Genomic Data Reveal a Complex Making of Humans

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Genomic Data Reveal a Complex Making of Humans Jan 7, 2016 6:58:41 GMT

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Post by Admin on Jan 7, 2016 6:58:41 GMT

The map below shows that hg Q is found in central Europe between an imaginary line that joins Marseille with Hambourg and another joining the Black Sea with Finland. It encompasses large portions of Scandinavia with in pockets in the UK, Iceland, Sicily, South Western Iberia, Cotentin, Dalmacia and South Sardinia. The voids are interesting too, it is absent from most of Western France, Spain, Italy, the Balkans and Slovenia, Belarus and central-western Poland.

The argument behind the Hun Q haplogroup admixture in Europe goes like this: as they were Asians, from central Siberia, apart from other haplogroups, they also carried the Q hg in them. This explains the presence of Q hg in the areas formerly occupied by the Hunnic Empire (central Europe); it is also found in Provence / Burgundy because many huns settled there after their defeat at Chalons. Furthermore, the Huns supposedly employed Scandinavian (i.e. Goth and Heruli) warriors and many Huns marched north with them after being beaten by the Romans, dispersing their Y chromosomes in that area. The Norse peoples (Vikings, Normans) descended from this admixture later spread the hunnic Q hg widely when they raided Europe (ca. 900 CE): this explains its presence France (Cotentin - Normandy), Great Britain (Danelagh), Sicily (conquered by Normans in 1091 CE) and, as they went across the Atlantic, in Iceland, the Shetland and Faroe Islands.

The Scyths were Asians, which after crossing the Araxes (Volga) River invaded Cimmeria ca. 713 BCE, causing them to flee in two directions: One group invaded Asia Minor (Phrygia) and settled in Sinope on the northern coast of Turkey. Another marched west after a fratricide battle on the shores of the Dniester (Tyras) River and then entered Thrace. These Cimmerians from the Chersonesus (Crimea) several centuries later, sent an embassy to Emperor Augustus in Rome with gifts, to ask for pardon for their raids one century before (Plutarch [8] and Strabo [9]).

But the largest part of these people, had migrated from their Crimean home and lived in the wooded lands of Central Europe, along the Danube River and at the sources of the Elbe and the Vistula rivers, which they settled long before the appearance of the Germanic tribes. [10] They were considered Celtic people and they took part in the attack upon Delphi in Greece (279 BCE) allied with the Illyrians, but were defeated. [12]

The Romans at that time occupied the coastal areas around the Mediterranean sea (green in map below), they ignored the homeland of these barbarians who " sallied forth against Italy, being called at first Cimmerians, and then, not inappropriately, Cimbri." [8]. Their twelve year campaing ended in defeat, and they retreated to the north, deep within the forests, into Jutland, which is now Denmark, where, according to Strabo [9] they occupied the country west of the Elbe. A map by Claudius Ptolemy (ca. 90 – ca. 168 CE) that is, roughly 220 years after their invasions, places the land of the Cimbri at the northernmost tip of Jutland.

Their campaign would explain the presence of their Q hg across the central parts of Europe. Its later dispersion from Denmark into Scandinavia and the rest of Europe would be identical to the "Hun's Q hg dispersal" already mentioned above. The presence of Cimbrian Y Chromosomes in the Valley of the Rhone belonged to the refugees escaping the defeat at Vercelli, crossing the Alpine passes into current Savoy and Haute Rhone. Or (chose your option): (1) the survivors of the Cimbri garrison that remained in Belgium (who later became the Aduatuci), after their defeat by Julius Caesar in 57 BCE (most were killed or sold as slaves). (2) Later moves towards the south (400 CE) of the Burgundians from Scandinavia, to current Poland, and finally to France, bearing Cimbrian admixture in their genomes.

An interesting paper (I. Rozhansky, 2010) [11] views the Cimbrians as carrying different haplogroups in their genome, but after being subjected to a bottleneck (the battles against Rome), male lineages were reduced and only a small part of it reached the Jutland refuge after a 1,700 km march. Their long settlement there (100 BC - 400 CE) subjected them to further genetic drift yielding two haplotypes of Q1a3 unique to Scandinavia which date back to a common ancestor 2200 - 2150 ya. (coincidental with the date of the Cimbrian Invasions).

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Genomic Data Reveal a Complex Making of Humans Jan 15, 2016 6:49:12 GMT

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Post by Admin on Jan 15, 2016 6:49:12 GMT

The team started by looking at the average genetic ancestry of the three largest groups in the United States: European Americans, African-Americans, and Latinos. Those categories are based on how 23andMe customers defined themselves. But as you might expect in a country where different groups of people have been meeting and mixing for hundreds of years, the genetic lines between the groups are quite blurred.

“You see all of those different ancestries in each of these groups,” Bryc explains. The average African-American genome, for example, is 73.2% African, 24% European, and 0.8% Native American, the team reports online today in The American Journal of Human Genetics. Latinos, meanwhile, carry an average of 18% Native American ancestry, 65.1% European ancestry (mostly from the Iberian Peninsula), and 6.2% African ancestry.

The new study adds an unprecedented level of detail to patterns that had been noticed in previous, more general studies. For example, the 23andMe data reveals that the proportion of different ancestries, even within one self-identified ethnic group, vary significantly by state. Latinos with the highest proportion of African ancestry (about 20%) are from Louisiana, followed by states such as Georgia, North Carolina, New York, and Pennsylvania. In Tennessee and Kentucky, Latinos tend to have high proportions of European ancestry. And in the Southwest, where states share a border with Mexico, Latinos tend to have higher proportions of Native American ancestry.

At least 3.5% of European Americans carry African ancestry, though the averages vary significantly by state. In South Carolina and Louisiana, about 12% of European Americans have at least 1% African ancestry. In Louisiana, too, about 8% of European Americans carry at least 1% Native American ancestry.

We find very low levels of African and Native American ancestry in Europeans with four grandparents born in Europe. We estimate that only 0.98% of Europeans carry African ancestry and 0.26% of Europeans carry Native American ancestry. These levels are substantially lower than the 3.5% and 2.7% of European Americans who carry African and Native American ancestry, respectively. Furthermore, for most European countries we observed no individuals with substantial non-European ancestry, and the presence of individuals with African and Native American ancestry is limited to countries that had major ports in the Atlantic trade and were known to have been highly connected to the trans-Atlantic slave trade. Indeed, African ancestry in individuals from Europe is not unexpected; approximately 9,000 Africans were brought to Europe between 1501 and 1867 (as documented by Eltis and Richardson’s maps of the slave trade, accessible at Emory University’s database). Excluding countries that had major and minor ports in the Atlantic with strong connections to the slave trade (namely Portugal, Spain, France, and United Kingdom) and Malta, which has been the site of migrations from Africa and the Middle East, we obtain a data set of 9,701 Europeans, where we find African and Native American ancestry is virtually absent, with only 0.04% of individuals carrying 1% or more African ancestry and 0.01% carrying 1% or more Native American ancestry, within the margins of survey error estimates.

Native American mtDNA in European Americans and African Americans and Not in Europeans

The frequency of Native American mtDNA haplogroups in European Americans and African Americans correlate with our estimates of genome-wide ancestry in European Americans and African Americans and are found in appreciable fractions of individuals who are estimated to carry Native American ancestry. The frequencies of haplogroups are shown in Table S8. These haplogroups are virtually absent in individuals with four grandparents from a European country (21 individuals out of 15,651). Furthermore, the majority of these Native American haplogroups in Europeans are found in individuals from Spain. Though it is possible these represent non-Native American haplogroups, prior literature and studies of genetic, archaeological, and paleontological evidence suggest that these haplogroups have Native American origins and is evidence of gene flow from the Americas to Spain. Excluding Spain, Native-American-specific haplogroups are detected in fewer than 0.05% of individuals with four grandparents from Europe and can be explained by survey errors in reporting all four grandparents’ birth places.

Patterns of Genetic Ancestry of Self-Reported European Americans

Our estimated rates of non-European ancestry in European Americans suggest that more than six million Americans, who self-identify as European, might carry African ancestry. Likewise, as many as five million Americans who self-identify as European might have at least 1% Native American ancestry. Louisiana’s high levels of African ancestry in European Americans are consistent with historical accounts of intermarriage in the New Orleans area.74,75

Regional differences in European subpopulation ancestry across states reflect known major historical migrations from Europe. Inferred British/Irish ancestry is found in European Americans from all states at mean proportions of more than 20% and represents a majority of ancestry (more than 50% mean proportion) in states such as Mississippi, Arkansas, and Tennessee. These states are similarly highlighted in the map of the self-reported “American” ethnicity in the US 2010 Census survey, which might reflect regions with lower subsequent migration from other parts of Europe. Inferred Eastern European ancestry is found at its highest levels in Illinois, Michigan, and Pennsylvania, potentially stemming from immigration during the late 19th and early 20th centuries, settling in metropolitan areas in the Northeast and Midwest. Inferred Iberian ancestry, found overall at lower mean proportions, still represents a measurable ancestry component in Florida, Louisiana, California, and Nevada, and might point to the early Spanish rule and colonization of the Americas. Scandinavian ancestry in European Americans is highly localized; most states show only trace mean proportions of Scandinavian ancestry, but it comprises a significant proportion, upward of 10%, of ancestry in European Americans from Minnesota and the Dakotas. The distributions of the European subpopulation ancestries in European Americans illustrate that the distribution of within-European ancestry is not homogenous among individuals from different states, and instead, reflects differences in population migrations and settlement patterns across the US.

Lastly, our recent dates for admixture suggest that introgression probably occurred in the Americas within the last 500 years. Hence, our estimates do not support that the African ancestry in European Americans stems from ancient population events that predate the migrations to the Americas. (For example, gene flow from Africa coinciding with the Moor invasion of the Mediterranean might have introduced African ancestry into the ancestral population of some European Americans.) Though such ancient events would probably not lead to inferred African ancestry because our supervised learning algorithm would apply a European label to such segments, it is possible that European population substructure could lead to inferred segments of African ancestry in some European Americans that derive from older historical admixture events, which are not seen in modern Europeans. However, these events would lead to admixture or introgression of segments several hundred or thousand years old, and our admixture dates for both Native American ancestry and African ancestry point to gene flow within the last 20 generations and is not consistent with any known historical migrations within Europe during this time period.

Am J Hum Genet. 2015 Jan 8; 96(1): 37–53.
doi: 10.1016/j.ajhg.2014.11.010

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Genomic Data Reveal a Complex Making of Humans Jan 31, 2016 6:22:32 GMT

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Post by Admin on Jan 31, 2016 6:22:32 GMT

Mitochondrial DNA is a DNA that is only inherited from mother to child, and it tracks back to the most recent common female ancestor of all humans (Mitochondrial Eve).

Ages of the major Haplotypes.

These are the estimated dates, some of the oldest could be as much as 17,000 years out, the youngest a couple of thousand. It also varies from study to study.

L0 170,000 years African, Mitochondrial EVE
L1 142,000 years African
L2 92,000 years African
L3 100,000 years African, out of Africa haplogroup.
N 63,300 years Europe (100k, my estimate)
M 64,800 years S W Asia into Asia, East Africa (100k, my estimate)
A 32,300 years Asia
R 61,000 years Near East
HV 50,000 years Europe
H 40,000 years Europe into the near East
V 13,600 years Europe
T J 50,000 years
J 34,400 years Near East into Europe
T 11,000 years Near East into Europe
U 51,700 years Eurasia, now mostly in North Africa
CZ 47,000 years Eurasia
C 28,300 years Asia into America
D 33,300 years Asia into America
K 15,000 years Europe
I 30,000 years Eurasia
E ? South Asia and Pacific
G ? East Asia
Q 50,000 years South East Asia and Pacific
Z ? Central Asia
S ? Aborigines
W ? Northern Eurasia, rare in S E Asia
X 30,000 years Europe into America
Y ? Asia

In 1987 population geneticists first demonstrated the existence of such a ‘mitochondrial Eve'3. After analysing mtDNA from 147 people from around the world to chart their genetic relationships, they used a ‘molecular clock’, based on the number of DNA mutations that arise with each generation, to estimate Eve's age. This woman, the researchers concluded, probably lived in Africa around 200,000 years ago. The finding provided evidence for the theory that modern humans evolved in Africa before migrating to other continents. Yet comparable studies later found that Adam, the common ancestor of the portion of the Y chromosome that passes from father to son, lived roughly 100,000 years ago. It’s possible that Adam and Eve lived aeons apart, and geneticists have come up with a number of explanations as to why.

Carlos Bustamante, a population geneticist at the Stanford University School of Medicine in California who led one of the latest studies, says that chance could explain the discrepancy between the ages of Adam and Eve. Polygamy could also help to explain the gap, he says. The calculation of when Adam or Eve lived depends on the number of breeding adults in a population, and polygamy reduces the number of males that pass on their Y chromosomes, thereby skewing the estimate.

Bustamante and his team sequenced the Y chromosomes of 69 males from around the world and uncovered about 9,000 previously unknown DNA sequence variations. They used these variations to create a more reliable molecular clock and found that Adam lived between 120,000 and 156,000 years ago. A comparable analysis of the same men's mtDNA sequences suggested that Eve lived between 99,000 and 148,000 years ago1. “This idea of a very recent common ancestor of all men is not that true,” Bustamante says.

Meanwhile, a team led by Paolo Francalacci, a population geneticist at the University of Sassari, Italy, came to a similar conclusion by studying the Y chromosomes of 1,200 men from the island of Sardinia. The team identified nearly 7,000 previously unknown Y-chromosome variations and used that detail to create their own molecular clock. The clock helped to pinpoint key events in Sardinian history, such as the rise of Neolithic populations there and the arrival of Africans as part of the Roman slave trade. It also suggested that Adam lived 180,000–200,000 years ago, similar to initial estimates of Eve’s age2.

Francalacci says that the difference between the two studies' estimates of Adam’s age could be due to the different populations they studied and how the molecular clocks were calculated. Bustamante says that, all in all, the two papers match up well. “It’s not so much we’re shifting the mitochondria down — which we are, a bit — but we’re pushing the Y farther back,” he says.

In February, for instance, researchers led by Michael Hammer, a population geneticist at the University of Arizona in Tucson, reported the discovery of an African American family whose Y chromosomes do not seem to directly descend from Adam's4. One possible explanation is that the Y chromosome came from an archaic species of human that interbred with Homo sapiens tens of thousands of years ago. Yet Hammer sees the discrepancy between the age of the Y-Adam and that of the mitochondrial eve as a “red herring”, and he, as many other population geneticists, bristles at the use of biblical names. Because of the random nature of genealogy, he says, two different genetic lineages are unlikely to have common ancestors who lived in the same population at the same time.

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Genomic Data Reveal a Complex Making of Humans Feb 2, 2016 5:49:08 GMT

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Post by Admin on Feb 2, 2016 5:49:08 GMT

A nonsynonymous single nucleotide polymorphism (SNP), rs17822931-G/A (538G>A; Gly180Arg), in the ABCC11 gene determines human earwax type (i.e., wet or dry) and is one of most differentiated nonsynonymous SNPs between East Asian and African populations. A recent genome-wide scan for positive selection revealed that a genomic region spanning ABCC11, LONP2, and SIAH1 genes has been subjected to a selective sweep in East Asians. Considering the potential functional significance as well as the population differentiation of SNPs located in that region, rs17822931 is the most plausible candidate polymorphism to have undergone geographically restricted positive selection. In this study, we estimated the selection intensity or selection coefficient of rs17822931-A in East Asians by analyzing two microsatellite loci flanking rs17822931 in the African (HapMap-YRI) and East Asian (HapMap-JPT and HapMap-CHB) populations. Assuming a recessive selection model, a coalescent-based simulation approach suggested that the selection coefficient of rs17822931-A had been approximately 0.01 in the East Asian population, and a simulation experiment using a pseudo-sampling variable revealed that the mutation of rs17822931-A occurred 2006 generations (95% credible interval, 1,023-3,901 generations) ago. In addition, we show that absolute latitude is significantly associated with the allele frequency of rs17822931-A in Asian, Native American, and European populations, implying that the selective advantage of rs17822931-A is related to an adaptation to a cold climate. Our results provide a striking example of how local adaptation has played a significant role in the diversification of human traits.

To identify the signature of recent positive selection in human
populations, a number of LD-based methods have
been developed (Sabeti et al. 2002; Voight et al. 2006;
Kimura et al. 2007; Grossman et al. 2010). However, such
methods generally do not allow us to estimate the selection
intensity of an advantageous allele. This study suggests that
the selection coefficient of rs17822931-A has been 0.01 in
East Asians (fig. 5A). The present approach using microsatellite
markers near a polymorphism subjected to positive
selection should be useful for estimating the selection intensity
of an advantageous allele even after a strong selective
sweep.

The estimated age of rs17822931-A was 2,006 generations.
Although the 95% credible interval was large
(1,023–3,901 generations; fig. 5B), the date of the
rs17822931-A mutation is in agreement with the generally
accepted ‘‘Out of Africa’’ scenario; the date for the divergence
of African and non-African populations is 3,500 generations
ago and that for the divergence of European and
Asian populations is 2,000 generations ago (Schaffner et al.
2005). When rs17822931-A was assumed to be selectively
neutral (i.e., s 5 0), the mean age of rs17822931-A
was 10,038 generations (95% credible interval: 3,742–
23,796 generations). The geographical distribution of
rs17822931-A (supplementary fig. S1, Supplementary Material
online) suggests that rs17822931-A appeared after an
‘‘Out of Africa’’ event. Thus, we may conclude that, without
the assumption of positive selection, it is difficult to explain
the rapid increase in the allele frequency of rs17822931-A in
East Asian populations.

Polymorphisms that are directly subjected to natural selection
must have functional significance. The functional
significance of rs17822931-G/A (G180R) has been recently
described (Toyoda et al. 2009). Immunofluorescence staining
of human ABCC11 protein in tissue specimens containing
ceruminous apocrine glands from human subjects with
the rs17822931-G/A (180G/R) or rs17822931-A/A (180R/R)
genotype revealed that the ABCC11 G180 protein is localized
in the intracellular granules and large vacuoles,
whereas neither granular nor vacuolar localization was detected
for R180. Furthermore, the level of R180 protein was
lower than that of G180 due to its proteasomal degradation
(Toyoda et al. 2009). Thus, the rs17822931-A mutation
seems to cause a loss of function of the ABCC11 protein.
To examine if the ABCC11 protein has no selective constraint,
the dN/dS ratios of human, chimpanzee, and macaque
were calculated (table 2). The results suggest that
purifying selection has operated against the ABCC11 gene
in the human lineage after divergence from chimpanzee.
Nevertheless, the frequency of rs17822931-A, a loss of
function mutation, has increased in non-African populations.

Thus, an ‘‘Out of Africa’’ event may have removed
a long-standing selective constraint on the ABCC11 gene.
What is the cause of the selective advantage of
rs17822931-A? Although the physiological function of earwax
is poorly understood (Matsunaga 1962), dry earwax
itself is unlikely to have provided a substantial advantage.
The rs17822931-GG and GA genotypes (wet earwax) are
also strongly associated with axillary osmidrosis, suggesting
that the ABCC11 protein has an excretory function in the
axillary apocrine gland (Nakano et al. 2009). The ancestral
environment of East Asians is thought to have been much
colder than that of Africans. As Yoshiura et al. (2006) suggested,
the ancestors of East Asians with the rs17822931-
AA genotype might have had some selective advantages,
such as less sweating, as an adaptation to the cold climate.
Because average daily and annual temperatures, on the
whole, correlate with absolute latitude (New et al. 2002),
in order to examine the ‘‘cold adaptation hypothesis,’’
the association between absolute latitude and allele frequency
was evaluated for 47 SNPs including rs17822931
in worldwide populations. Absolute latitude was found
to be associated with rs17822931-A allele frequency across
three regions (i.e., Asian, Native American, and European
populations), whereas significant associations in all three
regions were not observed for any control SNPs (supplementary
fig. S4 and table S4, Supplementary Material online).
Thus, we conclude that absolute latitude is not always
associated with allele frequency across human populations
and that the geographical distribution of rs17822931-A is
rather an exception. Therefore, the observed latitudinal
cline in the rs17822931-A allele frequency strongly supports
the cold adaptation hypothesis, although the possibility
that other conditions associated with latitude (e.g.,
sunlight and microbial environment) might play a role
cannot be excluded.

Mol Biol Evol. 2011 Jan;28(1):849-57.

mbe.oxfordjournals.org/content/28/1/849.full.pdf

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Genomic Data Reveal a Complex Making of Humans Feb 8, 2016 5:43:05 GMT

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Post by Admin on Feb 8, 2016 5:43:05 GMT

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Figure 1
Genealogy of A00, A0, and the Reference Sequence

Genotyping of a DNA sample that was submitted to a commercial genetic-testing facility demonstrated that the Y chromosome of this African American individual carried the ancestral state of all known Y chromosome SNPs. To further characterize this lineage, which we dubbed A00 (see Figure S1, available online, for proposed nomenclature), we sequenced multiple regions (totaling ∼240 kb) of the X-degenerate portion of this chromosome, as well as a subset of these regions (∼180 kb) on a chromosome belonging to the previously known basal lineage A1b (which we rename here as A0). We note that all sampling procedures described herein were approved by and performed according to the ethical standards of the University of Arizona Human Subjects Committee. The ancestral state of each polymorphic site was inferred with pairwise alignments between the human (UCSC Genome Browser hg18) and chimpanzee (panTro3) reference sequences, and mutations were assigned to the branches (i.e., A00 and A0) shown as thick lines in Figure 1 on the basis of an infinite-sites model (Table S1). To estimate the TMRCA of the Y chromosome tree that incorporates the newly discovered root defined by A00, we developed a likelihood-based method that uses mutation rates recently estimated by Kong et al.,14 who performed high-coverage whole-genome sequencing on 78 human pedigrees.

We estimated the TMRCA of human Y chromosomes as 338 kya (95% CI = 237–581 kya). Using a joint likelihood20 and the same mutation rate, we also estimated a divergence time between A0 chromosomes and the human reference as 202 kya (95% CI = 125–382 kya), a time that is older than that previously obtained by Cruciani et al. (142 kya).6 This discrepancy in the age of A0 is due to the fact that the earlier study did not utilize mutation rates based on recently obtained whole-genome sequence data.14–18 If we were to use the higher mutation rate (1.0 × 10−9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39 × 10−10 − 7.07 × 10−10), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ∼39 kya6 (i.e., versus ∼63 kya for the mutation rate used here). It is difficult to reconcile the younger estimate with the timing of the out-of-Africa dispersal on the basis of the analyses of autosomal DNA21 and the fossil record outside of Africa.22–25 Regardless of which mutation rate is applied, the analysis of relative ages of nodes26 shows that the TMRCA of the A00-rooted tree is 67% older (95% CI = 35%–126%) than that of the A0-rooted tree.

Figure 2
Map Showing Cameroon and the Approximate Location where Mbo Speakers Live

We then genotyped a set of six Y chromosome short tandem repeats (Y-STRs) (DYS19, DYS388, DYS390, DYS391, DYS392, and DYS39327) and found that the A00 chromosome carried the following alleles: 16-11-19-10-12-13. Upon searching a large pan-African database consisting of 5,648 samples from ten countries (Cameroon, Nigeria, Ghana, Senegal, Uganda, Tanzania, Malawi, Zimbabwe, Mozambique, and South Sudan), we identified 11 Y chromosomes that were invariant and identical to the A00 chromosome at five of the six Y-STRs (2 of the 11 chromosomes carried DYS19-16, whereas the others carried DYS19-15). These 11 chromosomes were all found in a sample of 174 (∼6.3%) Mbo individuals from western Cameroon (Figure 2). Seven of these Mbo chromosomes were available for further testing, and the genotypes were found to be identical at 37 of 39 SNPs known to be derived on the A00 chromosome (i.e., two of these genotyped SNPs were ancestral in the Mbo samples) (Table S1). Using the joint likelihood for the split of two lineages and a sublineage internal to one of them,20 we estimated that the most recent common ancestor of the African American and Mbo A00 chromosomes lived between 2.6 and 73 kya (95% CI, maximum likelihood estimate = 17 kya).

Figure 3
Median-Joining Network of A00 Haplotypes

In contrast to the estimates of all previous studies, our estimate of the Y chromosome TMRCA predates both that of known mtDNA lineages9,10 and of the likely time of origin of AMHs on the basis of current fossil evidence.31 Although we identified the A00 lineage in an African American, the unusual Y-STR profile associated with this individual’s Y chromosome allowed us to identify the same divergent lineage in a single ethnic group living in a small region of western Cameroon (Figure 2). Interestingly, contrary to previous Y chromosome and mtDNA studies, we did not identify the most basal lineage in a traditional hunter-gatherer population, such as the Khoisan or Pygmies.32–35 Rather, like the majority of groups that now occupy sub-Saharan Africa, the Mbo are a Bantu-speaking population. Given the large stochasticity expected in the genealogical process of a single locus,36,37 we should not be surprised that the Y chromosome genealogy does not match the currently accepted phylogeny of human populations on the basis of genome-wide data,38 which show that the earliest divergence events involved the ancestors of extant traditional hunter-gatherers.39–41 Given what we know about the coalescent process, the lack of dense sampling in sub-Saharan Africa (especially compared with Europe) has most likely contributed to the failure to identify more cases of incongruence between genealogical and population divergence.

The large sample size of African Americans was critical for the discovery of the A00 lineage given its very low frequency estimate in sub-Saharan Africa (0.19% [95% CI = 0.11%–0.35%]). However, even the large consumer-based African American data set examined here is a highly biased representation of sub-Saharan Africans because it captures only the genetic diversity inherited from ancestors living at a particular time and place (i.e., essentially the West African coastal source area of the Atlantic Slave Trade, which took place between the 15th and 19th centuries).42 It is likely that a much richer understanding of the Y chromosome phylogeny, as well as of genetic variation in general, would be achieved if more dense and even sampling were to be conducted across sub-Saharan Africa, especially given its high level of genetic diversity.

Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,41,43,44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ∼13 kya.47 Further surveys in sub-Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity. Finally, the discovery of the A00 lineage demonstrates the power of public participation in the scientific process—a venture that is likely to continue in the current era of personal genomics.

Am J Hum Genet. 2013 Mar 7; 92(3): 454–459.

Last Edit: Apr 13, 2018 2:01:36 GMT by Admin