Early agriculture and crop transmission among Bronze Age mobile pastoralists of Central Eurasia

Archaeological research in Central Eurasia is exposing unprecedented scales of trans-regional interaction and technology transfer between East Asia and southwest Asia deep into the prehistoric past. This article presents a new archaeobotanical analysis from pastoralist campsites in the mountain and desert regions of Central Eurasia that documents the oldest known evidence for domesticated grains and farming among seasonally mobile herders. Carbonized grains from the sites of Tasbas and Begash illustrate the first transmission of southwest Asian and East Asian domesticated grains into the mountains of Inner Asia in the early third millennium BC. By the middle second millennium BC, seasonal camps in the mountains and deserts illustrate that Eurasian herders incorporated the cultivation of millet, wheat, barley and legumes into their subsistence strategy. These findings push back the chronology for domesticated plant use among Central Eurasian pastoralists by approximately 2000 years. Given the geography, chronology and seed morphology of these data, we argue that mobile pastoralists were key agents in the spread of crop repertoires and the transformation of agricultural economies across Asia from the third to the second millennium BC.     

Does targeted management work for red-legged partridges <Emphasis Type="Italic">Alectoris rufa</Emphasis>? Twelve years of the ‘Finca de Matallana’ demonstration project

After the implementation of a management package for red-legged partridges (Alectoris rufa) (including habitat improvement, legal predator removal, supplementary feeding and watering and shooting restrain) in an agricultural Mediterranean area of Spain (308 ha), spring pair densities increased from 2.92 to 12.66/km² in 9 years, together with summer densities (from 24 to 98 birds/km²) and autumn densities (from 16.5 to 86 birds/km²). We recorded an overall decrease in the over-winter survival of partridges and an increase in their over-summer survival as time progressed. Productivity doubled in 5 years and densities of wild rabbits (Oryctolagus cuniculus) significantly increased. Hence, this study shows that a feasible and affordable combination of management tools worked to improve partridge populations, and also helped the recovery of wild rabbits. The study site supported the presence of 42 ‘red-listed’ species (including 21 species of raptors).     

Crop husbandry activities and wild plant gathering,use and consumption at the EPPNB Tell Qarassa North (south Syria)

The Early Pre-Pottery Neolithic B (EPPNB) in southwest Asia is a fundamental period in research on the origins of domesticated plants. However, there are few archaeobotanical data with which to characterise the plant-based subsistence and crop husbandry activities during this time, which hinders the understanding of the factors that triggered the appearance of plant domestication. In this paper, analyses of non-woody plant macro-remains provide new insights into subsistence activities such as crop cultivation (husbandry activities and storage) and plant use (wild plant gathering and food preparation) during the EPPNB at Tell Qarassa North (south Syria). We make comparisons between Tell Qarassa North and the evidence at earlier and later periods as to how plants were used, and highlight similarities and differences in the practices attested, as well as describing some of the consequences that these plant-related activities may have had in terms of labour and social organization during EPPNB.     

Plant microbiota modified by plant domestication

Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.     

Crop introduction and accelerated island evolution: archaeobotanical evidence from ‘<Emphasis Type="Italic">Ais Yiorkis</Emphasis> and Pre-Pottery Neolithic Cyprus

Charred plant remains from the Cypriot Pre-Pottery Neolithic site of Krittou Marottou ‘Ais Yiorkis, situated in the foothills of the Troödos Mountains and dated to ca. 7500 cal. b.c., demonstrate the early introduction of two-grained einkorn (Triticum monococcum sensu lato). Grain measurements of two-grained einkorn from ‘Ais Yiorkis are compared to those from Aceramic and early Neolithic sites elsewhere in Cyprus, in northern Syria and central Europe. The grains appear to be larger than domestic grains of a later date from the Levantine mainland. Recent work by Purugganan and Fuller (Evolution 65:171–183, 2011) demonstrates a slow evolutionary rate in increasing grain size relative to the rates of evolution in wild species subject to natural selection. When the measurements of two-grained einkorn wheat from ‘Ais Yiorkis are compared with these same allochronic data the results indicate an accelerated rate in attaining larger grain size on Cyprus than on the mainland. The possibility of a domestication ‘event’ or rapid fixation of larger grain size characteristic of domesticated cereal crops in the context of an initially small island population is suggested by the colonisation by farmers of Cyprus in the Cypro-Pre-Pottery Neolithic.     

Evolution of the population structure of Venturia inaequalis,the apple scab fungus,associated with the domestication of its host

Evaluating the impact of plant domestication on the population structure of the associated pathogens provides an opportunity to increase our understanding of how and why diseases emerge. Here, we investigated the evolution of the population structure of the apple scab fungus Venturia inaequalis in response to the domestication of its host. Inferences were drawn from multilocus microsatellite data obtained from samples collected on (i) the Central Asian Malus sieversii, the main progenitor of apple, (ii) the European crabapple, Malus sylvestris, a secondary progenitor of apple, and (iii) the cultivated apple, Malus×domestica, in orchards from Europe and Central Asia. Using clustering methods, we identified three distinct populations: (i) a large European population on domesticated and wild apples, (ii) a large Central Asian population on domesticated and wild apples in urban and agricultural areas, and (iii) a more geographically restricted population in M. sieversii forests growing in the eastern mountains of Kazakhstan. Unique allele richness and divergence time estimates supported a host‐tracking co‐evolutionary scenario in which this latter population represents a relict of the ancestral populations from which current populations found in human‐managed habitats were derived. Our analyses indicated that the domestication of apple induced a significant change in the genetic differentiation of populations of V. inaequalis in its centre of origin, but had little impact on its population dynamics and mating system. We discuss how the structure of the apple‐based agrosystem may have restricted changes in the population structure of the fungus in response to the domestication of its host.     

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.     

The structure of wild and domesticated emmer wheat populations,gene flow between them,and the site of emmer domestication

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. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Plant management among the Nahua and the Mixtec in the Balsas River Basin,Mexico: An ethnobotanical approach to the study of plant domestication

Different forms of management of wild, weedy, and domesticated plants carried out by the Nahua and the Mixtec in the Balsas River Basin, Mexico, are described. Along with cultivation of domesticated plants, these forms of plant management include gathering from wild populations; in situtolerance of plant individuals during clearings of natural vegetation; in situenhancement and protection of particular plants among populations of some species; as well as sowing or planting of propagules and transplantation of complete individuals of weedy and wild plants in controlled ex situenvironments. Processes of artificial selection and possible routes of domestication occurring in these forms of plant management are discussed.     

Agriculture and use of wild and weedy greens by thePiik AP Oom okiek of Kenya

This study documents patterns of use of wild and weedy greens in a previously little studied context among the Piik ap Oom Okiek of Kenya. The Piik ap Oom have a hunter-gatherer history and at the time of the study lived at low population densities in a high altitude forest habitat. Leafy greens, both wild and domesticated, were the most commonly eaten fresh plant food documented. Wild greens,Solanum nigrum L. andAmaranthus graecizans ssp.sylvestris L. were the most preferred. Patterns of harvesting wild greens, a few leaves from many plants and a variety of taxa together, resulted in greater dietary diversity associated with consumption of wild than domesticated greens. Greens provided contemporary Okiek households with nutritious and low maintenance plant food. Increased use of wild and weedy greens was an important benefit of the adoption of the agricultural complex by the Okiek.     

Physiological properties of a drought-resistant wild soybean genotype: Transpiration control with soil drying and expression of root morphology

Aims

Wild soybean accession PI 468917 [Glycine soja (Sieb. and Zucc.)] was examined for traits that could potentially be beneficial for development of drought resistant soybean cultivars.

Methods

Water use was examined in controlled environment chambers at three temperatures (25, 30, and 35 °C). Root morphology of plants grown in hydroponics was analyzed using digital imaging software.

Results

Wild soybean had lower transpiration efficiency in producing mass than the domesticated soybean cultivar Hutcheson at all temperatures. As soil dried, wild soybean decreased transpiration earlier (at a higher soil water content) than domesticated soybean, but only at 25 °C. Wild soybean had much greater root length than the modern soybean when grown at 25 or 30 °C in hydroponics, with the increase observed in the 0.25 to 0.50 mm diameter class. Wild soybean’s advantages dissipated at higher growth temperatures.

Conclusions

Wild soybean populations, potentially, can offer useful traits for improving drought resistance of modern soybean. Sensitive transpiration control in response to soil drying would contribute to ‘slow-wilting’ strategies known to be advantageous for drought resistance, and greater root length would enhance water acquisition from the soil profile. Use of the traits in breeding programs will require extending the temperature range for trait expression.     

Harvesting practices and early Neolithic barley cultivation at el-Hemmeh,Jordan

Recent research strongly suggests polyphetic origins of multiple cultigens across Southwest Asia approximately 11,000 years ago during the Pre-Pottery Neolithic A period. The harvesting practices that contributed to the dedicated use of cultivation as a plant exploitation strategy remain largely unidentified. Archaeobotanical data from el-Hemmeh, a settlement site dating to ca. 10850 cal. b.p., provides an opportunity to examine in close detail the harvesting strategies that may have contributed to the development of domesticated forms. Initial analyses indicate a variety of wild plant foods including barley, lentils, vetch, Pistacia cf. atlantica and fig were exploited, while the presence of large predomesticated barley grains and potential weed species suggest cereal cultivation was also pursued at the site. Barley rachis internodes from el-Hemmeh typically possess a wild morphology, but 22% of specimens show evidence of a forced or “ripped” disarticulation. This suggests barley may have been harvested while ears were partially immature and required subsequent processing in order to disarticulate spikelets.     

Construction of a high-density genetic map of <Emphasis Type="Italic">Ziziphus jujuba</Emphasis> Mill. using genotyping by sequencing technology

The Chinese jujube (Ziziphus jujuba Mill., 2n = 2 × = 24), one of the most popular fruit trees in China, is widely cultivated and utilized in Asia. High-density genetic linkage maps are valuable resources for molecular breeding and functional genomics; however, they are still under-developed for the jujube. The genotyping by sequencing (GBS) strategy could be an efficient and cost-effective tool for single nucleotide polymorphism (SNP) discovery based on the sequenced jujube genome. Here, we report a new high-density genetic map constructed using GBS technology. An F1 population with 145 progenies and their parents (‘Dongzao’ × ‘Zhongningyuanzao’) were sequenced on the Illumina HiSeq 4000 platform. In total, 79.8 Gb of raw data containing 256,708,177 paired-end reads were generated. After data filtering and SNP genotyping, 40,372 polymorphic SNP markers were developed between the parents and 2540 (1756 non-redundant) markers were mapped onto the integrated genetic linkage map. The map spanned 1456.53 cM and was distributed among 12 linkage groups, which is consistent with the haploid chromosome number of the jujube. The average marker interval was 0.88 cM. The genetic map allowed us to anchor 224 Mb (63.7 %) of scaffolds from the sequenced ‘Junzao’ genome, containing 52 newly anchored scaffolds, which extended the genome assembly by 7 Mb. In conclusion, GBS technology was applied efficiently for SNP discovery in this study. The high-density genetic map will serve as a unique tool for molecular-assisted breeding and genomic studies, which will contribute to further research and improvement of the jujube in the near future.     

Organic carbon in soils of Central Asia—status quo and potentials for sequestration

Expectations have been raised that carbon sequestration in soils could provide a short-term bridge to reduce the impacts of increasing carbon emissions until low-carbon technologies are available. To assess the role of Central Asia in this regard, the organic carbon in soils of Central Asia and losses in response to land use were quantified in a spatially explicit way. Based on literature information on soil organic carbon contents and in combination with the FAO-UNESCO Soil Map of the Word, the organic carbon stocks in the upper 30 cm of native soils of Central Asia were estimated to amount to 20,17?±?4,03 Pg. The extent of conversion of native land into agricultural land and the degradation of rangelands was assessed by a land use land cover change map of the region. This type of land use (change) was responsible for a reduction of the soil organic carbon by about 828?±?166 Tg C, or on average 4.1% of the total stocks. To this reduction, degradation of rangeland (observed on 4.9 Mha) with 50 Tg contributed only 6%. Most of the losses resulted from past conversion of rangelands into rainfed or irrigated agricultural land in the north of Kazakhstan. Hotspots of high soil organic matter depletion were former wetlands, drained for cultivation during the last decades. Assuming that improved agronomic and grazing management could be put in place and that therewith SOC levels in all of Central Asia’s cropland and degraded rangeland could be brought back to native levels in the next 50 years, each year 16.6 Tg C could be sequestered. This is equal to the sizeable amount of 15.5% of the 2004 annual anthropogenic C-emissions of the five Central Asian countries (107 Tg C yr^?1). However, Central Asia contributed only 1.4% of CO₂ that is set free worldwide by fossil fuel burning. Therefore, the mitigation effect on rising atmospheric CO₂ levels and climate change of such ambitious sequestration plans, if put into practice, would be hardly notable. The central Asian example shows that, unfortunately, the strategy of soil C sequestration as a stand-alone measure is not a viable bridge to a future in which alternative energy source can substitute fossil fuel burning, but can only be part of a set of mitigating measures.     

High heterotrophic CO<Subscript>2</Subscript> emissions from a Malaysian oil palm plantations during dry-season

Tropical peatlands are currently being rapidly cleared and drained for the establishment of oil palm plantations, which threatens their globally significant carbon sequestration capacity. Large-scale land conversion of tropical peatlands is important in the context of greenhouse gas emission factors and sustainable land management. At present, quantification of carbon dioxide losses from tropical peatlands is limited by our understanding of the relative contribution of heterotrophic and autotrophic respiration to net peat surface CO₂ emissions. In this study we separated heterotrophic and autotrophic components of peat CO₂ losses from two oil palm plantations (one established in ‘2000’ and the other in 1978, then replanted in ‘2006’) using chamber-based emissions sampling along a transect from the rooting to non-rooting zones on a peatland in Selangor, Peninsular Malaysia over the course of 3 months (June–August, 2014). Collar CO₂ measurements were compared with soil temperature and moisture at site and also accompanied by depth profiles assessing peat C and bulk density. The soil respiration decreased exponentially with distance from the palm trunks with the sharpest decline found for the plantation with the younger palms with overall fluxes of 1341 and 988 mg CO₂ m^?2 h^?1, respectively, at the 2000 and 2006 plantations, respectively. The mean heterotrophic flux was 909 ± SE 136 and 716 ± SE 201 mg m^?2 h^?1 at the 2000 and 2006 plantations, respectively. Autotrophic emissions adjacent to the palm trunks were 845 ± SE 135 and 1558 ± SE 341 mg m^?2 h^?1 at the 2000 and 2006 plantations, respectively. Heterotrophic CO₂ flux was positively related to peat soil moisture, but not temperature. Total peat C stocks were 60 kg m^?2 (down to 1 m depth) and did not vary among plantations of different ages but SOC concentrations declined significantly with depth at both plantations but the decline was sharper in the second generation 2006 plantation. The CO₂ flux values reported in this study suggest a potential for very high carbon (C) loss from drained tropical peats during the dry season. This is particularly concerning given that more intense dry periods related to climate change are predicted for SE Asia. Taken together, this study highlights the need for careful management of tropical peatlands, and the vulnerability of their carbon storage capability under conditions of drainage.     

Diversity and evolution of rice progenitors in Australia

In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest‐branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.     

Do human activity and infrastructure disturb domesticated reindeer? The need for the reindeer’s perspective

In recent decades, human–Rangifer (reindeer and caribou) interactions have increasingly been studied from a scientific perspective. Many of the studies have examined Norwegian wild reindeer or caribou in North America. It is often questioned whether results from these studies can be applied to reindeer in managed herds, as these animals have been exposed to domestication and are also more used to humans. In order to examine the domesticated reindeer’s reactions to various disturbance sources, we reviewed 18 studies of the effects of human activity and infrastructure on 12 populations of domesticated reindeer and compared these to studies on wild reindeer and caribou; based on this, we discuss the effects of domestication and tameness on reindeer responses to anthropogenic disturbance. We also consider the relevance of spatial and temporal scales and data collection methods when evaluating the results of these studies. The reviewed studies showed that domesticated reindeer exhibit avoidance behaviours up to 12 km away from infrastructure and sites of human activity and that the area they avoid may shift between seasons and years. Despite a long domestication process, reindeer within Sami reindeer-herding systems exhibit similar patterns of large-scale avoidance of anthropogenic disturbance as wild Rangifer, although the strength of their response may sometimes differ. This is not surprising since current Sami reindeer husbandry represents an extensive form of pastoralism, and the reindeer are not particularly tame. To obtain a true picture of how reindeer use their ranges, it is of fundamental importance to study the response pattern at a spatial and temporal scale that is relevant to the reindeer, whether domesticated or wild.     

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum

The domestication of diverse grain crops from wild grasses was a result of artificial selection for a suite of overlapping traits producing changes referred to in aggregate as ‘domestication syndrome’. Parallel phenotypic change can be accomplished by either selection on orthologous genes or selection on non‐orthologous genes with parallel phenotypic effects. To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes, we employed resequencing data from wild and domesticated accessions of Zea (maize) and Sorghum (sorghum). Many ‘classic’ domestication genes identified through quantitative trait locus mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum. However, the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance. This suggests that while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication, the optimization part of domestication targeted small and largely non‐overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.     

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

Key message

This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication.

Abstract

The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today’s crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.