Validation and reliability of the sex estimation of the human os coxae using freely available DSP2 software for bioarchaeology and forensic anthropology.

OBJECTIVES: A new tool for skeletal sex estimation based on measurements of the human os coxae is presented using skeletons from a metapopulation of identified adult individuals from twelve independent population samples. For reliable sex estimation, a posterior probability greater than 0.95 was considered to be the classification threshold: below this value, estimates are considered indeterminate. By providing free software, we aim to develop an even more disseminated method for sex estimation. MATERIALS AND METHODS: Ten metric variables collected from 2,040 ossa coxa of adult subjects of known sex were recorded between 1986 and 2002 (reference sample). To test both the validity and reliability, a target sample consisting of two series of adult ossa coxa of known sex (n = 623) was used. The DSP2 software (Diagnose Sexuelle Probabiliste v2) is based on Linear Discriminant Analysis, and the posterior probabilities are calculated using an R script. RESULTS: For the reference sample, any combination of four dimensions provides a correct sex estimate in at least 99% of cases. The percentage of individuals for whom sex can be estimated depends on the number of dimensions; for all ten variables it is higher than 90%. Those results are confirmed in the target sample. DISCUSSION: Our posterior probability threshold of 0.95 for sex estimate corresponds to the traditional sectioning point used in osteological studies. DSP2 software is replacing the former version that should not be used anymore. DSP2 is a robust and reliable technique for sexing adult os coxae, and is also user friendly.

Human ancient and extant mtDNA from the Gambier Islands (French polynesia): evidence for an early Melanesian maternal contribution and new perspectives into the settlement of easternmost Polynesia.

Molecular anthropology has been widely used to infer the origin and processes of the colonization of Polynesia. However, there are still a lack of representative geographical studies of Eastern Polynesia and unchallenged genetic data about ancient Polynesian people. The absence of both of these elements prevents an accurate description of the demographic processes of internal dispersion within the Polynesian triangle. This study provides a twofold analysis of ancient and modern mtDNA in the eastern part of French Polynesia: the Gambier Islands. The paleogenetic analyses conducted on burials of the Temoe Atoll (14(th) -17(th) centuries) represent the first fully authenticated ancient human sequences from Polynesia. The identification of the "Melanesian" Q1 mtDNA lineage in ancient human remains substantiates the Near Oceanic contribution to the early gene pool of this region. Modern samples originate from Mangareva Island. Genealogical investigations enable us to reliably identify the conservation of the Melanesian component in Easternmost Polynesia, despite recent European colonization. Finally, the identification of rare mutations in sequences belonging to haplogroup B4a1a1a provides new perspectives to the debate on the internal peopling of the Polynesian region. Altogether, the results laid out in our study put the emphasis on the necessity of controlled sampling when discussing the internal settlement of Polynesia.

Comparison between morphological and genetic data to estimate biological relationship: the case of the Egyin Gol necropolis (Mongolia).

Osseous and dental nonmetric (discrete) traits have long been used to assess population variability and affinity in anthropological and archaeological contexts. However, the full extent to which nonmetric traits can reliably be used as a proxy for genetic data when assessing close or familial relationships is currently poorly understood. This study represents the unique opportunity to directly compare genetic and nonmetric data for the same individuals excavated from the Egyin Gol necropolis, Mongolia. These data were analyzed to consider the general efficacy of nonmetric traits for detecting familial groupings in the absence of available genetic data. The results showed that the Egyin Gol population is quite homogenous both metrically and genetically confirming a previous suggestion that the same people occupied the necropolis throughout the five centuries of its existence. Kinship analysis detected the presence of potential family burials in the necropolis. Moreover, individuals buried in one sector of the necropolis were differentiated from other sectors on the basis of nonmetric data. This separation is likely due to an outside Turkish influence in the paternal line, as indicated by the results of Y-chromosome analysis. Affinity matrices based on nonmetric and genetic data were correlated demonstrating the potential of nonmetric traits for detecting relationships in the absence of genetic data. However, the strengths of the correlations were relatively low, cautioning against the use of nonmetric traits when the resolution of the familial relationships is low.

OPA1-related dominant optic atrophy is not strongly influenced by mitochondrial DNA background.

BACKGROUND: Leber's hereditary optic neuropathy (LHON) and autosomal dominant optic atrophy (ADOA) are the most frequent forms of hereditary optic neuropathies. LHON is associated with mitochondrial DNA (mtDNA) mutations whereas ADOA is mainly due to mutations in the OPA1 gene that encodes a mitochondrial protein involved in the mitochondrial inner membrane remodeling. A striking influence of mtDNA haplogroup J on LHON expression has been demonstrated and it has been recently suggested that this haplogroup could also influence ADOA expression. In this study, we have tested the influence of mtDNA backgrounds on OPA1 mutations. METHODS: To define the relationships between OPA1 mutations and mtDNA backgrounds, we determined the haplogroup affiliation of 41 French patients affected by OPA1-related ADOA by control-region sequencing and RFLP survey of their mtDNAs. RESULTS: The comparison between patient and reference populations did not revealed any significant difference. CONCLUSION: Our results argue against a strong influence of mtDNA background on ADOA expression. These data allow to conclude that OPA1 could be considered as a "severe mutation", directly responsible of the optic atrophy, whereas OPA1-negative ADOA and LHON mutations need an external factor(s) to express the pathology (i.e. synergistic interaction with mitochondrial background).

Inter- and extra-Indian admixture and genetic diversity in reunion island revealed by analysis of mitochondrial DNA.

Reunion Island is a French territory located in the western Indian Ocean. The genetic pattern of the Reunionese population has been shaped by contributions from highly contrasting regions of the world. Over the last 350 years, several migration waves and cultural and socio-economic factors have led to the emergence of six main ethnic groups in Reunion. India is one of the principal regions that contributed to the setting up of the Reunionese population. Diversity, demographic and admixture analyses were performed on mtDNA variation of the Reunionese of Indian ancestry, including the Malbar and Zarab ethnic groups, in order to question their history. Using a phylogeographical approach, we generated and analysed quantitative data on the contribution of the Indian parental populations. Furthermore, we showed that the settlement of Reunion Island by Indians did not involve a founder effect, except in the very beginning of the Reunionese settlement (at the end of the 17(th) century). The accuracy of our results was optimised by a re-evaluation of the classification of the Southern Asian mtDNA haplogroups. Finally, by comparing our results to a previous study dealing with the Reunionese population, we highlighted how ethno-historical data are critical for reconstructing the complex history of multiethnic populations.

Complete mitochondrial sequences for haplogroups M23 and M46: insights into the Asian ancestry of the Malagasy population.

Through the sequencing of the complete mitochondrial genome of three individuals of Malagasy ancestry, we completed the characterization of the island southeastern Asian specific M46 haplogroup. We assumed that the association of the np 3588 and np 16278 polymorphisms were M46 specific. In addition, we characterized a novel basal M subhaplogroup: M23. This clade can be defined by one coding region transition at np 10295 and one control region transition at np 16263. Our data suggest the arrival of South Asian migrants before the start of the 15th century and highlights the fact that future studies dealing with the settlement of Madagascar should consider at least three potential source populations (Africa, Indonesia, and India).

Genetic data analysis of 10 Y-STR loci in two ethnic groups of Asian ancestry (Gujarat and Guangdong-Fujian provinces) from Reunion Island (Indian Ocean).

One hundred and twenty-three unrelated individuals belonging to two ethnic groups (Shinwa and Zarab) of Asian ancestry from Reunion Island (Indian Ocean) were analyzed for 10 Y-STR loci. Haplotype diversity and frequencies were determined for loci DYS19, DYS385a/b, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and YCAIIa/b. The two ethnic groups do not share haplotypes, and a total of 98 distinct haplotypes were identified. Unique haplotypes were obtained for 49 Shinwa and 33 Zarab. Moreover, 52 of the identified distinct haplotypes revealed to have not been described to date.

New evidence of a mitochondrial genetic background paradox: impact of the J haplogroup on the A3243G mutation.

BACKGROUND: The A3243G mutation in the tRNALeu gene (UUR), is one of the most common pathogenic mitochondrial DNA (mtDNA) mutations in France, and is associated with highly variable and heterogeneous disease phenotypes. To define the relationships between the A3243G mutation and mtDNA backgrounds, we determined the haplogroup affiliation of 142 unrelated French patients - diagnosed as carriers of the A3243G mutation - by control-region sequencing and RFLP survey of their mtDNAs. RESULTS: The analysis revealed 111 different haplotypes encompassing all European haplogroups, indicating that the 3243 site might be a mutational hot spot. However, contrary to previous findings, we observed a statistically significant underepresentation of the A3243G mutation on haplogroup J in patients (p = 0.01, OR = 0.26, C.I. 95%: 0.08-0.83), suggesting that might be due to a strong negative selection at the embryo or germ line stages. CONCLUSION: Thus, our study supports the existence of mutational hotspot on mtDNA and a "haplogroup J paradox," a haplogroup that may increase the expression of mtDNA pathogenic mutations, but also be beneficial in certain environmental contexts.

mtDNA polymorphisms in five French groups: importance of regional sampling.

According to classical markers, France has been reported to be regionally heterogeneous. Here, we propose to test the homogeneity of the French mitochondrial gene pool by analysing D-Loop and coding regions polymorphisms in 210 individuals stemming from five regions. The data set obtained was also used to test the ability of mitochondrial DNA to detect well historically established admixtures (admixtures between British/Irish people and native Breton people in our case). For these purposes, the sampling procedure was subject to special care, concerning the individuals' geographical origin and maternal pedigree. The mtDNA analysis revealed some regional specificities in haplogroup distribution, which is discussed in terms of successive settlements of France. Statistical analyses were conducted to investigate mtDNA diversity and structure within and between British, Irish and French groups. They tended to show affinities between Morbihan region and Britain plus Ireland. Furthermore, genetic evidences were in line with the fact that Morbihan region results from an admixture event, agreeing with historical evidences of successive migrations from Britain and Ireland into Brittany. These results also tended to outline the fact that two geographically very adjacent samples (Morbihan and Finistère), sharing a cultural and linguistic area, can present a distinct genetic pattern. Although mtDNA analyses were able to identify a historically reported admixture event, we point out here the high influence of the sampling procedure and representativeness over the migrations hypothesis. We also underline the importance of regional sampling for studies on the spread and/or origin of specific European haplogroups (here U5a1a and U8).

Variability of the pattern of aging on the human skeleton: evidence from bone indicators and implications on age at death estimation.

Age at death assessment of adult skeletons is one of the most difficult problems in forensic and physical anthropology. Two fundamental sources of error are described: the complex variability in the process of skeletal aging and methodological bias. Taking into account these limits, we developed a new scoring system for the auricular surface of the ilium and the pubic symphysis. In order to address a large variability, we examine reference samples from Europe, North America, Africa, and Asia. Data were processed using Bayesian prediction in order to classify specimens in age range categories. Results show that combining indicators do not perform better than the auricular surface used as a single indicator. Morphological changes with aging are variable between Asian, African, and European populations, confirming the necessity to use population-specific standards. Bayesian prediction produces reliable classification and is applicable for subjects over 50 years old, a real methodological improvement.