Hawaiian genetic study shows 2-1 Asian-Melanesian admixture in Polynesians

Queen Liliuokalani of Hawaii in her youth

Native Hawaiians still make up some 38% of the population of Hawaii but most of them have mixed ancestry nowadays. This new study may help to understand them better and also includes some interesting findings about the overall origins of Polynesians, whose Melanesian ancestry is revealed as very significant.

Sung K. Kim et al., Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047881]

Abstract

The population genetic structure of Native Hawaiians has yet to be comprehensively studied, and the ancestral origins of Polynesians remain in question. In this study, we utilized high-resolution genome-wide SNP data and mitochondrial genomes of 148 and 160 Native Hawaiians, respectively, to characterize their population structure of the nuclear and mitochondrial genomes, ancestral origins, and population expansion. Native Hawaiians, who self-reported full Native Hawaiian heritage, demonstrated 78% Native Hawaiian, 11.5% European, and 7.8% Asian ancestry with 99% belonging to the B4 mitochondrial haplogroup. The estimated proportions of Native Hawaiian ancestry for those who reported mixed ancestry (i.e. 75% and 50% Native Hawaiian heritage) were found to be consistent with their self-reported heritage. A significant proportion of Melanesian ancestry (mean = 32%) was estimated in 100% self-reported Native Hawaiians in an ADMIXTURE analysis of Asian, Melanesian, and Native Hawaiian populations of K = 2, where K denotes the number of ancestral populations. This notable proportion of Melanesian admixture supports the “Slow-Boat” model of migration of ancestral Polynesian populations from East Asia to the Pacific Islands. In addition, approximately 1,300 years ago a single, strong expansion of the Native Hawaiian population was estimated. By providing important insight into the underlying population structure of Native Hawaiians, this study lays the foundation for future genetic association studies of this U.S. minority population.

In my understanding, the most interesting elements from this study are the ADMIXTURE analyses:

Figure 1. ADMIXTURE clustering of Native Hawaiians for K = 5 (A) and K = 6 (B). Figures 1A and 1B illustrate the clustering of Native Hawaiians and HGDP samples based on GWAS data.

As the general Admixture analysis was not really conclusive about the Melanesian and Asian affinities of Native Hawaiians, the authors also performed a supervised K=2 analysis:

Figure 4. Supervised ADMIXTURE results for K = 2...

This appears to show rather unmistakably that Hawaiians (and by extension surely also other Polynesians, very close in genetics and history across the Pacific Ocean) have an important amount of Melanesian genetics, consistent with the "Slow Boat" model and the relevance of Melanesian Y-DNA haplogroup C2a among all Polynesian populations.

See also in this blog: The genetic and phenotype complexity of the Oceanic language area.

Refinement in the knowledge of old African Y-DNA haplogroups

New important paper refining the understanding of old branches of mostly African patrilineages (which are important to understand the ancestry of all Humankind). 

Rossaria Scozzari et al., Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0049170]

Abstract

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

Figure 1. Revised topology of the deepest portion of the human MSY tree.

Besides B2, A3 has also been greatly improved in its understanding suggesting recent expansions. 

Haplogroup B2 is typical from Pygmies but also found through all the Sahel from Ethiopia to Mali, among other Central African populations and even among Southern African aborigines, the Khoisan peoples. 

Haplogroup A3 is important in Sudan and the Horn of Africa, as well as among the Khoisan peoples of Southern Africa. It's also occasionally found among Bantu speakers of Southern Africa, Egyptians, West Asian peoples and has also been reported in Sardinia.


New C subclade

Besides Africa a new haplogroup C7 was reported in an Italian individual. See supp. materials.

Advanced lithic tech 70,000 years ago in South Africa

A new paper argues for the importance of ill-researched early African stone technologies in human techno-cultural evolution, based mostly on the heat-treated microlithic technology used at Pinnacle Point and its persistence through time. 

Kyle S. Brown et al., An early and enduring advanced technology originating 71,000 years ago in South Africa. Nature 2012. Pay per view ··> LINK [doi:10.1038/nature11660]

Abstract

There is consensus that the modern human lineage appeared in Africa before 100,000 years ago^{1, 2}. But there is debate as to when cultural and cognitive characteristics typical of modern humans first appeared, and the role that these had in the expansion of modern humans out of Africa³. Scientists rely on symbolically specific proxies, such as artistic expression, to document the origins of complex cognition. Advanced technologies with elaborate chains of production are also proxies, as these often demand high-fidelity transmission and thus language. Some argue that advanced technologies in Africa appear and disappear and thus do not indicate complex cognition exclusive to early modern humans in Africa^{3, 4}. The origins of composite tools and advanced projectile weapons figure prominently in modern human evolution research, and the latter have been argued to have been in the exclusive possession of modern humans^{5, 6}. Here we describe a previously unrecognized advanced stone tool technology from Pinnacle Point Site 5–6 on the south coast of South Africa, originating approximately 71,000 years ago. This technology is dominated by the production of small bladelets (microliths) primarily from heat-treated stone. There is agreement that microlithic technology was used to create composite tool components as part of advanced projectile weapons^{7, 8}. Microliths were common worldwide by the mid-Holocene epoch, but have a patchy pattern of first appearance that is rarely earlier than 40,000 years ago^{9, 10}, and were thought to appear briefly between 65,000 and 60,000 years ago in South Africa and then disappear. Our research extends this record to ~71,000 years, shows that microlithic technology originated early in South Africa, evolved over a vast time span (~11,000 years), and was typically coupled to complex heat treatment that persisted for nearly 100,000 years. Advanced technologies in Africa were early and enduring; a small sample of excavated sites in Africa is the best explanation for any perceived ‘flickering’ pattern.

Supplementary materials (PDF) are freely available.

Supplementary Figure 2. Artifacts including crescent shaped backed blades (A-L) and notched blades (M-U) from the DBCS at PP5-6 show affinities with the Howiesons Poort industry. Backed blades are oriented with backed edge up and unmodified edge down. Notched blades are oriented parallel with axis of flake removal.

See also:

• Solutrean-style retouch 75,000 years ago in South Africa
  
• The Nubian techno-complex of Dhofar: yet another evidence for an early migration out-of-Africa via Arabia  
  
• Evidence of human beachcombing in South Africa: 164-120,000 years ago
• Decorated ostrich eggshells from MSA South Africa (at my old blog Leherensuge)
• Not yet metallurgy but the same basic concept... 75,000 years ago (at Leherensuge)
• More evidence for arrows 60,000 years ago (at Leherensuge)
  
• People ate processed sorghum 100,000 years ago in Mozambique (at Leherensuge)
  

Causes of skin and hair color variance in Europeans remain undetermined

Portuguese & N. Irish

Our ability to predict pigmentation traits from genetic loci remains limited but this new paper adds some honest research on the matter:

Sophie I. Candille et al., Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048294]

One of the findings is that women have darker skin shades than men in Europe (but not among peoples with dark skin from several continents, where men are darker). Another unstated but curiously counterintuitive finding is that Portuguese (from Porto) have on average the same skin tone as Polish (from Warsaw) do:

Table 1. Skin, hair, and eye pigmentation by sex and country.

However for hair and eye color, Polish have lighter shades, approaching the Irish (Dublin) extreme values, while Portuguese approach Italians (Rome) in hair color and show darker eyes on average than anybody else among the sampled populations.

Another curiosity of the survey is that Irish women show significantly lighter hair shades than Irish men, a phenomenon not appreciable elsewhere.

The authors found that, in general:

... in this European sample, pigmentation phenotypes are mainly stratified by country, whereas height is mainly stratified by sex.

They also found that:

Skin and eye pigmentation are correlated in Ireland. Hair and eye pigmentation are correlated in Portugal. Skin and hair pigmentation are correlated in Poland and Italy (Table S2).

What I find rather curious and suggestive of complex genetic influences affecting more than just one pigmentation trait at the same time. But which ones? And why do they seem to operate differently in different populations?

The GWAS analysis found these loci as significant:

Table 2. GWAS, replication, and combined association results for all signals with p-value<10⁻⁵ in the GWAS.

Apparently neither the SCIN nor the FLNB genes have been related with pigmentation before. Therefore the authors applied a strong test of reliability (replication in the table), correcting for geographical structure, which actually discarded all loci except the already known ones for eye color in relation to OCA2/HERC2, which were: rs1667394, rs8039195, rs1635168, rs16950987, and rs8028689.

However further analysis showed that rs1667394 is in linkage disequilibrium (LD) with rs12913832 (OCA2), which is the actual culprit of blue eyes (a well known SNP that explains some 45% of the eye color variance among Dutch).

In regard to the failure to detect markers of skin and hair color variance, they conclude that:

The fact that we did not detect reproducible associations with skin or hair color suggests that, unlike eye color, skin and hair pigmentation variation in Europe are not determined by major loci.

Furthermore, genes that have been shown to contribute to skin color variance in South Asians (rs1426654 SLC24A5, rs16891982 SLC45A2, and rs1042602 TYR) or in African-European admixed populations (rs1426654 in SLC24A5 again), fail to show any importance in intra-European variance for this trait. However rs1426654 is fixated in Northern Europeans (CEU), so it cannot show any variation.

Other SNPs (rs16891982 and r183671 in SLC45A2, which are in LD) may contribute to skin pigmentation, however the pattern mentioned (in which Italians and Portuguese are contrasted with Polish and Irish) rather reminds me of the variation for hair and eye color instead.

They also mention that rs885479 in MC1R has not provided any clear association in previous studies but that they did find some association with skin color, however they did not practice the replication test for this SNP.

In the end not much new other than some cold water but an straightforward study for the record.

See also:

• Predicting pigmentation phenotypes with genetic information (at Yan Klimentidis blog)
• Some population structured SNPs and also one epigenetic factor
• Category "Pigmentation"
• The height of Europeans and the myth of the North-South cline

Toba supervolcano matched with ice cores

No ashes or tephra was found in the ice sheets of Greenland or Antarctica but the supervolcano left other marks in form of very large acidity spikes (sulphates), etc:

Source: Science Daily

As you probably know, Toba caldera is located in Sumatra and its explosion was surely the largest supervolcano ever experienced by Humankind, leading to particularly cold period. 

We know since Petraglia 2007[PPV] that peoples with an African-derived techno-culture lived in South Asia before and after the dramatic episode. However it is unclear how exactly the volcano affected our ancestors beyond that.

Reference paper:

A. Svensson et al., Direct linking of Greenland and Antarctic ice cores at the Toba eruption (74 kyr BP). Climate of the Past, 2012. Open access ··> LINK [doi:10.5194/cpd-8-5389-2012]

 

12,000 years old human presence in Costa Rica

An early Native American site in the Reventazón river (Costa Rica) has been dated by radiocarbon to c. 12,000 years BP. 

The date is consistent with others in North America (as old as c. 17,000 BP) and South America (c. 13,000 BP) marking the likely first inhabitation of the Western Hemisphere. It is anyhow the oldest prehistoric date known for Costa Rica.

The site which is being dug prior to the completion of a hydroelectric project, has been researched for several years now and has provided stone tools and weapons, as well as some charcoal (fire residues) that have allowed to date it.

Source: Pileta de Prehistoria[es].

Genetic insights on tomato origins

Who doesn't love tomato? Well, my dad. But besides him... 

But one thing is loving tomato sauce, tomato salad, tomato in sandwich or other tomato based cuisine and another thing is to know much about its origins. 

While it is generally accepted that Europeans brought tomato from Mexico, the species has its greatest diversity in the Andean region. This new study should help us to better understand the nuances of tomato origins:

José Blanca et al., Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0048198]

Abstract

Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.

The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S. l. lycopersicum. It is also not clear whether the domestication occurred in the Andean region or in Mesoamerica. We characterized 272 accessions (63 S. pimpinellifolium, 106 S. l. cerasiforme, 95 S. l. lycopersicum and 8 derived from hybridization processes) were morphologically and genetically using the SolCap platform (7,414 SNPs). The two species were distinguished in a PCA analysis and displayed a rich geographic structure. Solanum lycopersicum var. cerasiforme and S. l. lycopersicum were also differentiated in the PCA and Structure analyses, which supports maintaining them as different varieties. Solanum pimpinellifolium and the Andean S. l. cerasiforme were more diverse than the non-Andean S. lycopersicum. Solanum lycopersicum var. cerasiforme was morphologically and molecularly intermediate between S. pimpinellifolium and tomato. Solanum lycopersicum var. cerasiforme, with the exception of several Ecuadorian and Mexican accessions, is composed of the products of admixture processes according to the Structure analysis. The non-admixtured S. l. cerasiforme might be similar to the ancestral cultivars from which the cultivated tomato originated, and presents remarkable morphological diversity, including fruits of up to 6 cm in diameter. The data obtained would fit a model in which a pre-domestication took place in the Andean region, with the domestication being completed in Mesoamerica. Subsequently, the Spaniards took plants from Mesoamerica to Spain and from there they were exported to the rest of the world.

Fig. 2A (with legend from fig. 1) - PCA analysis of the S. lycopersicum samples