New Archaeozoological Data from the Fayum “Neolithic” with a Critical Assessment of the Evidence for Early Stock Keeping in Egypt

Faunal evidence from the Fayum Neolithic is often cited in the framework of early stock keeping in Egypt. However, the data suffer from a number of problems. In the present paper, large faunal datasets from new excavations at Kom K and Kom W (4850–4250 BC) are presented. They clearly show that, despite the presence of domesticates, fish predominate in the animal bone assemblages. In this sense, there is continuity with the earlier Holocene occupation from the Fayum, starting ca. 7350 BC. Domesticated plants and animals appear first from approximately 5400 BC. The earliest possible evidence for domesticates in Egypt are the very controversial domesticated cattle from the 9^th/8^th millennium BC in the Nabta Playa-Bir Kiseiba area. The earliest domesticates found elsewhere in Egypt date to the 6^th millennium BC. The numbers of bones are generally extremely low at this point in time and only caprines are present. From the 5^th millennium BC, the numbers of sites with domesticates dramatically increase, more species are also involved and they are usually represented by significant quantities of bones. The data from the Fayum reflect this two phase development, with very limited evidence for domesticates in the 6^th millennium BC and more abundant and clearer indications in the 5^th millennium BC. Any modelling of early food production in Egypt suffers from poor amounts of data, bias due to differential preservation and visibility of sites and archaeological remains, and a lack of direct dates for domesticates. In general, however, the evidence for early stock keeping and accompanying archaeological features shows large regional variation and seems to be mainly dependent on local environmental conditions. The large numbers of fish at Kom K and Kom W reflect the proximity of Lake Qarun.     

The Origins of Domesticated Cattle

The origin of domestic cattle has perplexed archaeologists for more than a century. Researchers have proposed various theories, which offer alternative spatial and chronological models for the origin and spread of domesticated cattle. One point of discussion is whether domestic cattle had a single or multiple origins; however, most authorities considered that the first steps towards cattle domestication were taken in southwest Asia and that domesticated cattle entered Europe with pastoralists migrating from this region. Domesticated taurine cattle were thought to have entered Africa in successive waves from southwest Asia, while zebu cattle migrated into Africa at a later date from Arabia and the Indian subcontinent. Analysis of mitochondrial DNA (mtDNA) shows that taurine and zebu cattle divergence before the Holocene and were probably domesticated independently. Recent mtDNA sequence data shows that African and European taurine cattle were probably domesticated independently, but that there was a process of genetic introgression between taurine and zebu cattle in Africa. Ancient DNA studies over the last 10 years suggest that Northern European aurochsens apparently contributed little or nothing to domestic cattle while Southern European aurochsens apparently made a significant input. However, Middle Eastern aurochsen, unfortunately not typed yet, are expected to be to be very similar to European breeds as well, both because archeological data suggest that the major center of domestication for European Bos taurus breeds was the Fertile Crescent (9), and also because a mtDNA sequence from a Syrian specimen dated at 8,000–9,000 years ago shows a typical European haplotype found both in modern breeds and the Italian aurochsen. Evidence seems to suggest that small to moderate levels of local gene flow from wild Bos primigenius females in selected breeds were either accepted or may be reinforced by Neolithic breeders.     

Reproductive isolation between wild and domesticated chaya (Cnidoscolus aconitifolius) in sympatry

• Reproductive isolation is a necessary condition for plant domestication in their domestication centre where crops co‐occur with their wild progenitors. However, the identification of reproductive barriers and their relative contribution to reproductive isolation have been overlooked in plants under domestication.
• We assessed pre‐ and post‐pollination reproductive barriers and their relative contribution to reproductive isolation between wild and domesticated chaya (Cnidoscolus aconitifolius) in its domestication centre.
• We found that wild and domesticated chaya both exhibit a high degree of reproductive isolation. However, the reproductive isolation barriers exhibited some asymmetry: while pre‐pollination barriers (differential pollen production and pollinator specificity) were only detected in wild plants, post‐pollination barriers (pollen–pistil incompatibility and/or failure to set fruit) were observed in both wild and domesticated plants.
• We conclude that complete reproductive isolation has evolved in sympatry in co‐occurring domesticated and wild chaya.

     

Visual Cues Given by Humans Are Not Sufficient for Asian Elephants (Elephas maximus) to Find Hidden Food

Recent research suggests that domesticated species – due to artificial selection by humans for specific, preferred behavioral traits – are better than wild animals at responding to visual cues given by humans about the location of hidden food. \Although this seems to be supported by studies on a range of domesticated (including dogs, goats and horses) and wild (including wolves and chimpanzees) animals, there is also evidence that exposure to humans positively influences the ability of both wild and domesticated animals to follow these same cues. Here, we test the performance of Asian elephants (Elephas maximus) on an object choice task that provides them with visual-only cues given by humans about the location of hidden food. Captive elephants are interesting candidates for investigating how both domestication and human exposure may impact cue-following as they represent a non-domesticated species with almost constant human interaction. As a group, the elephants (n = 7) in our study were unable to follow pointing, body orientation or a combination of both as honest signals of food location. They were, however, able to follow vocal commands with which they were already familiar in a novel context, suggesting the elephants are able to follow cues if they are sufficiently salient. Although the elephants’ inability to follow the visual cues provides partial support for the domestication hypothesis, an alternative explanation is that elephants may rely more heavily on other sensory modalities, specifically olfaction and audition. Further research will be needed to rule out this alternative explanation.     

Development of PCR-based chloroplast DNA markers that characterize domesticated cowpea (Vigna unguiculata ssp. unguiculata var. unguiculata) and highlight its crop-weed complex

In 1992, Vaillancourt and Weeden discovered a very important mutation for studying cowpea evolution and domestication. A loss of a BamHI restriction site in chloroplast DNA characterized all domesticated accessions and a few wild (Vigna unguiculata ssp. unguiculata var. spontanea) accessions. In order to screen a larger number of accessions, primers were designed to check this mutation using PCR RFLP or direct PCR methods. Using these new primers, 54 domesticated cowpea accessions and 130 accessions from the wild progenitor were screened. The absence of haplotype 0 was confirmed within domesticated accessions, including primitive landraces from cultivar-groups Biflora and Textilis, suggesting that this mutation occurred prior to domestication. However, 40 var. spontanea accessions distributed from Senegal to Tanzania and South Africa showed haplotype 1. Whereas this marker could not be used to identify a precise center of origin, it did highlight the widely distributed cowpea crop-weed complex. Its very high frequency in West Africa could be interpreted as a result of either genetic swamping of the wild/weedy gene pool by the domesticated cowpea gene pool or as the result of domestication by ethnic groups focusing primarily on cowpea as fodder.     

Are the early holocene cattle in the eastern sahara domestic or wild?

Questions relating to the antiquity of domestic cattle in the Sahara are among the most controversial in North African prehistory. It is generally believed that cattle were first domesticated in southwest Asia, particularly Anatolia, or in southeast Europe, where their remains have been found in several sites dated between 9,000 and 8,000 years ago.1 The discovery, in several small sites in the Western Desert of Egypt, of large bovid bones identified as domestic cattle and having radiocarbon dates ranging between 9,500 and 8,000 B.P. has raised the possibility that there was a separate, independent center for cattle domestication in northeast Africa (Fig. 1).^2–4 However, it has not been universally accepted that these bones are from cattle or, if so, that the cattle were domestic.     

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30–75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.     

Modern taurine cattle descended from small number of near-eastern founders

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.     

A reconsideration of the domestication geography of tetraploid wheats

The domestication of tetraploid wheats started from their wild progenitor Triticum dicoccoides. In this paper, the geographical distribution of this progenitor is revised to include more sampling locations. The paper is based on a collection of wild and domesticated lines (226 accessions in total) analyzed by AFLP at 169 polymorphic loci. The collection includes the 69 wild lines considered by Mori et al. (2003) in their study on chloroplast DNA haplotypes of T. dicoccoides. The goal of the experiment was to reconsider which location thought to have generated the domesticated germplasm has the highest chance of being the actual site from which wild progenitors were sampled during domestication. Phylogenetic analysis of the nuclear AFLP databases indicates that two different genetic taxa of T. dicoccoides exist, the western one, colonizing Israel, Syria, Lebanon and Jordan, and the central-eastern one, which has been frequently sampled in Turkey and rarely in Iran and Iraq. It is the central-eastern race that played the role of the progenitor of the domesticated germplasm. This is supported by the cumulative results of the AFLP data from the collections of Ozkan et al. (2002) and of Mori et al. (2003), which indicate that the Turkish Karacadag population, intermixed with some Iraq-Iran lines, has a tree topology consistent with that of the progenitor of domesticated genotypes. The Turkish Kartal population belongs genetically to the central-eastern T. dicoccoides race but at the nuclear DNA level is less related to the domesticated gene pool. A general agreement between published work on tetraploid wheat domestication emerges from these results. A disagreement is nevertheless evident at the local geographical scale; the chloroplast DNA data indicate the Kartal mountains while AFLP fingerprinting points to the Karacadag Range as the putative site of tetraploid wheat domestication.     

Ancient mtDNA Analysis of Early 16th Century Caribbean Cattle Provides Insight into Founding Populations of New World Creole Cattle Breeds

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15^th to early 16^th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16^th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle.     

Changes in fruit shape inproboscidea parviftora ssp.parviflora (martyniaceae) with domestication

Aboriginal cultivators selected a phylogenetically novel fruit shape during the domestication ofProboscidea parviflora ssp.parviflora var.Hohokamiana. The extremely long rostrum of the domesticated var.Hohokamiana is unique for the Martyniaceae. Rostrum length and width are significantly correlated in the wild var.parviflora, but in var.Hohokamiana aboriginal cultivators apparently selected for a weaker correlation between these variables. In both varieties there is an allometric relationship between rostrum and “capsule” lengths, with the former increasing proportionately faster than the latter. The above allometric relationship and the decrease in correlation between rostrum length and width are advantageous to aboriginal cultivators because the proportionately longer and thinner rostra are better for basketmaking. Comparisons of the data presented herein with data from other plants suggest that similar growth factors have been responsible for changes in fruit shape resulting from domestication.     

Evidence of the domestication history of flax (Linum usitatissimum L.) from genetic diversity of the sad2 locus

A phylogenetic analysis was conducted on 34 alleles of 2.5 kb sized stearoyl-ACP desaturase II (sad2), obtained from 30 accessions of cultivated and pale flax (Linum spp.), to elucidate the history of flax domestication. The analysis supports a single domestication origin for extant cultivated flax. The phylogenetic evidence indicates that flax was first domesticated for oil, rather than fibre. The genetic diversity of the sad2 locus in cultivated flax is low when compared to that of the pale flax assayed. An absolute archaeological date could be applied to the synonymous substitution rate of sad2 in cultivated flax, yielding a high estimate of 1.60–1.71×10⁻⁷ substitutions/site/year. The occurrence of nonsynonymous substitutions at conserved positions of the third exon in alleles from cultivated flax suggests that the locus may have been subjected to an artificial selection pressure. The elevated synonymous substitution rate is also compatible with a population expansion of flax since domestication, followed by a population decline in historic times. These findings provide new insight into flax domestication and are significant for the continuous exploration of the flax germplasm for utilization.     

Factors influencing the priority of access to food and their effects on the carcass traits for Japanese Black (Wagyu) cattle

The factors influencing the priority of access to food and the effects of the priority of access to food on their carcass traits were analyzed for Japanese Black (Wagyu) cattle in a semi-intensive fattening production system. The records of 96 clinically healthy steers and heifers were analyzed. The calves at ∼3 to 4 months of age were allocated to pens with four animals per pen; all four animals in the same pen were of the same sex and of similar body size. The ranking of the animals’ priority of access to food (1^st, 2^nd, 3^rd and 4^th), which was determined by the farm manager, was used as an indicator of social dominance in the present study. Four models including sire line, maternal grandsire line and the difference in the animals’ birth dates as fixed effects were used to analyze factors influencing the priority of access to food. Ranking was represented by ordinal scores (highest=4, lowest=1) in Model 1, and the binary scores were assigned in Model 2 (highest=1; 2^nd, 3^rd and 4^th=0), Model 3 (1^st and 2^nd=1; 3^rd and 4^th=0) and Model 4 (1^st, 2^nd and 3^rd=1; lowest=0). The results showed that the difference in the animals’ birth dates had a significant effect on the establishment of the priority of access to food in Model 3 (P<0.05), suggesting that animals born earlier may become more dominant in the pen. The maternal grandsire line tended to affect the social rank score in Models 2 and 3 (P<0.10). Our results indicated that the maternal grandsire line may affect the temperament of calves through their mothers’ genetic performance and thereby more aggressive calves may be more dominant and have higher priority of access to food. On the other hand, there was a significant effect of the priority of access to food on beef marbling score (BMS; P<0.05), and the priority of access to food also tended to influence the carcass weight (P=0.09). The highest BMS was observed for animals with the first rank of the priority of access to food (P<0.05), and the higher-ranking animals had the tendency to be heavier carcass than the lower-ranking animals. Our findings emphasized the importance of information about the priority of access to food determined by farmers’ own observation on implementing best management practices in small-scaled semi-intensive beef cattle production systems.     

Cattle demographic history modelled from autosomal sequence variation

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.     

Multiple origins of the determinate growth habit in domesticated common bean (Phaseolus vulgaris)

Background and Aims

The actual number of domestications of a crop is one of the key questions in domestication studies. Answers to this question have generally been based on relationships between wild progenitors and domesticated descendants determined with anonymous molecular markers. In this study, this question was investigated by determining the number of instances a domestication phenotype had been selected in a crop species. One of the traits that appeared during domestication of common bean (Phaseolus vulgaris) is determinacy, in which stems end with a terminal inflorescence. It has been shown earlier that a homologue of the arabidopsis TFL1 gene – PvTFL1y – controls determinacy in a naturally occurring variation of common bean.

Methods

Sequence variation was analysed for PvTFL1y in a sample of 46 wild and domesticated accessions that included determinate and indeterminate accessions.

Key Results

Indeterminate types – wild and domesticated – showed only synonymous nucleotide substitutions. Determinate types – observed only among domesticated accessions – showed, in addition to synonymous substitutions, non-synonymous substitutions, indels, a putative intron-splicing failure, a retrotransposon insertion and a deletion of the entire locus. The retrotransposon insertion was observed in 70 % of determinate cultivars, in the Americas and elsewhere. Other determinate mutants had a more restricted distribution in the Americas only, either in the Andean or in the Mesoamerican gene pool of common bean.

Conclusions

Although each of the determinacy haplotypes probably does not represent distinct domestication events, they are consistent with the multiple (seven) domestication pattern in the genus Phaseolus. The predominance of determinacy in the Andean gene pool may reflect domestication of common bean prior to maize introduction in the Andes.     

Prehistoric sunflower (Helianthus Annuus L.) domestication in Mexico

Early remains of Helianthus annuus L. unearthed at the San Andrés site in the Gulf Coast region of Tabasco, Mexico, constitute the earliest record of domesticated sunflower. Accelerator mass spectrometry (AMS) age determinations of a large domesticated seed and achene produced dates of 4130 ± 40 years before the present (B.P.) and 4085 ± 50 B.P., respectively. These discoveries challenge the longstanding hypothesis that sunflower was domesticated in eastern North America. Moreover, when considered with other recent discoveries on plant domestication, these data suggest a reconsideration of the idea that the eastern United States was an independent hearth for domestication.     

群体遗传学下动物驯化研究进展

动物驯化是将野生动物改变为能够长期稳定饲养的家养动物的过程。作为新石器时代农业革命的内容,驯化是人类社会文明进步的重要标志之一。由于和人类的密切关系,驯化不仅改变了动物的野生状态,也改变了人类的生活习性和文明进程。动物驯化研究的关键问题包含驯化祖先是谁、驯化所产生的改变及驯化时间地点等。随着高通量基因组技术和对应分析方法的发展,目前研究动物驯化一般基于群体水平,在群体遗传学的框架下研究动物驯化过程中的重要事件。本文总结了群体遗传学下动物驯化研究的相关内容,包括群体动态历史、选择信号、基因交流等,着重介绍了基因选择初始时间和基因交流时间两个新的拓展内容及分析方法,概述了家猪(Sus scrofa f. domestica)、家鸡(Gallus gallus domesticus)、绵羊(Ovis aries)和山羊(Caprine hircus)等几种主要农业动物近期驯化研究的进展,以期为动物驯化研究提供了新的方向和视角。     

Dopamine Receptor Genes and Evolutionary Differentiation in the Domestication of Fighting Cocks and Long-Crowing Chickens

The chicken domestication process represents a typical model of artificial selection, and gives significant insight into the general understanding of the influence of artificial selection on recognizable phenotypes. Two Japanese domesticated chicken varieties, the fighting cock (Shamo) and the long-crowing chicken (Naganakidori), have been selectively bred for dramatically different phenotypes. The former has been selected exclusively for aggressiveness and the latter for long crowing with an obedient sitting posture. To understand the particular mechanism behind these genetic changes during domestication, we investigated the degree of genetic differentiation in the aforementioned chickens, focusing on dopamine receptor D2, D3, and D4 genes. We studied other ornamental chickens such as Chabo chickens as a reference for comparison. When genetic differentiation was measured by an index of nucleotide differentiation (N _ST) newly devised in this study, we found that the N_ST value of DRD4 for Shamo (0.072) was distinctively larger than those of the other genes among the three populations, suggesting that aggressiveness has been selected for in Shamo by collecting a variety of single nucleotide polymorphisms. In addition, we found that in DRD4 in Naganakidori, there is a deletion variant of one proline at the 24^th residue in the repeat of nine prolines of exon 1. We thus conclude that artificial selection has operated on these different kinds of genetic variation in the DRD4 genes of Shamo and Naganakidori so strongly that the two domesticated varieties have differentiated to obtain their present opposite features in a relatively short period of time.     

The Environmental Impact of Cambodia's Ancient City of Mahendraparvata (Phnom Kulen)

The Khmer kingdom, whose capital was at Angkor from the 9^th to the 14^th-15^th century, was founded in 802 by king Jayavarman II in a city called Mahandraparvata, on Phnom Kulen. Virtually nothing more is known of Mahandraparvata from the epigraphic sources, but systematic archaeological survey and excavation have identified an array of cultural features that point to a more extensive and enduring settlement than the historical record indicates. Recent remote sensing data have revolutionized our view, revealing the remains of a city with a complex and spatially extensive network of urban infrastructure. Here, we present a record of vegetation change and soil erosion from within that urban network, dating from the 8^th century CE. Our findings indicate approximately 400 years of intensive land use, punctuated by discrete periods of intense erosion beginning in the mid 9^th century and ending in the late 11^th century. A marked change in water management practices is apparent from the 12^th century CE, with implications for water supply to Angkor itself. This is the first indication that settlement on Mahendraparvata was not only extensive, but also intensive and enduring, with a marked environmental impact.