August 2009 (81:4)
Table of Contents
Comparison of Genetic Distance Measures Using Human SNP Genotype Data
Ondrej Libiger, Caroline M. Nievergelt, Nicholas J. Schork
Quantification of the genetic distance between populations is instrumental in many genetic research initiatives, and a large number of formulae for this purpose have been proposed. However, selection of an appropriate measure for assessing genetic distance between real-world human populations that diverged due to mechanisms that are not fully known can be a challenging task. We compared results from nine widely used genetic distance measures applied to high-density, whole genome SNP genotype data obtained on individuals from 51 world populations. Using population trees and generalized analysis of molecular variance, we found that contradictory inferences could be drawn from analyses that used different distance measures. We determined the grouping of the distance measures in terms of similarity and consistency of their values using concordance, consistency and Procrustes analyses. Overall, Cavalli-Sforza and Edwards' distance (CE) measure differed the most from the other measures. Wright's FST for diploid data, Latter's, Reynolds' and Nei's minimum distance measures each yielded values that were most consistent with the other eight distance measures in terms of ordering populations based on genetic distance. CE and Nei's geometric distance were least consistent. Simulation studies showed that CE is relatively more sensitive in distinguishing genetically very similar populations, while Reynolds' genetic distance provided the highest sensitivity for highly divergent populations. Finally, our study suggests that using CE may provide less power for studies concerning human migration history.
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Silvia E. Smith, M. Geoffrey Hayes, Graciela S. Cabana, Chad Huff, Joan Brenner Coltrain, and Dennis H. O'Rourke
Hrdlicka (1945) proposed a population replacement event in the Aleutian Islands approximately 1000 years ago based on a perceived temporal shift in cranial morphology.  The archaeological record, in contrast, indicates cultural, and presumed population, continuity for over 4000 years.  We use mtDNA haplogroup data in the series of prehistoric eastern Aleutian samples (n=86) studied craniometrically by Hrdlicka to test alternative hypotheses regarding population continuity or replacement in the region.  This molecular characterization, in conjunction with direct dating of individual specimens, provided increased resolution for hypothesis testing.  Results indicate an apparent shift in mtDNA haplogroup frequencies in the Eastern Aleutians approximately 1000 years ago, in concert with changes in mortuary practices and isotopic signatures reflecting resource acquisition strategies. The earliest Aleut populations were characterized by a high frequency of haplogroup A, as are most modern populations of the North American arctic.  Later prehistoric peoples in the Aleutians were characterized by a high frequency of haplogroup D, and a correspondingly lower frequency of haplogroup A, a pattern typified by modern Aleut populations.
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Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim Populations of Uttar Pradesh, IndiaMuthukrishnan Eaaswarkhanth1, Bhawna Dubey1, Poorlin Ramakodi Meganathan1,
Sabahat Noor and Ikramul Haque
This study aims to characterize genetic diversity and relationships between Shia, Sunni Muslim populations of north India and geographically targeted neighboring and global populations. A number of parameters of population genetics and forensic interests were examined based on the allele frequencies from 15 autosomal STR loci included in the AmpFlSTR® IdentifilerTM PCR Amplification kit panel from Applied Biosystems (D8S1179, D21S11, D7S820, CSF1PO, D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both the populations even after applying the Bonferroni correction. The CPE and CPD values for all 15 STR loci of Shia and Sunni Muslim populations were 0.999991, 0.99999 and 0.9999999999999999913, 0.9999999999999999965, respectively. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (Ho) oscillate between 0.5833 (D18S51) to 0.8595 (vWA) in Shia Muslims and 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and is lower than expected heterozygosity (He) for almost 11 out of the set of 15 STRs typed. The genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring north Indian, Middle Eastern, East Asian and European populations were analyzed by distance-based methods, including Neighbor-Joining trees and multidimensional scaling. In addition, the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool was estimated by admixture analysis. Although a certain degree of genetic contribution from Iran to both the Muslim populations was observed, results of the phylogenetic analyses based on autosomal STRs analyzed suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations.
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Isonymy Structure of Buenos Aires City
Rubén A. Bronberg, José E. Dipierri, Emma L. Alfaro, Italo Barrai, Alvaro Rodríguez-Larralde, Eduardo E. Castilla, Vincenza Colonna, Greta Rodríguez-Arroyo, Graciela Bailliet
The isonymy structure of Buenos Aires City  was studied based on its surname frequency. Information on 2,552,359 voters of the 28 Buenos Aires districts was used to estimate Lasker's coefficient of relationship by isonymy (Ri), surname diversity according to Fisher's ?, the coefficient of consanguinity due to random isonymy (F) and Nei's, Lasker's and Euclidean isonymic distances. These were correlated with geographic distances which were calculated by assigning an arbitrary point to each district and measuring distances on a map of the city. The Ri*105 and F*104 averages of the districts located south of Rivadavia Avenue were higher (Ri = 66.,08; F = 3.4) than  those situated north of that avenue (Ri = 46.60; F = 2.4) (p<0.001). Fisher's ? showed the opposite behaviour (North: 1055.5; South: 757.2). There was a significant correlation (p<0.001) of geographic distance with Nei's and Euclidean distances (0.496 and 0.503 respectively) but not significant with Lasker's distance (0.051). These results indicate isolation by distance in the city of Buenos Aires and reveal subdivision of the metropolitan population with greater consanguinity and a lesser variety of surnames in the districts located in the southern section of the city. This structure agrees with the fragmentation and social, cultural and economic differences observed among the districts of this Latin American metropolis.
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Seasonality in Birth Weight: A Review of Global Patterns and Potential Etiologies
Gabriel Chodick, Yonit Deoitch, Varda Shalev

Birth weight is the single most significant determinant of infant mortality and the chances of a newborn to experience healthy development.  Low birth weight also appears to be related with higher risks of several important chronic conditions such as ischemic heart disease, non insulin-dependent-diabetes, and cancer in adults. Thus, factors that influence in utero growth and birth weight may have a serious effect on health outcomes many years later in life. Analysis of seasonal   variations in birth weights may enable us to suggest specific factors influencing this measure. The current review summarizes literature on seasonal variations in birth weight. While etiologies for seasonal variation in developing regions are more clearly understood, it is yet unclear which factors affect apparent seasonal variation in birth weight in developed countries. In our analysis we observed a pattern of seasonal variations in developed countries which differed between low, mid and high latitude countries, and we suggest several mechanisms that may be responsible for this diversity.  Namely, we suggest that in mid latitude climates, the large annual temperature range may cause low birth weights during summer, while as in high and low latitude regions variations in sunlight exposure between seasons may attribute to low birth weights apparent during winter. The identification of the suggested causal environmental factors may have public health implications in the development of primary prevention programs for low birth weights and macrosomia in developed countries.

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Italian populations during the Copper Age: assessment of biological affinities through
morphological dental traits
Rita Vargiu, Andrea Cucina and Alfredo Coppa
The Copper Age (III millennium BC) was characterized by considerable socio-economic transformations and coincided with the discovery of metallurgy. The aim of this study is to reconstruct the peopling of Italy during this period of time based on dental morphology. Dental remains from 41 sites throughout Italy were analyzed; only three of them (Laterza, and two from Sicily) span from the Late Copper Age to the Early Bronze Age. In order to work with adequate samples, the collections were pooled into 9 geographically and culturally homogeneous groups. Dental morphological traits were scored using on 8,891 teeth from 1,302 individuals the ASUDAS rank-scale system. The correlation between the Mean Measure of Divergence (MMD) and geographic distances (calculated as air distances) was computed. Multidimensional Scaling (MDS) with the Minimum Spanning Tree (MST) and Maximum Likelihood (ML) methods were applied in order to assess the relationships between groups. The results revealed a substantial genetic homogeneity among the populations throughout the Italian peninsula during the Copper Age with the exception of Sardinia, which tends to diverge from the continental samples. Phenetic and geographic distances correlate highly significantly only when the southern samples from Sicily and/or Laterza are removed from the analysis, which indicates that these groups may have experienced genetic admixture with external populations.
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Brief Communication Complete Mitochondrial Sequences for Haplogroups M23 and M46: Insights into the Asian Ancestry of the Malagasy Population
Vincent Dubut, François Cartault, Christine Payet, Marie-Dominique Thionville, Pascal Murail
Through the sequencing of the complete mitochondrial genome of three individuals of Malagasy ancestry, we completed the characterization of the island southeastern Asian specific M46 haplogroup. We assumed that the association of the np 3588 and np 16278 polymorphisms were M46 specific. In addition, we characterized a novel basal M subhaplogroup: M23. This clade can be defined by one coding region transition at np 10295 and one control region transition at np 16263. Our data suggest the arrival of South Asian migrants before the start of the 15th century and highlights the fact that future studies dealing with the settlement of Madagascar should consider at least three potential source populations (Africa, Indonesia, and India).
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August 2010 (82:4)
June 2010 (82:3) In press
April 2010 (82:2)
February 2010 (82:1)
October-December 2009 (81:5-6)
Special Issue on the Lasker Prize winning articles 1992-2005
August 2009 (81:4)
April-June 2009 (81:2-3)
Special Issue on « Demography and Cultural Macroevolution »
February 2009 (81:1)
December 2008 (80:6)
October 2008 (80:5)
August 2008 (80:4)

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