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  #31  
Old 8th December 2006, 10:20 PM
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casadecoqui casadecoqui is offline
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Aaaaaaah! L1c are so special

Batini C, Coia V, Battaggia C, Rocha J, Pilkington MM, Spedini G, Comas D, Destro-Bisol G, Calafell F.

Phylogeography of the human mitochondrial L1c haplogroup: Genetic signatures of the prehistory of Central Africa.
Mol Phylogenet Evol. 2006 Oct 5;

Interindividual variation of human mitochondrial DNA has been extensively studied over the last two decades, and its usefulness for reconstructing evolutionary relationships of extant populations has been proved. However, some mitochondrial lineages still need to be studied using a combination of larger and tailored datasets and increased level of resolution in order to shed light on their origin and on the processes underlying their present distribution. In this study, we analyze the phylogeny of the L1c haplogroup of human mitochondrial DNA using sequence data from hypervariable regions 1 and 2 obtained from 455 individuals (extracted from a total sampling of 2542 individuals) belonging to sub-Saharan African and African-American populations. We propose a substantial revision of L1c phylogeny, by introducing one new sub-haplogroup (L1c4), two new L1c1 clades (L1c1b and L1c1c), and by reassigning the previous L1c1a1 sequences to a clade which we termed L1c5. The new phylogeny encompasses distinct lineages with different evolutionary histories. In fact, based on population frequency, internal variation and mismatch distribution, we propose that L1c1b, L1c1c and L1c2 originated in Bantu ancestors, whereas L1c1a, L1c4 and L1c5 evolved among Western Pygmies. The population structure of L1c is not comparable to any known mitochondrial or, even, Y-chromosomal haplogroup, and challenges the current view that most of mtDNA variation in Pygmies might reflect admixture with Bantu or a persistence of plesiomorphic characters. In fact, the unique feature of the L1c is that it retains a signature of a phase common to the ancestors of the Bantu and Western Pygmies, while encompassing some specific sub-clades which can indicate their divergence. This allowed us to attempt a phylogenetically based assessment of the evolutionary relationships between the two groups. Taking into consideration estimates of the time to the most recent common ancestor of L1c and its clades together with archaeological and paleoclimatological evidence, we propose that the ancestors of Bantu and Western Pygmies separated between 60 and 30kya.

**********************

If anyone has library access to this one, (I don't, library too far), I would appreciate a copy. Many thanks.
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  #32  
Old 10th December 2006, 02:07 PM
GregKiroKH2 GregKiroKH2 is offline
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The abstract is interesting to read. I do not see how to obtain a copy.

Cannot get this one:
Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis
Juan C. Martínez-Cruzado 1 *, Gladys Toro-Labrador 1, Jorge Viera-Vera 1, Michelle Y. Rivera-Vega 1 2, Jennifer Startek 1, Magda Latorre-Esteves 1 3, Alicia Román-Colón 1 4, Rebecca Rivera-Torres 1 5, Iris Y. Navarro-Millán 1 2, Enid Gómez-Sánchez 1, Héctor Y. Caro-González 1 6, Patricia Valencia-Rivera 1 7
Volume 128, Issue 1 , Pages 131 - 155

Published Online: 3 Feb 2005
http://www3.interscience.wiley.com/c...TRY=1&SRETRY=0

Cannot get the next one:

http://www.journals.uchicago.edu/AJH...414300671Guest

The Making of the African mtDNA Landscape

Antonio Salas,1,2,3 Martin Richards,2 Tomás De la Fe,1 María-Victoria Lareu,1 Beatriz Sobrino,1 Paula Sánchez-Diz,1 Vincent Macaulay,3 and Ángel Carracedo1


Am J Hum Genet. 2002 November; 71(5): 1082?1111.
Published online 2002 October 22.

Can read this one:
http://www.pubmedcentral.nih.gov/pic...6&blobtype=pdf

Cannot read this one:
Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set.

Forensic Science International, Volume 148, Issue 2-3, Pages 169-179

M. Allard, D. Polanskey, K. Miller, M. Wilson, K. Monson, B. Budowle

Quote:
Abstract
The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n = 217) were observed in the African American data set (n = 1148). These SNPs ranged from having 1?39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each) observed included 16093, 16129, 16189, 16311, 16362, 16519, 146, 150, 152, 189, and 195. These rapidly changing sites are consistent with other published analyses. Only 34 SNPs are needed to identify all clusters containing 10 or more individuals in the African American data set. The results show that the African American SWGDAM mtDNA data set contains variation consistent with that described in continental African populations. Thirteen of the 18 haplogroups previously observed in African populations were observed and include: L1a, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e1, L3e2, L3e3, L3e4 and L3f. Haplogroup L2a is the most commonly observed cluster (18.8%) in the African American data set. The next most common haplogroups in the African American data set include the clusters L1c (11.0%), L1b (9.1%), L3e2 (9.0%) and L3b (8.1%). Approximately 8% of the haplogroups observed within African Americans were common in European Caucasians or East Asians; these were H (n = 32), J (n = 4), K (n = 5), T (n = 2), U5 (n = 6), U6 (n = 9 also known from North Africa), A (n = 12), B (n = 7), C (n = 4), and M (n = 16), respectively. The European Caucasian and East Asian haplogroups are expected due to admixture between individuals with recent ancestry in Western Eurasia and sub-Saharan Africa. The genetic characterization of these relevant data sets is fully consistent with other published mtDNA genetic variation. The sequence diversity observed in this data set makes it a valuable tool for forensic applications.
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  #33  
Old 11th December 2006, 05:37 PM
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casadecoqui casadecoqui is offline
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Greg,

See below. Shall I send them to your e-mail one by one? I don't know how much space you have in your e-mail box. I don't think the file upload here takes pdfs greater than 2.0 MB.

Quote:
Originally Posted by GregKiroKH2
The abstract is interesting to read. I do not see how to obtain a copy.

I can send you this one
Cannot get this one:
Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis
Juan C. Martínez-Cruzado 1 *, Gladys Toro-Labrador 1, Jorge Viera-Vera 1, Michelle Y. Rivera-Vega 1 2, Jennifer Startek 1, Magda Latorre-Esteves 1 3, Alicia Román-Colón 1 4, Rebecca Rivera-Torres 1 5, Iris Y. Navarro-Millán 1 2, Enid Gómez-Sánchez 1, Héctor Y. Caro-González 1 6, Patricia Valencia-Rivera 1 7
Volume 128, Issue 1 , Pages 131 - 155

Published Online: 3 Feb 2005
http://www3.interscience.wiley.com/c...TRY=1&SRETRY=0

Cannot get the next one:
I can send you this one and it is also on our African DNA web site.

http://www.journals.uchicago.edu/AJH...414300671Guest

The Making of the African mtDNA Landscape

Antonio Salas,1,2,3 Martin Richards,2 Tomás De la Fe,1 María-Victoria Lareu,1 Beatriz Sobrino,1 Paula Sánchez-Diz,1 Vincent Macaulay,3 and Ángel Carracedo1


Am J Hum Genet. 2002 November; 71(5): 1082?1111.
Published online 2002 October 22.

Can read this one:
http://www.pubmedcentral.nih.gov/pic...6&blobtype=pdf

I'll have to check on this one. I think I have it.

Cannot read this one:
Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set.

Forensic Science International, Volume 148, Issue 2-3, Pages 169-179

M. Allard, D. Polanskey, K. Miller, M. Wilson, K. Monson, B. Budowle
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  #34  
Old 12th December 2006, 11:24 AM
GregKiroKH GregKiroKH is offline
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Quote:
Originally Posted by casadecoqui
Greg,

See below. Shall I send them to your e-mail one by one? I don't know how much space you have in your e-mail box. I don't think the file upload here takes pdfs greater than 2.0 MB.
I think I have enough space in my E-mail box. I would appreciate if you would send it to me, Ana
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  #35  
Old 12th December 2006, 11:29 AM
GregKiroKH GregKiroKH is offline
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L1c1b, Bantu Expansion

I was looking at some articles about the Bantu expansion. It seems as if people are still finding new things.

Quote:
The Bantu languages adopted the use of clicks from neighboring Khoisan populations, often through intermarriage, while the Dahalo are thought to have retained clicks from an earlier Khoisan-like language when they shifted to speaking a Cu****ic language. Grammatically, the Khoisan languages are generally fairly isolating. Suffixes are often used, but word order is overall more widely used than inflection. The geographic spread and order of the Bantu expansion 3500 years ago matches with the geographic distribution of the spread of farming. Holden (2001) specifies that sometime between 5000 BC and AD 5 the Bantu people spread throughout East and Southern Africa. http://www.public.asu.edu/~csteiner/

Accordingly, prehistorians hypothesize that the Bantu expansion is related to the spread of agriculture, which was not practiced in the areas now occupied by Bantu. They furthermore suggest that this process was set in motion by a new crop complex, bananas and other crops from southeast Asia, that allowed the ancestral Bantu to occupy the previously uncultivated forest zone immediately to the south and east. A second theory rests on archaeological evidence of iron smelting in Nigeria, just prior to the time of Christ. This new technology would have both allowed the early migrants to penetrate and cultivate the tropical rain forest and given them a substantial advantage against any indigenous groups that might have retarded their advance.
http://www.umanitoba.ca/faculties/ar...le2/bantu.html

Dr. Wilhelm Heinrich Immanuel Bleek (1827-1875) first used the term "Bantu" in its current sense in his 1862 book "A Comparative Grammar of South African Languages," in which he hypothesized that a vast number of languages located across central, southern, eastern, and western Africa shared so many characteristics that they must be part of a single language group.
The Bantu first originated around the Benue-Cross rivers area in southeastern Nigeria and spread over Africa to the Zambia area. Sometime in the second millennium BC, perhaps triggered by the drying of the Sahara and pressure from the migration of people from the Sahara into the region, they were forced to expand into the rainforests of central Africa (phase I). About 1000 years later they began a more rapid second phase of expansion beyond the forests into southern and eastern Africa. Then sometime in the first millennium new agricultural techniques and plants were developed in Zambia, probably imported from South East Asia via Austronesian-speaking Madagascar. With these techniques another Bantu expansion occurred centered on this new location (phase III).

By about AD 1000, it had reached modern day Zimbabwe and South Africa. In Zimbabwe a major southern hemisphere empire was established, with its capital at Great Zimbabwe. It controlled trading routes from South Africa to north of the Zambezi, trading gold, copper, precious stones, animal hides, ivory and metal goods with the Arab traders of the Swahili coast. By the 14th or 15th centuries the Empire had surpassed its resources and it had collapsed, with the city of Great Zimbabwe being abandoned.

Before the Bantu, the southern half of Africa is believed to have been populated by Khoisan speaking people, today occupying the arid regions around the Kalahari and a few isolated pockets in Tanzania. Pygmies inhabited central Africa, whereas Cu****es and other people speaking Afro-Asiatic languages inhabited north-eastern and northern Africa. Northwestern Africa, the Sahara, and the Sudan were inhabited by people speaking Mande and Atlantic languages (such as the Fulani and Wolof) and other people speaking Nilo-Saharan languages.
http://en.wikipedia.org/wiki/Bantu
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  #36  
Old 12th December 2006, 04:13 PM
GregKiroKH2 GregKiroKH2 is offline
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Found Links to Papers

I found the papers on the school's computer system, Ana. Thank you for the offer to send them to me. I really appreciated it.
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  #37  
Old 12th December 2006, 06:38 PM
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casadecoqui casadecoqui is offline
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No problem. I did manage to send the Making of the African landscape before I saw your note.

How about you send me the one on PR. The one I have is a scanned image and not a pdf. I used the article in a paper I wrote for the Genealogy Society of San Juan. Dr. Martínez-Cruzado let me use some of the images from his article.

I also couldn't find the SWGDAM article. I have access to MDConsult and other medical journals from home but not the Forensic International associated with Elseveir which is odd. anyway, I wasn't going to pay $30 for it.

Quote:
Originally Posted by GregKiroKH2
I found the papers on the school's computer system, Ana. Thank you for the offer to send them to me. I really appreciated it.
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  #38  
Old 12th December 2006, 11:22 PM
GregKiroKH2 GregKiroKH2 is offline
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Ok, The PR one is a part of a thesis by Jorge Viera-Vera called "THE ORIGINS OF THE AFRICAN ANCESTRY IN THE PUERTO RICAN POPULATION ACCORDING TO RESTRICTION ANALYSIS OF THE MITOCHONDRIAL DNA."
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  #39  
Old 13th December 2006, 12:04 PM
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casadecoqui casadecoqui is offline
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Thanks, Greg. I got it just fine. It is a very well done thesis.

Quote:
Originally Posted by GregKiroKH2
Ok, The PR one is a part of a thesis by Jorge Viera-Vera called "THE ORIGINS OF THE AFRICAN ANCESTRY IN THE PUERTO RICAN POPULATION ACCORDING TO RESTRICTION ANALYSIS OF THE MITOCHONDRIAL DNA."
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  #40  
Old 14th December 2006, 12:28 PM
GregKiroKH2 GregKiroKH2 is offline
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Quote:
Originally Posted by casadecoqui
Thanks, Greg. I got it just fine. It is a very well done thesis.
You are welcome, Ana. It was an interesting week
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