Articles and Interesting Links

[casadecoqui]

National Geographic News:

New article in the next issue of the Proceedings of the National Academy of Sciences:

Climate Change May Have Spurred Early Human Migration, Study Says

Rapid climate change may have enabled early humans to venture out of Africa and colonize the rest of the world, according to a new study.

[GregKiroKHR1bL1]

Latest African Aricles on the Internet

http://www.sciencemag.org/cgi/conten...ci;1172257/DC1
http://www.sciencemag.org/cgi/content/abstract/1172257

[GregKiroKHR1bL1]

African Gene Flow Patterns

I thought the following authors' ideas of unique female populations in Africa was interesting. These is even more interesting when thinking about the articles over the last ten years.

African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations.
http://www.genetics.org/cgi/content/full/177/4/2195

This can be combined with modern migration trends such as slavery.

Slavery can be traced to the earliest records, such as the Code of Hammurabi, which refers to slavery as an already established institution. Persons generally became enslaved in ancient Egypt by virtue of being captives (or prisoners) of war, committing criminal or other indecent acts, or indebtedness. In ancient Athens about 30% of the population consisted of slaves. In the Roman Empire, probably over 25% of the population was enslaved. The early medieval slave trade was mainly to the East: the Byzantine Empire and the Muslim world were the destinations, pagan Central and Eastern Europe, along with the Caucasus and Tartary, were important sources. Viking, Arab, Greek and Jewish merchants (known as Radhanites) were all involved in the slave trade during the Early Middle Ages. Male slaves were employed as servants, soldiers, or laborers, while female slaves were traded to Middle Eastern countries and kingdoms by Arab, Indian, or Oriental traders, some as domestic servants, and others as sex slaves. Christians were also selling Muslim slaves captured in war.
http://en.wikipedia.org/wiki/Slave_trade

[GregKiroKHR1bL1]

Interesting Article for Haplogroup L mtDNA

Relative Rates of Evolution in the Coding and Control Regions of African mtDNAs

Molecular Biology and Evolution 2007 24(10):2213-2221; doi:10.1093/molbev/msm147

Reduced median networks of African haplogroup L mitochondrial DNA (mtDNA) sequences were analyzed to determine the pattern of substitutions in both the noncoding control and coding regions. In particular, we attempted to determine the causes of the previously reported (Howell et al. 2004) violation of the molecular clock during the evolution of these sequences. In the coding region, there was a significantly higher rate of substitution at synonymous sites than at nonsynonymous sites as well as in the tRNA and rRNA genes. This is further evidence for the operation of purifying selection during human mtDNA evolution. For most sites in the control region, the relative rate of substitution was similar to the rate of neutral evolution (assumed to be most closely approximated by the substitution rate at 4-fold degenerate sites). However, there are a number of mutational hot spots in the control region, 3% of the total sites, that have a rate of substitution greater than the neutral rate, at some sites by more than an order of magnitude. It is possible either that these sites are evolving under conditions of positive selection or that the substitution rate at some sites in the control region is strongly dependent upon sequence context. Finally, we obtained preliminary evidence for "nonideal" evolution in the control region, including haplogroup-specific substitution patterns and a decoupling between relative rates of substitution in the control and coding regions.
http://mbe.oxfordjournals.org/cgi/co...act/24/10/2213

[GregKiroKHR1bL1]

A M91 Ancient Africans
B M60 Ancient Africans
C M130 Eden in the East
D M174 Ancient Asians
E M40 Old Africa
E3a M2 Bantu farmers
E3b M35 Abyssinia
G M201 Caucasus mountains
H M69 Ancient Dravidians
I M170 Gravettian culture
J 12f2a Arabia
J1 M62 Fertile Crescent Farmers
J2 M172 Fertile Crescent Farmers
L M20 Ancient Indians
N3 M46 Uralic languages
O M175 Rice agriculture
O3 M122 Rice agriculture
Q P36 Native Americans
R1a M17 Kurgan culture
R1b M269 Aurignacian culture
R2 M124 Asia, predominantly
southern

I guess nothing is new for most people. I am beginning to organize my data now.

[GregKiroKHR1bL1]

I guess nothing is new for most people. I am beginning to organize my data now.

[GregKiroKHR1bL1]

I Thought This Was Interesting (mostly from the Gen. Proj. 2005)

mtDNA
L0 Central Eastern African, much of sub-Saharan
L1 East, Southern. Central, West African. Explorer group and L0 group
L2_2758 Wide sub-Saharan distribution, four unique subsets
L3594 Central to out of Africa in Arabia or to north-western Africa
M10400 Red Sea-E. Africa, Nile Valley, Mediterranean to Australia, expanded north from Persia
D5178 Caspian Sea and Lake Baikal to Ancient American, East Asia
C13263 Caspian Sea and Lake Baikal to Ancient American, Central Asia
N10873 Eastern Mediterranean, western Asia
N1_10238 Ashkenazi Jew to Egypt to Greece to Persia to East of Black Sea
I10034 Western Eurasian, Caucasus to north Asia and western Europe
A4248 Caspian Sea and Lake Baikal to Ancient American, Eskimos, Asians
W1243 Caucasus to Northern Eurasian, west to Europe (Aurignacian)
X6371 North and East Africa, Western Eurasia, Early America
R12705 Surrounding area of the Near East, descendants dominated Europe
U11467 NW Eurasia into Scandinavia, N. Caucasus Mts., Near East, N. Africa, India, Ancestral K
K10550 NW Eurasia into Scandinavia, Northern Caucasus Mountains, Near East, N. Africa, India
R0_11719 West Eurasian
HV14766 Caucasus Mountains, Ethiopia (Arabian Slave), Anatolia, N. Poland
H7028 Turkey, Caucasus Mountains, Iberian Peninsula, Italy, Balkans, Europe,
V4580 Southern Europe to NW Africa, Scandinavia
J12612 Fertile Crescent , Arabia, India, Eastern Eurasia & Europe
T13368 Fertile Crescent, Indus Valley, Arabian Peninsula, NE Europe
R9_3970 Parent of hg F, Indochina, Malay Peninsula, island Southeast Asia
B Caspian Sea and Lake Baikal to Ancient American, Pacific Coast, South East Asia
Z Caspian Sea and Lake Baikal to Siberia and Asia
F Caspian Sea and Lake Baikal to Asia, East Asia, Central Siberia
P S. Pacific region, especially in New Guinea, Melanesia, indigenous populations of Australia
G East Asian, northeastern Siberia
Y_A14693G South Siberian populations
S Aboriginal Australians
O Branch from hg N
Q southern Pacific region
E southern Asia distribution
?* several parental haplogroups

[GregKiroKHR1bL1]

I think the Wiki reference made a small mistake or the wording is bad.

Chemically, pheomelanin differs from eumelanin in that its oligomer structure incorporates the amino acid L-cysteine, as well as DHI and DHICA units.

It should read something that has this information I give below in it because there is the black DHI eumelanin and the brown DHICA eumelanin. Pheomelanin incorporates L-cysteine and GSH. It differs from eumelanin because it does not have DHI and DHICA. Mix melanins have elements from eumelanin and pheomelanin.

DHI-melanin; black, insoluble,high MW
DHICA-melanin; brown, slightly soluble, intermediate MW
Pheomelanin; yellow/red, alkalisoluble, low MW

[GregKiroKHR1bL1]

We were having a conversation about the origins of the term "Redbone" at school the other day. I never hear of the word. However, we all were wondering about the genetics and molecular structures of the various types of melanin.

The 2 types are black eumelanin and brown eumelanin. A small amount of black eumelanin in the absence of other pigments causes grey hair. A small amount of brown eumelanin in the absence of other pigments causes yellow (blond) color hair. Chemically, pheomelanin differs from eumelanin in that its oligomer structure incorporates the amino acid L-cysteine, as well as DHI and DHICA units.

http://www.answers.com/topic/melanin?cat=health

http://music.musictnt.com/biography/sdmc_Phaeomelanin

http://en.wikipedia.org/wiki/Melanin

I found an excellent article which went into the details of Tyrosine → DOPA → dopaquinone.

Melanin Pigmentation in Mammalian Skin and Its Hormonal Regulation
http://physrev.physiology.org/cgi/co...full/84/4/1155

But my sister was a little bit lost with the chemistry. She wanted to know more about the social part of the issue.

1514 Spanish law of 19 October explicitly permits intermarriage with Indians; permission of intermarriages reenacted in 1515 and 1556; intermarriage with blacks neither encouraged nor prohibited.
1527 Spanish royal decree of 11 May recommends that male slaves ought to marry female slaves as much as possible: "with marriage and their love for wives and children and orderly married life they will become more calm and much sin and trouble will be avoided."
1638 Ordinance of the Director and Council of New Netherland prohibits adulterous intercourse between whites and heathens, blacks or other persons, upon threat of exemplary punishment of the white party.
1640 1 Laws of Virginia 552; "Robert Sweat is to do penance in church according to the law of England, for getting a negro woman with child, and the woman to be soundly whipped."
1662 First Virginia laws against intermarriage and against interracial sex: "if any christian shall committ ffornication with a negro man or woman, hee or shee soe offending shall pay double the ffines imposed by the former act (which set fines for fornication at 500 pounds of tobacco]."
1685 Dutch Cape law prohibits marriage between white men and slave women; some legal unions of white men with free women of color continued to take place, but with decreasing frequency.
1771 Viceroy of Portuguese Brazil orders degradation of an Amerindian chief, who, "disregarding the signal honours which he had received from the Crown, had sunk so low as to marry a Negress, staining his blood with this alliance."
1778 5 April: "Order of the Council of State forbidding all marriages between whites and blacks in France, on penalty of being expelled at once to the colonies."
1805 Spanish royal decree requires that persons of "pure blood" obtain permission of the viceroy or the audiencia in order to marry "ele-ments of Negro and Mulatto origin."
1837 5 June: Texas act provides "It shall not be lawful for any person of Caucasian blood or their descendants to intermarry with Africansor the descendants of Africans."
http://www.redboneheritagefoundation...e_timeline.htm

I found it all to be interesting. I guess, I have to think about it for a little time.

[clarkedenise]

Searching the Database

Here a link to the article: https://www3.nationalgeographic.com/...PLOS_paper.pdf

I believe there a link to the database as well.

https://www3.nationalgeographic.com/...resources.html

Go to "the Get supplemental data" link, it is a xls (Microsoft Excel) format. I participated in the public database, I found my mtDNA markers and their final Haplogroup designation was L1c2 instead of L1*, however they when I go to my Genographic page they still have my haplogroup at L1*. Has anyone else read the paper and search the database?

Dear Lee,
I searched the supplemental data link today, and like you, 10 of my markers corresponded to L1c2. I have three markers that are not part of L1c2, and they are 16213A, 16519C, and 16527T. Hope this helps.
Denise

[GregKiroKHR1bL1]

Questionable Results

I put a question mark that came from articles or post with questionable data . . . I think some assignments are harder than others.

mutations tend to increase in value but not always

DYS 390 = 23, DYS 492 = 13
Northern Germany, Scandinavia, Frisian

S28+/492=14 seems to
represent deep ancestry among
the Celts of southern Germany and northern Italy

S28+/492=12 seems to
represent more northern Celt deep ancestry

R1b DYS 390, 391, 392 and 393
Atlantic Modal: 24, 11, 13, 13
NW Irish: 25, 11, 14, 13
Scottish: 24, 10 13, 13
Anglo-Saxon: 23, 11, 13, 13
?N Italy 24, 10, 13, 14
L3 mtDNA Y-DNA related

M168 R1b separated from E3b
M89 R1b separated from G and I
M173 R1b separated from R1a

G2 al-Quraish 21, 10, 11, 15
E3b Levite 24, 10 (11), 11, 13
R1a 25, 10, 11, 13
DYS388 = 13
I1b2a 23, 10 (11), 11, 14 (15)
DYS388 =14, DYS19 = 14
I1a - Anglo-Saxon 22, 10, 11, 13
I1a-NORSE 23, 10, 11, 13

?E3a Portugal 24, 10, 11, 13
?E(xE3b) Austria 24, 10, 11, 13
?E3a Sub-Saharan 21, 10 (11), 11, 13 (14,15)

[GregKiroKH2]

People are beginning to use UEPs for haplogroup assignments instead of HVR-1 and 2 haplotypes. Do you know what they tested for besides the HVR-1 and 2 regions? I had to ask to find out, and so I tested my entire mitochondria to know for sure.

Here a link to the article: https://www3.nationalgeographic.com/...PLOS_paper.pdf

I believe there a link to the database as well.

https://www3.nationalgeographic.com/...resources.html

Go to "the Get supplemental data" link, it is a xls (Microsoft Excel) format. I participated in the public database, I found my mtDNA markers and their final Haplogroup designation was L1c2 instead of L1*, however they when I go to my Genographic page they still have my haplogroup at L1*. Has anyone else read the paper and search the database?

[GregKiroKH2]

The good thing about these sub-clades is that we can understand how our society became what it is today. Luckily for me, my R1b does not have many matches after 12 markers. Still, some of the older markers can tell us a unique story of history.

mutations tend to increase in value but not always

DYS 390 = 23, DYS 492 = 13
Northern Germany, Scandinavia, Frisian

S28+/492=14 seems to
represent deep ancestry among
the Celts of southern Germany and northern Italy

S28+/492=12 seems to
represent more northern Celt deep ancestry

R1b DYS 390, 391, 392 and 393
Atlantic Modal: 24, 11, 13, 13
NW Irish: 25, 11, 14, 13
Scottish: 24, 10 13, 13
Anglo-Saxon: 23, 11, 13, 13
N Italy 24, 10, 13, 14
L3 mtDNA Y-DNA related

M168 R1b separated from E3b
M89 R1b separated from G and I
M173 R1b separated from R1a

G2 al-Quraish 21, 10, 11, 15
E3b Levite 24, 10 (11), 11, 13
R1a 25, 10, 11, 13
DYS388 = 13
I1b2a 23, 10 (11), 11, 14 (15)
DYS388 =14, DYS19 = 14
I1a - Anglo-Saxon 22, 10, 11, 13
I1a-NORSE 23, 10, 11, 13

Great Post Dra. Ana & Greg,
I'm not surprise with these findings. As more data is accumulated on those of us who do have these admixtures, I think the results will prove to be insightful. Thanks for the articles.
Denise

[lee1906]

The Genographic Public Project mtDNA Database

Here a link to the article: https://www3.nationalgeographic.com/...PLOS_paper.pdf

I believe there a link to the database as well.

https://www3.nationalgeographic.com/...resources.html

Go to "the Get supplemental data" link, it is a xls (Microsoft Excel) format. I participated in the public database, I found my mtDNA markers and their final Haplogroup designation was L1c2 instead of L1*, however they when I go to my Genographic page they still have my haplogroup at L1*. Has anyone else read the paper and search the database?

[clarkedenise]

Article on Y, X, autosomal and mtDNA in African Americans

Great Post Dra. Ana & Greg,
I'm not surprise with these findings. As more data is accumulated on those of us who do have these admixtures, I think the results will prove to be insightful. Thanks for the articles.
Denise