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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 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
Low Countries
Common sense
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
Reduced mtDNA diversity in the Ngöbé Amerinds of Panamá. -
Genetics, Vol. 140, No. 1. (May 1995), pp. 275-283 Mitochondrial DNA (mtDNA) haplotype diversity was determined for 46 Ngöbé Amerinds sampled widely across their geographic range in western Panamá. The Ngöbé data were compared with mtDNA control region I sequences from two additional Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche and from one Na-Dene group, the Haida of the Pacific Northwest. The Ngöbé exhibit the lowest mtDNA control region sequence diversity yet reported for an Amerind group. Moreover, they carry only two of the four Amerind founding lineages first described by Wallace and coworkers. We posit that the Ngöbé passed through a population bottleneck caused by ethnogenesis from a small founding population and/or European conquest and colonization. Dating of the Ngöbé population expansion using the Harpending et al. approach to the analysis of pairwise genetic... - Rebekah Adele Canada
Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland -
Science, Vol. 320, No. 5884. (27 June 2008), pp. 1787-1789, doi:10.1126/science.1159750 The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This result suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo-Eskimos that replaced them. Thomas, Toomas Kivisild, Bjarne Grønnow, Pernille Andersen,... - Rebekah Adele Canada
International Society of Genetic Genealogy
Talk:International Society of Genetic Genealogy
Haplogroup Q-L275
MtDNA variation in the Altai-Kizhi population of southern Siberia: a synthesis of genetic variation. -
Human biology, Vol. 78, No. 4. (August 2006), pp. 477-494 The native peoples of Gorno Altai in southern Siberia represent a genetically diverse population and have been of great interest to anthropological genetics. In particular, the southern Altaian population is argued to be the best candidate for the New World ancestral population. In this study we sampled Altai-Kizhi from the southern Altaian village of Mendur-Sokkon, analyzed mtDNA RFLP markers and HVS-I sequences, and compared the results to other published mtDNA data from Derenko et al. (2003) and Shields et al. (1993) encompassing the same region. Because each independent study uses different sampling techniques in characterizing gene pools, in this paper we explore the accuracy and reliability of evolutionary studies on human populations. All the major Native American haplogroups (A, B, C, and D) were identified in the Mendur-Sokkon sample, including a single individual belonging to haplogroup X. The most common mtDNA... - Rebekah Adele Canada
Mitochondrial DNA of a late neolithic woman from Kaminnaia cave (Gorny Altai) -
Russian Journal of Genetics: Applied Research In Russian Journal of Genetics: Applied Research, Vol. 2, No. 3. (3 June 2012), pp. 214-221, doi:10.1134/s2079059712030082 The results of molecular genetic analysis of mitochondrial DNA of a Late Neolithic woman (middle of the 4th millennium BC) from Kaminnaia cave (Gorny Altai) are presented. It was determined that the studied sample belongs to the East Eurasian A4 haplogroup. A phylogeographic analysis indicates an informativity of the A4 variants for the reconstruction of early stages of ethnogenetic processes on the south of Western and Eastern Siberia. AS Pilipenko, VI Molodin, AG Romashchenko - Rebekah Adele Canada
Talk:Bennett Greenspan
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