Pulse domestication before cultivation

Comparative studies of the pulses of the Middle East and of their wild progenitors indicate that the pattern of pulse domestication is completely different from that of cereals in the same region. Wild legumes are not suitable for cultivation because of their conspicuous seed dormancy. Pre-adaptation of wild pulses for cultivation through loss of the seed dormancy mechanism apparently occurred in wild populations and may have been influenced by the gathering practices of man in pre-agricultural times. Pod indehiscence was of low value in pulse domestication and had evolved after the crop was well established and widespread.     

Genetic analyses reveal independent domestication origins of Eurasian reindeer

Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.     

Early Holocene cultivation before domestication in northern Syria

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

Ustilago maydis populations tracked maize through domestication and cultivation in the Americas

The domestication of crops and the development of agricultural societies not only brought about major changes in human interactions with the environment but also in plants' interactions with the diseases that challenge them. We evaluated the impact of the domestication of maize from teosinte and the widespread cultivation of maize on the historical demography of Ustilago maydis, a fungal pathogen of maize. To determine the evolutionary response of the pathogen's populations, we obtained multilocus genotypes for 1088 U. maydis diploid individuals from two teosinte subspecies in Mexico and from maize in Mexico and throughout the Americas. Results identified five major U. maydis populations: two in Mexico; two in South America; and one in the United States. The two populations in Mexico diverged from the other populations at times comparable to those for the domestication of maize at 6000-10000 years before present. Maize domestication and agriculture enforced sweeping changes in U. maydis populations such that the standing variation in extant pathogen populations reflects evolution only since the time of the crop's domestication.     

Modelling the developmental origins of health and disease in the early embryo

The concept that certain adult diseases, such as hypertension, type 2 diabetes and dyslipidaemia can originate from events occurring in utero arose from epidemiological studies in humans but has since been supported by numerous animal-based studies. Referred to as the "developmental origins of health and disease" or "DOHaD" hypothesis, nutritional studies to date have largely focused on two experimental paradigms involving either calorie or protein restriction for varying intervals during pregnancy, where the favoured animal models have been the sheep and rat. In recent times, attention has been directed towards the earliest stages of gestation, where there is emerging evidence to indicate that the pre-implantation embryo may be particularly sensitive to environmentally induced perturbations leading to impaired health in adulthood. In this article, we make the case for hESCs as a model of the human pre-implantation embryo. Working with comparatively large populations of embryonic cells from the species of clinical interest, the scope exists to investigate the effects of specific genetic manipulations or combinations of metabolites against contrasting genetic backgrounds, where the consequences can be evaluated in downstream tissue specific progenitor and/or terminally differentiated cells. In order to fully realize these potentials, however, both derivation and culture conditions need to be harmonized and refined so as to preclude the requirement for feeder cells and serum.     

The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere

This article aims to summarize the present archaeo(zoo)logical knowledge and reflections on the origins of Neolithic animal domestication. It targets the main characteristics of early Neolithic animal domestication set against a backdrop of two complementary scales, namely the global and macro-regional scales (the latter using the example of the Near East). It discusses the conceptual and methodological issues, arguing in favor of an anthropozoological approach taking into account the intentions and the dynamics of human societies and critically analyzes the reductionist neo-Darwinian concepts of co-evolution and human niche construction. It also provides a brief discussion on the birth of ungulate domestication and its roots, as well as appropriate bibliographic references to enlighten the current status of domestication research.     

Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars

Background and Aims

In spite of the abundance of archaeological, bio-archaeological, historical and genetic data, the origins, historical biogeography, identity of ancient grapevine cultivars and mechanisms of domestication are still largely unknown. Here, analysis of variation in seed morphology aims to provide accurate criteria for the discrimination between wild grapes and modern cultivars and to understand changes in functional traits in relation to the domestication process. This approach is also used to quantify the phenotypic diversity in the wild and cultivated compartments and to provide a starting point for comparing well-preserved archaeological material, in order to elucidate the history of grapevine varieties.

Methods

Geometrical analysis (elliptic Fourier transform method) was applied to grapevine seed outlines from modern wild individuals, cultivars and well-preserved archaeological material from southern France, dating back to the first to second centuries.

Key Results and Conclusions

Significant relationships between seed shape and taxonomic status, geographical origin (country or region) of accessions and parentage of varieties are highlighted, as previously noted based on genetic approaches. The combination of the analysis of modern reference material and well-preserved archaeological seeds provides original data about the history of ancient cultivated forms, some of them morphologically close to the current ‘Clairette’ and ‘Mondeuse blanche’ cultivars. Archaeobiological records seem to confirm the complexity of human contact, exchanges and migrations which spread grapevine cultivation in Europe and in Mediterranean areas, and argue in favour of the existence of local domestication in the Languedoc (southern France) region during Antiquity.     

Modelling of continuous microbial cultivation taking into account the memory effects

The problem of chemostat dynamics modelling for the purpose of control is considered. The "memory" of the culture is explicitly taken into account. Two possibilities for improving the quality of the proposed modelling approaches are discussed. A general model that accounts for the culture `memory' by means of different `memory' functions in the expressions of the specific growth rate and of the specific consumption rate and a polynomial function of the substrate concentration for the yield factor is proposed. The case where the maintenance energy is taken into account is also discussed. Two modifications of the general model (w-type and S-type) are presented. A zero-order `memory' function and a i-function with delay are applied in order to describe the `memory' effects. Continuous growth of the strain Saccharomyces cerevisiae on a glucose limited medium is considered as a case study. Detailed investigations of the variety of models, derived from the general model by applying different `memory' functions and different assumptions are carried out. The results are compared with those previously reported for the same process. It is shown that a significant improvement in predicting the substrate dynamics (not accompanied by any decrease in the quality of the model with respect to the biomass concentration) could be achieved, involving a first- or second-order polynomial function for the yield factor. It is also shown that the quality of the model mainly depends on the way that `memory' function is incorporated. The detailed investigations give priority to the w-type models. In this case past values of both biomass and substrate variables are considered. The time delay models with pure (constant) delay and those which account for the culture `memory' by zero-order `memory' function (adaptability parameter) are compared with respect to their utilization for the purpose of model-based control.     

Genetic analysis of wheat domestication and evolution under domestication

Wheat is undoubtedly one of the world's major food sources since the dawn of Near Eastern agriculture and up to the present day. Morphological, physiological, and genetic modifications involved in domestication and subsequent evolution under domestication were investigated in a tetraploid recombinant inbred line population, derived from a cross between durum wheat and its immediate progenitor wild emmer wheat. Experimental data were used to test previous assumptions regarding a protracted domestication process. The brittle rachis (Br) spike, thought to be a primary characteristic of domestication, was mapped to chromosome 2A as a single gene, suggesting, in light of previously reported Br loci (homoeologous group 3), a complex genetic model involved in spike brittleness. Twenty-seven quantitative trait loci (QTLs) conferring threshability and yield components (kernel size and number of kernels per spike) were mapped. The large number of QTLs detected in this and other studies suggests that following domestication, wheat evolutionary processes involved many genomic changes. The Br gene did not show either genetic (co-localization with QTLs) or phenotypic association with threshability or yield components, suggesting independence of the respective loci. It is argued here that changes in spike threshability and agronomic traits (e.g. yield and its components) are the outcome of plant evolution under domestication, rather than the result of a protracted domestication process. Revealing the genomic basis of wheat domestication and evolution under domestication, and clarifying their inter-relationships, will improve our understanding of wheat biology and contribute to further crop improvement.     

Human origins and the origins of humanity

As long asHomo sapiens was considered to be separated from the rest of the natural world by an unbridgeable if narrow gulf, there was no difficulty in defining, or at least in recognizing, what is «human» and what is not. But with the advent of evolutionary thought came the realization that the concept of humanity lacks any firm definition. While adminitting that any definition of humanness must be essentially intuitive and thus arbitrary, this article examines various innovations in the human fossil and archaeological records and discusses at what point humanness could be said to have been achieved. This task is complicated by the fact that there appears to be no correspondence whatever between biological and cultural innovation.     

Modelling the growth and bacteriocin production by Lactobacillus amylovorus DCE 471 in batch cultivation

A model was set up to describe the production of amylovorin L471 by Lactobacillus amylovorus DCE 471, on a laboratory scale, in which the cells are grown in MRS (deMau-Rogosa-Sharpe) broth. The main features of the dynamic model are : (i) increase of the biomass according to a logistic equation ; (ii) non-growth-associated consumption of substrate (maintenance metabolism) ; and (iii) primary metabolite kinetics for the bacteriocin production. The main purpose was to set up a simple empirical model to examine growth and bacteriocin production in different conditions. Parameters estimated from a fermentation with 20 g l⁻¹ glucose (w/v) could be used to predict the evolution of cell dry mass, glucose and lactic acid concentration of fermentations, performed with 5, 30, 40 and 60 g l⁻¹ initial glucose. The influence of the operating temperature (30, 37 and 45 °C) on the model parameters was also investigated. The proposed model was able to describe growth and bacteriocin production in all cases. The specific bacteriocin production rate was found to vary strongly with temperature, with 30 °C as the best value. Variation of the operating temperature from 37 to 30 °C appeared to significantly enhance the specific bacteriocin production.     

Inherited variability in multiple traits determines fitness in populations of an annual legume from contrasting latitudinal origins

Background and Aims

Variation in fitness depends on corresponding variation in multiple traits which have both genetically controlled and plastic components. These traits are subjected to varying degrees of local adaptation in specific populations and, consequently, are genetically controlled to different extents. In this study it is hypothesized that modulation of different traits would have contrasting relevance for the fitness of populations of diverse origins. Specifically, assuming that environmental pressures vary across a latitudinal gradient, it is suggested that inherited variation in traits differentially determines fitness in annual Lupinus angustifolius populations from contrasting latitudinal origins in western Spain.

Methods

Seeds of L. angustifolius from three contrasting origins were grown in a common garden. Traits related to more plastic vegetative growth and more genetically conserved phenology were measured, together with estimates of reproductive success. Fitness was estimated by the number of viable seeds per plant. Structural Equation Models were used to infer causal relationships among multiple traits and fitness, separating the direct and indirect effects of morphological, phenological and reproductive traits.

Key Results

Phenological, vegetative and reproductive traits accounted for most of the fitness variation. Fitness was highest in plants of southernmost origin, mainly due to earlier flowering. Fitness within each seed origin was controlled by variation in different traits. Southern origin plants that grew to a larger size achieved higher fitness. However, plant size in plants of northernmost origin was irrelevant, but early flowering promoted higher fitness. Variation in fruit and seed set had a greater effect on the fitness of plants of central origin than phenological and size variation.

Conclusions

It is concluded that modulation of a functional trait can be relevant to fitness in a given population (i.e. affecting intensity and direction), but irrelevant in other populations. This points to the need to consider integrated phenotypes when trying to unravel local adaptation effects over single traits.Key words: Lupinus, Structural Equation Models, fitness, phenology, functional traits, reproductive success, SLA, seed size     

Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification

The evolution of the polyploid Triticum wheats is distinctive in that domestication, natural hybridization and allopolyploid speciation have all had significant impacts on their diversification. In this review, I outline the phylogenetic relationships of cultivated wheats and their wild relatives and provide an overview of the recent progress and remaining issues in understanding the genetic and ecological factors that favored their evolution. An attempt is made to view the evolution of the polyploid Triticum wheats as a continuous process of diversification that was initiated by domestication of tetraploid emmer wheat and driven by various natural events ranging from interploidy introgression via hybridization to allopolyploid speciation of hexaploid common wheat, instead of viewing it as a group of discrete evolutionary processes that separately proceeded at the tetraploid and hexaploid levels. This standpoint underscores the important role of natural hybridization in the reticulate diversification of the tetraploid-hexaploid Triticum wheat complex and highlights critical, but underappreciated, issues that concern the allopolyploid speciation of common wheat.     

Self domestication and the evolution of language

We set out an account of how self-domestication plays a crucial role in the evolution of language. In doing so, we focus on the growing body of work that treats language structure as emerging from the process of cultural transmission. We argue that a full recognition of the importance of cultural transmission fundamentally changes the kind of questions we should be asking regarding the biological basis of language structure. If we think of language structure as reflecting an accumulated set of changes in our genome, then we might ask something like, “What are the genetic bases of language structure and why were they selected?” However, if cultural evolution can account for language structure, then this question no longer applies. Instead, we face the task of accounting for the origin of the traits that enabled that process of structure-creating cultural evolution to get started in the first place. In light of work on cultural evolution, then, the new question for biological evolution becomes, “How did those precursor traits evolve?” We identify two key precursor traits: (1) the transmission of the communication system through learning; and (2) the ability to infer the communicative intent associated with a signal or action. We then describe two comparative case studies—the Bengalese finch and the domestic dog—in which parallel traits can be seen emerging following domestication. Finally, we turn to the role of domestication in human evolution. We argue that the cultural evolution of language structure has its origin in an earlier process of self-domestication.     

Modelling and optimization of a recombinant BHK-21 cultivation process using hybrid grey-box systems

In this work a model-based optimization study of fed-batch BHK-21 cultures expressing the human fusion glycoprotein IgG1-IL2 was performed. It was concluded that due to the complexity of the BHK metabolism it is rather difficult to develop a kinetic model with sufficient accuracy for optimization studies. Many kinetic expressions and a large number of parameters are involved resulting in a complex identification problem. For this reason, an alternative more cost-effective methodology based on hybrid grey-box models was adopted. Several model structures combining the a priori reliable first principles knowledge with black-box models were investigated using data from batch and fed-batch experiments. It has been reported in previous studies that the BHK metabolism exhibits modulation particularities when compared to other mammalian cell lines. It was concluded that these mechanisms were effectively captured by the hybrid model, this being of crucial importance for the successful optimization of the process operation. A method was proposed to monitor the risk of hybrid model unreliability and to constraint the optimization results to acceptable risk levels. From the optimization study it was concluded that the process productivity may be considerably increased if the glutamine and glucose concentrations are maintained at low levels during the growth phase and then glutamine feeding is increased.     

Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World

BACKGROUND: Archaeobotany, the study of plant remains from sites of ancient human activity, provides data for studying the initial evolution of domesticated plants. An important background to this is defining the domestication syndrome, those traits by which domesticated plants differ from wild relatives. These traits include features that have been selected under the conditions of cultivation. From archaeological remains the easiest traits to study are seed size and in cereal crops the loss of natural seed dispersal. SCOPE: The rate at which these features evolved and the ordering in which they evolved can now be documented for a few crops of Asia and Africa. This paper explores this in einkorn wheat (Triticum monococcum) and barley (Hordeum vulgare) from the Near East, rice (Oryza sativa) from China, mung (Vigna radiata) and urd (Vigna mungo) beans from India, and pearl millet (Pennisetum glaucum) from west Africa. Brief reference is made to similar data on lentils (Lens culinaris), peas (Pisum sativum), soybean (Glycine max) and adzuki bean (Vigna angularis). Available quantitative data from archaeological finds are compiled to explore changes with domestication. The disjunction in cereals between seed size increase and dispersal is explored, and rates at which these features evolved are estimated from archaeobotanical data. Contrasts between crops, especially between cereals and pulses, are examined. CONCLUSIONS: These data suggest that in domesticated grasses, changes in grain size and shape evolved prior to non-shattering ears or panicles. Initial grain size increases may have evolved during the first centuries of cultivation, within perhaps 500-1000 years. Non-shattering infructescences were much slower, becoming fixed about 1000-2000 years later. This suggests a need to reconsider the role of sickle harvesting in domestication. Pulses, by contrast, do not show evidence for seed size increase in relation to the earliest cultivation, and seed size increase may be delayed by 2000-4000 years. This implies that conditions that were sufficient to select for larger seed size in Poaceae were not sufficient in Fabaceae. It is proposed that animal-drawn ploughs (or ards) provided the selection pressure for larger seeds in legumes. This implies different thresholds of selective pressure, for example in relation to differing seed ontogenetics and underlying genetic architecture in these families. Pearl millet (Pennisetum glaucum) may show some similarities to the pulses in terms of a lag-time before truly larger-grained forms evolved.     

Theoretical basis of the plant domestication

Summary Plant domestication is stimulated by economic demands. Crop plant formation is controlled primarily by natural selection in cultivation; artificial selection is only a useful addition. The ecotypical nature of the initial material has great bearing on the success of domestication. The weeds of a convergent group were well adapted to being cultivated; weeds of a divergent group can be domesticated only with difficulty. Wild plants in nature are extremely varied ecotypically: some can be domesticated easily, others with difficulty. Some wild plants and weeds can be cultivated without genetic change (naturalization), while a genetic transmutation is necessary for the domestication of others (acclimatization). New domesticated ecotypes can be produced: 1. as a result of reconstruction of the initial populations and new ecotype synthesis on the basis of individual genotypes; 2. by means of hybridization of wild or weed initial genotypes with cultivated ones; 3. by use of new mutations in cultivation and further plant breeding.     

Crop domestication and the disruption of species interactions

The process of crop domestication involves artificial selection for beneficial traits in plants, such as yield, standard development times for ease of harvest, and pest and disease resistance. This process has greatly improved crop performance and can allow farmers to produce viable harvests in previously un-profitable circumstances. However, there is growing evidence that domestication may impact species interactions perhaps through the amplification of effects across spatial scales and so have a pervasive influence on the functioning and sustainability of agro-ecosystems. This can occur directly, through unintentional alteration to crop traits that disrupt the host-finding ability of natural enemies; or indirectly through alterations to within-plant nutritional quality that impacts herbivore size and density and then ramifies throughout food chains. At the field level, the low variability in traits between individual plants means that particular weed and invertebrate communities are associated with each crop type. At the landscape level, the use of one or a few varieties across wide spatial scales, planted and harvested relatively synchronously, further reduces diversity. This process acting across multiple spatial scales represents a considerable selection pressure that may result in feedback-loops which favour the occurrence of particular traits within the community (e.g. resistance to pesticides). In order to properly balance the ‘pros and cons’ of the widespread adoption of new varieties, for the future, we must consider how particular traits influence interactions within the wider ecological community, and how these effects amplify across spatial scales. Here we argue that the process of domestication (with the primary goal of yield increases) and the widespread use of a few varieties has led to potentially detrimental impacts on species interactions, and suggest possible strategies for mitigating some of these negative impacts in the future.