User:JohnLloydScharf/Haplogroup H3 (mtDNA)

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In human mitochondrial genetics, Haplogroup H3 is a human mitochondrial DNA (mtDNA) haplogroup descended from Haplogroup H (mtDNA). Mitochondria in humans is a double-stranded circular molecule of 16,569 base pairs. H3 is the next most common sub-haplogroup after H1, characterized by the polymorphism T6776C; a basepair in the coding region from locations numbered from 575 to 16,000. H3 is European, without Near Eastern representatives. H3 is ∼9000 [Range 6,000 to 12,000] years old based on the coding-region data. H3 is ∼11,000 years old [Range 8,000 to 14,000] using locations numbered 16001-16568 of the Hypervariable region HVR1. [1]

Infobox for Haplogroup H3[edit]

Haplogroup H3
Possible time of origin ∼12,000 YBP[2]
Possible place of origin Not Yet Certain
Ancestor H2
Descendants H3a, H3b, H3c, H3d, H3e, H3f, H3g
Defining mutations A2706ArCRS, C7028CrCRS, T6776C[3]
Highest frequencies Not Yet Certain

H3 Association with Loss of Feeling as a result of Type II Diabetes[edit]

Mitochondrial dysfunction has been implicated in rare and common forms of type 2 diabetes (T2DM). While the associations are low, some mitochondrial haplogroups are statistically significant in their association with an increased risk of specific diabetes complications. H is slightly associated with retinopathy, H3 with neuropathy (loss of sense of feeling/touch), U3 with nephropathy, and V with renal failure. [4]

Origin and Expansion[edit]

Haplogroup H3 is common in western Europe, having expanded after the Last Glacial Maximum 19,000–20,000 years ago from the refugium in the Franco-Cantabrian region. [5] Given the date of origin, its expansion seems to be the Late Glacial Maximum or even the Younger Dryas 12,000 to 13,000 years before the present. H3 probably experienced first a bottleneck during the Last Glacial Maximum and then rapid growth during global warming. [6]

Distribution[edit]

  • In the study by Garcia et al(2011)[7] 320 samples were taken from NW Iberian Peninsula[50], NE Iberian Peninsula[4],France[10], West Islands from Europe[5], North Central Europe[75], Other Iberian Peninsula Samples[60], the Mediterranean Area[16], Scandinavia[33], and Northeast Europe[7]. The "Other Iberian Peninsula" samples had the highest percentage of H3 of all samples[8%] and within H samples[18%]found. All five samples from the West Islands[Ireland/British Isles] were H3 with the highest gene and nucleotide diversity, which is an indication of age of H3 from that source.

Archaeological Cultures and Sites Contemporary with H3 Dates of Origin[edit]

Phylogenic Tree of Ancestors and Decedents of H3[edit]

263, 750, 1438, 2706, 4769, 7028, 8860, 14766, and 15326 are the seven nucleotides are confirmed as rare polymorphisms associated with H2a2 or the revised Cambridge Reference Sequence. It is documented as the Homo sapiens mitochondrion, complete genome, NC_012920 in the Genbank [8] by the National Center for Biotechnology Information. This phylogenetic tree of haplogroup H3 subclades is drawn from Mannis van Oven, PhyloTree.[9]


Subclades[edit]

Save

H3a[edit]

H3b[edit]

H3c[edit]

H3d[edit]

H3e[edit]

H3f[edit]

References[edit]

  1. ^ Genome Res. 2005 January; 15(1): 19–24.doi: 10.1101/gr.3182305 PMCID: PMC540273 Copyright © 2005, Cold Spring Harbor Laboratory Press, High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium Luísa Pereira,1 Martin Richards,2 Ana Goios,1 Antonio Alonso,3 Cristina Albarrán,3 Oscar Garcia,4 Doron M. Behar,5 Mukaddes Gölge,6 Jiři Hatina,7 Lihadh Al-Gazali,8 Daniel G. Bradley,9 Vincent Macaulay,10,12 and António Amorim1, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540273/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540273/pdf/00150019.pdf
  2. ^ Soares, P; Ermini, L; Thomson, N; Mormina, M; Rito, T; Röhl, A; Salas, A; Oppenheimer, S; MacAulay, V (2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". American journal of human genetics. 84 (6): 740–59. PMC 2694979Freely accessible. PMID 19500773. doi:10.1016/j.ajhg.2009.05.001. The calibration points chosen (the European LGM and the colonization of Sahul) would stretch the diversity within haplogroup H (H1 and H3 dated to ∼12 kya in our time-dependent clock) while contracting that within haplogroup P (which dates to 58 [49.3; 66.8] kya with our corrected clock), producing an effect opposite to our correction for overestimation at lower time depths.
  3. ^ {{cite journal |title=The Molecular Dissection of mtDNA Haplogroup H Confirms That the Franco-Cantabrian Glacial Refuge Was a Major Source for the European Gene Pool |journal=Am J Hum Genet |date=September 20 2008 |first=Mannis |last=van Oven |coauthors=Chiara Rengo, Chiara Magri, Vincenza Battaglia, Anna Olivieri, Rosaria Scozzari, Fulvio Cruciani, Massimo Zeviani, Egill Briem, Valerio Carelli, Pedro Moral, Jean-Michel Dugoujon, Urmas Roostalu, Eva-Liis Loogväli, Toomas Kivisild, Hans-Jürgen Bandelt, Martin Richards, Richard Villems, A. Silvana Santachiara-Benerecetti, Ornella Semino, and Antonio Torroni |volume=75 |issue=5 |pages=910-918 |doi=10.1002/humu.20921 |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182122 |accessdate=2009-05-20|pmid=18853457
  4. ^ Achilli A, Olivieri A, Pala M, Hooshiar Kashani B, Carossa V, et al. 2011 Mitochondrial DNA Backgrounds Might Modulate Diabetes Complications Rather than T2DM as a Whole. PLoS ONE 6(6): e21029. doi:10.1371/journal.pone.0021029 http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=0FFD220F17A81DDA8D5F257AB396A640.ambra01?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0021029&representation=PDF
  5. ^ a b c d Roostalu et al (2007), Mol Biol Evol (2007) 24 (2): 436-448. doi: 10.1093/molbev/msl173 First published online: November 10, 2006, "Origin and Expansion of Haplogroup H, the Dominant Human Mitochondrial DNA Lineage in West Eurasia: The Near Eastern and Caucasian Perspective", U Roostalu1,*, I Kutuev*†, E-L Loogväli*, E Metspalu*, K Tambets*, M Reidla*, EK Khusnutdinova†, E Usanga‡, T Kivisild* and R Villems* Cite error: Invalid <ref> tag; name "Roostalu_et_al.282007.29" defined multiple times with different content (see the help page). Cite error: Invalid <ref> tag; name "Roostalu_et_al.282007.29" defined multiple times with different content (see the help page).
  6. ^ Pierron D, Chang I, Arachiche A, Heiske M, Thomas O, et al. 2011 Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe. PLoS ONE 6(6): e21543. doi:10.1371/journal.pone.0021543 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021543 http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0021543&representation=PDF
  7. ^ Heredity (2011) 106, 37–45; doi:10.1038/hdy.2010.47; published online 21 April 2010, Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge O García1,4, R Fregel2,4, J M Larruga2, V Álvarez3, I Yurrebaso1, V M Cabrera2 and A M González2, Sup.Ref. S12, http://www.nature.com/hdy/journal/v106/n1/extref/hdy201047x1.xls
  8. ^ PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from J01415. On Jul 8, 2009 this sequence version replaced gi:115315570. This sequence is a corrected version of the HUMMTCG reference sequence. The original Cambridge reference sequence (CRS) is preserved as GenBank J01415 gi:337188 [PMID:7219534] http://www.ncbi.nlm.nih.gov/nuccore/NC_012920 National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/
  9. ^ [http://www.phylotree.org/ Mannis van Oven, PhyloTree van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. http://www.phylotree.org. doi:10.1002/humu.20921]
  10. ^ http://www.snpedia.com/index.php/Rs2854128
  11. ^ http://www.snpedia.com/index.php/Rs2015062
  12. ^ http://www.snpedia.com/index.php/I1000015
  13. ^ http://www.snpedia.com/index.php/Haplogroup_H_(mtDNA)#Associated_Genosets http://www.snpedia.com/index.php/Gs1031
  14. ^ http://www.snpedia.com/index.php/Haplogroup_H_(mtDNA)#Associated_Genosets
  15. ^ http://www.snpedia.com/index.php/Haplogroup_H_(mtDNA)#Associated_Genosets
  16. ^ http://www.snpedia.com/index.php/Haplogroup_H_(mtDNA)#Associated_Genosets

See also[edit]

Phylogenetic tree of human mitochondrial DNA (mtDNA) haplogroups

  Mitochondrial Eve (L)    
L0 L1–6  
L1 L2   L3     L4 L5 L6
M N  
CZ D E G Q   O A S R   I W X Y
C Z B F R0   pre-JT   P   U
HV JT K
H V J T
  1. ^ van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. http://www.phylotree.org. doi:10.1002/humu.20921