Genomic Data Reveal a Complex Making of Humans

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Genomic Data Reveal a Complex Making of Humans Aug 11, 2016 21:36:34 GMT

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Post by Admin on Aug 11, 2016 21:36:34 GMT

Archaeologists need a new theory for the colonization of the Americas. Plant and animal DNA buried under two Canadian lakes squashes the idea that the first Americans travelled through an ice-free corridor that extended from Alaska to Montana.

The analysis, published online in Nature on 10 August and led by palaeogeneticist Eske Willerslev of the University of Copenhagen, suggests that the passageway became habitable 12,600 years ago1. That’s nearly 1,000 years after the formation of the Clovis culture — once thought to be the first Americans — and even longer after other, pre-Clovis cultures settled the continents.

Some 14,000 years ago, as North America was emerging from the last Ice Age, twin glaciers that blanketed central Canada receded, creating the ice-free corridor before the appearance of Clovis people across what is now the central United States. “That coincidence seemed too powerful to ignore,” says archaeologist and co-author David Meltzer of Southern Methodist University in Dallas, Texas. “People who have been cooling their heels in Alaska for thousands of years see this new land open up and they come blasting down this corridor into the new world.”

The ice-free-corridor theory began to crack in the 1990s, when researchers made a case that humans lived at Monte Verde in Chile more than 14,000 years ago. The discovery of other possible pre-Clovis sites in North America further shook the theory that Clovis people were the first Americans. But the idea that their ancestors at least trekked through the corridor persisted, says Meltzer, even though there was little consensus on when the passage opened or when it became habitable. “It’s 1,500 kilometres. You can’t pack a lunch and do it in a day.”

To build a picture of the habitat as it crept out of the Ice Age, Willerslev’s team analysed DNA in cores taken from beneath two lakes in what was the last stretch of the corridor to melt. The first plant life — thin grasses and sedges — dates back just 12,600 years. The region later became lusher, with sagebrush, buttercups and even roses, followed by willow and poplar trees. This habitat attracted bison first, and later mammoths, elk, voles and the occasional bald eagle. Around 11,500 years ago, the corridor began to resemble the pine and spruce boreal forests of today’s landscape.

The region’s bounty must eventually have tempted hunter-gatherers. But the dates rule out its use as a corridor by Clovis people and earlier Americans to colonize the Americas, says Willerslev. Instead, both probably skirted the Pacific coast, perhaps by boat.

During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr BP), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by approximately 12.6 cal. kyr BP, followed by open forest, with evidence of moose and elk at about 11.5 cal. kyr BP, and boreal forest approximately 10 cal. kyr BP. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr BP, are unlikely to have travelled by this route into the Americas. However, later groups may have used this north–south passageway.

Pedersen, M. W. et al. Nature (2016).

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Genomic Data Reveal a Complex Making of Humans Aug 13, 2016 21:24:58 GMT

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Post by Admin on Aug 13, 2016 21:24:58 GMT

This week the authors issued a note explaining the mistake in their October 2015 Science paper on the genome of a 4,500-year-old man from Ethiopia1 — the first complete ancient human genome from Africa. The man was named after Mota Cave, where his remains were found. Although the first humans left Africa some 100,000 years ago, a study published in 2013 found that some came back again around 3,000 years ago; this reverse migration has left its trace in African genomes.

West Eurasian haplogroups such as J and R1b can be found in East Africa at low to moderate frequencies as a result of ancient Arab migrations to the region. For example, J1 and J2 make up 21.6% in Cushitic speakers in Ethiopia and the combined frequency of J haplotypes increases to 26.6% in Ethiopian Semitic speakers. R1b is absent in Ethiopia but 40% of the Hausa people in neighbouring Sudan belong to R1b-V88. The study's initial conclusion that a large migration from Western Eurasia to East Africa is not affected but the geographic impact of this migration was overestimated. West Eurasian components are mostly concentrated in East Africa and only a few populations outside East Africa show detectable levels (Fig. 2).

The West Eurasian backflow mostly affected East Africa and only a few sub-Saharan populations. Llorente et al. (2015) further estimated that the proportion of West Eurasian ancestry is up to 50% in Amhara and Tygray peoples in Ethiopia (Fig. S6). The Mota individual is less than 3% West Eurasian because his generation of ancient Ethiopians missed the encounter with J people from the Arabian Peninsula by 1,500 years. Mota lived approximately 4,500 years ago in Ethiopia and the initial movement of West Eurasians to East Africa is dated approximately 3,000 years ago.

Andrea Manica, a population geneticist at the University of Cambridge, UK, who co-led the study, says the team made a mistake in its conclusion that the backflow reached western and central Africa. “The movement 3,000 years ago, or thereabouts, was limited to eastern Africa,” he says.

Manica says that the error occurred when his team compared genetic variants in the ancient Ethiopian man with those in the reference human genome. Incompatibility between the two software packages used caused some variants that the Ethiopian man shared with Europeans (whose DNA forms a large chunk of the human reference sequence) to be removed from the analysis. This made Mota man seem less closely related to modern European populations than he actually was — and in turn made contemporary African populations appear more closely related to Europeans. The researchers did have a script that they could have run to harmonize the two software packages, says Manica, but someone forgot to run it.

Ethiopians, in particular highland Ethiopians, seem to me likely an ancient stabilized hybrid population between a population from Arabia, and a local Sub-Saharan population. This population seems unlikely to have been related to the peoples of West-Central Africa, who are associated with the Bantus across eastern and southern Africa. The Bantu agricultural toolkit runs into ecological constraints in various regions, and it is in those regions that non-Bantu populations have persisted. Ethiopia, with its unique climate and topography, naturally remains non-Bantu (as well as the Horn of Africa as a whole).

The possible connections between Khoisan and Ethiopia may be a function of the fact that these areas harbor genetic variants which have disappeared in the intervening regions because of the Bantu expansion. I have a hard time accepting that the Bantu expansion was particular eliminationist, but I am starting to suspect that outside of Ethiopia population densities were very, very, low. The antiquity of this ancient hybridization event to me is attested by the fact that Ethiopians lack any of the other Middle Eastern components besides the one modal in Saudi Arabia.

Erratum to Gallego Llorente et al. 2015

Last Edit: Apr 13, 2018 1:48:49 GMT by Admin

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Genomic Data Reveal a Complex Making of Humans Aug 15, 2016 21:16:42 GMT

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Post by Admin on Aug 15, 2016 21:16:42 GMT

J1 (map A) in Europe is highly concentrated in the Caspian region spanning from Armenia to Ajebaijan and Eastern Europeans and Russians with J1 may harbour Armenian ancestry. According to the Armenian DNA Project, most of the Eastern European cases of J1* with DYS388 are ancestrally Armenian.

The "J1* with DYS388 = 13 or 14, L136-, P58- sub-clade" is considered by Dr. Roy King of Stanford University to be one of the markers of the Caucasian-speaking Hurrians and Urartians. James Honeychuck has prepared a MAP of the current distribution of this sub-clade. Many if not most of the Eastern European cases of J1* with DYS388 = 13 or 14 shown on this map could well be ancestrally Armenian.

J1e is predominantly Arab and Jewish, which is linked to the expansion of Neolithic pastorialists from the Fertile Crescent to the Arabian Peninsula. J2 (map B) has a widespread distribution but it is primarily found in northern Italy, which could be associated with the spread of farming from Anatolia to Europe. Genetic evidence suggests that the first settlers in the Italian Peninsula arrived from modern-day Turkey.

Professor Alberto Piazza, from the University of Turin, Italy, will say that there is overwhelming evidence that the Etruscans, whose brilliant civilisation flourished 3000 years ago in what is now Tuscany, were settlers from old Anatolia (now in southern Turkey).

Etruscan culture was very advanced and quite different from other known Italian cultures that flourished at the same time, and highly influential in the development of Roman civilisation. Its origins have been debated by archaeologists, historians and linguists since time immemorial.

Now modern genetic techniques have given scientists the tools to answer this puzzle. Professor Piazza and his colleagues set out to study genetic samples from three present-day Italian populations living in Murlo, Volterra, and Casentino in Tuscany, central Italy. “We already knew that people living in this area were genetically different from those in the surrounding regions”, he says. “Murlo and Volterra are among the most archaeologically important Etruscan sites in a region of Tuscany also known for having Etruscan-derived place names and local dialects. The Casentino valley sample was taken from an area bordering the area where Etruscan influence has been preserved.”

The scientists compared DNA samples taken from healthy males living in Tuscany, Northern Italy, the Southern Balkans, the island of Lemnos in Greece, and the Italian islands of Sicily and Sardinia. The Tuscan samples were taken from individuals who had lived in the area for at least three generations, and were selected on the basis of their surnames, which were required to have a geographical distribution not extending beyond the linguistic area of sampling. The samples were compared with data from modern Turkish, South Italian, European and Middle-Eastern populations.

“We found that the DNA samples from individuals from Murlo and Volterra were more closely related those from near Eastern people than those of the other Italian samples”, says Professor Piazza. “In Murlo particularly, one genetic variant is shared only by people from Turkey, and, of the samples we obtained, the Tuscan ones also show the closest affinity with those from Lemnos.”

Last Edit: Apr 13, 2018 1:47:12 GMT by Admin

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Genomic Data Reveal a Complex Making of Humans Aug 31, 2016 21:11:43 GMT

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Post by Admin on Aug 31, 2016 21:11:43 GMT

Lower rates of alcoholism in East Asian countries can be explained by the genetic safety mechanism, according to Peng et al. (2009). The ADH1B*47His allele is extremely common in East Asia (up to 90%) and it causes flushes on the face after consuming alcoholic beverages, which may serve as a deterrent to prevent people from consuming too much alcohol that the body cannot handle. Figure 1 (Borinskaya 2009) further shows that the ADH1B*47His allele is fairly common in southern Russia, the Caucasus region and as far as southern Europe (10-20%), while it's completely absent in Scandinavia and northern Europe, where the blue-eye mutation OCA2/HERC2 is common (above 90%). Northern Europeans are prone to develop alcoholism compared to Caucasians and southern Europeans probably due to the lack of the ADH1B*47His allele, which urges the body to consume alcohol in moderation.

ADH1B*47His allele frequency in East Asian populations
We analyzed a total of 2,275 individuals from 38 East Asian populations, especially those not included in the previous reports (northern Han Chinese, Tibetan and southern ethnic populations in China). Table 1 lists the frequencies of ADH1B*47His in the 38 populations. In general, the distribution pattern is consistent with the previous reports[14, 17], and most of the populations (31/38) have frequencies higher than 50%. In Han Chinese, the highest frequency is detected in Zhejiang province of south-eastern China (98.5%), and those in the west have relatively low frequencies (60-70%). The same pattern is also observed for the other ethnic populations from China and Southeast Asia (Cambodia and Thailand) except for Tibetan (14.1% on average), Bulang (1.7%, an ethnic population from south-western China) and Cambodian (20.6%). All the five Tibetan populations from different geographic regions have low frequencies (13-21%). We created a contour map based on the data from the 38 populations and those published before (Figure. 1). The distribution of the frequencies of ADH1B*47His confirms its prevalence in East Asia and a clear east-to-west cline is observed.

Figure 1
The distribution of the ADH1B*47His allele and the sites of early rice relics.

Selection on the ADH1B gene
To detect the molecular signature of recent selection on the ADH1B*47 polymorphism, we applied the LRH method and the iHS statistics using the genotype data from the HapMap project. The obtained iHS value for the core SNP (rs1229984) is -2.189 (the empirical p-value is 0.0269), an indication of selection. We then define the core region of ADH1B on the basis of five SNPs (rs4147536, rs1229984, rs1353621, rs1159918 and rs6810842) which determine the East Asian-dominant haplotype. We also select the flanking SNPs, extending both upstream and downstream to 250 Kb, to study the decay of LD from the core haplotype. We plot the haplotype-bifurcation diagrams[18] for the two East Asian populations (Figure. 2) from HapMap (JPT: Japanese in Tokyo, Japan; CHB: Han Chinese in Beijing, China). At a minimum threshold of 9%, we define two core-region haplotypes in the JPT+CHB population. The haplotype CTTCG, which covers the derived variant of ADH1B*47His has an extended predominance by showing a thick branch in the haplotype-bifurcation diagram, clearly suggesting a long-range LD.

Figure 2
The selection test for the ADH1B gene region.

Having established that the rice culture is likely the driving force of selection on the ADH1BArg47His polymorphism, the left question would be to explain the selective advantage of the ADH1B*47His allele. In southern China, people began to make fermented beverages long time ago. The potential benefits of having fermented beverage (or foods) can be explained by ethanol's combined analgesic, disinfectant and profound mind-altering effects[26]. In addition, fermentation helps to preserve and enhance the nutritional value of foods and beverages. Chemical analyses of ancient organics absorbed into pottery jars suggests that the earliest production of rice fermentation was carried out by the Neolithic people who lived in southern China about 9,000 years ago[6], not long after the origin of rice domestication in the same region. We believe that the custom could have prevailed rapidly among those early-agriculture populations in southern China during the Neolithic time, which have lasted thousands of years.

The ADH I has a low Km for ethanol, found in the liver, which metabolizes the most part of ethanol in the body. The derived ADH1B*47His allele is known to metabolize ethanol up to 100 times quicker than the ancestral ADH1B*47Arg allele, providing support that quick eradication of ethanol, and therefore lower local exposure should be protective. The recent case-control studies also suggested that the ADH1B*47His allele is the protective variant [27, 28, 29, 30]. The higher metabolic rate of ADH1B*47His may also lead to the accumulation of the toxic aldehyde intermediate that has been commonly associated with the flushing phenotype[31]. An association study in Han Chinese indicates that the individuals carrying ADH1B*47His have the lowest risk for alcoholism[32]. It was suggested that the flushing phenotype is biochemically equivalent to the effects of disulfiram (a drug used to prevent relapse)[33], which can influence drinking behaviour as a way of protection from over consumption of alcohol. It can also protect against the damage to human bodies caused by alcohol consumptions.

BMC Evolutionary Biology201010:15
DOI: 10.1186/1471-2148-10-15

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Genomic Data Reveal a Complex Making of Humans Oct 5, 2016 20:57:45 GMT

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Post by Admin on Oct 5, 2016 20:57:45 GMT

Previous studies have shown that African Americans in the US typically carry segments of DNA shaped by contributions from peoples of Europe, Africa, and the Americas, with variation in African and European admixture proportions across individuals and differences in groups across parts of the country.2, 3, 4 More recent studies that utilized high-density genotype data provide reliable individual ancestry estimates, illustrate the large variability in African and European ancestry proportions at an individual level, and are able to detect low proportions of Native American ancestry.3, 4, 5, 6, 7, 8, 9, 10, 11 Latinos across the Americas have differing proportions of Native American, African, and European genetic ancestry, shaped by local historical interactions with migrants brought by the slave trade, European settlement, and indigenous Native American populations.12, 13, 14, 15, 16, 17, 18 Individuals from countries across South America, the Caribbean, and Mexico have different profiles of genetic ancestry molded by each population’s unique history and interactions with local Native American populations.1, 19, 20, 21, 22, 23, 24, 25 European Americans are often used as proxies for Europeans in genetic studies.26 European Americans, however, have a history of admixture of many genetically distinct European populations.27, 28 Studies have shown that European Americans also have non-European ancestry, including African, Native American, and Asian, though it has been poorly quantified with some discordance among estimates even within studies.29, 30, 31, 32

That genetic ancestry of self-described groups varies across geographic locations in the US has been documented in anecdotal examples but has not previously been explored systematically. Most early studies of African Americans had limited resolution of ancestry because of small sample sizes and few genetic markers, and recent studies typically have limited geographic scope. Though much work has been done to characterize the genetic diversity among Latino populations from across the Americas, it is unclear the extent to which Latinos within the US share or mirror these patterns on a national or local scale. Most analyses have relied on mitochondrial DNA, Y chromosomes, or small sets of ancestry-informative markers, and few high-density genome-wide SNP studies have explored fine-scale patterns of African and Native American ancestry in individuals living across the US.

Figure 1
The Distribution of Ancestry of Self-Reported African Americans across the US

Patterns of Genetic Ancestry of Self-Reported African Americans
Genome-wide ancestry estimates of African Americans show average proportions of 73.2% African, 24.0% European, and 0.8% Native American ancestry (Table 1). We find systematic differences across states in the US in mean ancestry proportions of self-reported African Americans (Figure 1 and Table S2). On average, the highest levels of African ancestry are found in African Americans living in or born in the South, especially South Carolina and Georgia (Figure 1Aand Table S3). We find lower proportions of African ancestry in the Northeast, the Midwest, the Pacific Northwest, and California. The amount of Native American ancestry estimated for African Americans also varies across states in the US. More than 5% of African Americans are estimated to carry at least 2% Native American ancestry genome-wide (Figures S1 and 1D). African Americans in the West and Southwest on average carry higher levels of Native American ancestry, a trend that is largely driven by individuals with less than 2% Native American ancestry (Figure 1B). With a lower threshold of 1% Native American ancestry, we estimate that about 22% of African Americans carry some Native American ancestry (Figure S2).

We used the lengths of segments of European, African, and Native American ancestry to estimate a best-fit model of admixture history among these populations for African Americans (Figure S3). We estimate that initial admixture between Europeans and Native Americans occurred 12 generations ago, followed by subsequent African admixture 6 generations ago, consistent with other admixture inference methods dating African American admixture. A sex bias in African American ancestry, with greater male European and female African contributions, has been suggested through mtDNA, Y chromosome, and autosomal studies.6 On average, across African Americans, we estimate that the X chromosome has a 5% increase in African ancestry and 18% reduction in European ancestry relative to genome-wide estimates (see Table 1). Through comparison of estimates of X chromosome and genome-wide African and European ancestry proportions, we estimate that approximately 5% of ancestors of African Americans were European females and 19% were European males (Table S4).

Figure 2
The Distribution of Ancestry of Self-Reported Latinos across the US

Patterns of Genetic Ancestry of Self-Reported Latinos
Latinos encompass nearly all possible combinations of African, Native American, and European ancestries, with the exception of individuals who have a mix of African and Native American ancestry without European ancestry (see Figures S4A and S1). On average, we estimate that Latinos in the US carry 18.0% Native American ancestry, 65.1% European ancestry, and 6.2% African ancestry. We find the highest levels of estimated Native American ancestry in self-reported Latinos from states in the Southwest, especially those bordering Mexico (Figure 2C). We find the highest mean levels of African ancestry in Latinos living in or born in states in the South, especially Louisiana, the Midwest, and Atlantic (Figure 2A). Further stratification of individuals by their self-reported population affiliation (e.g., “Mexican,” “Puerto Rican,” or “Dominican”) reveals a diversity in genetic ancestry, consistent with previous work studying these populations (see Figure S5 and Table S5).10, 20, 24, 25, 68, 69 We find that Latinos who, besides reporting as “Hispanic,” also self-report as Mexican or Central American, carry more Native American ancestry than Latinos overall; those also who self-report as black, Puerto Rican, or Dominican have higher levels of African ancestry; and those who additionally self-report as white, Cuban, or South American have on average higher levels of European ancestry.

Admixture date estimates for Latino admixture suggest that Native American and European mixture occurred first, about 11 generations ago, followed by African admixture 7 generations ago. Consistent with previous studies that show a sex bias in admixture in Latino populations,12, 13, 14, 15, 16, 17, 18 we estimate 13% less European ancestry on the X chromosome than genome-wide (Table 1), showing proportionally greater European ancestry contributions from males. We inferred elevated African and Native American ancestry on the X chromosome, corresponding to higher female ancestry contributions from both Africans and Native Americans. Lastly, Latinos show higher proportions of inferred Iberian ancestry than both European Americans and African Americans (Figure S6).

Figure 3
Differences in African, Native American, and European Subpopulation Ancestry among Self-Reported European Americans from Different States

Patterns of Genetic Ancestry of Self-Reported European Americans
We find that many self-reported European Americans, predominantly those living west of the Mississippi River, carry Native American ancestry (Figure 3B). We estimate that European Americans who carry at least 2% Native American ancestry are found most frequently in Louisiana, North Dakota, and other states in the West. Using a less stringent threshold of 1%, our estimates suggest that as many as 8% of individuals from Louisiana and upward of 3% of individuals from some states in the West and Southwest carry Native American ancestry (Figure S7).

Consistent with previous anecdotal results,32 the frequency of European American individuals who carry African ancestry varies strongly by state and region of the US (Figure 3A). We estimate that a substantial fraction, at least 1.4%, of self-reported European Americans in the US carry at least 2% African ancestry. Using a less conservative threshold, approximately 3.5% of European Americans have 1% or more African ancestry (Figure S8). Individuals with African ancestry are found at much higher frequencies in states in the South than in other parts of the US: about 5% of self-reported European Americans living in South Carolina and Louisiana have at least 2% African ancestry. Lowering the threshold to at least 1% African ancestry (potentially arising from one African genealogical ancestor within the last 11 generations), European Americans with African ancestry comprise as much as 12% of European Americans from Louisiana and South Carolina and about 1 in 10 individuals in other parts of the South (Figure S8).

Figure 4
Distribution of African Ancestry in African Americans and European Americans

Most individuals who have less than 28% African ancestry identify as European American, rather than as African American (Figures 4 and 5A ). Logistic regression of self-identified European Americans and African Americans reveals that the proportion of African ancestry predicts self-reported ancestry significantly, with a coefficient of 20.1 (95% CI: 18.0–22.2) (Table S6 and Figure S9). For a full characterization of terms and logistic models, see Table S6 and Figure S9.

Fitting a model of European and Native American admixture followed later by African admixture, we find the best fit with initial Native American and European admixture about 12 generations ago and subsequent African gene flow about 4 generations ago.

Non-European ancestry in European Americans follows a sex bias in admixture contributions from males and females, as seen in African Americans and Latinos. The ratio between X chromosome and genome-wide Native American ancestry estimates in European Americans shows greater Native American female and higher European male ancestry contributions (Tables 1 and S4). Though we do not observe evidence of a sex bias in African ancestry contributions in European Americans overall, analysis of only those individuals with at least 1% African ancestry reveals 15% higher African ancestry on the X chromosome relative to genome-wide estimates (p value 0.013). This increase suggests female-African and male-European sex bias in European Americans that follows the same direction as in African Americans and Latinos, with greater male European and female African and Native American contributions.

AJHG Volume 96, Issue 1, p37–53, 8 January 2015