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Mitochondrial DNA analysis of human remains from the Yuansha site in Xinjiang, China
ShiZhu Gao,YinQiu Cui,YiDai Yang,RanHui Duan,Idelisi Abuduresule,Victor H. Mair,Hong Zhu,Hui Zhou
Science China Life Sciences , 2008, DOI: 10.1007/s11427-008-0034-8
Abstract: The Yuansha site is located in the center of the Taklimakan Desert of Xinjiang, in the southern Silk Road region. MtDNA was extracted from fifteen human remains excavated from the Yuansha site, dating back 2,000–2,500 years. Analysis of the phylogenetic tree and the multidimensional scaling (MDS) reveals that the Yuansha population has relatively close relationships with the modern populations of South Central Asia and Indus Valley, as well as with the ancient population of Chawuhu.
Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures  [PDF]
Alice A. Storey, J. Stephen Athens, David Bryant, Mike Carson, Kitty Emery, Susan deFrance, Charles Higham, Leon Huynen, Michiko Intoh, Sharyn Jones, Patrick V. Kirch, Thegn Ladefoged, Patrick McCoy, Arturo Morales-Mu?iz, Daniel Quiroz, Elizabeth Reitz, Judith Robins, Richard Walter, Elizabeth Matisoo-Smith
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039171
Abstract: Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.
Mitochondrial DNA Variation, but Not Nuclear DNA, Sharply Divides Morphologically Identical Chameleons along an Ancient Geographic Barrier  [PDF]
Dan Bar Yaacov,Karmit Arbel-Thau,Yael Zilka,Ofer Ovadia,Amos Bouskila,Dan Mishmar
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031372
Abstract: The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel) into two subspecies, Chamaeleo chamaeleon recticrista (CCR) and C. c. musae (CCM). CCR mostly inhabits the Mediterranean climate (northern Israel), while CCM inhabits the sands of the north-western Negev Desert (southern Israel). AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097), consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA) fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79), which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (~17,400 bp) generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient) local adaptation to mitochondrial-related traits.
Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds
Marianna Niemi, Auli Bl?uer, Terhi Iso-Touru, Veronica Nystr?m, Janne Harjula, Jussi-Pekka Taavitsainen, Jan Stor?, Kerstin Lidén, Juha Kantanen
Genetics Selection Evolution , 2013, DOI: 10.1186/1297-9686-45-2
Abstract: A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds.Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds.Archaeological and molecular genetic evidence suggests that sheep’s (Ovis aries) wild ancestor was the Asiatic mouflon (O. orientalis) and that it was domesticated about 11 000 years ago in the Fertile Crescent region [1]. The genetic history of the domestication of sheep has been investigated by analysing maternally inherited mitochondrial DNA (mtDNA) in modern sheep breeds. To date, five phylogenetically divergent mtDNA haplogroups descending probably
Heteroplasmy and Ancient Translocation of Mitochondrial DNA to the Nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) Complex  [PDF]
Xiuguang Mao, Ji Dong, Panyu Hua, Guimei He, Shuyi Zhang, Stephen J. Rossiter
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0098035
Abstract: The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.
GNB3, eNOS, and Mitochondrial DNA Polymorphisms Correlate to Natural Longevity in a Xinjiang Uygur Population  [PDF]
Muyesai Nijiati, Abulajiang Saidaming, Jun Qiao, Zuheng Cheng, Changchun Qiu, Yujing Sun
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081806
Abstract: Background In centenarian populations, application of the positive biology approach (examination of positive phenotypes in aging) has revealed that mitochondrial DNA (mtDNA) mutation accumulation may be linked to human longevity; however, the role of guanine nucleotide-binding protein (G protein) abnormalities modulated by G-protein beta-3 (GNB3) and nitrate (NO2) production associated with endothelial nitric oxide synthase (eNOS), commonly appearing in age-related diseases, remains undetermined. Objective The association between the mtDNA 5178A/C, mtDNA 10398A/G, GNB3 C825T, and eNOS polymorphisms and longevity in a Uygur population (Xinjiang region, China) were investigated. Methods A total of 275 experimental subjects aged ≥100 or with 4 generations currently living were screened for inclusion in the centenarian (>100 years) and nonagenarian groups (90–100 years), and 112 65–70 year old control subjects were selected. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to examine mtDNA 5178A/C, mtDNA 10398A/G, GNB3 C825T, and eNOS. Associations between polymorphic loci, genotypes, and longevity were analyzed. Results 165 included subjects (M:F = 107:58; mean age = 97±3 years; mean age 100–113 years) were assigned to the centenarian (M:F = 46/19; n = 65) and nonagenarian groups (M:F = 61/39; n = 100). Associations between mtDNA C5178A and A10398G polymorphisms with longevity in the centenarian group with mtDNA genotype frequencies 5178A and 10398G were 66.79% and 36.8%. Conclusions Applying the overwhelming longevity observed in Uygur populations, these findings demonstrate that mtDNA 5178A/C and 10398A/G, GNB3 C825T, and eNOS polymorphisms are useful as a genetic basis for longevity.
Mitochondrial DNA analysis of human remains from the Yuansha site in Xinjiang, China

GAO ShiZhu,CUI YinQiu,YANG YiDai,DUAN RanHui,Idelisi ABUDURESULE,Victor H MAIR,ZHU Hong &,ZHOU Hui,

中国科学C辑(英文版) , 2008,
Abstract: The Yuansha site is located in the center of the Taklimakan Desert of Xinjiang, in the southern Silk Road region. MtDNA was extracted from fifteen human remains excavated from the Yuansha site, dating back 2,000–2,500 years. Analysis of the phylogenetic tree and the multidimensional scaling (MDS) reveals that the Yuansha population has relatively close relationships with the modern populations of South Central Asia and Indus Valley, as well as with the ancient population of Chawuhu. Supported by the National Natural Science Foundation of China (Grant No. J0530184) and the “985” Foundation of Jilin University
Mitochondrial DNA Diversity of Modern, Ancient and Wild Sheep (Ovis gmelinii anatolica) from Turkey: New Insights on the Evolutionary History of Sheep  [PDF]
Sevgin Demirci, Evren Koban Ba?tanlar, Nihan Dil?ad Da?ta?, Evangelia Pi?kin, Atilla Engin, Füsun ?zer, Eren Yüncü, ?ükrü An?l Do?an, ?nci Togan
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081952
Abstract: In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum H?yük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E. To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations. Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).
Analysis of the matrilineal genetic structure of population in the early Iron Age from Tarim Basin, Xinjiang, China
YinQiu Cui,ShiZhu Gao,ChengZhi Xie,QuanChao Zhang,HaiJing Wang,Hong Zhu,Hui Zhou
Chinese Science Bulletin , 2009, DOI: 10.1007/s11434-009-0647-8
Abstract: Ancient mtDNA data of human remains were analyzed from four early Iron Age Tarim Basin sites (Yuansha, Zaghunluq, Sampula and Niya) in the southern Silk Road region. Haplogroup distributions show that ancient Tarim Basin population was comprised of well-differentiated Western and Eastern matrilineal lineages. Some West lineage of Tarim Basin population originated from Near East and Iran region. Of the East lineages, North and Northeast Asia originated lineages were the main components, and a few Southeast Asian lineages also existed, which indicated a more extensive origin and a more complex admixture. The genetic structure of ancient Tarim Basin population is relatively close to the modern populations of Xinjiang, which implied that the early Iron Age is an important period during the formation of the modern Xinjiang population.
Ancient DNA studies: new perspectives on old samples
Ermanno Rizzi, Martina Lari, Elena Gigli, Gianluca De Bellis, David Caramelli
Genetics Selection Evolution , 2012, DOI: 10.1186/1297-9686-44-21
Abstract: The field of ancient DNA studies began twenty-eight years ago with the extraction and sequencing of DNA material from the quagga, a South African equid (Equus quagga quagga) that went extinct in the 19th century [1] and from an Egyptian mummy [2]. These studies used bacterial cloning to amplify small DNA sequences (retrieved from skin fragments of these specimens) and showed that the origin of the extracted genetic material was mainly microbial or fungal. In general, endogenous DNA was composed of very low concentrations of short and damaged fragments of multi-copy loci, such as mitochondrial DNA (mtDNA).A few years later, with the development of PCR (polymerase chain reaction) it became possible to routinely amplify and study surviving ancient DNA molecules even if only in a single copy, resulting in a rapid increase and diversification of ancient DNA research [3-5]. However, due to the enormous power of PCR to amplify even a few copies of DNA sequences, modern DNA contamination has become a crucial problem. For this reason, many of the most extravagant reports on ancient DNA, including claims of DNA sequences surviving for millions of years in plants [6-8] and dinosaur bones [9], have been disputed and actually disregarded. Studies on ancient DNA need to deal with technical problems that are specific to this field. The first difficulty is the production of sufficient quantities of authentic DNA sequences to make a study conclusive. This difficulty is a consequence of post-mortem DNA degradation processes, which can cause miscoding lesions, potentially leading to sequence errors, or physical destruction of the DNA molecule, thus increasing the risk for preferential amplification of exogenous contaminant sequences (Table?1). To deal with this issue, researchers have outlined a series of guidelines to ensure the quality of ancient DNA data and the reliability of consequent conclusions [5]. Over the years, these guidelines have gradually evolved into a more detailed a
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