What is subclade testing?

Subclade testing can provide increased resolution of your placement on the Y-chromosome phylogenetic tree.  Before your subclade can be determined, you must first know what haplogroup you belong to.  Haplogroups are defined by unique mutation events such as single nucleotide polymorphisms, or SNPs.  These SNPs mark the branch of a haplogroup, and indicate that all descendents of that haplogroup at one time shared a common ancestor.  The Y-DNA SNP mutations were passed from father to son over thousands of years.  Over time, additional SNPs occur within a haplogroup, leading to new lineages.  These new lineages are considered subclades of the haplogroup.  Each time a new mutation occurs, there is a new branch in the haplogroup, and therefore a new subclade.  By testing for the presence of SNPs identified in previous research to be indicative of particular subclades, you can now determine the specific subclade you belong to within your determined haplogroup.

Haplogroup Q, possibly the youngest of the 20 Y-chromosome haplogroups (Figure 1), originated with the SNP mutation M242 in a man from Haplogroup P that likely lived in Siberia approximately 15,000 to 20,000 years before present (Bortolini et al 2003, Seielstad et al. 2003).  Descendents with the M242 mutation migrated eastward across Siberia until they reached the north-eastern point of Asia (Figure 2).  During this time, sea levels were over 100 metres lower than at present because water was locked up in large glaciers.  The lower water level exposed a bridge of land connecting Siberia and Alaska (Figure 3).  This area was called Beringia and it provided a passageway for migrants into the Americas.  Hapologroup Q represents a recent paternal founder population for the Native American radiation into the Americas.



Figure 1.  The phylogenetic tree of the 20 known Y-DNA haplogroups.  Haplogroup Q is circled in blue to indicate its relative position within the tree.  You can see from this tree that it was derived from Haplogroup P.




Figure 2.  Proposed migration path of men carrying M242, the defining mutation for Haplogroup Q.  The migration continued east to Beringia, the conduit for the passage of people into the Americas.  At sometime during the movement of tribes across this land bridge, the SNP mutation M3 arose.  As a result, Subclade Q1a3a is prevalent throughout North, Central and South America as this continent was populated by the men that arrived across Beringia.





Figure 3.  This figure provides further detail on Beringia, the land mass that connected Siberia to the Americas.  Between 10,000 and 15,000 years ago, the water level of the ocean was lower because extensive glaciation had large quantities of water locked up as ice.  As a result, dry land was exposed between Siberia and Alaska.  Due to the presence of glaciers during this time, it is still not clear if migrations occurred along the coastline or over the land and ice.  Nevertheless, American ancestors arrived via this land bridge.

Geographical Distribution of Y-DNA Haplogroup Q

This haplogroup is widespread at low frequencies throughout the Middle East, Asia and Siberia, and at high frequencies in the Americas (Figure 4, Table 1).  In Eurasia, Haplogroup Q is mainly found in Siberian populations and in particular within two Siberian populations (Karafet et al. 2002): the Kets (93.8%) and the Selkups (66.4%).  The Kets are thought to be the only survivors of ancient nomads that lived in Siberia and their population size is very small; as of 2002, there were fewer than 1500 Kets in Russia.  The Selkups have a slightly larger population size than the Kets, but it is still a relatively small population (approximately 4,250 in 2002).  The Selkups are thought to represent a long history of interbreeding between aboriginal Siberians and Samoyedic people.

Some studies have detected the presence of Haplogroup Q in the Polynesian Islands.  Although strong evidence points to ancestral populations from Southeast Asia, there are some indications that pre-European Polynesian culture may have American origins.  These include the distribution of sweet potato and bottle gourds that would have required contact between Polynesians and Native Americans, either through a Polynesian round-trip voyage to South America, or a one-way voyage by Native Americans to Polynesian islands.  The Native American-specific subclade of Haplogroup Q was detected at low frequencies on Rapa Island (Hurles et al. 2002) and Rapa Nui Island (Ghiani et al. 2006) but further analysis of mtDNA indicated that the detected Native American paternal lineages were not due to an ancient settlement. Rapa and Rapa Nui Islands are thought to have been settled approximately 1200 AD (Hunt and Lipo 2006).  Native American Y chromosomes may have been introduced to the islands prior to the 20th century from members of a Peruvian slave ship that arrived on the islands (Hurles et al. 2003).  Shortly after the arrival of the ship, there was a population crash in 1864 on Rapa Nui and only 20 adult males survived (Green 2000).  The genetic contribution of the slaves may have been enhanced in the population if they were resistant to the dysentery or smallpox that likely decimated the populations.




Figure 4.  Worldwide distribution of Haplogroup Q; the black area of each pie chart shows the frequency of Haplogroup Q within that area.  Clearly, the haplogroup is most prevalent across North, Central and South America.  Some native Siberian populations also have a high frequency of Haplogroup Q.  The haplogroup is detected across Asia and the Middle East, although at low frequencies.



Table 1.  Worldwide frequencies if Haplogroup Q.

The Subclades of Y-DNA Haplogroup Q

Current data indicate that there are 14 distinct lineages, or subclades, within Haplogroup Q that can be detected with a panel of 14 different SNPs.  The haplogroup first splits into Paragroup Q* and Subclade Q1.  There are three distinct lineages within Subclade Q1: Paragroup Q1*, Subclade Q1a, and Subclade Q1b.  The remaining 11 subclades within haplogroup Q are located within Q1a3, one of the seven distinct lineages within Subclade Q1a.  Details on the relationship of the subclades can be viewed in the “Phylogenetic Tree” section.

Since many of the SNP markers that define the subclades within Haplogroup Q have only recently been detected, there have been few studies that have incorporated them into the genealogical analyses.  In addition, Subclade Q1a3a has been the focus of most studies since it is detected at such high rates within the Americas.  Consequently, relatively little is known about some of the individual subclades (Table 2).  However, this means that any new information gathered about the subclades will be important for advancing our understanding of the history of human populations. 

Table 2.  Summary of current knowledge on the subclades of Haplogroup Q.

How the Subclades of Y-DNA Haplogroup Q are determined

1. Obtain a Y-DNA haplogroup predication based on the results from a Y-DNA STR test.
2. Confirm your haplogroup with a Y-DNA Haplogroup Backbone SNP test.  You should be positive for M242, the SNP that is used to confirm Haplogroup Q in the Y-DNA Haplogroup Backbone SNP Test panel.
3. Once your haplogroup has been confirmed as Q, you can then obtain the Y-DNA Haplogroup Q Subclade Test.  The table below (Table 3) provides a list of the 14 SNP markers used in this panel, including the location of the SNP, the specific mutation, and the subclade that is defined by each SNP.
4. Identify the location of your SNPs on the phylogenetic tree to determine your subclade.  Refer to Figure 5a and 5b for a step-by-step guide to help you locate your subclade.


Table 3.  List of the SNP markers used in the Y-DNA Haplogroup Q Subclade Test Kit.






Figure 5a.  Once you have you have the results of your SNP test, you can then follow this step-by-step flow chart to determine your subclade.  To begin, refer to the decision indicated with the red circle.  Do you have SNP mutation M242?  This should be a “yes”, otherwise you are not part of Haplogroup Q.  Next, determine if you have SNP P36.2.  If you lack this mutation, you are located within Paragroup Q*.  Likely you will be positive for SNP P36.2, and then you can check if you have MEH2.  First, we will follow the decision path if you do not have MEH2.  If you do not have MEH2, you may be positive for M378.  If so, you are part of Subclade Q1b.  A missing M378 mutation indicates you are located within Paragroup Q1*.  Now, we will follow the path assuming you are positive for MEH2.  The next SNP to check is M120.  If you have this mutation, you are part of Subclade Q1a1.  If M120 is missing, but you are positive for M25, you are located within Subclade Q1a2.  If you do not have mutation M25, check your results for P48.  Presence of this mutation would place you into Q1a4.  If you lack P48, we will have to continue on the next figure to locate your subclade. 





Figure 5b.  Again, start at the decision indicated with the red circle.  To continue from the previous figure, you have determined that you are missing mutation P48.  Do you have SNP mutation M3?  First, let’s assume that you do not have this mutation.  If you are missing M3, but have P89, you are part of Subclade Q1a5, whereas if you have M323 you are part of Q1a6.  If you do not have any of these mutations, you are considered part of Paragroup Q1a*.  Now we will return and see what path to follow if you are positive for M3.  SNP M3 places you within Subclade Q1a3, but there are several further lineages within this subclade.  A positive result for M19 means that you are part of Subclade Q1a3a1, M194 would place you into Subclade Q1a3a2, whereas presence of mutation M199 means that you are located within Subclade Q1a3a3.  If you lack any further mutations after M3, you are considered to be part of Paragroup Q1a3a*.

Geographical Distribution of the Subclades of Y-DNA Haplogroup Q

Table 4 summarizes a current review of the literature on the worldwide frequency distribution of Haplogroup Q subclades.  Since many SNPs have only been recently discovered, there is not a lot of information for many of the subclades.  Figure 6 provides a visual representation of the relative frequencies of the subclades across the world and provides some insight into the migration patterns of ancient humans that carried Haplogroup Q mutations.  Some interesting studies on the distribution of Haplogroup Q subclades are described below.

Native American Subclade Q1a3a

Most research on Haplogroup Q has been focused on subclade Q1a3a because it has provided insight into the recent migration history of people into America.  The Americas have been the most recently colonized countries in the world, and initial studies proposed a tripartite model of migration with three distinct lineages leading to the Amerind (North, Central and South America), Na-Dene (northwestern North America) and Eskimo-Aleut (subarctic) language families.  Later studies utilizing Y-chromosome SNP variation indicated that there were likely two major male migrations into the Americas, one of which was Haplogroup Q, and in particular Subclade Q1a3a.  The SNP mutation M3 that defines Subclade Q1a3a has been shown to be a major founding haplogroup of Native Americans.  Aside from Native Americans, this lineage is only found on the Chukotkka peninsula of north-eastern Siberia (Karafet et al. 1997).  South American populations have a high prevalence of SNP M19 that defines a distinct lineage within Q1a3a; it has been detected in 59% of Amazonian Ticuna men and in 10% of Wayuu men (located in the extreme north of Columbia; Ruiz-Linares 1999).  This subclade, Q1a3a1, seems to be unique to South American populations and suggests that population isolation and perhaps even the establishment of tribes of Native Americans began very shortly after they migrated to the Americas (Bortolini et al. 2003).  

Estimation of the time of origin of a unique mutation event, or time to most recent common ancestor (tMRCA), is based on the number of Y-STR (short tandem repeat) markers that separate men with different haplogroups and the estimated mutation rate (on average, how many years pass by between mutation events).  These estimates, however, are not always precise and may have large margins of error.  To help support or disprove a proposed time of origin for a haplogroup, ancient skeleton remains can be tested for the presence of SNPs that define particular haplogroups.  If SNPs indicative of a specific haplogroup are found to occur in the skeleton, it means that haplogroup is at least as old as the ancient bones.  Scientists found human remains in Alaska that were estimated to be approximately 10,300 years old, and with persistence they were finally able to extract DNA from the molars.  This human was positive for SNP M3, indicating that subclade Q1a3a is at least 10,300 years old (Kemp et al. 2007).  Previous attempts to estimate the age of this subclade have provided results ranging from 7,510 to 22,000 years before present (Bortolini et al. 2003, Karafet et al. 1999, Schurr 2004, Bianchi et al. 1998, and Underhill et al. 1996). 

Many studies have utilized Y-linked STR markers to further examine gene diversity within the Native American subclade.  These STR markers include Y-chromosome linked microsatellite markers DYS19, DYS389A, DYS389B, DYS390, DYS391 and DYS393.  Analysis of haplotype diversity within South America supports observations of cultural and environmental diversity and paleoecological data; eastern populations show more genetic differentiation relative to western populations (Tarazona-Santos et al. 2001).  Most preliminary studies on the colonization of the Americas have utilized information from mitochondrial DNA.  Interpreting the Y-chromosome information with previous mtDNA studies has enriched understanding of the interaction of populations during colonization.  Within Brazil, the Guarani were attracted to Jesuit missions during colonial times whereas other tribes remained hidden and isolated within the forests.  It is thought that the Guarani likely made a significant genetic contribution to populations of Brazil through admixture with colonists.  The Kaingang represent all non-Guarani indigenous people in Brazil and their contact with non-Native Americans during colonization is thought to be much less than the Guarani.  Analysis of the proportions of this subclade, along with mitochondrial data, suggest that admixture with non-Native Americans in the Guarani was restricted to non-American males, whereas the Kaingang admixture occurred via introduction of non-American females. 

Haplogroup Q subclades in India

Haplogroup Q is widely distributed throughout India (although at low frequencies) including Indo-European and Dravidian castes and tribes.  This widespread distribution may be due to a common ancestral relationship among the population groups or to recent gene flow between the groups.  Most Indian Y-STR haplotypes are unique from haplotypes associated with Central Asian Q haplogroups, and Subclades Q1a3 and Q1a6 only seem to be found in India (Sharma et al. 2007; Sengupta et al. 2006).  Of the three Indian men that were Q1a3, one was Indo-European (of 21), one Middle Dravidian Caste (of 85) and one Upper Indo-European Caste (of 86).

Haplogroup Q subclades in the Jewish population

Q1 was one of seven haplogroups present at >5% in a population of Ashkenazi Jewish men and represented one of the haplogroups with the largest difference in frequency between the Ashkenazi Jewish and Non-Jewish Europeans.  The authors suggest that Q1 is minor founding haplogroup of the Ashkenazi Jews (Behar et al. 2004).  Low haplotype diversity of Q1 within this population suggests that there was a profound bottleneck in the Roma population from which the Ashkenazi Jews are thought to be derived.  The subclade Q1a6 has been detected in 15% of Yemeni Jewish men (Shen et al. 2004).




Figure 6.  Relative frequency distribution of the subclades of Haplogroup Q.  The pie charts indicate the relative contribution of the different subclades in geographical areas where Haplogroup Q has been detected.  Clearly, Subclade Q1a3a is widely distributed throughout the Americas with Q1a3a1 also detected in South America.  The yellow pies in Pakistan and India likely represent Subclade Q1a3*, and not the Native American Subclade Q1a3a.


Table 4.  Frequency distribution of the subclades of Haplogroup Q detected worldwide.

Phylogenetic Tree for the Subclades of Y-DNA Haplogroup Q

The phylogenetic tree of the subclades of Haplogroup Q is illustrated below (Figure 7).  It is current as of August 2008 and will be updated if further information becomes available. 




Figure 7.  The phylogenetic tree of Haplogroup Q subclades as of August 2008 (www.isogg.org).  As the figure indicates, the markers in white are those markers included in the Y-DNA Haplogroup Q Subclade Test Panel, whereas the markers are not included in the panel.  Most of the subclades detected in this haplogroup are located within Subclade Q1a3.

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