ISBA 2014 titles

Some interesting talks and posters from the upcoming International Symposium on Biomolecular Archaeology. I don't see any abstracts on the site (yet?) but the titles are intriguing. Some that caught my eye:

• Investigating the maternal lineage diversity from an early medieval site in Southern Italy
• Ancient mitochondrial and Y chromosomal DNA reveals the western Carpathian Basin as a corridor of the Neolithic expansion
• Ancient mitochondrial DNA from the Northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process
• The effect of demography and natural selection on pigmentation heterogeneity in late Pleistocene and early Holocene Europeans
• The genomics of equine speciation and domestication
• Ancient population genetics: new insights on horse domestication
• Species identification and analysis of the Tyrolean Iceman's clothes using next generation sequencing of ancient DNA.
• Early evidence for the use of pottery: extending the ancient lipid record to the Pleistocene.
• Whey to go – first identification of lactose in prehistoric pottery
• Use of the earliest pottery on the Western and Eastern side of the Baltic
• The geographical distribution of the Polynesian cultural complex and its association with P33-C2a1 Y chromosomes: adding data from Aotearoa (New Zealand)
• Interdisciplinary investigation of an archaic hominin femur from the Swabian Jura (South-West Germany)
• Tracing the genetic history of farming populations of El Portalón Cave in the Sierra de Atapuerca, Spain.
• Ancient human genomes suggest three ancestral populations for present-day Europeans
• Ancient DNA from Early Neolithic farmers in Europe
• Genomic diversity and admixture in Stone-Age farmer and hunter-gatherer groups in Scandinavia
• Ancient DNA reveals the complex genetic history of the New World Arctic
• A prediction of the hybridisation potential between Hominin species using mitochondrial DNA
• Population Genomics of Vikings
• Tracing the genetic profile of Sus scrofa on Romanian territory from the Neolithic period until the Middle Ages
• The origins of the Aegean palatial civilizations from a population genetic perspective
• Ancient DNA evidence for a diversified origin of ancestor of Han Chinese

mtDNA history of Oceania (Duggan et al. 2014)

AJHG doi:10.1016/j.ajhg.2014.03.014

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Ana T. Duggan et al.

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.

Link

Polynesian mtDNA in extinct Amerindians from Brazil

From the paper:

In 1808 the Portuguese Crown declared “Just War” (Bellumiustum) against all Indian tribes that did not accept European laws (23). The fierce Botocudo were targeted in such wars and, in consequence, became virtually extinct by the end of the 19th century (24). Their importance for the history of the peopling of the Americas was revealed by studies reporting that the Botocudo had cranial features that consistently were described as intermediate between the polar Paleoamerican and Mongoloid morphologies (25, 26). Multivariate analyses of the cranial measures of different Amerindian and Paleoamerican groups from Brazil indeed concluded that the Botocudo Indians presented sufficient similarities with the Lagoa Santa Paleoamericans to be considered candidates to be their possible descendants (27).

Possible explanations:

The first scenario, prehistoric, is related to the possibility of genetic continuity between the Paleoamericans from Lagoa Santa and Botocudo Indians (26, 27, 37), which indeed originally had motivated this study. 

... 

Another imaginable pre-Columbian scenario involves opportunities for more recent direct contact between Polynesia and South America before the European arrival. Such possibility of a direct movement from Oceania across the Pacific Ocean to the Americas was raised by Cann (43) on a discussion of the origin of the Amerindian B haplogroup. This finding prompted Bonatto et al. (44) to evaluate the likelihood of a Polynesian-Amerindian contact having occurred and conclude against it, although they could rule out neither minor contact events nor nonmaternal genetic exchange. New evidence from human and nonhuman material has become available since then. For example, there were archeological findings of Polynesian chicken bones in the Arauco Peninsula, in Chile (45) and evidence has been found in Easter Island of pre-Columbian presence of sweet potato and bottle gourd, both typical of South America (46, 47). Independent of the plausibility or implausibility of the pre-Columbian arrival of Polynesians to the South American Pacific coast, there still would remain the need to explain how these migrants crossed the Andes and ended up in Minas Gerais, Brazil. We feel that such a scenario is too unlikely to be seriously entertained. 

... 

The last scenario that we wish to assess is the possible arrival of Polynesian haplogroups to Brazil in modern times through the African slave trade from Madagascar, where 20% of the mtDNA lineages belong to the B4a1a1a haplogroup (29).

It may be of relevance that both Tianyuan (~40ka) and Boshan (~8ka) from China belong to mtDNA haplogroup B and that B belongs to the R (and N) clade of the mtDNA phylogeny, i.e., a different branch of Out-of-Africa than C (which belongs to M). I wager that interesting things were taking place in East Eurasia and the New World until fairly recent times, and hopefully ancient DNA will help us complete the picture.

PNAS doi: 10.1073/pnas.1217905110

Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil

Vanessa Faria Gonçalves et al.

There is a consensus that modern humans arrived in the Americas 15,000–20,000 y ago during the Late Pleistocene, most probably from northeast Asia through Beringia. However, there is still debate about the time of entry and number of migratory waves, including apparent inconsistencies between genetic and morphological data on Paleoamericans. Here we report the identification of mitochondrial sequences belonging to haplogroups characteristic of Polynesians in DNA extracted from ancient skulls of the now extinct Botocudo Indians from Brazil. The identification of these two Polynesian haplogroups was confirmed in independent replications in Brazil and Denmark, ensuring reliability of the data. Parallel analysis of 12 other Botocudo individuals yielded only the well-known Amerindian mtDNA haplogroup C1. Potential scenarios to try to help understand these results are presented and discussed. The findings of this study may be relevant for the understanding of the pre-Columbian and/or post-Columbian peopling of the Americas.

Link

Sweet potato genome provides link between South America and Polynesia

The actual PNAS paper seems to be still under embargo, but here's a news story in Science about the new research:

By analyzing genetic markers specific to sweet potatoes in both modern samples of the plant and older herbarium specimens, the researchers discovered significant differences between varieties found in the western Pacific versus the eastern Pacific. This finding supports the so-called tripartite hypothesis, which argues that the sweet potato was introduced to the region three times: first through premodern contact between Polynesia and South America, then by Spanish traders sailing west from Mexico, and Portuguese traders coming east from the Caribbean. The Spanish and Portuguese varieties ended up in the western Pacific, while the older South American variety dominated in the east, which would explain the genetic differences the French team saw.

Apart from the famous Heyerdahl voyage (which has recently become the subject of a 2012 movie), there was some other research regarding the introduction of Polynesian chickens to Chile. I have not followed the genetics of that part of the world very closely, but it's my impression that such a link between Polynesia and South America has not been found in the human populations of the two regions.

Q2 mtDNA haplogroup in Oceania

PLoS ONE 7(12): e52022. doi:10.1371/journal.pone.0052022

The Q2 Mitochondrial Haplogroup in Oceania

Chris A. Corser et al.

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.

Link

First Polynesian settlement: 2838±8 BP

PLoS ONE 7(11): e48769. doi:10.1371/journal.pone.0048769

High Precision U/Th Dating of First Polynesian Settlement

David Burley et al.

Previous studies document Nukuleka in the Kingdom of Tonga as a founder colony for first settlement of Polynesia by Lapita peoples. A limited number of radiocarbon dates are one line of evidence supporting this claim, but they cannot precisely establish when this event occurred, nor can they afford a detailed chronology for sequent occupation. High precision U/Th dates of Acropora coral files (abraders) from Nukuleka give unprecedented resolution, identifying the founder event by 2838±8 BP and documenting site development over the ensuing 250 years. The potential for dating error due to post depositional diagenetic alteration of ancient corals at Nukuleka also is addressed through sample preparation protocols and paired dates on spatially separated samples for individual specimens. Acropora coral files are widely distributed in Lapita sites across Oceania. U/Th dating of these artifacts provides unparalleled opportunities for greater precision and insight into the speed and timing of this final chapter in human settlement of the globe.

Link

Hawaiian origins (Kim et al. 2012)

PLoS ONE 7(11): e47881. doi:10.1371/journal.pone.0047881

Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study

Sung K. Kim et al.

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.

Link

Ancient mtDNA of first New Zealanders

PNAS doi: 10.1073/pnas.1209896109

Complete mitochondrial DNA genome sequences from the first New Zealanders

Michael Knapp et al.

The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.

Link

Climate and body composition

Am J Phys Anthropol DOI: 10.1002/ajpa.21591


Ecogeographical associations between climate and human body composition: Analyses based on anthropometry and skinfolds

Jonathan C.K. Wells et al.

Abstract

In the 19th century, two “ecogeographical rules” were proposed hypothesizing associations of climate with mammalian body size and proportions. Data on human body weight and relative leg length support these rules; however, it is unknown whether such associations are attributable to lean tissue (the heat-producing component) or fat (energy stores). Data on weight, height, and two skinfold thickness were obtained from the literature for 137 nonindustrialized populations, providing 145 male and 115 female individual samples. A variety of indices of adiposity and lean mass were analyzed. Preliminary analyses indicated secular increases in skinfolds in men but not women, and associations of age and height with lean mass in both sexes. Decreasing annual temperature was associated with increasing body mass index (BMI), and increasing triceps but not subscapular skinfold. After adjusting for skinfolds, decreasing temperature remained associated with increasing BMI. These results indicate that colder environments favor both greater peripheral energy stores, and greater lean mass. Contrasting results for triceps and subscapular skinfolds might be due to adaptive strategies either constraining central adiposity in cold environments to reduce cardiovascular risk, or favoring central adiposity in warmer environments to maintain energetic support of the immune system. Polynesian populations were analyzed separately and contradicted all of the climate trends, indicating support for the hypothesis that they are cold-adapted despite occupying a tropical region. It is unclear whether such associations emerge through natural selection or through trans-generational and life-course plasticity. These findings nevertheless aid understanding of the wide variability in human physique and adiposity.

Link

Y-chromosome ties between Taiwan and Polynesia

Gene. 2011 Nov 3. [Epub ahead of print]

Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines from Taiwan and the Polynesian Islands of Samoa and Tonga.

Mirabal S, Herrera KJ, Gayden T, Regueiro M, Underhill PA, Garcia-Bertrand RL, Herrera RJ.
Source

Abstract
The Austronesian expansion has left its fingerprint throughout two thirds of the circumference of the globe reaching the island of Madagascar in East Africa to the west and Easter Island, off the coast of Chile, to the east. To date, several theories exist to explain the current genetic distribution of Austronesian populations, with the "slow boat" model being the most widely accepted, though other conjectures (i.e., the "express train" and "entangled bank" hypotheses) have also been widely discussed. In the current study, 158 Y chromosomes from the Polynesian archipelagos of Samoa and Tonga were typed using high resolution binary markers and compared to populations across Mainland East Asia, Taiwan, Island Southeast Asia, Melanesia and Polynesia in order to establish their patrilineal genetic relationships. Y-STR haplotypes on the C2 (M38), C2a (M208), O1a (M119), O3 (M122) and O3a2 (P201) backgrounds were utilized in an attempt to identify the differing sources of the current Y-chromosomal haplogroups present throughout Polynesia (of Melanesian and/or Asian descent). Specifically, while haplogroups C2a, S and K3-P79 suggest a Melanesian component in 23%-42% of the Samoan and Tongan Y chromosomes, the prominence of sub-haplogroup O3a2c* (P164), which has previously been observed at only minimal levels in Mainland East Asians (2.0-4.5%), in both Polynesians (ranging from 19% in Manua to 54% in Tonga) and Ami aborigines from Taiwan (37%) provides, for the first time, evidence for a genetic connection between the Polynesian collections and the Ami.

Link

mtDNA of Oceanians (Ballantyne et al. 2011)

Forensic Sci Int Genet. 2011 Sep 20. [Epub ahead of print]

MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania.

Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RA, Kayser M.

Abstract

Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.

Link

The spread of Austronesian farmers across the Pacific

This is the first of three interesting papers that appear ahead of print in Current Anthropology. Peter Bellwood reviews the spread of farming across the Pacific from its two sources (China including Taiwan, and the New Guinea highlands).

Related:

• Major East-West divide in Indonesian Y chromosomes
• More on geographical divide between Asian and Melanesian types in Indonesia (Cox et al. 2010)
• Demographic history of Oceania (Wollstein et al. 2010)

Current Anthropology http://www.jstor.org/stable/full/10.1086/658181

Holocene Population History in the Pacific Region as a Model for Worldwide Food Producer Dispersals

Peter Bellwood

Pacific prehistory (excluding Australia) since 3000 BC reflects the impacts of two source regions for food production: China from the Yangzi southward (including Taiwan) and the western Pacific (especially the New Guinea Highlands). The linguistic (Austronesian, Trans–New Guinea), bioanthropological/human genetic, and Neolithic archaeological records each carry signals of expansion from these two source regions. A combined consideration of the multiregional results within all three disciplines (archaeology, linguistics, and biology) offers a historical perspective that will never be obtained from one discipline or one region alone. The fundamental process of human behavior involved in such expansion—population dispersal linked to increases in human population size—is significant for explaining the early spreads of food production and language families in many parts of the world. This article is concerned mainly with the archaeological record for the expansion of early food producers, Austronesian languages, and Neolithic technologies through Taiwan into the northern Philippines as an early stage in what was to become the greatest dispersal of an ethnolinguistic population in world history before AD 1500.

Link

StepPCO for admixture estimation

The authors introduce wavelet transform as a method of estimating admixture proportions and dating the time of admixture. They claim to perform better than HAPMIX which is probably the state of the art when it comes to this sort of thing.

As I had pointed out in my review of HAPMIX, the problem with this type of tool is that quite often you don't have access to the parental populations of an admixed population, because either they no longer exist in unadmixed form themselves, or you are using inappropriate stand-ins for them. This is not much of a problem for unsupervised admixture analysis which makes no assumptions about which populations combined to form an admixed population, but looks only at individuals.

Indeed, I'd say there is plenty of room for researchers to come up with unsupervised versions of HAPMIX/StepPCO and/or to extend them so that they can handle tri-source populations, as they currently assume only two sources of admixture.

An interesting quote from the paper:

Average admixture proportions estimated by the StepPCO method for the African-Americans, Polynesians and Fijians are 19% European ancestry, 24.9% Melanesian ancestry, and 40.2% Melanesian ancestry respectively (Figure 6a). Individual admixture estimates vary substantially among the African-Americans, with some individuals exhibiting very low European ancestry (less than 5%), and some substantially higher (more than 40%). These results were substantiated by the frappe [13] analysis, which agree quite closely with the per-chromosome ancestry estimates from the StepPCO analysis (Figure 6b). A similar pattern is observed in Fiji, with Melanesian ancestry ranging from 22% to 63%. Despite the fact that the Polynesian sample is very diverse, coming from seven different islands [19] , the level of Melanesian ancestry is much more uniform across individuals (varying from 18 to 28%).

Contra the speculations of some, per-chromosome ancestry estimates do not differ greatly from those obtained from a genome-wide maximum likelihood algorithm like frappe; the latter implements the same algorithm as ADMIXTURE, the software I use in the Dodecad Project. Nor is there any evidence that maximum likelihood algorithms suppress low-level admixture: the Mandenka show 2% European admixture in the 2-way analysis by both StepPCO and HAPMIX, and they show 1.66% West Eurasian admixture in my K=3 global unsupervised admixture analysis which looked at 139 different populations.

The main advantage of HAPMIX/StepPCO over maximum likelihood methods is not their greater accuracy, but rather the fact that they can date admixture events, with the above-mentioned caveats. From the paper:

The spectral analysis of the StepPCO signal revealed that the average dominant frequency for the African-Americans is located at level 1.8, which would correspond to an abundance of low frequency wavelets (that is, wider ancestry blocks), while for the Fijians and the Polynesians the average dominant frequency is at level 3.06 and 3.63 respectively, which is indicative of much narrower ancestry blocks (Figure 7). Based on simulations, the WT center of 1.8 corresponds to an admixture time of 6 generations ago (95% CI: 4-8 generations) for the African Americans. Assuming a generation time of 30 years [33] , our results indicate that the admixture in the African Americans started about 180 years ago. Similarly, the simulations indicate that the WT center of 3.63 for the Polynesians corresponds to an admixture time of 90 generations (95% CI: 77-131 generations), or about 2,700 years ago (Figure 8). The time estimation for Fiji is based on simulated data with a 40% admixture rate (to match the higher admixture rate of Fiji), and here the WT center of 3.06 corresponds to an admixture time of 37 generations (95% CI: 29-39) or about 1,100 years ago.

The central estimate for African Americans seems plausible, given that admixture in that population took place since colonial times until more recently, as AA children of half-white heritage are usually considered (by society) as "black" (cf. Obama), and two centuries or so seems like a reasonable middle ground. The ~2.7ky for Polynesian admixture is also in agreement with the different method of Wollstein et al. (2010) of 3ky.

The software runs in R and is available online.

Genome Biology 2011, 12:R19 doi:10.1186/gb-2011-12-2-r19

Dating the age of admixture via wavelet transform analysis of genome-wide data

Irina Pugach et al.

Abstract

We describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixed human populations. The wavelet transform method offers better resolution than existing methods for dating admixture, and can be applied to either SNP or sequence data from humans or other species.

Link

Sailing across the Pacific to settle Polynesia (Soares et al. 2011)

I always have a hard time following these easy archaeological interpretations on the basis of uniparental markers, both because I'm convinced that they are not supported by the wide confidence intervals of age estimates, and because, as I've argued countless times, age of colonization != age of most recent common ancestor of colonists' descendants.

With respect to the latter point, let me just reiterate that:

• The common founder of a set of lineages may postdate the colonization event, if the number of colonists was small enough so that attrition was high enough, and a founder that lived long after the colonization effect contributed most of the present-day population
• The common founder of a set of lineages may predate the colonization event, if the number of colonists was high enough, so that multiple related lineages with a founder who lived before the event, survived into the modern population.

We should all take modern genetic-archaeological-prehistorical correlations (including my own!) with a huge grain of salt. Polynesia seems like the last place on earth likely to yield ancient DNA of any antiquity, due to the combination of heat and moisture, but, on the whole, a single well-dated and authenticated ancient DNA sample carries much more weight than all the modern DNA put together.

From the press release:

Surprising new evidence which overturns current theories of how humans colonised the Pacific has been discovered by scientists at the University of Leeds, UK.

The islands of Polynesia were first inhabited around 3,000 years ago, but where these people came from has long been a hot topic of debate amongst scientists. The most commonly accepted view, based on archaeological and linguistic evidence as well as genetic studies, is that Pacific islanders were the latter part of a migration south and eastwards from Taiwan which began around 4,000 years ago.

But the Leeds research – published today in The American Journal of Human Genetics – has found that the link to Taiwan does not stand up to scrutiny. In fact, the DNA of current Polynesians can be traced back to migrants from the Asian mainland who had already settled in islands close to New Guinea some 6-8,000 years ago.

...

Professor Richards and co-researcher Dr Pedro Soares (now at the University of Porto), argue that the linguistic and cultural connections are due to smaller migratory movements from Taiwan that did not leave any substantial genetic impact on the pre-existing population.

The American Journal of Human Genetics, 03 February 2011
doi:10.1016/j.ajhg.2011.01.009

Ancient Voyaging and Polynesian Origins

Pedro Soares et al.

Abstract
The “Polynesian motif” defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ∼4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3–4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a “voyaging corridor” between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.

Link

Demographic history of Oceania (Wollstein et al. 2010)

frappe analysis on the left: New Guinea Highlanders split at K=4 (light blue), with Polynesian-Fijians remaining aligned with East Asians; at K=5 the specificity of the East Eurasian component in Polynesians-Fijians (teal) is revealed; at K=5 the specificity of Borneo is apparent (red), but there are individuals of clearer East Asian ancestry remaining.

From the paper:

Among the three demographic models examined for the peopling of Near Oceania (Figure 4, models 2a–2c), the model receiving the highest support involves a split of New Guineans from a common European-East Asian (i.e., Eurasian) ancestor population. This finding does not support the southern dispersal hypothesis of separate human migrations from Africa to Near Oceania and to East Asia [33, 34]. The existence of a single ancestral population for all present-day non-Africans is supported, among other genetic evidence, by recent data from the Neandertal genome sequence, indicating that all present-day non-African genome sequences studied(including one from a Papua New Guinean) have equivalent amounts of Neandertal admixture [46].

However, the authors date the split of Near Oceanians from the common Eurasians at 27ky and of East Asians from Europeans at only 18ky. These dates are far too low, in my opinion, as there is evidence that Upper Paleolithic Europeans were already robust versions of modern Caucasoids.

Moreover, if Eurasian unity broke down at 27ky, then where were the Eurasians since the time they acquired "Neandertal admixture" until 27ky?

It is difficult to imagine Eurasians camping in the Near East or Europe (where Neandertals are attested) for tens of thousands of years before starting to split off at 27ky. And indeed, the fact that there are anatomically modern humans from South China and the Levant at around 100ky, make the idea that Eurasians got Neandertal admixture in one place before starting to disperse a few tens of thousands of years ago hard to believe.

I personally don't buy the idea that New Guineans have the same "Neandertal admixture" as Europeans. In fact, I doubt there is any substantial Neandertal admixture in Eurasians at all, and if there is, it is certainly not the 1-4% evenly distributed element across Eurasia that was discovered in the recent paper.

In any case, this issue is peripheral to this paper which offers important new data on the question of Oceanian origins.

Related:

• Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan
• 500K SNP study of Oceanian populations
• Genetic structure of Pacific Islanders
• Polynesians more Asian than Melanesian
• A rare genomic look at Aboriginal Australians

Curr Biol. 2010 Nov 10. [Epub ahead of print]

Demographic History of Oceania Inferred from Genome-wide Data.

Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking M, Kayser M.

Abstract

BACKGROUND: The human history of Oceania comprises two extremes: the initial colonizations of Near Oceania, one of the oldest out-of-Africa migrations, and of Remote Oceania, the most recent expansion into unoccupied territories. Genetic studies, mostly using uniparentally inherited DNA, have shed some light on human origins in Oceania, particularly indicating that Polynesians are of mixed East Asian and Near Oceanian ancestry. Here, we use ∼1 million single nucleotide polymorphisms (SNPs) to investigate the demographic history of Oceania in a more detailed manner.

RESULTS: We developed a new approach to account for SNP ascertainment bias, used approximate Bayesian computation simulations to choose the best-fitting model of population history, and estimated demographic parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians ∼27 thousand years ago (kya), suggesting separate initial occupations of both territories. The genetic admixture in Polynesian history between East Asians (∼87%) and Near Oceanians (∼13%) occurred ∼3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (∼65%) and additional Near Oceanian (∼35%) ancestry not found in Polynesians, with this admixture occurring considerably after the initial settlement of Remote Oceania. Our data support a greater contribution of East Asian women than men in the admixture history of Remote Oceania and highlight population substructure in Polynesia and New Guinea.

CONCLUSIONS: Despite the inherent ascertainment bias, genome-wide SNP data provide new insights into the genetic history of Oceana. Our approach to correct for ascertainment bias and obtain reliable inferences concerning demographic history should prove useful in other such studies.

Link

More Uniform Sampling of Human Genetic Diversity (Xing et al. 2010)

Some observations on the paper:

New World populations (Totonac and Bolivian) are placed between Nepalese and Kyrgyzstanis, indicating higher affinity of these American samples to central Asians than to eastern Asians.

This is more likely an artifact of the mixed (Caucasoid-Amerindian) ancestry of these American samples, rather than an indication of their Central Asian origin, as the authors seem to believe. This is an important caveat, as American Indians and Central Asians are "pulled together" by their shared West Eurasian ancestry of post-Columbus and Neolithic/Chalcolithic Age origin respectively, and correspondingly "pulled away" by Mongoloids proper from East Asia who lack that admixture.

Polynesians also deviate from East Asians towards Europeans, less strongly than Central Asians, and this reflects low-level admixture between ancestral Polynesians and colonial-era Europeans.

The Eurasian PCA is interesting:

At the sub-continental level, we focus first on Eurasia, where most of our samples have been selected (Figure 4A). Overall, PC1 and PC2 mainly reflect the geographic distribution of the populations, with the majority of genetic variation accounted for by their locations. PC1 (accounting for 62.7% of the variance) reflects an east-west gradient, while PC2 (3.3% of the variance) reflects a north-south gradient.

There is absolutely no reason (based on geographical distance) for PC1 to account for twenty times more variance than PC2. PC1 reflects the racial contrast between Caucasoids and Mongoloids, while PC2 reflects the much weaker latitudinal adaptation and south-to-north spread of humans into the higher latitudes.

Another thing to notice is how tightly clustered Caucasoids are, from the Atlantic to Iraq (a distance of about 4,000km), which is -conservatively- about half the distance between Pakistan and South India. This is due to the fact that South Asians were formed by admixture of two elements: an extraneous Caucasoid one and an indigenous Paleo-Indian one. Notice also that this variable admixture (highest Caucasoid component in Brahmins) is not really compatible with an indigenous origin of the caste system, as has been proposed on non-scientific grounds.

More spread (given geographical distance) is also observed in Central Asia and Southeast Asia, and this is explained by relatively recent admixture between Caucasoids and Mongoloids (in the former) and Paleo-Indian-like morphological "Australoids" and Mongoloids (in the latter).

The results of ADMIXTURE analysis (for Eurasian individuals) are presented in graphical format in the paper itself, for (K=7).

Not much to comment on this that hasn't been seen before:

One observation is the existence of some "red" West Asian component in the N. European sample, which is not found in Slovenians. This may parallel the peculiarity of the Caucasoid components observed for Russians and Lithuanians recently, although the several Caucasoid components detected in that study are folded into 2 in the current one.

Notice also, how "red" is the main extraneous component in Indian Brahmins. As expected, even Brahmins are predominantly of "indigenous" origin, as these Brahmins are from Tamil Nadu and Andhya Pradesh, and not from North India. The West Asian affiliations of the main Caucasoid component are evident, and agree with Behar et al. (2010) where South Asians had a major overlap with West Asians (light green) and a minor one with Europeans (dark blue). In this paper, with a lower K the different European and West Asian subclusters are not visible.

The most interesting part of the study -for me- was the inclusion of three novel African samples, the Luhya, Alur, and Hema. Notice the blue component in these people, which resolves partially to orange at K=12. This is an indication of Eurasian affinities that are mostly lacking in other black Africans.

The Luhya are Bantu speakers from Kenya, so they are not indigenous to East Africa, but have probably picked up some native East African ancestry from their non-Bantu neighbors.

The Hema are from the Democratic Republic of Congo, but they are Nilo-Saharan pastoralists. Their fairly noticeable West Eurasian component may reflect origins outside the Congo. Are these another member of the non-Bantu pastoralists expanding from East Africa to the south? It would be interesting to take a look at these people's Y chromosomes.

All in all, a very interesting paper which adds important new populations to the discussion of human origins. Also of note, the free availability of the paper's genotype data and supplementary material at the Jorde Lab.

Genomics doi:10.1016/j.ygeno.2010.07.004

Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping

Jinchuan Xing et al.

High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

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"Aunty": 600-year old Maori woman reconstructed

Iwi face to face with "Aunty"

The face of a Maori woman who died on the Wairau bar in Marlborough more than 600 years ago has been revealed using digital technology.

Skulls found on the Wairau Bar in 1939 have been used to help digitally recreate the faces of the people who once lived there.

Local iwi Rangitane have affectionately renamed the woman as "aunty".

Video from above story.

Maori ancestor face mapped

It's not easy to visualise what our ancestors might have looked like, but now digital technology has allowed a group of researchers to reconstruct the face of a Maori woman using her 600 year old skull.

The woman the local iwi Rangitane have come to call "Aunty" lived in New Zealand's Marlborough region. Her skull was recovered several decades ago, but it's taken until now to repatriate the remains and reconstruct her face.

Audio from above story.

Bacteria and the human peopling of the Pacific

A new paper in Science looks at the peopling of the Pacific from the perspective of genetic diversity of the bacterium H. pylori which is found in people's stomachs.

Related to: Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan

Science doi:10.1126/science.1166083

The Peopling of the Pacific from a Bacterial Perspective

Yoshan Moodley et al.

Abstract

Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.

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Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan

The same Bayesian methodology was used by the first author to conclude that the spread of Indo-European languages began in Asia Minor during the Neolithic.



From the paper:

The innovationist "pulse-pause" scenario posits that the Austronesians originated in Taiwan around 5500 years ago and spread through the Pacific in a sequence of expansion pulses and settlement pauses (2, 4–6).

...

The divergence time estimates for the age of the Austronesian language family support the pulse-pause scenario (Fig. 2). The estimated root age of Austronesian across all the post–burn-in trees has a mean of 5230 years [95% highest posterior density (HPD) interval, 4750 to 5800 years B.P.). The divergence time estimates were robust across a range of calibrations and different models (28).

The concordance of Bayesian linguistics with the pulse-pause archaeological model is remarkable. So, how was the slow-boat model supported in the first place?

In contrast, proponents of the slow-boat scenario argue that the Austronesians emerged from an extensive sociocultural network of maritime exchange in Wallacea (in the region of modern day Sulawesi and the Moluccas) around 13,000 to 17,000 years B.P. based on the dating of mitochondrial lineages (11, 12).

...

Our estimates for the age of the Austronesian expansion are considerably younger than the deep age estimates of the slow-boat scenario (11, 12, 15). One possibility is that these deep estimates are artifacts due to problems with accurately dating genetic change. There is increasing evidence that rates of genetic change estimated over thousands of years are substantially higher than the long-term substitution rate (21). This violation of the molecular clock leads to the systematic overestimation of recent divergence times.

The problem was that a calibrated evolutionary mutation rate was used to estimate these ages, making them about 3 times older than the Austronesian expansion. Sound familiar?

Science DOI: 10.1126/science.1166858

Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement

R. D. Gray et al.

Abstract

Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.

Link

500K SNP study of Oceanian populations

Related: Genetic structure of Pacific Islanders

Molecular Biology and Evolution, doi:10.1093/molbev/msn128

Gene Flow and Natural Selection in Oceanic Human Populations, Inferred from Genome-wide SNP Typing

Ryosuke Kimura et al.

It is suggested that the major prehistoric human colonizations of Oceania occurred twice, namely, about 50,000 and 4,000 years ago. The first settlers are considered as ancestors of indigenous people in New Guinea and Australia. The second settlers are Austronesian-speaking people who dispersed by voyaging in the Pacific Ocean. In this study, we performed genome-wide SNP typing on an indigenous Melanesian (Papuan) population, Gidra, and a Polynesian population, Tongans, by using the Affymetrix 500K assay. The SNP data were analyzed together with the data of the HapMap samples provided by Affymetrix. In agreement with previous studies, our phylogenetic analysis indicated that indigenous Melanesians are genetically closer to Asians than to Africans and European Americans. Population structure analyses revealed that the Tongan population is genetically originated from Asians at 70% and indigenous Melanesians at 30%, which thus supports the so-called "Slow train" model. We also applied the SNP data to genome-wide scans for positive selection by examining haplotypic variation, and identified many candidates of locally selected genes. Providing a clue to understand human adaptation to environments, our approach based on evolutionary genetics must contribute to revealing unknown gene functions as well as functional differences between alleles. Conversely, this approach can also shed some light onto the invisible phenotypic differences between populations.

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