Genetica. 2009 Sep 30. [Epub ahead of print]
Mitochondrial sequence variation in ancient horses from the Carpathian Basin and possible modern relatives.
Priskin K, Szabó K, Tömöry G, Bogácsi-Szabó E, Csányi B, Eördögh R, Downes CS, Raskó I.
Movements of human populations leave their traces in the genetic makeup of the areas affected; the same applies to the horses that move with their owners This study is concerned with the mitochondrial control region genotypes of 31 archaeological horse remains, excavated from pre-conquest Avar and post-conquest Hungarian burial sites in the Carpathian Basin dating from the sixth to the tenth century. To investigate relationships to other ancient and recent breeds, modern Hucul and Akhal Teke samples were also collected, and mtDNA control region (CR) sequences from 76 breeds representing 921 individual specimens were combined with our sequence data. Phylogenetic relationships among horse mtDNA CR haplotypes were estimated using both genetic distance and the non-dichotomous network method. Both methods indicated a separation between horses of the Avars and the Hungarians. Our results show that the ethnic changes induced by the Hungarian Conquest were accompanied by a corresponding change in the stables of the Carpathian Basin.
Link
Showing posts with label Avars. Show all posts
Showing posts with label Avars. Show all posts
October 03, 2009
September 20, 2009
History of the people of the Hungarian plain in the 1st millennium
Hum Biol. 2008 Dec;80(6):655-67
History of the peoples of the Great Hungarian Plain in the first millennium: a craniometric point of view
Holló G, Szathmáry L, Marcsik A, Barta Z.
Holló G, Szathmáry L, Marcsik A, Barta Z.
We carried out an examination relying on six dimensions of 1,573 crania coming from the Great Hungarian Plain. The crania represent seven archeological periods: Sarmatian age (1-4th century), the period of transition (about 400-420), Hun and Gepidic epochs (about 420-455 and 455-567, respectively), early Avar age (about 568-670), late Avar period (about 670-895), the epoch of the Hungarian conquest and settlement (about 895-1000), and the Arpadian age (about 1000-1301). We were curious about the anatomical background behind cultural changes of the various populations that inhabited this area. After having noticed some discontinuities between the populations, as revealed by univariate analysis of single dimensions, we performed a principal-components analysis to see whether or not the diverse components showed eventual breaks in the sequence of the populations. Knowing that all the dominant populations had Asian roots, except for the Gepids of Germanic origin, we expected a considerable difference between the Gepidic population and all the other inhabitants. We also assumed that a conquest itself with a large-scale assimilation was unlikely to leave breaklike traits in anatomical patterns, except for aggressive conquests. We found that the second principal component (which correlated with cranial breadth and partly with height) showed a remarkable hiatus in both sexes between Gepids and early Avars. Having done a statistical proof (simultaneous tests for general linear hypotheses) of the observed phenomenon, we found that the gap referring to subsequent populations was significant only in males. A possible reason for this result is that the Avar conquest was much more radical than has been thought. In addition, considering that men were more likely to die in wars, women survived and were assimilated into the conquerors' populations with higher probability, so it is not surprising that the results of multicomparison tests are significant only in men.
Link
Link
April 09, 2008
Origins of Mongoloid mtDNA in Slavs
A very interesting article which addresses the issue of the Mongoloid mitochondrial component in Slavs. I like this kind of paper that looks at the minor features of populations, rather than their broad general characteristics that are well known by now, and indeed were known even before genetics came into the picture.
From the paper:
Russian Journal of Genetics, 10.1007/s11177-008-3016-9
On the origin of Mongoloid component in the mitochondrial gene pool of Slavs
B. A. Malyarchuk, M. A. Perkova and M. V. Derenko
Abstract The data on mitochondrial DNA (mtDNA) restriction polymorphism in Czech population (n = 279) are presented. It was demonstrated that in terms of their structure, mitochondrial gene pools of Czechs and other Slavic populations (Russians, Poles, Slovenians, and Bosnians) were practically indistinguishable. In Czechs, the frequency of eastern-Eurasian (Mongoloid) mtDNA lineages constituted 1.8%. The spread of eastern-Eurasian mtDNA lineages belonging to different ethnolinguistic groups in the populations of Europe was examined. Frequency variations of these DNA lineages in different Slavic groups was observed, with the range from 1.2 and 1.6% in Southern and Western Slavs, respectively, to 1.3 to 5.2% in Eastern Slavs, the Russian population of Eastern Europe. The highest frequency of Mongoloid component was detected in the mitochondrial gene pools of Russian populations from the Russian North and the Northwestern region of Russia. This finding can be explained in terms of assimilation of northern-European Finno-Ugric populations during the formation of the Russian population of these regions. The origin of Mongoloid component in the gene pools of different groups of Slavs is discussed.
Link
From the paper:
The overwhelming majority of mtDNA clusters, identified in Czechs, were of the western-Eurasian origin. The frequency of eastern-Eurasian (Mongoloid) mtDNA lineages in this population constituted 1.8% (haplogroups A, N9a, and M). African lineage (with the frequency of 0.4%) belonging to haplogroup L2a and marked by the +13803HaeIII variant was also detected.
...
Low frequency of Mongoloid mtDNA variant in Letts and Lithuanians suggests that Mongoloid component was probably not typical of Balto-Slavic protogene pool. Thus, it seems reasonable that accumulation of Mongoloid mtDNA lineages in Slavs and their ancestors was intensified only in the last 4000 years.
...
The highest frequencies of the Mongoloid component are typical of the Russian populations from Russian Pomor’e and Northwestern region. These populations, however, differ in the mtDNA haplogroup composition. It was established that assimilation of the indigenous pre-Slavic population of Eastern Europe by true Slavs was of great importance to the process of the development of Russian population.
...
It is suggested that after the decay of Avar Khaganate the populations included into it were assimilated by Slavic tribes [34]. It is thereby suggested that rather high frequencies of eastern-Eurasian mtDNA lineages observed in the gene pools of some populations of Western and Southern Slavs (especially on the territoryof former Avar Khaganate) can be considered as a consequence of the process described.
Concerning the population of Eastern Europe, it should be noted that the forest zone of Eastern Europe was the area of intense population admixture [35]. It seems likely, that formation of the complex of Mongoloid traits happened not later than in Upper Paleolithic. For this reason, it is suggested that East Siberian populations could have much time for migration to Eastern Europe [35]. The number of such migrations still remains unclear, since in the northwest of Eastern Europe Mongoloid component is detected 10 000–8000 years ago; in Dnepr–Donetsk tribes, 7000–6000 years ago, and on the territory of Ivanovo oblast (Sakhtysh), 6000–5000 years ago [35, 36]. The data on mtDNA variation in Russian populations are consistent with anthropological data, since they point to the substantial differences in the frequencies of Mongoloid mtDNA lineages between the Russian populations of the Russian North, Northwest, and the central/southern regions of the European part of Russia (Table 3). We hope that future investigations would provide
the possibility of analyzing the chronology of the development of the Mongoloid component diversity in the gene pools of Russians and other Slavic populations.
Russian Journal of Genetics, 10.1007/s11177-008-3016-9
On the origin of Mongoloid component in the mitochondrial gene pool of Slavs
B. A. Malyarchuk, M. A. Perkova and M. V. Derenko
Abstract The data on mitochondrial DNA (mtDNA) restriction polymorphism in Czech population (n = 279) are presented. It was demonstrated that in terms of their structure, mitochondrial gene pools of Czechs and other Slavic populations (Russians, Poles, Slovenians, and Bosnians) were practically indistinguishable. In Czechs, the frequency of eastern-Eurasian (Mongoloid) mtDNA lineages constituted 1.8%. The spread of eastern-Eurasian mtDNA lineages belonging to different ethnolinguistic groups in the populations of Europe was examined. Frequency variations of these DNA lineages in different Slavic groups was observed, with the range from 1.2 and 1.6% in Southern and Western Slavs, respectively, to 1.3 to 5.2% in Eastern Slavs, the Russian population of Eastern Europe. The highest frequency of Mongoloid component was detected in the mitochondrial gene pools of Russian populations from the Russian North and the Northwestern region of Russia. This finding can be explained in terms of assimilation of northern-European Finno-Ugric populations during the formation of the Russian population of these regions. The origin of Mongoloid component in the gene pools of different groups of Slavs is discussed.
Link
March 03, 2007
AAPA 2007 abstracts
The 2007 meeting of the American Association of Physical Anthropologists will be held in about a month. As in previous years, here are some interesting abstracts to be presented at the meeting (pdf).
(up to page 94)
Homo floresiensis Cranial and Mandibular Morphology
J.Y. Anderson, University of New Mexico
These results suggest the Flores material does not represent a population derived from Australomelanesians, and do not represent a non-pathological dwarfed population of Homo sapiens. These results do not completely rule out a representation of a microcephalic dwarfed population, at the same time it is suggested possible affinities to earlier hominin groups is equally parsimonious.
Do Qafzeh and Skhūl represent the ancestors of Upper Paleolithic modern humans? A dental perspective.
S.E. Bailey et al.
If these fossils represent the source of early Upper Paleolithic people, there is no need to invoke admixture with Neandertals to explain archaic dental features observed in some early Upper Paleolithic humans.
Ancient Cemetery Social Patterning Project: Ancient DNA in Tirup Cemetery.
L.E. Baker et al.
Reconstructing the settlement history of the central Andes from mitochondrial DNA analyses.
K. Batai et al.
We found that among central Andean ancient and modern population samples, haplogroup B frequencies increased through time, while haplogroup A frequencies declined. At this point, we do not yet have sufficient data to determine whether these patterns indicate different population histories between ancient coastal and modern highland populations, or a larger temporal trend in entire central Andes region
Analysis of Genetic Diversity in Ethnic Populations of Afghanistan
P. Bermudez et al.
The Middle East has the distinction of being a major crossroads of human migration. The genetic diversity of Afghanistan, however, has long remained a missing piece to this rich and complex puzzle. To explore both the diversity within Afghanistan and to understand the relative genetic contributions from various groups throughout the Eurasian continent, buccal swabs were collected from 252 unrelated Afghani men for mitochondrial DNA analysis. Each of these men hailed from
one of four major ethnic groups inhabiting the region: the Pashtun, Hazara, Tajik or
Nooristani. The Indo-Iranian speaking Pashtun represent the largest ethnic group in Afghanistan; the Tajiks have a complex genetic history that likely involves admixture between Turkic groups and smaller distinct ethnic groups within Afghanistan; the Hazara, on the other hand, are thought to represent remnants of Ghengis Khan’s army left behind as it expanded through Asia; and the Nooristani have biological links to populations in northern Pakistan and the
claim of descent from Alexander the Great’s army. All samples were analyzed for HVS1
and SNP variation. In all of these populations, Western Eurasian haplogroups (H, HV, R, J, I, U, X) were most common, with the highest frequency occurring in the Nooristanis, while the remaining East Eurasian haplogroups including D, G, and various other M types. The results of this study will be instrumental in expanding our knowledge of Afghani genetic history, in addition to broadening our understanding of population migrations throughout West and Central Asia.
Dental variation in Holocene Khoesan populations.
W. Black et al.
Are the Koh an indigenous population of the Hindu Kush? II: a dental morphology investigation.
S. Blaylock and B.E. Hemphill
Little is known about the population history of the ethnic groups in Chitral District, Pakistan, an area long been regarded as the “crossroads of Asia.” Some scholars emphasize that the Koh lifeway is the consequence of long-standing indigenous isolation. Others stress the equestrian
tradition among Koh villagers indicate they are descendants of Central Asians who emigrated across the Hindu Kush Mountains during the second millennium BC. To still others, an array of Persian linguistic inclusions indicates the Koh are more recent emigrants from the Iranian Plateau. This investigation tests these hypotheses for Koh origins through assessment of dental
morphology variations of the permanent dentition scored as 17 tooth-trait combination in accordance with the Arizona State University Dental Morphology System in a sample of 134 Kho school children from Chitral City. These data were contrasted with 17 additional samples. Comparisons are in two stages and include cluster analysis, multidimensional scaling and principal coordinates analysis. First, sex-pooled and sex-specific data compared Koh to six contemporary ethnic groups from India. Results indicate the Koh share equidistant affinities to Indo-European speaking west-Central Indian and Dravidianspeaking South Indian ethnic groups.
Second, sex-pooled data compared the Koh to 13 prehistoric samples from Neolithic to Early Iron Age sites located in the Indus Valley, Central Asia and the Iranian Plateau. Results indicate that the Koh share little affinity to prehistoric Indus Valley groups. Rather, the Koh share nearly equal affinities to prehistoric inhabitants of the Iranian Plateau and Central Asia.
A Howells grasp on prehistoric and recent Japan: A precursor to the Kennewick connection.
C. L. Brace, N. Seguchi.
Using many more samples, our results are compatible with what Howells showed for his Japanese comparisons, and,using the neighbor-joining technique, we can go on to show that Kennewick ties with the Ainu who are the descendants of the Jōmon.The Jōmon then are the probable ancestors of
the first inhabitants of the western hemisphere.
Admixture in Mexico City: implications for admixture mapping.
E. Cameron et al.
"The average proportions of Native American, European and West African admixture were estimated as 65%, 30% and 5% respectively."
"In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95% credible interval 3.8 – 22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is
paralleled, and possibly maintained, by socioeconomic stratification."
Intracontinental Distribution of Haplotype Variation: Implications for Human Demographic History.
M.C. Campbell et al.
"These results suggest that diverse African populations were more subdivided with lower levels of gene flow during human history."
Social stratification in a Christian cemetery? An assessment of stress indicators and social status at Anglo-Saxon Raunds.
E.F. Craig, J.L. Buckberry
"The occurrence of statistically more individuals with both cribra orbitalia and tibial periostitis in plain graves rather than graves with stone arrangements, and LEH in plain graves rather than graves with a cover or marker, suggests that individuals buried in more elaborate graves enjoyed better levels of health and may been of higher social status than those buried in plain graves."
Variability of the Stature of the Central European Population from the Neolithic Age to Present
M. Dobisíková, S. Katina, P. Velemínský
The aim of our contribution is to characterize the changes of the stature in adult populations that have lived in Central Europe from the Neolithic period up to the present. Our sample consisted of 802 male and 704 female skeletons. The evaluation was conducted taking into account the demographic structure of the groups studied. We confronted the findings with the living
conditions of the populations known to have a significant impact on human stature, in
addition to genetic factors. We thus considered the socioeconomic status of the populations that might have influenced the quality of nutrition. We focused our attention on the socioeconomic aspect of populations of the early Middle Ages and the recent population. We compared socially higher placed part of the society with socially poorer classes (agricultural groups) (177 male, 178 female) in the early-medieval population of Great Moravia. No statistically significant
differences were found among individual social groups. To calculate the stature of last populations we used the regression equations developed by Breitiger (1937) and Bach (1965). The
calculation was based only on the length of the femur that is directly involved in body length. The impact of the secular trend was evaluated in the recent population. We compared two autopsy skeletal samples from the beginning and ends of the 20th century (107 male, 53 female). Statistically significant differences between them was found. Finally, we proposed regression equations for calculating the stature of the contemporary Czech population usable in forensic practice.
A phylogeographic analysis of haplogroup D5 and its implications for the peopling of East Asia.
M.C. Dulik
While genetic studies have focused on the Altai region of South Siberia as a possible place of origin for Native Americans, it is also possible that it played a similarly significant role in the peopling of East Asia. A Siberian connection to other East Asian populations has already been proposed based on archaeological, linguistic and classical genetic marker evidence. In this study, we examined a rare and ancient haplogroup, D5c, in an effort to elucidate early population movements in East Asia. Previous studies suggested that D5 first emerged in China and
spread northwards from there. However,given the number of D5c individuals (12) and the range of variation in D5 from the Altai region, it is conceivable that this haplogroup instead originated in South Siberia and spread from there during the initial movements of Paleolithic peoples. To est this hypothesis, we obtained complete mtDNA sequences for individuals represented by aplogroups D4 and D5 and acquired additional sequences available through GenBank and published literature. We then analyzed the entire dataset with the reduced median network approach and
phylogeographic modeling. Our results suggest that Southern Siberia did play a
critical role in the spread of the D5 haplogroup. This focus on relatively unique
mtDNA lineages specific to certain populations allowed us to better understand
the processes of ancient settlement and subsequent population movements that helped shape the current genetic landscape of East Asia.
More than meets the eye: LB1, the transforming hominin.
R.B. Eckhard et al.
LB1 is not a microcephalic.
D. Falk1 et al.
Is there biological meaning to “Hispanic” in New Mexico?
H.J.H. Edgar, C.M. Willermet
Establishing the nature of the differences between skull samples from two populations.
S.P. Evans et al.
A sample of 1188 skulls from the Romano-British site at Poundbury shows differences from the 18th century sample of 822 skulls from Spitalfields. Both sites are in the south of England, but 1400 years apart in time. The differences between the sites could be due to immigrations over time and/or to adaptation to the environment. The aim of the study was to establish the nature of the differences, in particular the relative importance of genetic and acquired traits.
Frequencies of 22 selected non-metric traits in juvenile, female and male skulls were analysed. Initial logistic regression analyses established that there was a substantial difference between the two sites and between juveniles and adults, with some sexual dimorphism. The modified mean
measure of divergence, used to calculate overall distances between the groups, showed the juvenile groups to be closer to each other than to adults from their respective sites. Across sites, males were most distant from each other. The largest distance was between Spitalfields juveniles and males. Principal coordinate analysis, followed by a jackknife stability analysis, revealed a pattern indicating that this came about through growth and adaptation. Omitting traits in turn, procrustes methods were used to identify the most influential, all of which
were acquired through ageing or lifestyle. Without these traits there was no significant
difference between the two juvenile groups and no sexual dimorphism. These results show the importance of the behavioural environment in determining morphology, and the resilience of populations to genetic change.
Peopling of the Pacific: resolving the controversy.
J.S. Friedlaender et al.
"Our survey of mitochondrial DNA, Ychromosome, and over 600 short tandem repeat polymorphisms and 200 insertiondeletions from over 40 Pacific populations indicates Polynesians have their genetic
origins to both Melanesian and Taiwanese (Southeast Asian) populations in significant degrees. In Island Melanesia, there is a small but clear ancient genetic footprint in certain Oceanic-speaking populations (i.e., linguistically related to Polynesian). The survey results underscore the extraordinary diversity of Island Melanesian populations from one language group to another, and from island to island. This is the result of the small sizes of the populations and the very long extent of modern human settlement there (over 30,000 years)."
Multivariate studies of cranial form: the impact of Howells' research on defining Homo sapiens.
J.B. Gaines et al.
Demographic simulations of the admixture between foragers and farmers in central European Neolithic.
P. Galeta, J. Bruzek.
William White Howells: A physical anthropologist in the making.
E. Giles
The relationship of Nubians with their neighbors, the Egyptians.
By, K. Godde.
The Phylogeography of Haplogroup N1a
Gokcumen O et al.
Recent studies have revealed a complex geographic distribution of haplogroup N1a. This rare and distinctive lineage is widely distributed across Eurasia and Africa, but always found at very low frequencies. However, despite its rarity, the genetic diversity within N1a has remained relatively high (h=0.9605). The reduced median network of N1a haplotypes not only reflects
this level of diversity, but also exhibits several relatively well-defined branches. The
distribution of N1a is intriguing because of revealing previously unrecognized connections between populations. What makes N1a even more interesting is the prevalence of this lineage in ancient European populations. Haak et al. (2005) found that 25% of their European Neolithic
samples belonged to N1a and dated to ~5000 BCE, whereas the frequency of this lineage in contemporary Europeans is only ~0.2%. In addition, an Iron Age skeleton from Kazakhstan had an N1a haplotype, suggesting the existence of this lineage in the Altai Republic in ~500BCE (Ricaut et al. 2004). Indeed, we found several haplogroup N1a mtDNAs in indigenous Altaians and Altaian Kazakhs. To further elucidate the phylogeography of this lineage in Central Asia, we sequenced the whole mtDNA genomes of our N1a haplotypes, and analyzed the resulting data with several quantitative methods and simulation programs to estimate their expansion times and spatial
distribution in Eurasia. Our findings suggest that there are two well-defined sublineages
within N1a, and that the dispersal of this haplogroup could be associated with the Neolithic expansion and with prehistoric interactions between Central Asian and European populations.
Understanding human races: the retreat of neutralism.
Henry Harpending
Discussion and debate about human races has been dominated for decades by neutral theory and statistics. Since this literature never posed a real question, it has never produced an answer. Lewontin's 1972 paper with its claim that a value of 1/8 of a statistic like Fst is “small” and that this means that human race differences are insignificant is a staple of our textbooks. Recently geneticists have had a closer look and pointed out that Fst of 1/8 describes differences among sets of half sibs and few claim that half sibs are insignificantly related. Anthony Edwards has shown that the significance of differences is in the correlation structure of a large number of traits, again denying the Lewontin assertion that human differences are small. Alan Templeton in 1998 claimed that human races were less differentiated that races of some other large mammals, but he compared human nuclear DNA statistics with statistics from mtDNA in the other species. An appropriate comparison shows that human are more, not less, differentiated than other large mammal species. Since neutral differences are a passive
record of demographic history they are not very significant for issues of functional biology. Newly available data sources allow us to study the natural selection of race differences instead of their drift. It appears that there is a lot of ongoing evolution in our species and the loci under strong selection on different continents only partially overlap. Human race differences may be increasing rapidly.
Acceleration of adaptive evolution in modern humans.
J. Hawks and G. Cochran
Humans vastly increased in numbers during the past 40,000 years. Recent surveys of human genomic variation have suggested a large surplus of recent positive selection, indicated by excess linkage disequilibrium and skewed SNP frequency spectra. We applied estimates of prehistoric and historic population sizes to estimate the importance of population growth in explaining the number of recent adaptive mutations. Our estimates are consistent with genomic evidence in suggesting that the rate of generation of positively selected genes has increased as much as a hundredfold during the past 40,000 years.
Do skeletal features reflect this genomic evidence of selection? Under positive
selection, rapid appearance of new variants during the terminal Pleistocene and early
Holocene would cause maximal phenotypic change during the last 2000-4000 years. We compared original and published series of Holocene cranial data from Europe, Jordan, Nubia, South Africa, and China, in addition to Late Pleistocene samples from Europe and West Asia, to test the hypothesis that the genomic acceleration in positive selection correlates with phenotypic evolution during this time period. A constellation of features in the face and cranial vault, notably including endocranial volume, changed globally during this time period and documents common patterns of selection in different regions. Holocene changes were similar in pattern and chronologically faster than those at the archaic-modern transition, which themselves were rapid compared to earlier hominid evolution. In genomic and craniometric terms, the origin of modern humans was a minor event compared to more recent evolutionary changes.
Patterns of admixture in Mexican Americans assessed from 101,150 SNPs.
M.G. Hayes et al.
"No significant differences were observed between the 10 subsets, allowing us to average the admixture estimates across the subsets: 68% European, 27% Asian (as a proxy for Native American), and 6% African."
Gender, wealth, and status in Bronze Age Central Asia: a dental pathology investigation.
B.E. Hemphill.
Sahara passage: the post-glacial recolonisation of North Africa by mitochondrial L* haplotypes.
AD Holden. P Forster.
Secular trends of the European male facial skull from the Migration Period to the present.
E. Jonke et al.
We examined secular trends in the facial skull over three Central European samples spanning more than 13 centuries. Data are 43 conventional cephalometric landmark points for samples dating from 680–830 CE, from the mid-19th Century, and from living Austrian young adult males. Methods of geometric morphometrics demonstrate shape differences across the samples, and also
differences in allometry. There is a stronginteraction between these, so that group mean differences are different for small and large individuals (equivalently, allometry is
different from period to period). The oldest sample, from the Migration Period, exhibits
allometric features that may possibly be Turkic. There are implications for the
craniofacial biologist interested in growth trends or growth predictions in ethnically
mixed populations. There are also implications for the discussion concerning the morphology of the Avars (an ethnic group of probably Central Asian origin who conquered large parts of Central Europe during the Migration Period and who interbred with other incoming groups after their conquest by Charlemagne), and also the relation of these findings to current thinking on gnathic reduction trends.
Roman Gladiators - The Osseous Evidence.
F. Kanz, K. Grossschmidt
Paternal heritage for the Indonesian peoples.
T. M. Karafet et al.
Feeding the children: Isotopic evidence for weaning practices in the ancient Greek colony of Apollonia (5th-2nd centuries BC).
C. Kwok, A. Keenleyside.
Misconceptions about the postcranial skeleton of Homo floresiensis.
S.G. Larson et al.
A comparison of mitochondrial DNA and Y chromosome DNA variation on Manus Island.
K.E. Latham et al.
(up to page 94)
Homo floresiensis Cranial and Mandibular Morphology
J.Y. Anderson, University of New Mexico
These results suggest the Flores material does not represent a population derived from Australomelanesians, and do not represent a non-pathological dwarfed population of Homo sapiens. These results do not completely rule out a representation of a microcephalic dwarfed population, at the same time it is suggested possible affinities to earlier hominin groups is equally parsimonious.
Do Qafzeh and Skhūl represent the ancestors of Upper Paleolithic modern humans? A dental perspective.
S.E. Bailey et al.
If these fossils represent the source of early Upper Paleolithic people, there is no need to invoke admixture with Neandertals to explain archaic dental features observed in some early Upper Paleolithic humans.
Ancient Cemetery Social Patterning Project: Ancient DNA in Tirup Cemetery.
L.E. Baker et al.
Reconstructing the settlement history of the central Andes from mitochondrial DNA analyses.
K. Batai et al.
We found that among central Andean ancient and modern population samples, haplogroup B frequencies increased through time, while haplogroup A frequencies declined. At this point, we do not yet have sufficient data to determine whether these patterns indicate different population histories between ancient coastal and modern highland populations, or a larger temporal trend in entire central Andes region
Analysis of Genetic Diversity in Ethnic Populations of Afghanistan
P. Bermudez et al.
The Middle East has the distinction of being a major crossroads of human migration. The genetic diversity of Afghanistan, however, has long remained a missing piece to this rich and complex puzzle. To explore both the diversity within Afghanistan and to understand the relative genetic contributions from various groups throughout the Eurasian continent, buccal swabs were collected from 252 unrelated Afghani men for mitochondrial DNA analysis. Each of these men hailed from
one of four major ethnic groups inhabiting the region: the Pashtun, Hazara, Tajik or
Nooristani. The Indo-Iranian speaking Pashtun represent the largest ethnic group in Afghanistan; the Tajiks have a complex genetic history that likely involves admixture between Turkic groups and smaller distinct ethnic groups within Afghanistan; the Hazara, on the other hand, are thought to represent remnants of Ghengis Khan’s army left behind as it expanded through Asia; and the Nooristani have biological links to populations in northern Pakistan and the
claim of descent from Alexander the Great’s army. All samples were analyzed for HVS1
and SNP variation. In all of these populations, Western Eurasian haplogroups (H, HV, R, J, I, U, X) were most common, with the highest frequency occurring in the Nooristanis, while the remaining East Eurasian haplogroups including D, G, and various other M types. The results of this study will be instrumental in expanding our knowledge of Afghani genetic history, in addition to broadening our understanding of population migrations throughout West and Central Asia.
Dental variation in Holocene Khoesan populations.
W. Black et al.
Are the Koh an indigenous population of the Hindu Kush? II: a dental morphology investigation.
S. Blaylock and B.E. Hemphill
Little is known about the population history of the ethnic groups in Chitral District, Pakistan, an area long been regarded as the “crossroads of Asia.” Some scholars emphasize that the Koh lifeway is the consequence of long-standing indigenous isolation. Others stress the equestrian
tradition among Koh villagers indicate they are descendants of Central Asians who emigrated across the Hindu Kush Mountains during the second millennium BC. To still others, an array of Persian linguistic inclusions indicates the Koh are more recent emigrants from the Iranian Plateau. This investigation tests these hypotheses for Koh origins through assessment of dental
morphology variations of the permanent dentition scored as 17 tooth-trait combination in accordance with the Arizona State University Dental Morphology System in a sample of 134 Kho school children from Chitral City. These data were contrasted with 17 additional samples. Comparisons are in two stages and include cluster analysis, multidimensional scaling and principal coordinates analysis. First, sex-pooled and sex-specific data compared Koh to six contemporary ethnic groups from India. Results indicate the Koh share equidistant affinities to Indo-European speaking west-Central Indian and Dravidianspeaking South Indian ethnic groups.
Second, sex-pooled data compared the Koh to 13 prehistoric samples from Neolithic to Early Iron Age sites located in the Indus Valley, Central Asia and the Iranian Plateau. Results indicate that the Koh share little affinity to prehistoric Indus Valley groups. Rather, the Koh share nearly equal affinities to prehistoric inhabitants of the Iranian Plateau and Central Asia.
A Howells grasp on prehistoric and recent Japan: A precursor to the Kennewick connection.
C. L. Brace, N. Seguchi.
Using many more samples, our results are compatible with what Howells showed for his Japanese comparisons, and,using the neighbor-joining technique, we can go on to show that Kennewick ties with the Ainu who are the descendants of the Jōmon.The Jōmon then are the probable ancestors of
the first inhabitants of the western hemisphere.
Admixture in Mexico City: implications for admixture mapping.
E. Cameron et al.
"The average proportions of Native American, European and West African admixture were estimated as 65%, 30% and 5% respectively."
"In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95% credible interval 3.8 – 22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is
paralleled, and possibly maintained, by socioeconomic stratification."
Intracontinental Distribution of Haplotype Variation: Implications for Human Demographic History.
M.C. Campbell et al.
"These results suggest that diverse African populations were more subdivided with lower levels of gene flow during human history."
Social stratification in a Christian cemetery? An assessment of stress indicators and social status at Anglo-Saxon Raunds.
E.F. Craig, J.L. Buckberry
"The occurrence of statistically more individuals with both cribra orbitalia and tibial periostitis in plain graves rather than graves with stone arrangements, and LEH in plain graves rather than graves with a cover or marker, suggests that individuals buried in more elaborate graves enjoyed better levels of health and may been of higher social status than those buried in plain graves."
Variability of the Stature of the Central European Population from the Neolithic Age to Present
M. Dobisíková, S. Katina, P. Velemínský
The aim of our contribution is to characterize the changes of the stature in adult populations that have lived in Central Europe from the Neolithic period up to the present. Our sample consisted of 802 male and 704 female skeletons. The evaluation was conducted taking into account the demographic structure of the groups studied. We confronted the findings with the living
conditions of the populations known to have a significant impact on human stature, in
addition to genetic factors. We thus considered the socioeconomic status of the populations that might have influenced the quality of nutrition. We focused our attention on the socioeconomic aspect of populations of the early Middle Ages and the recent population. We compared socially higher placed part of the society with socially poorer classes (agricultural groups) (177 male, 178 female) in the early-medieval population of Great Moravia. No statistically significant
differences were found among individual social groups. To calculate the stature of last populations we used the regression equations developed by Breitiger (1937) and Bach (1965). The
calculation was based only on the length of the femur that is directly involved in body length. The impact of the secular trend was evaluated in the recent population. We compared two autopsy skeletal samples from the beginning and ends of the 20th century (107 male, 53 female). Statistically significant differences between them was found. Finally, we proposed regression equations for calculating the stature of the contemporary Czech population usable in forensic practice.
A phylogeographic analysis of haplogroup D5 and its implications for the peopling of East Asia.
M.C. Dulik
While genetic studies have focused on the Altai region of South Siberia as a possible place of origin for Native Americans, it is also possible that it played a similarly significant role in the peopling of East Asia. A Siberian connection to other East Asian populations has already been proposed based on archaeological, linguistic and classical genetic marker evidence. In this study, we examined a rare and ancient haplogroup, D5c, in an effort to elucidate early population movements in East Asia. Previous studies suggested that D5 first emerged in China and
spread northwards from there. However,given the number of D5c individuals (12) and the range of variation in D5 from the Altai region, it is conceivable that this haplogroup instead originated in South Siberia and spread from there during the initial movements of Paleolithic peoples. To est this hypothesis, we obtained complete mtDNA sequences for individuals represented by aplogroups D4 and D5 and acquired additional sequences available through GenBank and published literature. We then analyzed the entire dataset with the reduced median network approach and
phylogeographic modeling. Our results suggest that Southern Siberia did play a
critical role in the spread of the D5 haplogroup. This focus on relatively unique
mtDNA lineages specific to certain populations allowed us to better understand
the processes of ancient settlement and subsequent population movements that helped shape the current genetic landscape of East Asia.
More than meets the eye: LB1, the transforming hominin.
R.B. Eckhard et al.
LB1 is not a microcephalic.
D. Falk1 et al.
Is there biological meaning to “Hispanic” in New Mexico?
H.J.H. Edgar, C.M. Willermet
Establishing the nature of the differences between skull samples from two populations.
S.P. Evans et al.
A sample of 1188 skulls from the Romano-British site at Poundbury shows differences from the 18th century sample of 822 skulls from Spitalfields. Both sites are in the south of England, but 1400 years apart in time. The differences between the sites could be due to immigrations over time and/or to adaptation to the environment. The aim of the study was to establish the nature of the differences, in particular the relative importance of genetic and acquired traits.
Frequencies of 22 selected non-metric traits in juvenile, female and male skulls were analysed. Initial logistic regression analyses established that there was a substantial difference between the two sites and between juveniles and adults, with some sexual dimorphism. The modified mean
measure of divergence, used to calculate overall distances between the groups, showed the juvenile groups to be closer to each other than to adults from their respective sites. Across sites, males were most distant from each other. The largest distance was between Spitalfields juveniles and males. Principal coordinate analysis, followed by a jackknife stability analysis, revealed a pattern indicating that this came about through growth and adaptation. Omitting traits in turn, procrustes methods were used to identify the most influential, all of which
were acquired through ageing or lifestyle. Without these traits there was no significant
difference between the two juvenile groups and no sexual dimorphism. These results show the importance of the behavioural environment in determining morphology, and the resilience of populations to genetic change.
Peopling of the Pacific: resolving the controversy.
J.S. Friedlaender et al.
"Our survey of mitochondrial DNA, Ychromosome, and over 600 short tandem repeat polymorphisms and 200 insertiondeletions from over 40 Pacific populations indicates Polynesians have their genetic
origins to both Melanesian and Taiwanese (Southeast Asian) populations in significant degrees. In Island Melanesia, there is a small but clear ancient genetic footprint in certain Oceanic-speaking populations (i.e., linguistically related to Polynesian). The survey results underscore the extraordinary diversity of Island Melanesian populations from one language group to another, and from island to island. This is the result of the small sizes of the populations and the very long extent of modern human settlement there (over 30,000 years)."
Multivariate studies of cranial form: the impact of Howells' research on defining Homo sapiens.
J.B. Gaines et al.
Demographic simulations of the admixture between foragers and farmers in central European Neolithic.
P. Galeta, J. Bruzek.
William White Howells: A physical anthropologist in the making.
E. Giles
The relationship of Nubians with their neighbors, the Egyptians.
By, K. Godde.
The Phylogeography of Haplogroup N1a
Gokcumen O et al.
Recent studies have revealed a complex geographic distribution of haplogroup N1a. This rare and distinctive lineage is widely distributed across Eurasia and Africa, but always found at very low frequencies. However, despite its rarity, the genetic diversity within N1a has remained relatively high (h=0.9605). The reduced median network of N1a haplotypes not only reflects
this level of diversity, but also exhibits several relatively well-defined branches. The
distribution of N1a is intriguing because of revealing previously unrecognized connections between populations. What makes N1a even more interesting is the prevalence of this lineage in ancient European populations. Haak et al. (2005) found that 25% of their European Neolithic
samples belonged to N1a and dated to ~5000 BCE, whereas the frequency of this lineage in contemporary Europeans is only ~0.2%. In addition, an Iron Age skeleton from Kazakhstan had an N1a haplotype, suggesting the existence of this lineage in the Altai Republic in ~500BCE (Ricaut et al. 2004). Indeed, we found several haplogroup N1a mtDNAs in indigenous Altaians and Altaian Kazakhs. To further elucidate the phylogeography of this lineage in Central Asia, we sequenced the whole mtDNA genomes of our N1a haplotypes, and analyzed the resulting data with several quantitative methods and simulation programs to estimate their expansion times and spatial
distribution in Eurasia. Our findings suggest that there are two well-defined sublineages
within N1a, and that the dispersal of this haplogroup could be associated with the Neolithic expansion and with prehistoric interactions between Central Asian and European populations.
Understanding human races: the retreat of neutralism.
Henry Harpending
Discussion and debate about human races has been dominated for decades by neutral theory and statistics. Since this literature never posed a real question, it has never produced an answer. Lewontin's 1972 paper with its claim that a value of 1/8 of a statistic like Fst is “small” and that this means that human race differences are insignificant is a staple of our textbooks. Recently geneticists have had a closer look and pointed out that Fst of 1/8 describes differences among sets of half sibs and few claim that half sibs are insignificantly related. Anthony Edwards has shown that the significance of differences is in the correlation structure of a large number of traits, again denying the Lewontin assertion that human differences are small. Alan Templeton in 1998 claimed that human races were less differentiated that races of some other large mammals, but he compared human nuclear DNA statistics with statistics from mtDNA in the other species. An appropriate comparison shows that human are more, not less, differentiated than other large mammal species. Since neutral differences are a passive
record of demographic history they are not very significant for issues of functional biology. Newly available data sources allow us to study the natural selection of race differences instead of their drift. It appears that there is a lot of ongoing evolution in our species and the loci under strong selection on different continents only partially overlap. Human race differences may be increasing rapidly.
Acceleration of adaptive evolution in modern humans.
J. Hawks and G. Cochran
Humans vastly increased in numbers during the past 40,000 years. Recent surveys of human genomic variation have suggested a large surplus of recent positive selection, indicated by excess linkage disequilibrium and skewed SNP frequency spectra. We applied estimates of prehistoric and historic population sizes to estimate the importance of population growth in explaining the number of recent adaptive mutations. Our estimates are consistent with genomic evidence in suggesting that the rate of generation of positively selected genes has increased as much as a hundredfold during the past 40,000 years.
Do skeletal features reflect this genomic evidence of selection? Under positive
selection, rapid appearance of new variants during the terminal Pleistocene and early
Holocene would cause maximal phenotypic change during the last 2000-4000 years. We compared original and published series of Holocene cranial data from Europe, Jordan, Nubia, South Africa, and China, in addition to Late Pleistocene samples from Europe and West Asia, to test the hypothesis that the genomic acceleration in positive selection correlates with phenotypic evolution during this time period. A constellation of features in the face and cranial vault, notably including endocranial volume, changed globally during this time period and documents common patterns of selection in different regions. Holocene changes were similar in pattern and chronologically faster than those at the archaic-modern transition, which themselves were rapid compared to earlier hominid evolution. In genomic and craniometric terms, the origin of modern humans was a minor event compared to more recent evolutionary changes.
Patterns of admixture in Mexican Americans assessed from 101,150 SNPs.
M.G. Hayes et al.
"No significant differences were observed between the 10 subsets, allowing us to average the admixture estimates across the subsets: 68% European, 27% Asian (as a proxy for Native American), and 6% African."
Gender, wealth, and status in Bronze Age Central Asia: a dental pathology investigation.
B.E. Hemphill.
Sahara passage: the post-glacial recolonisation of North Africa by mitochondrial L* haplotypes.
AD Holden. P Forster.
Secular trends of the European male facial skull from the Migration Period to the present.
E. Jonke et al.
We examined secular trends in the facial skull over three Central European samples spanning more than 13 centuries. Data are 43 conventional cephalometric landmark points for samples dating from 680–830 CE, from the mid-19th Century, and from living Austrian young adult males. Methods of geometric morphometrics demonstrate shape differences across the samples, and also
differences in allometry. There is a stronginteraction between these, so that group mean differences are different for small and large individuals (equivalently, allometry is
different from period to period). The oldest sample, from the Migration Period, exhibits
allometric features that may possibly be Turkic. There are implications for the
craniofacial biologist interested in growth trends or growth predictions in ethnically
mixed populations. There are also implications for the discussion concerning the morphology of the Avars (an ethnic group of probably Central Asian origin who conquered large parts of Central Europe during the Migration Period and who interbred with other incoming groups after their conquest by Charlemagne), and also the relation of these findings to current thinking on gnathic reduction trends.
Roman Gladiators - The Osseous Evidence.
F. Kanz, K. Grossschmidt
Paternal heritage for the Indonesian peoples.
T. M. Karafet et al.
Feeding the children: Isotopic evidence for weaning practices in the ancient Greek colony of Apollonia (5th-2nd centuries BC).
C. Kwok, A. Keenleyside.
Misconceptions about the postcranial skeleton of Homo floresiensis.
S.G. Larson et al.
A comparison of mitochondrial DNA and Y chromosome DNA variation on Manus Island.
K.E. Latham et al.
November 06, 2006
ASHG 2006 abstracts
The meeting of the American Society of Human Genetics took place this October and the abstracts of the meeting are online in a big pdf file. A few items of interest:
The genetic variation and population history in the Baltic Sea region
Estimating the split time of Human and Neanderthal populations
Genomic diversity and population structure of Native Americans
The rare nonsynonymous SCN5A-S1103Y variant in Caucasians is due to recent African Admixture as revealed by 100k SNP genotyping.
Allele frequency estimates from DNA pools for 317,000 SNPs for multiple European and worldwide populations and discovery of Ancestry Informative Markers for Europe.
Mitochondrial haplogroups are associated with asthma and total serum IgE levels
The genetic variation and population history in the Baltic Sea region
Sharp genetic borders within a geographically restricted region are known to exist among the populations around the northern Baltic Sea on the northern edge of Europe. We studied the population history of this area in greater detail from paternal and maternal perspectives with Y chromosomal and mitochondrial DNA markers. Over 1700 DNA samples from Finland, Karelia, Estonia, Latvia, Lithuania and Sweden were genotyped for 18 Y-chromosomal biallelic polymorphisms and 8 microsatellite loci, together with 18 polymorphisms from the coding area of mtDNA and sequencing of the HVR1. Y chromosomal haplogroups from the biallelic data indicate both various phases of gene flow and existence of genetic barriers within the Baltic region. Haplogroup N3, being abundant on the eastern side of the Baltic, differentiates between eastern and western sides of the Baltic Sea, just like R1b that has a reverse frequency pattern to N3. The typically Scandinavian haplogroup Ia1 has a high frequency of up to 40%, separating not only Sweden but also Western Finland from the other populations. The frequency of haplogroup R1a1, most characteristic to Slavic peoples, varied substantially across the populations. In addition to biallelic markers, Y-chromosomal microsatellite loci were analyzed for a more detailed approach to the history of the paternal lineages in the region. We also analyzed mtDNA markers with special interest for sub-haplogroups of H and U, that among other haplogroups, show substantial variation between the populations (e.g. haplogroups H1, H2, T and J1). In conclusion, our current Y-chromosomal and mtDNA data suggest various incidents of gene flow from different sources, each reaching partly different areas of the Baltic region, which can be thus seen as a meeting point of a not only culturally but also genetically diverse set of populations.Asian Nomads traces in the mitochondrial gene pool of Slavs.
Mitochondrial DNA (mtDNA) variability was studied in a sample of 179 individuals representing Czech population from west Bohemia. MtDNA analysis revealed that the majority of Czech mtDNAs belongs to the common West Eurasian mitochondrial haplogroups. However, about 3 per cent of Czech mtDNAs encompass East Eurasian lineages (A, N9a, D4, M*). Comparative analysis of published data has shown that different Slavonic populations contain small but marked amount of East Eurasian mtDNAs (e.g. 1.3 per cent in Eastern Slavs, 1.8 per cent in Western Slavs, and 1.2 per cent in Southern Slavs). It is noteworthy that Baltic populations (Latvians, Lithuanians and Estonians) have avoided a marked influence of maternal lineages of East Eurasian origin (0.3-0.6 per cent). The two East Eurasian mtDNA haplogroups, Z1 and D5, are present in gene pools of North European Finnic populations (Saami, Finns, and Karelians). Unlike them, Slavonic populations in general are characterized by heterogeneous mtDNA structure, defined, in addition to Z1 and D5, by haplogroups A, C, D4, G2a, M*, N9a, F and Y. Therefore, different scenarios of female-mediated East Eurasian genetic influence on Northern and Eastern Europeans should be highlighted: (1) the most ancient, probably originated in the early Holocene, influx of Asian tribes, which brought a few selected East Asian mtDNA haplotypes (like Z and D5) to Fennoscandia (Tambets et al. 2004), and (2) gradual gene flows of historic times occurred mostly in the Middle Ages due to migrations of nomadic peoples (such as the Huns, Avars, Bulgars, Mongols) to Eastern and Central European territories inhabited mainly by Slavonic tribes. We suggest that the presence of East Eurasian mtDNA haplotypes is not original feature of gene pool of the proto-Slavs, but mostly is a consequence of admixture with Central Asian nomadic tribes, who migrated into Central and Eastern Europe in the early middle Ages.Use of Forensic Markers in the Assessment of Population Stratification.
Assignment of individuals to population groups is important to genetic case control association studies, admixture mapping, medical risk assessment, genealogy, and forensic studies. Polymorphic sequences can be used to infer ancestry but their utility for such an application is related to the number of alleles and relative frequency differences of these alleles between the population groups under study. Multiple study designs differing in numbers and types of polymorphic markers with differing levels of informativeness make comparison of studies difficult. The use of commercially-available highly-informative markers that are used internationally in forensic applications could provide a universal first tier analysis for assignment of individuals to population groups prior to inclusion in association and admixture studies. We evaluated the utility of the PowerPlex kit of 16 markers from Promega for this purpose. Multiple population groups including African, Bengalis, Chinese, Japanese, Koreans, Crypto Jews, Sephardic Jews, and Dutch were genotyped using the PowerPlex kit. The data were analyzed with STRUCTURE (Pritchard et al.) using an admixture model, correlated alleles and 3 clusters. Africans, Asians (Bengalis, Koreans, Chinese and Japanese), and Caucasians (Dutch, Sephardic Jews, and Crypto Jews) were clearly delineated. Individuals showing admixture were detectable and their removal resulted in more discrete clustering. An independently collected and genotyped set of Dutch individuals was indistinguishable from the original Dutch group providing reproducibility across data sets. The sensitivity conferred by the number of markers used in the analysis was assessed by removing markers. Delineation of population groups was apparent when 14 markers were used, although clusters were noisier; however it was not possible to delineate population groups when only 8 markers were used. The use of forensic markers is a promising strategy for clustering individuals into population groups and will be an inevitable outcome of their forensic use.Evaluation of Ancestry and Linkage Disequilibrium Sharing in Admixed Population in Mexico
National Institute of Genomic Medicine, Mexico. More than 80% of the Mexican population is considered Mestizo, resulting from the admixture of ethnic groups with Spaniards. To generate an initial estimate of ancestral contribution (AC) of populations from Europe, Africa and Asia to the Mexican Mestizos, we genotyped 104 samples from the states of Sonora (n=20), Yucatan (n=17), Guerrero (n=21), Zacatecas (n=19), Veracruz (n=18) and Guanajuato (n=8) using the 100K Affymetrix SNP array, and used data from the International HapMap Project as the parental population information. From 3,055 ancestry informative SNPs reported by Smith et al. and Choudhry et al., we identified 105 present in the 100K array and used them to calculate AC from each population to our sample. To infer AC we used Structure software under the admixture model. Based on this analysis, the average AC in our samples is 58.96% European, 10.03% African and 31.05% Asian. Sonora shows the highest European contribution (70.63%) and Guerrero the lowest (51.98%) where we also observe the highest Asian contribution (37.17%). African contribution ranges from 7.8% in Sonora to 11.13% in Veracruz. Based on these data, we grouped our population according to European AC (<50%,>70%). We used the Carlson algorithm to derive European tagSNPs from the 100K marker set. To explore Linkage Disequlibrium Sharing (LDS) between Mestizos and Europeans, we calculated the proportion of tagSNP-marker pairs that maintained an r2≥0.8 in each evaluated population. In general, comparison of LDS between European and Asian population is ~73%, whereas comparison with African population is ~40%. Mestizos from Guerrero show the lowest LDS (74%), whereas those from Sonora show the highest (77%). Similar results are seen in the group of lower (<50%)>70%) European ancestry. Our results suggest that the Mexican Mestizo population shows ancestry-based stratification that will requiere the appropriate corrections to avoid spurius results in association studies. Our results show that admixed populations have unique patterns of LD depending on levels of ancestral contribution.European mitochondrial haplogroups exhibit differential risk of developing presbycusis.
The genetic basis of human presbycusis (age-related hearing loss) is unknown. This common disorder is characterized by difficulty understanding conversation, particularly in noisy backgrounds. Audiograms of presbycusics show sloping hearing loss, with greatest deficiencies at the highest frequencies, and over time an individual’s hearing loss progresses into the lower frequencies that are more important for understanding speech. We investigated the hypothesis that the mitochondrial (mt) genome plays a role in presbycusis. Subjects of European ancestry, all over age 58, were tested using both classical and advanced audiometric measures and then genotyped to determine mt haplogroups. We found that subjects belonging to haplogroup H (N=93) had better hearing than other Europeans (N=80), with the greatest differences observed in the right ear at 3 kHz (p=0.017) and 10-14 kHz (p=0.016). The difference at 3 kHz correlates with the common noise notch location, and thus may indicate a difference in susceptibility to noise damage. Distortion product otoacoustic emissions also indicated better hair cell health in haplogroup H subjects, at higher frequencies and in the right ear (average DPOAEfor 4-6 kHz, p= 0.010). These results support the hypothesis that a mitochondrial factor influences susceptibility to the development of presbycusis. We are currently investigating the mt genome for causative mutations linked to the haplogroups.
Estimating the split time of Human and Neanderthal populations
Previous genetic studies of Neanderthal ancestry have used mtDNA and thus have been limited in their conclusions on the relationship of humans and Neanderthals. We present here the first use of Neanderthal genomic DNA to assess the joint history of human and Neanderthal populations. Our data consist of 37kb of short fragments of genomic DNA sequenced in Neanderthal. By studying the degree to which modern human diversity is shared with Neanderthal we can assess the time at which the human and Neanderthal populations split. We use a flexible simulation based approach that demonstrates the power of using human variation data in such analyses. We find that the two populations split ~400,000 years, predating the emergence of modern humans. Our best fitting model predicts that the Neanderthal lineage will be outgroup to the human population ~52% of the time.The Genetic Structure of Human Populations in Africa.
Africa contains the greatest levels of human genetic variation and is the source of the worldwide range expansion of all modern humans. Knowledge of the genetic population boundaries within Africa has important implications for the design and implementation of genetic epidemiologic studies of Africans and African Americans, and for reconstructing modern human origins. A dataset consisting of ~3.7 million genotypes has been generated from the Marshfield panel of 773 microsatellites and 392 in-del polymorphic genetic markers. These markers were genotyped in ~3,200 individuals from >100 diverse ethnic populations across Africa as well as in 118 African Americans and in the CEPH Human Genome Diversity Panel, consisting of 1048 individuals from 51 globally diverse populations. Preliminary analysis of population structure using the program STRUCTURE1 indicates considerably more substructure amongst global populations (estimate for the number of genetic clusters, K, is 12) and amongst African populations (K = 9) than had previously been recognized2. Population clusters are correlated with self-described ethnicity and shared cultural and/or linguistic properties (e.g. Pygmies, Khoisan-speakers, Bantu-speakers, etc). African Americans have predominantly West African Bantu (~80%) and European (~17%) ancestry, although individual admixture levels vary considerably. These results justify the need to include a broad range of geographically and ethnically diverse African populations in studies of human genetic variation. 1Pritchard JK, et al. Genetics 155:945-59 (2000) 2Rosenberg NA, et al. Science 298:2381- 5 (2002).Patterns of admixture in Latino populations
We examined the diversity of 13 Latino populations from seven countries (Mexico, Guatemala, Costa Rica, Colombia, Chile, Argentina and Brazil) typing 745 autosomal microsatellite markers in 250 individuals. Estimates of genetic ancestry for these populations varied substantially. Native American ancestry varied between 19.6% and 70.3%, European ancestry between 26.9% and 70.6%, and African ancestry between 1.1% and 9.8%. Genetic structure analysis provides evidence of a genetic continuity between pre- and post-Columbian populations for specific geographic regions. For instance, a Chibchan-Paezan ancestry is detectable in Latinos from lower Central America and northwest South America. Individual admixture estimates vary considerably between populations. Some Latinos (e.g. Mexico City) show marked variation in individual admixture, whereas others (e.g. Antioquia and Costa Rica) show little variation. This variation is likely to reflect the history of admixture of each geographic region examined: some Latino populations are still undergoing substantial admixture whereas others underwent admixture mostly in early colonial times. These results have important implications for admixture mapping and association mapping studies in Latino populations.
Genomic diversity and population structure of Native Americans
We examined 745 autosomal microsatellite markers in 432 individuals sampled from 24 indigenous populations in the Americas. These data were analyzed jointly with similar data available in 54 other indigenous populations from across the world (including an additional 5 Native American groups). The populations from the Americas show lower diversity and more differentiation than populations from other continental regions (global Fst=0.08). Signals of long-range linkage disequilibrium are detectable to a greater extent in Native Americans than in other populations, as are signals of recent bottlenecks followed by population growth. A negative correlation is observed between population diversity and geographic distance from the Bering Strait, an observation consistent with the north-to-south dispersal of humans upon initial entry into the continent. A higher diversity is observed in western vs. eastern South American populations, potentially reflecting differences in long-term effective population size or in colonization routes within South America. Phylogenetic trees relating Native American populations show a marked differentiation between Canadian and other Native populations. Canadian natives also show a detectable shared ancestry with contemporary Siberian populations, which is less visible for more southerly Americans. A substantial agreement is observed between phylogenetic relatedness and population affiliation according to the linguistic classification of Greenberg.
The rare nonsynonymous SCN5A-S1103Y variant in Caucasians is due to recent African Admixture as revealed by 100k SNP genotyping.
The SCN5A-S1103Y variant is an established and confirmed risk factor conferring an odds ratio up to 8.5 for cardiac ventricular arrhythmias and sudden cardiac death (Splawski et al, Science, 2002, Burke et al., Circulation, 2005, Plant et al., J. Clin. Invest. 2006). In Africans it is a common nonsynonymous SNP (MAF=8%), but it is rarely observed in Caucasians (Chen et al, J. Med. Genet. 2002). In a Bavarian family appearing of entirely Caucasian descent and affected with long QT Syndrome we have detected this variant in heterozygote state as the only causal nonsynonymous variation upon diagnostic ion channel resequencing. To resolve the question, whether in the family the variant was (a) of ancient African descent, (b) due to recent African admixture or (c) a de novo mutation, we analyzed the genetic segment it resided on. Dense SNP genotyping in admixed individuals allows to infer the ethnicity of chromosomal regions if allele frequencies are known in the original populations. Ethnicity inference for any given locus can be carried out by applying the product rule to a sliding window of neighboring SNPs or via modeling ancestry by hidden Markov Chain Monte Carlo Methods (Tang et al. Am. J. Hum. Genet, 2006). By 100k SNP genotyping of the Bavarian family, we demonstate that the S1103 variant is due to recent African admixture (b) and could rule out possibilities (a) and (c). This application demonstrates that inferring ethnicity of chromosomal regions by high density SNP genotyping is a powerful approach with prospects also to admixture mapping of disease loci and population stratification correction of genomewide association mapping of complex disease loci.
Allele frequency estimates from DNA pools for 317,000 SNPs for multiple European and worldwide populations and discovery of Ancestry Informative Markers for Europe.
The identification of Ancestry Informative Markers (AIMs) and inference of individual genetic history is useful in many applications, including studies of geography and evolution of human populations, forensic sciences, pharmacogenomics, admixture mapping and association studies of complex diseases. While many AIMs have been reported that define strong genetic differences between major continents, it is more difficult to identify markers that reflect subtle, within-continent diversity, such as the heterogeneous ancestry of European Americans contributed by different populations within Europe. We have analyzed DNA pools, each for a different population, on Illumina HumanHap300 BeadArrays to estimate allele frequencies for ~317,000 Single Nucleotide Polymorphisms for 9 European, 6 African, and 2 Amerindian populations in the Human Genome Diversity Project collection. We have also evaluated the performance of this method by analyzing three HapMap pools (YRI, CHB, and JPT), for which the true allele frequencies are already known from the International HapMap Project. We found that the allele frequency estimates differed between replicate chips by less than +/-5% for 95% of the SNPs, and that the estimated frequencies and the true frequencies differed by +/-5-10% for 90% of the SNPs. The data for nine European populations, from western Caucasus, Scotland, Tuscany, Sardinia, France, Iberia, Russia, Northern Italy, and a Basque region, showed a clear excess of SNPs having large allele frequency differences (e.g. >30%) between most pairs of populations, compared to what would be expected given the sample sizes. These results provide a valuable resource of European AIMs for monitoring within-continent stratification in association studies. We are currently validating the most informative SNPs by individually genotyping samples that formed the pools as well as those from additional European populations.
Mitochondrial haplogroups are associated with asthma and total serum IgE levels
Maternal history of asthma and/or atopy is a major risk factor for the subsequent development of asthma and allergy in childhood. Although mitochondrial mutations have been implicated in several maternally inherited monogenic disorders, no studies of mitochondrial polymorphisms and asthma have been reported.Weevaluated whether common mitochondrial haplogroups are associated with asthma and total serum IgE levels. 8 common mitochondrial single nucleotide polymorphisms (mtSNP) were genotyped in two cohorts of European ancestry: 512 adult women with incident asthma and 517 matching controls participating in the Nurses’ Health Study (NHS) and 654 children ages 5-12 years with mild to moderate asthma participating in the Childhood Asthma Management Program (CAMP). Genotyping was performed using TaqMan® probe hybridization assays. 93 random NHS samples were run in duplicate for all assays and demonstrated 100% concordance. In the CAMP Study, genotype data from probands’ mothers was also 100% concordant across all assays. Completion rates in both cohorts were > 95% for all markers. mtSNP 9055 was seen at higher frequency in NHS asthma cases (frequency 11.1%) than controls (8.0%, p = 0.02). Association analysis using haplo.score identified two haplogroups associated with asthma: one haplogroup at a frequency of 3.83% among cases compared to 1.27% among controls (p=0.0002) and another at a frequency of 9.97% among cases and 11.3% among controls (p=0.04). The CAMP Study is a case-only (family-based) cohort, thus precluding evaluation of mitochondrial SNP associations with asthma status. However, quantitative analysis of mitochondrial haplogroups identified two haplogroups of 11.0% and 1.87% frequency that were associated with log-transformed total serum IgE levels, an important intermediate phenotype in asthma and atopy (p=0.006 and 0.01, respectively). These data suggest that common mitochondrial haplogroups influence asthma diathesis.
May 02, 2005
More on Y-chromosomes in Bosnia Herzegovina
The recent paper on Bosnia Herzegovina gives some new insights into the origins of the populations residing there, as well as their relationships to other populations of the region. According to the authors:
In the PC analysis (Figure 3), the first PC shows that the three populations are genetically extremely close to each other, and closely related to other populations of the Balkans. However, the second PC tends to separate the Croat group not only from both Serbs and Bosniacs, but also from the Croats of Croatia.Here are some of my observations:
- Haplogroups C and Q are lacking in Bosnia Herzegovina, indicating that the region was not affected by Central Asian descended groups arriving either from eastern Europe or Asia Minor. We can infer the absence of Q from the absence of P*(xR) in these samples; note that P*(xR) was found in mainland Croatians and two islands believed to have received it either from the Avars or the Ottomans.
- Serbs have a frequency of about 7.5% K*(xP) which is lacking in Croats and is found in a frequency of 1.2% in Bosniacs (aka Muslims). It is not clear what this represents.
- J-M267 is found in 2.4% of Bosniacs and is lacking in Serbs and Croats, indicating perhaps that this was brought by Muslims.
- E3b dominates over the other "Neolithic" haplogroups G and J. This probably reinforces the association of J with more "coastal" migrations observed before, and this probably applies to G as well, which is found in higher frequencies in Greece and Italy than in these Balkan populations.
- R1a1 is found at frequencies less than 15.3%, and this is much lower than the 34% observed in the Croatian mainland and closer to the 10% frequency observed in Greece.
- Haplogroup I-M170 is found at frequencies comparable to those of the Croatian mainland, except in the Croatians of Bosnia where it is much higher, perhaps due to drift. These frequencies differentiate these populations from the Greeks and Albanians where I-M170 is lower.
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