Poland and eight from the U.S. and Canada.

For three loci, Cbf3, Dhn9, and ORF1, additional wild accessions were resequenced, resulting in sample sizes of 52, 45, and 47.

PCR amplification, sequencing, and fragment assembly follow the methods of Morrell et al. (17), i.e., direct sequencing of PCR products using Big Dye V. 3.1 (Applied Biosystems, Foster City, CA) followed by assembly of sequence fragments with PHRED/PHRAP/CONSED (40–42). POLYPHRED V. 5.04 was used for polymorphism detection (43). For the Cbf3 locus, sequence from five wild accessions were computationally phased by using PHASE V. 2.1 (44–46). Error detection using triplets of SNPs (ref. 38 and D. M. Toleno, P.L.M., and M.T.C., unpublished data) was used to confirm the accuracy of haplotypes at all loci.
Data Analysis. Tests for geographic structure at individual loci (Table 1) used the nearest neighbor test (33) as implemented in LIBSEQUENCE (47). Diversity statistics for haplotype segments were calculated with GDA 1.1 (48). The haplotype diagrams in SI Fig. 7 where generated by using SNAP MAP (49). Great circle distance among samples (SI Figs. 4 and 6) was calculated by using the FIELDS package in the R statistical language and programming environment. Unless specified, all other analyses used custom scripts written in R.

To estimate the probability that individual cultivated barley accessions derive from wild barley either within or outside the Fertile Crescent, we used a model-based genetic assignment algorithm implemented in the computer program STRUCTURE V. 2.1 (34, 50). As in previous studies employing resequencing data (51), we have recoded haplotypes as unique alleles, as required by the STRUCTURE data model. Portions of each locus that have a partially independent genealogical history, as indicated by the presence of a detectable recombination event (52), are treated as individual haplotype segments. All parsimony-informative (nonsingleton) mutations were used to define haplotype segments.

A STRUCTURE analysis, based on 61 haplotype segments from the 18 loci previously surveyed in wild barley (31), was used to assign each wild barley individual to a cluster of origin without using prior information as to the geographic origin of individual samples. Assignment of cultivated barleys was based on data from seven loci that showed geographic structure (Table 1) and were highly informative for assignment (53) (SI Table 4) into the two groups defined by all 18 loci.

We explored several options in STRUCTURE, with initial analyses based on a minimal set of assumptions regarding the data. The initial setup used a model with uncorrelated allele frequencies among populations with no admixture; sampled segments were treated as unlinked, and the geographic location of origin was not used to assist clustering. This setup reflects prior data from wild barley populations suggesting that major portions of the range of wild barley have large differences in haplotype frequency (18) with moderate levels of gene flow (17) but no evidence of recent population admixture.

The probability of assignment of domesticated barleys to eastern or western clusters was inferred with K = 2; allele frequencies were estimated with wild barley treated as a learning sample. In this analysis, geographic population of origin was used to cluster wild barleys but not used for domesticates. Cultivated barleys have a known collection location, but their probability of derivation from various portions of the range or their wild progenitor is unknown and inferred based on allele frequencies in the wild barley learning sample. Ten replicate runs of STRUCTURE were carried out, with 100,000 replicates for burn-in and 200,000 replicates during analysis. Reported probabilities of assignment are based on the run with the highest likelihood.

To explore variation in assignment due to model specification, the panel of wild individuals was resampled with replacement to create 20 test samples from both the eastern and western cluster and 20 samples with the allele at each locus drawn randomly and with equal probability from either cluster. Multiple replicate searches were used to explore the impact of model specification on assignment of these test samples where the genetic contribution of each source population is known. Data models tested included a linkage model that accounts for the use of adjacent chromosomal segments (this must be specified along with an admixture model) and with map distances among segments based on the midpoint distance in kilobases. We also explored combinations of models with or without correlated allele frequencies, admixture, and the use of location of origin for wild barley samples to assist clustering. Test samples were clustered with wild barley as a learning sample. The addition of admixture, correlated allele frequencies, and the linkage model resulted in lower probabilities of assignment of test samples to their known population of origin and increased variance of assignment in all test samples. Using prior information on population of origin for wild samples resulted in higher probability of assignment of test samples to their population of origin.
 

The double domestication of rice.

Biologists from Washington University in St. Louis and their collaborators from Taiwan have examined the DNA sequence family trees of rice varieties and have determined that the crop was domesticated independently at least twice in various Asian locales.

Jason Londo, Washington University in Arts & Sciences biology doctoral candidate, and his adviser, Barbara A. Schaal, Ph.D., Washington University Spencer T. Olin Professor of Biology in Arts & Sciences, ran genetic tests of more than 300 types of rice, including both wild and domesticated, and found genetic markers that reveal the two major rice types grown today were first grown by humans in India and Myanmar and Thailand (Oryza sativa indica) and in areas in southern China (Oryza sativa japonica).

A paper describing the research was published June 9, 2006, in the on-line issue of the Proceedings of the U.S. National Academy of Science.

“We look where the genetic signature of clusters on a haplotype tree (family tree),” explained Londo. “We chose samples across the entire range of rice and looked for DNA sequences that were shared by both wild and domesticated types. These two major groups clustered out by geography.”

DNA is comprised of vast, varied combinations of chemical subunits known as base pairs. Londo, Schaal and their collaborators concentrated on finding genetic markers shared by both cultivated and wild rice types that ranged from 800 to 1,300 base pairs.

Cultivated rice has a genetic signature that defines it as cultivated, Schaal explained.

“What you do is go out and sample all the wild rice across regions and you look for that signature in the wild,” said Schaal, who has done similar work with cassava and jocote, a tropical fruit. “You find that the unique signature of cultivated rice is only found in certain geographic regions. And that’s how you make the determination of where it came from.”

Great site for a more in depth picture.

So far, the oldest domesticated rice grains have been found in Korea, at about 15,000 years old. The earliest found in China appear to be about 13,000 years old.

 

 

The Turkish/Northern Syrian origin of lentils.

Identification of the lentil’s wild genetic stock

  The origin of lentil from the taxon Lens culinaris subsp. orientalis has been proved by morphological evidence and breeding experiments. This wild form exhibits variation in many characters and is distributed over a vast area from the Middle-East to central Asia. Characters that are polymorphic in the wild progenitor but monomorphic in the cultigen can be utilized for better identification of the genetic stock which gave rise to the domesticated lentil. Three characters of that kind have been identified in lentil: chromosomal architecture, crossability potential and restriction pattern of chloroplast DNA. Nearly all accessions of the cultivated lentil tested to these three characters have been found monomorphic, but considerable polymorphism exists in the wild accessions. Three subsp. orientalis accessions have been shown to share the above characters with the cultigen and hence can be regarded as members of the genetic stock from which lentil was domesticated. These three accessions originated from eastern Turkey and northern Syria.

Also, the oldest lentils found were 11,000 years old from a Greek cave. Since the lentil is not native to Greece, it’s not a stretch to figure out these must have been cultivated. This would mean the growing of lentils predates cereals in Greece, meaning farming started earlier than believed in Europe (by about two thousand years) and that cultivation of lentils predates the cultivation of cereals.

Hallan Cemi Tepe, home of the first pork chop

Some Preliminary Observations Concerning Early Neolithic Subsistence Behaviors in Eastern Anatolia

Michael Hosenberg, .Clark Nesbitt, Richard K Redding, Thornas F Strasser

In 1991 a salvage excavation was begun at Hallan Cemi Tepesi, a largely aceramic (so some pottery) site in the Taurus foothills of eastern Turkey.’ The results of the 1991 through 1993 field seasons permitted some preliminary observations concerning the material culture of the site’s early Neolithic inhabitants. Of particular note was the relatively high degree of cultural complexity implied by that material culture (see Rosenberg and Davis 1992; Rosenberg 1994). Also of note was the evidence suggesting that, at its earliest stages, the Neolithic tradition in eastern Anatolia evolved with only minimal influence from the contemporaneous Levantine complex.

Excavations at Hallan Cemiare ongoing and the results of the 1994 field season make it necessary to once again modify some of the tentative conclusions concerning the site’s stratigraphy. More importantly, the ongoing analyses of the botanical and fauna1 remains, as well as of relevant aspects of the artifact assemblage, now make it possible to begin making some preliminary observations about the subsistence behaviors of the site’s inhabitants. The picture that is emerging from these ongoing analyses is often at odds with prior expectations. For example, though sedentism is indicated, it was apparently not based on the exploitation of cereals. The site’s inhabitants also appear to have been experimenting with animal domestication. In all. the Hallan Cemi data promise to significantly alter our understanding of the origins of food production and animal husbandry in south-western Asia.
The Botanical Assemblage Carbonized plant remains are consistently well preserved in the Hallan Cemi depos- its. Collection was largely by means of flotation involvinga sample of the site’s deposits, though individual seeds, nuts, etc. were also collected by hand in some instances. What follows is for the most part based on the formal analysis of a limited number of flotation samples from the 1992 season  as well as more preliminary analysis of samples from other contexts. Analysis of the sample balance is ongoing.

In the samples analyzed to date, relatively few seeds of wild grasses were found and most were in fragmentary condition. None have yet been identified as belongingto the cereal grasses. Compared to other sites of this period in Iraq and the Levant, this relative paucity of wild grasses is surprising It is, however, consistent with the dearth of sickle blades in the Hallan Cerni chipped stone assemblage (Rosenberg 1994: 128).

In contrast, pulses are common. They are mostly fragmentary and thus cannot be identified beyond I Viciailarlgrzis. However, identifiable examples of both lentils (Lens sp.) and bitter vetch (l’icia enilia) were found. Nuts are also common. These include wild almond (Anq@alussp.), pistachio (Pisracia S-.) and another thin-walled nut that remains to be identified. During both the 1993 and 1994 seasons, deposits in several parts of the mound yielded concentrations of wild almond (Fig. 5). Wild almonds contain potential toxins, yet almonds were clearly of great economic importance at Hallan Cemi despite that latent toxicity. This suggests the existenc eof processes for mitigating that latent toxicity and rendering almonds into an edible product. Judgingfrom the concentrations of charred almonds encountered in 1993 and 1994, roasting seems to have played a part in the processing of almonds.

It is also perhaps noteworthy that small, shallow sand and gravel pits occur scattered about the site. Though it is not clear whether these shallow pits were used for food preparation and, if so, for what foods, it is conceivable that these sand pits also played a role in the processingof almonds. Also common in the botanical assemblage are the seeds of sea club-rush (Bolboschoems ntaririnzus), a species of Po&gonzim, and Gundelia tournefortii. The presence of Guidelia totirizefortii is particularly interesting, as it is not often reported to be found at sites of this period. Gztndelia is a perennial tumbleweed belonging to the daisy family (Composirae). Though typically native to steppe habitats, it does occur in open woodland, such as appears to have then existed in the vicinity of Hallan e m i .The fruit consists of a woody and fibrous capitulum enclosing a single waxy achene (weight ca. 0.03 gm) in the single fertile floret at the center of the capitulum. The achene, as its waxy appearance suggests, is rich in fatty oils.

‘ According to Rouena Gale, who graciously provided these data, Fraxinus, Quercus, Prunus, Pistacia, and Salix or Popuftrs are represented in the wood charcoal from the site. Questionably, buckthorn (cf. Frangula alnus) is also present. The SalidPopults charcoal probably indicates the proximity of riverine forests to the site, ivhilc the olhrr specics are consistent \vith a mixed oak forest. 

 Collectingthe fruit simply involves shaking the plant upside down, as this causes the fruits to drop out. The achene, however, is tightly enclosed at the base of the capitulum and cannot be extracted without breaking open the fruit. One widely used method for extract- ing fat-rich seeds from tough shells in nuts is roasting. It is, therefore, noteworthy that, in addition to being found as scattered single fruits, a 5 cm thick lens, consisting of hundreds of more or less intact charred Grtndelia fruits, was found in the central open area. Perhaps a batch was being roasted and, for whatever reason, the fruits were burnt too completely for consumption of the seed, resulting in them being discarded as a unit.

The Fauna1 Assemblage

Animal exploitation was an important subsistence activity at Hallan Cemi, as attested to by the more than 2 tons of animal bone thus far unearthed. Of the 22,000+ bones (in- cluding small fragments) examined to date, 2,097 could be assigned to mammalian taxa and 91 1 to non-mammalian taxa. The bones and horn cores of sheep (Ovis sp.) and goats (Capm sp.) are the single most numerous mammalian component of the fauna1 assem- blage, comprising ca. 43% of all mammalian bone. Sheep outnumber goats at approxi- mately 6: 1. Red deer (Cervus elephlrs) follow at ca. 27% of all mammalian bone, followed in turn by canids (including two species of fox – L’zrlpes vrrlpes and Ciirlpes corsac – and either dog or jackal) at ca. 13%, pig (Sus sp.) at ca. 12%, brown bear (Ursus arclos) at ca. 3%, cape hare (Lepus capensis) at 2%. Stone marten (Martesjiona), wild cat (Fefis catzrs), beaver (Castor jiber), and European hedgehog (Erinacerrs ezrropaeus) also occur, but at less than 1% each. The remains of wild cattle (Bos primigenizrs) were not present in the samples analyzed so far, but are known to be present at the site (see Rosenberg 1994:Fig. 10). Non-mammalian taxa include two types of fish (catfish and a species of cyprinid), lizards, turtles of the genus Marrremjs and birds. Of these, turtle bones are by far the most numerous at 84% of the non-mammalian bone, followed by bird (10%), fish (6%), and lizard.

 Morphologically, the sheep and goats are wild. Moreover, approximately 66% of the sheep-goat remains (for which an age could be determined) come from individuals that survived to at least 42 months of age. This is a pattern consistent with the results of the hunting of a wild population (cf. Hesse 1982).

 In the case of pigs, the sample analyzed to date contains two measurable lower third molars and one measurable upper second molar. The two lower third molars measure 38.4 and 40.0 mm in length, which places them in the area of overlap between wild and domes- tic taxa. The upper second molar, however, measures 21.8 mm in length, within the range for domestic pig (cf. Flannery 1982). While this sample is obviously small, other lines of evidence are consistent with incipient pig domestication. The survivorship curve for pigs is in marked contrast to that for sheep-goats (Fig. 6). At least 10% of the individuals were less than 6 months of age when consumed, 29% never reached the age of 12 months, and only 3 1% survived to the age of 36 months. This pattern of consumption is similar to that found by one of the authors (Redding) at sites in Egypt, Iraq, and the Levant that yielded domestic pigs.

The present day economic importance of sheep and goats in the Near East has tended to foster the implicit presumption that they were the earliest animal domesticates in that area. However, the possible early domestication of pigs is not surprising when one considers certain facts. As Redding (n.d.) has noted: 1) the fecundity and growth rate of pigs make them superior producers of protein relative to all other native Near Eastern domesticates; 2) the labor required for pig maintenance is lower than for other Near Eastern domesticates; 3) young pigs tame readily and will imprint on humans; and, 4) juvenile or neonate pigs are relatiely easy to obtain. These qualities make the pig an ideal candidate for early experiments with animal domestication.

However, as also noted, pigs are more difficult to control or herd than sheep or goats. This makes pigs a poor choice of domesticate (relative to sheep and goats) in situations where intensified production of animals is desired. Pigs are also competitors with humans for cereals. This makes pigs a poor choice of domesticate (relative to sheep and goats) in contexts where cereal Ygrass exploitation is a significant component of the human subsis- tenceeconomy. However, in situationswhere, for whatever reason, cereals were not a significant component of the human subsistence economy (as was apparently the case at Hallan Cemi), pigs would seem superior to sheep and goats at the early stages of animal domestication.

Lastly, it should be noted that domesticated pigs are present at Cayonii(Lawrence 1980) and pigs, in general, are particularly common (relative to sheep and goats) in the lower levels of that site (Lawrence 1982). Whether domesticated pigs precede domesti cated sheep and goats at that site is not made clear in the published reports.

The Ground Stone Assemblage

Ground stone tools of types generally thought to be subsistencerelated constitute the next largest tools artifact assemblage after chipped stone tools. Sandstone of varying types appears to have been the most commonly used raw material for both mobile (i e., hand stones, pestles) and stationary (i.e., querns, mortars) types. Limestone and various kinds of metamorphic rocks were also used. While much of this assemblageremains to be analyzed in detail, it is now possible to make some preliminary observationsabout the assemblage as a whole.

The handstonesare typically ovate to sub-rectangular in form – having often been purposehlly ground or pecked to shape – with either one or two flat to slightly convex workingsurfaces. They rarely exceed 15 cm on the longest dimension. In many cases, one or both of the horizontal surfaces were reused as what are sometimes informally called ‘nuttingstones’.’ Such ‘nuttingstones’ also occur on simple water-worn pebbles and stones ‘ As a rule ‘nutting stones’ are characterized by relatively small, very shallow, irregularly circular deprcssi- ons produced by batteringthat appear to have been shaped into a variety of configurations. Pestles are less common than handstones.

 They are typically cylindrical to slightly conical in form and circular to slightly squared in section. They rarely exceed 30 cm in length and are usually less well shaped than are the handstones. The querns are of both trough and basin type and range up to 50+ cm in overall length on the intact examples. The exteriors of these are also often pecked or ground to shape, with ovate and sub-rectangular forms the most common (Fig. 7). Bowl mortars are less common than querns and they range up to almost 20 cm in depth. The most common forms are ovate and sub-rectangular/squared, but the evidence for purposehlexterior shaping is less clear than for the querns.

 It has been suggested (Moore 1985; Goring-Morris 1987) that a prevalence of quernsover mortars in an assemblage implies an emphasis on the exploitation of seeds, as op- posed to nuts. Though Wright (1994:241) notes that the ethnographic record provides cause to question such a strict correlation, she does go on to note (1994:242-243) that grinding (as opposed to pounding) is most beneficial in the processing of cereals. In view of the preliminary botanical evidence (see above) suggesting that at Hallan Cemi grasses played a smaller dietary role than did nuts and pulses, the higher frequency of quernsover mortars in the ground stone assemblage is puzzling.

 Lastly, it was earlier suggested (Rosenberg and Davis 1992) that many of the querns and mortars were purposehllyrendered useless through intentional perforation of the bottoms. At that time, this conclusion was based solely on the fact that the perforationswere very often relatively large and that their edges were thick and not convergent with the base (see Fig. 7). This conclusion has now been supported by two new lines of evidence. First, during the 1994 season, we recognized for the first time four intact bases that had been punched out of stationary grinding stones by a (presumably) heavy blow to the interior working surface. Second, during the 1994 season, several (intact) perforated grindingstones were found that had apparently been spirally scored near the base of the interior surface. Such scoring would no doubt facilitate breakage and may have been carried out for precisely that purpose. No unperforated grinding stones exhibit this scarring. Why these grinding stones were intentionally rendered useless remains unknown. However, destruction associated with human death is an obvious, albeit untestable, possibility that is brought  to mind by a similar destruction pattern for prehistoric Mimbres ceramic vessels in the American southwest (e.g., see Fiedel 1987:213).

Concluding Comments

The subsistencepatterns emerging from the Hallan Cemidata are significant for two reasons. First, they are the first clear indication that we have for the existence of subsis- tence systems in southwestern Asia that did not revolve around reliance on the exploitation of grasses. Hallan Cemiwas, nevertheless, occupied year-round. This would appear to challenge theories that place cereal grass exploitation at the center of explanations (e.g., cr cdri Henry 1989) for the increased sedentism we see in southwestern Asia at the end of the Pleistocene. Second, the Hallan Cemi data suggest that pigs were the earliest animal domesticate, at least in eastern Anatolia. The data from Cayonii have long obliquely hinted at this. However, the consistently greater economic importance of ovicaprids in southwestern Asia aceramic sites has tended to foster the presumption that the earliest attempts at animal domestication would focus on these economically more important animals. The fauna1 data from Hallan Cemi are consistent with the data from these other sites, in that ovicapridswere here too much more intensively exploited than were pigs. It would appear, though, that factors other than economic importance (see above) were paramount in the selection of the earliest food animal domesticate. It is perhaps only with subsequent changes in plant food subsistence (to the exploitation of grasses), or the subsequent need to further intensify food animal production, that the knowledge gained in working with pigs was applied to ovicaprids.

 

The appalling spelling, the authors, not mine!

So, it looks like lentils preceded grains. Were these grains domesticated or wild?