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:

• Ancient Viking mtDNA from Denmark
• Iron Age, Viking Age, and Eskimo mtDNA
• Ancient mtDNA from Iron Age Denmark
• mtDNA of an early Danish sample
• Modern Scandinavians descended (maybe) from Neolithic TRB but not Mesolithic Pitted Ware ancestors
• Some mtDNA links between Asia and Europe

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

Guess their origin

Vote in the poll and/or comment.

Where are they from?
	Austria
	Denmark
	Ireland
	Italy
	Netherlands
	Portugal
	Romania
	Scotland
	Spain
	Switzerland
Free polls from Pollhost.com

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

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

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

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

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

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

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

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.

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