人类线粒体DNA单倍体群
[[
File:Peopling of eurasia.jpg|thumb|right|350px|根据线粒体DNA建议的“走出非洲”迁徙路线。]]
![](http://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/MtDNA_haplogroup_distribution_among_2%2C054_individuals_across_26_populations_from_the_1000_Genomes_Project.png/350px-MtDNA_haplogroup_distribution_among_2%2C054_individuals_across_26_populations_from_the_1000_Genomes_Project.png)
![](http://upload.wikimedia.org/wikipedia/commons/thumb/a/ab/World_map_of_prehistoric_human_migrations.jpg/340px-World_map_of_prehistoric_human_migrations.jpg)
人类线粒体DNA单倍体群(Human mitochondrial DNA Haplogroup)是遗传学上依据线粒体DNA差异而定义出来的单倍体群。单倍群用于表示线粒体系统发育树上的主要分支点。了解母系血统的演化路径,可使研究者追溯母系遗传的人类起源,线粒体研究显示人类起源于非洲地区。单倍群的字母名从A到Z不等,按照发现的先后顺序命名,与实际的遗传关系不相干。
线粒体单倍群起源于一个假想的女性,是所有现存人类的母系最近共同祖先,一般称作线粒体夏娃。
线粒体DNA的变异速度称作人线粒体分子钟,这是尚在研究的领域,有报告称每8000年发生一次突变。[2]
线性透视
[编辑]![](http://upload.wikimedia.org/wikipedia/commons/thumb/8/80/MtDNA_haplogroup_tree_and_distribution_map.gif/350px-MtDNA_haplogroup_tree_and_distribution_map.gif)
![](http://upload.wikimedia.org/wikipedia/commons/thumb/a/a4/Migration_route_of_Human_mtDNA_haplogroups.png/350px-Migration_route_of_Human_mtDNA_haplogroups.png)
此进化树来自Van Oven (2009)[4],2022年6月一份研究提出了单倍群L的另一种系统发育路径。[5]
主要mtDNA单倍群
[编辑]泛单倍群L
[编辑]泛单倍群 L是人mtDNA单倍群中最基本的,其他单倍群都从L3单倍群演化而来。主要分布在非洲。
- 单倍型类群 L0
- L1-7
泛单倍群M
[编辑]泛单倍群M主要分布在亚洲和美洲,其后代有单倍型类群 M、单倍型类群 C、单倍型类群 Z、单倍型类群 D、单倍型类群 E、单倍型类群 G、单倍型类群 Q等。
泛单倍群N
[编辑]泛单倍群N主要分布在澳洲、美洲,在亚洲亦有,其后代有单倍型类群 N、单倍型类群 O、单倍型类群 A、单倍型类群 S、单倍型类群 I、单倍型类群 W、单倍型类群 X、单倍型类群 Y以及泛单倍群R。
泛单倍群R
[编辑]泛单倍群R主要分布在欧洲、北美、大洋洲,在亚洲和美洲亦有,其后代有单倍型类群 R、单倍型类群 B、单倍型类群 F、单倍型类群 H、单倍型类群 V、单倍型类群 J、单倍型类群 T、单倍型类群 U、单倍型类群 K。
年代
[编辑]单倍群 | 估计起源时间(万年前)[6] | 可能起源地 |
---|---|---|
L | 20 | 非洲 |
L1-6 | 17 | 东非 |
L2-6 | 15 | 东非 |
L0 | 15 | 东非 |
L1 | 14 | 中非 |
L3-6 | 13 | |
L5 | 12 | |
L2 | 9 | |
L3 | 7 | 东非 |
N | 7 | 东非或西亚 |
M | 6 | 东非,西亚或南亚 |
R | 6 | 南亚或东南亚 |
U | 5.5 | 东北非或印度(南亚) |
RT'JT | 5.5 | 中东 |
JT | 5 | 中东 |
U8 | 5 | 西亚 |
R9 | 4.7 | |
B4 | 4.4 | |
F | 4.3 | |
U4'9 | 4.2 | 中亚 |
U5 | 3.5 | 西亚 |
U6 | 3.5 | 北非 |
J | 3.5 | |
X | 3 | |
K | 3 | |
U5a | 2.7 | |
HV | 2.7 | 近东 |
J1a | 2.7 | 近东 |
T | 2.7 | 两河流域 |
K1 | 2.7 | |
I | 2.6 | |
J1 | 2.4 | 近东 |
W | 2 | |
U4 | 2 | 中亚 |
X2 | 2 | |
H | 2 | 西亚 |
U5a1 | 1.8 | 欧洲 |
J1b | 1.1 | |
V | 1.4 | |
X2a | 1.3 | 北美 |
H1 | 1..2 | |
H3 | 12 | |
X1 | 1 |
地理分布
[编辑]2004年一篇论文总结,现代西亚、北美与欧洲人群中最普遍的单倍群是H, J, K, N1, T, U4, U5, V, X, W。[7]
非洲单倍群:L0, L1, L2, L3, L4, L5, L6, T, U5a
澳洲单倍群:M42a, M42c, M14, M15, Q, S, O, N, P. (Refs 1, 2, 3, 4, 5, 6)
亚洲单倍群:F, C, W, M, D, N, K, U, T, A, B, C, Z, U many number variants to each section
研究软件
[编辑]分配
[编辑]- mtHap: James Lick's tool (multiple input formats).
- YSEQ mt Clade Finder: FASTA based haplogroup tool. Replaced HAPLOFIND.[8]
- HaploGrep: VCF based tool.[9][10]
- Haplocheck: Mitoverse's tool for both WGS and WES.[11]
- Haplotracker: A short fragment tool.[12]
- Haplogroup Finder: Ian Logan's SNP to haplogroup tool.
测年
[编辑]- mtDNA Mutation Computer Model: Ian Logan's mutation calculator.
系统发生
[编辑]- FTDNA's mtDNA Haplotree: The largest mtDNA tree.
- YFull's MTree: An mtDNA tree. Faster loading (simpler).
- PhyloTreemt: A traditional mtDNA tree (last updated 2016-02-18).[13]
- HIP: Haplogroup trees.
地图
[编辑]古地图
[编辑]- HIP Haplomap: Ancient uniparental map.
- AH DNA: Nicky Rosenblatt's ancient uniparental map.[14]
- Ancient DNA: An aDNA map made with Map Maker.
现代地图
[编辑]- HRAS mtDNA: A heatmap generator.
数据库
[编辑]古代
[编辑]- AmtDB: An database of ancient mtDNA samples.[15]
- All Ancient DNA Dataset: Carlos Quiles' uniparental database (with BAM).
现代
[编辑]- GenBank mtDNA Sequence Checker: Ian Logan's GenBank based accession matching tool.
- mitoYDNA: A uniparental database.
- MITOMAP: An mtDNA genome database.[16]
参看
[编辑]参考资料
[编辑]- ^ Rishishwar L, Jordan IK. Implications of human evolution and admixture for mitochondrial replacement therapy.. BMC Genomics. 2017, 18 (1): 140. PMC 5299762
. PMID 28178941. doi:10.1186/s12864-017-3539-3
.
- ^ Loogvali, Eva-Liis; Kivisild, Toomas; Margus, Tõnu; Villems, Richard, O'Rourke, Dennis , 编, Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria, PLOS ONE, 2009, 4 (12): e8260, Bibcode:2009PLoSO...4.8260L, PMC 2794369
, PMID 20041137, doi:10.1371/journal.pone.0008260
- ^ Kivisild T. Maternal ancestry and population history from whole mitochondrial genomes.. Investig Genet. 2015, 6: 3. PMC 4367903
. PMID 25798216. doi:10.1186/s13323-015-0022-2
.
- ^ 4.0 4.1 van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human Mutation. February 2009, 30 (2): E386–94. PMID 18853457. S2CID 27566749. doi:10.1002/humu.20921
.
- ^ Maier P, Runfeldt G, Estes R, Vilar M. African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing. Nature. 2022, 12 (1): 10747. Bibcode:2022NatSR..1210747M. PMC 9232647
. PMID 35750688. S2CID 250021505. doi:10.1038/s41598-022-13856-0
.
- ^ Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary (PDF). Cell. 2009: 82–83 [89]. (原始内容 (PDF)存档于2009-12-29).
- ^ Villems, Richard; Usanga, Esien; Mikerezi, Ilia; Gölge, Mukaddes; Claustres, Mireille; Michalodimitrakis, Emmanuel N.; Pappa, Kalliopi I.; Anagnou, Nicholas P.; Chaventré, André; Moisan, Jean-Paul; Richard, Christelle; Grechanina, Elena; Balanovska, Elena V.; Rudan, Pavao; Puzyrev, Valery; Stepanov, Vadim; Khusnutdinova, Elsa K.; Gusar, Vladislava; Balanovsky, Oleg P.; Peričić, Marijana; Barać, Lovorka; Golubenko, Maria; Lunkina, Arina; Laos, Sirle; Pennarun, Erwan; Parik, Jüri; Tolk, Helle-Viivi; Reidla, Maere; Tambets, Kristiina; Metspalu, Ene; Kivisild, Toomas; Derenko, Miroslava V.; Malyarchuk, Boris A.; Roostalu, Urmas; Loogväli, Eva-Liis. Disuniting Uniformity: A Pied Cladistic Canvas of mtDNA Haplogroup H in Eurasia. Molecular Biology and Evolution. November 1, 2004, 21 (11): 2012–2021. PMID 15254257. doi:10.1093/molbev/msh209
–通过academic.oup.com.
- ^ Capri, Miriam; Castellani, Gastone; Franceschi, Claudio; Lomartire, Laura; Sevini, Federica; Vianello, Dario. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Human Mutation. 2013-06-12, 34 (9): 1189–1194. eISSN 1098-1004.
- ^ Binna, Robert; Kloss-Brandstätter, Anita; Kronenberg, Florian; Pacher, Dominic; Schönherr, Sebastian; Specht, Günther; Weissensteiner, Hansi. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Human Mutaton: Variation, Informatics, and Disease. 2010-10-19, 32 (1): 25–32. eISSN 1098-1004.
- ^ Kronenberg, Florian; Forer, Lukas; Schönherr, Sebastian; Weissensteiner, Hansi. Haplogrep 3 - an interactive haplogroup classification and analysis platform. Nucleic Acids Research. 2023-04-23, 51 (1): 263–268. eISSN 1362-4962.
- ^ García-Olivares, Victor; et al. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Scientific Reports. 2021-10-15, 11 (20510). eISSN 2045-2322. 已忽略未知参数
|orig-date=
(帮助) - ^ Kim, Dong-han; Kim, Kijeong; Kim, Kyung-yong; Kim, Yoonyeong; Kwon, Chulhwan. Haplotracker: a web application for simple and accurate mitochondrial haplogrouping using short DNA fragments. 2020-04-23. bioRxiv 10.1101/2020.04.23.057646v1
.
- ^ Kayser, Manfred; van Oven, Mannis. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human Mutation. 2008-10-13, 30 (2): 386–394. doi:10.1002/humu.20921
. eISSN 1098-1004.
- ^ Various. Rosenblatt's ancient DNA map. Anthrogenica. 2017-05-30.
- ^ Chyleński, Maciej; Ehler, Edvard; Juras, Anna; Moravčík, Ondřej; Novotný, Jiří; Pačes, Jan. AmtDB: a database of ancient human mitochondrial genomes. Nucleic Acids Research. 2018-09-24, 47 (D1): 29–32. eISSN 1362-4962.
- ^ Brown, Michael D.; Kogelnik, Andreas M.; Lott, Marie T.; Navathe, Shamkant B.; Wallace, Douglas C. MITOMAP: A Human Mitochondrial Genome Database. Nucleic Acids Research. 1996-01-01, 24 (1): 177–179. eISSN 1362-4962.
外部链接
[编辑]- mtDNA .pdf map(页面存档备份,存于互联网档案馆)
- Map of macro-单倍型类群 N (页面存档备份,存于互联网档案馆) by John S. Walden
- Indian maternal gene pool, Journal of Human Genetics
- The Making of the African mtDNA Landscape, American Journal of Human Genetics
- Do the Four Clades of the mtDNA 单倍型类群 L2 Evolve at Different Rates?, American Journal of Human Genetics
- The Matrilineal Ancestry of Ashkenazi Jewry: Portrait of a Recent Founder Event, American Journal of Human Genetics
- MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations (页面存档备份,存于互联网档案馆)
- HaploGrep: mtDNA haplogroup determination based on PhyloTree.org (页面存档备份,存于互联网档案馆)
- HaploFind – fast automatic haplogroup assignment pipeline for human mitochondrial DNA (页面存档备份,存于互联网档案馆)
最近的共同线粒体祖先 | ||||||||||||||||||||||||||||||||
L0 | L1 | |||||||||||||||||||||||||||||||
L2 | L3 | L4 | L5 | L6 | L7 | |||||||||||||||||||||||||||
M | N | |||||||||||||||||||||||||||||||
CZ | D | E | G | Q | A | I | O | R | S | W | X | Y | ||||||||||||||||||||
C | Z | B | F | pre-HV | pre-JT | P | UK | |||||||||||||||||||||||||
HV | JT | U | K | |||||||||||||||||||||||||||||
H | V | J | T |