YHRD frequency calculation

YHRD has a new tool available called "Frequency calculation". At present, you can enter a minimal Y-chromosome haplotype, and you get the frequency of your haplotype in three European "meta-populations" viz. Western European, Eastern European, and South-eastern European.

My results indicate a frequency of my haplotype in the ratio of 1 : 1.20 : 4.98 in the three meta-populations - which sounds reasonable. By calculating such an odds ratio, you may get a quick guess of where in Europe a haplotype may be common, or may have originated.

Y-chromosomal to autosomal STR variance

This may be relevant to Peter Frost's theory which I blogged about earlier.

Averaged over regional populations and over Y chromosome loci, the ratio equals 1.14, 0.51, 0.97, 0.93, 1.06, and 0.61, respectively, for sub-Saharan African hunter-gatherers (the number of populations, k, is 3), sub-Saharan African “farmers” (k=3), Eurasia (k = 21), East Asia (k = 18), Oceania (k = 2), and America (k = 5). Outlying values for American and sub-Saharan African farming populations, 0.61 and 0.51, may indicate lower effective population size for males than for females in these populations.

Source: The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time (PDF)

What was really Aaron's lineage? (Cohen modal haplotype)

One of the first spectacular applications of Y-chromosome testing was the discovery that Jewish Cohanim exhibited a particular Y-chromosome haplotype, called the Cohen Modal Haplotype (CMH). Jewish Cohens are believed to be descended from the priests of biblical Israel by patrilineal descent, and hence their Y chromosomes should be descended from that of Aaron, the first priest.

In retrospect, the first letter announcing this discovery supported its case by showing a spectacular difference between Cohanim and non-Cohanim Jews. The Cohanim had trace frequencies of haplogroup E3b, and a particular DYS19 allele at high frequency. This finding did prove different histories for priests and non-priests. However, it did not prove descent from a single individual because the YAP- DYS19B combination is not a monophyletic lineage.

In another study, the authors discovered a more extended version of the same haplotype (DYS19-14, DYS388-16, DYS390-23, DYS391-10, DYS392-11, DYS393-12) at high frequency in the Lemba of Southern Africa, as well as in Jews. This was interpreted as evidence for a Jewish origin of the Lemba. This seems likely, given the anomalous existence of a Middle-Eastern haplotype and the oral history of the Lemba. However, once again, it was not proven that people belonging to the CMH were all descended from the biblical Aaron.

A small note: if two men have the same haplotype, it does not mean that they are descended from the same ancestor. This is due to the fact that microsatellites defining haplotypes mutate quite fast, so two unrelated men may have the same haplotype by chance. In fact, the probability of such an accident increases as the number of microsatellites decreases.

The Cohen modal haplotype belongs to a Y-chromosome haplogroup called J or HG-9. A haplogroup is defined by a unique event polymorphism, and men who belong to the same haplogroup are indeed descended from a single man. But, in the case of J, that single man lived more than 10,000 years ago, long before the time of Aaron. However, J is split into two lineages that are also more than 10,000 years old: J2 (or Eu9) and J1 (or Eu10).

If the people who have the CMH are always in Eu9 or in Eu10, then the CMH really reflects priestly descent. But, if it is found in both, then by definition the CMH does not in itself reflect priestly descent, because the common ancestor of a Eu9-CMH and a Eu10-CMH lived earlier than 10,000 years ago, i.e., much earlier than the putative time of Aaron's priesthood (~3 thousand years).

This brings us to yet another study (pdf) which discovered a high frequency of the CMH in Jews. According to this study:

The most-frequent haplotype in all three Jewish groups (the CMH [haplotype 159 in the Appendix]) segregated on a Eu 10 background, together with the three modal haplotypes in Palestinians and Bedouin (haplotypes 144, 151, and 166).

This would suggest that the CMH belonged to J1. However, the author only identified that most CMHs belonged to J1. In the appendix of the same study, it is shown that haplotype 108 is also the CMH, but belongs to haplogroup J2.

Admittedly, 22 CMH-bearing Jews from the study belong to J1, and only 3 ones belong to J2, but this clearly demonstrates that the CMH is not in itself evidence of priestly descent. In principle, Aaron could have been either J1 or J2.

More importantly, the occurrence of the CMH in Cohanim overestimates their descent from Aaron, because at least some of the CMH bearers belong to J1 and some to J2, and they can't both be descended from Aaron.

At this stage, it would appear that we could conclude that the "real" priestly lineage was J1+CMH, because J1+CMH is more frequent than J2+CMH in Jews. Things are however not that simple.

In yet another study the authors state that:

By typing a limited number of Italian Cohanim (A. N. unpublished obs.) for the STRs used here, we determined that the Cohen Modal Haplotype (`an important component in the sharing of Ashkenazic and Sephardic Israelite Y chromosomes', Thomas et al. 2000) does indeed belong to network 1.2.

Network 1.2 falls under the J2 haplogroup. Hence it appears that Cohen Jews, as opposed to Jews in general may belong mainly to haplogroup J2.

At present, no new published information is available on this matter. Several studies have now proven that the CMH occurs in both J1 and J2 backgrounds and does not represent a single lineage. Moreover, Jews themselves are split between the J1 and J2 varieties.

More importantly, the CMH was first identified because of its high frequency compared to other haplotypes. The strength of this evidence is diminished by the finding that CMH chromosomes belong to two unrelated lineages. Furthermore, the dating of CMH chromosomes to Aaron's time should be reconsidered, and the molecular variation within J1 and J2-background CMH and its neighbors should be considered separately.

In conclusion, the true genetic identity of Aaron remains elusive.

UPDATE:

I just discovered the supplementary materials of this comprehensive article on Ashkenazi Jewish Y-chromosome variation.

According to my count, 28 of the Jewish CMHs belong to J1 (6.3%) and 25 belong to J2 (5.7%). This casts further doubt to the CMH as Aaron's lineage, and even if the CMH was Aaron's lineage, it raises the question as to whether he belonged to J1 or J2.

UPDATE II:

In Anatolia, the CMH occurs in:

2 x J2*, 1 x J2f1, 5 x J2f* (total 8 x J2 or 1.5%)
7 x J1* and 1 x J1c (total 8 x J1 or 1.5%)

It is noteworthy that in region 6 (south), 4/33=12% belong to the J1-CMH.

UPDATE III:

Among Armenians, the CMH occurs at a frequency of 1.9%, ranging up to 4.4% in the West region.

New paper on Indian Y-chromosome variation

A new paper on Y-chromosome variation in India has become available as an unedited preprint in the AJHG site. This is a huge study which covered linguistic/caste groups from the entire country and used 69 binary markers and 10 microsatellites to create a very thorough sampling of Indian Y-chromosomal variation. It will take some time to digest all the new information, plus the supplemental materials of the paper that remain to be put online. I will blog more about this soon. In bullet form, some findings of the paper which caught my attention:

• R1a1's molecular variance is highest in NW India and its age is substantial
  
• R1a1's variance is high in tribals
  
• The phylogeny of J2 has been refined and it is now split into two newly discovered clades, called J2a and J2b.
• J2 is almost entirely absent from tribals and is represented at a higher frequency in upper castes than middle castes than lower castes.
  

UPDATE:

The samples:

High-resolution assessment of Y-chromosome binary haplogroup composition was conducted on 728 Indian samples representing 36 populations, including 17 tribal populations, from six geographic regions and different social and linguistic categories. They comprise (Austro-Asiatic) Ho, Lodha, Santal, (Tibeto-Burman) Chakma, Jamatia, Mog, Mizo, Tripuri, (Dravidian) Irula, Koya Dora, Kamar, Kota, Konda Reddy, Kurumba, Muria, Toda (Indo-European) Halba. The 18 castes include (Dravidian) Iyer, Iyengar, Ambalakarar, Vanniyar, Vellalar, Pallan and (Indo-European) Koknasth Brahmin, Uttar Pradhesh Brahmin, West BengalBrahmin, Rajput, Agharia, Gaud, Mahishya, Maratha, Bagdi, Chamar, Nav Buddha, Tanti. With exception of the Koya Dora and Konda Reddy groups, these samples have been previously described (Basu et al. 2003).

J2 is divided into two main clades: J2a*-M410 and J2b*-M12:

New phylogenetic resolution has been achieved within the J2-M172 clade with the discovery of the M410 nucleotide A to G substitution (Table 2). Now all J2-M172 derived lineages can be assigned to one of two sister clades, namely J2a*-M410 and J2b*-M12, necessitating an updated revision of the previous “haplogroup by lineage” YCC nomenclature for J2 (Jobling et al. 2003). The J2*-M172 phylogenetic revisions are presented in supplemental dataA5. We include the DYS413≤18 allele repeat node in the phylogeny as suggested by Di Giacomo et al. (2004). It is notable that no J2*-M172 haplogroup lacking both M410 and M12 derived alleles has yet been observed. The DYS413 locus was typed in M410 derived samples from India, Pakistan and Turkey. The vast majority displayed the ≤18 allele repeat, although 16/118 in Turkey had alleles ≥19, as did 5/17 in Pakistan and 5/28 in India, 4 of which were restricted to the Dravidian-speaking Iyengar and Iyer upper castes.

5 New Clades in haplogroups C, L, Q, and I:

We report 5 new clades that improve the haplogroup topology within the Y-chromosome genealogy. The new subclade C5-M356, accounts for 85% of the former C* haplogroups. While its overall frequency is only 1.4% in the Indian sample, it occurs in all linguistic groups, and in both tribes and castes. It also occurs in 1 Dravidian Brahui in Pakistan (Table 3). The new L3-M357 subclade which accounts for 86% of L-M20(xL1xL2) chromosomes in Pakistan; but occurs sporadically (3/728) in India. All Indian haplogroup Q representatives belong to the new M346-subclade. This new Q clade will aid in future studies attempting to narrow the candidate Asian/Siberian precursors of Native American chromosomes. The G5-M377 substitution is independent of G1-M285 and G2-P15 subclades (Cinnioglu et al. 2004) and occurs in Pakistan. The M379 polymorphism defines the I1c2 subclade, that occurs only our Pakistani data.

Indigenous Indian haplogroups:

On the basis of the combined phylogeographic distributions of haplotypes observed
among populations defined by social and linguistic criteria, candidate haplogroups that most plausibly arose in situ within the boundaries of present day India include C5-M356, F*-M89, H*-M69 (and its sub-clades H1-M52 and H2-APT), R2-M124 and L1-M76. The congruent geographic distribution of H*-M69 and potentially paraphyletic F*-M89 Y-chromosomes in India suggests that they might share a common demographic history.

R1a1 and R2:

The widespread geographic distribution of haplogroup R1a1-M17 across Eurasia and the current absence of informative subdivisions defined by binary markers leave its geographic origin uncertain. However the contour map of R1a1-M17 variance shows the highest variance in the northwest region of India (Figure 3).

...

In haplogroups R1a1 and R2 the associated mean microsatellite variance is highest in tribes (Table 8), not castes. This is a clear contradiction to what would be expected from an explanation involving a model of recent occasional admixture.

...

Specifically, they could have actually arrived in southern India from southwest Asian source region multiple times with some episodes being considerably earlier than others. Considerable archeological evidence exists regarding the presence of Mesolithic peoples in India (Kennedy 2000), some of whom could have entered the
subcontinent from the northwest during the late Pleistocene period. The high variance of R1a1 in India (Table 8), the spatial frequency distribution of R1a1 microsatellite variance (Figure 3) clines and expansion time (Table 7) support this view.

Clustering of R1a1 haplotypes:

The ages of the Y-microsatellite variation (Table 7) for R1a1 and R2 in India suggest that the pre-historical context of these haplogroups will likely be complex. A PC plot of R1a1-M17 Y-microsatellite data (Figure 4) shows several interesting features: (a) one tight population cluster comprising S. Pakistan, Turkey, Greece, Oman and West Europe, (b) one loose cluster comprising all the Indian tribal and caste populations, with the tribal populations occupying an edge of this cluster, and (c) Central Asia
and Turkey occupy intermediate positions. The upper and lower bounds of the divergence time between the two clusters is 12 kya and 8 kya, respectively. The pattern of clustering does not support the model that the primary source of the R1a1-M17 chromosomes in India was Central Asia or the Indus valley via Indo-European speakers.

The spread of J2a:

Figure 2 demonstrates the eastward expansion of J2a-M410 to Iraq, Iran and Central Asia coincident with painted pottery and ceramic figurines, well documented in the Neolithic archeological record (Cauvin 2000). Near the Indus valley, the Neolithic site of Mehrgarh beginning around 5000 BCE (Kenoyer 1998) displays the presence of these types of material culture correlated with the spread J2a-M410 in Pakistan. While the association of agriculture with J2a-M410 is recognized, it is not necessarily the only explanation for its history. Despite an apparent exogenous frequency spread pattern of hg J2a towards North and Central India from the west (Figure 2), it is premature to attribute it to a simplistic demic expansion of early agriculturalists and pastoralists from the Middle East. It reflects the overall net process of spread that may contain numerous as yet unrevealed movements embedded within the general pattern. It may also reflect a combination of elements of earlier prehistoric Holocene epi-paleolithic peoples from the Middle East, subsequent Bronze Age Harappans of uncertain provenance and succeeding Iron Age Indo-Aryans from Central Asia (Kennedy 2000). Further, the relative position of the Indian tribals (Fig. 4), the high microsatellite variance among them (Table 8), the estimated age (14 kya) of microsatellite variation within R1a1 (Table 7) and the variance peak in the west (Fig. 3) are entirely inconsistent with a model of recent gene flow from castes to tribes and a large genetic impact of the Indo-Europeans on the autochthonous gene pool of India. Instead, our overall inference is that an early Holocene expansion in NW India (including the Indus) contributed R1a1-M17 chromosomes both to the Central Asian and S Asian tribes prior to the arrival of the Indo-Europeans.

J2a in upper caste Indians:

The J2 clade is nearly absent among Indian tribals, except among Austro-Asiatic speaking tribals (11%). Among the Austro-Asiatic tribals, the predominant J2b2 hg occurs only in the Lodha.

...

Haplogroup J2a-M410 is confined to upper caste Dravidian and Indo-European speakers, with little occurrence in the middle and lower castes. This absence of even modest admixture of J2a in south Indian tribes and middle and lower castes is inconsistent with the L1 data. Overall, therefore, our data provide overwhelming support to an Indian origin of Dravidian speakers.

Haplogroup frequencies:



American Journal of Human Genetics (in press)

Polarity and Temporality of High Resolution Y-chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists

Sanghamitra Sengupta, Lev A. Zhivotovsky, Roy King, S. Q. Mehdi, Christopher A. Edmonds, Cheryl-Emiliane T. Chow, Alice A. Lin, Mitashree Mitra, Samir K. Sil, A. Ramesh, M.V. Usha Rani, Chitra M. Thakur, L. Luca Cavalli-Sforza, Partha P. Majumder and Peter A. Underhill

Abstract

While considerable cultural impact on social hierarchy and language in south Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of south Asia. We sought to resolve this conflict using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially and linguistically representative ethnic groups of south Asia. We have found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10-15 kya, attesting to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from central Asia to explain the observed genetic variation in south Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment towards distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene era – not Indo-European – expansions have shaped the distinctive south Asian Y-chromosome landscape.

Pinhasi et al. on the origin and spread of agriculture

PubMed has an interesting abstract. I will update the entry with the link and post my comments once the paper becomes available.

UPDATE:

From the paper:

As far as we know, no cultural-diffusion model to date has been able to derive a speed compatible with the observed range (0.6–1.3 km/y).

...

The values of a and m have been carefully derived in previous work from plots of the population number versus time (a) and records of individual movements (m). Data from anthropological studies gathered hitherto yield estimates of 0.029–0.035/y for a, 900–2,200 km2/generation for m, and 29–35 y for T (Text S3). Using these ranges, the above formula yields a speed range of 0.6–1.1 km/y. Thus, the speed range predicted by demic diffusion, namely 0.6–1.1 km/y, is compatible with that observed, namely 0.6–1.3 km/y (obtained above from Figure 2). Our conclusion at this point is that demic diffusion predicts a speed compatible with the archaeological observations, whereas no cultural-diffusion model has been developed so far that can explain the observed speed.

PLoS Biology (early access)

Tracing the Origin and Spread of Agriculture in Europe.

Pinhasi R, Fort J, Ammerman AJ.

The origins of early farming and its spread to Europe have been the subject of major interest for some time. The main controversy today is over the nature of the Neolithic transition in Europe: the extent to which the spread was, for the most part, indigenous and animated by imitation (cultural diffusion) or else was driven by an influx of dispersing populations (demic diffusion). We analyze the spatiotemporal dynamics of the transition using radiocarbon dates from 735 early Neolithic sites in Europe, the Near East, and Anatolia. We compute great-circle and shortest-path distances from each site to 35 possible agricultural centers of origin-ten are based on early sites in the Middle East and 25 are hypothetical locations set at 5 degrees latitude/longitude intervals. We perform a linear fit of distance versus age (and vice versa) for each center. For certain centers, high correlation coefficients (R > 0.8) are obtained. This implies that a steady rate or speed is a good overall approximation for this historical development. The average rate of the Neolithic spread over Europe is 0.6-1.3 km/y (95% confidence interval). This is consistent with the prediction of demic diffusion (0.6-1.1 km/y). An interpolative map of correlation coefficients, obtained by using shortest-path distances, shows that the origins of agriculture were most likely to have occurred in the northern Levantine/Mesopotamian area.

Link

Western world's oldest map was created by southern Italian Greeks

Archaeologists find western world's oldest map

The oldest map of anywhere in the western world, dating from about 500 BC, has been unearthed in southern Italy. Known as the Soleto Map, the depiction of Apulia, the heel of Italy's "boot", is on a piece of black-glazed terracotta vase about the size of a postage stamp.

...

"The map offers, to date, for the Mediterranean, and more generally for western civilisation, the oldest map of a real space," the university said recently.

Its engraved place names are indicated by points, just as on maps today, and are written in ancient Greek.

The sea on the western side, Taras (Taranto), today's Gulf of Taranto, is named in Greek. But the rest of the map is in Messapian, the ancient tongue of the local tribes, although the script is ancient Greek.

...

Apart from being the oldest geographical map from classical antiquity ever found, it is the first material proof that the ancient Greeks were drawing maps of real places before the Romans.

It was known from ancient Greek literature that the concept of a map existed and that some had been drawn but none had been found.

The ancient Chinese had a well-defined system of map-making, but modern cartography descends from techniques laid down by the ancient Greeks.

...

The Soleto map also gives vital new clues to the cultural exchange between the newly arrived Greeks and the Messapi.

They lived in the area but probably came originally from Greece as their language is believed to be a dialect of Illyrian.

Recent positive selection in cis-Regulation in Humans

One more paper which suggests that a locus, which shows significant differences between humans and other primates, continued to evolve after the human-specific allele was fixed. Recent selection -within the human lineage- favored different variants in Caucasoids and Asians:

Selection drove an increase in the frequency of the three-repeat allele in Europe and East Africa and independently increased the frequency of the two-repeat allele in India and China, according to the significantly reduced lnRθ values in each of the populations implicated by the FST data.

PLoS Biology Volume 3 Issue 12

Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans

Matthew V. Rockman et al.

Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory. Independent lines of phylogenetic and population genetic evidence support a history of selective sweeps driving the evolution of the human prodynorphin promoter. In experimental assays of chimpanzee–human hybrid promoters, the selected sequence increases transcriptional inducibility. The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution. In addition, the pattern of linked nucleotide and microsatellite variation among and within modern human populations suggests that recent selection, subsequent to the fixation of the human-specific mutations and the peopling of the globe, has favored different prodynorphin cis-regulatory alleles in different parts of the world.

Link

Large Bronze Age settlement discovered in Armenia

ARMENIAN ARCHAEOLOGISTS FIND LARGE ANCIENT SETTLEMENT OF EARLY BRONZE AGE

YEREVAN, 16.11.05. On the western slopes of Aragats, near the village of Tsakhkasar, archaeologists got on the tracks of an ancient settlement of the Early Bronze Age (the fourth millenium BC) referring the Archaeological Culture Kur-Araks. Director of the Institute of Archaeology and Ethnography of the Armenian National Academy of Sciences, Aram Kalantaryan, told ARMINFO. The monument is unique for its unprecedented scale of an ancient settlement. It occupies a territory of about 100 ha, while the Kur Araks lowland towns are known to occupy not more than 10 ha. The settlement was surrounded with cyclopean fortress. Archaeologists have excavated a 300 sq/m ancient cultural layer so far and found a unique bronze reaping-hook. Unfortunately, irrigation canals were laid there yet in 1930, which has partially damaged the monument.

Kalantaryan said that an Armenian-American joint expedition near the village of Gegharot, on the northern slope of Aragats, found another unique monument of the Late Bronze Age - a sanctuary of the 15th-12th centuries BC. He called the find `a real fount of the ancient material culture of Armenia`. The sanctuary is unique for the latest such complex found by archaeologists in the village of Metsamor belonged to later period. Archaeologists found a woman`s breast bronze decoration and semiprecious stones, including a cut rock crystal.

Kalantaryan also informed ARMINFO of another find, an ancient pagan temple of Antic Age on the bank of the Araks near the ancient town of Artashat. Archaeologists suppose it was the very temple the Armenian chroniclers Movses Khorenatsi and Agatangeghos wrote about in their works on Grigor Lusavorich. Kalantaryan expressed satisfaction that for the first time since the independence of Armenia the state budget for 2006 envisages funds for archaeological excavations. While, the present season was partially financed from the governmental reserve fund.

Interestingly, the Kura-Arax culture is implicated in Gamkrelidze and Ivanov's theory of Indo-European origins.

Gummy smiles are less attractive

People who show their upper gums when they smile were judged as less attractive; however, women were more tolerant of gum-showers than men.

Angle Orthod. 2005 Sep;75(5):778-84.

Influence of sex on the perception of oral and smile esthetics with differen gingival display and incisal plane inclination.

Geron S and Atalia W.

This study was designed to determine the esthetic perception of men and women to variations in upper and lower gingival display at smile and speech and to incisal plane tilting. Composed photographs of smile and speech with varying amounts of gingival exposure of the upper and lower teeth and gingiva at smile and at speech and with varying degrees of incisal plane tilting were rated for attractiveness by two groups of lay people. The images were presented as male or female images. A total of 300 questionnaires, including 7500 images, were evaluated by 100 subjects. The results showed that images were scored as less attractive as the amount of upper and lower gingival display was increased during smile and speech. The amount of gingival exposure graded in the esthetic range was up to one mm for the upper incisors and zero mm for the lower incisors. Incisal plane tilting was graded as unesthetic when above two degrees of deviation from the horizontal. Male and female evaluators scored images differently with upper gingival exposure. Female evaluators gave statistically significant higher scores than male evaluators to upper gingival exposure images at smile and speech of both males and females, suggesting that females are more tolerant of upper gingival exposure. Images were scored differently when presented as male or female images. Female images were scored lower by both male and female evaluators, suggesting that additional efforts should be taken in female patients to achieve an esthetic result.

Link

Y-chromosomal microsatellites in Northern and Southern Russians

Genetika. 2005 Aug;41(8):1125-31.

[Polymorphism of Y-chromosomal microsatellites in Russian populations from the northern and southern Russia as exemplified by the populations of Kursk and Arkhangel'sk Oblast]

[Article in Russian]

Khrunin AV et al.

Allelic polymorphisms at five Y-chromosomal microsatellite loci (DYS19, DYS390, DYS391, DYS392, and DYS393) were typed in 87 individuals from male population samples from two geographically isolated regions (Arkhangelsk oblast and Kursk oblast) of the European part of Russia. The populations examined demonstrated substantial differences in the distribution of the DYS392 (P = 0.005) and DYS393 (P = 0.003) alleles. Estimates of genetic relationships between these populations and some other European populations (including Eastern-Slavic) showed that irrespectively of the measure of genetic distance chosen, Arkhangelsk population was closer to the populations belonging to the Finno-Ugric linguistic group (Saami and Estonians) and to the Estonian geographical neighbors, Latvians, while Kursk population was the member of a cluster formed by Eastern-Slavic populations (Russians of Novgorod oblast, Ukrainians, and Belarussians). Phylogenetic analysis of the most frequent haplotypes indicated that these differences between Kursk and Arkhangelsk populations were associated with high prevalence in the latter of major haplotypes characteristic primarily of the Finno-Ugric populations.

Link

Corded Ware people were not mobile pastoralists

A new study disproves the idea that the Corded Ware people had a mobile, pastoral type of subsistence.

Journal of Archaeological Science (Article in press)

Mobility in Central European Late Eneolithic and Early Bronze Age: tibial cross-sectional geometry

Vladimír Sládek et al.

Abstract

An absence of settlement features during the Central European Corded Ware period (Late Eneolithic, 2900–2300 BC) has been interpreted as a reflection of mobile pastoral subsistence. Recent analyses of the Late Eneolithic archeological context reveal that the Late Eneolithic exhibit evidence of sedentary agricultural activities similar to the Early Bronze Age. Since the archeological analyses are not clear cut, we tested mobility pattern differences between the Late Eneolithic and Early Bronze Age using biomechanical analysis of the tibial midshaft cross-sections. The total sample of the 130 tibiae representing five archaeological cultures was used. The results of the tibial midshaft geometry do not support the hypothesis about different mobility in the Late Eneolithic and Early Bronze Age. This conclusion is supported by nonsignificant differences between the Corded Ware females and the Early Bronze Age females. Higher absolute values for the Corded Ware males should be explained either by stochastic variation or by differing amounts of physical demands despite a generally similar pattern of subsistence of the Late Eneolithic and Early Bronze Age. One of the Early Bronze Age samples, the Wieselburger group, is an exception because the individuals show both reduced overall size and bending resistance of the tibial parameters not only in comparison with the Late Eneolithic but also to the rest of the Early Bronze Age. The results suggest that the behavioral processes which affected the tibial midshaft biology operated during the Late Eneolithic and Early Bronze Age as a mosaic across time and between/within cultures.

Link

N1a in Brahmnins

Interesting tidbit from an earlier post:

The N1a haplogroup was not observed among the native American, east Asian, Siberian, Central Asian, and western European populations. The geographic distribution of haplogroup N1a is restricted to regions neighboring the Eurasian steppe zone. Its frequency is very low, less than 1.5% (Table 6), in the populations located in the western and southwestern areas of the Eurasian steppe. Haplogroup N1a is, however, more frequent in the populations of the southeastern region of the Eurasian steppe, as in Iran (but only 12 individuals were studied) and southeastern India (Karnataka and Andhra Pradesh territories). More precisely, in India haplogroup N1a is absent from the Dravidic-speaking population and is present in only five Indo-Aryan-speaking individuals, four of whom belonged to the Havik group, an upper Brahman caste (Mountain et al. 1995).

The presence of haplogroup N1a in upper caste Hindus and not in Dravidians further strengthens the case for it being associated with the Neolithic Indo-Europeans. According to this theory, the diffusion of Neolithic people led to the Indo-Europeanization of large parts of Eurasia. The recent discovery of a high frequency of N1a in Linearbandkeramik people is also consistent with this theory, and so is its presence in prehistoric Scytho-Siberians who were Iranic speakers at the edge of the Indo-European world.

Peter Forster's Neolithic Project

Peter Forster, one of the authors of the new study on ancient European farmers has a Neolithic Project. It provides mtDNA testing, as well as interpretation of results obtained from other testing services:

The Neolithic Project is an independent continuation of the ancient DNA work on the first European farmers from 7500-year-old Neolithic sites, published with our German and Estonian colleagues in the leading magazine Science. For details on our recent publication, see the Press Release below.

Our venture Genetic Ancestor Ltd is now asking members from the public who are of European descent (including those living outside Europe) to provide DNA samples for exploring the genetic fate of the first farmers who colonised Europe about 7500 years ago.

There is a major archaeological puzzle to solve. Why did the first prehistoric farmers enter Europe, completely transform the culture from primitive hunting and gathering to sophisticated farming, house-building and pottery, but then apparently not leave a large number of typical farming N1a female lineages in the European population today?

These farming N1a lineages now make up less than 0.2 percent of European female lineages. Why?

We aim to analyse a large number of modern European saliva samples to find out where in Europe the ancient farming lineages have survived until today, in order to address this question.

If you register for this new project, we will send you a home test by post, for sending us your saliva sample. Your registration fee of 35 US-Dollars will contribute to covering our costs for the home test, postage, handling, and lab materials. We are able to keep these lab costs lower than usual, because we only carry out expensive detailed lab analysis on the small percentage of those samples which have been identified (using a novel inexpensive preliminary genetic screening test) for the farming mtDNA types identified in the ancient remains.

More info on the offered services.

mtDNA of early central European farmers

A new study in Science examines ancient mtDNA from Central Europe and more precisely from the Linearbandkeramik (LBK) and the related Alföldi Vonaldiszes Kerámia (AVK) cultures. The farmers of the LBK are responsible for the spread of agriculture in Central and Northern Europe, and hence their genetic composition is of particular interest:

From a total of 57 LBK/AVK individuals analyzed, 24 individuals (42%) revealed reproducibly successful amplifications of all four primer pairs from at least two independent extractions usually sampled from different parts of the skeleton. Eighteen of the sequences belonged to typical western Eurasian mtDNA branches; there were seven H or V sequences, five T sequences, four K sequences, one J sequence, and one U3 sequence (table S1). These 18 sequences are common and widespread in modern Europeans, Near Easterners, and Central Asians, and thus these 18 lineages lack the detailed temporal or geographic discrimination required to test the hypotheses we are examining, even though some of them have previously been suggested to be of Neolithic origin on the basis of modern DNA studies (15). We therefore concentrated on the mtDNA types identified in the other six individuals.

The most striking result is that 6 of the 24 Neolithic skeletons are of the distinctive and rare N1a branch. For verification, we sequenced 517 clones derived from independent extractions from different parts of the six individuals. All six showed the suite of mutations characteristic of the N1a lineage. Five of these six individuals display different N1a types, whereas Flomborn 1 and Derenburg 3 show identical N1a types (Table 1).

It is not surprising that the early Neolithic farmers belonged mainly to several well-known Caucasoid haplogroups. What is surprising is that a particular lineage, N1a which occurs at a low frequency in modern Europeans was found at a very high frequency in the ancient farmers. Moreover, it occurred in different sites, hence it appears to be a genuine distinguishing feature of the LBK, and not simply a peculiarity of some local population.

The reduction of frequency of N1a in the modern sample is 150-fold. As the authors suggest, genetic drift alone cannot account for this enormous reduction, and the reduction can be explained either because (a) modern central Europeans are primarily descended from Paleolithic ones and not from the Neolithic culture bearers, or (b) the genetic legacy of the early farmers has been wiped out by subsequent population movements into Central Europe:

These simulations reject the simple hypothesis in which modern Europeans are direct descendants of these first farmers and have lost N1a mainly by genetic drift. Hence the simulations confirm that the first farmers in Central Europe had limited success in leaving a genetic mark on the female lineages of modern Europeans. This is in contrast to the success of the Neolithic farming culture itself, which subsequently spread all over Europe, as the archaeological record demonstrates. One possible explanation is that the farming culture itself spread without the people originally carrying these ideas. This includes the possibility that small pioneer groups carried farming into new areas of Europe, and that once the technique had taken root, the surrounding hunter-gatherers adopted the new culture and then outnumbered the original farmers, diluting their N1a frequency to the low modern value. Archaeological research along the Western periphery of LBK and isotope studies of some of our sampled individuals seem to support the idea that male and female hunter-gatherers were integrated into the Neolithic communities (3, 10, 29). This hypothesis implies that N1a was rare or absent in Mesolithic Europeans, which may be a reasonable assumption given the rarity of the N1a type anywhere in the world (Fig. 3). An alternative hypothesis is a subsequent post–early-Neolithic population replacement in Europe, eliminating most of the N1a types. Archaeological evidence for such an event is as yet scant.

In the supplemental data we can see that there are some modern matches to the 6 ancient mtDNA sequences belonging to haplogroup N1a.

• The sequence of Derenburg 3/Flomborn 1 occurs in the Chuvashi, in Slovakia, in Yemen, in Mashhad \Ostan-e-Khorasan, in Turkmen from Turkmenistan, in Iran, in Estonia, and in Sweden
• The sequence of Derenburg 1 occurs in Cairo Egypt, and Armenia.
• The sequence of Halberstadt 2 is not found elsewhere.
• The sequence of Unterwiederstedt 5 is not found elsewhere.
• The sequence of Ecsegfalva 1 is not found elsewhere
  

In conclusion, it appears that modern central Europeans are very little physically descended from the early Neolithic culture bearers of the same region. What we really need now is for other early Neolithic samples from other parts of Europe, Western Eurasia, and Northern Africa to be studied, to see whether N1a was a peculiarity of the LBK, or it was a genuine feature of the first farmers.

PS: It should be noted that an alternative explanation for the great reduction in the frequency of N1a would be some form of negative selection. This suggestion is entirely speculative, but it should be kept in mind.

Update: I have added a link to this study to the Ancient DNA compendium.

Update 2: The major weakness of the study -apart from not having anything to say about selection- is that it assumes that haplogroup N1a was brought into Central Europe by the Neolithic farmers. However, there is no reason to suppose that this is the case. The authors arbitrarily label N1a as Neolithic, but they have no evidence that N1a was brought by the immigrant farmers and does not represent an indigenous component. Indeed, their own map shows that the particular cluster of N1a found in modern Europeans is not found in Greece or Turkey where the Neolithic of Europe originated. So, it is just as likely that N1a may be indigenous to central Europe and the Neolithic was associated with some of the other 18 sequences that were found in the Linear Pottery sample. Indeed, if N1a turns out to be Paleolithic, then the conclusions of their study will be completely reversed, and the great decrease in frequency of N1a would indicate an almost complete replacement of Paleolithic people by Neolithic farmers.

In conclusion: the authors don't present any evidence for N1a being Neolithic by either measuring a high frequency in originary areas of the Neolithic (Anatolia and Greece), or by sampling ancient populations from the originary areas. Hence, their conclusions are entirely arbitrary.

Science, Vol 310, Issue 5750, 1016-1018 , 11 November 2005

Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites

Wolfgang Haak et al.

The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.

Link

Surfing the genetic wave of advance

Molecular Biology and Evolution (advance access)

The Fate of Mutations Surfing on the Wave of a Range Expansion

Seraina Klopfstein et al.

Abstract

Many species, including humans, have dramatically expanded their range in the past; and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance, and thus reach a larger spatial distribution and a much higher frequency than would be expected in stationary populations. We study here this surfing phenomenon in more details, by performing extensive computer simulations under a two-dimensional stepping-stone model. We find that the probability of survival of a new mutation depends to a large degree on its proximity to the edge of the wave. Demographic factors such as deme size, migration rate and local growth rate also influence the fate of these new mutations. We also find that the final spatial and frequency distribution depends on the local deme size of a subdivided population. This latter result is discussed in the light of human expansions in Europe, as it should allow one to distinguish between mutations having spread with Paleolithic or Neolithic expansions. By favoring the spread of new mutations, a consequence of the surfing phenomenon is to increase the rate of evolution of spatially expanding populations.

Link

Y-haplogroups in several populations

Electrophoresis has a new article describing a new haplogroup typing kit. Of interest is a table of haplogroup frequencies from several populations:



Electrophoresis (early view)

Introduction of an single nucleodite polymorphism-based Major Y-chromosome haplogroup typing kit suitable for predicting the geographical origin of male lineages

María Brión et al.

Abstract

The European Consortium High-throughput analysis of single nucleotide polymorphisms for the forensic identification of persons - SNPforID, has performed a selection of candidate Y-chromosome single nucleotide polymorphisms (SNPs) for making inferences on the geographic origin of an unknown sample. From more than 200 SNPs compiled in the phylogenetic tree published by the Y-Chromosome Consortium, and looking at the population studies previously published, a package of 29 SNPs has been selected for the identification of major population haplogroups. A Major Y-chromosome haplogroup typing kit has been developed, which allows the multiplex amplification of all 29 SNPs in a single reaction. Allele genotyping was performed with a single base extension reaction (minisequencing) detected by CE. The validation of the multiplex was performed in a total of 1126 unrelated males distributed among 12 worldwide populations. The approach takes advantage of the specific geographic distribution of the Y-chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage.

Link

Hamilton's Rule invalid?

Hamilton's rule specifies when altruistic behavior is adaptive and is the cornerstone of kin selection theory. A new paper argues that it is invalid:

Hamilton’s rule, and the model of kin selection on which it is based, was derived in the 1960s, when there was great emphasis on the individual, and on the gene, as the unit of selection. The concept of inclusive fitness encapsulated the notion that a gene that lowered the fitness of its bearer could promote behaviors that increased the fitness of consanguineous relatives, therefore increasing the frequency of the gene. Therefore it was the inclusive fitness of the gene that was assumed to predict the evolutionary increase or decrease of that gene. The extension of this concept into more teleological parlance became the selfish gene hypothesis. Hamilton’s model of kin selection has had a great influence on biology, anthropology, economics, and other fields. My results indicate, however, that although kin selection may occur, Hamilton’s rule is invalid.

Human Biology
Volume 77, Number 4, August 2005

Kin Selection in Human Populations: Theory Reconsidered

B. J. Williams

Abstract:

Past considerations of kin selection have assumed a dyadic fitness exchange relationship between altruist and recipient. This approach does not account for all alleles affected by altruistic behavior. This can be corrected by focusing on matings rather than on individuals. I present a model that tries to account for fitness changes resulting from altruistic acts, not only for the altruist and recipient but also for their spouses, in an evolving population. Results from this model indicate that Hamilton's rule fails to predict when the altruism allele will increase in frequency and, more important, suggest that kin selection can, at most, account for low levels of a gene for altruism but only if fairly extreme conditions are met.

Link

More on R1a1 age and haplogroup J2 in upper caste Hindus

A reader has brought to my attention a paper which appeared in 2001 in the Indian Journal of Genetics, and which is quite interesting for the discussion of the origins of haplogroup R1a1, as well as for the problem of the genetic makeup of the Proto-Indo-Europeans.

The Indian researchers have studied the microsatellite diversity of their northern Indian sample, and have estimated the corresponding age of haplogroup R1a1 (referred to as HG3). This age is 5,200 years. However, age is calculated based on assumptions about (i) the mutation rate, i.e., how fast microsatellites mutate, as well as (ii) the generation length. The 2001 paper makes assumptions which lead to an age that is 2.17 times younger than the assumptions of the recent South Siberian study. If we convert these estimates to the younger scale, we obtain ages of 5,193 years for Central Asia and 5,244 years for Eastern Europe. In other words, the age of R1a1 seems to be comparable in the three regions. The discrepancy of the ages in the two papers also underscores how the dating of prehistoric events depends to a great degree to assumptions which vary from researcher to researcher.

More fascinating is the finding that the main haplogroup distinguishing the northern Indian brahmins from the lower castes is J2 (referred to as HG9). I have long argued that haplogroup J2, associated with the early Neolithic expansions was also the PIE lineage par excellence, and this certainly supports this theory. It may very well be that in early times, the Indo-Iranians emerged as J2-bearing Indo-Europeans diffused into the R1a1-bearing east, with the resulting J2/R1a1 then settling on the Iranian plateau and invading India from the north.

The frequency of this haplogroup is highest (23.5%) among the upper-ranked caste Brahmin and is lower (17.1%) among the middle-ranked caste Rajput. It is known that after the entry of the Aryan speakers into India, the Brahmins were the torchbearers and promoters of Aryan rituals (Karve 1961). Therefore it is likely that this group had the highest genetic contact with the Aryan-speaking peoples. This observation is consistent with the high frequency of HG-9 observed among them. This haplogroup may have percolated into the middle-ranked Rajput either through admixture with Brahmins or directly with the Aryan-speaking immigrants. Since historians (Thapar 1975) have noted that some of the Central Asian pastoral nomads are ancestors of Rajputs, it is more likely that this haplogroup (HG-9) was introduced into the Rajputs directly by the Central Asians than indirectly through admixture with the Brahmins. It is noteworthy that HG-9 is absent among the low-ranked caste group, Chamar.

UPDATE I:

Interestingly though, in Oman the age of R1a1 is 11,400 years or 5,178 equivalent years using the same assumptions about generation length and mutation rate as above. In Iran and Pakistan it is 6,300 and 6,200 years old. Hence, all these ages seem very close to each other, and -given their confidence intervals- we cannot at present determine the point of origin of haplogroup R1a1.

UPDATE II:

Also of interest is Cordaux's extensive study of Indian Y chromosomes. Interestingly, the odds ratio for an Indian J2 being a caste vs. a tribal is 4 times more likely, whereas for an Indian R1a1 it is only 2.3 times more likely. This further supports the idea that haplogroup J2 significantly differentiates between Hindu caste members and indigenous non-caste populations. Unfortunately, Cordaux does not report differences within the Hindu caste hierarchy; it would be interesting to see whether J2 is even more prevalent among the upper castes within this hierarchy.

Journal of Genetics, 80(3): 125-135

High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from Central Asia and West Asia into India

N. Mukherjee et al.

Abstract

Linguistic evidence suggests that West Asia and Central Asia have been the two major geographical sources of genes
in the contemporary Indian gene pool. To test the nature and extent of similarities in the gene pools of these regions we have collected DNA samples from four ethnic populations of northern India, and have screened these samples for a set of 18 Y-chromosome polymorphic markers (12 unique event polymorphisms and six short tandem repeats). These data from Indian populations have been analysed in conjunction with published data from several West Asian and Central Asian populations. Our analyses have revealed traces of population movement from Central Asia and West Asia into India. Two haplogroups, HG-3 and HG-9, which are known to have arisen in the Central Asian region, are found in reasonably high frequencies (41.7% and 14.3% respectively) in the study populations. The ages estimated forthese two haplogroups are less in the Indian populations than those estimated from data on Middle Eastern populations. A neighbour-joining tree based on Y-haplogroup frequencies shows that the North Indians are genetically placed between the West Asian and Central Asian populations. This is consistent with gene flow from West Asia and Central Asia into India.

Link

Y chromosomes of South Siberians

A very interesting paper about South Siberia, a contact region between Caucasoids and Mongoloids right in the middle of Asia. First, the anthropological picture, which has been established for quite some time:

Unfortunately, archaeological records alone with the lack of human skeletal remains are inconclusive about the anthropological traits, which were characteristic for the Upper Paleolithic Siberian population. East Asian features thought to have been derived from early modern East Asians exist in the tooth from the Denisova Cave in the Altai region and in human remains from the Afontova Gora II site and indicate that the East Asians had moved into southwestern Siberia by 21,000 B.P. or even earlier (Alekseev 1998). Yet, the Upper Paleolithic artifacts from the 23,000-year-old Mal’ta site near Lake Baikal in south-central Siberia (Medvedev et al. 1996) have been found in association with skeletal remains that bear similar morphology with contemporary anatomically modern humans teeth from Europe thus providing the evidence for links between Siberia and the West during the Upper Paleolithic. Thus, on assuming that during the Upper Paleolithic the population of South Siberia was closely related to other East Asian populations, then during the Neolithic, admixture with populations from Eastern Europe probably occurred. The prevalence of European features among steppe zone inhabitants of Tuva, Altai, Khakassia, and West Mongolia became the most significant since the Bronze Age or even earlier (Alexeev and Gohman 1984; Alexeev 1989). The boundary of the Eastern European influence is clearly fixed at Lake Baikal. To the east of Baikal no palaeoanthropological find bears any traces of European admixture (Alekseev 1998).

Of importance is the discovery that R1a1 chromosomes in Siberians and Eastern Europeans are differentiated, and are both quite old, predating the spread of the Kurgan culture.

Divergency estimates based on Y-chromosome microsatellite variation indicate that, despite the haplotype diversity value of Eastern European R1a1-lineages exceeds that in South Siberia, the estimated ages for this haplogroup are almost equal in both regional groups—11,270±4,070 years in South Siberia and 11,380±3,200 years in Eastern Europe. These values are very close to the divergence time between the two regional groups studied (10,310±3,140 years). These results suggest that an isolation of the regional groups occurred soon after the origin of the R1a1 haplogroup.

Finally, here are the haplogroup frequencies in the various populations tested.



Update: The most frequent haplotype (#40) in Siberians, defined over (DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439) is: 16 11 14 14 18 25 11 11 13 14 11 10. This was not found in the extensive Russian sample, so it may represent a quite distinctive Central Asian haplotype.

Interestingly, a search in YHRD with this haplotype revealed only a single match in the Hungarian-speaking sample Lunca de Sus, Romania [Csángó]. This may serve to illustrate the paucity of relevant samples in YHRD. If we exclude DYS438 and DYS439 which are not typed in all samples in YHRD, then additional matches are found in Central Anatolian Turks, Szekely (also Hungarian-speaking) from Romania and in Ljubljana, Slovenia. If we further remove the fast-mutating DYS385 markers, then the following matches are found.



Let's hope that more Central Asian and Siberian samples are added to YHRD soon!

Human Genetics (Early view)

Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions

Miroslava Derenko et al.

Abstract In order to investigate the genetic history of autochthonous South Siberian populations and to estimate the contribution of distinct patrilineages to their gene pools, we have analyzed 17 Y-chromosomal binary markers (YAP, RPS4Y711, SRY-8299, M89, M201, M52, M170, 12f2, M9, M20, 92R7, SRY-1532, DYS199, M173, M17, Tat, and LLY22 g) in a total sample of 1,358 males from 14 ethnic groups of Siberia (Altaians-Kizhi, Teleuts, Shors, Tuvinians, Todjins, Tofalars, Sojots, Khakassians, Buryats, Evenks), Central/Eastern Asia (Mongolians and Koreans) and Eastern Europe (Kalmyks and Russians). Based on both, the distribution pattern of Y-chromosomal haplogroups and results on AMOVA analysis we observed the statistically significant genetic differentiation between the populations of Baikal and Altai–Sayan regions. We suggest that these regional differences can be best explained by different contribution of Central/Eastern Asian and Eastern European paternal lineages into gene pools of modern South Siberians. The population of the Baikal region demonstrates the prevalence of Central/Eastern Asian lineages, whereas in the populations of Altai and Sayan regions the highest paternal contribution resulted from Eastern European descent is revealed. Yet, our data on Y-chromosome STRs variation demonstrate the clear differences between the South Siberian and Eastern European R1a1-lineages with the evolutionary ages compatible with divergence time between these two regional groups.

Link

What's a modern girl to do?

Maureen Dowd writes an interesting piece in the New York Times about the evolution of the relationship between the two genders, and how early feminism appears to have been reversed in favor of more traditional gender roles. Interesting reading overall, but his snippet caught my attention:

A 2005 report by researchers at four British universities indicated that a high I.Q. hampers a woman's chance to marry, while it is a plus for men. The prospect for marriage increased by 35 percent for guys for each 16-point increase in I.Q.; for women, there is a 40 percent drop for each 16-point rise.

mtDNA of Latvians

Interesting new study on a Baltic-speaking population. From the conclusions:

Overall, the present study fills a gap which existed and shows that the maternal lineages of Baltic-speaking populations, Latvians and Lithuanians, and of their Slavonic- and Finno-Ugric-speaking neighbours, in particular Estonians, form a close cluster. This cluster also includes Germans, as well as Germanic-speaking Scandinavians, suggesting a recent shared maternal ancestry as well as pre-historic and historic time gene flows across linguistic borders. However, this maternal gene flow (migration of females) contrasts with an apparent lack of westward flow of hg N3 Y chromosomes (migration of males). The Baltic-speaking populations largely share a mosaic of frequencies that, in Europe, brings them together specifically with the Finnic-speaking populations, both those living in the Baltic area and those living in the Volga Basin. It remains to be seen whether rapidly advancing technologies for complete genome variation studies may in future reveal autosomal genes with a spread closely matching that of either of the contrasting haploid genetic systems of the Y chromosome and mtDNA.

Haplogroup frequencies in Latvians and others:



The paper also mentions briefly some information about the age of haplogroup N3:

Meanwhile, it is interesting to note that the calculations of Kasperaviciuteet al. (2004) suggested very similar expansion times, around 7000 - 8000 BP, for the Lithuanian and Estonian hg N3 Y chromosomes, which are probably also applicable to Latvians. Therefore, it is indeed possible that the spread of hg N3 among the ancestral populations of Estonians, on the one hand, and the Baltic-speaking populations on the other, pre-date the advent of the Neolithic age in the East Baltic and may be part of the post-LGM re-colonisation of the region.

The authors refer to an article (Ann Hum Genet 68, 438-452) which gives estimates of the age of haplogroup N3:

The lower gene diversity and nearly star-like median joining network of Lithuanian HgN3 chromosomes suggests a bottleneck involving HgN3 chromosomes in Lithuania; therefore, a demographic analysis using a Bayesian-based coalescence approach was performed (Table 6). A signal of population growth was detected both in Lithuanians and Estonians (the Latvian sample was excluded from this analysis because of the small sample size), and also for the combined dataset, corrected for differences in sample sizes. The dates of the start of the population growth depended greatly on the mutation rate estimate used for calculations, and varied from ~1000 years (using the mutation rate obtained from father-son pairs (Kayser et al. 2000b)) to ~7-8000 years (using the phylogenetic mutation rate estimate (Zhivotovsky et al. 2004)). The true date probably lies in between these estimates. Interestingly, similar dates were obtained for HgR1a Lithuanian chromosomes and all Y chromosomes, indicating that population growth was characteristic for the whole population, while a reduction of diversity is seen only among HgN3 chromosomes.

Hence, the authors of the current paper arbitrarily picked the earliest date as supportive of their pre-Neolithic hypothesis, even though the data can't distinguish between Neolithic and pre-Neolithic. Moreover, even using the phylogenetic mutation rate, the confidence intervals are consistent with both the Paleolithic and Neolithic dates.



This underscores the importance of appreciating the many factors which contribute to error in time estimates using molecular data on living populations.

Annals of Human Genetics (Online early)

Mitochondrial DNA Portrait of Latvians: Towards the Understanding of the Genetic Structure of Baltic-Speaking Populations

L. Pliss et al.

Mitochondrial DNA (mtDNA) variation was investigated in a sample of 299 Latvians, a Baltic-speaking population from Eastern Europe. Sequencing of the first hypervariable segment (HVS-I) in combination with analysis of informative coding region markers revealed that the vast majority of observed mtDNAs belong to haplogroups (hgs) common to most European populations. Analysis of the spatial distribution of mtDNA haplotypes found in Latvians, as well as in Baltic-speaking populations in general, revealed that they share haplotypes with all neighbouring populations irrespective of their linguistic affiliation. Hence, the results of our mtDNA analysis show that the previously described sharp difference between the Y-chromosomal hg N3 distribution in the paternally inherited gene pool of Baltic-speaking populations and of other European Indo-European speakers does not have a corresponding maternal counterpart.

Link

Using complex words make you look less intelligent

The secret of impressive writing? Keep it plain and simple (EurekAlert)

Writers who use long words needlessly and choose complicated font styles are seen as less intelligent than those who stick with basic vocabulary and plain text, according to new research from the Princeton University in New Jersey, to be published in the next edition of Applied Cognitive Psychology.

This implies that efforts to impress readers by using florid font styles and searching through a thesaurus may have the opposite effect.

Study author Daniel Oppenheimer based his findings on students' responses to writing samples for which the complexity of the font or vocabulary was systematically manipulated. In a series of five experiments, he found that people tended to rate the intelligence of authors who wrote essays in simpler language, using an easy to read font, as higher than those who authored more complex works.

"It's important to point out that this research is not about problems with using long words but about using long words needlessly," said study author Daniel Oppenheimer.

"Anything that makes a text hard to read and understand, such as unnecessarily long words or complicated fonts, will lower readers' evaluations of the text and its author."

The samples of text included graduate school applications, sociology dissertation abstracts, and translations of a work of Descartes. Times New Roman and italicised Juice font were used in samples to further assess the effect of fluency on rating levels.

Interestingly, by making people aware that the source of low fluency was irrelevant to judgement, Oppenheimer found that they overcompensated and became biased in the opposite direction. In a final experiment, he provided samples of text printed with normal and low printer toner levels. The low toner levels made the text harder to read, but readers were able to identify the toner as being responsible for the difficulty, and therefore didn't blame the authors.

"The continuing popularity amongst students of using big words and attractive font styles may be due to the fact that they may not realise these techniques could backfire," Oppenheimer noted.

"One thing seems certain: write as simply and plainly as possible and it's more likely you'll be thought of as intelligent."