Ancient mtDNA haplogroups: a new insight into the genetic history of European populations

In the present work, DNA was extracted from 63 skeletal samples recovered at the Neolithic site of San Juan ante Portam Latinam (SJAPL) (Araba, Basque Country). These samples have proved useful as genetic material for the performance of population studies. To achieve this it was necessary to overcome the methodological problems arising when working with damaged DNA molecules. We succeeded in performing an amplification and restriction analysis of the polymorphisms present in the mtDNA. Ninety seven percent of the samples were classified as belonging to one of the nine mtDNA haplogroups described in Caucasians. This work shows that restriction analysis is a useful methodological tool to perform reliable population genetic analysis on archaeological remains. Tha analysis of ancient and modern haplogroup distribution can shed more light on the genetic evolution of human populations. Moreover, a more exhaustive data on prehistoric populations will allow to build stronger hypothesis on the genetic relationships among human populations.     

Ancient DNA reveals a migration of the ancient Di‐qiang populations into Xinjiang as early as the early Bronze Age

Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty‐nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y‐chromosomal DNA analyses combined with the archaeological studies revealed that the Di‐qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age. Am J Phys Anthropol 157:71–80, 2015. © 2014 Wiley Periodicals, Inc.     

Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas

Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.     

古代DNA研究实验技术

现代分子生物技术的发展,使从古代样品中获取微量DNA成为现实。在过去的十多年里,古DNA研究取得了重大进展,但实验方案还需要加以改进,其结果的分析与推论也需要多方面的验证。本综述着重介绍了古DNA研究的实验技术及可靠性分析。 Experimental Techniques for Ancient DNA Research YANG Shu-juan1,LAI Xu-long1,2,TANG Xian-hua1,SHENG Gui-lian1,2 1.Faculty of Earth Sciences,China University of Geosciences,Wuhan,430074,China; 2.Institute of Life Sciences,China University of Geosciences,Wuhan,430074,China Abstract:The development of modern molecular biological techniques makes it possible to study minimum DNA from ancient materials.During past decade,a lot of significant achievements on ancient DNA research have been made in many fields especially in molecular evolutionary biology.The nature of degradation and contamination of ancient DNA from ancient biological materials pose a dominating problem in ancient DNA research.Therefore,the experiments should be modified based on the modern molecular techniques and more factors should be considered when the results are analyzed.In this paper,authors review the general experimental protocols on sampling,extraction and amplification as well as authenticity of ancient DNA. Key words：ancient DNA;authenticity;ancient DNA techniques     

Present-Day DNA Contamination in Ancient DNA Datasets

Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.     

Dissecting the molecular architecture and origin of Bayash Romani patrilineages: genetic influences from South-Asia and the Balkans

The Bayash are a branch of Romanian speaking Roma living dispersedly in Central, Eastern, and Southeastern Europe. To better understand the molecular architecture and origin of the Croatian Bayash paternal gene pool, 151 Bayash Y chromosomes were analyzed for 16 SNPs and 17 STRs and compared with European Romani and non-Romani majority populations from Europe, Turkey, and South Asia. Two main layers of Bayash paternal gene pool were identified: ancestral (Indian) and recent (European). The reduced diversity and expansion signals of H1a patrilineages imply descent from closely related paternal ancestors who could have settled in the Indian subcontinent, possibly as early as between the eighth and tenth centuries AD. The recent layer of the Bayash paternal pool is dominated by a specific subset of E1b1b1a lineages that are not found in the Balkan majority populations. At least two private mutational events occurred in the Bayash during their migrations from the southern Balkans toward Romania. Additional admixture, evident in the low frequencies of typical European haplogroups, J2, R1a, I1, R1b1b2, G, and I2a, took place primarily during the early Bayash settlement in the Balkans and the Romani bondage in Romania. Our results indicate two phenomena in the Bayash and analyzed Roma: a significant preservation of ancestral H1a haplotypes as a result of considerable, but variable level of endogamy and isolation and differential distribution of less frequent, but typical European lineages due to different patterns of the early demographic history in Europe marked by differential admixture and genetic drift.     

Ancient DNA studies

Now that the hype surrounding Jurassic Park has settled down and we have become relatively used to dramatic headlines announcing the recovery of DNA from exotic fossilized remains, scientists working on ancient DNA are beginning to reflect on the long-term prospects and implications of the subject.¹ The science of ancient DNA has grown exponentially since its birth only ten years ago, and despite serious technical difficulties, it promises to become a revolutionary research tool in anthropology and molecular evolution. The use of bone DNA typing in particular has already yielded useful insights into Polynesian prehistory as well as spectacular applications in the forensic identification of skeletal remains.     

Ancient DNA evidence supports the contribution of Di‐Qiang people to the han Chinese gene pool

Han Chinese is the largest ethnic group in the world. During its development, it gradually integrated with many neighboring populations. To uncover the origin of the Han Chinese, ancient DNA analysis was performed on the remains of 46 humans (～1700 to 1900 years ago) excavated from the Taojiazhai site in Qinghai province, northwest of China, where the Di‐Qiang populations had previously lived. In this study, eight mtDNA haplogroups (A, B, D, F, M*, M10, N9a, and Z) and one Y‐chromosome haplogroup (O3) were identified. All analyses show that the Taojiazhai population presents close genetic affinity to Tibeto‐Burman populations (descendants of Di‐Qiang populations) and Han Chinese, suggesting that the Di‐Qiang populations may have contributed to the Han Chinese genetic pool. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.     

Culture modifies expectations of kinship and sex‐biased dispersal patterns: A case study of patrilineality and patrilocality in tribal yemen

Studies of the impact of post‐marital residence patterns on the distribution of genetic variation within populations have returned conflicting results. These studies have generally examined genetic diversity within and between groups with different post‐marriage residence patterns. Here, we directly examine Y chromosome microsatellite variation in individuals carrying a chromosome in the same Y haplogroup. We analyze Y chromosome data from two samples of Yemeni males: a sample representing the entire country and a sample from a large highland village. Our results support a normative patrilocality in highland Yemeni tribal populations, but also suggest that patrilocality is violated often enough to break down the expected correlation of genetic and geographic distance. We propose that a great deal of variation in male dispersal distance distributions is subsumed under the “patrilocal” label and that few human societies are likely to realize the idealized male dispersal distribution expected under strict patrilocality. In addition, we found almost no specific correspondence between social kinship and genetic patriline at the level of the clan (large, extended patrilineal kinship group) within a large, highland Yemeni village. We discuss ethnographic accounts that offer several cultural practices that explain exceptions to patrilocality and means by which social kinship and genetic patriline may become disentangled. © 2013 Wiley Periodicals, Inc.     

Ancient DNA perspectives on American colonization and population history

Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.     

North Indian Muslims: Enclaves of foreign DNA or Hindu converts?

The mtDNA composition of two Muslim sects from the northern Indian province of Uttar Pradesh, the Sunni and Shia, have been delineated using sequence information from hypervariable regions 1 and 2 (HVI and HVII, respectively) as well as coding region polymorphisms. A comparison of this data to that from Middle Eastern, Central Asian, North East African, and other Indian groups reveals that, at the mtDNA haplogroup level, both of these Indo-Sunni and Indo-Shia populations are more similar to each other and other Indian groups than to those from the other regions. In addition, these two Muslim sects exhibit a conspicuous absence of West Asian mtDNA haplogroups suggesting that their maternal lineages are of Indian origin. Furthermore, it is noteworthy that the maternal lineage data indicates differences between the Sunni and Shia collections of Uttar Pradesh with respect to the relative distributions of Indian-specific M sub-haplogroups (Indo Shia > Indo Sunni) and the R haplogroup (Indo Sunni > Indo Shia), a disparity that does not appear to be related to social status or geographic regions within India. Finally, the mtDNA data integrated with the Y-chromosome results from an earlier study, which indicated a major Indian genetic (Y-chromosomal) contribution as well, suggests a scenario of Hindu to Islamic conversion in these two populations. However, given the substantial level of the African/Middle Eastern YAP lineage in the Indo-Shia versus its absence in the Indo-Sunni, it is likely that this conversion was somewhat gender biased in favor of females in the Indo-Shia.     

Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history

We study the major levels of Y-chromosome haplogroup variation in 15 Sudanese populations by typing major Y-haplogroups in 445 unrelated males representing the three linguistic families in Sudan. Our analysis shows Sudanese populations fall into haplogroups A, B, E, F, I, J, K, and R in frequencies of 16.9, 7.9, 34.4, 3.1, 1.3, 22.5, 0.9, and 13% respectively. Haplogroups A, B, and E occur mainly in Nilo-Saharan speaking groups including Nilotics, Fur, Borgu, and Masalit; whereas haplogroups F, I, J, K, and R are more frequent among Afro-Asiatic speaking groups including Arabs, Beja, Copts, and Hausa, and Niger-Congo speakers from the Fulani ethnic group. Mantel tests reveal a strong correlation between genetic and linguistic structures (r = 0.31, P = 0.007), and a similar correlation between genetic and geographic distances (r = 0.29, P = 0.025) that appears after removing nomadic pastoralists of no known geographic locality from the analysis. The bulk of genetic diversity appears to be a consequence of recent migrations and demographic events mainly from Asia and Europe, evident in a higher migration rate for speakers of Afro-Asiatic as compared with the Nilo-Saharan family of languages, and a generally higher effective population size for the former. The data provide insights not only into the history of the Nile Valley, but also in part to the history of Africa and the area of the Sahel.     

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.     

一种实用可靠的古代 DNA 获取方法

古代DNA序列信息能够为物种演化研究提供最直接的分子证据,但获取古代DNA的技术仍存在诸多瓶颈,尤其是扩增中存在受损伤DNA模板的干扰、获取成本高和实验周期长等问题．改进了异丙醇沉淀提取法,并采用了尿嘧啶糖苷酶(UNG)去除受损伤DNA模板后进行扩增的方法,最终可以高效地获取真实的古代DNA序列．实验利用距今4 300～3 900年前的猪牙样本,将改进的古 DNA 获取方法与常规方法进行比较研究,结果表明,改进的异丙醇沉淀法提取结合UNG处理后进行PCR扩增的方法,可以在保证古代DNA获取成功率并提高获得的DNA序列可靠性的前提下,将经费投入和实验周期都各减少至常规方法的50%以下．这可以为开展大规模古代样本检测提供一种切实可行的 DNA 获取方法．     

Detection of DNA in Ancient Bones Using Histochemical Methods

We describe histochemical techniques for detecting DNA within the osteocytic lacunae of ancient bones. The bones examined were fragments of femurs from two human individuals found in the Pompeian C. I. Polybius house and fragments of metacarpals from two horses (Equus sp.) found in the Pompeian “Casti Amanti” house. Both buildings were buried by the 79 A. D. Vesuvius eruption. Fragments of femurs from a modern horse, a modern swine and a modern amphibian also were studied as controls. Some bone sections were stained with two different DNA-specific fluorochromes, 4′ -′ 6-diamidino-2-phenylindole (DAPI) and chromomycin A3 (CMA), while others were stained by the Feulgen reaction. All of the techniques gave a positive reaction within the osteocytic lacunae. Histological analysis of the undecalcified, ground and unstained sections agreed well with results of bone sections stained with either the fluorochromes or the Feulgen reaction. Bones showing good histology also were positive by our DNA-specific stain. Histochemical and histological analyses correlated well with the success of DNA extraction and amplification. Using conventional DNA-specific histochemical techniques in conjunction with histological analysis can be useful in the study of DNA extracted from ancient bone remains while reducing both the amount of time and cost.     

Detection of DNA in Ancient Bones Using Histochemical Methods

We describe histochemical techniques for detecting DNA within the osteocytic lacunae of ancient bones. The bones examined were fragments of femurs from two human individuals found in the Pompeian C. I. Polybius house and fragments of metacarpals from two horses (Equus sp.) found in the Pompeian “Casti Amanti” house. Both buildings were buried by the 79 A. D. Vesuvius eruption. Fragments of femurs from a modern horse, a modern swine and a modern amphibian also were studied as controls. Some bone sections were stained with two different DNA-specific fluorochromes, 4' -' 6-diamidino-2-phenylindole (DAPI) and chromomycin A3 (CMA), while others were stained by the Feulgen reaction. All of the techniques gave a positive reaction within the osteocytic lacunae. Histological analysis of the undecalcified, ground and unstained sections agreed well with results of bone sections stained with either the fluorochromes or the Feulgen reaction. Bones showing good histology also were positive by our DNA-specific stain. Histochemical and histological analyses correlated well with the success of DNA extraction and amplification. Using conventional DNA-specific histochemical techniques in conjunction with histological analysis can be useful in the study of DNA extracted from ancient bone remains while reducing both the amount of time and cost.     

Congruent Avian Phylogenies Inferred from Mitochondrial and Nuclear DNA Sequences

Recent molecular studies addressing the phylogenetic relationships of avian orders have had conflicting results. While studies using nuclear DNA sequences tend to support traditional taxonomic views, also supported by morphological data [(paleognaths (galloanseres (all other birds)))], with songbirds forming a clade within Neoaves (all other birds), analyses with complete mtDNA genomes have resulted in topologies that place songbirds as one of the earliest-diverging avian lineages. Considering that over half of the extant bird species are songbirds, these different results have very different implications for our understanding of avian evolution. We analyzed data sets comprising nearly 4 kb of mitochondrial DNA (mtDNA) (complete 12S, ND1, ND2, and cytochrome b) plus 600 bp of the nuclear gene c-mos for 15 birds that were chosen to represent all major avian clades and to minimize potential long-branch attraction problems; we used a partition-specific maximum likelihood approach. Our results show congruence with respect to the ingroup among phylogenies obtained with mtDNA and the nuclear gene c-mos, separately or combined. The data sets support a traditional avian taxonomy, with paleognaths (ratites and tinamous) occupying a basal position and with songbirds more derived and forming a monophyletic group. We also show that, for mtDNA studies, turtles may be a better outgroup for birds than crocodilians because of their slower rate of sequence evolution.     

Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA

We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen.