人類線粒體DNA單倍體群

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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。]]

人類線粒體DNA單倍體群（Human mitochondrial DNA Haplogroup）是遺傳學上依據線粒體DNA差異而定義出來的單倍體群。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遺傳的人類起源，線粒體研究顯示人類起源於非洲地區。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]

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]

L（线粒体夏娃）
- L0
- L1-6
  - L1
  - L2-6
    - L5
    - L2'3'4'6
      - L2
      - L3'4'6
        L6
        
        L3'4
        L4
        
        L3
        M
        M8: CZ (C, Z)
        
        M9: E
        
        M12'G: G
        
        M29'Q: Q
        
        D
        
        N
        N1: I
        
        N2: W
        
        N9: Y
        
        A
        
        S
        
        X
        
        R
        R0 (FMKA pre-HV)
        HV: (H, V)
        
        pre-JT或R2'JT
        JT: (J, T)
        
        R9: F
        
        R11'B: B
        
        P
        
        U（UK改来）
        U8: K
        
        O

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
- 单倍型类群 L1
- L2-7
  - L3'4'6
    - 单倍型类群 L2
    - L346
      - L34
        单倍型类群 L3
        
        单倍型类群 L4
      - 单倍型类群 L6
  - L5'7
    - 单倍型类群 L5
    - 单倍型类群 L7

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).
PhyloTree_mt: 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.