水稻的起源与驯化——来自基因组学的证据

 水稻是世界上最重要的粮食作物, 约1 万年前开始被驯化。由于水稻与其祖先野生种存在一定的遗传分化, 水稻的起源和驯化问题长期存在争议。本文综述了水稻起源和驯化方面的研究成果, 特别是近年来基因组学方面的证据, 认为水稻2 个亚种独立起源于野生祖先种内很早就分化的不同类群, 但一些驯化基因--控制重要农艺性状的基因, 可能首先在一个亚种中被驯化, 然后通过基因渐渗, 扩散到另一个亚种中。因此, 水稻驯化的关键是研究驯化基因的起源和扩散方式。随着大规模基因组测序技术的发展和相应数据分析方法的建立, 在全基因组水平对水稻及其祖先进行大规模分析, 已成为揭示水稻起源与驯化之谜的必由之路。     

The limits of selection during maize domestication

The domestication of all major crop plants occurred during a brief period in human history about 10,000 years ago. During this time, ancient agriculturalists selected seed of preferred forms and culled out seed of undesirable types to produce each subsequent generation. Consequently, favoured alleles at genes controlling traits of interest increased in frequency, ultimately reaching fixation. When selection is strong, domestication has the potential to drastically reduce genetic diversity in a crop. To understand the impact of selection during maize domestication, we examined nucleotide polymorphism in teosinte branched1, a gene involved in maize evolution. Here we show that the effects of selection were limited to the gene's regulatory region and cannot be detected in the protein-coding region. Although selection was apparently strong, high rates of recombination and a prolonged domestication period probably limited its effects. Our results help to explain why maize is such a variable crop. They also suggest that maize domestication required hundreds of years, and confirm previous evidence that maize was domesticated from Balsas teosinte of southwestern Mexico.     

Affinities of 'hyopsodontids' to elephant shrews and a Holarctic origin of Afrotheria

Macroscelideans (elephant shrews or sengis) are small-bodied (25-540 g), cursorial (running) and saltatorial (jumping), insectivorous and omnivorous placental mammals represented by at least 15 extant African species classified in four genera. Macroscelidea is one of several morphologically diverse but predominantly African placental orders classified in the superorder Afrotheria by molecular phylogeneticists. The distribution of modern afrotheres, in combination with a basal position for Afrotheria within Placentalia and molecular divergence-time estimates, has been used to link placental diversification with the mid-Cretaceous separation of South America and Africa. Morphological phylogenetic analyses do not support Afrotheria and the fossil record favours a northern origin of Placentalia. Here we describe fossil postcrania that provide evidence for a close relationship between North American Palaeocene-Eocene apheliscine 'hyopsodontid' 'condylarths' (early ungulates or hoofed mammals) and extant Macroscelidea. Apheliscine postcranial morphology is consistent with a relationship to other ungulate-like afrotheres (Hyracoidea, Proboscidea) but does not provide support for a monophyletic Afrotheria. As the oldest record of an afrothere clade, identification of macroscelidean relatives in the North American Palaeocene argues against an African origin for Afrotheria, weakening support for linking placental diversification to the break-up of Gondwana.     

Large-scale processes and the Asian bias in species diversity of temperate plants

An important issue in the study of biodiversity is the extent to which global patterns of species richness reflect large-scale processes and historical contingencies. Ecological interactions in local assemblages may constrain the number of species that can coexist, but differences in diversity in similar habitats within different regions (diversity anomalies) suggest that this limit is not firm. Variation in rate of species production could influence regional and perhaps local diversity independently of the ecological capacity of an area to support coexisting species, thereby creating diversity anomalies. Temperate Zone genera of plants that are disjunct between similar environments in eastern Asia and eastern North America (EAS-ENA) have twice as many species in Asia as in North America. Because lineages of these genera in Asia and North America are mostly sister pairs, they share a common history of adaptation and ecological relationship before disjunction. Thus, the diversity anomaly in EAS-ENA genera is not an artefact of taxon or habitat sampling but reflects differences in the net diversification (speciation-extinction) of the lineages in each of the continents. Here we propose that the most probable cause of the EAS-ENA anomaly in diversity is the extreme physiographical heterogeneity of temperate eastern Asia, especially compared with eastern North America, which in conjunction with climate and sea-level change has provided abundant opportunities for evolutionary radiation through allopatric speciation.     

Two new carnivores from an unusual late Tertiary forest biota in eastern North America

Late Cenozoic terrestrial fossil records of North America are biased by a predominance of mid-latitude deposits, mostly in the western half of the continent. Consequently, the biological history of eastern North America, including the eastern deciduous forest, remains largely hidden. Unfortunately, vertebrate fossil sites from this vast region are rare, and few pertain to the critically important late Tertiary period, during which intensified global climatic changes took place. Moreover, strong phylogenetic affinities between the flora of eastern North America and eastern Asia clearly demonstrate formerly contiguous connections, but disparity among shared genera (eastern Asia-eastern North America disjunction) implies significant periods of separation since at least the Miocene epoch. Lacustrine sediments deposited within a former sinkhole in the southern Appalachian Mountains provide a rare example of a late Miocene to early Pliocene terrestrial biota from a forested ecosystem. Here we show that the vertebrate remains contained within this deposit represent a unique combination of North American and Eurasian taxa. A new genus and species of the red (lesser) panda (Pristinailurus bristoli), the earliest and most primitive so far known, was recovered. Also among the fauna are a new species of Eurasian badger (Arctomeles dimolodontus) and the largest concentration of fossil tapirs ever recorded. Cladistical analyses of the two new carnivores strongly suggest immigration events that were earlier than and distinct from previous records, and that the close faunal affinities between eastern North America and eastern Asia in the late Tertiary period are consistent with the contemporaneous botanical record.     

串珠藻目的现代地理分布和起源

对串珠藻目的现代地理分布和可能的起源进行了初步分析。初步确定串珠藻目植物的现代地理分布中心在东亚和东南亚地区 ,北美和大洋州是两个次分布中心。推测串珠藻目植物可能的起源地在古北大陆和古南大陆相连接的地区 ,可能的起源时间在三叠纪之前。文中对串珠藻目植物可能的起源和散布途径也作了推测 ,对其现代分布格局及成因也进行了初步分析     

从接受美学审视文学翻译策略取向

从接受美学的角度探讨了中国文学翻译策略选择的不同取向，认为文学翻译不是简单的归化为主或异化为主的问题，而是根据读者的文化接受程度不同可划分为四个取向阶段：归化为主、少量异化为辅阶段，归化为主、大量异化为辅阶段，异化为主、大量归化为辅阶段和异化为主、少量归化为辅阶段。     

徐州植物区系组成及其特点

本文论述了徐州植物区系的组成及其特点。结果表明,徐州现有种子植物850种,隶属于130科,486属。本地植物以北温带、泛热带、东亚和东亚——北美成分为主体。区系特点表现为:1）地理成分复杂;2）区系起源古老;3） 北温带成分占优势。     

Genetic evidence for Near-Eastern origins of European cattle

The limited ranges of the wild progenitors of many of the primary European domestic species point to their origins further east in Anatolia or the fertile crescent. The wild ox (Bos primigenius), however, ranged widely and it is unknown whether it was domesticated within Europe as one feature of a local contribution to the farming economy. Here we examine mitochondrial DNA control-region sequence variation from 392 extant animals sampled from Europe, Africa and the Near East, and compare this with data from four extinct British wild oxen. The ancient sequences cluster tightly in a phylogenetic analysis and are clearly distinct from modern cattle. Network analysis of modern Bos taurus identifies four star-like clusters of haplotypes, with intra-cluster diversities that approximate to that expected from the time depth of domestic history. Notably, one of these clusters predominates in Europe and is one of three encountered at substantial frequency in the Near East. In contrast, African diversity is almost exclusively composed of a separate haplogroup, which is encountered only rarely elsewhere. These data provide strong support for a derived Near-Eastern origin for European cattle.     

深层碎屑岩含油气储层发育特征

基于深层油气藏的最新数据,对世界范围内深层碎屑岩油气藏富集规律及储层发育特征进行了统计分析.中南美和北美(不包括美国本土48州)深层碎屑岩发现的油气探明和控制(2P)可采储量最多,其中北美发现的石油2P可采储量最多,而中南美发现的天然气和凝析油2P可采储量最多.全球深层碎屑岩油气最富集的六大盆地依次为墨西哥湾、东委内瑞拉、阿拉伯、南里海、塔里木和圣克鲁斯-塔里哈盆地.在深层条件下,尽管储层通常表现为物性整体差,但仍可发育优质储层.深层油气勘探应立足于对“甜点”的预测,重点考虑颗粒薄膜、孔隙流体超压和盐岩发育对深层砂岩储层原生孔隙的保存作用.     

Stimulated influences of Lake Agassiz on the climate of central North America 11,000 years ago

Eleven thousand years ago, large lakes existed in central and eastern North America along the margin of the Laurentide Ice Sheet. The large-scale North American climate at this time has been simulated with atmospheric general circulation models, but these relatively coarse global models do not resolve potentially important features of the mesoscale circulation that arise from interactions among the atmosphere, ice sheet, and proglacial lakes. Here we present simulations of the climate of central and eastern North America 11,000 years ago with a high-resolution, regional climate model nested within a general circulation model. The simulated climate is in general agreement with that inferred from palaeoecological evidence. Our experiments indicate that through mesoscale atmospheric feedbacks, the annual delivery of moisture to the Laurentide Ice Sheet was diminished at times of a large, cold Lake Agassiz relative to periods of lower lake stands. The resulting changes in the mass balance of the ice sheet may have contributed to fluctuations of the ice margin, thus affecting the routing of fresh water to the North Atlantic Ocean. A retreating ice margin during periods of high lake level may have opened an outlet for discharge of Lake Agassiz into the North Atlantic. A subsequent advance of the ice margin due to greater moisture delivery associated with a low lake level could have dammed the outlet, thereby reducing discharge to the North Atlantic. These variations may have been decisive in causing the Younger Dryas cold event.     

Space geodetic evidence for rapid strain rates in the New Madrid seismic zone of central USA

In the winter of 1811-1812, near the town of New Madrid in the central United States and more than 2,000 km from the nearest plate boundary, three earthquakes within three months shook the entire eastern half of the country and liquefied the ground over distances far greater than any historic earthquake in North America. The origin and modern significance of these earthquakes, however, is highly contentious. Geological evidence demonstrates that liquefaction due to strong ground shaking, similar in scale to that generated by the New Madrid earthquakes, has occurred at least three and possibly four times in the past 2,000 years (refs 4-6), consistent with recurrence statistics derived from regional seismicity. Here we show direct evidence for rapid strain rates in the area determined from a continuously operated global positioning system (GPS) network. Rates of strain are of the order of 10(-7) per year, comparable in magnitude to those across active plate boundaries, and are consistent with known active faults within the region. These results have significant implications for the definition of seismic hazard and for processes that drive intraplate seismicity.     

A deep-bodied ginglymodian fish from the Middle Triassic of eastern Yunnan Province, China, and the phylogeny of lower neopterygians

The Ginglymodi are a group of ray-finned fishes that make up one of three major subdivisions of the infraclass Neopterygii.Ex- tant ginglymodians are represented by gars,which inhabit freshwater environments of North and Central America and Cuba.Here, we report the discovery of well-preserved fossils of a new ginglymodian,Kyphosichthys grandei gen.et sp.nov.,from the Middle Triassic(Anisian)marine deposits(Guanling Formation)in Luoping,eastern Yunnan Province,China.The discovery documents the first known fossil record of highly deep-bodied ginglymodians,adding new information on the early morphological diversity of this group.The studies of functional morphology of extant deep-bodied fishes indicate that Kyphosichthys is not a fast swim- mer but has a good performance in precise maneuvering,representing a morphological adaptation to structurally complex habitats (e.g.thick macrophyte beds,rocky areas,or coral reefs),which differs from the other members of this group.A cladistic analysis with the new fish taxon included supports the hypothesis that the Ginglymodi are more closely related to the Halecomorphi than to the Teleostei.Represented by Felberia,Kyphosichthys,and Dapedium,a highly deep and short fish body type has inde- pendently evolved at least three times in the stem-group neopterygians,ginglymodians,and basal teleosts within the lower neop- terygians of the Triassic.     

Experimental infection of bats with Geomyces destructans causes white-nose syndrome

White-nose syndrome (WNS) has caused recent catastrophic declines among multiple species of bats in eastern North America. The disease's name derives from a visually apparent white growth of the newly discovered fungus Geomyces destructans on the skin (including the muzzle) of hibernating bats. Colonization of skin by this fungus is associated with characteristic cutaneous lesions that are the only consistent pathological finding related to WNS. However, the role of G. destructans in WNS remains controversial because evidence to implicate the fungus as the primary cause of this disease is lacking. The debate is fuelled, in part, by the assumption that fungal infections in mammals are most commonly associated with immune system dysfunction. Additionally, the recent discovery that G. destructans commonly colonizes the skin of bats of Europe, where no unusual bat mortality events have been reported, has generated further speculation that the fungus is an opportunistic pathogen and that other unidentified factors are the primary cause of WNS. Here we demonstrate that exposure of healthy little brown bats (Myotis lucifugus) to pure cultures of G. destructans causes WNS. Live G. destructans was subsequently cultured from diseased bats, successfully fulfilling established criteria for the determination of G. destructans as a primary pathogen. We also confirmed that WNS can be transmitted from infected bats to healthy bats through direct contact. Our results provide the first direct evidence that G. destructans is the causal agent of WNS and that the recent emergence of WNS in North America may represent translocation of the fungus to a region with a naive population of animals. Demonstration of causality is an instrumental step in elucidating the pathogenesis and epidemiology of WNS and in guiding management actions to preserve bat populations against the novel threat posed by this devastating infectious disease.     

Ancestry of unisexual salamanders.

In eastern North America there are populations of all-female salamanders that incorporate the nuclear genomes of two or three of four sympatric bisexual species. The hybrids can be diploid, triploid, tetraploid or pentaploid, and 18 different combinations have been reported. All hybrids require sperm from a sympatric male of one of the bisexual species to reproduce, but the sperm may or may not be incorporated in the egg. Some of the hybrids are believed to represent separate, clonal species, but little is known of the origin of this hybrid complex. Vertebrate mitochondrial DNA is inherited maternally, allowing identification of the female parent that gave rise to hybrid lineages. A portion of the cytochrome b gene was sequenced from diploid and triploid hybrids that represent combinations of all four species. Nearly all hybrids had a similar mitochondrial genome sequence, independent of nuclear genome composition and ploidy, and the sequence was distinct from that of any of the four bisexual species. The hybrids maintain a mitochondrial lineage that has evolved independently of their nuclear genome and represent the most ancient known unisexual vertebrate lineage.     

Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (~2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.     

Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (??2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.     

Evidence from mitochondrial DNA that African honey bees spread as continuous maternal lineages

African honey bees have populated much of South and Central America and will soon enter the United States. The mechanism by which they have spread is controversial. Africanization may be largely the result of paternal gene flow into extant European populations or, alternatively, of maternal migration of feral swarms that have maintained an African genetic integrity. We have been using both mitochondrial and nuclear DNA restriction fragment length polymorphisms to follow the population dynamics between European and African bees. In earlier reports, we suggested that if African honey bees had distinctive mitochondrial (mt) DNA, then it could potentially distinguish the relative contributions of swarming and mating to the Africanization process. Because mtDNA is maternally inherited, it would not be transmitted by mating drones and only transported by queens accompanying swarms. Furthermore, the presence of African mtDNA would reflect unbroken maternal lineages from the original bees introduced from Africa. The value of mtDNA for population studies in general has been reviewed recently. Here we report that 19 feral swarms, randomly caught in Mexico, all carried African mtDNA. Thus, the migrating force of the African honey bee in the American tropics consists of continuous African maternal lineages spreading as swarms. The mating of African drones to European queens seems to contribute little to African bee migration.     

北美超低渗致密油藏提高采收率技术现状

在过去的十年中，北美致密油气的开发技术日渐成熟，其中，最具代表性的技术是水力压裂和水平钻井技术的结合。然而，现有依靠天然能量的衰竭式开发只能采出超低渗储层中的少部分原油（采出程度低于10%），导致致密储层中仍存在大量剩余油。因此，非常规超低渗油藏提高采收率技术的研究日趋重要。目前，全世界90%以上的致密油产量来自美国，其开采技术在非常规致密油的开发领域具有明显优势。并且，在过去的十年间，北美的石油公司已经对针对致密低渗油藏的提高采收率（EOR）技术进行了许多现场测试。鉴于美国在非常规致密油的勘探开发中具有领先地位，重点对北美致密油资源开发中提高采收率措施的现场经验进行了总结和评价，并指出了其目前面临的主要困难和挑战。此项研究对于中国未来超低渗致密油藏提高采收率技术的发展具有指导和借鉴意义。     

基于12S rRNA 基因序列推断中国及北美部分滑蜥属（有鳞目:石龙子科）物种的生物地理和亲缘关系

许多东亚和北美的生物类群之间呈现较近的亲缘关系,格雷分布即指这种生物洲际间断分布的现象.本文通过线粒体DNA (mtDNA) 12S rRNA基因序列分析,证明北美的滑蜥属Scincella (Squamata: Scincidae)物种Sc. lateralis 与中国的滑蜥属南滑蜥种组呈现典型的格雷分布. 南滑蜥种组包括宁波滑蜥Sc. modesta,秦岭滑蜥Sc. tsinlingensis,南滑蜥Sc. reevesii,和一个采自广东鼎湖山自然保护区的未命名种Scincella indet..这个鼎湖山未命名种并不具备滑蜥属所特有的鉴别性特征“睑窗”,但显示它与Sc. modesta,Sc. tsinlingensis都是由Sc. reevesii演化而来的近缘种.证实了之前认为亚洲的蜓蜥属Sphenomorphus 与滑蜥属Scincella是复系的观点,目前美洲物种Sp. cherriei应隶属于滑蜥属Scincella,具睑窗或不具睑窗的物种分别出现在系统树的不同分支中）.支持前人将Kaestlea travancorica从滑蜥属中划分出去的观点.根据分子钟估算,北美的滑蜥从它们的中国祖先分化出来的时间可追溯到第三纪中新世,约7.3-21.6百万年前,当时白令陆桥还露出海平面而且气候湿润. 该研究为洲际分布的物种的系统发育和生物地理研究提供了理论依据.