Tracing the Y-DNA Founders ou...

Date study began: February 19, 2007

Published: March 11, 2007

Tracing the Y-DNA Founders out of Africa

Using marker DYS 393 we will follow this marker out of Africa and to various expansions around the world. The more frequent and sustained these expansions occurred in any given lineage the greater the expansion. Consequently the more genetic diversity. Therefore the better the chances are of an off modal value of DYS 393 becoming modal in a subsequent expansion.

It is sometimes useful in our genealogical searches to start from the founders and work our way forward in time.

This has been done on the The Genealogy of Mexico web-page by identifying the founders (conquistadors) and locating where they or their descendants settled over time.

With this in mind, this paper will for the time being set aside SNP's and only use them as reference points for founder lineages and geographical locations and concentrate primarily on modal values of marker DYS 393 and work our way forward in time. The premises working here are that the founders left the most descendants and great population expansions in both paleolithic and neolithic times. These expansions had a greater effect on increasing effective mutation rates (i.e. deviation from ancestral-founder markers). Sometimes bottlenecks served to change modal values for DYS 393 from ancestral values.

The very slow mutating marker 393 with a mutation rate of .00076 will be used in this study. This works out to 1 mutation every 1,316 generations or 26,320 years with a generation being 20 years or 39,480 years with a generation being 30 years.

For an off modal value at DYS 393 to take over as modal there would have to be a depopulation and subsequent expansion or early expansion in which this off modal value took part early on. The earliest populations out of Africa would not have had the numbers to mutate from modal until great population expansions.

Most of the world in ancient times had an unfavorable climate, soil unsuitable for planting crops, mountains, deserts, forests or areas where crops, game and domesticatable animals and water were scarce. In rare locations around the world there were areas of aquatic life and flat grass lands ideal for hunting game in Paleolithic times as well as areas of ideal climate and soil conducive to growing crops in Neolithic times. It is these rare areas where conditions were favorable for survival that drew that ancients.

From the table below, the value of marker 393 when it left Africa with the founder lineages, was 13. We will look for these founder lineages in these favorable areas where their lineage was likely to expand.

Marker DYS393

YDNA Haplogroup	Age of linage	Modal Value at Marker 393	Area of expansion	Modal Source and *Expansion Source
C* (M130)	50K	13/14	South India	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. (note: two samples found and one additional from China was 12 at 393).
C* (M130)	<50K	13	Mongolia	-*The Genetic Legacy of the Mongols
C2b (M208)	<50K	14	Polynesia	-*The Effective Mutation Rate at Y Chromosome Short Tandem Repeats
C3 (M217)	20K	13	China and India	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. ,
C3c (M48)	1K	13	Mongolia	-*Genetic Evidence for the Mongolian Ancestry
C5 (M356)	?	13/14	India	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists.
D1 (M15)	30K	13	Paleolithic Japan	Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta *Dual origins of the Japanese
E* (M96)	30-40K	13	Sub Saharan Africa	E3b Y-DNA Project Note: only two samples *Origin, Diffusion, and Differentiation of Y Haplo. E and J
E3a (M2)	30K	13	Bantu expansion	Bantu Y-lineages in Sub-Saharan Africa *Deep Ancestry by Wells
E3b (M35)	20K	13	Neolithic North Africa	E3b Y-DNA Project *Origin, Diffusion, and Differentiation of Y Haplo. E and J
E3b1a (M78)	14.7K	13	Paleolithic Balkans	E3b Y-DNA Project *Origin, Diffusion, and Differentiation of Y Haplo. E and J
E3b1b (M81)	5.6K	13	Neolithic Northwest Africa	IBERIAN SUB-CLUSTER IS REVEALED by Robert Tarin *Origin, Diffusion, and Differentiation of Y Haplo. E and J
F* (M89)	45K	13	Paleolithic India	* Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta **
F2 (M427\M428)	<45K	14	Paleolithic China	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. , Sengupta paper w/ access to expanded dataset
G* (M201)	30K	13	Paleo.Neolithic India	-*Excavating Y-chromosome haplotype strata in Anatolia (note 1 sample)
G1a (P20)	<30K	13	Neolithic Caucasus	-*Excavating Y-chromosome haplotype strata in Anatolia
G2* (P15)	<30K	14	Neolithic Middle East	*Excavating Y-chromosome haplotype strata in Anatolia
H* (M69)	30K	13/14	India	*Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta
H1 (M52)	25K	12	India	*Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta
H2 (APT)	<30K	13	India	*Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta
I1a (M253)	20K	13	Frisia	Distribution of Repeat Values at Various STR Sites for Haplogroup I1a**The origins of the British by Oppenheimer , Phylogeography of Y-Chromo. Haplo. I Reveals Distinct Domains
I1b (P37.2)	15K	13	Balkans	Excavating Y-chromosome haplotype strata in Anatolia *The origins of the British by Oppenheimer , Phylogeography of Y-Chromo. Haplo. I Reveals Distinct Domains
I1c (M223)	16K	14	Paleolithic Frisia	I1c Clan FTDNA Project *The origins of the British by Oppenheimer , Phylogeography of Y-Chromo. Haplo. I Reveals Distinct Domains
J (M304)	15K	12	Neolithic Middle East	-*Origin, Diffusion, and Differentiation of Y Haplo. E and J , Excavating Y-chromosome haplotype strata in Anatolia
K* (M9)	40K	?	Eurasian steppe	**Deep Ancestry by Wells
K2 (M70)	30K	13	Near East	K2 Y-DNA Project , Excavating Y-chromosome haplotype strata in Anatolia *Deep Ancestry by Wells
L1 (M76)	<30K	11	India	*Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta
L3 (M357)	<30K	12	India	*Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta
N* (M231)	13K	13	Southeast Asia	Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta , Excavating Y-chromosome haplotype strata in Anatolia *Route of Y-DNA Haplogroup N
N3 (TAT)	11K	14	Siberia	Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta *Route of Y-DNA Haplogroup N
O* (M175)	35K	?	Paleo.Neolithic China	**Male Demography in East Asia: A North–South Contrast in Human Population Expansion Times
O1 (M119)	<35K	13	China	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. , Sengupta paper w/ access to expanded dataset
O2a (M95)	<35K	14	China and India	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. ,
O3 (M122)	<35K	12	China and India	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. ,
O3a5 (M134)	<35K	12	Northeast India	-*Northeast Indian Passageway: A Barrier or Corridor for Human Migrations?
P* (M45)	35K	13	Paleolithic Southern Siberia	P-M45 Haplotypes in Mongolians, Chipewayan, and Amerindians , ** Deep Ancestry by Wells
Q* (M242)	17.5K	13	Siberia and America	Allele Frequencies at Six Microsatellite Loci in Lineages within the P-M45 Haplogroup in Amerindians, Chipewayan, and Mongolians , Excavating Y-chromosome haplotype strata in Anatolia *Deep Ancestry by Wells , Y-Chromosome Evidence for Differing Ancient Demographic Histories in the Americas
Q3 (M3)	10K	13	America	Allele Frequencies at Six Microsatellite Loci in Lineages within the P-M45 Haplogroup in Amerindians, Chipewayan, and Mongolians. *Deep Ancestry by Wells
R*(M207)	30K	13	Central Asia>India	Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions , Research by Sengupta *Deep Ancestry by Wells
R1a (M17)	12.5K	13	Ukraine	Y Haplogroup R1a1 by Dennis Garvey , Excavating Y-chromosome haplotype strata in Anatolia *Deep Ancestry by Wells
R1b (M343)	30K	13/12	Iberia/ Balkans	-*Y Haplogroup R1b by Dennis Garvey , Excavating Y-chromosome haplotype strata in Anatolia
R1b2b (M73)	?	13	Siberia	Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. , Sengupta paper w/ access to expanded dataset *Male Demography in East Asia: A North–South Contrast in Human
R1b2b (M73)	?	14	Northeastern Pakistan	*Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of central Asian pastoralists. , Sengupta paper w/ access to expanded dataset
R2 (M124)	25K	14	India	-A Synthesis of Haplogroup R2 Excavating Y-chromosome haplotype strata in Anatolia , Research by Sengupta **Deep Ancestry by Wells ,

C* (M130) - is the oldest surviving lineage to leave Africa. Its journey took it through Southern India and on to Australia. From southeast Asia this lineage went north up the coast of East Asia and is only found sporadically there. It eventually expanded in Mongolia. Two samples from this journey through India are shown to have DYS 393 of 13 and 14. Haplogroup C* attains its highest diversity in India.

C3 (M217) - is a subclade of the oldest surviving lineage to leave Africa. This line ended up in expanding in Mongolia/Northern China. This area would have been away from the Neolithic of China and possibly more prone to drift given the Northern climate and Nomadic lifestyle. This subclade may have expanded with its horse culture in Neolithic times. Given this populations lack of diversity (per the source article above) it is no surprise DYS 393 exhibits the ancestral 13 as modal.

D1 (M15) - is a Paleolithic remnant of the Jamon culture seen in the Ainu of Japan. This culture was successful enough to hold off the farmers in the form of Haplogroup O coming in from China. The only other expansion of

D is in Tibet, which Spencer Wells says was a recent expansion. Tibet has the most diversity of Haplogroup D anywhere.

After D left Africa and headed up the coast of Asia it never really expanded but left genetic traces of its migration. D has the ancestral value of 13 at DYS 393 as modal which reflects it lack of major expansions in the world.

E* (M96) - some of this haplogroup likely left Africa early on leaving E3a in Africa and E3b in the middle east. An ancestral Brother of E, Haplogroup D both with the YAP mutation left Africa earlier and in the case of Haplogroup D initiated expansions in Tibet and Japan. All subclades of E show founder values of 13 at marker DYS 393 and were mainly limited to Africa.

E3a (M2) - associated with the Bantu expansion this line was limited in the natural resources (domestic animals and empire building crops) needed to expand past the hunter gather stage in ancient times. E3a remained in Africa. The modal value of DYS 393 remains the ancient value of 13 and is documented here as a reference for Haplogroup E.

E3b (M35) - the consistency of E3b at marker DYS 393 (value of 13) and its subclades and its relatively young age (20K) reveals that once some of Y Haplogroup E* left Africa its frequency expanded mainly in the direction of the Neolithic expansion in North Africa in the form of E3b. This expansion took advantage of the same daylight hours and good climatic conditions exhibited in the middle east, by moving laterally west and entering Africa again to the north of the Sahara this time. Given the stableness of marker 393 in E3b's subclades there would likely be a small population that grew exponentially with the expansion, around the area of the middle east that meets North Africa. This linage participated in an expansion out of the Balkans from Neolithic times possibly with the Danubian culture.

Note: there is some evidence of modal 14 at DYS 393 in Eastern Europe as evidenced in y-search.

F* (M89) - is the second wave to leave Africa and is modal 13 at DYS 393. It represents 95% of non-Africans and expanded out from the Middle East and/or India. This linage is the ancestor of Haplogroups G, H, I, J, K, L, M, N, O, P, Q and R. Haplogroup F's numbers out of Africa would have been small and is still modal 13 at DYS 393. It would be the descendant populations of F to expand in Paleolithic and Neolithic times to go off modal with this value depending on the age and rate of expansion.

G* (M201) - a direct descendant of F* maintains 13 at DYS 393 and likely came to be in India and spread to the the Caucasus region. G1 is most frequent in the southern Caucasus. G1a (DYS 393=13) is a subclade of G1.

G2 (P15) - makes it way to the middle east and expands with the Neolithic farmers into Europe. G2 may have become off modal, to 14 at DYS 393 during a depopulation as pandemics swept the early Neolithic due to their proximity with diseases the domestication of animals.

H* (M69) - is confined to India for the most part and expanded during the Paleolithic and Neolithic periods as evidenced by it's population today. It is the second most populous country in the world. Currently modal values at DYS 393 are split between 13 and 14 representing a slow and continued growth between paleolithic and neolithic times.

H1 (M52) - may have been influenced by the neolithic expansion in the west of India as evidenced by the prevalence of Haplogroup J there. This late expansion could have changed its modal at DYS 393 to 12.

I1a (M253) - made its way north from the Balkans into Scandinavia from the east and into Frisia from the North. The flooding that formed the North Sea may have created an expansion point due to a bounty of food. With I1a's heaviest concentration in Southern Sweden, this migration through Scandanavia ended after the flooding of the area of the North Sea. Stranding most of I1a on the Scandanavian side. The modal for DYS 393 remained ancestral at 13 as the trip through Scandinavia may have kept I1a's numbers low.

I1b (P37.2) - remained in the Balkans after the Last Glacial Maximum (LGM). This would be geographically relatively close to the ancestral Haplogroup F and it remains at modal 13 at DYS marker 393.

I1c (M223) - made its way up the Danube before the younger dryas from Haplogroup I's holdout in the Balkans to the area of Frisia. Frisia is the most densely populated part of Europe today and fueled a large expansion in Paleolithic times due to its level topology and grasses while the rest of Europe, save the refugiums (Iberia and Balkans) were in open woodland areas or artic tundra. There is archaeological evidence (The People of Earth by Fagan) showing the ancients wintering along the Danube which connects Frisia with the Balkans. I1c was likely born of a Haplogroup I ancestor during this expansion. DYS 393 is modal 14 which can be attributable to the age and population of this expansion and to the small Haplogroup I founder population in this area.

Note: the only sample on the Internet of I1c2 (M379) is from India and is ancestral 13 at DYS 393 (see table 3 of Sengupta paper w/ access to expanded dataset).

J (M304) - given the numerous mutations that make up the J portion of the Haplogroup Tree (see http://www.isogg.org/tree/ISOGG_HapgrpJ.html), the overlapping haplotypes in ysearch and the young age (15K) of this branch, it is evident that the J branch grew rapidly in a relatively short period of time. It is apparent that J was the primary benefactor of Neolithic Farming. The modal value for DYS 393 in Haplogroup J must have changed early on to 12 as it appears to be modal in all subclades. The early Neolithic would have experienced depopulation due to diseases that would have developed early on due to pandemics brought on by their proximity to newly domesticated animals. This would have been a problem at least until they developed immunities to them. Perhaps this is when there was a modal change at DYS 393. The change would have been from an expansion population with the newly acquired modal value of 12.

K2 (M70) - descends from Haplogroup K in the Eurasian steppe. This clan probably moved into the middle east in a late expansion spread through the area of the Mediterranean. DYS 393 remains ancestral at 13.

L - is limited to India and surrounding areas such as the Caucasus, Turkey the Middle East and Pakistan. The modal value of L1 (M76) at DYS 393 is 11 which would be off the modal value of 13 by two steps. This represents multiple founder lineages in this older (30K) Paragroup (L*). L3 (M357) with a value of 12 at DYS 393 is only one step off of the ancestral value of 13 found in K2 and F. Some lineages of L may have been lost in a possible attempt to head north before the LGM while India itself was not affected or in a clash of cultures. Many lineages were likely caught away from refugiums and perished. Also many lineages in the west of India would have expanded faster than the east due to advantages brought by the Neolithic Farmers. India is the second most populous country in the world.

N* (M231) - came about in Southeast Asia were in shows limited expansion. The value of DYS 393 remains ancestral (same value as K2 and F) at 13.

N3 (TAT) - represents a migration of N to the north into Siberia with a new founder with a modal value of 14 at DYS 393 instead of the ancestral 13 found in N*.

O* (M175) - likely had an ancestral value (same value as K2 and F) of 13 at DYS 393 (not enough data to confirm this). This linage is mainly confined to China with some expansion into India. The population of China is the largest in the world indicating both Paleolithic and Neolithic expansions from areas favorable to game hunting in North Western China in paleolithic times and agriculture in South Eastern China in Neolithic times. Off modal values of subclades of O (12 and 14) in the area of an expansion of O into India show separate founders one step above and below the ancestral value of 13.

P* (M45) - today is found in Central Asia and Siberia in low numbers, likely due to the harsh environment in which this haplogroups descendants make their home. The low numbers kept the modal value of DYS 393 at the ancestral (same value as K2 and F) value of 13.

Q* (M242) - expanded out of a small Siberian refugium supporting a small founder population that retains its paternal ancestral (P*) marker of 13 at DYS 393. Harsh environmental conditions kept the initial population small. This paragroup expanded in the Americas to give rise to Q3 and modals of 14 at DYS 393 in expansion populations in Peru and Mexico.

R*(M207) - came to be in Central Asia and some moved south into India as part of India's expansion. It is a rare linage and retains its ancestral (P*) value of 13 at DYS 393 in India.

R1a (M17) - came from R1 in central Asia and expanded in the Ukraine after the younger dryas. Perhaps due to its young age it has retained paragroup R* ancestral value of 13 at DYS 393.

R1b (M343) - along with brother clade R1b2b (M73) expanded out from 3 refugiums each, across Europe and Siberia. Western R1b who is ancestral modal at DYS 393 (equal to 13), likely crossed the Northern part of Europe into Western Europe in better climactic times 30K years ago. Eastern R1b would have been caught up in glaciation in the north of Europe with possibly only a residual population with the off modal value of 12 at DYS 393 making it into the Balkan refugium. It is not known when R1b2b (M73) expanded into Northern China but five samples from three locations across Northern China and Japan all have 13 at DYS 393. Eleven of twelve R1b2b (M73) samples from Southern China and Pakistan have modal 14 at DYS 393. Source of M73 data (Table 3).

R2 (M124) - is limited to India and is off modal from ancestral (R*) with 14 at DYS 393.

_____________________________________________________________________________________________________

From the Migration of Haplogroup C*below it can be seen that there was no branching of this group except within C*. Haplogroup C's numbers remain relatively small today. There are only minor traces of C* on the east Asian coast of China so it was never a factor in the Neolithic growth of China. This haplogroup always seemed to settle in remote unhospitable places like Mongolia and Northern Australia with the exception of India where it is the most diverse. The slow growth of this haplogroup is probably the reason it has kept its modal at 13 for DYS 393.

In the three graphics below in this section are likely migration patterns of Paragroups and subclades with expansions and DYS 393 values in parenthesis, starting with C* then DE* and then F*:

Africa>C India (13)>Australia

>C Mongolia (13)

>C3 Mongolia (13)

C3 India (13)>C3 China (13)

The consistency of the E3b's value of 13 (above) at DYS 393 reflects it's relatively young age. E3b expansion is from the Middle East and likely a result of Neolithic Farming. E3b seems to have played a part in a late expansion from the Balkans.

Africa>E* Middle East>E3b Middle East (13)>E3b North Africa (13)

>E3b Balkans (13)

Haplogroup D* follows a similar pattern as Haplogroup C* (above). D* as C* has low population numbers today and did not leave any branches other than sublades for being such an old linage. It is even thought to have traveled with C* up the coast of East Asia to be found today in Japan. D* shares the YAP mutation with E*.

Africa>D* Middle East>D* Southeast Asia>D1 Japan (13)>Tibet D2

F* (above) and descendants appear to have participated in a Paleolithic and Neolithic expansion out of India. India is the crossroads in the expansion out of Africa.

Africa>F* India (13)>F2 China (14)

Africa>F* India (13)>G* India (13)>G1a Caucasus (13)

>G2 Middle East (14)

Africa>F* India (13)>H* India (13 or 14)>H1 India (12)

>H2 India (13)

Africa>F* India (13) or Middle East>I1a Frisia (13)

>I1b Balkans (13)

>I1c Frisia (14)

Africa>F* Middle East>J* Middle East (12)

Africa>F* India (13)>K* Southern Central Asia>K2 Near East (13)

Africa>F* India (13)>K* Southern Central Asia>L* India >L1 India (11)

>L3 India (12)

Africa>F* India (13)>K* Southern Central Asia>N* Southeast Asia (13)>N3 Siberia (14)

Africa>F* India (13)>K* Southern Central Asia>Southeast Asia>O1 China (13)

>O2a China & India (14)

>O3 China & India (12)

>O3a5 India (12)

Africa>F* India (13)>K* Southern Central Asia>P* Siberia (13)

Africa>F* India (13)>K* Southern Central Asia>P* Siberia (13)>Q* Siberia & Americas (13)>Q3 Americas (13)

>P* Central Asia>R* Central Asia>R* India (13)

>R1a Ukraine (13)

>R1b Balkans (12)

>R1b Iberia (13)

>R1b2b Siberia (13)

>R1b2b India (14)

>P* Central Asia>R* Central Asia>R* India (13)>R2 India (14)

____________________________________________________________________________________________________

In conclusion, by following the very slow mutating marker DYS 393 out of Africa to ancient refugiums and/or current major population centers, we can see how lineages evolved. By knowing a founder value of a lineage (i.e. those with a given SNP) we can see that migrations by an off modal subpopulation (e.g. I1c) or depopulation and subsequent expansion (e.g. Eastern R1b) caused marker DYS 393 to go off modal (i.e. deviate from its ancestrial value). Also we can see how low population numbers by very old lineages (e.g. C* and D*) kept the ancient modal value at marker DYS 393; at 13.

Gary Felix

Mexico DNA Project Administrator

The Genealogy of Mexico DNA Project

_________________________________________________________________________________________________________