July 31, 2010

Ancient Nordic mtDNA (Melchior et al. 2010)

The reduction of mtDNA haplogroup I in modern Scandinavians has been observed before (by the same author). Inferences from the 2 Bell Beaker and 1 Bronze Age samples which belong to U subgroups should be cautious, however these contrast with later groups as well as with the earlier Neolithic Scandinavian TRB samples. Table 5 has haplogroup frequencies in various age-place groups. From the paper:

Table 5 shows the occurrence of haplogroups among ancient Danes and Britons and modern Danes and Scandinavians. Using G-tests, no significant deviations were observed among the extant populations or between the ancient Britons and the ancient Danes, despite the two ancient population samples show a surplus of Hg T and Hg I, respectively. We have previously observed a high frequency of Hg I's among Iron Age villagers (Bøgebjerggård) and individuals from the early Christian cemetery, Kongemarken [16], [17]. This trend was also found for the additional sites reported here, Simonsborg, Galgedil and Riisby. The overall frequency of Hg I among the individuals from the Iron Age to the Medieval Age is 13% (7/53) compared to 2.5% for modern Danes [35]. The higher frequencies of Hg I can not be ascribed to maternal kinship, since only two individuals share the same common motif (K2 and K7 at Kongemarken). Except for Skovgaarde (no Hg I's observed) frequencies range between 9% and 29% and there seems to be no trend in relation to time.
There are two main explanations for the reduction in haplogroup I frequency: (a) negative selection and/or (b) the movement of non-I bearing populations into the region of interest. Unless selection occurred very recently (in the last millennium), the lack of a temporal trend adds some weight in favor of (b) and contra (a).

Of interest:
Several haplogroups which are rare or absent among the extant population of southern Scandinavia were observed. Hg's R0a and U7 have been discussed previously [15], [17]. Here we note the finding of Hg N1a in the Medieval Riisby (Table 3), which seems to be common among early European LBK farmers [10], a rare Hg T2 motif in the Iron Age settlement Simonsborg (Table 2) and Hg U5a and Hg U4 at the Early Bronze Age site Bredtoftegård and Neolithic Damsbo (Table 1).
A recent paper on mtDNA haplogroup R0a.

A main conclusion from this paper is that the mtDNA gene pool does not appear to change "monotonically" with time, as the Neolithic Bell Beaker and Bronze Age groups resemble Mesolithic ones rather than the Neolithic TRB. Thus, it is safe to say that simple one-time admixture scenaria between "Paleolithic" and "Neolithic" gene pools grossly oversimplify reality.

The more we learn about prehistory, the less we can believe in the paradigm of static people changing their subsistence, technology, language from the Paleolithic to the present. Migrationism is overdue for a comeback as an explanatory tool for the plethora of unexpected results that the bones of ancient humans present us with.

The persistence of mtDNA-U gene pools down to the Bronze Age leads the authors to consider the Iron Age as the origin of the modern Scandinavian mtDNA gene pool:
However, the frequency of Hg U4 and U5 declines significantly among our more recent Iron Age and Viking Age Danish population samples to the level observed among the extant Danish population. Our study therefore would point to the Early Iron Age and not the Neolithic Funnel Beaker Culture as suggested by Malmström et al. (2009) [14], as the time period when the mtDNA haplogroup frequency pattern, which is characteristic to the presently living population of Southern Scandinavia, emerged and remained by and large unaltered by the subsequent effects of genetic drift.
I find that a reasonable suggestion, as it was in the Iron Age that the Germanic language group seems to have emerged in southern Scandinavia and northern Germany, and started to experience its demographic expansion that rendered it one of the largest in modern Europe. So, it makes sense that the mtDNA composition of that age would persist down to the present-day inhabitants.

Related:
PLoS ONE 5(7): e11898. doi:10.1371/journal.pone.0011898

Genetic Diversity among Ancient Nordic Populations

Linea Melchior et al.

Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (~2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

Link

Koreans in genomic context (Jung et al. 2010)

The sample codes:
A total of 320 subjects from 24 regional groups were analyzed in this study. They include Yoruba (YRI), European (CEU), Japanese (JPT), Chinese (CHB), Amerindians (AI), and several population groups from Southern and Northern Asia comprising Chinese from the Jilin area (JL), Vietnamese (VN), Cambodians (CB), Mongolians (MH), and Koreans from ten cities in South Korea

Table 1 has complete sample codes, including those for different Korean cities.


The MDS plot is shown on the left. Of interest is the Asian-specific one (right), which shows Vietnamese-Cambodians on the bottom, Mongolians on the top-left, Koreans-Japanese on top and Chinese close to them but towards the Vietnamese-Cambodian direction. Not very surprising as Koreans are basically north Mongoloid, Japanese have origins in the Korean peninsula, while Chinese are both north and south in origin.

The STRUCTURE analysis is also quite interesting: see top row which is the Korean-Chinese-Japanese only admixture analysis: clear Chinese- (green), Japanese- (red), and Korean- (yellow) centered clusters emerge, paralleling what our eyes tell us about the distinctiveness of these three ethnic groups. Notice, however, sample JJ (Jeju island) which lacks Korean yellow (K=4).

From the paper:
In addition, genetic structure analysis using the STRUCTURE method revealed the existence of five major populations, African, Caucasian, Amerindian, North-East Asian, and Southern Asian. Therefore, in between, there were significant admixtures such as Mongolian with Caucasian, Vietnamese (or Cambodian) with unknown Southern original settlers, and Amerindians with both North-East Asians and Caucasians (Fig. 2).
I have commented before on all these admixtures, so let's summarize: Mongolia represents the eastern limit of the Caucasoid expansion, where a small Caucasoid component exists in a predominantly Mongoloid population; Southeast Asians represent a fusion of Mongoloids with "Australoid"-like indigenous populations of the tropical belt from South Asia to Micronesia; Amerindians are partially admixed with Europeans, and partially admixed with NE Asians; the latter component is marked, perhaps, by Y-chromosome haplogroup C3, and may correspondto the second wave of expansion into the Americas.

PLoS ONE 5(7): e11855. doi:10.1371/journal.pone.0011855

Gene Flow between the Korean Peninsula and Its Neighboring Countries

Jongsun Jung et al.

SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.

Link

July 30, 2010

Guess their origin (answer: Irish)


Here are readers' guesses:


See page 45 for explanation.

July 29, 2010

NordicDB paper on Finns, Danes, and Swedes

On the left is an MDS plot using ~45k SNPs. Some explanation on the datasets: CAPS are Swedish; SGENE and MS are Finnish (Helsinki region); Aneurysm is Finnish (Helsinki and Kupio).

A striking feature of the plot is the distinctiveness of the different Finish samples (light vs. dark brown points). This is not so difficult to explain if one considers that the light brown squares (DGI-FIN) are from Botnia. This parallels the results of Salmela et al. (2008) or Jakkula et al. (2008) in underscoring the internal structure of the population of Finland

The familiar V shape was also observed in the PCA produced by McEvoy et al. (2009) or Nelis et al. (2009). In my opinion, it is produced by the differential representation of the two main population elements of the Nordic countries, namely the Germanic and Finnic elements.

Here is the website of NordicDB.

European Journal of Human Genetics doi: 10.1038/ejhg.2010.112

NordicDB: a Nordic pool and portal for genome-wide control data

Monica Leu et al.

A cost-efficient way to increase power in a genetic association study is to pool controls from different sources. The genotyping effort can then be directed to large case series. The Nordic Control database, NordicDB, has been set up as a unique resource in the Nordic area and the data are available for authorized users through the web portal (http://www.nordicdb.org). The current version of NordicDB pools together high-density genome-wide SNP information from ~5000 controls originating from Finnish, Swedish and Danish studies and shows country-specific allele frequencies for SNP markers. The genetic homogeneity of the samples was investigated using multidimensional scaling (MDS) analysis and pairwise allele frequency differences between the studies. The plot of the first two MDS components showed excellent resemblance to the geographical placement of the samples, with a clear NW–SE gradient. We advise researchers to assess the impact of population structure when incorporating NordicDB controls in association studies. This harmonized Nordic database presents a unique genome-wide resource for future genetic association studies in the Nordic countries.

Link

July 28, 2010

Ancient DNA provides clues to donkey domestication


Proceedings of the Royal Society B doi: 10.1098/rspb.2010.0708

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Birgitta Kimura et al.

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

Link

July 27, 2010

Neolithic and modern Chinese craniofacial variation (Wu et al. 2010)

The PCA loadings on the cranial variables used are shown in Table 2. As usual for craniometric analyses, PC1 is an overall "size" factor, with positive loadings on all variables.

PC2 which distinguishes north from south is associated with high face (nasion-prosthion height), narrow nose (nasal breadth), and high eye sockets (orbital height). Notice that the sign is reversed for Modern-day vs. Neolithic Chinese, but the combination of traits is preserved (e.g. low eye sockets with broad noses).

PC3 is associated with broad and short skulls and eye sockets, and low noses.

Table 3 in the paper shows the differences between the Neolithic-era and modern Chinese, with the six significant changes being: lower skull, narrower face, narrower nose, higher orbits, lower face, narrower orbits in the modern sample.

The results of the craniometric analysis are quite similar to those arrived by genetics, which show that north-south being the main axis of differentiation within East Asia.

It is also quite interesting that this distinction also finds parallels in Y-chromosome distribution, with "northern C3" and "southern O3", while an earlier study found greater differentiation between northern and southern Chinese based on mtDNA rather than Y-chromosomes.

The north-south genetic structure of the Han Chinese was made most evident in this recent paper.

You can also take a look at some (non-Han) ethnic groups of China, where differences between northern/southern populations, similar to those discovered in this paper are quite evident.

International Journal of Osteoarchaeology doi:10.1002/oa.1190

Craniofacial variation between southern and northern Neolithic and Modern Chinese

X. J. Wu et al.

Abstract

Previous studies propose that the Yangtze River is the geographic boundary separating northern and southern Chinese populations. In order to test this hypothesis, 19 Neolithic and 15 Modern human cranial samples from north of the Qinling Mountain Range, south of the Yangtze River and in between were chosen for morphometric analysis. Our results indicate that cranial variation exists in Holocene Neolithic and Modern northern and southern Chinese. In the Neolithic sample, the northern Chinese crania are characterised by greater upper face height and orbit height, while the southern Chinese skulls are depicted by a wider nose. The morphology of the crania between the Qinling Mountain range and the Yangtze River feature a mosaic of characters that suggest affiliation with both north and south groups. In the Modern day sample, northern crania are characterised by a broad and wide face, and a tall nose. From the Neolithic to Modern day, a series of microevolutionary processes that apply to both the northern and southern samples can be discerned. Overall, the head gets lower, the face and nose become narrower and the orbits tend to be narrower and higher. Our results support the suggestion that the Qinling Mountain Range and the Yangtze River represent a natural barrier to the movement of Chinese populations. Climatic variation and the transition to an agricultural lifestyle are proposed as the primary factors influencing human craniofacial morphologies.

Link

July 26, 2010

Malana (Himachal Pradesh) autosomal and Y-chromosome study

It would be risky to draw too many conclusions from this: all I can say is that a fairly isolated sample from north India which turns out to be J2- and R1a-dominated is not inconsistent with my own past speculations.

UPDATE

From the paper:
Malana, a remote plateau in the upper reaches (Altitude 2,633 meters) of Parvati valley in Kullu district of Himachal Pradesh, India is an abode to mysterious group of people commonly known as Malanis. Rosser (1955) describes Malana as a hermit village with an aspect of cohesiveness and intense group loyalty that sustains a virulent and suspicious community attitude towards outsiders. Formidable mountain barriers namely Chandrakhani (3,677m); Deo-Tibba (3,732 m) and Rashol Jot (3,238 m) on three sides coupled with the curious efforts of the people to retain their cultural and social uniqueness have ensured virtual biological isolation of the village from the surrounding societies.

and:
We predicted Y chromosome haplogroups from Y-STR data by the use of the Haplogroup Predictor program. The observed haplotypes, predicted haplogroups of the Malana population and the Bayesian probability are reported in Table 4. We found only four haplogroups in the Malana population. Haplogroup J2a1h accounted for 60% of all Y chromosomes. Other haplogroups were R1a (~27%), H (10%) and L (3%). The Bayesian probability was greater than 62% in all the samples.
Hum Biol. 2010 Apr;82(2):123-41.

The Most Ancient Democracy in the World is a Genetic Isolate: An Autosomal and Y-Chromosome Study of the Hermit Village of Malana (Himachal Pradesh, India).

Giroti R, Talwar I.

Abstract

Malana, a small village in Kullu District of Himachal Pradesh, India, has historically been considered a hermit village. Today it has a census size of 1,101 individuals. Geographic, linguistic, and population barriers have contributed to its seclusion. Little is known about the extent to which the population genetically differentiated during the years of isolation. To address this issue, we genotyped 48 Malani individuals at 15 highly polymorphic autosomal STR loci. We found that Malanis have lost some genetic variability compared with the present-day cosmopolitan caste populations and highly mobile pastoral cultures of India. But there is no evidence that they have gone through a severe bottleneck; the average population still shows a mean of 6.86 alleles per locus compared to a mean of 7.80-8.93 for nonisolated populations. An analysis of molecular variance (AMOVA) differentiates Malanis from the rest of the comparison populations. The population structure revealed by multidimensional scaling analysis of standard genetic distances lends support to the AMOVA. Our results are consistent with the social heterogeneity of the Malanis. We also analyzed 17 Y-chromosome STRs in 30 individuals to assess the paternal gene pool. The Malanis are characterized by a generally low Y-chromosome haplotype diversity. A network analysis indicates that two closely related haplotypes account for a large proportion of Malani Y chromosomes. We predicted Y-chromosome haplogroups and found that J2 and R1a were the most prevalent. Genetic drift and limited gene flow leading to reduced genetic diversity were important in determining the present genetic structure of the highly endogamous Malana village.

Link

July 22, 2010

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.

Link

Genomics reveal demographic history of cattle populations

The genomic distinction between B. taurus and B. indicus populations was also detected in another recent paper.

Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2531-9.

Cattle demographic history modelled from autosomal sequence variation.

Murray C, Huerta-Sanchez E, Casey F, Bradley DG.

Abstract

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.

Link

July 21, 2010

Internal diversification of mtDNA haplogroup R0a

Molecular Biology and Evolution, doi:10.1093/molbev/msq178

Internal diversification of mitochondrial haplogroup R0a reveals post-Last Glacial Maximum demographic expansions in South Arabia

Viktor Černý et al.

Abstract

Widespread interest in the first successful Out of Africa dispersal of modern humans 60 – 80 KYA via a southern migration route has overshadowed the study of later periods of South Arabian prehistory. In this work we show that the post-Last Glacial Maximum period of the past 20,000 years, during which climatic conditions were becoming more hospitable, has been a significant time in the formation of the extant genetic composition and population structure of this region. This conclusion is supported by the internal diversification displayed in the highly resolved phylogenetic tree of 89 whole mitochondrial genomes (71 being newly presented here) for haplogroup R0a – the most frequent and widespread haplogroup in Arabia. Additionally, two geographically specific clades (R0a1a1a and R0a2f1) have been identified in non-Arabic speaking peoples such as the Soqotri and Mahri living in the southern part of the Arabian Peninsula where a past refugium was identified by independent archaeological studies. Estimates of time to the most recent common ancestor of these lineages match the earliest archaeological evidence for seafaring activity in the peninsula in the sixth millennium BC.

Link

July 20, 2010

Craniofacial differences between bottle-fed and breastfed people

Eur J Paediatr Dent. 2010 Jun;11(2):87-92.

Comparative study of the craniofacial growth depending on the type of lactation received

Sánchez-Molins M, Grau Carbó J, Ustrell Torrent JM.

Abstract

AIM: Several organizations consider mother's milk the optimal nutrition source for newborns [AAP, 1998; Gartner et al., 1997; Mohrbacher and Stock, 2002; WHO, 1989]. However, there is little scientific evidence supporting the idea that breastfeeding has a positive influence on the development of the orofacial structures. MATERIALS AND METHODS: The study of cases and controls (observational, analytical and retrospective) and lateral teleradiographs of the cranium of 197 patients (106 breast-fed and 91 bottle-fed) were compared. Ricketts, Steiner and McNamara values were used for the cephalometric analysis. Differences between the two groups were analysed by applying the T-test and ANOVA. Statistical significance levels were set at p less than 0.05. Non-nutritive infantile sucking habits have been compared; differences between the two groups were analysed by applying the Chi-square test. RESULTS: First, the upper incisors were found to be protruded in the bottle-fed group. Second, subjects belonging to the breast-fed group displayed a brachycephalic mandible arch, while those fed with bottle had a dolichocephalic Steiner mandibular plane. Third, both facial depth and distance of the pogonion to the perpendicular nasion presented a certain tendency to a retruded mandibular bone in the bottle-fed group. And fourth, the frequency of use of dummy and thumb suction were greater in the bottle feed group, without statistical significance. CONCLUSION: In addition to the multiple advantages that mother's milk offers to newborns, breastfeeding also helps correct orofacial development (not only for the incisors position, but also for the vertical and sagittal relations of the mandible with upper maxillary and cranial basis).

Link

July 16, 2010

Breastfeeding and IQ (Steer et al. 2010)

The new article references an older article by Caspi et al, which studied the moderation of the association between breastfeeding and IQ by a genetic variant in FADS2:
Children's intellectual development is influenced by both genetic inheritance and environmental experiences. Breastfeeding is one of the earliest such postnatal experiences. Breastfed children attain higher IQ scores than children not fed breast milk, presumably because of the fatty acids uniquely available in breast milk. Here we show that the association between breastfeeding and IQ is moderated by a genetic variant in FADS2, a gene involved in the genetic control of fatty acid pathways. We confirmed this gene–environment interaction in two birth cohorts, and we ruled out alternative explanations of the finding involving gene–exposure correlation, intrauterine growth, social class, and maternal cognitive ability, as well as maternal genotype effects on breastfeeding and breast milk. The finding shows that environmental exposures can be used to uncover novel candidate genes in complex phenotypes. It also shows that genes may work via the environment to shape the IQ, helping to close the nature versus nurture debate.
The current study's sample:
In all, 5934 children of white European origin had genetic data with additional information on breastfeeding and IQ. Of these 83% were breastfed within the first month. These children had means (SDs) of 108 (16), 100 (17) and 105 (16) for verbal, performance and full-scale IQ respectively.
The breastfeeding association:
Breastfeeding showed a strong association with full-scale IQ with breastfed children scoring 8 points higher IQ on average in unadjusted analyses as has been previously reported [2], [3]. There were strong associations between breastfeeding and most confounders (see Table S2). The breastfeeding effect attenuated to a 3-point advantage after adjustment for these confounders (see Table 2).
The important caveat, referring to this earlier paper by Der et al. From the current paper:
A limitation of this study was the risk of bias due to the lack of controlling for other potentially important factors such as maternal IQ [34], maternal fish consumption during lactation and the ratio of omega-6 to omega-3 fatty acids. These data were not available within ALSPAC. However data on maternal educational qualifications were available. This measure is likely to be highly correlated with maternal IQ and more strongly related than other measures of education such as years of schooling. In addition, adjustment for educational qualifications did not change the conclusions despite being an important predictor of child IQ (p less than 0.001).
What Der et al. had proposed is that smart mothers breastfeed more, so the association between IQ and breastfeeding reflects the heredity of maternal IQ rather than benefits of the breastfeeding practice itself. The current study has used maternal educational qualifications as a proxy for IQ. This is unsatisfactory as education is not as tightly coupled with IQ as would be necessary to let us discount maternal IQ as a source of the breastfed children IQ's increase:

As I have noted in a previous post, extreme care is needed when using proxy variables. You can mentally analyze the IQ-educational attainment relationship into two parts:
  1. Different educational levels (e.g., high school graduates vs. Master's holders) have different average IQ
  2. Within educational levels (e.g., high school graduates) there is variation in IQ. Moreover, there is IQ overlap between educational levels
Using educational level as a proxy for IQ allows us to capture part of the maternal IQ variation. However, if maternal IQ and breastfeeding within an educational level are correlated, then the use of educational level as a proxy for IQ underestimates for the strength of the relationship.

The "meat" of the paper involves the effect of genotype on the IQ/breastfeeding association:






The fact that genotype in the two studied loci modifies the IQ/breastfeeding relationship is evident and needs no further comment.

The discussion of the paper goes into some detail on the technical reasons for the discrepancy between this study and Caspi et al.
PLoS ONE 5(7): e11570. doi:10.1371/journal.pone.0011570

FADS2 Polymorphisms Modify the Effect of Breastfeeding on Child IQ

Colin D. Steer et al.

Background
Breastfeeding is important for child cognitive development. A study by Caspi et al has suggested that rs174575 within the FADS2 gene moderates this effect so that children homozygous in the minor allele (GG genotype) have similar IQs irrespective of feeding method.

Methods and Principal Findings
In our study of 5934 children aged 8 years, no genetic main effect with IQ was found for rs174575. However, an interaction with this polymorphism was observed such that breastfed GG children performed better than their formula fed counterparts by an additional 5.8 points [1.4, 10.1] (interaction p = 0.0091). Interaction results were attenuated by about 10% after adjustment for 7 factors. This study also investigated rs1535, another FADS2 polymorphism in linkage disequilibrium with rs174575, together with performance and verbal IQ, finding similar results although effect sizes were generally reduced.

Conclusions and Significance
This study did not replicate the findings of Caspi et al. In contrast to their study, GG children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed GG children performed worse than other children on formula milk. Further studies are required to replicate these findings.

Link

July 14, 2010

mtDNA of Yemeni and Ethiopian Jews

From the paper:
Mitochondrial DNA analysis also revealed a high diversity of sub-Saharan African and Eurasian haplotypes in both the Yemenite and Ethiopian Jewish populations (see Fig. 2). Specifically, common haplotypes (haplotypes present at [5%) in Yemenite Jews include the African haplogroup L3x1 and Eurasian haplogroups R0a (renamed from (preHV)1 (Torroni et al., 2006), HV1, J2a1a [renamed from J1b (Palanichamy et al., 2004)] K, R2, U, and U1, and in Ethiopian Jews include African haplogroups L2a1b2 and L5a1 and Eurasian haplogroups R0a and M1a1 (see Fig. 2). Overall, sub-
Saharan African L haplotypes [hereafter referred to as L(xM,N), i.e., all African haplotypes except M and N, following the nomenclature of Behar et al. (2008)], comprise a large proportion of the genetic variation in both Jewish populations, representing 20% in the Yemenite Jews and 50% in Ethiopian Jews. This high frequency contrasts with other Jewish populations, such as Near Eastern and Ashkenazi Jews, who almost entirely lack L(xM,N) haplogroups (Thomas et al., 2002; Richards et al., 2003).
I think that the authors' conclusion that Yemenite Jews are partially descended from Israeli exiles is premature. Sure, they can exclude large-scale introgression of Yemeni mtDNA, but the universe of possibilities is not limited to either Israeli or Yemenite.

The way I see it, only a large-scale study of all global Jewish populations may uncover verified ancient Jewish lineages for both Y-chromosomes and mtDNA. The recent studies on Jews have uncovered several genetic sub-clusters of Jews, and only lineages that occur in 2 or more of these clusters, and preferably geographically separated ones have a strong claim of representing original Jewish lineages. There is a limit on what can be uncovered about the past from the study of living populations.

American Journal of Physical Anthropology doi: 10.1002/ajpa.21360

Mitochondrial DNA reveals distinct evolutionary histories for Jewish populations in Yemen and Ethiopia

Amy L. Non et al.

Abstract

Southern Arabia and the Horn of Africa are important geographic centers for the study of human population history because a great deal of migration has characterized these regions since the first emergence of humans out of Africa. Analysis of Jewish groups provides a unique opportunity to investigate more recent population histories in this area. Mitochondrial DNA is used to investigate the maternal evolutionary history and can be combined with historical and linguistic data to test various population histories. In this study, we assay mitochondrial control region DNA sequence and diagnostic coding variants in Yemenite (n = 45) and Ethiopian (n = 41) Jewish populations, as well as in neighboring non-Jewish Yemeni (n = 50) and Ethiopian (previously published Semitic speakers) populations. We investigate their population histories through a comparison of haplogroup distributions and phylogenetic networks. A high frequency of sub-Saharan African L haplogroups was found in both Jewish populations, indicating a significant African maternal contribution unlike other Jewish Diaspora populations. However, no identical haplotypes were shared between the Yemenite and Ethiopian Jewish populations, suggesting very little gene flow between the populations and potentially distinct maternal population histories. These new data are also used to investigate alternate population histories in the context of historical and linguistic data. Specifically, Yemenite Jewish mitochondrial diversity reflects potential descent from ancient Israeli exiles and shared African and Middle Eastern ancestry with little evidence for large-scale conversion of local Yemeni. In contrast, the Ethiopian Jewish population appears to be a subset of the larger Ethiopian population suggesting descent primarily through conversion of local women.

Link

July 13, 2010

Early Holocene human remains from the Argentinean Pampas

Related:

American Journal of Physical Anthropology doi:10.1002/ajpa.21347

Early Holocene human remains from the Argentinean Pampas: Additional evidence for distinctive cranial morphology of early South Americans

Héctor M. Pucciarelli et al.

The cranial morphology of Early Holocene American human samples is characterized by a long and narrow cranial vault, whereas more recent samples exhibit a shorter and wider cranial vault. Two hypotheses have been proposed to account for the morphological differences between early and late-American samples: (a) the migratory hypothesis that suggests that the morphological variation between early and late American samples was the result of a variable number of migratory waves; and (b) the local diversification hypothesis, that is, the morphological differences between early and late American samples were mainly generated by local, random (genetic drift), and nonrandom factors (selection and phenotypic plasticity). We present the first craniometric study of three early skulls from the Argentinean Pampas, dated 8,000 cal. years BP (Arroyo Seco 2, Chocorí, and La Tigra), and one associated with mega-faunal remains (Fontezuelas skull). In addition, we studied several Late Holocene samples. We show that the skulls from the Argentinean Pampas are morphologically similar to other Early Holocene American skulls (i.e., Lagoa Santa from Brazil, Tequendama, Checua, and Aguazuque from Colombia, Lauricocha from Peru, and early Mexicans) that exhibit long and narrow cranial vaults. These samples differ from the Late Holocene American samples that exhibit a shorter and wider cranial vault. Our results underscore the important differences in cranial morphology between early and late-American samples. However, we emphasize the need for further studies to discuss alternative hypotheses regarding such differences.

Link

Genome-wide association study of neuroticism

This genome-wide study suggests that common variation is not related to neuroticism, and that individual loci have at most a 2% share in its heritability. It is interesting to compare this study with the recent one on height, where a larger number of individuals (~4k) were studied on a smaller number of SNPs (~300k). Are there many SNPs with effects on neuroticism that may have been detected if a larger number of individuals were sampled? I doubt it for two reasons (i) the number of individuals sampled here is not that lower than in the height study, and (ii) neuroticism is a made-up construct that can be imperfectly measured with psychometric testing, while height is a physical reality that can be measured objectively. So, while neuroticism does have a correspondence to brain function, it is much more difficult to discover what it is.

PLoS ONE 5(7): e11504. doi:10.1371/journal.pone.0011504

A Genome-Wide Association Study of Neuroticism in a Population-Based Sample

Federico C. F. Calboli et al.

Abstract

Neuroticism is a moderately heritable personality trait considered to be a risk factor for developing major depression, anxiety disorders and dementia. We performed a genome-wide association study in 2,235 participants drawn from a population-based study of neuroticism, making this the largest association study for neuroticism to date. Neuroticism was measured by the Eysenck Personality Questionnaire. After Quality Control, we analysed 430,000 autosomal SNPs together with an additional 1.2 million SNPs imputed with high quality from the Hap Map CEU samples. We found a very small effect of population stratification, corrected using one principal component, and some cryptic kinship that required no correction. NKAIN2 showed suggestive evidence of association with neuroticism as a main effect (p less than 10−6) and GPC6 showed suggestive evidence for interaction with age (p≈10−7). We found support for one previously-reported association (PDE4D), but failed to replicate other recent reports. These results suggest common SNP variation does not strongly influence neuroticism. Our study was powered to detect almost all SNPs explaining at least 2% of heritability, and so our results effectively exclude the existence of loci having a major effect on neuroticism.

Link

July 12, 2010

Mathematical structure of Platonic dialogues (?)

J. B. Kennedy proposes that Plato organized his dialogues in mathematical form. His argument is mostly found in 'Plato's Forms, Pythagorean Mathematics, and Stichometry', but there is some interesting additional material in his site, and, apparently, a planned book on the subject. The story has found its way to the popular press, without, unfortunately, a lack of journalistic hyperbole thrown in.

I was first suspicious of the notion of a Plato Code, as the name itself reminds one of the discredit Bible Code, but Kennedy proposes something more down-to-earth, namely that Plato used Pythagorean musical principles in the organization of his dialogues. Three main claims stand out: (i) that dialogues have an internal organization in which high points are placed in 1/12ths, corresponding to notes of a musical scale, (ii) that positive and negative turns of the dialogue correspond to consonant intervals of the scale, and this may allow us to discover what Plato "really thought" in open-ended dialogues, and (iii) that different dialogues have a different length of their 1/12th unit, which stretch from 100 lines for the Apology to 1000 lines for the Republic and 1200 lines for the Laws. Kennedy makes several interesting observations on his material, including an apparent lack of this mathematical structure in some of the Platonica that are universally acknowledged to be spurious.

Is it plausible that Plato went into all this trouble? Kennedy cites some pieces of evidence in favor of his Platonic stichometry thesis. In my opinion, the thesis is plausible: the "secret structure" may sound like a conspiracy theory, yet Plato himself (in the 7th epistle) argued against revealing the highest doctrines to the polloi, and (in the Republic) proposed that the advanced study of geometry and astronomy should be revealed -after preparation- to the guardian class. The idea that Plato had a secret mathematical doctrine, discussed only within the walls of the Academy, also finds support in Aristotle, who recounts the tale of Plato's Lecture on the Good, which ended in disaster when Plato attempted to present his geometrical arguments about the One to a lay audience. And, the relationship between the world created by the demiurge, music, and mathematical proportion is famously presented in the Timaeus.

Could it be that as the Timaean demiurge looked at the eternal model of number and proportion to fashion the universe as an expression of a musical scale, so did Plato, as the demiurge of his philosophical universe? It is an intriguing idea.

Even though Kennedy's thesis does not sound like a simple case of quackery, and circumstantial evidence lends it a level of initial credibility, the main weakness of the paper is its lack of statistical elaboration, and its reliance on expert judgments.

Perhaps there is evidence that key themes coincide with 1/12ths, but how many key themes are placed in-between notes? A thorough breakdown of the dialogues based on who is speaking, the topic of discussion, the tone, etc. would allow us to better appreciate whether or not the proposed structure actually exists.

July 11, 2010

mtDNA of Tibet

American Journal of Physical Anthropology doi:10.1002/ajpa.21350

A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum

Zhendong Qin et al.

ABSTRACT

As the highest plateau surrounded by towering mountain ranges, the Tibetan Plateau was once considered to be one of the last populated areas of modern humans. However, this view has been tremendously changed by archeological, linguistic, and genetic findings in the past 60 years. Nevertheless, the timing and routes of entry of modern humans into the Tibetan Plateau is still unclear. To make these problems clear, we carried out high-resolution mitochondrial-DNA (mtDNA) analyses on 562 Tibeto-Burman inhabitants from nine different regions across the plateau. By examining the mtDNA haplogroup distributions and their principal components, we demonstrated that maternal diversity on the plateau reflects mostly a northern East Asian ancestry. Furthermore, phylogeographic analysis of plateau-specific sublineages based on 31 complete mtDNA sequences revealed two primary components: pre-last glacial maximum (LGM) inhabitants and post-LGM immigrants. Also, the analysis of one major pre-LGM sublineage A10 showed a strong signal of post-LGM population expansion (about 15,000 years ago) and greater diversity in the southern part of the Tibetan Plateau, indicating the southern plateau as a refuge place when climate dramatically changed during LGM.

Link

July 10, 2010

Dolichofacial bed wetters

The abstract mentions a study of the cephalic index (which measures the shape of the head), but uses the adjective "dolichofacial" (which refers to a long face). It is not clear to me what exactly correlates with nocturnal enuresis, but, it is quite interesting that something does. In any case, the cephalic and facial indices are generally correlated in Caucasoid populations. This is why the long-faced/long-headed (aka Nordic-Mediterranean) and broad-faced/broad-headed (aka Alpine) combinations are termed harmonic, while the long-faced/broad-headed (aka Dinaric-Armenoid) and broad-faced/long-headed (aka Cro-Magnoid) are termed dysharmonic.

My completely speculative hypothesis is that the phenomenon is related to balance, as a long head would tend to rotate around the neck much easier than a short one, due to the greater torque that develops in an oblong object (in the supine position). Our heads do not normally wobble left and right because of our neck muscles, and the added effort needed to maintain a longer head in supine position may cause discomfort/strain during sleep, and hence enuresis.


Sleep Breath. 2010 Jul 6. [Epub ahead of print]

Facial patterns and primary nocturnal enuresis in children.

Carotenuto M, Esposito M, Pascotto A.

Abstract

PURPOSE: Aims of our study are evaluating: (1) the prevalence of dolicofacial pattern among enuretic and control-group children, (2) the prevalence of an abnormal head posture in bedwetters, and (3) the correlation with sleep-related breathing disorders (SRBD) identified by polysomnography (PSG) recording. Nocturnal enuresis is a multifactorial disease, but has been related also to obstructive sleep-disordered breathing in both adults and children. Anatomical factors recognized to predispose to SRBD include adenotonsillar hypertrophy, neuromuscular disorders, craniofacial abnormalities associated with macroglossia, retrognathia or maxillary hypoplasia, and obesity. METHODS: Two hundred seventy enuretic children aged 7-12 years (mean 9.62 +/- 2.31) were compared with a control-matched group of 274 children. To screen nocturnal sleep habits, all subjects' mothers filled out the Sleep Disturbance Scale for Children. Among these scales, only SBD scale was taken into account. Sleep breathing disorders (SBD) scale is composed of three items: sleep breathing difficulties, sleep apnea, and snoring. Cephalic index was calculated for each patient in order to identify facial patterns. An overnight PSG was performed in 28 (15 males, 13 females), randomly chosen, enuretic children and in 38 healthy volunteer controls (18 males, 20 females) matched for age (8.73 +/- 0.79 vs. 9.12 +/- 1.23; p = 0.147) and sex distribution (chi-square = 0.062; p = 0.803). RESULTS: Bedwetters show different sleep habits, higher prevalence of dolicofacial pattern, and abnormal head posture more than controls. CONCLUSIONS: Our preliminary study support further investigation of usage of the cephalic index as a predictor of SRBD.

Link

July 09, 2010

Admixture mapping panels for African Americans (Chen et al. 2010)

From the paper:
Averaged genome-wide, the individual proportion of European ancestry was 0.192 ± 0.098, 0.193 ± 0.098, and 0.264 ± 0.106 among normotensive subjects and 0.196 ± 0.119, 0.196 ± 0.119, and 0.268 ± 0.109 among hypertensive subjects, for the panels based on δ, FST, and 21k random markers, respectively.
also:
The number of generations since the original admixture event based on our sample of African Americans was estimated at 7.44 ± 3.35 and 7.33 ± 3.01 generations for the panels based on δ and FST, respectively.
Obviously admixture between Europeans and Sub-Saharan Africans did not occur instantaneously, but these numbers provide a good time frame of about 2-3 centuries ago (if we also take into account that African Americans studied here where not born yesterday). This seems like a reasonable midpoint between the present and the initiation of the Atlantic slave trade.

BMC Genomics
doi:10.1186/1471-2164-11-417

Development of admixture mapping panels for African Americans from commercial high-density SNP arrays

Guanjie Chen et al.

Abstract (provisional)

Background
Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs) for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined.

Results
We developed two panels of AIMs (~2,000 markers each) based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area.

Conclusions
Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1) no de novo genotyping needs to be done, thereby saving costs, and (2) markers can be filtered for various quality measures and replacement markers (to minimize gaps) can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1) the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2) clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from SNP chip genotype data provides a fresh opportunity to conduct admixture mapping for disease genes in admixed populations when genome-wide association data exist or are planned.

July 08, 2010

Persistence of gender gap in top science and math performance

From the press release:
A study that examined 30 years of standardized test data from the very highest-scoring seventh graders has found that performance differences between boys and girls have narrowed considerably, but boys still outnumber girls by more than about 3-to-1 at extremely high levels of math ability and scientific reasoning.

At the same time, girls slightly outnumber boys at extremely high levels of verbal reasoning and writing ability.
Intelligence Volume 38, Issue 4, July-August 2010, Pages 412-423

Sex differences in the right tail of cognitive abilities: A 30 year examination

Jonathan Wai et al.

Abstract

One factor in the debate surrounding the underrepresentation of women in science technology, engineering and mathematics (STEM) involves male–female mathematical ability differences in the extreme right tail (top 1% in ability). The present study provides male–female ability ratios from over 1.6 million 7th grade students in the right tail (top 5% in ability) across 30 years (1981–2010) using multiple measures of math, verbal, and writing ability and science reasoning from the SAT and ACT. Male–female ratios in mathematical reasoning are substantially lower than 30 years ago, but have been stable over the last 20 years and still favor males. Over the last two decades males showed a stable or slightly increasing advantage in science reasoning. However, more females scored in the extreme right tail of verbal reasoning and writing ability tests. The potential role of sociocultural factors on changes in the male–female ability ratios is discussed and the introduction of science reasoning as a potential new factor in the debate is proposed. The implications of continued sex differences in math and science reasoning is discussed within the context of the many important interlocking factors surrounding the debate on the underrepresentation of women in STEM.

July 07, 2010

Genetic structure of cattle in Eurasia

The mixed (east-west) affiliation of Mongolian cattle parallels the mixed affiliation of Mongolians themselves. The Caucasoids do not appear to have penetrated east of Lake Baikal, and some Caucasoid-influenced populations that live to the east of that frontier are thought to have originated there. Thus, the evidence from cattle complements that from physical anthropology and human population genetics to fix the border between the Western and Eastern Eurasian spheres of influence.

Anim Sci J. 2010 Jun 1;81(3):281-9.

Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers.

Lin BZ, Sasazaki S, Mannen H.

Abstract

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.

Link

July 06, 2010

The WEIRDest people in the world

There is a freely available version of this article here (pdf).

Behav Brain Sci. 2010 Jun;33(2-3):61-83. Epub 2010 Jun 15.

The weirdest people in the world?

Henrich J, Heine SJ, Norenzayan A.

Abstract

Behavioral scientists routinely publish broad claims about human psychology and behavior in the world's top journals based on samples drawn entirely from Western, Educated, Industrialized, Rich, and Democratic (WEIRD) societies. Researchers - often implicitly - assume that either there is little variation across human populations, or that these "standard subjects" are as representative of the species as any other population. Are these assumptions justified? Here, our review of the comparative database from across the behavioral sciences suggests both that there is substantial variability in experimental results across populations and that WEIRD subjects are particularly unusual compared with the rest of the species - frequent outliers. The domains reviewed include visual perception, fairness, cooperation, spatial reasoning, categorization and inferential induction, moral reasoning, reasoning styles, self-concepts and related motivations, and the heritability of IQ. The findings suggest that members of WEIRD societies, including young children, are among the least representative populations one could find for generalizing about humans. Many of these findings involve domains that are associated with fundamental aspects of psychology, motivation, and behavior - hence, there are no obvious a priori grounds for claiming that a particular behavioral phenomenon is universal based on sampling from a single subpopulation. Overall, these empirical patterns suggests that we need to be less cavalier in addressing questions of human nature on the basis of data drawn from this particularly thin, and rather unusual, slice of humanity. We close by proposing ways to structurally re-organize the behavioral sciences to best tackle these challenges.

Link

July 05, 2010

The genius of Archimedes

The conference program of the conference that took place in Syracuse a few weeks ago. The proceedings from Springer.

A few interesting papers from the volume:

Archimedes’ Cannons Against the Roman Fleet?

Cesare Rossi

In the paper is discussed the possibility that Archimedes built and used against the Roman fleet a steam cannon. It is well-known that Archimedes, during the siege of Syracuse, designed and built several war machines to fight against the Romans. Among these war machines, the legend about the large concave mirrors that concentrated the sun rays burning the Roman ships is rather interesting. On this topic are also interesting some drawings by Leonardo Da Vinci where a steam cannon is described and attributed to Archimedes. Starting from passages by ancient Authors (mainly Plutarchos, Petrarca and Da Vinci), the author investigates on the possibility that Archimedes built a steam cannon and used it to hit the Roman ships with incendiary proiectiles.

Archimedes Arabicus. Assessing Archimedes’ Impact on Arabic Mechanics and Engineering

Constantin Canavas

Archimedes is an author who is frequently quoted in Arabic texts in relationship with mathematics and mechanics, including hydraulic devices such as water-clocks. The present study traces transmission paths and evidence for an assessment of the impact of the Archimedean works on the Arabic tradition of mechanics and hydraulics.


The Heritage of Archimedes in Ship Hydrostatics: 2000 Years from Theories to Applications


Horst Nowacki

Archimedes left to posterity his famous treatise “On Floating Bodies”, which establishes the physical foundations for the floatability and stability of ships and other maritime objects. Yet since this treatise was long lost and also simply ignored by practitioners, it took many centuries before Archimedes’ brilliant insights were actually applied in ship design and ship safety assessment. This article traces the tedious acceptance of Archimedes’ principles of hydrostatics and stability in practical applications. It will document important milestones and explain how this knowledge was passed down through the centuries and ultimately spread into ship design practice.

Archimedean Science and the Scientific Revolution

Agamenon R. E. Oliveira

According to Richard Westfall (Westfall, 1977) the Scientific Revolution of the seventeenth century was dominated by two themes: the Platonic-pythagorean tradition “which looked on nature in geometric terms” and mechanical philosophy “which conceived of nature as a huge machine”. This paper is an attempt to study the appropriation of Archimedean science in the Scientific Revolution in Western Europe.

The Influence of Archimedes in the Machine Books from the Renaissance to the 19th Century

Francis C. Moon

The influence of Archimedes on the so-called theatre of machines books is reviewed using original manuscripts from the 15th to the 19th centuries. The evidence shows continuity of knowledge of ancient Greek theory of machines as well as Archimedes principles of statics, hydrostatics and concepts of centers of gravity on the development of machine science.

July 04, 2010

Mediterranean diet changes gene expression to fight disease

The FASEB Journal. 2010;24:2546-2557 doi: 10.1096/fj.09-148452

In vivo nutrigenomic effects of virgin olive oil polyphenols within the frame of the Mediterranean diet: a randomized controlled trial

Valentini Konstantinidou et al.

The aim of the study was to assess whether benefits associated with the traditional Mediterranean diet (TMD) and virgin olive oil (VOO) consumption could be mediated through changes in the expression of atherosclerosis-related genes. A randomized, parallel, controlled clinical trial in healthy volunteers (n=90) aged 20 to 50 yr was performed. Three-month intervention groups were as follows: 1) TMD with VOO (TMD+VOO), 2) TMD with washed virgin olive oil (TMD+WOO), and 3) control with participants’ habitual diet. WOO was similar to VOO, but with a lower polyphenol content (55 vs. 328 mg/kg, respectively). TMD consumption decreased plasma oxidative and inflammatory status and the gene expression related with both inflammation [INF- (INF), Rho GTPase-activating protein15 (ARHGAP15), and interleukin-7 receptor (IL7R)] and oxidative stress [adrenergic β2-receptor (ADRB2) and polymerase (DNA-directed) (POLK)] in peripheral blood mononuclear cells. All effects, with the exception of the decrease in POLK expression, were particularly observed when VOO, rich in polyphenols, was present in the TMD dietary pattern. Our results indicate a significant role of olive oil polyphenols in the down-regulation of proatherogenic genes in the context of a TMD. In addition, the benefits associated with a TMD and olive oil polyphenol consumption on cardiovascular risk can be mediated through nutrigenomic effects.

Link

July 03, 2010

Y chromosomes of Arbereshe from Calabria

From the paper:
The Arbereshe are one of the largest linguistic minorities in Italy. They are the result of complicated movements of Albanians around the end of the 15th and beginning of the 16th century, often linked to the invasion of the Balkans by the Ottoman Empire. Despite that, it is generally agreed that most of the immigrants started moving from the south of Albania (Toskeria), with, very often, intermediate steps in Greece, particularly in the Peloponnese (Zangari 1941). Further evidence is provided by linguistic research, according to which Arberisht, the language spoken by Arbereshe, is part of the Tosk dialect group of Albanian, a language originally spoken in Toskeria (Babiniotis 1998).
On the sample:
The Arbereshe Y-chromosome variation was investigated by sampling individuals from different villages of the Pollino area (Calabria) who bear one of the founding surnames of the population. The genotyping was performed using 12 microsatellites (STRs) and 31 unique event polymorphisms (UEPs), defining, respectively, haplotypes and haplogroups. The Italian and Balkan genetic backgrounds were explored using the large amount of data provided by recent Y-chromosome studies in the two peninsulas and by literature data on STRs from forensic research.
Comparison of Y-haplogroup frequency and diversity between Albanians from Tirana and Arbereshe from Calabria (from Table III):


The presence of F*(xG,I,J,K) in Albanians is interesting as this occurs in Romania and Bosnia Herzegovina (all groups), and in South Apulia, It could potentially be haplogroup H and may reflect a Gypsy element that was not present when the Arbereshe moved to Italy from the Balkans.

Haplogroup I shows similar frequencies, but:
I-M170 is the most common Balkan haplogroup (Pericic et al. 2005a,b) and the second most frequent Arbereshe clade. Nevertheless, analysis of its network reveals unexpected results: most of the Arbereshe I-M170 haplotypes are not included in the Balkan cluster (Figure 3), but are located in the long branches containing mainly Italian chromosomes. Comparisons with literature data (Semino et al. 2000; Barac et al. 2003, Rootsi et al. 2004) show that the core haplotype of the Balkan cluster (16-14-15-13-31-24-11-11-13; locus order as above) is consistent with the almost Balkan exclusive I2a (formerly I1b) clade. The proposed interpretation of the Arbereshe as a proxy of the founder Albanian population leads us to hypothesize that the I2a clade was less common in the southern Balkans 500 years ago than nowadays. The very tight shape of the I2a cluster in the network suggests a very recent expansion of this haplogroup in the southern Balkans. Furthermore, I2a is still rare in
mountain populations such as the Albanians of Kosovo (Pericic et al. 2005a,b) and in a randomly selected Arbereshe sample from Rootsi et al. (2004).
This is an interesting finding in the light of recent evidence for selection in Y-haplogroup I.

The situation with J2 is also quite interesting as this is rarer in Arbereshe (3%) than Albanians (17%):
The scarcity of J2 chromosomes in the Arbereshe sample (1/40) is very difficult to explain, given that they are very common in both the Italian peninsula and the southern Balkans. Literature data on J2 indicate that most of the haplotypes included in the Balkan (B) cluster of the network (Figure 3) have an STR configuration consistent with the J2-M12 sub-clade (Di Giacomo et al. 2004; Semino et al. 2004; Cruciani et al. 2007). In contrast, most of the haplotypes in the other clusters agree with the STR configuration given for the J2-M67 clade, with its sub-clade J2-M92 (Di Giacomo et al. 2004). It is unconvincing to attribute the rarity of J2 in the Arbereshe to random sampling or to the effect of genetic drift. Furthermore, the Arbereshe sample analysed by Semino et al. (2004) also completely lacks the typically Balkan J2-M12 chromosomes. If we interpret our Arbereshe sample as representative of the founding Albanian population, we may hypothesize that the J2 haplogroup was considerably less diffuse in the southern Balkans five centuries ago than today.
What we can conclude from this study is that the founding Albanian population was J2- and I2a- lite compared to modern Albanians. The source for the I2a seems to be either the Albanization of people from the West Balkans and/or selection, although it would be difficult to see a massive increase in frequency in only five centuries. The I2a-deficiency of the Arbereshe also gives support to the theory that the Albanians are relatively recent arrivals from the northeast; this theory has been upheld in the past on the basis of the (i) their historical obscurity until the last millennium, and (ii) the paucity of native sea terms and Greek loanwords in Albanian, which is difficult to explain if Albanians always occupied their current location on the Adriatic.

The source of J2 is less clear, and could be either the Albanization of Greeks (the only Balkan population with a sizeable J2 frequency) or remnants of Muslim Anatolians from Ottoman times. However, modern Albanians belong mainly to clade J2b, while Anatolians belong to J2a. Thus, I tend to dismiss the Anatolian connection.

The low frequency of R1*x(R1a1) in the Arbereshe, together with the high E1b1b1a frequency are quite convincing of the Balkan origins of this population.

Ann Hum Biol.
2010 Jun 22. [Epub ahead of print]

Linking Italy and the Balkans. A Y-chromosome perspective from the Arbereshe of Calabria.

Boattini A, Luiselli D, Sazzini M, Useli A, Tagarelli G, Pettener D.

Abstract

Background: The Arbereshe are an Albanian-speaking ethno-linguistic minority who settled in Calabria (southern Italy) about five centuries ago. Aim: This study aims to clarify the genetic relationships between Italy and the Balkans through analysis of Y-chromosome variability in a peculiar case study, the Arbereshe. Subject and methods: Founder surnames were used as a means to identify a sample of individuals that might trace back to the Albanians at the time of their establishment in Italy. These results were compared with data of more than 1000 individuals from Italy and the Balkans. Results: The distributions of haplogroups (defined using 31 UEPs) and haplotypes (12 STRs) show that the Italian and Balkan populations are clearly divergent from each other. Within this genetic landscape, the Arbereshe are characterized by two peculiarities: (a) they are a clear outlier in the Italian genetic background, showing a strong genetic affinity with southern Balkans populations; and (b) they retain a high degree of genetic diversity. Conclusion: These results support the hypothesis that the surname-chosen Arbereshe are representative of the Y-chromosome genetic variability of the Albanian founder population. Accordingly, the Arbereshe genetic structure can contribute to the interpretation of the recent biological history of the southern Balkans. Intra-haplogroup analyses suggest that this area may have experienced important changes in the last five centuries, resulting in a marked increase in the frequency of haplogroups I2a and J2.

Link

July 02, 2010

Admixture in Uyghurs (again)

Gene Expression points me to this letter which suggests that Western Eurasian admixture in Uyghurs has been overestimated in previous studies. They base their claim on the alleged low population coverage of previous studies. I don't buy their argument, mainly because of Behar et al. (2010) which has as good a coverage of Eurasia as one might hope for, and finds (expectedly) Uyghurs to be about a 50-50 Caucasoid/Mongoloid mix. The same is also true for Hazara, shown by the authors as majority Mongoloid, but revealed by Behar et al. (2010) to be about 50-50 as well.

The authors make another claim:
STRUCTURE cannot distinguish recent admixture from a cline of other origin, and these analyses cannot prove admixture in the Uyghurs; however, historical records indicate that the present Uyghurs were formed by admixture between Tocharians from the west and Orkhon Uyghurs (Wugusi-Huihu, according to present Chinese pronunciation) from the east in the 8th century CE.14 The Uyghur Empire was originally located in Mongolia and conquered the Tocharian tribes in Xinjiang. Tocharians such as Kroran have been shown by archaeological findings to appear phenotypically similar to northern Europeans,15 whereas the Orkhon Uyghur people were clearly Mongolians. The two groups of people subsequently mixed in Xinjiang to become one population, the present Uyghurs. We do not know the genetic constitution of the Tocharians, but if they were similar to western Siberians, such as the Khanty, admixture would already be biased toward similarity with East Asian populations.
First of all, the authors forget about the eastern Iranian peoples (Sakas) who most surely were present among the ancestors of the Uyghurs. Second, there is no reason to think that Tocharians were similar to the Khanty, a population with a substantial presence of northern Eurasian Y-haplogroup N does not make a link with Uyghurs likely.

Am J Hum Genet. 2009 December 11; 85(6): 934–937.

Genetic Landscape of Eurasia and “Admixture” in Uyghurs

Hui Li et al.

Link

Recent Tibetan adaptation for high altitude

From the New Scientist:
Mountain-dwelling Tibetans have genetically adapted to life at altitude in the past 3000 years – the fastest genetic change known to have occurred in humans.

Rasmus Nielsen at the University of California, Berkeley, and his colleagues looked at the DNA of people living in two villages at 4300 and 4600 metres above sea level in Tibet. At these heights, oxygen levels are about 40 per cent lower than at sea level and lowlanders experience hypoxia, which is associated with headaches, fatigue, smaller fetuses and more deaths in infancy.

Tibetans don't suffer from hypoxia, but it has been unclear why. Nielsen's team compared the DNA of 50 Tibetans with that of 40 Han Chinese people from Beijing and 200 people of European ancestry from Denmark, all of whom live at altitudes below 2000 metres.

By comparing the DNA of the three groups, the team identified the specific genetic differences between the Tibetan and Han populations, thought to have diverged around 2750 years ago.
Science Vol. 329. no. 5987, pp. 72 - 75
DOI: 10.1126/science.1189406

Genetic Evidence for High-Altitude Adaptation in Tibet

Tatum S. Simonson et al.

Abstract

Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in several regions that contain genes whose products are likely involved in high-altitude adaptation. Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia-response pathways in humans.

Link
Science Vol. 329. no. 5987, pp. 75 - 78
DOI: 10.1126/science.1190371

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

Xin Yi et al.

Abstract

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP’s association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.

Link