农业的起源、传播与影响

农业是文明形成和发展的基础。约1万年以前,农业在西亚、中美洲和东亚地区几乎同时独立出现。西亚的两河流域被认为是小麦、大麦、燕麦等作物的起源中心;中美洲则是玉米、马铃薯和花生等农作物的诞生地;中国拥有两套独立的原始农业系统,分别是起源于长江中下游地区的稻作农业和黄河中游地区的粟-黍旱作农业,孕育了中华农耕文明。西亚的小麦农业、东亚的稻作和粟-黍农业逐步传播到世界上大多数地区,促进了早期农业全球化。15世纪末,新航路的开辟和众多贸易路线的出现加快了欧亚大陆和美洲大陆农作物的传播和融合,加速了农业全球化进程。农业的发展改变了人类改造和适应环境的能力;促进了人类定居,导致人群结构的重大变革,出现劳动分工和商品交换等,为人类提供了稳定的食物供应及储存,推动了人口的增长。农业起源和发展极大地增强了人类活动的强度和范围,深刻地影响着全球生态和气候环境。     

How ancient DNA may help in understanding the origin and spread of agriculture

The origin and spread of agriculture have been central questions in archaeology for the last 75 years and are increasingly being addressed by a multidisciplinary approach involving biologists, ecologists, geographers and anthropologists as well as archaeologists. Molecular genetics has the potential to make an important contribution, especially by enabling the number of times that a crop or animal was domesticated to be determined. Molecular genetics can also assign approximate dates to domestication events, identify the wild progenitor of a domesticate, and provide new forms of evidence relevant to agricultural spread. With wheat, molecular genetical studies of modern plants have suggested that einkorn was domesticated just once but that emmer might have been domesticated more than once. Ancient DNA studies of animal remains have benefited from progress made with equivalent analyses of human bones, and with plant material there have been clear demonstrations of DNA preservation in desiccated seeds. Charred remains have also been shown to contain ancient DNA but this finding is unexpected in view of the high temperatures to which these seeds have supposedly been exposed. Ancient DNA studies of wheat remains have been used in taxonomic identification and in assessment of the possible bread-making quality of the wheat grown at an Early Bronze Age site in Greece.     

Can the spread of agriculture in Europe be followed by tracing the spread of the weed Silene latifolia. A RAPD study

On the basis of gene frequency data of three flavone glycosylating genes, populations of the agricultural weed Silene latifolia (Caryophyllaceae) in Europe can be divided into two chemical races: an eastern and a western race. Morphological data also show a clear east-west division. When the two datasets are combined at least nine different geographical races can be distinguished using cluster analysis. Because these observations are hard to explain by selection, it has been proposed that these different races probably originated as a consequence of migration during the spread of agriculture over Europe in the past. To discriminate between selection and genetic drift many more selectively neutral easy-to-score characters are needed. In order to test whether random amplified polymorphic DNAs (RAPDs) might be suitable for this purpose, we performed a small-scale RAPD analysis on 16 geographical different populations. Using Jaccard's coefficient of similarity, we calculated genetic distances by pair-wise comparisons of both unique and shared amplification products, and a dendrogram was subsequently constructed using an unweighted pair-group method with arithmetical averages (UPGMA). On the basis of the dendrogram two clusters were discerned that clearly coincide with the aforementioned east-west division in populations. As there has been little or no artificial selection on this weed, its migration routes may be a good reflection of the different geographical routes agriculture has taken. We propose that a phylogenetic analysis of RAPD data of many more populations may provide additional information on the spread of agriculture over Europe.     

Evidence for phylogeographic structure in Lolium species related to the spread of agriculture in Europe. A cpDNA study

In order to explain the present distribution area of natural populations of two forage grasses species (Lolium perenne and L. rigidum), we studied genetic variation for maternally inherited chloroplast DNA (cpDNA) in 447 individual plants from 51 natural populations sampled throughout Europe and the Middle East. The detection of polymorphism by restriction analysis of PCR-amplified cpDNA fragments resulted in the identification of 15 haplotypes. Hierarchical analysis of chloroplastic diversity showed a high level of within-population diversity while, for both species, we found that about 40% of the total diversity still remains among populations. The use of previous isozymes data enabled us to estimate the pollen to seed flow ratio: pollen flow appears to be 3.5 times greater than seed flow for L. perenne and 2.2 times higher for L. rigidum. A stepwise weighted genetic distance between pairs of populations was calculated using the haplotypes frequencies of populations. A hierarchical clustering of populations clearly divides the two species, while two main clusters of L. perenne populations show a strong geographical structure. Different scenario are proposed for explaining the distribution area of the two species. Finally, evidence attesting that these geographical structures are related to the spread of agriculture in Europe are presented and discussed. Received: 5 November 1999 / Accepted: 24 November 1999     

Tracing the patterns of non-marine turtle richness from the Triassic to the Palaeogene: from origin to global spread

Turtles are key components of modern vertebrate faunas and their diversity and distributions are likely to be affected by anthropogenic climate change. However, there is limited baseline data on turtle taxonomic richness through time or assessment of their past responses to global environmental change. We used the extensive Triassic–Palaeogene (252–223 Ma) fossil record of terrestrial and freshwater turtles to investigate diversity patterns, finding substantial variation in richness through time and between continents. Globally, turtle richness was low from their Triassic origin until the Late Jurassic. There is strong evidence for high richness in the earliest Cretaceous of Europe, becoming especially high following the Cretaceous Thermal Maximum and declining in all continents by the end-Cretaceous. At the K–Pg boundary, South American richness levels changed little while North American richness increased, becoming very high during the earliest Palaeogene (Danian). Informative data are lacking elsewhere for this time period. However, the Selandian–Thanetian interval, approximately 5 myr after the K–Pg mass extinction, shows low turtle richness in Asia, Europe and South America, suggesting that the occurrence of exceptional turtle richness in the post-extinction Paleocene fauna of North America is not globally representative. Richness decreased over the Eocene–Oligocene boundary in North America but increased to its greatest known level for Europe, implying very different responses to dramatic climatic shifts. Time series regressions suggest number of formations sampled and palaeotemperature are the primary influencers of face-value richness counts, but additional factors not tested here may also be involved.     

Paleopathology and the origin of agriculture in the Levant

This study addresses changes in health which were consequential to the Neolithic transition in the southern Levant, judged on the basis of the study of specific and nonspecific stress indicators, trauma, and degenerative joint disease in 200 Natufian (hunter‐gatherer) skeletons (10,500–8300 BC) and 205 Neolithic (agricultural) skeletons (8300–5500 BC) from the southern Levant. The comparison of the health profiles of pre‐Neolithic (Natufian) and Neolithic populations reveals a higher prevalence of lesions indicative of infectious diseases among the Neolithic population, and an overall reduction in the prevalence of skull trauma among males. No change over time was observed in the prevalence of degenerative joint disease. These results indicate that in the southern Levant the Neolithic transition did not simply lead to an overall deterioration in health but rather resulted in a complex health profile which was shaped by 1) an increase exposure to disease agents, 2) changes in diet, 3) population aggregation in larger and denser settlements, 4) changes in activity patterns and the division of labor, and possibly 5) a higher resistant immunological system and response capacity to environmental aggressions (mainly infections). Am J Phys Anthropol 143:121–133, 2010. © 2010 Wiley‐Liss, Inc.     

Tracing the origin and evolution of plant TIR-encoding genes

Toll-interleukin-1 receptor (TIR)-encoding proteins represent one of the most important families of disease resistance genes in plants. Studies that have explored the functional details of these genes tended to focus on only a few limited groups; the origin and evolutionary history of these genes were therefore unclear. In this study, focusing on the four principal groups of TIR-encoding genes, we conducted an extensive genome-wide survey of 32 fully sequenced plant genomes and Expressed Sequence Tags (ESTs) from the gymnosperm Pinus taeda and explored the origins and evolution of these genes. Through the identification of the TIR-encoding genes, the analysis of chromosome positions, the identification and analysis of conserved motifs, and sequence alignment and phylogenetic reconstruction, our results showed that the genes of the TIR-X family (TXs) had an earlier origin and a wider distribution than the genes from the other three groups. TIR-encoding genes experienced large-scale gene duplications during evolution. A skeleton motif pattern of the TIR domain was present in all spermatophytes, and the genes with this skeleton pattern exhibited a conserved and independent evolutionary history in all spermatophytes, including monocots, that followed their gymnosperm origin. This study used comparative genomics to explore the origin and evolutionary history of the four main groups of TIR-encoding genes. Additionally, we unraveled the mechanism behind the uneven distribution of TIR-encoding genes in dicots and monocots.     

Tracing the spread of fibronectin type III domains in bacterial glycohydrolases

The evolutionary spread of 22 fibronectin type III (Fn3) sequences among a dozen bacterial enzymes has been traced by searching databases with the non-Fn3 parts of the enzyme sequences. Numerous homologues were found that lacked the Fn3 domains. In each case the related sequences were aligned, phylogenetic trees were constructed, and the occurrences of Fn3 units on the trees were noted. Comparison with phylogenetic trees prepared from the Fn3 segments themselves allowed inferences to be made about when the Fn3 units were shuffled into their present positions.Correspondence to: R.F. Doolittle     

Predicting the spatio-temporal spread of West Nile virus in Europe

West Nile virus is a widely spread arthropod-born virus, which has mosquitoes as vectors and birds as reservoirs. Humans, as dead-end hosts of the virus, may suffer West Nile Fever (WNF), which sometimes leads to death. In Europe, the first large-scale epidemic of WNF occurred in 1996 in Romania. Since then, human cases have increased in the continent, where the highest number of cases occurred in 2018. Using the location of WNF cases in 2017 and favorability models, we developed two risk models, one environmental and the other spatio-environmental, and tested their capacity to predict in 2018: 1) the location of WNF; 2) the intensity of the outbreaks (i.e. the number of confirmed human cases); and 3) the imminence of the cases (i.e. the Julian week in which the first case occurred). We found that climatic variables (the maximum temperature of the warmest month and the annual temperature range), human-related variables (rain-fed agriculture, the density of poultry and horses), and topo-hydrographic variables (the presence of rivers and altitude) were the best environmental predictors of WNF outbreaks in Europe. The spatio-environmental model was the most useful in predicting the location of WNF outbreaks, which suggests that a spatial structure, probably related to bird migration routes, has a role in the geographical pattern of WNF in Europe. Both the intensity of cases and their imminence were best predicted using the environmental model, suggesting that these features of the disease are linked to the environmental characteristics of the areas. We highlight the relevance of river basins in the propagation dynamics of the disease, as outbreaks started in the lower parts of the river basins, from where WNF spread towards the upper parts. Therefore, river basins should be considered as operational geographic units for the public health management of the disease.     

The origin and spread of the new daisy rust in Britain

Since 1997, wild and cultivated daisies in Britain and other European countries have been suffering from a rust fungus epidemic that menaces the future cultivation of horticultural varieties. The causal fungus was first discovered in Australia 100 years ago and may have evolved there from another rust fungus on daisies previously introduced from Europe. At present, ornamental daisies can be grown successfully only when protected by fungicide sprays.     

Tracing the origin of the RACTK1 K(+) channel

Potassium secretion by the kidney is vital for the maintenance of K(+) homeostasis. RACTK1, a putative inwardly rectifying potassium channel cloned from cultured rabbit collecting duct cells, has been proposed to play a role in this process. However, the lack of homology with any other cloned potassium channel and the inability to reproduce the results across different laboratories has brought into question the existence of RACTK1. Recently, it has been suggested that RACTK1 is a contamination from Escherichia coli. In this work we add conclusive evidence supporting the bacterial origin of RACTK1. Using both genomic PCR and RT-PCR we were unable to detect RACTK1 in a number of mammalian species. In addition sequencing of RACTK1 cDNA confirmed a complete homology between RACTK1 and a region of E. coli genomic DNA. Finally, a hypothesis on how RACTK1 could have been generated from a contamination by E. coli genomic DNA is presented.     

栽培茶树的驯化起源与传播

茶作为世界上最重要的饮品之一, 其栽培类型的驯化起源一直是人们关注的热点。本文总结了近年相关研究的进展, 讨论了存在的问题, 并对未来的研究方向提出建议。长江流域及以南地区分布有众多栽培茶树的野生近缘种, 特别集中于云南、贵州、广西等地; 一方面南方各族语言中“茶”发音的相似, 暗示了茶知识起源的单一性, 最可能起源于古代的巴蜀或云南, 另一方面遗传分析揭示栽培的茶存在多个起源中心, 即使Camellia sinensis (L.) O. Kuntze的几个栽培变种也可能起源于不同的地区; 文献记载, 茶的栽培中心曾经从西向东再向南迁移, 遗传多样性的变化也揭示了这一可能性, 但考古发现却提示最早的栽培茶可能出现在长江流域的最东部。我们推测在茶知识及栽培品种的传播过程中, 各地野生近缘植物的基因渗入栽培类型中, 或各地居民直接用当地野生茶培育出新的栽培茶类型, 从而导致遗传上的复杂性和语言上的一致性并存。茶树的祖先类型、起源地点、起源时间以及栽培品种的演变历程都还需要更为明确的证据, 未来应该以整个茶组植物为对象, 将茶文化、群体遗传学、谱系地理、人类学、气候变化、考古等多学科研究进行整合分析。     

A craniometric perspective on the transition to agriculture in Europe

Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.     

The role of hybridization in the origin and spread of asexuality in Daphnia

The molecular mechanisms leading to asexuality remain little understood despite their substantial bearing on why sexual reproduction is dominant in nature. Here, we examine the role of hybridization in the origin and spread of obligate asexuality in Daphnia pulex, arguably the best‐documented case of contagious asexuality. Obligately parthenogenetic (OP) clones of D. pulex have traditionally been separated into ‘hybrid’ (Ldh SF) and ‘nonhybrid’ (Ldh SS) forms because the lactase dehydrogenase (Ldh) locus distinguishes the cyclically parthenogenetic (CP) lake dwelling Daphnia pulicaria (Ldh FF) from its ephemeral pond dwelling sister species D. pulex (Ldh SS). The results of our population genetic analyses based on microsatellite loci suggest that both Ldh SS and SF OP individuals can originate from the crossing of CP female F₁ (D. pulex × D. pulicaria) and backcross with males from OP lineages carrying genes that suppress meiosis specifically in female offspring. In previous studies, a suite of diagnostic markers was found to be associated with OP in Ldh SS D. pulex lineages. Our association mapping supports a similar genetic mechanism for the spread of obligate parthenogenesis in Ldh SF OP individuals. Interestingly, our study shows that CP D. pulicaria carry many of the diagnostic microsatellite alleles associated with obligate parthenogenesis. We argue that the assemblage of mutations that suppress meiosis and underlie obligate parthenogenesis in D. pulex originated due to a unique historical hybridization and introgression event between D. pulex and D. pulicaria.     

Origins and spread of agriculture in Italy: a nonmetric dental analysis

Dental morphological traits were employed in this study as direct indicators of biological affinities among the populations that inhabited the Italian peninsula from the Upper Paleolithic-Mesolithic to Medieval times. Our analysis aims at contributing to the ongoing debate regarding the origin and spread of agriculture in the peninsula by contrasting the dental evidence of archaeological and modern molecular samples. It is not possible to generalize given the complex and dynamic nature of these populations. However, the results from the principal component analysis, maximum likelihood, mean measure of divergence, and multidimensional scaling do indicate a net separation of the Paleo-Mesolithic sample from the other groups that is not related to dental reduction. This suggests that the shift in dental morphology was the product of Neolithic populations migrating into the peninsula from other areas. Nonetheless, the Paleo-Mesolithic populations share several discriminative traits with the Neolithic group. The biological relevance of such evidence suggests that, to some minor extent, the spread of agriculture did not occur by total population replacement. Because of regional small sample sizes, this hypothesis cannot be tested on a micro-regional scale. It is, however, feasible to depict a scenario where processes of genetic mixture or replacement probably took place at different rates on a macro-regional level.     

Neolithic dairy farming at the extreme of agriculture in northern Europe

The conventional ‘Neolithic package’ comprised animals and plants originally domesticated in the Near East. As farming spread on a generally northwest trajectory across Europe, early pastoralists would have been faced with the challenge of making farming viable in regions in which the organisms were poorly adapted to providing optimal yields or even surviving. Hence, it has long been debated whether Neolithic economies were ever established at the modern limits of agriculture. Here, we examine food residues in pottery, testing a hypothesis that Neolithic farming was practiced beyond the 60th parallel north. Our findings, based on diagnostic biomarker lipids and δ¹³C values of preserved fatty acids, reveal a transition at ca 2500 BC from the exploitation of aquatic organisms to processing of ruminant products, specifically milk, confirming farming was practiced at high latitudes. Combining this with genetic, environmental and archaeological information, we demonstrate the origins of dairying probably accompanied an incoming, genetically distinct, population successfully establishing this new subsistence ‘package’.     

Intensive agriculture reduces soil biodiversity across Europe

Soil biodiversity plays a key role in regulating the processes that underpin the delivery of ecosystem goods and services in terrestrial ecosystems. Agricultural intensification is known to change the diversity of individual groups of soil biota, but less is known about how intensification affects biodiversity of the soil food web as a whole, and whether or not these effects may be generalized across regions. We examined biodiversity in soil food webs from grasslands, extensive, and intensive rotations in four agricultural regions across Europe: in Sweden, the UK, the Czech Republic and Greece. Effects of land‐use intensity were quantified based on structure and diversity among functional groups in the soil food web, as well as on community‐weighted mean body mass of soil fauna. We also elucidate land‐use intensity effects on diversity of taxonomic units within taxonomic groups of soil fauna. We found that between regions soil food web diversity measures were variable, but that increasing land‐use intensity caused highly consistent responses. In particular, land‐use intensification reduced the complexity in the soil food webs, as well as the community‐weighted mean body mass of soil fauna. In all regions across Europe, species richness of earthworms, Collembolans, and oribatid mites was negatively affected by increased land‐use intensity. The taxonomic distinctness, which is a measure of taxonomic relatedness of species in a community that is independent of species richness, was also reduced by land‐use intensification. We conclude that intensive agriculture reduces soil biodiversity, making soil food webs less diverse and composed of smaller bodied organisms. Land‐use intensification results in fewer functional groups of soil biota with fewer and taxonomically more closely related species. We discuss how these changes in soil biodiversity due to land‐use intensification may threaten the functioning of soil in agricultural production systems.