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本帖最后由 ranhaer 于 2009-9-19 20:53 编辑

Improved resolution of the human Y-chromosomal phylogeny using targeted next-generation sequencing. Q. Ayub, Y. Xue, C. Tyler-Smith Human Evolution, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.

   The non-recombining part of the Y chromosome provides unique insights into male-specific aspects of human genetics and history. We are using next-generation Illumina sequencing to fully re-sequence targeted regions of the Y and resolve the Y-chromosomal phylogeny by characterization of additional single nucleotide polymorphisms (SNPs) on lineages of interest. Initially ~6 Mb of Y sequence (NCBI36:Y-chromosome: 12,308,579-18,230,132) is being generated for an African haplogroup A male. The strategy involves sequence enrichment by long template PCR of genomic DNA (10-20 ng/reaction) using overlapping fragments of 5.5 - 6.5 kbp. Currently ~70% of primer pairs work using a standard touchdown PCR protocol. Fragments obtained from a single individual are pooled and used for library preparation and IIlumina sequencing. Re-sequencing generates accurate high coverage data; SNP calling and their subsequent validation will be presented. Most SNPs are expected to be rare but some are likely to resolve deep divisions within African populations. Subsequently, we aim to (1) determine the time depth of the human Y phylogeny, (2) resolve multifurcations in the major lineages by discovering additional SNPs on the relevant and (3) discover SNPs that mark any lineage of particular interest. In addition, we will be able to provide a subset of all primers that work well with this protocol to investigators who are interested in Y-chromosomal phylogenies so that comparable standard datasets can be generated for use by the community.

霰弹法测试Y染色体的全序列! 。目的在于1,确定Y的年代深度;2,细化系统树;3,发现更多SNP. 同时作者愿意提供整套引序物共他人使用,以便公众能够分享这一成果!
On the borderline between the east and the west: the maternal genetic background of Karelians. S. Koivumäki1, T. Lappalainen2, P. Lahermo2 1) Medical Genetics, University of Turku, Turku, Finland; 2) 2 Finnish Genome Center, University of Helsinki, Helsinki, Finland.

   Introduction: The frontier between Finland and Russia represents one of the most conspicuous socioeconomic gaps in the world. Based on the mean gross national product, there is a ten-fold difference between Russian Karelian Republic and Finnish Karelia. Otherwise these populations share the same geophysical environment. For these reasons, Karelia has been a very interesting field of research for multifactorial disease studies. However, this area has undergone many demographic incidents, such as wars and famine, which may cause local differences in the gene pool. In this study, we wanted to elucidate the maternal genetic background of Karelians. Materials: Blood samples were collected from healthy unrelated individuals without known foreign background from four Karelian districts; Aunus(n=218), Viena(n=87), Tver(n=61) and Finnish Karelia (n=70), The sample collection was performed according to the Basic Principles of the Declaration of Helsinki. Methods: The entire mitochondrial DNA was sequenced in 32 reactions per sample with the BigDye® Terminator v3.1 Cycle Sequencing Kit in the Applied Biosystem’s 3730 Genetic Analyzer sequencing machine. Sequence alignments were made by the SeqScape® Software, Version 2.5 (Applied Biosystem). Results: Haplogroup H was very common in all populations. However, H1a is almost absent in Finnish Karelia. Also U and its subhaplogroups were common. Specially U5b1b1 reached over 16% in Viena Karelians. U4 was most common among Tver Karelians. Conclusions: The maternal genetic background seem to be complex in this area. There is clear regional differences. Also there is solid evidence of gene flow from various sources. Representation of the clearly Asian haplogroups is strikingly low.

卡累利亚人的mtDNA--处在东西之间。 他们的语言属于乌拉尔语。
本帖最后由 ranhaer 于 2009-9-19 21:10 编辑

A detailed phylogeography of mtDNA haplogroup C1d: another piece in the Native American puzzle.
U. A. Perego1,2, N. Angerhofer1, M. Pala2, J. E. Gomez-Palmieri1, A. Olivieri2, K. H. Ritchie1, B. Hooshiar Kashani2, V. Carossa2, H. Lancioni3, N. Myres1, A. Gómez-Carballa4, B. Zimmermann5, G. Huber5, M. Bodner5, W. Parson5, A. Salas4, H.-J. Bandelt6, S. R. Woodward1, A. Torroni2, A. Achilli2,3 1)
   Recent studies based on complete mitochondrial DNA (mtDNA) sequences revealed that two almost concomitant paths of migration from Beringia led to the dispersal of the first Americans (Paleo-Indians) approximately 15-17 thousand years ago (kya). This first expansion was followed by later more restricted diffusion events from the same dynamically changing Beringian source. Thus, five pan-American (A2, B2, C1, D1, and D4h3a) and four geographically confined (D2, D3, X2a, and C4c) mtDNA haplogroups represent the current female legacy of the ancient migratory events that gave rise to the native populations of the double continent. Regarding haplogroup C1, all its members appear to belong to one of three branches: C1b (characterized by the control-region transition at np 493), C1c, and C1d (with the control-region transition at np 16051). These three sub-haplogroups are found throughout the Americas, thus supporting the scenario that they most likely differentiated at the early stages of the Paleo-Indian southward migration. If considered as three separate founders, C1b, C1c, and C1d would bring the currently known number of native pan-American lineages to seven. As a whole, the C1 haplogroup has an estimated age of 17.0-19.6 ky, while the three individual branches are dated 16.5-17.0 ky, 17.2-17.6 ky, and 7.6-9.7 ky, respectively. The extremely young age estimate of C1d has been attributed, at least for the moment, to a major under-representation of C1d mtDNAs (only nine complete sequences published to date) in the current Native American mtDNA phylogeny. We have addressed this issue in the current study by completely sequencing more than 60 novel mtDNAs belonging to haplogroup C1d, which were carefully selected on the basis of both control-region variation and geographic/ethnic origin. Phylogeographic analyses have provided not only an accurate evaluation of the expansion time of C1d in the Americas, but also a detailed picture of its current distribution in both general mixed and indigenous populations.

A detailed phylogeography of mtDNA haplogroup C1d: another piece in the Native American puzzle.
U. A. Perego1,2, N. Angerhofer1, M. Pala2, J. E. Gomez-Palmieri1, A. Olivieri2, K. H. Ritchie1, B. Hoo ...
ranhaer 发表于 2009-9-19 21:06
7.6-9.7 ky, 这个年代意义重大啊,有全文吗,斑竹?

The evolution of the 16051G mtDNA lineage in American human populations
Figueiro, G1; Ackermann, E1; Hidalgo, PC1; Sans, M1
1: Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay.
Latin American populations provide an excellent model to analyze microevolutionary processes. The Native Americans conform the base of the present populations, and before mixing, they have suffered different processes as migration and genetic drift. Some of these process can be seen analyzing mitochondrial DNA (mtDNA).
Mt DNA (mtDNA) of Native American populations is defined by the presence of the four major (founding) haplogroups A, B, C, and D, each of them with several variants originated in Northeast Asia and Beringia. Recently, it was determined that haplogroup C is divided the founding components C1b, C1c y C1d, widely distributed in the Americas. We detected a lineage of haplogroup C1d specific for Uruguay in prehistoric (late Holocene) remains, as well as in a sample of living Uruguayan individuals. Additionally, two early Holocene individuals from site Arroyo Seco 2, in the Province of Buenos Aires, Argentina carry mtDNA sequences that correspond to haplogroup C1d. Based on the possible connection between the Argentinean and Uruguayan prehistoric populations we analyzed the variation, dispersal and age of haplogroup C1d.
Based on these analyses, we obtained an age of of 11450 years before present (ybp) for the origin of haplogroup C1d, with a 95% confidence interval of 7034.6 – 16841 ybp. The interval concurs with some of the most recent estimations of the age of peopling of the Americas, being nevertheless in discrepancy with other calculations that place the peopling of the continent at 19000 ybp. The presence of variants of haplogroup C1d in prehistoric remains of Argentina and Uruguay opens an independent line of evidence in the investigation of early contacts between populations suggested by archaeological data.
Effect of natural selection on North Asian mitochondrial haplogroup variation. M. Derenko1, B. Malyarchuk1, T. Grzybowski2, G. Denisova1, U. Rogalla2, M. Perkova1, I. Dambueva3, I. Zakharov4 1) Geneti ...
ranhaer 发表于 2009-9-12 08:49
Adygei106OCA2rs1800414 (His615Arg)G8/6/20120.02
African Americans176OCA2rs1800414 (His615Arg)G8/6/20120
Ami70OCA2rs1800414 (His615Arg)G8/6/20120.74
Atayal82OCA2rs1800414 (His615Arg)G8/6/20120.63
Baima Dee74OCA2rs1800414 (His615Arg)G11/18/20110.27
Bangladeshi236OCA2rs1800414 (His615Arg)G5/18/20090.01
Buryat286OCA2rs1800414 (His615Arg)G5/18/20090.13
Cambodians, Khmer46OCA2rs1800414 (His615Arg)G8/6/20120.39
Cheyenne112OCA2rs1800414 (His615Arg)G11/21/20110
Chuvash82OCA2rs1800414 (His615Arg)G8/6/20120.04
Colombian248OCA2rs1800414 (His615Arg)G6/8/20110
Danes100OCA2rs1800414 (His615Arg)G8/6/20120
Druze202OCA2rs1800414 (His615Arg)G8/6/20120
European Americans120OCA2rs1800414 (His615Arg)G6/8/20110
Europeans, Mixed176OCA2rs1800414 (His615Arg)G8/6/20120
Ewenki228OCA2rs1800414 (His615Arg)G6/8/20110.23
Finns66OCA2rs1800414 (His615Arg)G8/6/20120
French196OCA2rs1800414 (His615Arg)G5/18/20090
Germans398OCA2rs1800414 (His615Arg)G5/18/20090
Ghanaian72OCA2rs1800414 (His615Arg)G5/18/20090
Greeks98OCA2rs1800414 (His615Arg)G8/6/20120
Gujarati176OCA2rs1800414 (His615Arg)G10/14/20110.01
Hakka78OCA2rs1800414 (His615Arg)G8/6/20120.72
Han90OCA2rs1800414 (His615Arg)G8/6/20120.77
Han112OCA2rs1800414 (His615Arg)G8/6/20120.69
Han90OCA2rs1800414 (His615Arg)G6/8/20110.63
Han174OCA2rs1800414 (His615Arg)G5/18/20090.45
Han238OCA2rs1800414 (His615Arg)G5/18/20090.57
Han222OCA2rs1800414 (His615Arg)G5/18/20090.63
Han80OCA2rs1800414 (His615Arg)G6/8/20110.55
Han218OCA2rs1800414 (His615Arg)G6/8/20110.55
Han214OCA2rs1800414 (His615Arg)G6/8/20110.67
Han236OCA2rs1800414 (His615Arg)G6/8/20110.65
Han414OCA2rs1800414 (His615Arg)G10/14/20110.55
Hausa76OCA2rs1800414 (His615Arg)G8/6/20120
Hazara186OCA2rs1800414 (His615Arg)G8/6/20120
Hungarian176OCA2rs1800414 (His615Arg)G8/6/20120.01
Indian, Mixed214OCA2rs1800414 (His615Arg)G5/18/20090
Indonesian210OCA2rs1800414 (His615Arg)G5/18/20090.11
Irish224OCA2rs1800414 (His615Arg)G8/6/20120
Italians176OCA2rs1800414 (His615Arg)G8/6/20120
Japanese92OCA2rs1800414 (His615Arg)G8/6/20120.64
Japanese88OCA2rs1800414 (His615Arg)G6/8/20110.52
Japanese206OCA2rs1800414 (His615Arg)G5/18/20090.55
Japanese174OCA2rs1800414 (His615Arg)G5/18/20090.47
Japanese578OCA2rs1800414 (His615Arg)G6/8/20110.6
Jews, Ashkenazi230OCA2rs1800414 (His615Arg)G8/6/20120
Jews, Ethiopian72OCA2rs1800414 (His615Arg)G8/6/20120
Jews, Sephardic52OCA2rs1800414 (His615Arg)G8/6/20120
Kachari30OCA2rs1800414 (His615Arg)G8/6/20120
Karitiana110OCA2rs1800414 (His615Arg)G11/21/20110
Kazakh84OCA2rs1800414 (His615Arg)G11/18/20110.15
Keralite58OCA2rs1800414 (His615Arg)G8/6/20120
Khalkha346OCA2rs1800414 (His615Arg)G5/18/20090.21
Khamba62OCA2rs1800414 (His615Arg)G11/18/20110.19
Khanty96OCA2rs1800414 (His615Arg)G8/6/20120
Komi-Zyrian92OCA2rs1800414 (His615Arg)G8/6/20120
Koreans106OCA2rs1800414 (His615Arg)G8/6/20120.62
Koreans278OCA2rs1800414 (His615Arg)G6/8/20110.56
Koreans282OCA2rs1800414 (His615Arg)G6/8/20110.54
Kuwaiti26OCA2rs1800414 (His615Arg)G8/6/20120
Lao Loum230OCA2rs1800414 (His615Arg)G8/6/20120.55
Malaysians20OCA2rs1800414 (His615Arg)G8/6/20120
Masai38OCA2rs1800414 (His615Arg)G8/6/20120
Maya, Yucatan96OCA2rs1800414 (His615Arg)G8/6/20120
Mbuti74OCA2rs1800414 (His615Arg)G8/6/20120
Melanesian, Nasioi44OCA2rs1800414 (His615Arg)G8/6/20120
Micronesians66OCA2rs1800414 (His615Arg)G8/6/20120.05
Mongolian124OCA2rs1800414 (His615Arg)G11/18/20110.22
Mongolian122OCA2rs1800414 (His615Arg)G6/15/20120.8
Oroqen162OCA2rs1800414 (His615Arg)G6/8/20110.11
Papuan New Guinean42OCA2rs1800414 (His615Arg)G8/6/20120
Pashtun182OCA2rs1800414 (His615Arg)G8/6/20120
Pima, Arizona102OCA2rs1800414 (His615Arg)G11/21/20110
Qiang72OCA2rs1800414 (His615Arg)G11/18/20110.38
Quechua42OCA2rs1800414 (His615Arg)G8/6/20120
Russians92OCA2rs1800414 (His615Arg)G8/6/20120
Russians64OCA2rs1800414 (His615Arg)G8/6/20120
Samaritans76OCA2rs1800414 (His615Arg)G8/6/20120
Sardinian68OCA2rs1800414 (His615Arg)G8/6/20120
Surui84OCA2rs1800414 (His615Arg)G8/6/20120
Thai228OCA2rs1800414 (His615Arg)G6/8/20110.43
Tibetan232OCA2rs1800414 (His615Arg)G6/8/20110.09
Tsaatan90OCA2rs1800414 (His615Arg)G6/15/20120.92
Turks400OCA2rs1800414 (His615Arg)G5/18/20090.02
Uyghur92OCA2rs1800414 (His615Arg)G11/18/20110.16
Yakut100OCA2rs1800414 (His615Arg)G8/6/20120.09
Yoruba148OCA2rs1800414 (His615Arg)G8/6/20120
Yoruba120OCA2rs1800414 (His615Arg)G6/8/20110
. ...东亚人群浅色素先相关基因: OCA2 and HERC2  

欧洲的蓝色虹膜和亚洲的浅肤色与OCA2 和HERC2面临的选择相关

     OCA2 和HERC2是第15号染色体上距离10 kb的两个基因。这一区域的突变已经被证明对色素沉淀有影响,比如2型白化病。 在欧洲,一个三个SNP组成的单倍型(rs4778138, rs4778241, rs7495174)和三个独立SNP(rs12913832, rs916977, rs1667394) 被证明与蓝色虹膜有关。我们将这个单倍型标识为BEH1。我们发现,三个独立SNP的第一个,rs12913832,与其他SNP(rs1129038)接近连锁不平衡. 我们将这两个SNP标识为BEH2。我们也发现,其余两个单个SNP也是连锁不平衡的,因此标识为 BEH3。此外在东亚,rs1800414已经被确定为色素沉淀相关表型。
    我们对64-70 个人群的样本检测了这8个SNP,然后分析4个单倍型在全世界的分布。我们发现,浅色素基因在东亚东部人群中最高频,在东亚东南部中频,在东亚西部低频并且在世界其他地方罕见。BEH1和BEH3有相同的分布:在非洲和东亚为低频至中频,在亚洲西南、欧洲、西伯利亚西部、太平洋岛屿和美洲土著中高频。 BEH2和这两个不同,它在东非、印度、西伯利亚东部和美洲低频,而在东欧、西北欧和西伯利亚西部高频。

    然后我们通过REHH检测这些SNP是否面临选择。结果,rs1800414在东亚人群中面临选择。BEH2在欧洲和亚洲西南不面临选择。因此,浅色素基因在东亚面临选择。这应取决于在高纬度地区的UV光照(相对于非洲)以及制造维生素D对浅肤色的需要。 同时,蓝色虹膜在欧洲也面临选择。这很有可能来自性选择,但也不排除其他因素也会造成影响。
ranhaer 发表于 2009-9-12 08:51
查了一下alfred和NCBI,OCA2上的rs4778138与 rs1800414变异均在东亚人群中高频,不过rs1800414(his615arg)仅限于东亚人群,而rs4778138则分布普遍(包括非洲),不过在高纬度地区频度偏低,提示这个变异与色素调节的相关度不大。


本帖最后由 lll 于 2017-12-11 05:55 编辑

28# imvivi001 巴西的karitiana人混入了较多类似安达曼人的基因,但370A比例居然比汉族还高
28# imvivi001 巴西的karitiana人混入了较多类似安达曼人的基因,但370A比例居然比汉族还高
lll 发表于 2017-12-11 05:49
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