Neandertal origin of MC1R haplotypes related to skin color

Mol Biol Evol (2014) doi: 10.1093/molbev/msu180

Neanderthal Origin of the Haplotypes Carrying the Functional Variant Val92Met in the MC1R in Modern Humans

Qiliang Ding et al.

Skin color is one of the most visible and important phenotypes of modern humans. Melanocyte-stimulating hormone and its receptor played an important role in regulating skin color. In this paper, we present evidence of Neanderthal introgression encompassing the melanocyte-stimulating hormone receptor gene MC1R. The haplotypes from Neanderthal introgression diverged with the Altai Neanderthal 103.3 KYA, which postdates the anatomically modern human – Neanderthal divergence. We further discovered that all of the putative Neanderthal introgressive haplotypes carry the Val92Met variant, a loss-of-function variant in MC1R that is associated with multiple dermatological traits including skin color and photoaging. Frequency of this Neanderthal introgression is low in Europeans (~5%), moderate in continental East Asians (~30%), and high in Taiwanese aborigines (60-70%). Since the putative Neanderthal introgressive haplotypes carry a loss-of-function variant that could alter the function of MC1R and is associated with multiple traits related to skin color, we speculate that the Neanderthal introgression may have played an important role in the local adaptation of Eurasians to sunlight intensity.

Link

Music and population structure (Brown et al. 2013)

Proceedings of the Royal Society B doi: 10.1098/rspb.2013.2072

Correlations in the population structure of music, genes and language

Steven Brown et al.

We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers.

Link

The role of Taiwan in the Austronesian expansion

Of interest:

It is of interest that only two of the Pacific populations,
NZA and NZEP, both from New Zealand, are
impacted by mainland Chinese groups in the admixture
proportions (Table 4). The fact that the NZA population
is of Asian descent is the likely explanation for its connection.
In contrast, all the Austronesian Pacific populations
studied (as well as Madagascar), exhibit
widespread influences from Taiwanese aborigines, these
influences are even greater, in most instances, than the
impact from populations more geographically proximal
(for example Indonesia). Notably, the three Taiwanese
aboriginal groups that seem largely responsible for the
aforementioned effects (Paiwan, Puyuma and Saisiyat)
have been largely understudied. The Ami, which not
only is the largest tribe (population wise) within Taiwan
but the most represented in the literature, only affects
the New Zealand groups and Madagascar but not Samoa
and Tonga (Table 4), indicating that it is essential to
include a complete survey of these tribal groups when
ascertaining phylogenetic relationships.

Am J Phys Anthropol Volume 150, Issue 4, pages 551–564, April 2013

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Sheyla Mirabal et al.

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the “Out of Taiwan” hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.

Link

Southeast Asian Neolithic dogs

From the paper:

Nevertheless, the close phylogenetic clustering of haplotypes from Thailand, Brunei, Bali, and the Philippines suggests these populations originated from the same source, consistent with a single migration event, whereas the dingoes, NGSDs, and dogs from Taiwan appear sufficiently distinct from these to reflect a distinct migration event (Fig. 2b-c). The clustering of the three Island Southeast Asian populations with Thailand also was more consistent with origination from Mainland Southeast Asia than Taiwan (in agreement with mtDNA findings of Oskarsson et al. 2011).

and:

In light of findings from the present study, it seems clear that both post-Victorian and Neolithic exchanges link eastern and western Eurasian dogs. However, the cause of post-Victorian haplotype sharing between Western breed dogs and Southeast Asian village dogs apparently reflects very recent introduction of Western dogs to the East rather than extraction of Eastern dogs to create Western breeds during the Victorian Era.

and:

Specifically, our aging of this European haplogroup to 5,800 (±SE = 1750) or 8,400 (±SE = 2500) years (depending on the dingo calibration to 3,500 or 5,000 years, respectively) suggests that the connection between pre-Victorian European and Southeast Asian dogs traces only to the Neolithic period and is not of sufficient antiquity to support the hypothesis of a single origin of dogs from Southeast Asia. Thus, although future studies are needed to combine the Y SNPs and STR markers in a geographically broader sampling of dogs than was considered here, our findings support the hypothesis for a massive Neolithic expansion of dogs from Southeast Asia rather than a Paleolithic origin of dogs from this region.

This massive Neolithic expansion of Southeast Asian dogs is testable by looking at early European dogs; these ought not to belong to haplogroup H1. It would also be interesting to speculate about the trade routes and/or population movements that facilitated the spread of dogs from SE Asia to Europe during the Neolithic.

Mol Biol Evol (2013) doi: 10.1093/molbev/mst027

Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals

Benjamin N. Sacks et al.

Dogs originated >14,000 BP, but the location(s) where they first arose is uncertain. The earliest archaeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5–7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archaeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 SNPs and 5 STRs, from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia directly from Taiwan, independently of later dispersals of dogs through Thailand to Island Southeast Asia.

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

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

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

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

mtDNA and human dispersals in Southeast Asia

Yann Klimemtidis points me to this new paper. From the press release:

Prevailing theory suggests that the present-day populations of Island Southeast Asia (ISEA) originate largely from a Neolithic expansion from Taiwan driven by rice agriculture about 4,000 years ago - the so-called "Out of Taiwan" model.

However an international research team, led by the UK’s first Professor of Archaeogenetics, Martin Richards, has shown that a substantial fraction of their mitochondrial DNA lineages (inherited down the female line of descent), have been evolving within ISEA for a much longer period, possibly since modern humans arrived some 50,000 years ago.

Moreover, the lineage can be shown to have actually expanded in the opposite direction - into Taiwan - within the last 10,000 years.

Says Professor Richards: “I think the study results are going to be a big surprise for many archaeologists and linguists on whose studies conventional migration theories are based. These population expansions had nothing to do with agriculture, but were most likely to have been driven by climate change - in particular, global warming and the resulting sea-level rises at the end of the Ice Age between 15,000-7,000 years ago.”

Molecular Biology and Evolution 2008 25(6):1209-1218; doi:10.1093/molbev/msn068

Climate Change and Postglacial Human Dispersals in Southeast Asia

Pedro Soares et al.

Modern humans have been living in Island Southeast Asia (ISEA) for at least 50,000 years. Largely because of the influence of linguistic studies, however, which have a shallow time depth, the attention of archaeologists and geneticists has usually been focused on the last 6,000 years—in particular, on a proposed Neolithic dispersal from China and Taiwan. Here we use complete mitochondrial DNA (mtDNA) genome sequencing to spotlight some earlier processes that clearly had a major role in the demographic history of the region but have hitherto been unrecognized. We show that haplogroup E, an important component of mtDNA diversity in the region, evolved in situ over the last 35,000 years and expanded dramatically throughout ISEA around the beginning of the Holocene, at the time when the ancient continent of Sundaland was being broken up into the present-day archipelago by rising sea levels. It reached Taiwan and Near Oceania more recently, within the last ~8,000 years. This suggests that global warming and sea-level rises at the end of the Ice Age, 15,000–7,000 years ago, were the main forces shaping modern human diversity in the region.

Link

Paternal genetic affinity between western Austronesians and Daic populations

BMC Evol Biol. 2008 May 15;8(1):146.

Paternal genetic affinity between western Austronesians and Daic populations.

Li H, Wen B, Chen SJ, Su B, Pramoonjago P, Liu Y, Pan S, Qin Z, Liu W, Cheng X, Yang N, Li X, Tran D, Lu D, Hsu MT, Deka R, Marzuki S, Tan CC, Jin L.

ABSTRACT: BACKGROUND: Austronesian is a linguistic family spread in most areas of the Southeast Asia, the Pacific Ocean, and the Indian Ocean. Based on their linguistic similarity, this linguistic family included Malayo-Polynesians and Taiwan aborigines. The linguistic similarity also led to the controversial hypothesis that Taiwan is the homeland of all the Malayo-Polynesians, a hypothesis that has been debated by ethnologists, linguists, archaeologists, and geneticists. It is well accepted that the Eastern Austronesians (Micronesians and Polynesians) derived from the Western Austronesians (Island Southeast Asians and Taiwanese), and that the Daic populations on the mainland are supposed to be the headstream of all the Austronesian populations. RESULTS: In this report, we studied 20 SNPs and 7 STRs in the non-recombining region of the 1,509 Y chromosomes from 30 China Daic populations, 23 Indonesian and Vietnam Malayo-Polynesian populations, and 11 Taiwan aboriginal populations. These three groups show many resemblances in paternal lineages. Admixture analyses demonstrated that the Daic populations are hardly influenced by Han Chinese genetically, and that they make up the largest proportion of Indonesians. Most of the population samples contain a high frequency of haplogroup O1a-M119, which is nearly absent in other ethnic families. The STR network of haplogroup O1a* illustrated that Indonesian lineages did not derive from Taiwan aborigines as linguistic studies suggest, but from Daic populations. CONCLUSION: We show that, in contrast to the Taiwan homeland hypothesis, the Island Southeast Asians do not have a Taiwan origin based on their paternal lineages. Furthermore, we show that both Taiwan aborigines and Indonesians likely derived from the Daic populations based on their paternal lineages. These two populations seem to have evolved independently of each other. Our results indicate that a super-phylum, which includes Taiwan aborigines, Daic, and Malayo-Polynesians, is genetically educible.

Link

Austronesian expansion in Admiralty Islands of Melanesia

Molecular Biology and Evolution, doi:10.1093/molbev/msn078

The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia

Manfred Kayser et al.

The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of non-recombining Y-chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origin, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia, and perhaps as consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y-chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and of human history in the Pacific region.

Link

mtDNA haplogroup E in Southeast Asia

Mol Biol Evol. 2008 Mar 21 [Epub ahead of print]

Climate Change and Post-Glacial Human Dispersals in Southeast Asia.

Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, Chen YM, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB.

Modern humans have been living in Island Southeast Asia (ISEA) for at least 50,000 years. Largely because of the influence of linguistic studies, however, which have a shallow time depth, the attention of archaeologists and geneticists has usually been focused on the last 6000 years - in particular, on a proposed Neolithic dispersal from China and Taiwan. Here we use complete mitochondrial DNA (mtDNA) genome sequencing to spotlight some earlier processes that clearly had a major role in the demographic history of the region but have hitherto been unrecognised. We show that haplogroup E, an important component of mtDNA diversity in the region, evolved in situ over the last 35,000 years and expanded dramatically throughout ISEA around the beginning of the Holocene, at the time when the ancient continent of Sundaland was being broken up into the present-day archipelago by rising sea levels. It reached Taiwan and Near Oceania more recently, within the last approximately 8000 years. This suggests that global warming and sea-level rises at the end of the Ice Age, 15,000-7000 years ago, were the main forces shaping modern human diversity in the region.

Link

Genetic structure of Pacific Islanders

A very interesting freely available article. See also this recent blog post, Polynesians more Asian than Melanesian. Like previous studies on e.g., Europeans, European Americans, Native Americans, Indians, the scientific study of humanity by grouping individuals in clusters (i.e., races and subraces) is leading the way for a deeper understanding of the origins of the world's populations and ethnic groups.


PLoS Genetics Vol. 4, No. 1, e19 doi:10.1371/journal.pgen.0040019

The Genetic Structure of Pacific Islanders

Jonathan S. Friedlaender et al.

Human genetic diversity in the Pacific has not been adequately sampled, particularly in Melanesia. As a result, population relationships there have been open to debate. A genome scan of autosomal markers (687 microsatellites and 203 insertions/deletions) on 952 individuals from 41 Pacific populations now provides the basis for understanding the remarkable nature of Melanesian variation, and for a more accurate comparison of these Pacific populations with previously studied groups from other regions. It also shows how textured human population variation can be in particular circumstances. Genetic diversity within individual Pacific populations is shown to be very low, while differentiation among Melanesian groups is high. Melanesian differentiation varies not only between islands, but also by island size and topographical complexity. The greatest distinctions are among the isolated groups in large island interiors, which are also the most internally homogeneous. The pattern loosely tracks language distinctions. Papuan-speaking groups are the most differentiated, and Austronesian or Oceanic-speaking groups, which tend to live along the coastlines, are more intermixed. A small “Austronesian” genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups. Although the Polynesians are also distinctive, they tend to cluster with Micronesians, Taiwan Aborigines, and East Asians, and not Melanesians. These findings contribute to a resolution to the debates over Polynesian origins and their past interactions with Melanesians. With regard to genetics, the earlier studies had heavily relied on the evidence from single locus mitochondrial DNA or Y chromosome variation. Neither of these provided an unequivocal signal of phylogenetic relations or population intermixture proportions in the Pacific. Our analysis indicates the ancestors of Polynesians moved through Melanesia relatively rapidly and only intermixed to a very modest degree with the indigenous populations there.
Link

Walking speed in different cities

The New Scientist reports on a study regarding the average walking speed over a distance of 18 meters in different cities. The times to walk 18m are listed below

1) Singapore (Singapore); 10.55
2) Copenhagen (Denmark); 10.82
3) Madrid (Spain); 10.89
4) Guangzhou (China): 10.94
5) Dublin (Ireland); 11.03
6) Curitiba (Brazil); 11.13
7) Berlin (Germany); 11.16
8) New York (United States of America); 12.00
9) Utrecht (Netherlands); 12.04
10) Vienna (Austria); 12.06
11) Warsaw (Poland); 12.07
12) London (United Kingdom); 12.17
13) Zagreb (Croatia); 12.20
14) Prague (Czech Republic); 12.35
15) Wellington (New Zealand); 12.62
16) Paris (France); 12.65
17) Stockholm (Sweden); 12.75
18) Ljubljana (Slovenia); 12.76
19) Tokyo (Japan); 12.83
20) Ottawa (Canada); 13.72
21) Harare (Zimbabwe); 13.92
22) Sofia (Bulgaria); 13.96
23) Taipei (Taiwan): 14.00
24) Cairo (Egypt); 14.18
25) Sana'a (Yemen); 14.29
26) Bucharest (Romania); 14.36
27) Dubai (United Arab Emirates); 14.64
28) Damascus (Syria); 14.94
29) Amman (Jordan); 15.95
30) Bern (Switzerland); 17.37
31) Manama (Bahrain); 17.69
32) Blantyre (Malawi); 31.60

The Arabs' leisurly pace is rather obvious from this list. Also, predictably "tall" nations tend to be on the top of the list, but so is Singapore; perhaps in a crowded city-state fast walking may be a culturally acquired trait.

The website of the study has more info.

New edition of YHRD database is online

From the curators of YHRD:

Hi Dienekes,

we have launched release 20 of the YHRD database, the largest update ever with 4,755 new haplotypes. See the news below and a geographical overview as an attachment.

December 28 YHRD update (Lutz Roewer, Sascha Willuweit)

The largest update since the database was started in 2000! Release 20 is out with 46,720 haplotypes in 386 populations. 44,863 haplotypes of these are completely typed for 9 and 17,824 for 11 loci. Twenty-nine populations were added today: from Ningxia in China (Han), from Qinghai in China (Salar), from Hungary including Romani speakers, from Germany (Bonn), from Sweden (Saami from Jokkmokk), from Norway (Bergen), from Libya (Tripolis), from Yemen (Sanaa), from Mexico (Chihuahua and Mexico City), from Serbia (Novi Sad), from Siberia (Stony Tunguska Evenks, Yakut speaking Evenks, Yakuts, Yukaghir, Tuva), from Western Russia (Belgorod, Kaluga, Mineralnye Vody, Nizhnii Novgorod, Orel, Pskov, Saratov, Tula, Vladimir, Volot, Yaroslavl) and from Southeastern Poland. Ten populations were updated: from Colombia (province Antioquia), from Ningxia in China (Hui), from Taiwan (Han), from Norway (Eastern, Central, Northern, Southern, Western parts and from Oslo) as well as from Russia (Novgorod). In two populations erroneous allele calls were corrected: Taraz (Kazakhstan) and Andalucia/Extremadura (Spain). We would like to thank the following colleagues for submissions, updates and corrections: Bofeng Zhu and his group (Shaanxi, P.R.China), Pamszav Horolma and her group (Budapest, Hungary), Anke Junge and her group (Bonn, Germany), Cheng-Hwai Tzeng and his group (Taipei, Taiwan), Andreas Karlsson and his group (Linkoeping, Sweden), Anibal Gaviria and his group (Medellin, Colombia), Thomas Rothaemel and his group (Hannover, Germany), Berit Myhre Dupuy and her group (Oslo, Norway), Uta Immel and her group (Halle, Germany), Hector Rangel-Villalobos and his group (Ocotlan, Mexico), Miljen Maletin and his group (Novi Sad, Serbia), Brigitte Pakendorf and her group (Leipzig, Germany), Marcin Wozniak and his group (Bydgoszcz, Poland), Grzegorz Kaczmarczyk and his group (Krakow, Poland) and Maria Jose Farfan and her group (Sevilla, Spain).

We wish you a happy new year !

Lutz Roewer, Sascha Willuweit
YHRD curators

mtDNA of island Southeast Asia

A new preprint has appeared in the American Journal of Human Genetics site about the mtDNA origins of island SE Asians.

American Journal of Human Genetics (preprint)

A mitochondrial stratigraphy for Island Southeast Asia

Catherine Hill et al.

Island Southeast Asia (ISEA) was first colonized by modern humans at least 45,000 years ago, but the extent to which the modern inhabitants trace their ancestry to the first settlers is a matter of debate. It is widely held in both archaeology and linguistics that they are largely descended from a second wave of dispersal, proto-Austronesian-speaking agriculturalists who originated in China and spread to Taiwan ~5,500 years ago. From there they are thought to have dispersed into Island Southeast Asia ~4,000 years ago, assimilating the indigenous populations. Here, we demonstrate that mtDNA diversity in the region is extremely high and includes a large number of indigenous clades. Only a fraction of these date back to the time of first settlement, and the majority appear to mark dispersals in the late Pleistocene or early
Holocene most likely triggered by post-glacial flooding. There are much closer genetic links to Taiwan than to the mainland, but most of these probably pre-dated the mid-Holocene ‘out of Taiwan’ event as traditionally envisioned. Only ~20% at most of modern mtDNAs in ISEA could be linked to such an event, suggesting that if an agriculturalist migration did take place it was demographically minor, at least as regards the involvement of women.

Link (pdf)

mtDNA and human movements in Oceania

Definitions of Remote Oceania and Near Oceania.

Mol Biol Evol. 2006 Jul 19; [Epub ahead of print]

Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes.

Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, Penny D.

The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning ca. 3000 years ago when people sailed eastwards into the Pacific from Near Oceania where evidence of human settlement dates from as early as 40 000 years ago. Archaeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began ca. 5500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia, or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania we have assembled and analyzed a dataset of 137 mtDNA genomes from Oceania, Australia, Island Southeast Asia and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS) we report the consensus network of 165 most parsimonious trees for the Oceanic dataset, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm the female settlers of Remote Oceania were descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.

Link

Origin of Eastern Islanders

Annals of Human Genetics (Online Early)

Genetic Change in the Polynesian Population of Easter Island: Evidence from Alu Insertion Polymorphisms

E. González-Pérez et al.

Summary

The origin of Pacific islanders is still an open issue in human population genetics. To address this topic we analyzed a set of 18 Alu insertion polymorphisms in a total of 176 chromosomes from native Easter Island inhabitants (Rapanui). Available genealogical records allowed us to subdivide the total island sample into two groups, representative of the native population living in the island around 1900, and another formed by individuals with some ancestors of non-Rapanui origin. Significant genetic differentiation was found between these groups, allowing us to make some biodemographic and historical inferences about the origin and evolution of this geographically isolated island population. Our data are consistent with equivalent and recent contributions from Amerindian and European migrants to the 1900s Rapanui population, with an accelerated increase in the European gene flow during the 20th century, especially since the 1960s. Comparative analysis of our results with other available Alu variation data on neighbouring populations supports the "Voyaging Corridor" model of Polynesian human settlement, which indicates that pre-Polynesians are mainly derived from Southeast Asian and Wallacean populations rather than from Taiwan or the Philippines. This study underlines the importance of sampling and taking into account historical information in genetic studies to unravel the recent evolution of human populations.

Link

Polynesian inflow into Bismarck archipelago Melanesians

American Journal of Physical Anthropology
(Early View)

Brief communication: Mitochondrial DNA variation suggests extensive gene flow from Polynesian ancestors to indigenous Melanesians in the northwestern Bismarck Archipelago

Jun Ohashi et al.

Abstract

Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck Archipelago before their arrival. To examine the extent of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase and lysine transfer RNA (COII/tRNALys) intergenic 9-bp deletion were analyzed in the following three Oceanian populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck Archipelago, 2) Tongans as AN-speaking Polynesians, and 3) Gidra as non-Austronesian-speaking Melanesians in the southwestern lowlands of Papua New Guinea. Phylogenetic analysis of mtDNA sequences revealed that more than 60% of mtDNA sequences in the Balopa Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences with the 9-bp deletion and the Polynesian motif (i.e., T16217C, A16247G, and C16261T) suggested that the expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago.

Link

Genetics of Austronesian speaking populations

Journal of Human Genetics (online early)

Genetic characterization of four Austronesian-speaking populations

Rachel A. Chow et al.

Abstract Ascertaining the genetic relationships between Austronesian populations is paramount to understanding their dispersal throughout the islands of the Pacific and Indian Oceans. The start of the Austronesian expansion has been dated to approximately 6,000 years ago, and from linguistic and archeological evidence, the origin of this dispersal may have been the island of Formosa. Consequently, the Taiwanese aboriginal populations and their phylogenetic relationship to the Austronesian-speaking groups from Madagascar at the occidental fringes of the expansion are of great interest. In this study, allelic frequencies from six polymorphic point mutation loci were assessed in the Austronesian-speaking populations of Madagascar, the Atayal aborigines of Formosa, and the general populations of Bali and Java. These allelic frequencies were compared and analyzed with the corresponding values from eight other worldwide populations from geographically targeted regions. The group from Madagascar is genetically distinct from their east-African neighbor from Zimbabwe. Our data also indicates that the Ami and the Atayal aborigines in the island of Taiwan, which occupy adjacent territories, differ sharply genetically. Genetic differences were also found between the populations of Bali and Java, belying their geographical proximity. Our results indicate that the east-African population from Madagascar phylogenetically segregates intermediate between mainland east-African and east-Asian groups, corroborating linguistic data indicating the Austronesian influence on this population.

Link