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
[編輯]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]
主要mtDNA單倍群
[編輯]泛單倍群L
[編輯]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
泛單倍群M
[編輯]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
[編輯]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
[編輯]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
[編輯]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 |
地理分布
[編輯]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
[編輯]分配
[編輯]- 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
[編輯]- mtDNA Mutation Computer Model: Ian Logan's mutation calculator.
系統發生
[編輯]- 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.
地圖
[編輯]古地圖
[編輯]- 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
[編輯]- HRAS mtDNA: A heatmap generator.
數據庫
[編輯]古代
[編輯]- AmtDB: An database of ancient mtDNA samples.[15]
- All Ancient DNA Dataset: Carlos Quiles' uniparental database (with BAM).
現代
[編輯]- GenBank mtDNA Sequence Checker: Ian Logan's GenBank based accession matching tool.
- mitoYDNA: A uniparental database.
- MITOMAP: An mtDNA genome database.[16]
參看
[編輯]參考資料
[編輯]- ^ 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 , 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
- ^ 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]. (原始內容 (PDF)存檔於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 –透過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. 已忽略未知參數
|orig-date=
(幫助) - ^ 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.
外部連結
[編輯]- 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
- 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)
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 |