Ancient mtDNA Research Articles

Simulating the effects of kinship and postmarital residence patterns on mitochondrial DNA diversity in mortuary contexts.

We explore the observable outcome in mtDNA diversity of different kinship systems and associated postmarital residence patterns in the archeological record, using simulations at the intrapopulation level. Four kinship systems were simulated from a set of variable fertility and mortality scenarios. Initial conditions consisted of six clusters of variable size and a random number of assigned haplotypes, with individuals migrating between groups and reproducing for 15 generations. Each 15-generation span was simulated 500 times to obtain representative intrasite mtDNA diversity distributions for each kinship system. Additional simulations were devised to consider the effect of migration and different rates of adherence to kinship norms. Matrilineal kinship generates low male and female haplotype diversities that are statistically indistinguishable from each other, while female diversity in bilateral kinship with matrilocality is significantly lower than that observed in male diversity. Furthermore, mtDNA diversity generated by patrilineal kinship is very high. The effect of noncompliance with kinship rules is low; migration has a considerable impact on diversity, eventually obscuring the effect of kinship practices. The results of the simulations can be applied to ancient mtDNA data from archeological contexts, as exemplified with data from two studies. On a broader scale, the kinship system followed by the sampled population, can lead to either over- or underestimation of mtDNA population diversity. The results of the simulations can be used in the design of inferential frameworks to discern kinship scenarios in the archeological record, based on mtDNA and other types of evidence.

Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas

Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.

Hunter-gatherer genetic persistence at the onset of megalithism in western Iberia: New mitochondrial evidence from Mesolithic and Neolithic necropolises in central-southern Portugal

Despite its strategic importance at the furthermost edge of the Neolithic expansion in Europe, archaeogenetic data from Mesolithic and Neolithic human remains from Portugal are still very limited. Here we present ancient mtDNA evidence (mostly unpublished) to fill the gap and discuss the pattern of “genetic resurgence” of hunter-gatherer (Mesolithic) ancestry, widely reported elsewhere in Europe, among the first megalith builders (Middle Neolithic) of western Iberia.A total of 11 Mesolithic and Neolithic necropolises located in the central and southern regions of Portugal dated to ca. 6200–3000 BC were studied. These sites comprise all Mesolithic–Neolithic cultural stages and include several funerary architectures and spaces. Reproducible mtDNA HVRI haplotypes were obtained from 23 individuals from six different archaeological sites spread across a >3000-year transect, from the Late Mesolithic to the Late Neolithic.Our results support a three-stage explanatory demographic and populational model: i) local hunter-gatherer populations constituted a highly homogeneous genetic pool; ii) the first farming practices were introduced by human groups carrying new, extraneous haplogroups and exhibiting the signature of admixture events occurring at the time of first contact with local hunter-gatherers; iii) the genetic pattern detected among the megalith-building populations, showing hunter-gatherer along with farming ancestry, may be explained by the segmentary principles, and attendant endogamic practices, that structured Neolithic societies.

Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA

Simple SummaryRetracing the ancient human migration routes in the remote islands of the Pacific relies on robust models of the origins and spread of animals that were commensal to long-distance ocean voyages. Domestic pigs (Sus scrofa) in Polynesia belong to a rare mitochondrial DNA group whose geographic origins are disputed. We report new complete genome ancient DNA that suggests all founding populations of pigs in Polynesia, first settled by people about 2800–700 years ago, can be traced back to northern peninsular Southeast Asia.Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the “Pacific Clade” that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China’s Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800–700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia.

Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages.

Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.

Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors.

The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA (“NUMTs”). NUMTs are considered “mtDNA fossils” as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).

Uniparental origins of the admixed Argentine Patagonia.

We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history. The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information. Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers. Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762-2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region. The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed.

Mitochondrial DNA variation and cancer.

Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.

New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples.

Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.

Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia

BackgroundThe earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period.ResultsFrom these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D.ConclusionsThe presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.

Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals

Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating “hidden support”. Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.

Machine learning ATR-FTIR spectroscopy data for the screening of collagen for ZooMS analysis and mtDNA in archaeological bone

Faunal remains from archaeological sites allow for the identification of animal species that enables the better understanding of the relationships between humans and animals, not only from their morphological information, but also from the ancient biomolecules (lipids, proteins, and DNA) preserved in these remains for thousands and even millions of years. However, due to the costs and efforts required for ancient biomolecular analysis, there has been considerable research into development of accurate and efficient screening approaches for archaeological remains. FTIR spectroscopy is one such approach that has been considered for screening of proteins, but its widespread use has been hindered by the fact that its predictive accuracy can vary widely depending on the extent of sample preservation and the instrument used. Further, screening methods for ancient DNA (aDNA) analysis are scarce. Here we present a new approach to vastly improve upon FTIR-based screening methods prior to ZooMS (Zooarchaeology by Mass Spectrometry) and aDNA analysis through the use of random forest-based machine learning. To do so, we use ATR-FTIR to examine three sets of archaeological bone assemblages and analyse them by ZooMS (for taxonomic identification). Two of these are from Palaeolithic contexts, dominated by terrestrial fauna and include specimens with a variety of preservational conditions. The third set consists of Holocene faunal remains, with variable levels of preservation and is dominated by cetaceans. Using the Holocene faunal remains, we were able to more consistently evaluate ATR-FTIR-based screening for mtDNA as well as ZooMS success. We report on the potential of machine learning in ATR-FTIR-based screening for ancient mtDNA analysis, and our machine learning models conclusively improve the accuracy prior to usage of ATR-FTIR-based screening for ZooMS by 20–40%. The results also suggest this approach potentially allows for a universal screening system, applicable across multiple sites and largely independent of the spectrometers used.

AYChr-DB: a database of ancient human Y haplogroups.

Ancient Y-Chromosomal DNA is an invaluable tool for dating and discerning the origins of migration routes and demographic processes that occurred thousands of years ago. Driven by the adoption of high-throughput sequencing and capture enrichment methods in paleogenomics, the number of published ancient genomes has nearly quadrupled within the last three years (2018–2020). Whereas ancient mtDNA haplogroup repositories are available, no similar resource exists for ancient Y-Chromosomal haplogroups. Here, we present aYChr-DB—a comprehensive collection of 1797 ancient Eurasian human Y-Chromosome haplogroups ranging from 44 930 BC to 1945 AD. We include descriptors of age, location, genomic coverage and associated archaeological cultures. We also produced a visualization of ancient Y haplogroup distribution over time. The aYChr-DB database is a valuable resource for population genomic and paleogenomic studies.

Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease.

Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.

Heating histories and taphonomy of ancient fireplaces: A multi-proxy case study from the Upper Palaeolithic sequence of Abri Pataud (Les Eyzies-de-Tayac, France)

While the use of fire has long been recognised as a crucial innovation in the cultural evolution of humankind, much research has focused on the (debated) chronology of its earliest use and control, and less on the ways in which fire was used in the deep past. At its latest by the Upper Palaeolithic, hunter-gatherers routinely used fire to heat a wide range of materials, adjusting parameters like temperature, exposure time and fuel type to the specific requirements of the treated materials, for instance in food preparation or tool production.Comparing analyses of the chemical and physical properties of modern materials, heated under a range of controlled conditions in a laboratory, to archaeological ones might allow the reconstruction of the “heating history” of excavated materials and hence to infer the function of particular fires in the past - provided changes affecting the properties of the heated archaeological material during burial time are taken into consideration. To investigate the feasibility of such an approach, heated materials sampled from ~40,000 to 25,000 year old fireplaces (hearths) and their sedimentary matrices from the Upper Palaeolithic Abri Pataud rock shelter in South-Western France are used here to study (1) the fuel type(s) used by the site’s occupants, (2) the temperatures reached in fireplaces and (3) the potential changes in human activities related to fireplaces over time, with the influence of post-depositional processes taken into explicit consideration throughout. For this purpose, we used a range of methods to analyse macroscopically visible as well as “invisible” (microscopic and molecular) heat-altered materials.The results suggest that charred organic materials (COM) encountered in the samples predominantly result from the fuel used in fireplaces, including the earliest reported use of dung as fuel. Earlier suggestions about the use of bone as fuel at the Abri Pataud are not supported by this study. The heating temperature of COM increased gradually from 350 °C in the Aurignacian to 450 °C in Gravettian levels. Py-GC–MS studies identified a range of organic compounds, biomolecules derived from plant as well as animal sources, still preserved in the sediments after exposure to heat and burial in the rock shelter more than 20,000 years ago. Mammalian mtDNA was identified in sediment samples retrieved from the fireplaces, including ancient mtDNA fragments that originated from one or more modern human-like mitochondrial genome(s). This makes the Abri Pataud the first archaeological site for which ancient modern human mtDNA has been retrieved from sediment samples.The absence of specific organic compounds (furans) in the Aurignacian levels and their presence in the Gravettian ones, the changes in temperatures reached through the Aurignacian-Gravettian sequence as well as changes in the character of the fireplaces (presence/absence of lining river pebbles) suggest that the functions of hearths changed through time.These results highlight the potential of multi-proxy analyses of macro- and microscopic traces of ancient fireplaces, and especially of a shift in focus towards molecular traces of such activities. Systematic sampling of fireplaces and their sedimentary matrix should become a standard part of the excavation protocol of such features, to improve our understanding of the activities of humans in the deep past.

Comparison of Ancient Haplotypes with Modern Island Reed Vole Populations

Ancient (Medvezhyi Klyk Cave, Primorsky krai, Russia) and modern (island and coastal populations of Peter the Great Bay) mtDNA haplotypes of the reed vole were compared. Both ancient and modern vole haplotypes were divided into two groups. The first group included three ancient haplotypes dated >30 000 years BP and modern vole haplotypes from the islands of the Rimsky-Korsakov Archipelago. The second group involved ancient haplotypes dated 2000–5000 years BP and modern vole haplotypes of young island populations and mainland populations. Two widely distributed haplotypes H1 and H7 were found in the second group, the latter identical to one of the ancient haplotypes. The voles of Matveyev and Bolshoy Pelis islands retained the most ancient haplotypes. The main haplogroup changed on the coastal territory after the isolation of islands of the Rimsky-Korsakov Archipelago.

Zooarchaeology, ancient mtDNA, and radiocarbon dating provide new evidence for the emergence of domestic cattle and caprines in the Tao River Valley of Gansu Province, northwest China

The Gansu-Qinghai region of Northwest China was an important region for cultural exchange and the adoption of new animal domesticates during the fourth through second millennia BCE. This paper summarizes previously published zooarchaeological reports from Neolithic and Bronze Age sites in Gansu and Qinghai Provinces in order to synthesize the changing uses of domesticated taxa and the timing of the arrivals of new domesticates into northwest China. We present new zooarchaeologial data collected during archaeological investigations by the Tao River Archaeological Project (TRAP) at the sites of Dayatou, Qijiaping, and Huizuiwa. These sites allow us to explore changes in animal use at a local scale of analysis, revealing the increasing importance of caprine pastoralism through time. Our analyses also include the first directly dated sheep and goat bones for the region, with the earliest samples dating to 1900-1750 cal. BCE. We conclude that although there is a suggestion that cattle, sheep, and goats arrived in the Gansu-Qinghai region during the 4th millennium BCE, we do not believe that there is definitive evidence for cattle, sheep, and goats until after about 2500 BCE.

Ancient mtDNA from the extinct Indian cheetah supports unexpectedly deep divergence from African cheetahs

The Indian cheetah was hunted to extinction by the mid-20th century. While analysis of 139 bp of mitochondrial DNA (mtDNA) has confirmed that the Indian cheetah was part of the Asiatic subspecies (Acinonyx jubatus venaticus), the detailed relationships between cheetah populations remains unclear due to limited genetic data. We clarify these relationships by studying larger fragments of cheetah mtDNA, both from an Indian cheetah museum specimen and two African cheetah, one modern and one historic, imported into India at different times. Our results suggest that the most recent common ancestor of cheetah mtDNA is approximately twice as ancient as currently recognised. The Indian and Southeast African (Acinonyx jubatus jubatus) cheetah mtDNA diverged approximately 72 kya, while the Southeast and Northeast African (Acinonyx jubatus soemmeringii) cheetah mtDNA diverged around 139 kya. Additionally, the historic African cheetah sampled from India proved to have an A. j. jubatus haplotype, suggesting a hitherto unrecognised South African route of cheetah importation into India in the 19th century. Together, our results provide a deeper understanding of the relationships between cheetah subspecies, and have important implications for the conservation of A. j. venaticus and potential reintroduction of cheetahs into India.

Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs.

The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the Yellow River and Yangtze River basins (YYRB). These are the first complete ancient mtDNA of Chinese dogs from the cradle of early Chinese civilization. We found that most ancient dogs (18/26) belong to the haplogroup A1b lineage that is found in high frequency in present-day Australian dingoes and precolonial Pacific Island dogs but low frequency in present-day China. Particularly, a 7,000-year-old dog from the Tianluoshan site in Zhejiang province possesses a haplotype basal to the entire haplogroup A1b lineage. We propose that A1b lineage dogs were once widely distributed in the YYRB area. Following their dispersal to South China, and then into Southeast Asia, New Guinea and remote Oceania, they were largely replaced by dogs belonging to other lineages in the last 2,000 years in present-day China, especially North China.

Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy

Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy.The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.