Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach

The Yuan Dynasty (AD 1271–1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites.     

Ancient Maltese genomes and the genetic geography of Neolithic Europe

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Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal

Archaeological evidence supports the inhabitation of the Lake Baikal region since the Paleolithic. Both metric and nonmetric osteological studies suggest that Neolithic Cis-Baikal populations are the ancestors of contemporary inhabitants of the region. To date, ancient DNA data have not been used to corroborate this biological continuity hypothesis. This study presents a temporal snapshot of the Cis-Baikal Neolithic by examining mtDNA diversity in two cemetery populations situated on the Angara River downstream of Lake Baikal. The 800 years separating the use of the two cemeteries is thought to represent a biocultural hiatus in the Cis-Baikal region, one that ended when a new group migrated into the area. To assess the likelihood that genetic continuity exists between these two Neolithic groups, we examined both mtDNA coding region and hypervariable region I (HVI) polymorphisms from skeletal remains excavated from both cemeteries (Lokomotiv and Ust'-Ida). The mtDNA haplogroup distributions of the two cemetery populations differ significantly, suggesting that they were biologically distinct groups. When the biological distance between these Neolithic groups is compared with modern Siberian and other East Eurasian groups, the posthiatus group (Serovo-Glazkovo) generally aligns with contemporary Siberians, while the prehiatus (Kitoi) individuals are significantly different from all but modern Kets and Shorians living in the Yenisey and Ob River basins to the west of Lake Baikal. These results suggest that the Lake Baikal region experienced a significant depopulation event during the sixth millennium BP, and was reoccupied by a new immigrant population some 800 years later.     

Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

The increasing ability to extract and sequence DNA from noncontemporaneous tissue offers biologists the opportunity to analyse ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. In this study, we provide a critical assessment of Bayesian Markov chain Monte Carlo (MCMC) analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates because of model misspecification when the data come from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However, when model misspecification is only mild, then the 95% highest posterior density intervals provide adequate frequentist coverage of the true rates.     

Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany

The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800-2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool.     

Sex roles and sex ratios in animals

In species with separate sexes, females and males often differ in their morphology, physiology and behaviour. Such sex-specific traits are functionally linked to variation in reproductive competition, mate choice and parental care, which have all been linked to sex roles. At the 150th anniversary of Darwin's theory on sexual selection, the question of why patterns of sex roles vary within and across species remains a key topic in behavioural and evolutionary ecology. New theoretical, experimental and comparative evidence suggests that variation in the adult sex ratio (ASR) is a key driver of variation in sex roles. Here, we first define and discuss the historical emergence of the sex role concept, including recent criticisms and rebuttals. Second, we review the various sex ratios with a focus on ASR, and explore its theoretical links to sex roles. Third, we explore the causes, and especially the consequences, of biased ASRs, focusing on the results of correlational and experimental studies of the effect of ASR variation on mate choice, sexual conflict, parental care and mating systems, social behaviour, hormone physiology and fitness. We present evidence that animals in diverse societies are sensitive to variation in local ASR, even on short timescales, and propose explanations for conflicting results. We conclude with an overview of open questions in this field integrating demography, life history and behaviour.     

Population Genetics and Signatures of Selection in Early Neolithic European Farmers

Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.     

Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses

Equine mitochondrial DNA sequence variation was investigated in three indigenous Irish horse populations (Irish Draught Horse, Kerry Bog Pony and Connemara Pony) and, for context, in 69 other horse populations. There was no evidence of Irish Draught Horse or Connemara Pony sequence clustering, although the majority of Irish Draught Horse sequences (47%) were assigned to haplogroup D. Conversely, 31% of the Kerry Bog Pony sequences were assigned to the rare haplogroup E. In addition to the extant population analyses, ancient DNA sequences were generated from three out of four Irish archaeological specimens, all of which were assigned to haplogroup A.     

Sexing pollen reveals female bias in a dioecious plant

* Information on angiosperm sex ratios has largely been restricted to surveys of flowering individuals. These often deviate from equality, with male bias more commonly reported. Female-biased sex ratios are concentrated in a few taxa and have been linked to the possession of heteromorphic sex chromosomes and bias introduced during the gametophytic stage of the life cycle. It has been proposed that differences in gamete quantity and quality could give rise to female bias, although there is no direct evidence with which to evaluate this possibility. * Here, we use flow cytometry to investigate microgametophytic 'sex ratios' in a flowering plant. We demonstrate that differences in DNA content between the sexes in Rumex nivalis, a species with heteromorphic sex chromosomes, make it possible to distinguish female- vs male-determining pollen nuclei. * We found a small but significant female bias in microgametophytes produced by males (mean 0.515) with significant variation among family means (range 0.463-0.586), and 18 of 22 families averaging > 0.50. * The observed female bias at the gametophytic stage of the life cycle is consistent with the direction of bias previously reported for seeds and vegetative and reproductive plants in wild populations of R. nivalis, but is insufficient to fully explain the degree of bias.     

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this “RAD-sex” method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, “male genotypes” became males and some “female genotypes” also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.     

Sex differences in incubation behaviour but not mortality risk in a threatened shorebird

Sex‐related variation in survival is common in birds and, as it influences effective population size and population growth, is important for conservation and species management. Here we assessed incubation behaviour and sex‐related survival in a threatened sexually monomorphic shorebird, the St Helena Plover Charadrius sanctaehelenae. Males incubated at night, the period of highest activity of cats, which are likely to be predators of breeding birds. In spite of behavioural differences between the sexes, adult survival was not significantly different between males and females, suggesting that sex‐biased behaviour need not lead to sex‐related survival, and thus behavioural differences may not impact upon the adult sex ratio.     

Sex ratios in natural populations ofAphelinus mali (Hym.: Aphelinidae) in relation to host size and host density

In an apple orchard at Armidale, the Northern Tablelands of NSW, population sex ratios ofAphelinus mali (Haldeman), an endoparasitoid of the woolly apple aphid,Eriosoma lanigerum (Hausmann) varied from 0.51 (proportion of males) at low host densities to female-biased at high host densities (proportion of males ranged from 0.35–0.39). This shift in sex ratio seems to be caused by the differences in allocation of sons and daughters to hosts of different sizes. In the fieldA. mali parasitizes all life stages (four nymphal instars and adult) of the woolly aphid upon encountering. According to Hughes'(1979) optimal diet model, such general host acceptance seems to be the best strategy. However, it allows the host nymphs or adults to continue to develop or reproduce until about to mummify (pupate). No mortality was observed when first or second-instar hosts were parasitized in the laboratory. Field collected small mummified hosts yielded male-biased sex ratios whereas large mummified hosts produced mainly females. In the laboratory, progeny from smaller hosts (first to third-instars) produced sex ratios which were not significantly different from 0.5 whereas progeny from larger hosts (third and fourth-instars) produced female-biased sex ratio. During winter (June–August) and early spring (September–October) when the host populations in the orchard were predominantly nymphs, the parasitoid tended to allocate equal resources to male and female offspring. In contrast, at peak population densities in summer and autumn (December–May) when larger hosts were available, the sex ratios were female-biased. The host size ofE. lanigerum andA. mali is, therefore, an important component in the dynamics of host-parasitoid interactions.     

利用孕妇血浆DNA检测胎儿性别的研究

本文探讨应用孕妇血浆中游离DNA进行无创性产前性别诊断的可行性。用柱分离法提取73例孕妇血浆中DNA,用巢式PCR技术检测其胎儿SRY基因。 结果73位孕妇血浆DNA含量为0.0062~0.3399μg/μL。巢式PCR检测胎儿SRY基因的灵敏度为97.37%（37/38）,假阴性率2.86%(1/35),特异度85.71%（30/35）,假阳性率13.16%(5/38),总符合率91.78%（67/73）。采用孕妇血浆胎儿DNA和巢式PCR技术可以快速简便的进行无创性产前性别诊断,诊断结果的准确率为91.8%,对性连锁遗传病的预防具有重要意义。 Abstract:To investigate the feasibility and possibility of application of fetal DNA from maternal plasma for noninvasive prenatal diagnosis of fetal sex,plasma DNAs in blood samples of 73 pregnant women at the gestational period of 26 to 41 weeks were extracted by column separation and nested polymerase chain reaction were employed to amplify the SRY gene.A comparison was made between the amplification results and the real sex of the fetus after their delivery.The concordance rate of SRY gene amplification results of plasma free DNA with real fetal sex was 91.78% (67/73),the sensitivity rate was 97.37% (37/38),and the specific rate was 85.71% (30/35).The cell-free fetal DNA in maternal blood can be one of the valuable material sources for noninvasive prenatal diagnosis and the method of nested PCR could be useful for fetal sex determination.The specific rate of the test was 91.78%.It is of significance to prevent sex-linked inheritant diseases.     

Spatial association of genetically similar Atlantic salmon juveniles and sex bias in spatial patterns in a river

Atlantic salmon ( Salmo salar ) juveniles were electrofished along a 300-m stretch of a river to test for possible associations between genetic similarity and geographical distance between individuals. Multilocus DNA fingerprinting showed that genetically similar juveniles (1–4 years old) were found closer together in the river than less related individuals. However, the association between genetic similarity and geographical distance, although significant, was not strong. This may indicate that factors other than genetic relatedness influence the positioning in the river. A sex bias in the relationship between genetic similarity and geographical distance was caused by a difference between sexually mature and immature males. The study shows that sampling of salmon juveniles should be spread over a wide stretch of the river in order to avoid sampling relatives. Moreover, by including several year classes, the overall degree of genetic similarity is effectively reduced compared with sampling individuals of similar age.     

Feasibility and utility of microsatellite markers in archaeological cattle remains from a Viking Age settlement in Dublin

Nineteen cattle bones from the Viking 10th and early 11th century levels in Dublin were assessed for presence of reliable genotypes from three autosomal markers. Due to the good preservational condition of the samples, it was possible to amplify and type at least two out of three of the microsatellite markers (CSRM60, HEL1 and ILSTS001) in 11 specimens. Full three-loci genotypes were obtained from a subset of seven of these samples. A comparative analysis was performed using data from the same three markers in 11 extant British, Irish and Nordic cattle breeds. Although the medieval remains displayed lower levels of diversity than the modern European breeds, the results fit within the ranges obtained from the extant populations. The results indicate a probable origin for the ancient Irish cattle as the remains group significantly more closely with breeds from the British Isles than with those from Scandinavia. The data collected indicate that microsatellites may be useful for the further study of ancient cattle.     

Effects of Host Size and Parasite Burden on Sex Ratio in the Mosquito Parasite Octomyomermis muspratti

The ratio of Octomyomermis muspratti to the host mosquito at the time of exposure had little effect on the ratio of male to female parasites that resulted. However, the ratio of males to females increased as the number of parasites/host increased. Hosts with a single nematode produced fewer than 1% males in comparison with hosts with 8 parasites which produced about 40% males; hosts with 10 or more nematodes generally produced more male than female nematodes. Males of O. muspratti usually emerged before females because of the earlier death of multiply-infected mosquitoes. The size of the host at the time of invasion bad no significant influence on nematode sex ratios. Since mating is apparently necessary for reproduction in O. muspratti, the low male to female ratios that occur will be important in developing successful mass production techniques.     

Effect of Aedes aegypti (Diptera:Culicidae) Age on Sex Ratios in Romanomermis culicivorax (Nematoda:Mermithidae)

First, second, third, early and late fourth-instar larvae, and pupae of Aedes aegypti were infected with Romanomerrais culicivorax and reared at 20, 25, and 30 C. An increase in the ratio of male to female nematodes was observed with increase in host age at the time of infection at each temperature. The number of pupal and late fourth-instar infections was low, but R. culicivorax continued to develop in adult A. aegypti. Since male nematodes were recovered from both male and female hosts infected as late fourth instars or pupae, the sex of the host did not influence the sex of the nematode.     

Distribution of Ixodes ricinus in the British Isles: investigation of historical records

Ixodes ricinus Linnaeus (Acari: Ixodidae) is the most abundant and widely distributed tick in the British Isles, and is a vector for a number of bacterial, viral and protozoal pathogens of both medical and veterinary importance. This report provides an update to the historical distribution data of I. ricinus, published by the Biological Records Centre (BRC), Monks Wood in The Provisional Atlas of the Ticks (Ixodidae) of the British Isles by K. P. Martyn (1988), and is supplemented with additional BRC records since 1988, additional data from published scientific literature and unpublished field studies, and enhanced with spatial and temporal information on tick stages collected and their host associations. Records have been mapped at 10 km resolution and enhanced to 5 km, 1 km and 0.1 km. Differentiation between records representing one-off collections from those representing populations of I. ricinus has been achieved through the classification of the records into either reported or established populations. Detailed seasonality and host associations of records are investigated, highlighting the value in obtaining additional detailed contemporary data to aid risk assessments and research within this field.