Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.

The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.

Analysis of the Preserved Amino Acid Bias in Peptide Profiles of Iron Age Teeth from a Tropical Environment Enable Sexing of Individuals Using Amelogenin MRM.

The first dental proteomic profile of Iron Age individuals (ca. 2000-1000 years B.P.), collected from the site of Long Long Rak rock shelter in northwest Thailand is described. A bias toward the preservation of the positively charged aromatic, and polar amino acids is observed. It is evident that the 212 proteins identified (2 peptide, FDR <1%) comprise a palimpsest of alterations that occurred both ante-mortem and post-mortem. Conservation of amino acids within the taphonomically resistant crystalline matrix enabled the identification of both X and Y chromosome linked amelogenin peptides. A novel multiple reaction monitoring method using the sex specific amelogenin protein isoforms is described and indicate the teeth are of male origin. Functional analysis shows an enrichment of pathways associated with metabolic disorders and shows a capacity for harboring these conditions prior to death. Stable isotope analysis using carbon isotopes highlights the strongly C3 based (≈80%) diet of the Long Long Rak cemetery people, which probably comprised rice combined with protein from freshwater fish among other food items. The combination of proteomics and stable isotope analysis provides a complementary strategy for assessing the demography, diet, lifestyle, and possible diseases experienced by ancient populations.

Fetal-sex determination of human placental tissues.

It is now demonstrated that the sex-specific maternal-placental-fetal interaction plays an important role in placental functions and pathologies. Determination of fetal-sex may therefore be an important consideration in studies using placenta samples. In this present study, we describe a simple, fast, and cheap protocol, which allows the fetal-sex determination of placental tissues from various starting materials (villi or formalin-fixed, paraffin-embedded (FFPE) tissues, isolated cytotrophoblasts or cellular debris from whole cell lysates, and cDNA) by a single duplex PCR reaction followed by agarose gel electrophoresis.

The use of soil pollen to determine the sex of overhead individuals of a temperate dioecious shrub.

PREMISE OF THE STUDY: In dioecious species, determining the sex of individual plants from one-time phenological observations is rarely feasible when some individuals capable of reproducing are not flowering or fruiting at the time of observation. Currently, sexing those individuals requires long-term phenological data on individuals and populations, but such data are rarely available or feasible to collect. We tested the hypothesis that differences in soil pollen concentrations beneath the crowns of female and male plants would exist and be sufficient to reliably determine the sex of the individual plant overhead in a dioecious species. We predicted that soil pollen concentrations beneath male plants would be significantly higher than beneath female plants because only males produce pollen and pollen should accumulate in the soil underneath the male plants over repeated flowering events. METHODS: We collected samples from surface soil under both sexes of the insect-pollinated dioecious shrub, Aucuba japonica (Garryaceae). KEY RESULTS: Pollen grains were present in surface soil in both Oe and A horizons, and mean pollen concentration under males was significantly higher than under females. Pollen concentrations beneath males were positively correlated with male plant height, potentially reflecting greater pollen production by larger individuals. CONCLUSIONS: Considering the small plant size and relatively low pollen production of A. japonica, this method may hold promise for sexing other dioecious species in the absence of direct phenological data. Our phenology-free and relatively low-cost method for sexing dioecious plants may be especially useful in tropical forests where many species are dioecious.

Odontometric sex estimation in humans using measurements on permanent canines. A comparison of an early Neolithic and an early medieval assemblage from Germany.

SUMMARY: This study analyzed whether cervical canine dimensions measured at the enamel-cement junction can provide a basis for sex estimation in human skeletal remains and whether discriminant functions developed for one assemblage can be successfully applied also to others. Cervical canine dimensions were recorded for an Early Neolithic (Linear Pottery Culture) and an early medieval skeletal assemblage from Germany. Only individuals in whom sex estimation based on standard diagnostic criteria could be performed with a high degree of certainty were included. Sexual dimorphism in cervical canine dimensions was higher in the early medieval assemblage. Values in females of the Early Neolithic assemblage exceeded those of the early medieval assemblage, while there were no significant differences in males. Discriminant analysis led to a maximum correct classification of sex (cross validation results) of 94.0% in the early medieval and of 79.2% in the Early Neolithic assemblage. Applying the discriminant functions developed on one assemblage to the other led to poor classification results. Cervical canine dimensions are highly correlated with sexually dimorphic skeletal traits and may provide a good basis for sexing archaeological individuals. It is suggested that due to population differences in canine dimensions, either assemblage specific discriminant functions should be developed or the applicability of existing formulae obtained on other assemblages to the assemblage under study should be carefully checked.

Odontometric sex estimation on three populations of the Iron Age from Abruzzo region (central-southern Italy).

BACKGROUND: In archaeological contexts, sex identification is a necessary step for a complete reconstruction of the biological profile of the individuals and to know demographic patterns of the population, nutritional stress, diseases, growth and development, and distribution of pathological conditions. METHODS: This study is based on the skeletal remains of 149 individuals from three protohistoric populations in close temporal and geographic proximity in Abruzzo region (central-southern Italy): Opi, Alfedena and Bazzano. It has been possible to develop logistic regression equations based on dental measurements of permanent teeth of adult individuals whose sex had previously been estimated based on pelvic and cranial features. These equations were subsequently applied to the permanent dentition of immature individuals and adult individuals whose sex was estimated as uncertain or unknown in order to estimate their sex. RESULTS: The mandibular canine is the tooth with the greatest sexual dimorphism in adults, followed by both maxillary and mandibular first and second molars, providing a correct assignment of sex ranging from 83.7% and 95.9% of cases, depending on the dimensions used for the construction of these equations. Of the 29 individuals in the target sample (14 adultus, 10 juvenilis and 5 infans), sex estimation was possible for 23 (10 adultus, 8 juvenilis and 5 infans), representing an applicability rate of 79.31% of the individuals. CONCLUSIONS: The results indicate that odontometrics is a useful tool for sex estimation and allows to increase the data to perform more complete paleodemographic studies on archaeological populations.

[DNA extraction and sex determination for human teeth dated 3000 years ago unearthed in Xi'an].

OBJECTIVE: To extracted DNA from ancient human teeth dated 3000 years ago unearthed in Xi'an and determine the genders for the individuals. METHODS: Thirty five ancient human teeth were studied. A 'Reverse-root-canal' technique and a Chelex-100 solution were used to extract the DNA. Specific primers for Amelogenin gene were designed for PCR amplification. RESULTS: Genomic DNA was successfully extracted from 30 samples, for which 8 were determined to be males and 22 were females. CONCLUSION: The 'Reverse-root-canal' technique may be used for extracting DNA from ancient human teeth. Genetics method can supplement physical anthropology for determination of sex for ancient samples.

DNA extraction and sex determination for human teeth dated 3000 years ago unearthed in Xi'an / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To extracted DNA from ancient human teeth dated 3000 years ago unearthed in Xi'an and determine the genders for the individuals.</p><p><b>METHODS</b>Thirty five ancient human teeth were studied. A 'Reverse-root-canal' technique and a Chelex-100 solution were used to extract the DNA. Specific primers for Amelogenin gene were designed for PCR amplification.</p><p><b>RESULTS</b>Genomic DNA was successfully extracted from 30 samples, for which 8 were determined to be males and 22 were females.</p><p><b>CONCLUSION</b>The 'Reverse-root-canal' technique may be used for extracting DNA from ancient human teeth. Genetics method can supplement physical anthropology for determination of sex for ancient samples.</p>

Identification of circulating fetal cell markers by microarray analysis.

OBJECTIVE: Different fetal cell types have been found in the maternal blood during pregnancy in the past, but fetal cells are scarce, and the proportions of the different cell types are unclear. The objective of the present study was to identify specific fetal cell markers from fetal cells found in the maternal blood circulation at the end of the first trimester. METHOD: Twenty-three fetal cells were isolated from maternal blood by removing the red blood cells by lysis or combining this with removal of large proportions of maternal white blood cells by magnetic-activated cell sorting. Fetal cells identified by XY fluorescence in situ hybridization and confirmed by reverse-color fluorescence in situ hybridization were shot off microscope slides by laser capture microdissection. The expression pattern of a subset of expressed genes was compared between fetal cells and maternal blood cells using stem cell microarray analysis. RESULTS: Twenty-eight genes were identified as fetal cell marker candidates. CONCLUSION: Of the 28 fetal marker candidate genes, five coded for proteins, which are located on the outer surface of the cell membrane and not expressed in blood. The protein product of these five genes, MMP14, MCAM, KCNQ4, CLDN6, and F3, may be used as markers for fetal cell enrichment.

Odontometric sex discrimination in the Herculaneum sample (79 AD, Naples, Italy), with application to juveniles.

Sex determination of subadult skeletal remains with satisfactory accuracy represents one of the most important limitations of archaeological research and forensic practice. Teeth are one of the most durable physical elements of an individual that remain after death, and constitute a potential source of information about the biological sex of that individual. This study was based on the skeletal remains of 117 individuals from the ancient city of Herculaneum (Naples, Italy), victims of the eruption of the nearby volcano Vesuvius on 24/25 August, 79 AD. It has been possible to develop discriminant function formulae based on dental dimensions of adult individuals whose sex had previously been determined based on descriptive osteologic criteria. These formulae were subsequently applied to the permanent dentitions of immature individuals of the same population in order to estimate their sex. The results show that the canine is the tooth with the greatest sex dimorphism in adults, providing percentages of correct assignment of sex between 76.5% and 100% depending on the dimension used. Of the 30 subadult individuals in the target sample, estimation of sex was possible for 22 individuals. Sex assignments matched those determined from descriptive characteristics of the ilia and mandible in 73.33% of the cases. The results provide some optimism that this method may be applicable to juvenile archaeological samples.

Dietary antioxidants, lipid peroxidation and plumage colouration in nestling blue tits Cyanistes caeruleus.

Carotenoid pigments are responsible for many of the red, yellow and orange plumage and integument traits seen in birds. One idea suggests that since carotenoids can act as antioxidants, carotenoid-mediated colouration may reveal an individual's ability to resist oxidative damage. In fact, there is currently very little information on the effects of most dietary-acquired antioxidants on oxidative stress in wild birds. Here, we assessed the impacts on oxidative damage, plasma antioxidants, growth and plumage colouration after supplementing nestling blue tits Cyanistes caeruleus with one of three diets; control, carotenoid treatment or α-tocopherol treatment. Oxidative damage was assessed by HPLC analysis of plasma levels of malondialdehyde (MDA), a by-product of lipid peroxidation. Contrary to predictions, we found no differences in oxidative damage, plumage colouration or growth rate between treatment groups. Although plasma lutein concentrations were significantly raised in carotenoid-fed chicks, α-tocopherol treatment had no effect on concentrations of plasma α-tocopherol compared with controls. Interestingly, we found that faster growing chicks had higher levels of oxidative damage than slower growing birds, independent of treatment, body mass and condition at fledging. Moreover, the chromatic signal of the chest plumage of birds was positively correlated with levels of MDA but not plasma antioxidant concentrations: more colourful nestlings had higher oxidative damage than less colourful individuals. Thus, increased carotenoid-mediated plumage does not reveal resistance to oxidative damage for nestling blue tits, but may indicate costs paid, in terms of oxidative damage. Our results indicate that the trade-offs between competing physiological systems for dietary antioxidants are likely to be complex in rapidly developing birds. Moreover, interpreting the biological relevance of different biomarkers of antioxidant status represents a challenge for evolutionary ecology.

An endoscopic method for identifying sex of hatchling Chinese box turtles and comparison of general versus local anesthesia for coelioscopy.

OBJECTIVE: To establish a safe and effective endoscopic method for visualizing the gonads and identifying the sex of hatchling Chinese box turtles and to compare the effects of general versus local anesthesia during coelioscopy. DESIGN: Clinical trial. ANIMALS: 58 hatchling Chinese box turtles (Cuora flavomarginata). PROCEDURES: Turtles were randomly assigned to be anesthetized with a mixture of ketamine, medetomidine, and morphine (n = 29) or to receive local anesthesia with lidocaine in the prefemoral region (29). Coelioscopy was performed with a rigid 1.9- or 2.7-mm telescope following insufflation with sterile lactated Ringer's solution. Ease of endoscopic sex identification and quality of anesthesia were scored. Body weights were recorded before and 7 and 14 days after surgery. RESULTS: Gonads were easily visualized and sex was easily identified in all 58 turtles without complications. Endoscopy scores and pre- and postoperative weights did not differ significantly between groups. However, anesthesia scores were significantly worse for animals that received local anesthesia alone, compared with those that underwent general anesthesia. All anesthetized turtles recovered within 21 minutes after administration of the reversal agents, atipamezole and naloxone. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggested that coelioscopy with a rigid endoscope and lactated Ringer's solution for insufflation was a safe and effective method for identifying the sex of hatchling Chinese box turtles. General anesthesia was effective and effects were rapidly reversible; local anesthesia with lidocaine alone was considered insufficient for coelioscopy.

Genetic analysis of the skeletal remains attributed to Francesco Petrarca.

We report on the mitochondrial DNA (mtDNA) analysis of the supposed remains of Francesco Petrarca exhumed in November 2003, from the S. Maria Assunta church, in Arquà Padua (Italy) where he died in 1374. The optimal preservation of the remains allowed the retrieval of sufficient mtDNA for genetic analysis. DNA was extracted from a rib and a tooth and mtDNA sequences were determined in multiple clones using the strictest criteria currently available for validation of ancient DNA sequences, including independent replication. MtDNA sequences from the tooth and rib were not identical, suggesting that they belonged to different individuals. Indeed, molecular gender determination showed that the postcranial remains belonged to a male while the skull belonged to a female. Historical records indicated that the remains were violated in 1630, possibly by thieves. These results are consistent with morphological investigations and confirm the importance of integrating molecular and morphological approaches in investigating historical remains.

[Cremation--biological source for gender research]. / Leichenbrand--biologische Quelle für Genderforschung.

This article presents a project designed for prehistoric gender research. It focuses on the late Bronze Age to early Iron Age urnfield in Cottbus "Alvensleben-Kaserne", Brandenburg. The cremation remains were emptied from the urns layer by layer. This provided excellent conditions for a critical reconstruction of the funeral rituals related to the cremation. Detailed recording of each bone fragment in each layer made possible the discovery of the ritual deposition of burnt bones according to the anatomical order. Cremated bones, a primarily biological source, are also a substantial resource for cultural historical research, e.g., on funeral practices as well as social structures.

Genetic dissection of hyperthermia-induced neural tube defects in mice.

BACKGROUND: Maternal hyperthermia has been shown to induce neural tube defects (NTD) in humans and in experimental animal systems. We report the first genetic dissection of maternal hyperthermia-induced NTD in mice. METHODS: After maternal exposure on E8.5 to 43 degrees C water bath for 10 min, we observed exencephaly frequencies among E15.5-17.5 fetuses from the following crosses and backcrosses, SWV/Fnn(SWV)xSWV, C57BL/6J(C57)xC57, SWVxC57 (F1), F1xSWV and SWVxF1. RESULTS: The fetuses with maternal hyperthermia exposure developed exencephaly in a strain-dependent manner and the exencephaly frequencies among the above crosses were 46.2, 14.3, 13.6, 11.3, and 27.0%, respectively, expressed over total live fetuses. The fetal death rates were 47.3, 24.6, 37.1, 4.3, and 35.5%, respectively, expressed over total implants. CONCLUSION: The data demonstrate that a single fetal genetic locus, plus a maternal effect, have likely caused the strain differences in the susceptibility to hyperthermia-induced exencephaly. A maternal effect alone may have caused the higher prenatal mortality rates in the SWVxF1 cross versus the reciprocal cross. Analysis of gender ratios among those affected from these crosses excludes an X- or Y-linked effect in causing the higher numbers of affected females.

Sex assessment on the basis of long bone circumference.

Discriminant functions have long been used to classify individuals into groups according to the dimensions of their bones. Although lengths, widths, and diameters have been extensively used, the circumferences have not been adequately validated. In this work, the importance that the circumferences of long bones can have in assigning the sex of ancient human remains is demonstrated. The functions produced by using just one circumference achieved accuracies higher than 80%, and circumference at the radial tuberosity of the radius is able to classify 92.8% of skeletons from the Late Roman site of Mas Rimbau/Mas Mallol (Spain). When functions are produced by using more than one circumference, they can achieve the uppermost classification attained in this sample. The functions also showed that the arm circumference functions are more useful than those of the leg, probably because male individuals of the population had greater mechanical stress than did females. The classification percentages, as well as other statistical values for the functions, demonstrated the great ability of long bone circumferences in helping to classify the sex of individuals of other sites of the Mediterranean area besides the ones examined in this study.

Sex ratio and fledging success of supplementary-fed Tengmalm's owl broods.

A nest box population of Tengmalm's owls (Aegolius funereus) in northern Sweden was studied to investigate the effects of extra food on the sex ratio between hatching and fledging in this sexually size-dimorphic species. The brood size and brood sex ratio of supplementary-fed and control broods were compared. Newly hatched nestlings were blood sampled and sexed by polymerase chain reaction (PCR) amplification of the sex-linked CHD1Z and CHD1W genes. The brood sex ratio at hatching was strongly male biased (65%); this was also the case in broods where all eggs hatched (72%). There was no relationship between hatch order and sex ratio, and hatching sex ratio did not vary significantly with laying date. Brood size decreased between hatching and fledging, but did not differ between fed and control broods at either stage. Brood sex ratio did not differ between hatching and fledging, and fledging sex ratio did not differ between fed and control broods. It was concluded that, at least during the year in which the study was carried out, feeding had no effect on brood reduction, and that male and female nestlings did not show any differential mortality. The mechanisms behind the male-biased sex ratio at hatching, and any possible adaptive reasons for it, are not known.