Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set -
PLoS Genet, Vol. 5, No. 4. (10 April 2009), e1000448, doi:10.1371/journal.pgen.1000448 The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunterâgatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunterâgatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic eventsâsize changes, population splits, and gene flowâultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunterâgatherers and agricultural populations from Africa and estimated separation... - Rebekah Adele Canada
Genetic Structure of Europeans: A View from the North–East -
PLoS ONE, Vol. 4, No. 5. (8 May 2009), e5472, doi:10.1371/journal.pone.0005472 Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and... - Rebekah Adele Canada
Population structure and genome-wide patterns of variation in Ireland and Britain -
European Journal of Human Genetics, Vol. 18, No. 11. (23 June 2010), pp. 1248-1254, doi:10.1038/ejhg.2010.87 Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654... - Rebekah Adele Canada
Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays -
PLoS ONE, Vol. 3, No. 12. (5 December 2008), e3862, doi:10.1371/journal.pone.0003862 Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close... - Rebekah Adele Canada
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes -
Current Biology, Vol. 23, No. 7. (April 2013), pp. 553-559, doi:10.1016/j.cub.2013.02.044 Qiaomei Fu, Alissa Mittnik, Philip Johnson, Kirsten Bos, Martina Lari, Ruth Bollongino, Chengkai Sun, Liane Giemsch, Ralf Schmitz, Joachim Burger, Anna Ronchitelli, Fabio Martini, Renata Cremonesi, Jiří Svoboda, Peter Bauer, David Caramelli, Sergi Castellano, David Reich, Svante Pääbo, Johannes Krause - Rebekah Adele Canada
Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites -
NATURE COMMUNICATIONS, doi:10.1038/ncomms3928 Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder... - Rebekah Adele Canada
Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers -
PLoS ONE, Vol. 8, No. 12. (12 December 2013), e83570, doi:10.1371/journal.pone.0083570 Evenks and Evens, Tungusic-speaking reindeer herders and hunter-gatherers, are spread over a wide area of northern Asia, whereas their linguistic relatives the Udegey, sedentary fishermen and hunter-gatherers, are settled to the south of the lower Amur River. The prehistory and relationships of these Tungusic peoples are as yet poorly investigated, especially with respect to their interactions with neighbouring populations. In this study, we analyse over 500 complete mtDNA genome sequences from nine different Evenk and even subgroups as well as their geographic neighbours from Siberia and their linguistic relatives the Udegey from the Amur-Ussuri region in order to investigate the prehistory of the Tungusic populations. These data are supplemented with analyses of Y-chromosomal haplogroups and STR haplotypes in the Evenks, Evens, and neighbouring Siberian populations. We demonstrate that whereas the... - Rebekah Adele Canada
Unraveling the complex maternal history of Southern African Khoisan populations -
Am. J. Phys. Anthropol. (1 December 2013), pp. n/a-n/a, doi:10.1002/ajpa.22441 The Khoisan populations of southern Africa are known to harbor some of the deepest-rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre-Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also... - Rebekah Adele Canada
Demographic Histories, Isolation and Social Factors as Determinants of the Genetic Structure of Alpine Linguistic Groups -
PLoS ONE, Vol. 8, No. 12. (2 December 2013), e81704, doi:10.1371/journal.pone.0081704 Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations... - Rebekah Adele Canada
Tracing Arab-Islamic Inheritance in Madagascar: Study of the Y-chromosome and Mitochondrial DNA in the Antemoro -
PLoS ONE, Vol. 8, No. 11. (22 November 2013), e80932, doi:10.1371/journal.pone.0080932 Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human... - Rebekah Adele Canada
The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies -
Journal of Human Genetics, Vol. 59, No. 2. (05 December 2013), pp. 66-77, doi:10.1038/jhg.2013.120 Since the determination in 1981 of the sequence of the human mitochondrial DNA (mtDNA) genome, the Cambridge Reference Sequence (CRS), has been used as the reference sequence to annotate mtDNA in molecular anthropology, forensic science and medical genetics. The CRS was eventually upgraded to the revised version (rCRS) in 1999. This reference sequence is a convenient device for recording mtDNA variation, although it has often been misunderstood as a wild-type (WT) or consensus sequence by medical geneticists. Recently, there has been a proposal to replace the rCRS with the so-called Reconstructed Sapiens Reference Sequence (RSRS). Even if it had been estimated accurately, the RSRS would be a cumbersome substitute for the rCRS, as the new proposal fuses—and thus confuses—the two distinct concepts of ancestral lineage and reference point for human mtDNA. Instead, we prefer to maintain the... - Rebekah Adele Canada
Stature in Holocene foragers of North India: Stature in Holocene Foragers of North India -
American Journal of Physical Anthropology (1 December 2013), pp. n/a-n/a, doi:10.1002/ajpa.22439 The Ganga Plain of North India provides an archaeological and skeletal record of semi-nomadic Holocene foragers in association with an aceramic Mesolithic culture. Prior estimates of stature for Mesolithic Lake Cultures (MLC) used inappropriate equations from an American White reference group and need revision. Attention is given to intralimb body proportions and geo-climatic provenance of MLC series in considering the most suitable reference population. Regression equations from ancient Egyptians are used in reconstructing stature for MLC skeletal series from Damdama (DDM), Mahadaha (MDH), and Sarai Nahar Rai (SNR). Mean stature is estimated at between 174 (MDH) and 178 cm (DDM and SNR) for males, and between 163 cm (MDH) and 179 cm (SNR) for females. Stature estimates based on ancient Egyptian equations are significantly shorter (from 3.5 to 7.1 cm shorter in males; from 3.2 to 7.5 cm... - Rebekah Adele Canada
Genetic affinities of Ukrainians from the maternal perspective -
Am. J. Phys. Anthropol. (1 September 2013), pp. n/a-n/a, doi:10.1002/ajpa.22371 The area of what is now the Ukraine has been the arena of large-scale demographic processes that may have left their traces in the contemporary gene pool of Ukrainians. In this study, we present new mitochondrial DNA data for 607 Ukrainians (hypervariable segment I sequences and coding region polymorphisms). To study the maternal affinities of Ukrainians at the level of separate mitochondrial haplotypes, we apply an original technique, the haplotype co-occurrence analysis. About 20% of the Ukrainian maternal gene pool is represented by lineages highly specific to Ukrainians, but is scarcely found in other populations. About 9% of Ukrainian mtDNA lineages are typical for peoples of the Volga region. We also identified minor gene pool strata (1.6–3.3%), each of which is common in Lithuanians, Estonians, Saami, Nenets, Cornish, and the populations of the North Caucasus. Am J Phys Anthropol, 2013. © 2013 Wiley... - Rebekah Adele Canada
Parameters of the human genome. -
Proceedings of the National Academy of Sciences of the United States of America, Vol. 88, No. 17. (1 September 1991), pp. 7474-7476 Chromosome arm lengths are the critical parameters of the human genome. The physical length is required to scale radiation hybrid and other maps to megabases. The genetic lengths in males and females are required for probabilities of exclusion and synteny, choice of well-spaced loci for linkage tests, and comparison with centromeric maps based on nondisjunction. Interpolation of new data into a map is possible only when the length is known, including the distances from centromere and telomeres to the nearest markers. Current evidence on physical parameters including the reliable measurements of relative lengths from flow cytometry but only a crude estimate of genome size (3200 megabases). Evidence on genetic parameters includes chiasma counts and linkage maps corrected for failure to sample telomeres, giving an autosomal size of 2809 centimorgans in males... - Rebekah Adele Canada
Reconciling migration models to the Americas with the variation of North American native mitogenomes -
Proceedings of the National Academy of Sciences (12 August 2013), doi:10.1073/pnas.1306290110 In this study we evaluated migration models to the Americas by using the information contained in native mitochondrial genomes (mitogenomes) from North America. Molecular and phylogeographic analyses of B2a mitogenomes, which are absent in Eskimo–Aleut and northern Na-Dene speakers, revealed that this haplogroup arose in North America ∼11–13 ka from one of the founder Paleo-Indian B2 mitogenomes. In contrast, haplogroup A2a, which is typical of Eskimo–Aleuts and Na-Dene, but also present in the easternmost Siberian groups, originated only 4–7 ka in Alaska, led to the first Paleo-Eskimo settlement of northern Canada and Greenland, and contributed to the formation of the Na-Dene gene pool. However, mitogenomes also show that Amerindians from northern North America, without any distinction between Na-Dene and non–Na-Dene, were heavily affected by an additional and distinctive Beringian genetic... - Rebekah Adele Canada
RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference -
The American Journal of Human Genetics, Vol. 93, No. 2. (8 August 2013), pp. 278-288, doi:10.1016/j.ajhg.2013.06.020 Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. Current methods can only detect continental-level ancestry (i.e., European versus African versus Asian) accurately even when using millions of markers. Here, we present RFMix, a powerful discriminative modeling approach that is faster (<30×) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians. Finally, we demonstrate that African Americans in HapMap contain modest (but nonzero) levels of Native American... - Rebekah Adele Canada
Testing out a Logo for the E-M75 Project... -
Haplogroup E-M96
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American Capital
Beringian Standstill and Spread of Native American Founders -
PLoS ONE, Vol. 2, No. 9. (5 September 2007), e829, doi:10.1371/journal.pone.0000829 Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the intial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder... - Rebekah Adele Canada
mtDNA variation in the Chibcha Amerindian Huetar from Costa Rica. -
Human biology, Vol. 66, No. 6. (December 1994), pp. 963-977 The genetic variation in a Chibcha-speaking Amerindian tribe from lower Central America, the Huetar, was analyzed using nucleotide sequences of the hypervariable segments of the mitochondrial DNA (mtDNA) control region, the frequencies of 10 Amerindian-specific mtDNA haplotypes, and the regional distribution of private protein polymorphisms. The sequencing of 713 base pairs (bp) in the control regions of 27 individuals revealed 11 distinct lineages. These were defined by 24 variable sites and a 6-bp deletion between nucleotide pairs (np) 106 and 111. The 6-bp deletion is a new mtDNA marker that will be valuable for Amerindian taxonomic research. Control region sequences and mtDNA haplotype analyses reveal that Huetar mtDNAs are distributed in "Amerindian clusters" A, B, and D. A maximum-likelihood phylogenetic tree suggests a single origin for the 6-bp Huetar deletion in the sample. mtDNA haplotype analysis and the presence... - Rebekah Adele Canada
Decrypting the Mitochondrial Gene Pool of Modern Panamanians -
PLoS ONE, Vol. 7, No. 6. (4 June 2012), e38337, doi:10.1371/journal.pone.0038337 The Isthmus of Panama–the narrow neck of land connecting the northern and southern American landmasses–was an obligatory corridor for the Paleo-Indians as they moved into South America. Archaeological evidence suggests an unbroken link between modern natives and their Paleo-Indian ancestors in some areas of Panama, even if the surviving indigenous groups account for only 12.3% of the total population. To evaluate if modern Panamanians have retained a larger fraction of the native pre-Columbian gene pool in their maternally-inherited mitochondrial genome, DNA samples and historical records were collected from more than 1500 volunteer participants living in the nine provinces and four indigenous territories of the Republic. Due to recent gene-flow, we detected ~14% African mitochondrial lineages, confirming the demographic impact of the Atlantic slave trade and subsequent African immigration into Panama... - Rebekah Adele Canada
Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins -
BMC Evolutionary Biology, Vol. 11, No. 1. (07 October 2011), 293, doi:10.1186/1471-2148-11-293 BACKGROUND:The Asian origin of Native Americans is largely accepted. However uncertainties persist regarding the source population(s) within Asia, the divergence and arrival time(s) of the founder groups, the number of expansion events, and migration routes into the New World. mtDNA data, presented over the past two decades, have been used to suggest a single-migration model for which the Beringian land mass plays an important role.RESULTS:In our analysis of 568 mitochondrial genomes, the coalescent age estimates of shared roots between Native American and Siberian-Asian lineages, calculated using two different mutation rates, are A4 (27.5 +/- 6.8 kya/22.7 +/- 7.4 kya), C1 (21.4 +/- 2.7 kya/16.4 +/- 1.5 kya), C4 (21.0 +/- 4.6 kya/20.0 +/- 6.4 kya), and D4e1 (24.1 +/- 9.0 kya/17.9 +/- 10.0 kya). The coalescent age estimates of pan-American haplogroups calculated using the same two mutation... - Rebekah Adele Canada
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