Phylogeography of Y chromosome haplogroups A & B in Africa Naidoo, Thijessen
A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Medicine Johannesburg, 2014
Abstract: Evolution and historical events over the past 300 000 years have contributed in shaping the gene pool of sub-Saharan African populations. By examining patterns of Y chromosome variation, through the screening of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), the present study aimed to characterise the phylogeography of ancient African Y chromosome haplogroups found in populations across sub-Saharan Africa, as well as understand the genetic affinities of these populations. In order to screen the large number of the markers required, seven multiplex single base extension assays were developed. These were used to refine the resolution of Y chromosomes commonly found in Africa, but also included a few markers to delineate the common non-African Y chromosome haplogroups, following a hierarchical screening process. In total, 1667 males were screened, and these data were compiled together with comparative published data. The resultant SNP and STR dataset was used in illustrating, more specifically, the phylogeographies of haplogroups A and B. The wide geographic distribution of haplogroup A, together with its position at the root of the phylogeny and high diversity, support an early diversification of the haplogroup into its subclades, which subsequently spread across Africa. The distribution of major haplogroup B subclades, however, are possibly due to post-glacial migrations in the case of haplogroup B-M112, and recent population expansions, leading to the common presence of haplogroup B-M152 across sub-Saharan Africa. The spread of haplogroup E, however, created the biggest impact on African populations; with its expansion likely resulting in the diminished presence of many of the subclades of haplogroups A and B. The Y chromosome compositions of present sub-Saharan African populations are, thus, the result of several diversification events, followed by migration, and mixing of population groups, over the course of modern human existence.
Djehuti Member # 6698
posted
^ Lioness says only hg A & B carriers are the only true and pure Africans. Carriers of all other clades are automatic Eurasians. LOL
the lioness, Member # 17353
posted
^ this troll doesn't speak for me he's an agent.
If anybody has anything to say about what I say it has zero value unless I am quoted.
This is a good thread. It is a recent article on African DNA. I have made no comments on it. The thread is untouchable
But we have a troll in our midst trying to start something
Ish Gebor Member # 18264
posted
quote:Originally posted by Djehuti: ^ Lioness says only hg A & B carriers are the only true and pure Africans. Carriers of all other clades are automatic Eurasians. LOL
I am not sure why the lions ass posted this, dissertation.
quote:The spread of haplogroup E, however, created the biggest impact on African populations; with its expansion likely resulting in the diminished presence of many of the subclades of haplogroups A and B.
The Y chromosome compositions of present sub-Saharan African populations are, thus, the result of several diversification events, followed by migration, and mixing of population groups, over the course of modern human existence.
the lioness, Member # 17353
posted
I post new articles I see on African DNA, thats the reason
Ish Gebor Member # 18264
posted
quote:Originally posted by the lioness,: I post new articles I see on African DNA, thats the reason
So what is your view on this paper?
Oshun Member # 19740
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More context is needed:
quote:Originally posted by the lioness,: The distribution of major haplogroup B subclades, however, are possibly due to post-glacial migrations in the case of haplogroup B-M112, and recent population expansions, leading to the common presence of haplogroup B-M152 across sub-Saharan Africa.
What's being argued here? Migrations from within Africa or a back migration? And what data helped them arrive to their conclusion?
quote:The spread of haplogroup E, however, created the biggest impact on African populations; with its expansion likely resulting in the diminished presence of many of the subclades of haplogroups A and B. The Y chromosome compositions of present sub-Saharan African populations are, thus, the result of several diversification events, followed by migration, and mixing of population groups, over the course of modern human existence.
diversification events that mostly involved who??? Europeans/Asians? Africans????
the lioness, Member # 17353
posted
quote:Originally posted by Oshun: More context is needed:
quote:Originally posted by the lioness,: The distribution of major haplogroup B subclades, however, are possibly due to post-glacial migrations in the case of haplogroup B-M112, and recent population expansions, leading to the common presence of haplogroup B-M152 across sub-Saharan Africa.
What's being argued here? Migrations from within Africa or a back migration? And what data helped them arrive to their conclusion?
quote:The spread of haplogroup E, however, created the biggest impact on African populations; with its expansion likely resulting in the diminished presence of many of the subclades of haplogroups A and B. The Y chromosome compositions of present sub-Saharan African populations are, thus, the result of several diversification events, followed by migration, and mixing of population groups, over the course of modern human existence.
diversification events that mostly involved who??? Europeans/Asians? Africans????
You have only read the abstract
This is a dissertation. It has 134 pages of text, read some of that first
4.5 Potential impact of the Last Glacial Maximum An examination of TMRCA estimates for the major A and B subclades found in the study resulted in an interesting observation. With the exception of haplogroup A-M14, haplogroups A-M13, A-M51, B-M150 and B-M112 appeared to have very similar TMRCAs (14.2 14.5 kya). Seeing that A-M13 and A-M51 are sister clades (with the same being true for B-M150 and B-M112), common TMRCAs between them may reflect the point at which they split from each other (Platt, D. E. personal communication, 2012). However, the same reasoning cannot be used to explain similar TMRCAs across haplogroups (e.g. A-M51 versus B-M112). These TMRCAs appear to coincide with the end of the Last Glacial Maximum (LGM). During the LGM (19 26 kya) the climate in Africa was generally colder and more arid, which caused desert and semi-desert areas to expand (Clark, et al., 2009). This led to the abandonment of certain areas and population contractions into still habitable refugia. The end of the LGM brought about increased precipitation and re-colonisation of previously uninhabitable zones (Barham and Mitchell, 113 2008). It might be that these haplogroups emerged following the subsiding of the LGM. The possibility also exists that the population contractions and bottlenecks caused by the LGM are responsible for the similar TMRCAs, which estimate the point of population expansion, and not the ages of the haplogroups.
Djehuti Member # 6698
posted
quote:Originally posted by the lioness,: ^ this troll doesn't speak for me he's an agent. .........
But we have a troll in our midst trying to start something
LOL I merely imitate what YOU do all the time, so now you call me a troll!
Sorry but your hipocrisy game won't work. By the way, who am I an agent for? Your boss Mathilda?? LOL
Ish Gebor Member # 18264
posted
quote:Originally posted by the lioness,:
quote:Originally posted by Oshun: More context is needed:
quote:Originally posted by the lioness,: The distribution of major haplogroup B subclades, however, are possibly due to post-glacial migrations in the case of haplogroup B-M112, and recent population expansions, leading to the common presence of haplogroup B-M152 across sub-Saharan Africa.
What's being argued here? Migrations from within Africa or a back migration? And what data helped them arrive to their conclusion?
quote:The spread of haplogroup E, however, created the biggest impact on African populations; with its expansion likely resulting in the diminished presence of many of the subclades of haplogroups A and B. The Y chromosome compositions of present sub-Saharan African populations are, thus, the result of several diversification events, followed by migration, and mixing of population groups, over the course of modern human existence.
diversification events that mostly involved who??? Europeans/Asians? Africans????
You have only read the abstract
This is a dissertation. It has 134 pages of text, read some of that first
4.5 Potential impact of the Last Glacial Maximum An examination of TMRCA estimates for the major A and B subclades found in the study resulted in an interesting observation. With the exception of haplogroup A-M14, haplogroups A-M13, A-M51, B-M150 and B-M112 appeared to have very similar TMRCAs (14.2 14.5 kya). Seeing that A-M13 and A-M51 are sister clades (with the same being true for B-M150 and B-M112), common TMRCAs between them may reflect the point at which they split from each other (Platt, D. E. personal communication, 2012). However, the same reasoning cannot be used to explain similar TMRCAs across haplogroups (e.g. A-M51 versus B-M112). These TMRCAs appear to coincide with the end of the Last Glacial Maximum (LGM). During the LGM (19 26 kya) the climate in Africa was generally colder and more arid, which caused desert and semi-desert areas to expand (Clark, et al., 2009). This led to the abandonment of certain areas and population contractions into still habitable refugia. The end of the LGM brought about increased precipitation and re-colonisation of previously uninhabitable zones (Barham and Mitchell, 113 2008). It might be that these haplogroups emerged following the subsiding of the LGM. The possibility also exists that the population contractions and bottlenecks caused by the LGM are responsible for the similar TMRCAs, which estimate the point of population expansion, and not the ages of the haplogroups.
What exactly are you trying to say by this citation, in this dissertation?
Djehuti Member # 6698
posted
^ What indeed is she trying to say?? Meanwhile, I find it interesting that the most common paternal clades in the African continent are those of E-(M96 previously PN2). And we still have yet to discover the theoritcal clade CF(P143) much less CT!
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