Ancient Specimens Research Articles

Next-Generation Sequencing of Ancient and Recent Fungarium Specimens.

Fungaria are an unmatched resource for providing genetic data from authoritative, taxonomically-correct fungal species, especially type specimens. These specimens serve to anchor species hypotheses by enabling the correct taxonomic placement of taxa in systematic studies. The DNA from ancient specimens older than 30 years is commonly fragmented, and sometimes highly contaminated by exogenous, non-target fungal DNA, making conventional PCR amplification and Sanger sequencing difficult or impossible. Here, we present the results of DNA extraction, PCR amplification of the ITS2 region, and Illumina MiSeq Nano sequencing of nine recent and 11 ancient specimens, including seven type specimens. The taxa sampled included a range of large and fleshy, to small and tough, or small, melanized specimens of Discina, Gyromitra, Propolis, Stictis, and Xerotrema, with a culture of Lasiosphaeria serving as a positive control. DNA was highly fragmented and in very low quantity for most samples, resulting in inconclusive or incorrect results for all but five samples. Taxonomically-correct sequences were generated from the holotype specimens of G. arctica, G. korshinskii, and G. leucoxantha, from the neotype of G. ussuriensis, and from the positive control. Taxonomic assignments were confirmed through morphology, top BLASTn hits, and maximum likelihood phylogenetic analyses. Though this study was not cost-effective due to the small number of samples submitted and few generating correct sequences, it did produce short DNA barcode fragments for four type specimens that are essential for their correct taxonomic placement in our ongoing systematic studies.

Brassica and Sinapis Seeds in Medieval Archaeological Sites: An Example of Multiproxy Analysis for Their Identification and Ethnobotanical Interpretation.

The genus Brassica includes some of the most important vegetable and oil crops worldwide. Many Brassica seeds (which can show diagnostic characters useful for species identification) were recovered from two archaeological sites in northern Italy, dated from between the Middle Ages and the Renaissance. We tested the combined use of archaeobotanical keys, ancient DNA barcoding, and references to ancient herbarium specimens to address the issue of diagnostic uncertainty. An unequivocal conventional diagnosis was possible for much of the material recovered, with the samples dominated by five Brassica species and Sinapis. The analysis using ancient DNA was restricted to the seeds with a Brassica-type structure and deployed a variant of multiplexed tandem PCR. The quality of diagnosis strongly depended on the molecular locus used. Nevertheless, many seeds were diagnosed down to species level, in concordance with their morphological identification, using one primer set from the core barcode site (matK). The number of specimens found in the Renaissance herbaria was not high; Brassica nigra, which is of great ethnobotanical importance, was the most common taxon. Thus, the combined use of independent means of species identification is particularly important when studying the early use of closely related crops, such as Brassicaceae.

Changing diets over time: knock-on effects of marine megafauna overexploitation on their competitors in the southwestern Atlantic Ocean

AbstractThis study compares the δ15N values and the trophic position of two seabird species throughout the late Holocene in three regions in the southwestern Atlantic Ocean to assess the hypothesis that the decimation of megafauna led to changes in the trophic position of mesopredators. Modern and ancient mollusk shells were also analyzed to account for changes in the isotopic baseline through time. Results revealed that modern Magellanic penguins have higher δ15N values than their ancient conspecifics in the three regions, after controlling for changes in the isotopic baseline. This was also true for modern Imperial shags compared with ancient unidentified cormorants/shags from the two areas where ancient specimens were recovered (southern Patagonia and the Beagle Channel). Such temporal variability might be caused by three non–mutually exclusive processes: decreased availability of pelagic squat lobster resulting from decreasing primary productivity through the late Holocene, increased availability of small fishes resulting from the sequential depletion of other piscivores (South American fur seal and sea lion and Argentine hake) since the late eighteenth century, and modification of the migratory patterns of Magellanic penguins. Although disentangling the relative contribution of all those processes is impossible at this time, the results reported here demonstrate that the ecology of Magellanic penguins and Imperial shags has undergone major changes since the late Holocene.

Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.

Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.

Papyrus production revisited: differences between ancient and modern production modes

Papyrus, produced from the white pith of Cyperus papyrus L., has been used for millennia as the major writing support by ancient cultures, but there was no continuous papyrus production until modern times. Therefore, papyrus production had to be rediscovered. Modern Egyptian papyrus producers claim that their sheets possess ‘the same physical and chemical properties as ancient papyri’. To study if this is accurate, commercially available papyrus sheets were compared to ancient papyri and papyri produced according to Pliny’s historic description. Material characterization was performed with a focus on the potentially color-bearing lignin. Two-dimensional nuclear magnetic resonance spectroscopy, derivatization followed by reductive cleavage, and pyrolysis–gas chromatography/mass spectrometry were complemented with microscopy and tests for surface pH and sodium content. The lignin data in the native pith and commercial sheets were compared to 10 ancient samples from the Papyrus Museum Vienna. The analytical data clearly show the involvement of a strong alkaline treatment followed by chlorine bleaching for commercial papyri, as expressed by higher pH values, altered lignin structures, and chlorinated lignin compounds. The inclusion of an alkaline step in ancient papyrus manufacture is discussed but dismissed, since the alkali-treatment causes a huge decrease in lignin content, that was not found for the analysed ancient specimen. We assume that this additional treatment was introduced to obtain yellowish papyrus sheets meeting optical expectations of modern spectators. Linguistic and art historic evidence indicates that such a step would not have made sense in antiquity, since it was desired to produce white papyri.

Gradual domestication of root traits in the earliest maize from Tehuacán

Efforts to understand the phenotypic transition that gave rise to maize from teosinte have mainly focused on the analysis of aerial organs, with little insights into possible domestication traits affecting the root system. Archeological excavations in San Marcos cave (Tehuacán, Mexico) yielded two well-preserved 5,300 to 4,970 calibrated y B.P. specimens (SM3 and SM11) corresponding to root stalks composed of at least five nodes with multiple nodal roots and, in case, a complete embryonic root system. To characterize in detail their architecture and anatomy, we used laser ablation tomography to reconstruct a three-dimensional segment of their nodal roots and a scutellar node, revealing exquisite preservation of the inner tissue and cell organization and providing reliable morphometric parameters for cellular characteristics of the stele and cortex. Whereas SM3 showed multiple cortical sclerenchyma typical of extant maize, the scutellar node of the SM11 embryonic root system completely lacked seminal roots, an attribute found in extant teosinte and in two specific maize mutants: root with undetectable meristem1 (rum1) and rootless concerning crown and seminal roots (rtcs). Ancient DNA sequences of SM10—a third San Marcos specimen of equivalent age to SM3 and SM11—revealed the presence of mutations in the transcribed sequence of both genes, offering the possibility for some of these mutations to be involved in the lack of seminal roots of the ancient specimens. Our results indicate that the root system of the earliest maize from Tehuacán resembled teosinte in traits important for maize drought adaptation.

Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.

Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.

Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups.

Simple SummaryThe genetic diversity of southern African sheep remains under-studied. We present here the complete mitochondrial genomes of archaeological southern African sheep, as well as the genomes from three indigenous southern African breeds—Damara, Namaqua Afrikaner, and Ronderib Afrikaner. We show that southern African sheep exhibit limited genetic diversity which is consistent with our understanding of their migration south from northernmost Africa. Intriguingly, many of the modern sheep show close relationships with the archaeological sheep, implying an ancestor-descendant relationship. Similarly, the sheep that do not exhibit a close relationship with the archaeological sheep nonetheless cluster closely with each other and do not show a close relationship with European and Asian sheep. This suggests that they too are descendants of indigenous sheep and not the product of historic introductions of exotic breeds.We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period.

Seismic performance of the ancient pagoda wall strengthened with GFRP bars embedded in the horizontal mortar joint under in-plane cyclic loading

The low strength and bonding of the mortar joints of the ancient pagoda wall result in the vulnerability to earthquake. To protect ancient pagodas under earthquakes, the seismic performances of the ancient pagoda wall strengthened with glass fiber reinforced plastic (GFRP) bars embedded in the horizontal mortar joint were studied. Six half-scale ancient pagoda wall specimens with semicircular arched openings, including two undamaged strengthened specimens, one severely damaged strengthened specimen, and three un-strengthened specimens, were tested under in-plane cyclic loading. The results indicated that the seismic performances of the strengthened specimens were effectively improved. Specifically, GFRP bars can effectively inhibit the generation of stepped cracks, and the failure modes of the strengthened specimens were changed from brittle shear failure to ductile shear failure. The shear bearing capacity of the strengthened specimens increased by 25% compared with the un-strengthened specimens. Moreover, the ultimate displacement, the energy dissipation capacity and the stiffness of the strengthened specimens were obviously increased. GFRP bars embedded in the horizontal mortar joint and glutinous rice mortar filled into mortar joint to strengthen the severely damaged specimen could effectively recover the seismic performance of the specimen. Furthermore, the calculation formulas of the shear bearing capacity of the strengthened ancient pagoda walls with semicircular arched openings were developed.

Metody issledovaniya ieroglifi­ cheskih nadpisej na drevnejshih artefaktah — vvedenie v problemu: istoriya, arheologiya, lingvistika

It was given brief information about the Chinese language and Chinese language communities (from antiquity to the present day) and it was shown the history of the formation of the Chinese language. The oldest monuments of the Chinese language are the inscriptions on the bones and tortoise shells (Jiaguwen), which were used for fortune telling, as well as inscriptions on bronze vessels (Jinwen). In this paper, for the study of hieroglyphic inscriptions on the most ancient artifacts, it is proposed to use a method based on photometry of the investigated surface of the samples and subsequent digital processing of the obtained data on a computer in order to determine the characteristics and parameters of the test sample. To test the method, we used onyx, jasper, and jade specimens, the surface of which is similar to the surface of ancient specimens. Some features of this method for the study of ancient artifacts are noted. The possibility of obtaining reliable results in the study of the most ancient hieroglyphic signs is shown.

Archaeological Recovery of Late Pleistocene Hair and Environmental DNA from Interior Alaska

ABSTRACT Ancient hair and remnant plant DNA are important environmental proxies that preserve for millennia in specific archaeological contexts. However, recovery has been rare from late Pleistocene sites and more may be found if deliberately sought. Once discovered, singular hair fragments are not easily identified to taxa through comparative analyses and environmental DNA (eDNA) extraction can be difficult depending on preservation or contamination. In this paper, we present our methods for the combined recovery of ancient hair specimens and eDNA from sediments to improve our understanding of late Pleistocene environments from the Holzman site along Shaw Creek in interior Alaska. The approach serves as a useful case study for learning more about local environmental changes.

Canids (Caninae) from the Past of Venezuela

There are three extant species of wild canids in Venezuela: Urocyon cinereoargenteus, Cerdocyon thous, and Speothos venaticus, excluding the feral domestic dog (Canis familiaris). However, a review of paleontological material that was published previously, along with newly reported ancient specimens, reveals a distinct historical diversity for the same region. The gray fox, U. cinereoargenteus, is the only small-sized taxon and the only Vulpini (true fox) identified to date in the fossil record of Venezuela; its presence is limited to the late Pleistocene of the Mene de Inciarte site, Zulia State. In contrast, large canids are more abundant. Aenocyon dirus (subtribe Canina), the dire wolf from the late Pleistocene, was reported from the sites El Mene de Inciarte, Muaco in Falcón State, and for the first time in El Breal de Orocual (ORS20) in Monagas State. The genus Protocyon, a native South American canid (subtribe Cerdocyonina), is recognized in the country from late Pleistocene Inciarte (Protocyon troglodytes sensu lato), and late Pliocene–early Pleistocene Orocual (ORS16) (Protocyon orocualensis sp. nov.). Finally, we report a possible genus Theriodictis from the late Pleistocene Orocual; this is a Cerdocyonina not previously mentioned for the northern region of South America. These records present broader diversity and suggest a more complex evolutionary history than previously thought for South American canids.

Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens.

Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.

Mammals from Belarus in the collections of natural history museums of Ukraine

A review of collection samples of mammals received from the territory of Belarus (within its modern borders) and stored in natural museums of Ukraine is given. Information on the materials of 5 museums is summarized – Dybowski Zoological Museum at Lviv National University (ZMD), Zoological Museum of Kyiv National University (ZMKU), Museum of Nature at the Kharkiv University (MNKU), State Natural History Museum of NASU (Lviv, SNHM) and National Museum of Natural History of NAS of Ukraine (Kyiv, NMNH). Within the latter, two (out of three available) collections were studied – the collections of the Department of Zoology (NNPM-z) and the Department of Museology (NNPM-m). Samples from Belarus were found in the collections of ZMD (5 specimens), SMNH (2 sp.), NMNH-z (68 sp.), NMNH-p (36 sp.), NMNH-m (7 sp.), MNKU (3 sp.). In total, there are 121 specimens of 13 mammal species in the collections. The number of samples is dominated by rodents, in particular Spermophilus suslicus (61 sp.), Sus scrofa (31 sp.) and Sylvaemus tauricus (7 sp.). Ancient specimens predominate (1885–1915), among which specimens from the collection of O. Brauner (NNPM) dominate. Certain groups of mammals appear in collections only in the last period of accumulation of collections, in particular murine rodents (collections of the 1990s). The largest number of samples was collected in the southern and western regions of Belarus within the Brest, Minsk, Grodno and Gomel oblasts. The most diverse are the collections from the vicinities of Mozyr in the Gomel oblast, mostly samples from the Brauner's collections of 1900–1915, which are now stored in the NNPM. The oldest are the samples of the black rat (Rattus rattus) from the collections of Benedykt Dybowski in 1885 in the family estates of Vojnov and Niankov of the Novogrudok district of the Grodno oblast. The most valuable is a sample of 61 skulls of ground squirrels Spermophilus odessanus (suslicus s. lato), collected during 1947–1954 in different districts of Brest, Grodno and Minsk oblasts. The series Sylvaemus tauricus from Central Polissia (7 sp.), collected in the 1990-1995 and transferred to the NNPM, is also significant.

Developmental features of the canid proximocaudal femur.

We continued direct morphological studies of the canid coxofemoral joint, considering early-life spatial relationships around the locus of the proximocaudal joint capsule insertion. Our primary goal was to elucidate the postnatal developmental gross anatomy of the proximocaudal femur, among juveniles across Canidae. From an original database of 267 independent (museum) specimens from 11 canid taxa and 1 hybrid taxon, we identified 29 ancient or modern candidate juvenile specimens (nine taxa and one hybrid taxon). Based on optimal ability to recognize landmarks, the best photographic data were categorized into five groups of four each (n= 20). The data groups approximated early juvenile, early-mid juvenile, mid-juvenile, mid-late juvenile; and young adult stages. In this descriptive photographic essay, we demonstrate the developmental spatial proximity among (a) the dorsal meeting of the respective lateral and medial extensions from the growth centers of the femoral head and greater trochanter; (b) the caudodorsal aspect of the coxofemoral joint capsule attachment; (c) a segment of the proximocaudal femoral shaft physis; and (d) an eventual associated mineralized prominence. The latter occurs frequently but not universally, suggesting natural population variability across taxa. Across taxa and juvenile age categories, the morphology thus supports developmental conservation among ancient and modern Canidae. The biomechanical and biological cause-effect implications are not yet clear. For zoological purposes, we apply the term postdevelopmental mineralized prominence to the residual caudolateral surface feature. We extend the original anatomical work of Morgan in zoological and phylogenic arenas, using direct observation of cleared skeletal specimens.

An accurate assignment test for extremely low-coverage whole-genome sequence data.

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.

Historical management of equine resources in France from the Iron Age to the Modern Period

Alongside horses, donkeys and their first-generation hybrids represent members of the Equidae family known for their social, economic and symbolic importance in protohistoric and historical France. However, their relative importance and their respective roles in different regions and time periods are difficult to assess based on textual, iconographic and archaeological evidence. This is both due to incomplete, partial and scattered historical sources and difficulties to accurately assign fragmentary archaeological remains at the proper taxonomic level. DNA-based methods, however, allow for a robust identification of the taxonomic status of ancient equine osseous material from minimal sequence data. Here, we leveraged shallow ancient DNA sequencing and the dedicated Zonkey computational pipeline to obtain the first baseline distribution for horses, mules and donkeys in France from the Iron Age to the Modern period. Our collection includes a total of 873 ancient specimens spanning 128 sites and comprising 717 horses, 100 donkeys, 55 mules and a single hinny individual. While horses were ubiquitous and the most dominant species identified, our dataset reveals the importance of mule breeding during Roman times, especially between the 1st and 3rd centuries CE (Common Era), where they represented between 20.0% and 34.2% of equine assemblages. In contrast, donkeys were almost absent from northern France assemblages during the whole Roman period, but replaced mules in rural and urban commercial and economic centers from the early Middle Ages. Our work also identified donkeys of exceptional size during Late Antiquity, which calls for a deep reassessment of the true morphological space of past equine species. This study confirmed the general preference toward horses throughout all time periods investigated but revealed dynamic management strategies leveraging the whole breadth of equine resources in various social, geographic and temporal contexts.

The KD Sr/Ca in cultured massive Porites spp. corals are reduced at low seawater pCO2

Coral skeletal Sr/Ca has valuable potential as a proxy of sea surface temperatures (SSTs). However seawater pCO2 can influence skeletal Sr incorporation and Sr/Ca-SST calibrations derived from present day corals may not be applicable to ancient specimens or older sections of modern corals deposited under lower seawater pCO2 than the present day. In this study we analysed skeletal Sr/Ca in multiple genotypes of massive Porites spp. cultured over a range of seawater pCO2 (from 180 to 750 μatm) and temperature (25 °C and 28 °C). Multiple linear regression analysis indicates that the Sr/Ca aragonite partition coefficient, KD Sr/Ca is inversely related to seawater temperature and positively related to seawater pCO2 (equivalent to changes in skeletal Sr/Ca of 0.046 mmol mol−1 °C−1 and 0.0002 mmol mol−1µatm−1 respectively). Applying present day Sr/Ca-SST equations to older coral skeletons growing at lower pCO2 could underestimate seawater temperatures. However KD Sr/Ca vary significantly between some coral genotypes cultured at the same seawater pCO2 indicating that other unidentified processes also influence skeletal Sr/Ca and it is unknown how these processes varied when ancient corals were deposited. We do not observe a significant relationship between KD Sr/Ca and coral calcification rate after combining all coral genotypes to allow identification of the correct KD Sr/Ca to apply to coral records.

Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations.

The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.

Mitochondrial DNA analysis of ancient sheep from Kazakhstan: evidence for early sheep introduction

Kazakhstan covers a vast territory, and it has always been a land of nomadic pastoralism, where domesticated horses and sheep were moved by nomadic people across the steppe. Previous reports suggest that sheep breeds from Kazakhstan have an intermediate genetic composition between Asian and European breeds; however, this data appears to be limited. Therefore, we studied the genetic diversity of ancient domestic sheep from two Late Bronze Age settlements, Toksanbai and Kent, located in the Pre-Caspian region of Kazakhstan and central Kazakhstan, respectively. We have applied ZooMS analysis for taxonomic identification of small ruminant remains to select ancient specimens of domestic sheep (Ovis aries). To assign sheep mitochondrial DNA (mtDNA) haplogroups, the single nucleotide polymorphisms (SNPs) from the control region were analyzed by real-time PCR and direct sequencing. Identical distribution of mtDNA haplogroups A (8/14; 57%), B (5/14; 36%), and C (1/14; 7%) was observed in the specimens from Toksanbai (n = 14) and Kent (n = 14). Ovine haplogroup A was predominant in both settlements. Both archeological sites had similar patterns of haplogroup distribution, indicating early sheep introduction into the region. These results are important to gain a better understanding of sheep migrations in the Eurasian steppe and highlight the importance of genomic analysis of earlier local lineages.