The relationship of the Mimbres to other southwestern and Mexican populations

Previous aDNA research in the Southwest provides a framework to understand the Mimbres population which maintains a unique identity in the archeology of the desert Southwest of North America. Both the mitochondrial DNA (mtDNA) haplogroups and haplotypes of a sample of 46 Mimbres individuals were identified from skeletal remains and compared to those of other ancient and modern populations in the American Southwest and Mexico. The haplogroup frequency distribution of the Mimbres resembles that of other Southwestern populations, suggesting a close relationship between the Mimbres and the neighboring populations and population continuity for a long period of time. However, their relatively low frequency of haplogroup A (11% n = 5) is consistent with a clinal distribution of haplogroup A from Mesoamerica to the Southwest. Moreover, unlike other Southwestern populations, the Mimbres share haplotypes with populations to the south, such as the Cora, Huichol, and Nahua, suggesting gene-flow from Mesoamerica. Here we discuss this data in light of the origin of the Mimbres population and their relationship to other Southwestern and Mexican populations.     

Ancient DNA,a Neolithic legging from the Swiss Alps and the early history of goat

Ancient DNA from a Neolithic legging (1st half of the 3rd millennium BC) found at Lenk, Schnidejoch (2750 m a.sl.) in the Swiss Alps has demonstrated, that modern distribution of genetic variation does not reflect past spatio-temporal signatures. The legging was made from the skin of a domestic goat (Capra hircus), belonging to the caprine haplogroup B1, which is marginal in Europe today, but represents a third highly diverse goat haplogroup entering Europe already in the Neolithic. Population expansion of lineage B therefore happened more than 4500 years ago, but their members were at some point almost completely replaced by goats of today's common A and C haplogroups.     

Mitochondrial DNA Analysis of Ancient Domestic Goats in the Southern Caucasus: A Preliminary Result from Neolithic Settlements at Göytepe and Hacı Elamxanlı Tepe

This study presents preliminary results of mitochondrial DNA analyses of modern and ancient domestic goats in the southern Caucasus in order to examine their phylogenetic relationship with modern and ancient goats. For this purpose, seven ancient samples were obtained from two early agricultural villages in west Azerbaijan (Göytepe and Hacı Elamxanlı tepe, dated to ca. 6000–5500 cal bc , the Pottery Neolithic period), in addition to five modern goat samples in the same region. In the study, mitochondrial DNA segments of the control region (216 bp for the Neolithic samples and 481 bp for the modern samples) were amplified, and phylogenetic analyses were performed using previously published reference DNA sequences. As a result, all the haplotypes found in this study were grouped in the haplogroup A of goats. The finding of the haplogroup A among domestic goats in the southern Caucasus in the early sixth millennium bc can be interpreted as part of the geographic expansion of this lineage from the areas of initial domestication to surrounding areas that include also South and Southeast Europe. In the southern Caucasus, the haplogroup A probably continued to be a major lineage among domestic goats since their emergence in this area to the present. In contrast, this lineage has not been detected among local wild goats including Capra aegagrus , indicating the external origin of domestic goats. This possibility is consistent with archaeological records that indicate sudden appearance of agricultural lifeways in the southern Caucasus and cultural connections with northern Mesopotamia. Copyright © 2016 John Wiley & Sons, Ltd.     

Ancestral Puebloan mtDNA in context of the greater southwest

Ancient DNA (aDNA) was extracted from the human remains of seventy-three individuals from the Tommy and Mine Canyon sites (dated to PI-II and PIII, respectively), located on the B-Square Ranch in the Middle San Juan region of New Mexico. The mitochondrial DNA (mtDNA) haplogroups of 48 (65.7%) of these samples were identified, and their frequency distributions were compared with those of other prehistoric and modern populations from the Greater Southwest and Mexico. The haplogroup frequency distributions for the two sites were statistically significantly different from each other, with the Mine Canyon site exhibiting an unusually high frequency of haplogroup A for a Southwestern population, indicating the possible influence of migration or other evolutionary forces. However, both sites exhibited a relatively high frequency of haplogroup B, typical of Southwestern populations, suggesting continuity in the Southwest, as has been hypothesized by others (8, 9, 29, 45 and 57). The first hypervariable region of twenty-three individuals (31.5%) was also sequenced to confirm haplogroup assignments and compared with other sequences from the region. This comparison further strengthens the argument for population continuity in the Southwest without a detectable influence from Mesoamerica.     

Cats of the Pharaohs: Genetic Comparison of Egyptian Cat Mummies to their Feline Contemporaries

The ancient Egyptians mummified an abundance of cats during the Late Period (664 - 332 BC). The overlapping morphology and sizes of developing wildcats and domestic cats confounds the identity of mummified cat species. Genetic analyses should support mummy identification and was conducted on two long bones and a mandible of three cats that were mummified by the ancient Egyptians. The mummy DNA was extracted in a dedicated ancient DNA laboratory at the University of California - Davis, then directly sequencing between 246 and 402 bp of the mtDNA control region from each bone. When compared to a dataset of wildcats (Felis silvestris silvestris, F. s. tristrami, and F. chaus) as well as a previously published worldwide dataset of modern domestic cat samples, including Egypt, the DNA evidence suggests the three mummies represent common contemporary domestic cat mitotypes prevalent in modern Egypt and the Middle East. Divergence estimates date the origin of the mummies' mitotypes to between two and 7.5 thousand years prior to their mummification, likely prior to or during Egyptian Predyanstic and Early Dynastic Periods. These data are the first genetic evidence supporting that the ancient Egyptians used domesticated cats, F. s. catus, for votive mummies, and likely implies cats were domesticated prior to extensive mummification of cats.     

Ancient Iberian horses: a method to recover DNA from archaeological samples buried under sub-optimal conditions for preservation

Existing methods to extract, amplify, and sequence ancient DNA (aDNA) from horse bone and teeth were optimized to recover DNA from a depositional environment of highly permeable acidic soil. DNA was successfully retrieved using 0.10g of bone powder from horse (Equus sp.) remains dating to 25 K years utilizing the methods optimized for this archaeological material. The genetic analyses were performed in a facility that is dedicated to ancient DNA research (Paleo-DNA Laboratory, Thunder Bay, ON, Canada) and has not been previously used to analyse modern or ancient horse DNA. Research was replicated to obtain reliable sequencing results for six samples from the Iberian Peninsula that were consistent with published sequences of Equus caballus. The archaeological sequence data obtained support hypotheses that promote the significance that the Iberian Peninsula has had to the multi-focal centres of origin for horse domestication and distribution of modern horse breeds. The data presented may provide evidence of the existence of an Iberian refugium for Equus during the last glacial period, 10 K years BP. Further molecular data analyses will enhance the ideas presented by this data and our understanding of horse domestication and phylogeny. The optimization of molecular techniques to successfully obtain DNA using minimally destructive, cosmetically sensitive techniques from archaeological remains endeavours to foster further cooperation between museums and researchers.     

DNA analysis of archaeological sheep remains from China

Recent research has thrown considerable light on the history of the domestic sheep, but has not extended to ancient sheep specimens. In the present study, ancient DNA analysis was carried out on eight archaeological sheep remains recovered from Erlitou archaeological site in Henan Province (ca. 2100–1800 B.C.) to explore the genetic structure of ancient sheep and the phylogenetic relationship between ancient and modern sheep. We analyzed the control region sequences and coding regions of mitochondrial DNA from the remains by direct sequencing and restriction fragment length polymorphism analysis, respectively. Our results reveal that all ancient sheep belong to lineage A defined by modern sheep sequences. Phylogenetic analysis shows that neither argali (Ovis ammon) nor urial (Ovis vignei) mtDNA is closely related to Erlitou ancient sheep. In addition, our results suggest that ancient DNA analysis can serve as a powerful tool in tracing prehistoric population movement.     

Early history of Chinese domestic sheep indicated by ancient DNA analysis of Bronze Age individuals

China has a long history of sheep husbandry, and has several indigenous sheep breeds. However, the exact geographic origin of Chinese domestic sheep remains unclear. To provide valuable genetic information for origin of Chinese domestic sheep, we performed an ancient DNA study on 22 sheep excavated from four Bronze Age archaeological sites in Northern China. Two lineages (A and B) were observed in ancient Chinese sheep, of which lineage A was predominant reaching a frequency of 95.5%. Furthermore, phylogenetic network showed that the most frequent haplotype in ancient sheep was the founder of lineage A. These results suggest that Lineage A may hold the key to understanding the origin of Chinese domestic sheep. Sequence sharing and principal component analysis showed that the ancient Chinese sheep had a close affinity to modern Chinese sheep. However, there was no significant breed structure among three modern Chinese sheep groups, making it difficult to determine their relationship to ancient Chinese sheep. Lastly, our results imply that ancient DNA analysis could provide a new way to investigate prehistoric East-West contact.     

Mitochondrial haplogroup M discovered in prehistoric North Americans

We analyzed two mid-Holocene (∼5000 years before present) individuals from North America that belong to mitochondrial DNA (mtDNA) haplogroup M, a common type found in East Asia, but one that has never before been reported in ancient or living indigenous populations in the Americas. This study provides evidence that the founding migrants of the Americas exhibited greater genetic diversity than previously recognized, prompting us to reconsider the widely accepted five-founder model that posits that the Americas were colonized by only five founding mtDNA lineages. Additional genetic studies of prehistoric remains in the Americas are likely to reveal important insights into the early population history of Native Americans. However, the usefulness of this information will be tempered by the ability of researchers to distinguish novel founding lineages from contamination and, as such, we recommend strategies to successfully accomplish this goal.     

Ancient DNA Analysis of Anatolian Goat Remains Excavated from a Urartian Castle in Eastern Turkey

In recent years, mitochondrial diversity of goats has been extensively studied, in order to shed light on domestication processes. There are limited studies on genetic diversity and demographic history of Anatolian goat breeds, and these studies have focused only on modern goats. Until today, no research has been conducted on DNA analysis of ancient Anatolian goats. In the present study, seven ancient DNA samples of goat remains from Van‐Yoncatepe archaeological site in Eastern Anatolia, Turkey, dating 1000 BC, were successfully extracted and amplified for the first time. A 230‐bp fragment of mitochondrial DNA Hypervariable Region 1 of the samples was analyzed. All of the ancient sequences belonged to haplogroup A, which is the most widely distributed and frequently encountered haplogroup in modern goats. The results also pointed out that Anatolian ancient goats might have contributed to the genetic structure of modern goats in the Near East, the Mediterranean Region and South‐Southeastern Asia. Copyright © 2014 John Wiley & Sons, Ltd.     

Wild or domesticated: DNA analysis of ancient water buffalo remains from north China

Recent zooarchaeological studies on water buffalo (Bubalus sp.) remains from China and south Asia question the traditional view that water buffalo were first domesticated in Neolithic China over 7000 years ago. The results from several recent population genetic studies of modern domesticated buffalo (Bubalus bubalis) are not consistent with each other, placing the original center of buffalo's domestication in south Asia, southeast Asia, or China. This paper reports a study using an ancient DNA approach to analyze water buffalo remains from Neolithic sites in north China to investigate their affinities with modern domesticated water buffalo, and to shed light on the origin of modern domesticated water buffalo in China.A 169 bp fragment of D-loop mitochondrial DNA was successfully amplified and verified for 13 of 24 bone samples obtained from seven archaeological sites along the Wei River valley in Shaanxi Province, China. The bone samples which yielded positive DNA can be dated to 8000–3600 cal. BP. The phylogenetic analysis of the obtained DNA sequences along with modern water buffalo sequences indicated that the ancient water buffalos were not the direct ancestor of modern domesticated water buffalo. However, the phylogenetic analysis, along with BLAST searches of these ancient DNA sequences, did demonstrate their relatedness to water buffalo more so than to any other bovid species, confirming the existence of indigenous wild (but now extinct) water buffalo species (B. mephistopheles) in ancient China.The DNA analysis of these ancient remains failed to establish direct links between modern domesticated water buffalo (B. bubalis) and indigenous water buffalo (B. mephistopheles) from ancient China. If further DNA studies of more ancient remains from other regions of China confirm the observation of solely indigenous water buffalo species in ancient China, it would suggest modern water buffalo might not have been first domesticated in China.     

MtDNA origins of an enslaved labor force from the 18th century Schuyler Flatts Burial Ground in colonial Albany,NY: Africans,Native Americans,and Malagasy?

A burial ground located in the Town of Colonie, NY along the Hudson River revealed fourteen individuals dated from the 17th through the early 19th centuries. Bioarchaeological analysis suggested some of these individuals were of African ancestry who had worked and died on the property owned by the prominent Schuyler family. Mitochondrial DNA (mtDNA) analysis was carried out on skeletal remains of seven adults using restriction fragment length polymorphism typing and direct sequencing of the control region to infer their origins and relatedness. Results show that none of the individuals were maternally related, with four individuals identified as African haplogroup L, one identified as Native American haplogroup X, and two identified as haplogroup M and M7. Individuals of African ancestry correlate with published mtDNA data on African Americans and their geographical origins corroborate with the various exit points during the African slave trade to New York State. Individuals identified as haplogroup M7 and M resemble lineages found in Madagascar. Historical documents suggest several hundred people were imported from Madagascar through illegal trading to New York by the end of the 17th century. This study highlights the diverse origins of the enslaved labor force in colonial New York and contributes to our understanding of African American history in the northeast.     

The limits of biomolecular palaeopathology: ancient DNA cannot be used to study venereal syphilis

To determine whether ancient DNA (aDNA) can be used to study the palaeopathology of venereal syphilis, we carried out a comprehensive analysis of the preservation of human and pathogen DNA in a set of 46 bones of various ages, most of which displayed osteological indications of the disease. Bones came from seven English cemetery sites that were in use during the 9th–19th centuries. Twelve of the 46 bones consistently yielded mitochondrial DNA (mtDNA) sequences after replicate polymerase chain reactions (PCRs), and a further 13 bones yielded mtDNA sequences with less reproducibility. The sequence data enabled tentative mitochondrial haplogroups to be assigned to nine of the bones, and the identities and frequencies of these haplogroups were compatible with the geographical origins of the bones. Twenty-one bones consistently gave negative results with all mtDNA PCRs, indicating that at least these bones were not contaminated with modern human DNA, and those bones that gave positive results only yielded one sequence each, again suggesting that widespread modern contamination had not occurred. Mycobacterium tuberculosis sequences were obtained from seven bones, including three of five bones with tuberculous lesions. The cloned and direct sequences obtained from both the mtDNA and M. tuberculosis PCR products showed features typical of degraded aDNA. All of these results suggest that at least some of the 46 bones that we studied were suitable for aDNA analysis. All 46 bones were tested with nine different treponemal PCRs, each optimised to give a detection limit of ≤5 genomes. Although various bones gave PCR products of the expected size with one or more of these PCRs, sequencing showed that none of these products were authentic treponemal amplicons. Our failure to detect treponemal DNA in bones that were suitable for aDNA analysis, using highly sensitive PCRs, suggests that treponemal DNA is not preserved in human bone and that it is therefore not possible to use aDNA analysis to study venereal syphilis. Any past or future paper claiming detection of treponemal aDNA should therefore be accompanied by a detailed justification of the results.     

Mitochondrial DNA from 3000-year old chickens at the Teouma site,Vanuatu

Chickens were part of the Lapita cultural complex, transported into and through the Pacific by prehistoric colonists; as such they can be used as a proxy for tracking prehistoric migration and interaction. The Lapita site of Teouma in Vanuatu is well known for the recovery of complete dentate stamped pots and a cemetery containing the largest collection of Lapita period skeletons ever found. Chicken bones recovered from these excavations provide the first ancient DNA sequences from any commensal organism directly associated with a Lapita context. The ancient mtDNA sequences obtained from two Teouma chicken bones are compared with previously published archaeologically derived ancient DNA sequences to extend our understanding of the spread of chickens in Pacific prehistory. The results also show that the haplogroup E signature was present in very early populations of chickens transported into Remote Oceania. This study also adds to the suite of available data relating to isotopic signatures for commensal animals during the early settlement of Vanuatu and may reveal a different diet for Teouma chickens than those from other early prehistoric assemblages in the Pacific.     

MtDNA haplotype identification of aurochs remains originating from the Czech Republic (Central Europe)

Abstract

This study presents the results of the analysis of mtDNA bone samples morphologically determined to be aurochs (Bos primigenius) from four various archaeological finds in the Czech Republic (Central Europe). The results from two of them — the Pleistocene sample from Praha-?eporyje and the Neolithic sample from Vedrovice — probably represent contamination by modern DNA. Sequences identified in the Eneolithic Kutná Hora-Denemark site (～5 thousand BP) confirm the presence of haplogroup P in the geographically partly isolated Czech basin. This finding (the first of its kind within the Czech Republic) is consistent with other published findings showing the domination of this aurochs haplogroup line in Europe. The combination of large individual size and ‘domestic’ mtDNA suggest, if inconclusively, that the Early Medieval fourth sample from Vy?ehrad could potentially represent an aurochs/domestic cattle hybrid.     

Viking age horse graves from Kaunas region (Middle Lithuania)

Balts' territories have one peculiarity—large amounts of horse bones are found in burial grounds. This phenomenon is typical to the Prussians (5th–11th centuries) and Lithuanians (Kaunas region 8th–11th centuries) Horse burials of the 8th–11th centuries reflect the archaeological culture of Middle Lithuania most significantly. Several horse burial types have been defined on the basis of individuals; osteological signs and the archaeological data of the horse remains. A typical horse grave is when the whole horse was buried. Sometimes only a head or a head with forelegs, or scattered horse remains are found in a burial. The large number of burial grounds with an abundance of horse graves testifies to a very expressive ritual of horse offering in the Balts' region. On the basis of the data obtained, we determined that mostly 4–10 year old horses were buried in the grounds of Middle Lithuania. From the bone measurements, it has been determined that the length of metacarpals ranges between 180 and 216 mm (the average length 193.1±0.99 mm); the length of metatarsals between 218 and 253 mm (average length 233.9±0.73 mm).These data demonstrate that horses of different types were buried in Marvelė and Veršvai burial grounds (wither height 120–136 cm). A certain number of the larger horses (wither height 136–144 and 153 cm; length of metacarpals 210–222 mm) might not have belonged to local breeds. We have come to the conclusion that the most similar horse skeletons (according to the osteometric data) were found in Latvia. Copyright © 2001 John Wiley & Sons, Ltd.     

甘肃武威磨咀子出土汉代彩绘木马颜料 分析与修复保护

武威磨咀子考古出土的汉代彩绘木马,不仅数量多,而且形体较大,具有河西汉马的典型特征;根据彩绘木马的材质状况,其类型属于潮湿而糟朽木器,急需进行修复保护。为此,针对目前彩绘木马的保存现状,本修复工作运用现代X-射线衍射分析技术,对木马彩绘颜料进行了分析,物相结果表明:黑色为墨,白色为石膏,红色为朱砂、铅丹。同时遵循原始制作工艺,选用汉代棺板木作为复原材料对残缺部件进行了复原修复,采用无色、透明的有机玻璃(MMA)材料为其制作了辅助支撑底座,使用Paraloid B-72试剂对表面严重糟朽木质、彩绘层实施加固,使用聚醋酸乙烯酯对脱落部件实施粘接,利用原始铆眼套合与加楔技术对木马部件进行了组装;最后,通过安装辅助支撑底座使受损彩绘木马得到了妥善保护,修复取得良好效果。     

太原晋卿赵鞅墓车马坑马骨的保护与修复

春秋晚期的晋卿赵鞅墓车马坑马骨历经2500年的埋藏,有一定程度的腐朽;易地保护的切割,造成严重损伤;多次搬迁,造成箱内切块严重开裂破碎;出土后的长期裸露存放,形成一定程度的表面风化.为解决马骨的破损与风化,以及马骨承托底土的整体性问题,本工作采取的研究与保护措施有:对马骨骨组织结构进行电镜观察和力学性能检测、置换和轻化承托底土、隔绝地面水气、修补切割缝、修复屿骨、作防风化处理.经过两年的艰苦工作,晋卿赵鞅墓车马坑马骨的科技保护与修复完成了既定目标,达到了预期效果.     

Mitochondrial DNA diversity in a Transbaikalian Xiongnu population

Xiongnu was a confederation of nomadic pastoral tribes (~200 bc–100 ad) that founded the first nomadic empire in Central Asia. According to archeological and historical data, the tribes played a key role in ethnic and cultural processes in Central Asia and adjacent regions of Eurasia. Genetic studies of the Xiongnu published to date have focused on remains from burial grounds in present-day Mongolia, in the southern part of the ancient Xiongnu area. However, paleoanthropological materials from numerous Xiongnu cemeteries and settlements in Transbaikalia (the southern region of Eastern Siberia, Russia) in the northern part of the Xiongnu Empire have not been examined genetically. Here, we analyzed mitochondrial DNA variation in a Transbaikalian Xiongnu population based on ancient DNA obtained from skeletal remains (n = 18) at four burial grounds to complement available Xiongnu genetic diversity data. We detected 16 mitochondrial DNA haplotypes belonging to seven East Eurasian haplogroups (A, B5, C, D4, G2a, N9a, and Y) in the Transbaikalian Xiongnu series. We observed substantial similarity between Transbaikalian and Mongolian Xiongnu series with respect to main haplogroup composition and frequencies. We observed several mitochondrial DNA clusters (N9a, Y, B5, and A16) and 11 of 16 haplotypes that were previously undetected in the Xiongnu gene pool. We also observed high similarity between the Xiongnu and contemporary indigenous populations of eastern Central Asia, particularly Mongolian-speaking groups. These findings extend our knowledge of Xiongnu genetic diversity.