ARCHAEOLOGICAL DATA REVEAL SLOW RATES OF EVOLUTION DURING PLANT DOMESTICATION

Domestication is an evolutionary process of species divergence in which morphological and physiological changes result from the cultivation/tending of plant or animal species by a mutualistic partner, most prominently humans. Darwin used domestication as an analogy to evolution by natural selection although there is strong debate on whether this process of species evolution by human association is an appropriate model for evolutionary study. There is a presumption that selection under domestication is strong and most models assume rapid evolution of cultivated species. Using archaeological data for 11 species from 60 archaeological sites, we measure rates of evolution in two plant domestication traits—nonshattering and grain/seed size increase. Contrary to previous assumptions, we find the rates of phenotypic evolution during domestication are slow, and significantly lower or comparable to those observed among wild species subjected to natural selection. Our study indicates that the magnitudes of the rates of evolution during the domestication process, including the strength of selection, may be similar to those measured for wild species. This suggests that domestication may be driven by unconscious selection pressures similar to that observed for natural selection, and the study of the domestication process may indeed prove to be a valid model for the study of evolutionary change.     

Evaluating the self‐domestication hypothesis of human evolution

“Self‐domestication” has been invoked to understand important aspects of human evolution, integrating physiological, behavioral, and morphological information in a novel way. It proposes that selection for reduced aggression on animals undergoing domestication provides a model for selection favoring prosocial behaviors in humans and for a set of seemingly independent features, which arose as a result of developmental correlation. We review the history of the idea and examine patterns of domestication. A lack of empirical studies on evolutionary rates and variation thwarts meaningful comparison with domestication. The neural crest hypothesis for domestication has great explanatory power but it is difficult to test. We suggest a scenario in which the morphological byproducts of domestication can act as an honest signal of reduced xenophobia. Future studies should test if alternative explanations for the features deemed to result from self‐domestication are mutually exclusive and generate data to test predictions of these hypotheses.     

Global investigation of the co‐evolution of MIRNA genes and microRNA targets during soybean domestication

Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome‐wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA–target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA–target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA–target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA–target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co‐evolution of MIRs and miRNA targets during soybean domestication.     

家马的驯化起源与遗传演化特征

人类文明发展历史中, 家马(Equus ferus caballus)曾是推动文化交流、促进人类社会发展的主要动力。关于家马何时、何地被驯化以及在此过程中其遗传演化如何被人类影响等一直备受关注。近年来随着遗传学技术的发展, 人们对该问题有了更为深入的理解。本文回顾了近二十年来相关研究所取得的成果, 探讨了家马的驯化起源中心和驯化过程中的遗传演化特征, 并对未来的研究方向以及遗传资源保护提出了建议。分子标记遗传学和考古学研究认为家马可能来自多个驯化起源地种群, 然而最近的古DNA研究结果表明, 现代家马的驯化起源可能比之前人们所猜测的更加复杂, 古代博泰马被认为是最早被驯化的家马, 然而最近被证实并不是现代家马的直系祖先。如此复杂的驯化问题可能从多学科的层次才能解析清楚。人类社会活动直接或间接影响了家马的演化历程, 特别是工业革命以来家马的遗传基础发生了巨大变化, 其遗传多样性开始急剧衰退, 不少地方品种正逐渐走向衰落甚至灭绝。为确保农业生态安全不受威胁, 建议加强家马遗传资源保护与动物遗传学和文化地理之间的联系研究。     

Early agricultural pathways: moving outside the 'core area' hypothesis in Southwest Asia

The origins of agriculture in the Near East has been associated with a 'core area', located in south-eastern Turkey, in which all major crops were brought into domestication within the same local domestication system operated by a single cultural group. Such an origin leads to a scenario of rapid invention of agriculture by a select cultural group and typically monophyletic origins for most crops. Surprisingly, support for a core area has never been directly tested with archaeological evidence. Over the past decade a large amount of new archaeological and genetic evidence has been discovered which brings new light on the origins of agriculture. In this review, this new evidence was brought together in order to evaluate whether a core region of origin is supported. Evidence shows that origins began earlier than previously assumed, and included 'false starts' and dead ends that involved many more species than the typical eight founder crops associated with the core area. The rates at which domestication syndrome traits became fixed were generally slow, rather than rapid, and occurred over a geographically wide range that included the North and South Levant as well as the core area. Finally, a survey of the estimated ages of archaeological sites and the onset of domestication indicates that the domestication process was ongoing in parallel outside of the core area earlier than within it. Overall, evidence suggests a scenario in which crops were domesticated slowly in different locations around the Near East rather than emanating from a core area.     

Diversity in organization and the origin of gene orders in the mitochondrial DNA molecules of the genus Saccharomyces

Sequencing of the Saccharomyces cerevisiae nuclear and mitochondrial genomes provided a new background for studies on the evolution of the genomes. In this study, mitochondrial genomes of a number of Saccharomyces yeasts were mapped by restriction enzyme analysis, the orders of the genes were determined, and two of the genes were sequenced. The genome organization, i.e., the size, presence of intergenic sequences, and gene order, as well as polymorphism within the coding regions, indicate that Saccharomyces mtDNA molecules are dynamic structures and have undergone numerous changes during their evolution. Since the separation and sexual isolation of different yeast lineages, the coding parts have been accumulating point mutations, presumably in a linear manner with the passage of time. However, the accumulation of other changes may not have been a simple function of time. Larger mtDNA molecules belonging to Saccharomyces sensu stricto yeasts have acquired extensive intergenic sequences, including guanosine-cytosine-rich clusters, and apparently have rearranged the gene order at higher rates than smaller mtDNAs belonging to the Saccharomyces sensu lato yeasts. While within the sensu stricto group transposition has been a predominant mechanism for the creation of novel gene orders, the sensu lato yeasts could have used both transposition- and inversion-based mechanisms.     

Grinding up wheat: a massive loss of nucleotide diversity since domestication

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample of 101 individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify 2 genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms--by 69% in bread wheat and 84% in durum wheat--with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3--giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness--an important trait for end-use quality in wheat.     

Heterothallism in Saccharomyces cerevisiae isolates from nature: effect of HO locus on the mode of reproduction

Understanding the evolution of sex and recombination, key factors in the evolution of life, is a major challenge in biology. Studies of reproduction strategies of natural populations are important to complement the theoretical and experimental models. Fungi with both sexual and asexual life cycles are an interesting system for understanding the evolution of sex. In a study of natural populations of yeast Saccharomyces cerevisiae , we found that the isolates are heterothallic, meaning their mating type is stable, while the general belief is that natural S. cerevisiae strains are homothallic (can undergo mating-type switching). Mating-type switching is a gene-conversion process initiated by a site-specific endonuclease HO; this process can be followed by mother–daughter mating. Heterothallic yeast can mate with unrelated haploids (amphimixis), or undergo mating between spores from the same tetrad (intratetrad mating, or automixis), but cannot undergo mother–daughter mating as homothallic yeasts can. Sequence analysis of HO gene in a panel of natural S. cerevisiae isolates revealed multiple mutations. Good correspondence was found in the comparison of population structure characterized using 19 microsatellite markers spread over eight chromosomes and the HO sequence. Experiments that tested whether the mating-type switching pathway upstream and downstream of HO is functional, together with the detected HO mutations, strongly suggest that loss of function of HO is the cause of heterothallism. Furthermore, our results support the hypothesis that clonal reproduction and intratetrad mating may predominate in natural yeast populations, while mother–daughter mating might not be as significant as was considered.     

Reproductive Isolation during Domestication

It has been hypothesized that reproductive isolation should facilitate evolution under domestication. However, a systematic comparison of reproductive barrier strength between crops and their progenitors has not been conducted to test this hypothesis. Here, we present a systematic survey of reproductive barriers between 32 economically important crop species and their progenitors to better understand the role of reproductive isolation during the domestication process. We took a conservative approach, avoiding those types of reproductive isolation that are poorly known for these taxa (e.g., differences in flowering time). We show that the majority of crops surveyed are isolated from their progenitors by one or more reproductive barriers, despite the fact that the most important reproductive barrier in natural systems, geographical isolation, was absent, at least in the initial stages of domestication for most species. Thus, barriers to reproduction between crops and wild relatives are closely associated with domestication and may facilitate it, thereby raising the question whether reproductive isolation could be viewed as a long-overlooked "domestication trait." Some of the reproductive barriers observed (e.g., polyploidy and uniparental reproduction), however, may have been favored for reasons other than, or in addition to, their effects on gene flow.     

Comparison of fermentative capacities of industrial baking and wild-type yeasts of the species Saccharomyces cerevisiae in different sugar media

AIMS: To compare the fermentative capacity of wild and domesticated isolates of the genus Saccharomyces. METHODS AND RESULTS: The fermentative capacity of yeasts from a variety of wild and domesticated sources was tested in synthetic dough media that mimic major bread dough types. Domesticated yeast strains were found to have better maltose-utilizing capacity than wild yeast strains. The capacity to ferment sugars under high osmotic stress was randomly distributed amongst wild and baking strains of Saccharomyces. CONCLUSION: The domestication of bakers' yeast has enhanced the ability of yeasts to ferment maltose, without a similar impact on the fermentative capacity under high osmotic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: This study, combined with molecular studies of both wild and domesticated yeast, showed that domestication of bakers' yeast has resulted in improved maltose utilization, apparently via the duplication and mutation of the MAL genes.     

Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions

Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time-course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off-flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in ‘fast motion’ in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.     

Application of the reuseable, KanMX selectable marker to industrial yeast: construction and evaluation of heterothallic wine strains of Saccharomyces cerevisiae, possessing minimal foreign DNA sequences

The characterisation of wine yeasts and the complex metabolic processes influencing wine fermentation and the quality of wine might best be achieved by exploiting the standard classical and recombinant genetic techniques which have been successfully used with laboratory strains. However, application of these techniques to industrial strains has been restricted because such strains are typically prototrophic and often polyploid. To overcome this problem, we have identified commercial wine strains with good mating and sporulation properties from which heterothallic derivatives were constructed by disruption of the HO gene. Consequently, these haploids are amenable to genetic analysis, whilst retaining desirable wine-making properties. The approach used was an adaptation of a previously published gene disruption procedure for laboratory yeast and is based on the acquisition of geneticin resistance from a removable KanMX marker. The present work is the first report of the application of a construct of this type to the disruption of the HO gene in wine yeasts that are in common commercial use. Most of the 4.9-kb disruption construct was successfully removed from the genome of the haploid derivative strains by loop-out of the KanMX marker through meiotic recombination. Sequencing of the HO region confirmed the reduction of foreign sequences to a 582-bp fragment comprised largely of a single direct repeat at the target gene. The removal of the active foreign gene (conferring antibiotic resistance) allows the application of other constructs based on the KanMX module without the need to resort to other selectable marker systems. Laboratory-scale fermentation trials typically showed minimal differences between the HO disruptants and the parental wine strains in terms of fermentation kinetics and formation of key metabolites.     

Molecular approaches to origin,ancestry and domestication history of crop plants: Barley and clover as examples

Knowledge of the origin and domestication history of crop plants is important for studies aiming at avoiding the erosion of genetic resources due to the loss of ecotypes and landraces and habitats and increased urbanization. Such knowledge also strengthens the capacity of modern farming system to develop and scale-up the domestication of high value potential crops that can be achieved by improving the knowledge that help to identify and select high value plant species within their locality, identify and apply the most appropriate propagation techniques for improving crops and integrate improved crop species into the farming systems. The study of domestication history and ancestry provide means for germplasm preservation through establishment of gene banks, largely as seed collections, and preservation of natural habitats. Information about crop evolution and specifically on patterns of genetic change generated by evolution prior, during, and after domestication, is important to develop sound genetic conservation programs of genetic resources of crop plants and also increases the efficiency of breeding programs. In recent years, molecular approaches have contributed to our understanding of the aspects of plant evolution and crops domestication. In this article, aspects of crops domestication are outlined and the role of molecular data in elucidating the ancestry and domestication of crop plants are outlined. Particular emphasis is given to the contribution of molecular approaches to the origin and domestication history of barley and the origin and ancestry of the Egyptian clover.     

Reaction System for Violaxanthin De-Epoxidase with PSII Membranes

PSII membranes were used as a substrate for violaxanthin de-epoxidase(VDE) that had been solubilized from spinach thylakoids by sonication.Inclusion of Tween 20 in the assay mixture was essential, althoughthe detergent apparently inhibited the activity in the conventionalassay with purified violaxanthin and lipid as substrate. Themaximum enhancing effect of the detergent was observed nearits critical micellar concentration. It is likely that the monomerof the detergent helped VDE react with the substrate in themembranes. Dependence of the activity on the substrate concentrationsuggested that VDE functions at least at two sites in the membranes,probably on both their lumenal and stromal surfaces. The abilityof the enzyme to function on the stromal surface in in vitroassays was demonstrated by using intact thylakoids as the substrate.Under such conditions where the endogenous VDE was functioningin the lumen, the exogenously added VDE converted an-theraxanthinto zeaxanthin in the absence of Tween 20. This result suggeststhat, in the reaction with PSII membranes, the detergent wasrequired for VDE to react with violaxanthin but not with antheraxanthin.Otherwise, the detergent was necessary for the reaction on thelumenal surface. (Received September 5, 1997; Accepted October 19, 1997)     

The influence of phase transitions in phosphatidylethanolamine models on the activity of violaxanthin de-epoxidase

In the present study, the influence of the phospholipid phase state on the activity of the xanthophyll cycle enzyme violaxanthin de-epoxidase (VDE) was analyzed using different phosphatidylethanolamine species as model lipids. By using (31)P NMR spectroscopy, differential scanning calorimetry and temperature dependent enzyme assays, VDE activity could directly be related to the lipid structures the protein is associated with. Our results show that the gel (L beta) to liquid-crystalline (L alpha) phase transition in these single lipid component systems strongly enhances both the solubilization of the xanthophyll cycle pigment violaxanthin in the membrane and the activity of the VDE. This phase transition has a significantly stronger impact on VDE activity than the transition from the L alpha to the inverted hexagonal (HII) phase. Especially at higher temperatures we found increased VDE reaction rates in the presence of the L alpha phase compared to those in the presence of HII phase forming lipids. Our data furthermore imply that the HII phase is better suited to maintain high VDE activities at lower temperatures.     

HO gene polymorphism in Saccharomyces industrial yeasts and application of novel HO genes to convert homothallism to heterothallism in combination with the mating-type detection cassette

Southern blot analysis of industrial yeasts showed that all top-fermenting yeasts, distiller's yeasts and a proportion of wine yeasts tested in the present study produced a hybridization signal (approximately 7 kb), corresponding to a Saccharomyces cerevisiae-type HO gene (Sc-HO). It also showed that bottom-fermenting yeasts gave rise to 7-kb and 4-kb hybridization signals, corresponding to the Sc-HO gene and the lager yeast HO gene (Lg-HO), respectively. Two wine yeasts produced a 4-kb hybridization signal, corresponding to Lg-HO; and one wine yeast produced 2.5-kb and 1.5-kb hybridization bands, corresponding to a S. uvarum-type HO gene (Uv-HO). Partial nucleotide sequences of HO genes amplified from these wine yeasts perfectly matched those of Lg-HO and Uv-HO, respectively. HO disruption vectors were constructed by inserting a dominant selective marker PGK1p-neo and the mating-type detection cassette MFalpha1p-PHO5 within the Lg-HO or Uv-HO gene. From transformants carrying a single-disrupted ho gene, mating-competent progenies were easily obtained through meiosis. Moreover, mating-competent derivatives appearing at very low frequency could be obtained from a double-disrupted ho transformant without meiosis (even from a wine yeast lacking sporulation ability), because the sensitive phosphatase-staining method allowed detection of the Pho+ mating-competent derivatives from confluent colonies by the random spore method. Our study describes a rapid and convenient method for isolating mating-competent clones from industrial yeasts.     

The complex history of the domestication of rice

BACKGROUND: Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. SCOPE: Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. CONCLUSIONS: The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.     

The influence of phase transitions in phosphatidylethanolamine models on the activity of violaxanthin de-epoxidase

In the present study, the influence of the phospholipid phase state on the activity of the xanthophyll cycle enzyme violaxanthin de-epoxidase (VDE) was analyzed using different phosphatidylethanolamine species as model lipids. By using ³¹P NMR spectroscopy, differential scanning calorimetry and temperature dependent enzyme assays, VDE activity could directly be related to the lipid structures the protein is associated with. Our results show that the gel (L_β) to liquid-crystalline (L_α) phase transition in these single lipid component systems strongly enhances both the solubilization of the xanthophyll cycle pigment violaxanthin in the membrane and the activity of the VDE. This phase transition has a significantly stronger impact on VDE activity than the transition from the L_α to the inverted hexagonal (H_II) phase. Especially at higher temperatures we found increased VDE reaction rates in the presence of the L_α phase compared to those in the presence of H_II phase forming lipids. Our data furthermore imply that the H_II phase is better suited to maintain high VDE activities at lower temperatures.