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。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。
线性透视
编辑
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.
外部連結
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 | |||||||||||||||||||||||||||||