Sunday, August 28, 2011

Haplogroup H3 (mtDNA) In Constant Revision

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]
  • 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
  • Highest frequencies: Not Yet Certain

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

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.[3.]

Origin and Expansion

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.


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

Magdalenian: one of the later cultures of the Upper Paleolithic in western Europe, dating from around 17,000 BP to 9,000 BP.

Azilian:The Azilian is a name given by archaeologists to an industry of the Epipaleolithic in northern Spain and southern France.It probably dates to the period of the Allerød Oscillation around 10,000 years ago (uncalibrated) and followed the Magdalenian culture.This potter style gives its name to the main culture of the Mediterranean Neolithic: Cardium Pottery Culture or Cardial Culture, or Impressed Ware Culture, which eventually extended from the Adriatic sea to the Atlantic coasts of Portugal and south to Morocco. Antonio Gilman, Neolithic of Northwest Africa, ''Antiquity'',vol 48, no. 192 (1974), pp 273-282.

Tardenoisian: archaeological culture of the Epipaleolithic period from north-western France and Belgium. Similar cultures are known further east in central Europe (late Mesolithic) and west across Spain. The Tardenoisian lasted from about 7500 BC until the Neolithic.

Franchthi Cave:

Nevalı Çori

Phylogenic Tree of Ancestors and Decedents of H3
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]

[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,

2.] Soares, P; Ermini, L; Thomson, N; Mormina, M; Rito, T; Röhl, A; Salas, A; Oppenheimer, S et al. (2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock", American journal of human genetics 84 (6): 740–59. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773.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.] 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;jsessionid=0FFD220F17A81DDA8D5F257AB396A640.ambra01?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0021029&representation=PDF

[4.]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*

[5.] 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

[6] 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,

[7.]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] National Center for Biotechnology Information

[8.][ 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. doi:10.1002/humu.20921]

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