Abnormalities in Pleistocene Homo

 

An excess of congenital defects is certainly compatible with high levels of inbreeding, and the publication of the Denisova genome clearly suggested "extremely low" genetic diversity in that Pleistocene human. It'll be interesting to see if more ancient DNA data will reveal high levels of inbreeding consistent with the abundance of genetic abnormalities evident in the anthropological record.

PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587
An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo

Xiu-Jie Wu et al.

We report here a neurocranial abnormality previously undescribed in Pleistocene human fossils, an enlarged parietal foramen (EPF) in the early Late Pleistocene Xujiayao 11 parietal bones from the Xujiayao (Houjiayao) site, northern China. Xujiayao 11 is a pair of partial posteromedial parietal bones from an adult. It exhibits thick cranial vault bones, arachnoid granulations, a deviated posterior sagittal suture, and a unilateral (right) parietal lacuna with a posteriorly-directed and enlarged endocranial vascular sulcus. Differential diagnosis indicates that the perforation is a congenital defect, an enlarged parietal foramen, commonly associated with cerebral venous and cranial vault anomalies. It was not lethal given the individual’s age-at-death, but it may have been associated with secondary neurological deficiencies. The fossil constitutes the oldest evidence in human evolution of this very rare condition (a single enlarged parietal foramen). In combination with developmental and degenerative abnormalities in other Pleistocene human remains, it suggests demographic and survival patterns among Pleistocene Homo that led to an elevated frequency of conditions unknown or rare among recent humans.

Link

Millet use ~11 thousand years ago in northern China

 

PNAS March 6, 2012 vol. 109 no. 10 3726-3730
Early millet use in northern China
Xiaoyan Yang et al.
It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5–11.0 cal kyBP) and Donghulin (11.0–9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place.
Link

Late Middle Pleistocene teeth from South China (Liu et al. 2013)

From the paper:

The Panxian Dadong P3 falls in the upper left quadrant, an area that, with the exception of two out of the nine Atapuerca-SH specimens and S7-34, is exclusively occupied by recent humans. Thus this geometric morphometric analysis indicates that the general crown conformation of the Panxian Dadong P3 resembles some European Middle Pleistocene hominins, Chinese Upper Pleistocene hominins, and particularly the recent human specimens. 

According to the above comparisons, the Panxian Dadong P3 preserves some primitive and highly polymorphic traits, but in general its conformation is derived. Its occlusal morphology is simple, and the contour is symmetrical with a lingual cusp that is narrower than the buccal one. All these features make the Panxian Dadong P3 most similar to Upper Pleistocene hominins and recent humans in our comparative samples.

I suspect that the age of these teeth will render them useless for ancient DNA work.
Journal of Human Evolution doi:10.1016/j.jhevol.2012.10.012
Late Middle Pleistocene hominin teeth from Panxian Dadong, South China
Wu Liu et al.
The hominin teeth and evidence of hominin activities recovered from 1991 to 2005 at the Panxian Dadong site in South China are dated to the late Middle Pleistocene (MIS 8–6 or ca. 130–300 ka), a period for which very little is known about the morphology of Asian populations. The present study provides the first detailed morphometric description and comparisons of four hominin teeth (I1, C1, P3 and P3) from this site. Our study shows that the Panxian Dadong teeth combine archaic and derived features that align them with Middle and Upper Pleistocene fossils from East and West Asia and Europe. These teeth do not display any typical Neanderthal features and they are generally more derived than other contemporaneous populations from Asia and Africa. However, the derived traits are not diagnostic enough to specifically link the Panxian Dadong teeth to Homo sapiens, a common problem when analyzing the Middle Pleistocene dental record from Africa and Asia. These findings are contextualized in the discussion of the evolutionary course of Asian Middle Pleistocene hominins, and they highlight the necessity of incorporating the Asian fossil record in the still open debate about the origin of H. sapiens.
Link

Paternal origins of Chinese cattle

Paternal origins of Chinese cattle

The taurine/indicine north/central vs. south China makes sense. Also of interest, the dominance (within the taurine group) of Y2 over Y1 haplogroup. I had wished for more eastern data points when Edwards et al. was published and it now appears clear that at least in the case of China there is a predominance of the Y2 (southern) haplogroup within the taurine group of patrilineages.

Anim Genet. 2013 Jan 24. doi: 10.1111/age.12022. [Epub ahead of print]

Paternal origins of Chinese cattle.

Li R, Zhang XM, Campana MG, Huang JP, Chang ZH, Qi XB, Shi H, Su B, Zhang RF, Lan XY, Chen H, Lei CZ.

logy, Northwest A&F University, Yangling, Shaanxi, 712100, China. Abstract

To determine the genetic diversity and paternal origin of Chinese cattle, 302 males from 16 Chinese native cattle breeds as well as 30 Holstein males and four Burma males as controls were analysed using four Y-SNPs and two Y-STRs. In Chinese bulls, the taurine Y1 and Y2 haplogroups and indicine Y3 haplogroup were detected in seven, 172 and 123 individuals respectively, and these frequencies varied among the Chinese cattle breeds examined. Y2 dominates in northern China (91.4%), and Y3 dominates in southern China (90.8%). Central China is an admixture zone, although Y2 predominates overall (72.0%). The geographical distributions of the Y2 and Y3 haplogroup frequencies revealed a pattern of male indicine introgression from south to north China. The three Y haplogroups were further classified into one Y1 haplotype, five Y2 haplotypes and one Y3 haplotype in Chinese native bulls. Due to the interplay between taurine and indicine types, Chinese cattle represent an extensive reservoir of genetic diversity. The Y haplotype distribution of Chinese cattle exhibited a clear geographical structure, which is consistent with mtDNA, historical and geographical information.

Link

Ancient DNA from Tianyuan Cave

Ancient DNA from Tianyuan Cave

Another new PNAS paper that hasn't yet appeared in the journal website. Still, from this description at ScienceNews this appears to be Very Important, as it pertains to a 40,000-year-old modern human, which, if I'm not mistaken is the oldest modern human tested so far:

Ancient DNA from cell nuclei and maternally inherited mitochondria indicates that this individual belonged to a population that eventually gave rise to many present-day Asians and Native Americans, says a team led by Qiaomei Fu and Svante Paabo, evolutionary geneticists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003, carries roughly the same small proportions of Neandertal and Denisovan genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

The Max Planck press release adds some information:

The genetic profile reveals that this early modern human was related to the ancestors of many present-day Asians and Native Americans but had already diverged genetically from the ancestors of present-day Europeans.

This is an important finding because some published demographic models had Europeans and East Eurasians diverging as recently as ~20 thousand years ago. It now appears that they did so already at around the time of the Upper Paleolithic revolution, when unambiguous evidence of modern humans across Eurasia exists.

UPDATE I: While we wait for this paper to appear on the PNAS website, it might be useful to wonder whether the Tianyuan sample might fall on the East Asian/Amerindian group or the more general "Ancestral South Indian" (ASI)/East Eurasian group.

According to current dating, haplogroup M itself is ~50 thousand years old, and most of the subclades therein coalesce to younger than 40ky times. It's possible that the Tianyuan sample dates from a period where ASI/East Asian differentiation had only just begun or was just about to begin.

The press release makes clear that Tianyuan was already "Asian" rather than generalized Eurasian, proving that East/West Eurasian differentiation had begun by ~40kya. It will be interesting to see whether it can be placed on a more specific "East Eurasian" group rather than a generalized "Asian" one.

UPDATE II: The paper is now online.

UPDATE III: From the paper:

Thus, it is related to the mtDNA that was ancestral to present-day haplogroup B (Fig. 1), which has been estimated to be around 50,000 y old (18) (50. 7 ka BP; 95% CI: 38.1–68.3 ka BP). We note that the age of the Tianyuan individual is compatible with this date.

So, it appears to be within macro-haplogroup N, with haplogroup B being, I think, a fairly unambiguously East Asian/Native American clade of the phylogeny. It will certainly be interesting to see how the much more successful -and younger- M subclades ended up dominating East Eurasia.

UPDATE IV: The TreeMix analysis clearly places Tianyuan within the Asian group, but does not resolve whether Papuans are an outgroup to East Asians/Tianyuan:

I guess that is expected (see my UPDATE I), since Tianyuan dates from a period where within-Asia differentiation had only just begun or was about to begin.

UPDATE V: With respect to sharing of alleles with archaic Eurasian hominins, the Tianyuan sample is within the modern range of variation.

PNAS doi: 10.1073/pnas.1221359110

DNA analysis of an early modern human from Tianyuan Cave, China

Qiaomei Fu et al.

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (~30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Link

Ancient Y chromosomes from China

Ancient Y chromosomes from China

This appears to be an abstract of a 2012 dissertation from Jilin University (using Google Translate):

Northern China is the hub of East Asia connecting North Asia, Central Asia and the European civilization, it is a vast variety of natural ecological environment, suitable for farming, nomadic, hunting and fishing and other economic lifestyle coexist, since ancient times is fertile ground for human life, many ancient ethnic groups in here thrive and leave a valuable intangible cultural heritage. Ancient ancestors of the region but also a number of occasions by force to seize power, large-scale war had thrown the history of the North China southward to accelerate China Southern, northern populations gene fusion. Part of the ancient nation even Expeditionary Europe, its descendants across the country to play a role in promoting the exchange of population of the entire Eurasian continent. These events northern populations occupy an important position in the history of human migration. Therefore, this region of the ancient population genetics research for the original genetic retrospective of the Chinese nation, and speculated Eurasia population migration, fusion mode has great significance. This study of 13 archaeological sites in northern China - Xinjiang river cemetery, Hami Tianshan Road cemetery, Barkol the black Gouliang cemetery, the Ning Xia Pengyang cemetery, Xining Tao Wangjiazai cemetery, of Shanxi Jiangxian cross Kitamura cemetery, Hebei Yuxian three hurdles cemetery, Temple Zaigou site Niuheliang site, Sahara Trench cemetery, DADIANZI site, large piedmont ruins, wells ditch sub cemetery - human remains unearthed parent molecular genetics research, summed up the various ancient population Y chromosome haplotype groups paternal genetic diversity of the distribution rules and characteristics, combined with related ancient the modern crowd molecular genetics data reveal ancient population of the different regions of northern China, to explore the genetic makeup of the different periods of the ancient population dynamic process, in order to clarify the north fusion between ethnic origin, flow and crowd differentiation provides evidence of molecular genetics. The results are as follows: First, five archaeological site northeast western Liaoning Province 78 males unearthed ancient human remains of 44 cases of samples Y-DNA results are attributed to the C, N and O three single haplotype groups. Haplogroup N in western Liaoning Province the ancient population for a long, extensive presence, and account for a large proportion, dated to 5500-3000 years ago, is the most important ingredient in the genetic composition of the area of the ancient population paternal; based on single frequency of the haplotype groups O ancient population of western Liaoning Province and their cultural attributes and lifestyle of the crowd, and the combination of the relevant ancient population Y-SNP findings, we speculate that the haplogroup O northward by the Central Plains, emigrated to the the ancient agricultural population of western Liaoning Province carried haplogroup. The emergence of haplogroup C may be related to the nomads of the south of the North Asia. These data suggest that paternal genetic structure of the indigenous populations of the western Liaoning Province while maintaining continuity, integration into the ancient Central Plains and North Asian populations paternal genetic component. , From 64 cases of the Northwest men of ancient human remains successful Y-DNA results of 46 cases of samples, attributable to four single haplotype N, O, Q and R groups. Paternal genetic make-up of the ancient population of the Northwest Territories has obvious geographical specificity, for example, the westernmost Creek crowd as the main western lineage of R1a1 haplogroup; the adjoining Inner Mongolia Pengyang crowd all individuals can be attributed to a single type groups Q, North Asian populations in the high-frequency haplogroup; while the the approaching the Central Plains Dow Wangjiazai crowd of paternal Y-DNA to the East Asian haplogroup O, similar to the modern Han population. Comprehensive analysis of the ancient population of the Northwest Territories paternal genetic structure, in the paternal genetic form of the ancient population of the Northwest Territories there are significantly different, the reason for these different genetic data obtained speculated, is mainly due to the different groups of people have different paternal origin, everyone group accepted by the ancestors of the crowd gene contribution is different, and the from Sire terms, fewer exchanges between people own unique genetic component, so that it is preserved. Third, the success obtained from ancient human remains of the 48 cases in North China's male Y-DNA results of 29 cases of samples, attributable to the N, O and Q three single haplotype groups. The largest proportion of haplogroup O, diversity highest in two archaeological sites of the ancient Central Plains region of North China have been found; the haplogroup Q high frequency existence of Shanxi was the ancient nomads " Di "active area; haplogroup N appears that there may be the exchange of genes between populations in the Central Plains and western Liaoning Province. Comprehensive analysis of the Y-DNA of the various regions of the ancient population study results, northwest and northeast regions of the ancient population of most East Asian specific single haplotype groups can be found in the ancient population of the Central Plains, Ancient crowd paternal genetic diversity high. Central Plains region, since the Shang and Zhou dynasties is the Huaxia their descendants Han settlements, so the characteristics of the ancient population genetic structure in the Central Plains region of North China from one side of corroboration ancestors of the Han - Huaxia the Source is diverse rather than a single the integration of the different sources of the ancient population genetic component in the process of its formation. Based on the above analysis of the results, the paternal genetic structure of the ancient population in northern China in different regions have different distribution patterns: Northeast western Liaoning Province, while maintaining continuity in the of indigenous populations paternal genetic, you can see that the foreign genetic component exists in the population of the region, the foreign genetic component is likely to come from the Central Plains and North Asia and other regions. About 3000-2500 years ago, and the increasing trend of foreign genetic component. Northwest Territories of paternal inheritance there are significant differences between different geographical area of ancient population. 5 northwest of the ancient population of this study, Y chromosome genetic data, the reasons for these differences may be due to different populations have different sources of paternal and less genetic exchange between different populations, so that the the inherent genetic structure is maintained; in North China, the the patrilineal genetic structure is located in the ancient Central Plains region of the ancient population with modern Han closest, the modern Han paternal genes contributors.

The full text appears to be behind a paywall. Any native speakers who can add some information and/or correct possible mistranslations, feel free to do so in the comments.

A different look at the Olympic Medal Count

A different look at the Olympic Medal Count

The Athens Olympics are now over and Greece won 16 medals. The best-performing nations, according to the official medal count are the United States, China, Russia, Australia and Japan. A different look at the medal count of the Olympics comes from the Australian Bureau of Statistics which has compiled a world ranking based on population per gold medal. The Bahamas, Norway, Australia, Hungary and Cuba lead this ranking, with Greece placing 8th. At the bottom of the table, Syria, Mexico, Colombia, Nigeria and India.

mtDNA from Xinjiang

mtDNA from Xinjiang

A new study quantifies the level of Caucasoid admixture in various populations of the Xinjiang province of China, which ranges from 0% in the Han Chinese to 43% in the Uygur.

Mol Biol Evol. 2004 Aug 18 [Epub ahead of print]

Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China.

Yao YG

Previous studies have shown that there were extensive genetic admixtures in the Silk Road region. In the present study, we analyzed 252 mtDNAs of five ethnic groups (Uygur, Uzbek, Kazak, Mongolian, and Hui) from Xinjiang Province, China (where once was the via route of the Silk Road), together with some reported data from the adjacent regions in Central Asia. In a simple way, we classified the mtDNAs into different haplogroups (monophyletic clades in the rooted mtDNA tree) according to the available phylogenetic information and compared their frequencies to show the differences among the matrilineal genetic structures of these populations with different demographic histories. With the exception of 8 unassigned M(*), N(*) and R(*) mtDNAs, all the mtDNA types identified here belonged to defined subhaplogroups of haplogroups M and N (including R) and consisted of subsets of both the eastern and western Eurasian pools, thus providing direct evidence in supporting the suggestion that Central Asia be the place of the genetic admixture of the East and the West. Although our samples were from the same geographic location, a decreasing tendency of the western Eurasian-specific haplogroup frequency was observed, with the highest frequency present in Uygur (42.6%) and Uzbek (41.4%), followed by Kazak (30.2%), Mongolian (14.3%), and Hui (6.7%). No western Eurasian type was found in Han Chinese samples from the same place. The frequencies of the eastern Eurasian-specific haplogroups also varied in these samples. Combined with the historical records, ethno-origin, migratory history, and marriage custom might play different roles in shaping the matrilineal genetic structure of different ethnic populations resided in this region.

Link (pdf)

mtDNA of ancient central Asians

mtDNA of ancient central Asians

An interesting new paper confirms the anthropological and archaeological picture of a westward spread of Caucasoids in Central Asia in early prehistoric times, followed by the spread of Mongoloids in the opposite direction during the 1st millennium BC. The Caucasoid-Mongoloid hybrid population resulting from these interactions is similar in terms of mtDNA with present-day Central Asians with some noted differences (e.g., presence of additional West Eurasian haplogroups). In the ancient samples, West Eurasian haplogroups H, HV, I, T*, T1, U*, U1, U5, U5a1 and W were represented:

• HV sequences have matches in the Central Mediterranean region
• H sequences are split between the common Cambridge Reference Sequence (CRS) found in many populations, and two other sequences found in the Central Mediterranean and the Caucasus
• The I sequence is present in a modern Central Asian and also in individuals from the Caucasus
• The W sequence is widespread in West Eurasia
• T* sequences are widespread in Europe, the Near East and the Central Mediterranean region
• T1 is widespread in West Eurasia, but also found sporadically in East Eurasia
• The U1a sequences are found in Turks, Armenians and Caucasians
• The U5a sequence has been found in an Egyptian
• The U5a1 sequence is frequent in the Caucasus and present in Europe, while a different U5a1 was reported previously in Mongolia

The East Eurasian haplogroups belong to A*, M*, M4 and G2:

• The M* sequence was observed in an Indian individual
• The M4 sequence has not been previously reported
• The G2 sequence is found in present-day China and Central Asia
• One A sequence is found in present-day Central Asians and Indians, while the other two have a motif found in a modern Chukchi

Most (78%) of the sequences are of West Eurasian (Caucasoid) origin, but before the 7th c. BC, East Eurasian (Mongoloid) sequences are absent, although they could be present up to 20.6% (p<0.05).
Proc R Soc Lond B Biol Sci. 2004 May 7;271(1542):941-7. 

Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient central Asians.
Lalueza-Fox C et al.

This study helps to clarify the debate on the Western and Eastern genetic influences in Central Asia. Thirty-six skeletal remains from Kazakhstan (Central Asia), excavated from different sites dating between the fifteenth century BC to the fifth century AD, have been analysed for the hypervariable control region (HVR-I) and haplogroup diagnostic single nucleotide polymorphisms (SNPs) of the mitochondrial DNA genome. Standard authentication criteria for ancient DNA studies, including multiple extractions, cloning of PCR products and independent replication, have been followed. The distribution of east and west Eurasian lineages through time in the region is concordant with the available archaeological information: prior to the thirteenth-seventh century BC, all Kazakh samples belong to European lineages; while later an arrival of east Eurasian sequences that coexisted with the previous west Eurasian genetic substratum can be detected. The presence of an ancient genetic substratum of European origin in West Asia may be related to the discovery of ancient mummies with European features in Xinjiang and to the existence of an extinct Indo-European language, Tocharian. This study demonstrates the usefulness of the ancient DNA in unravelling complex patterns of past human migrations so as to help decipher the origin of present-day admixed populations.

Link (pdf)