Inference of human population history from individual whole-genome sequences

The history of human population size is important for understanding human evolution. Various studies have found evidence for a founder event (bottleneck) in East Asian and European populations, associated with the human dispersal out-of-Africa event around 60 thousand years (kyr) ago. However, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH), a Korean male (SJK), three European individuals (J. C. Venter, NA12891 and NA12878 (ref. 9)) and two Yoruba males (NA18507 (ref. 10) and NA19239). We infer that European and Chinese populations had very similar population-size histories before 10-20?kyr ago. Both populations experienced a severe bottleneck 10-60?kyr ago, whereas African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60 and 250?kyr ago, possibly due to population substructure. We also infer that the differentiation of genetically modern humans may have started as early as 100-120?kyr ago, but considerable genetic exchanges may still have occurred until 20-40?kyr ago.     

Early Pliocene hominids from Gona, Ethiopia

Comparative biomolecular studies suggest that the last common ancestor of humans and chimpanzees, our closest living relatives, lived during the Late Miocene-Early Pliocene. Fossil evidence of Late Miocene-Early Pliocene hominid evolution is rare and limited to a few sites in Ethiopia, Kenya and Chad. Here we report new Early Pliocene hominid discoveries and their palaeoenvironmental context from the fossiliferous deposits of As Duma, Gona Western Margin (GWM), Afar, Ethiopia. The hominid dental anatomy (occlusal enamel thickness, absolute and relative size of the first and second lower molar crowns, and premolar crown and radicular anatomy) indicates attribution to Ardipithecus ramidus. The combined radioisotopic and palaeomagnetic data suggest an age of between 4.51 and 4.32 million years for the hominid finds at As Duma. Diverse sources of data (sedimentology, faunal composition, ecomorphological variables and stable carbon isotopic evidence from the palaeosols and fossil tooth enamel) indicate that the Early Pliocene As Duma sediments sample a moderate rainfall woodland and woodland/grassland.     

Reproductive isolation caused by colour pattern mimicry

Speciation is facilitated if ecological adaptation directly causes assortative mating, but few natural examples are known. Here we show that a shift in colour pattern mimicry was crucial in the origin of two butterfly species. The sister species Heliconius melpomene and Heliconius cydno recently diverged to mimic different model taxa, and our experiments show that their mimetic coloration is also important in choosing mates. Assortative mating between the sister species means that hybridization is rare in nature, and the few hybrids that are produced are non-mimetic, poorly adapted intermediates. Thus, the mimetic shift has caused both pre-mating and post-mating isolation. In addition, individuals from a population of H. melpomene allopatric to H. cydno court and mate with H. cydno more readily than those from a sympatric population. This suggests that assortative mating has been enhanced in sympatry.     

随谈"兄终弟继"之争

只要是同一血亲家族,不论隔房远近,散居异地或改为他姓,都视为同一家族。“兄终弟继”的目的是为了传宗接代,而不是为了财产继承。宋代广源州侬全福与特磨道侬夏卿在唐代同祖于山东青州,本是一家之人。侬智高起兵反宋是不得已的、正义的,并曾得到侬夏卿的很多帮助。     

“非个人化”：近年写实小说创作叙述话语的人文立场

通过对近年写实小说在创作上态度、方式、方法、模式等方面的分析,揭示出近年写实小说创作叙述话语“非个人化”的人文立场,并指出这种人文立场必将为当下中国文学创作的发展带来一次较大契机。     

巴人源流与巴人迁徙

巴人源流始于廪君之先,出自巫蜒;荆蛮弓鱼族巴师勇锐,歌舞以凌殷人;巴有人骠勇,泛称白虎蛮、板木盾蛮,雄踞川东北上千年.廪君族西迁,弓鱼族北迁、南迁,板木盾蛮亦流徒西、北地区.     

Conservation biology: lion attacks on humans in Tanzania

Large carnivores inspire opposition to conservation efforts owing to their impact on livestock and human safety. Here we analyse the pattern of lion attacks over the past 15 years on humans in Tanzania, which has the largest population of lions in Africa, and find that they have killed more than 563 Tanzanians since 1990 and injured at least 308. Attacks have increased dramatically during this time: they peak at harvest time each year and are most frequent in areas with few prey apart from bush pigs (Potamochoerus larvatus), the most common nocturnal crop pest. Our findings provide an important starting point for devising strategies to reduce the risk to rural Tanzanians of lion attacks.     

Extensible Framework for Rao-Blackwellized Filtering

The Rao-Blackwellized Particle Filter (RBPF) is widely used for high dimensional nonlinear systems, often with a linear Gaussian substructure. However, the RBPF is just a specific method in the class of Rao-Blackwellized Filtering (RBF). This paper analyzes the recursive structure of the RBF from a more general perspective. The research starts from a general system model and studies the interconnected relationships between the two subspaces during the iterations. The results illustrate the working mechanisms of the RBF with an extensible framework for easily building Rao-Blackwellized algorithms with common nonlinear filters. Several examples are given to illustrate how to build new filters using this framework.     

A primitive fish close to the common ancestor of tetrapods and lungfish

The relationship of the three living groups of sarcopterygians or lobe-finned fish (tetrapods, lungfish and coelacanths) has been a matter of debate. Although opinions still differ, most recent phylogenies suggest that tetrapods are more closely related to lungfish than to coelacanths. However, no previously known fossil taxon exhibits a concrete character combination approximating the condition expected in the last common ancestor of tetrapods and lungfish -- and it is still poorly understood how early sarcopterygians diverged into the tetrapod lineage (Tetrapodomorpha) and the lungfish lineage (Dipnomorpha). Here we describe a fossil sarcopterygian fish, Styloichthys changae gen. et sp. nov., that possesses an eyestalk and which exhibits the character combination expected in a stem group close to the last common ancestor of tetrapods and lungfish. Styloichthys from the Lower Devonian of China bridges the morphological gap between stem-group sarcopterygians (Psarolepis and Achoania) and basal tetrapodomorphs/basal dipnomorphs. It provides information that will help in the study of the relationship of early sarcopterygians, and which will also help to resolve the tetrapod-lungfish divergence into a documented sequence of character acquisition.     

A single origin of phenylketonuria in Yemenite Jews

Phenylketonuria (PKU) is a metabolic disease caused by recessive mutations of the gene encoding the hepatic enzyme phenylalanine hydroxylase (PAH). The incidence of PKU varies widely across different geographic areas, and is highest (about 1 in 5,000 live births) in Ireland and western Scotland, and among Yemenite Jews. A limited number of point mutations account for most of the PKU cases in the European population. Here we report that a single molecular defect--a deletion spanning the third exon of the PAH gene--is responsible for all the PKU cases among the Yemenite Jews. Examination of a random sample of Yemenite Jews using a molecular probe that detects the carriers of this deletion indicated a high frequency of the defective gene in this community. Although the deleted PAH gene was traced to 25 different locations throughout Yemen, family histories and official documents of the Yemenite Jewish community showed that the common ancestor of all the carriers of this genetic defect lived in San'a, the capital of Yemen, before the eighteenth century.     

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.     

Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.     

Complex speciation of humans and chimpanzees

Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al. suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and--even if the null model could be rejected--they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow (see ref. 2, for example). I therefore believe that their claim of hybridization is unwarranted.     

SARS冠状病毒的起源和进化初探

发展了一种研究基因序列进化的随机替代模型,根据一组从某个最近共同祖先演化而来的若干序列,可以预测此共同祖先序列,并计算随机替代概率矩阵,确定了从祖先序列的各个碱基到进化序列的各个碱基之间的替代概率。将这一模型应用于分析包括SARS冠状病毒在内的4种冠状病毒全基因组的演化规律,确定了在若干较保守的编码蛋白基因序列中同义替代位点的最近共同祖先序列以及分歧进化后的累计同义替代数目。结果表明,SARS病毒和其他几种已知的冠状病毒具有相当的进化历程,但存在不同的进化途径,支持了SARS病毒在造成此次大规模感染人体之前已经历了较长的进化历程的猜测。     

Huanglong Cave, a new late Pleistocene hominid site in Hubei Province, China

For the past two decades, the modern human origins debate has received significant interest from both the scientific community and the public. The two hypothe- ses “Out of Africa” and “Mutiregional evolution” are focuses of this debate[1-3]. In partic…     

Life-history trade-offs favour the evolution of animal personalities

In recent years evidence has been accumulating that personalities are not only found in humans but also in a wide range of other animal species. Individuals differ consistently in their behavioural tendencies and the behaviour in one context is correlated with the behaviour in multiple other contexts. From an adaptive perspective, the evolution of animal personalities is still a mystery, because a more flexible structure of behaviour should provide a selective advantage. Accordingly, many researchers view personalities as resulting from constraints imposed by the architecture of behaviour (but see ref. 12). In contrast, we show here that animal personalities can be given an adaptive explanation. Our argument is based on the insight that the trade-off between current and future reproduction often results in polymorphic populations in which some individuals put more emphasis on future fitness returns than others. Life-history theory predicts that such differences in fitness expectations should result in systematic differences in risk-taking behaviour. Individuals with high future expectations (who have much to lose) should be more risk-averse than individuals with low expectations. This applies to all kinds of risky situations, so individuals should consistently differ in their behaviour. By means of an evolutionary model we demonstrate that this basic principle results in the evolution of animal personalities. It simultaneously explains the coexistence of behavioural types, the consistency of behaviour through time and the structure of behavioural correlations across contexts. Moreover, it explains the common finding that explorative behaviour and risk-related traits like boldness and aggressiveness are common characteristics of animal personalities.     

儒家文化与构建两岸和谐关系

孔子所创立的以“和”文化为核心的儒家学说,作为宝贵的文化遗产影响中华民族两千多年,海峡两岸同文同种,同宗同源,儒学已经成为两岸人民共同的精神财富。儒学思想对于促进人与人、人与社会的和谐,推动两岸和谐社会的构建都具有重要而独特的价值,两岸同仁应大力弘扬儒学精华,为构建两岸和谐社会服务。     

Bone histology indicates insular dwarfism in a new Late Jurassic sauropod dinosaur

Sauropod dinosaurs were the largest animals ever to inhabit the land, with truly gigantic forms in at least three lineages. Small species with an adult body mass less than five tonnes are very rare, and small sauropod bones generally represent juveniles. Here we describe a new diminutive species of basal macronarian sauropod, Europasaurus holgeri gen. et sp. nov., and on the basis of bone histology we show it to have been a dwarf species. The fossils, including excellent skull material, come from Kimmeridgian marine beds of northern Germany, and record more than 11 individuals of sauropods 1.7 to 6.2 m in total body length. Morphological overlap between partial skeletons and isolated bones links all material to the same new taxon. Cortical histology of femora and tibiae indicates that size differences within the specimens are due to different ontogenetic stages, from juveniles to fully grown individuals. The little dinosaurs must have lived on one of the large islands around the Lower Saxony basin. Comparison with the long-bone histology of large-bodied sauropods suggests that the island dwarf species evolved through a decrease in growth rate from its larger ancestor.     

醉翁榆(Ulmus gaussenii Cheng)的濒危特征与机制

对安徽特有濒危植物醉翁榆(Ulmus gaussenii)的地理分布、生境条件、种群数量动态、空间分布格局、种间关系、遗传变异等种群生态学特征及其濒危机制进行了综合分析.研究表明,现有醉翁榆种群均为高群集分布,景观破碎化程度加剧,年龄结构不合理,且已经演化为小种群,种群已处于相对不稳定阶段.自然生境的严重破坏对醉翁榆种群的生存构成严重威胁,是造成部分野生种群个体数量急剧减少的主要原因.醉翁榆生殖过程中胚胎败育可能是导致醉翁榆濒危的根本原因.所以应加强对醉翁榆遗传学和传粉生物学的研究,以期为醉翁榆以及其他近缘濒危植物保护提供理论指导.     

校园旅游开发浅析

近几年,校园旅游作为一个新兴产业“千呼万唤始出来”,正因为如此,它必然存在着许多问题,并且更需要人们对其关注。文章就校园旅游的现状及存在的问题进行了分析,并对其发展潜力进行发掘,提出几点对策建设。