人類線粒體DNA單倍體群

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。單倍群用於表示線粒體系統發育樹上的主要分支點。了解母系血統的演化路徑，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。單倍群的字母名從A到Z不等，按照發現的先後順序命名，與實際的遺傳關係不相干。

線粒體單倍群起源於一個假想的女性，是所有現存人類的母系最近共同祖先，一般稱作線粒體夏娃。

線粒體DNA的變異速度稱作人線粒體分子鐘，這是尚在研究的領域，有報告稱每8000年發生一次突變。^[2]

線性透視

此進化樹來自Van Oven (2009)^[4]，2022年6月一份研究提出了單倍群L的另一種系統發育路徑。^[5]

L（線粒體夏娃）
- 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改來）
        U8: K
        
        O

主要mtDNA單倍群

泛單倍群L

泛單倍群 L是人mtDNA單倍群中最基本的，其他單倍群都從L3單倍群演化而來。主要分布在非洲。

單倍型類群 L0
L1-7
- 單倍型類群 L1
- L2-7
  - L3'4'6
    - 單倍型類群 L2
    - L346
      - L34
        單倍型類群 L3
        
        單倍型類群 L4
      - 單倍型類群 L6
  - L5'7
    - 單倍型類群 L5
    - 單倍型類群 L7

泛單倍群M

泛單倍群M主要分布在亞洲和美洲，其後代有單倍型類群 M、單倍型類群 C、單倍型類群 Z、單倍型類群 D、單倍型類群 E、單倍型類群 G、單倍型類群 Q等。

泛單倍群N

泛單倍群N主要分布在澳洲、美洲，在亞洲亦有，其後代有單倍型類群 N、單倍型類群 O、單倍型類群 A、單倍型類群 S、單倍型類群 I、單倍型類群 W、單倍型類群 X、單倍型類群 Y以及泛單倍群R。

泛單倍群R

泛單倍群R主要分布在歐洲、北美、大洋洲，在亞洲和美洲亦有，其後代有單倍型類群 R、單倍型類群 B、單倍型類群 F、單倍型類群 H、單倍型類群 V、單倍型類群 J、單倍型類群 T、單倍型類群 U、單倍型類群 K。

年代

More information 單倍群, 估計起源時間（萬年前）[6] ...

單倍群	估計起源時間（萬年前）^[6]	可能起源地
L	20	非洲
L1-6	17	東非
L2-6	15	東非
L0	15	東非
L1	14	中非
L3-6	13
L5	12
L2	9
L3	7	東非
N	7	東非或西亞
M	6	東非，西亞或南亞
R	6	南亞或東南亞
U	5.5	東北非或印度（南亞）
RT'JT	5.5	中東
JT	5	中東
U8	5	西亞
R9	4.7
B4	4.4
F	4.3
U4'9	4.2	中亞
U5	3.5	西亞
U6	3.5	北非
J	3.5
X	3
K	3
U5a	2.7
HV	2.7	近東
J1a	2.7	近東
T	2.7	兩河流域
K1	2.7
I	2.6
J1	2.4	近東
W	2
U4	2	中亞
X2	2
H	2	西亞
U5a1	1.8	歐洲
J1b	1.1
V	1.4
X2a	1.3	北美
H1	1..2
H3	12
X1	1

Close

地理分布

2004年一篇論文總結，現代西亞、北美與歐洲人群中最普遍的單倍群是H, J, K, N1, T, U4, U5, V, X, W。^[7]

非洲單倍群：L0, L1, L2, L3, L4, L5, L6, T, U5a

澳洲單倍群：M42a, M42c, M14, M15, Q, S, O, N, P. (Refs 1, 2, 3, 4, 5, 6)

亞洲單倍群：F, C, W, M, D, N, K, U, T, A, B, C, Z, U many number variants to each section

研究軟件

分配

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.

測年

mtDNA Mutation Computer Model: Ian Logan's mutation calculator.

系統發生

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.

地圖

古地圖

HIP Haplomap: Ancient uniparental map.
AH DNA: Nicky Rosenblatt's ancient uniparental map.^[14]
Ancient DNA: An aDNA map made with Map Maker.

現代地圖

HRAS mtDNA: A heatmap generator.

數據庫

古代

AmtDB: An database of ancient mtDNA samples.^[15]
All Ancient DNA Dataset: Carlos Quiles' uniparental database (with BAM).

現代

GenBank mtDNA Sequence Checker: Ian Logan's GenBank based accession matching tool.
mitoYDNA: A uniparental database.
MITOMAP: An mtDNA genome database.^[16]

參看

參考資料

[1]
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 .
[2]
Loogvali, Eva-Liis; Kivisild, Toomas; Margus, Tõnu; Villems, Richard, O'Rourke, Dennis , 編, 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 
[3]
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]
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 .
[5]
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 .
[6]
Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary (PDF). Cell. 2009: 82–83 [89]. （原始內容 (PDF)存檔於2009-12-29）.
[7]
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  –透過academic.oup.com.
[8]
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.
[9]
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.
[10]
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.
[11]
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. 已忽略未知參數|orig-date= (幫助)
[12]
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 .
[13]
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.
[14]
Various. Rosenblatt's ancient DNA map. Anthrogenica. 2017-05-30.
[15]
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.
[16]
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.

外部連結

mtDNA .pdf map（頁面存檔備份，存於網際網路檔案館）
Map of macro-單倍型類群 N （頁面存檔備份，存於網際網路檔案館） 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 單倍型類群 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
- List of mtDNA haplogroup projects （頁面存檔備份，存於網際網路檔案館）
MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations （頁面存檔備份，存於網際網路檔案館）
HaploGrep: mtDNA haplogroup determination based on PhyloTree.org （頁面存檔備份，存於網際網路檔案館）
HaploFind – fast automatic haplogroup assignment pipeline for human mitochondrial DNA （頁面存檔備份，存於網際網路檔案館）

人類粒線體DNA單倍體群

最近的共同粒線體祖先

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

[pmid28178941-1] [1]
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 .

[2] [2]
Loogvali, Eva-Liis; Kivisild, Toomas; Margus, Tõnu; Villems, Richard, O'Rourke, Dennis , 編, 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 

[pmid25798216-3] [3]
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 .

[vanOven2009-4] [4]
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 .

[5] [5]
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 .

[soares_supplementary-6] [6]
Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary (PDF). Cell. 2009: 82–83 [89]. （原始內容 (PDF)存檔於2009-12-29）.

[7] [7]
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  –透過academic.oup.com.

[Vnl2013-8] [8]
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.

[Kls2010-9] [9]
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.

[Sch2023-10] [10]
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.

[Grc2021-11] [11]
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. 已忽略未知參數|orig-date= (幫助)

[Kim2020-12] [12]
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 .

[vnv2008-13] [13]
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.

[Ant2017-14] [14]
Various. Rosenblatt's ancient DNA map. Anthrogenica. 2017-05-30.

[Ehl2018-15] [15]
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.

[Kgl1996-16] [16]
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.

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

[9]

[10]

[11]

[12]

[13]

[14]

[15]

[16]