Y-DNA Haplogroup I, “EUROPE’S NATIVE SONS” All males can trace their Y-DNA lineage back to a Y-DNA ancestor, which originated in Africa about 60,000 years ago (60kya). Although the Y-DNA is inherited from father to son usually without any changes, occasionally differences arise via mutations. Since these mutations or variations add up through generations, the more differences that are found when comparing DNA equals more time elapsed and more genetic distance. Armed with information about the rates, types and number of variations we can create lineage maps or phylogenetic trees and make calculated estimates to trace our roots back to our forebears (e.g. to find the time to most recent common ancestor, TMRCA aka coalescence).
 Figure 1. Figure of Trees. The figure on the left is an African acacia tree silhouette and symbolically shows the root of humans in Africa with their subsequent variation and flourishing in the rest of the world. Next to this is a figure of the major Y-chromosome haplogroups, drawn according to their phylogenetic relationships.
Ancestral Markers
The Y-DNA contains two main types of ancestral markers:
- SNPs (single nucleotide polymorphisms)
- STRs (short tandem repeats, aka microsatellites).
SNPs are a change in a single nucleotide in the DNA and occur infrequently; once they occur they are stable and typically define a whole chromosome and become its signature.
STRs change by the number of repeats and change at a much faster rate than SNPs.
By testing the combination of SNPs and STRs in our Y-DNA, we can gain information on our paternal ancestry, ranging from ancient history (thousands and tens of thousands of years ago) with the much slower mutating SNPs, to recent history (100-1000 years ago) with faster mutating STRs. More simply, SNPs allow us to track ancient or deep ancestry, while STRs allow us to track recent ancestry in the range of immediate family history over several generations and the relatively modern use of surnames. (see Figure 2).
Figure 2. Diagram of variation on the Y-DNA. A schematic timeline is shown over a cytogenetic picture or "ideogram" of the Y-DNA (centromere also marks the BC-AD timeline division). Estimations of ancestry for STR and SNP variation in Y-DNA are shown above. Shown below is the portion of the Y-DNA that harbors informative variation. kya = thousand years ago.
Y-DNA Haplogroups
Haplogroups are groups or a population derived from a common ancestor. Y-DNA haplogroups are defined by slowly evolving SNPs, and each SNP characterizes or identifies a particular paternal haplogroup or branch of the Y-DNA phylogenetic tree. (Note: mtDNA SNPs are used to determine haplogroups for maternal lineages).
By contrast, the faster changing STRs are employed to determine haplotypes for the Y-DNA, where haplotypes are defined as a collection of variations in STR markers observed on the Y-DNA and can be thought of as a signature, one which tracks more recent genetic history. Frequent haplotypes, commonly known as modal haplotypes can often be associated with defined populations and geographical regions, and can be informative or predictive of haplogroups that also show geographical preferences. For example, from your haplotype determined through the Genebase Y-DNA STR Marker Test, you may already have a prediction of deeper genetic origins and a prediction of your Y-DNA haplogroup.
There are 20 major Y-DNA haplogroups (designated by the letters A through T) stemming in a branching fashion from the Y-chromosome prototype, aka “Y-DNA Adam” (haplogroup A), which may be seen as the root or trunk of the tree (see Figure 3). Each branch and haplogroup after “Y-DNA Adam” is defined by a novel SNP or genetic change. The Genebase Y-DNA backbone SNP Test Panel is used to determine Y-DNA haplogroups and additional panels are available to further resolve Y-DNA lineage into sub-haplogroups or subclades.
Figure 3. This phylogenetic tree of the Y-DNA haplogroups is presented in a more typical inverted fashion below, with the A-T haplogroups defined by SNP markers as they branch from the root. In order to identify your personal haplogroup, simply follow the branches from the ‘enter’ point with the SNPs identified, here exemplified for haplogroup I with the green highlighting.
The Haplogroup I story …so far
Early origins
Y-DNA haplogroup I represents a large constituent of Y-DNA found throughout Europe. This haplogroup is found at approximately a frequency of 20% in Europe, which means that roughly 1 out of every 5 males in Europe carries a Y-DNA of this lineage. Haplogroup I is tied to a number of major populations – Vikings, Celts, Anglo Saxons and Slavs - in European history, making it an important contributor to Europe’s emergence as a major center of human development.
The frequency of haplogroup I varies regionally and in a few notable areas, such as Scandinavia and the Balkans, this frequency reaches 40-70% making it the dominant Y-haplogroup in these regions. A distinguishing feature of haplogroup I is its almost complete absence outside of Europe. Haplogroup I not found in Africa and at marginal levels in regions of the Middle East and Asia, with borders juxtaposed to Europe. The estimated frequency of haplogroup I in the United States is near 10%, a consequence of relatively recent European explorations, colonizations and emigrations over the last 300-400 years. Alexander Hamilton, a founding father of the U.S. is a famous representative of this clade. The frequency of haplogroup I in Americans identified with a European background in the U.S. is ~19% - the same as its overall frequency in Europe. It is clear that Haplogroup I has contributed significantly to the paternal ancestry for much of modern Western Civilization.
Figure 4. The emergence of modern humans. A schematic timeline is shown with the approximate appearance of Homo sapiens, with particular attention to the estimated origins of different ancestral Y-chromosomal haplogroups. Below the timeline is shown key geological and anthropological events. Kya = thousand years ago, hg = haplogroup, LGM = last glacial maximum.
Haplogroup I is a descendent of suprahaplogroup F (encompassing haplogroup descendents G-T, see Figure 3). Haplogroup F is thought to represent a second and later stage of human migration out of Africa 50 thousand years ago (kya) (see Figures 4 and 5). Haplogroup I (and its sister clade J, which have an estimated TMRCA ~38kya) are thought to have reached Europe via the Middle East, using the Levant corridor that is part of the ancient fertile crescent created by the river systems of the Tigris, Euphrates and Nile Rivers. It is worth noting that haplogroup J is present in and highly typical of the Middle East, while haplogroup I is nearly non-existent here and exclusive to Europe. A small percentage of haplogroup I in Lebanon has actually been reasoned to come from European invaders during the Crusades rather than from ancient indigenous populations in this Middle Eastern region.
Haplogroup I persisted in Europe during the last glacial maximum (LGM, 18-20kya) that covered a large portion of Europe and pushed the habitable range of humans southward. (see Figures 4 and 5) Estimates put the TMRCA and origin of haplogroup I at 24-28kya, coinciding with the success of Gravettian and Aurignacian cultures (both named for archaeological sites in France) that spread over Europe. Two significant pockets of refuge from the glacial reach existed; one present in the Balkans around the Dinaric Alps and the other present in Franco-Cantabria around the Iberian Peninsula. These and other refuges harbored the haplogroups I and R that would come to predominate in Europe after the glacial retreat and the warming of the Holocene era.
Figure 5. Proposed scenario of the movements of human populations bearing haplogroup I. The figure shows likely origin of haplogroup I from the Middle East via the Levantine corridor and its residence in two pockets (gray ovals) during the last glacial maximum in Europe. Subclades of haplogroup I are color coded and corresponding SNPs listed in the legend. The routes and locations are based on evidence from several studies of Y-DNA I haplogroups and haplotypes.
SNPy trails and the spread of Haplogroup I
The human populations with haplogroup I expanded around 15kya, which coincides with estimates for the TMRCA and divergence of subclades of I. It is at this time that subclade I1 is thought to populate Fennoscandia (present day countries of Norway, Sweden, and Finland). The migration likely took place through present day France, Germany and Denmark, though the exact routes are not known with certainty. Subsequent expansion and migration of an I1 subclade and its subclades populated the British Isles and Iceland. The Vikings were the likely candidates for the spread of I1 subclades and there are studies that link the Celtic, Anglo-Saxon and Germanic heritages to I1. The Balkan refuge, representing subclade I2 likely spread northeast into Russia. The populations comprising I2 are tightly linked with Slavs. The subclade, I2a2, found almost exclusively in Sardinia where it makes up nearly 40% of all haplogroups on this island is also present in France and Iberia and makes these locations the likely source of this unique branch of I.
Haplogroup I is found throughout Europe, although there is regional variation in its frequency. It is especially prevalent in Scandinavian nations and Nordic populations in the north and Balkan nations and Slavic populations in the southeast (see Figure 6). Haplogroup I is similar in distribution to haplogroup R, overlapping R1a in Eastern Europe and R1b in Western Europe. Together, haplogroups I and R constitute 60-90% of the European Y chromosomes. These haplogroups are also similar with respect to their spread to the New World by Western European colonization efforts. The current profile of haplogroup I reflects a great deal of history (and prehistory) in the European culture and its continued investigation may provide new clues on the important events that shaped the course of Western Civilization.
For additional information on the subclades of haplogroup I, consult the section below and refer to Table 3.
Figure 6. A map illustrating the phylogeography of Y-chromosome haplogroup I in Europe. The frequency of haplogroup I is shown as the blue portion of the pie charts distributed over different locations. It is clear that there is a higher frequency around the Balkans and Scandinavia. Another abundant pocket of haplogroup I is located on the island of Sardinia, west of Italy. See Table 3 for a detailed account of the frequency and distribution of haplogroup I.
How the Subclades of Y-DNA Haplogroup I are DeterminedThe further refinement of Y-chromosome ancestry can be obtained by using the Y-DNA Haplogroup I Subclade Testing Panel from Genebase. This panel is based upon a collection of 12 SNPs (see Table 1) that identify 11 sub-branches or subclades of Y-DNA Haplogroup I.
Table 1. The 12 SNPs of the Y-DNA Haplogroup I Subclade Test
The following phylogenetic tree illustrates the relationships of the various branches "Subclades" of Y-DNA Haplogroup I:
Figure 7. Diagram of the current phylogenetic tree for Y-DNA haplogroup I and its subclades. The location of subclade-defining SNPs is shown above the subclade names (boxed). The root of this tree is equivalent to the terminal branch shown for haplogroup I in the previous phylogenetic tree figures.
The procedure for identifying your Y-DNA Haplogroup I Subclade is as follows:
Your Y-DNA Subclade will be automatically determined for you after your Sublcade test is completed. However, if you are interested in finding out how your subclade was determined, just follow these steps:
Step 1. Examine your test results from the Genebase Y-DNA Haplogroup I Subclade Testing Panel. Keep track of all your positive or derived SNP states and consult the Haplogroup I Subclade phylogenetic tree diagram (see Figure 7).
Step 2. Start with the root or main branch of haplogroup I, which is ascertained by the presence of SNP M170 or M258. According to your test results, follow or trace the branches with your SNPs from the Genebase Y-chromosome Haplogroup I Subclade Testing Panel. The point at which you no longer have mutations to follow is the branch or subclade of haplogroup I to which you belong!
Geographical Distribution of the Subclades of Y-DNA Haplogroup IThe following reference map illustrates how the various subclades of Y-DNA Haplogroup I are distributed throughout Europe.
Figure 8. A map illustrating the phylogeography of the subclades of haplogroup I in Europe. The frequency of six different subclades is shown by color in the pie charts. No color indicates the portion of haplogroups other than I observed for each location. The results illustrate a peak of subclade I1 around Scandinavia and I2 around Southeastern Europe. Note also the unique peak of subclade I2a2 in Sardinia. Subclades not currently identified: I1a, I1b1, I2a2a, I2b1a and I2b1b. A small fraction (1/523) of I2a1a was observed in a Turkish population, but is too small to be shown. Paragroup I* represents M170+ status, but lacking further subclade marker identification. See Table 3 for further details on the frequency and distribution of the subclades.
Detailed Accounts for the Subclades of Haplogroup IThe following section provides information on individual Y-DNA Haplogroup I Subclades. This is gathered from the current literature and will be updated as ongoing studies are released and progress in this field is made available.
I1. M253The I1 subclade, defined by SNP M253 is prominent in Scandinavia and other Nordic countries, which includes Sweden (40-50%), Norway (40%), Finland (20%) and Denmark (40%). It is the most prevalent I subhaplogroup in Sweden and TMRCA estimates are 6,000-8,000 years ago. This is after the time when the glaciers are believed to have retreated from Fennoscandia. The Saami population around Lappland in the northern regions of Fennoscandia also has high levels of this subclade. I1 levels diminish moving in the eastern direction from Finland toward Russia and its frequency is low in other Eastern European regions (5-1%). This and additional information from mtDNA haplogroups has provided evidence that the Saami came from a Southern European source rather than from Siberia and the East.
The presence of haplogroup I1 in Scandinavia is linked with Viking (Norwegian or Danish) excursions in the North Atlantic and the dissemination of haplogroup I1 in England, Ireland, Scotland and Iceland. It is also found at high levels in Germany (~25%) and the Netherlands (~17%). Subclade I1 is associated with the Anglo-Saxons who were believed to be descendents of Celtic and Germanic groups emanating from the Low Countries and Frisia (areas near the Netherlands, Belgium, Luxembourg, Germany and Denmark). Estimates of TMRCA for the Anglo-Saxon I1 subclade range from 1,500 to 4,000 years ago. There is also speculation that the spread of Anglo-Saxons (and subclade I1) to England took place through a land bridge, known as Doggerland that connected continental Europe to England around 10kya.
I1a. M21The I1a subclade can be described by the presence of SNP M21. Currently little information exists concerning the frequency and distribution of this subclade. Check this site regularly for updates on this subclade as new information will be posted as studies become available.
I1b. M227The M227 SNP identifies subclade I1b and appears to be a relatively new SNP mutation. It is present at modest levels (0.5-2.0%) in Eastern Europe and the Balkans and is likely to be a minor subclade. Check this site regularly for updates on this subclade as new information will be posted as studies become available.
I1b1. M72The M72 SNP identifies subclade I1b1. Currently little information exists concerning the frequency and distribution of this subclade. Check this site regularly for updates on this subclade as new information will be posted as studies become available.
I2The I2 subclade is the group descended from the refugium centered in the Balkans and has maintained its predominance in this region, which is marked by the Dinaric Alps running along the Adriatic Sea. It is the most prevalent haplogroup in Bosnia, Herzegovinia, Croatia and Serbia. It is also found abundantly on several islands in the Adriatic (Brač, Hvar, Krk and Korčula) and Mediterranean (Sardinia) Seas. Note that this is not a universal phenomenon since the corresponding I2 subclades are absent from Sicily and Corsica and below 5% on Crete. It appears to be primarily associated with Slavic groups in Eastern Europe. I2 subclade levels diminish to much lower levels in Western Europe and where they are associated with the Atlantic coastline.
I2a. P37.2The I2a subclade can be described by the presence of SNP P37.2 and is the most frequent haplogroup in the Balkan region, with a frequency peaking in Herzegovinia (60-70%). A high frequency is also found in Bosnia (40-50%) and Croatia (32%). The Croatian islands frequencies (Hvar = 66%, Korčula 52%, Brač =36% and Krk = 9.5%) show a decreasing trend in a northwestern direction. A similar drop off is seen moving to the northeast through Russia. In fact, the drop off in all directions creates a rather clear I2a peak in the Balkans that radiates outward over many Slavic populations to the east and south. The I2a subclade divergence is estimated near 11kya and it may have paralleled the spread of the R1a haplogroup in the Holocene period after the cold reversal and retreat of the glaciers from Europe.
I2a2. M26I2a2 is described by the presence of the M26 SNP and this interesting subclade of haplogroup I represents over 1/3 of the Y-chromosomes on the Mediterranean island of Sardinia. Its particular pre-eminence here and low levels in only a few other Western European populations has led researchers to conclude that this subclade either originated on Sardinia or was part of its ancestral colonization. Subsequently, in the absence of invasion and re-peopling, I2a2 became a founding and highly representative Y-chromosome on this island. Another way to view this is that there may have been a ‘Sardinian haplogroup I Adam’ from which one out of three Sardinian males can trace their Y-chromosome. Interestingly, the neighboring island of Corsica lacks this subclade altogether and appears to have an overall low frequency of haplogroup I. This could have been due to a smaller initial population of I2a2 coupled with successful colonization by other populations over time and replacement of this unique I subclade. An estimate for the I2a2 Sardinian subclade TMRCA is ~21kya and expansion of the population around 14kya.
I2b1. M223The M223 SNP is a marker for the I2b1 subclade, although it has been linked with the I1 subclade by geographical distribution. This subclade has been detected as a modest fraction of Y-chromosome haplogroup I in Sweden (5% of 42% total I). A similar trend is found throughout Europe where it contributes between 1 and 25% of the total pool of haplogroup I. Its highest frequency is located around Denmark, Germany and the Netherlands. It was previously assigned as subclade I1b2a (also known as I1c in older studies), but the present phylogenetic tree from ISOGG places this group in the I2b subclade.
I2b1a. M284The M284 SNP is a marker for the I2b1a subclade and may have arisen in Britain or Scotland where it appears to be uniquely found. The large study of ~1,000 Europeans by Rootsi did not identify anyone with this variation. There is little additional information concerning the frequency and distribution of this subclade. Check this site regularly for updates as new information will be posted as studies become available.
I2b1b. M379The I2b1b subclade can be described by the presence of SNP M379. Currently, little information exists concerning the frequency and distribution of this subclade. Check this site regularly for updates on this subclade as new information will be posted as studies become available.
I2a1a. P41.2This subclade can be identified by the presence of SNP P41.2. A very minor frequency (1/523 males or <1.0%) of this subclade has been detected in Turkey (Anatolia). There is little additional information concerning the frequency and distribution of this subclade. Check this site regularly for updates on this subclade as new information will be posted as studies become available.
I2a2a. M161This subclade can be described by the presence of SNP M161. Currently, little information exists concerning the frequency and distribution of this subclade. Check this site regularly for updates on this subclade as new information will be posted as studies become available.
Consult Table 3 for additional details on the frequency of haplogroup I and its subclades in different regions.
Modal Haplotypes Associated with Y-DNA Haplogroup IYour unique set of Y-DNA STR markers obtained through the Y-DNA STR test is referred to as your "Haplotype". This is not to be confused with your "Haplogroup" which is determined by testing the SNP markers in your Y-DNA through Y-DNA SNP backbone and subclade testing.
When the Y-DNA STR markers are tested for large groups of people from around the world, the haplotypes which occur with the highest frequencies within certain populations are called "Modal Haplotypes".
For example, a ‘Dinaric’ modal haplotype is common among Y-chromosomes in the Balkans but not typical of haplogroup I Y-chromosomes from Scandinavia or the British Isles.
Confirmation of haplogroup assignment is always made by SNP testing. Conversely, haplogroup assignment does not indicate that you will have the modal haplotype, recalling the fact that STRs are rapidly changing markers. Table 2 provides a list of modal haplotypes associated with Haplogroup I.
Table 2. Modal Haplotypes associated with Y-DNA Haplogroup I
Barac et al. 2003 Eur. J. Hum. Genet. ● Contu et al. 2008 PLoS ONE ● Goff ● Karlsson et al. 2006 Eur. J. Hum. Genet. ● Nordvedt ● Tambets et al. Am. J. Hum. Genet.
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25. Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DF, Blue-Smith J, Wells RS, Comas D, Bertranpetit J, Tyler-Smith C; Genographic Consortium. Y-chromosomal diversity in Lebanon is structured by recent historical events. Am J Hum Genet. 2008 Apr;82(4):873-82. Epub 2008 Mar 27. PMID: 18374297
26. Zei G, Lisa A, Fiorani O, Magri C, Quintana-Murci L, Semino O, Santachiara-Benerecetti AS. From surnames to the history of Y chromosomes: the Sardinian population as a paradigm. Eur J Hum Genet. 2003 Oct;11(10):802-7. PMID: 14512971
Not free to Public: Abstract-only available
1. Capelli C, Brisighelli F, Scarnicci F, Arredi B, Caglia' A, Vetrugno G, Tofanelli S, Onofri V, Tagliabracci A, Paoli G, Pascali VL. Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic-Neolithic encounter. Mol Phylogenet Evol. 2007 Jul;44(1):228-39. Epub 2006 Dec 13. PMID: 17275346
2. Fechner A, Quinque D, Rychkov S, Morozowa I, Naumova O, Schneider Y, Willuweit S, Zhukova O, Roewer L, Stoneking M, Nasidze I. Boundaries and clines in the West Eurasian Y-chromosome landscape: Insights from the European part of Russia. Am J Phys Anthropol. 2008 May 9. [Epub ahead of print] PMID: 18470899
3. Francalacci P, Morelli L, Underhill PA, Lillie AS, Passarino G, Useli A, Madeddu R, Paoli G, Tofanelli S, Calò CM, Ghiani ME, Varesi L, Memmi M, Vona G, Lin AA, Oefner P, Cavalli-Sforza LL. Peopling of three Mediterranean islands (Corsica, Sardinia, and Sicily) inferred by Y-chromosome biallelic variability. Am J Phys Anthropol. 2003 Jul;121(3):270-9. PMID: 12772214
4. Hammer MF, Chamberlain VF, Kearney VF, Stover D, Zhang G, Karafet T, Walsh B, Redd AJ. Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases. Forensic Sci Int. 2006 Dec 1;164(1):45-55. Epub 2005 Dec 5. PMID: 16337103
5. Helgason A, Nicholson G, Stefánsson K, Donnelly P. A reassessment of genetic diversity in Icelanders: strong evidence from multiple loci for relative homogeneity caused by genetic drift. Ann Hum Genet. 2003 Jul;67(Pt 4):281-97. PMID: 12914564
6. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008 May;18(5):830-8. Epub 2008 Apr 2. PMID: 18385274
7. Kasperaviciūte D, Kucinskas V, Stoneking M. Y chromosome and mitochondrial DNA variation in Lithuanians. Ann Hum Genet. 2004 Sep;68(Pt 5):438-52. Erratum in: Ann Hum Genet. 2005 Jul;69(Pt 4):499. PMID: 15469421
8. Lappalainen T, Laitinen V, Salmela E, Andersen P, Huoponen K, Savontaus ML, Lahermo P. Migration waves to the Baltic Sea region. Ann Hum Genet. 2008 May;72(Pt3):337-48. Epub 2008 Feb 19. PMID: 18294359
9. Marjanovic D, Fornarino S, Montagna S, Primorac D, Hadziselimovic R, Vidovic S, Pojskic N, Battaglia V, Achilli A, Drobnic K, Andjelinovic S, Torroni A, Santachiara-Benerecetti AS, Semino O. The peopling of modern Bosnia-Herzegovina: Y-chromosome haplogroups in the three main ethnic groups. Ann Hum Genet. 2005 Nov;69(Pt 6):757-63. PMID: 16266413
10. Nasidze I, Ling EY, Quinque D, Dupanloup I, Cordaux R, Rychkov S, Naumova O, Zhukova O, Sarraf-Zadegan N, Naderi GA, Asgary S, Sardas S, Farhud DD, Sarkisian T, Asadov C, Kerimov A, Stoneking M. Mitochondrial DNA and Y-chromosome variation in the caucasus. Ann Hum Genet. 2004 May;68(Pt 3):205-21. PMID: 15180701
11. Novelletto A. Y chromosome variation in Europe: continental and local processes in the formation of the extant gene pool. Ann Hum Biol. 2007 Mar-Apr;34(2):139-72. Review. PMID: 17558587
Key Investigators:
Luigi Luca Cavalli-Sforza
Stanford University, Stanford, California, USA
Michael F. Hammer
University of Arizona, Tucson, Arizona, USA
Mark A. Jobling
University of Leicester, Leicester, United Kingdom
Ivan Nasidze
Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany
Siiri Rootsi
University of Tartu and Estonian Biocentre, Tartu, Estonia
Pavao Rudan
Institute for Anthropological Research, Zagreb, Croatia
Ornella Semino
Università di Pavia, Pavia, Italy
Kari Stefansson
University of Iceland, Reykjavik, Iceland
Mark Stoneking
Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany
Peter A. Underhill
Stanford University, Stanford, California, USA
Richard Villems
University of Tartu and Estonian Biocentre, Tartu, Estonia
Need to cite this tutorial in your essay, paper or website? Use the following format:
Learn about Y-chromosome Haplogroup I. Genebase Tutorials. Retrieved December 15, 2008, from http://www.genebase.com/tutorial/item.php?tuId=12
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