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本帖最后由 Ryan 于 2013-7-18 13:47 编辑

为考虑人族内的 生殖隔离问题,开一个资料收集贴。
本帖最后由 Ryan 于 2013-7-18 13:45 编辑

PLoS Genet 1(4): e56. doi:10.1371/journal.pgen.0010056

Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies
Lars Feuk,Jeffrey R MacDonald,Terence Tang,  Andrew R Carson,Martin Li,Girish Rao, Razi Khaja,Stephen W Scherer


With a draft genome-sequence assembly for the chimpanzee available, it is now possible to perform genome-wide analyses to identify, at a submicroscopic level, structural rearrangements that have occurred between chimpanzees and humans. The goal of this study was to investigate chromosomal regions that are inverted between the chimpanzee and human genomes. Using the net alignments for the builds of the human and chimpanzee genome assemblies, we identified a total of 1,576 putative regions of inverted orientation, covering more than 154 mega-bases of DNA. The DNA segments are distributed throughout the genome and range from 23 base pairs to 62 mega-bases in length. For the 66 inversions more than 25 kilobases (kb) in length, 75% were flanked on one or both sides by (often unrelated) segmental duplications. Using PCR and fluorescence in situ hybridization we experimentally validated 23 of 27 (85%) semi-randomly chosen regions; the largest novel inversion confirmed was 4.3 mega-bases at human Chromosome 7p14. Gorilla was used as an out-group to assign ancestral status to the variants. All experimentally validated inversion regions were then assayed against a panel of human samples and three of the 23 (13%) regions were found to be polymorphic in the human genome. These polymorphic inversions include 730 kb (at 7p22), 13 kb (at 7q11), and 1 kb (at 16q24) fragments with a 5%, 30%, and 48% minor allele frequency, respectively. Our results suggest that inversions are an important source of variation in primate genome evolution. The finding of at least three novel inversion polymorphisms in humans indicates this type of structural variation may be a more common feature of our genome than previously realized.


来自HHMI霍德华休斯医学院的研究人员通过比较人类和人类血缘最近的“亲戚”—黑猩猩的基因组发现基因倒位现象(inversions)并不如科学家之前所认为的那么少见,这也许解释了这两个物种之间的许多进化之谜,也为人类疾病发生找到了部分根源。这一研究成果公布在10月28号的美国科学公共图书馆遗传学版上(Public Library of Science Genetics ,PLoS Genetics)。




本帖最后由 Ryan 于 2013-7-17 22:49 编辑

PLoS ONE 7(7): e40224. doi:10.1371/journal.pone.0040224

Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis
Jianzhong Ma mail,   Christopher I. Amos

Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct “populations” of inversion homozygotes of different orientations and their 1:1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases.
本帖最后由 Ryan 于 2013-7-18 13:29 编辑

Genome Biol. 2007;8(10):R230.

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

Marques-Bonet T, Sànchez-Ruiz J, Armengol L, Khaja R, Bertranpetit J, Lopez-Bigas N, Rocchi M, Gazave E, Navarro A.
SourceUnitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Catalonia, Spain. tomas.marques@upf.edu


     The role that chromosomal rearrangements might have played in the speciation processes that have separated the lineages of humans and chimpanzees has recently come into the spotlight. To date, however, results are contradictory. Here we revisit this issue by making use of the available human and chimpanzee genome sequence to study the relationship between chromosomal rearrangements and rates of DNA sequence evolution.

     Contrary to previous findings for this pair of species, we show that genes located in the rearranged chromosomes that differentiate the genomes of humans and chimpanzees, especially genes within rearrangements themselves, present lower divergence than genes elsewhere in the genome. Still, there are considerable differences between individual chromosomes. Chromosome 4, in particular, presents higher divergence in genes located within its rearrangement.

     A first conclusion of our analysis is that divergence is lower for genes located in rearranged chromosomes than for those in colinear chromosomes. We also report that non-coding regions within rearranged regions tend to have lower divergence than non-coding regions outside them. These results suggest an association between chromosomal rearrangements and lower non-coding divergence that has not been reported before, even if some chromosomes do not follow this trend and could be potentially associated with a speciation episode. In summary, without excluding it, our results suggest that chromosomal speciation has not been common along the human and chimpanzee lineage.




本帖最后由 Ryan 于 2013-7-18 13:22 编辑

动物学研究 2012, 33(1) 108-118 DOI:   10.3724/SP.J.1141.2012.01108   

廖承红1, 宿兵2

1. 海南大学 农学院, 海口 570288;
2. 中国科学院昆明动物研究所 遗传资源与进化国家重点实验室, 昆明 650223

随着人类和黑猩猩全基因组测序工作宣布完成, 以及其他灵长类基因组测序工作的逐步开展, 目前已经积累了大量的灵长类基因组数据, 一个崭新的研究领域——灵长类比较基因组学应运而生。该文主要通过对人类和其他非人灵长类系统关系和基因组结构的比较, 从系统进化、基因组结构和基因表达调控等方面评述该领域的研究进展, 阐述人类、黑猩猩与其他非人灵长类之间的主要生物学差异, 揭示人类进化的生物学机制。

关键词: 灵长类   比较基因组   进化


我觉得长臂猿和人类特别是M168-L3 系的主流人群的脸型颅型最接近,是否测过他们的基因?
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