Migration rates of human populations from surname distributions

Migration is an important factor in the biological evolution of human populations, and surnames provide one of the simplest records of identification. The distribution of surnames can supply quantitative information on the structure of human populations. Surnames considered as alleles of a gene transmitted only by the male line can be assumed to be neutral markers and therefore satisfy the expectations of the neutral theory of evolution, which is entirely described by random genetic drift, mutation and migration. As data on surnames are easier to collect than those from genes, the information yield is potentially increased, but the validity of the conclusions must be tested in actual samples. The purpose of this report is to compare the estimates of migration rates in Italy, as inferred by the surname distribution found in the telephone directories and other sources, with the corresponding estimates from official demographic sources. Our findings show that in these samples the ratio of surnames to individuals makes it possible to calculate reliable estimates of migration rates.     

华南湍蛙东、南沿海种群间系统发育关系研究

测定了华南湍蛙东南沿海8个种群共55个样品以及2个外群香港湍蛙的线粒体上ND2和CO1两个基因片段,比对后有2382 bp的序列,发现446个变异位点,391个为简约信息位点.分别用NJ法和Mrbayes法建立系统发育树,得到一致的结果:华南湍蛙东、南各种群主要分为四支,其中广西龙胜种群与湖南张家界种群聚在一起形成A支;广西防城种群(B支)与A形成姐妹群;广东深圳种群与香港大屿山种群形成姐妹群构成C支;而广东南昆山种群与南岭种群及福建三港种群形成姐妹群D.     

DNA sequence and analysis of human chromosome 8

The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.     

DNA sequence and analysis of human chromosome 9

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.     

DNA sequence and analysis of human chromosome 18

Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.     

Evolutionary analyses of the human genome

The completion of the human genome will greatly accelerate the development of a new branch of science--evolutionary genomics. We can now directly address important questions about the evolutionary history of human genes and their regulatory sequences. Computational analyses of the human genome will reveal the number of genes and repetitive elements, the extent of gene duplication and compositional heterogeneity in the human genome, and the extent of domain shuffling and domain sharing among proteins. Here we present some first glimpses of these features.     

成都麻羊与四川各地黑山羊品种(群体)mtDNA D-1oop序列多态性研究

采用mtDNA多态性标记对成都麻羊与四川各地黑山羊品种(群体)D-loop序列多态性进行分析.结果表明,供试山羊品种(群体)mtDNA片段长度为16kb左右,mtDNA D-loop片段长度为1210～1212bp,共检测到10种单倍型,群体间共有多态座位83个,单一多态座位23个,简约信息座位24个,平均核苷酸歧异度为0.001510,D-loop序列多态性较贫乏.经聚类,成都麻羊与四川各地黑山羊品种(群体)分为两大类,成都麻羊首先与金堂黑山羊(D=0.203)聚在一起后,再依次与乐至黑山羊(D=0.223)、建昌黑山羊(D=0.477)、白玉黑山羊(D=0.593)形成一大类;合江黑山羊与江安黑山羊(D=0.231)先聚在一起后,再与自贡黑山羊(D=0.337)聚为1类,营山黑山羊与嘉陵黑山羊(D=0.242)聚为1类,2类形成另一大类.最后两个大类聚在一起.聚类结果与供试山羊品种(群体)来源和生态地理分布相一致.     

The DNA sequence and analysis of human chromosome 14

Chromosome 14 is one of five acrocentric chromosomes in the human genome. These chromosomes are characterized by a heterochromatic short arm that contains essentially ribosomal RNA genes, and a euchromatic long arm in which most, if not all, of the protein-coding genes are located. The finished sequence of human chromosome 14 comprises 87,410,661 base pairs, representing 100% of its euchromatic portion, in a single continuous segment covering the entire long arm with no gaps. Two loci of crucial importance for the immune system, as well as more than 60 disease genes, have been localized so far on chromosome 14. We identified 1,050 genes and gene fragments, and 393 pseudogenes. On the basis of comparisons with other vertebrate genomes, we estimate that more than 96% of the chromosome 14 genes have been annotated. From an analysis of the CpG island occurrences, we estimate that 70% of these annotated genes are complete at their 5' end.     

Evolutionary change from induced to constitutive expression of an indirect plant resistance

Induced plant resistance traits are expressed in response to attack and occur throughout the plant kingdom. Despite their general occurrence, the evolution of such resistances has rarely been investigated. Here we report that extrafloral nectar, a usually inducible trait, is constitutively secreted by Central American Acacia species that are obligately inhabited by ants. Extrafloral nectar is secreted as an indirect resistance, attracting ants that defend plants against herbivores. Leaf damage induces extrafloral nectar secretion in several plant species; among these are various Acacia species and other Fabaceae investigated here. In contrast, Acacia species obligately inhabited by symbiotic ants nourish these ants by secreting extrafloral nectar constitutively at high rates that are not affected by leaf damage. The phylogeny of the genus Acacia and closely related genera indicate that the inducibility of extrafloral nectar is the plesiomorphic or 'original' state, whereas the constitutive extrafloral nectar flow is derived within Acacia. A constitutive resistance trait has evolved from an inducible one, obviously in response to particular functional demands.     

The DNA sequence and analysis of human chromosome 13

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.     

Construction and analysis of recombinant DNA for human chorionic somatomammotropin

DNA complementary to mRNA coding for the human polypeptide hormone, chorionic somatomammotropin, has been purified by specific restriction endonuclease digestion and religation before cloning into bacterial plasmids. The primary structure of a major portion of this mRNA species is deduced from the nucleotide sequence of the recombinant DNA.     

The DNA sequence and comparative analysis of human chromosome 5

Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.     

Positive identification of an immigration test-case using human DNA fingerprints

The human genome contains a set of minisatellites, each of which consists of tandem repeats of a DNA segment containing the 'core' sequence, a putative recombination signal in human DNA. Multiallelic variation in the number of tandem repeats occurs at many of these minisatellite loci. Hybridization probes consisting of tandem repeats of the core sequence detect many hypervariable minisatellites simultaneously in human DNA, to produce a DNA fingerprint that is completely individual-specific and shows somatic and germline stability. These DNA fingerprints are derived from a large number of highly informative dispersed autosomal loci and are suitable for linkage analysis in man, and for individual identification in, for example, forensic science and paternity testing. They can also be used to resolve immigration disputes arising from lack of proof of family relationships. To illustrate the potential for positive or inclusive identification, we now describe the DNA fingerprint analysis of an immigration case, the resolution of which would have been very difficult and laborious using currently available single-locus genetic markers.     

精神分裂症起因的进化生物学分析

精神分裂症受基因因素,自然环境因素以及心理应激因素等多种因素共同影响,但目前多数研究都只关注于其中一项,很少有假说能兼顾各种因素.针对精神分裂症研究的这种局限,从进化的角度,利用达尔文医学和进化心理学的方法对精神分裂症进行剖析,以推测其可能的进化史因,并解释环境因素与遗传因素等在精神分裂症发生发展中的作用.同时,对影响精神分裂症发病率的多种环境因素进行了分析,并讨论了精神分裂症的性别特异性、年龄特异性等发病特性,在此基础上提出和论证了一个新的精神分裂症病因的理论假说:"精神分裂症相关基因是一组用于应对不利生存环境的基因,受环境因素的反馈控制.当环境过于恶劣时,这些基因的过度表达就会引发精神分裂症."     

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.