Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters.

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.

About 42% of 154 remains from the "Battle of Le Mans", France (1793) belong to women and children: Morphological and genetic evidence.

Mass graves were discovered in Le Mans and 154 skeletons were exhumed, representing a remarkable historical series of human remains from western France. We aimed to characterise the age-class and sex of these subjects, and to determine whether their profile fits with that of the Catholic and Royal Army of Vendée, who fought against the Republican Army during the Battle of Le Mans (12th-13th December, 1793). This atypical army was composed of male soldiers, but also of civilian people who followed the troops, including the elderly, children and women. In total 154 skeletons from nine mass graves were exhumed from 2009 to 2010. Two morphological methods were used to determine the sex of the subjects: the Probabilist Sexual Diagnosis (DSP) and Secondary Sexual Diagnosis (DSS) methods. Samples were handled cautiously to avoid any pre-laboratory contamination. Molecular genetic sex-typing using a recently developed assay was used to maximise sex-diagnosis of the ancient DNA samples, and 97 successful profiles including immatures were generated. Using morphological and genetic data combined, we successfully determined the sex of 93% of the subjects; 62% were male and 31% female. About 87% of subjects could be considered adults (>18 years old), 6% adolescents (15-19 years old) and 7% infants (<15 years old). Our results of an unexpected population profile for an armed conflict (42% were women and children), in addition to traumatological and historical elements, tend to confirm that these subjects were involved in the Battle of Le Mans, either actively (Republican Army, the Catholic and Royal Army) or passively (collateral victims from the civilian population of Le Mans). They represent 5-6% of the estimated 2500-3000 victims.

Determined about sex: sex-testing in 45 primate species using a 2Y/1X sex-typing assay.

Sex-testing using molecular genetic technique is routinely used in the fields of forensics, population genetics and conservation biology. However, none of the assay used so far allows a non-ambiguous and successful sex determination for human and non-human primate species. The most widely used method, AMELY/X, and its alternatives suffer from a set of drawbacks in humans and can rarely be used in New World primate species. Here, we designed a new sex-typing assay using a multiplexed PCR amplification of UTX and UTY-homologous loci and combined male-specific SRY locus. This method was successfully tested on 1048 samples, including 82 non-human primates from 45 Anthropoidea and Lemuriformes species and 966 human samples from 24 populations (Africans, Europeans, and South Americans). This sex-typing method is applicable across all primate species tested from Hominoidea to Indriidae, and also on various populations with different background origins; it represents a robust and cheap sex-typing assay to be used both by the anthropologist and primatologist communities.

Tuberculosis epidemiology and selection in an autochthonous Siberian population from the 16th-19th century.

Tuberculosis is one of most ancient diseases affecting human populations. Although numerous studies have tried to detect pathogenic DNA in ancient skeletons, the successful identification of ancient tuberculosis strains remains rare. Here, we describe a study of 140 ancient subjects inhumed in Yakutia (Eastern Siberia) during a tuberculosis outbreak, dating from the 16(th)-19(th) century. For a long time, Yakut populations had remained isolated from European populations, and it was not until the beginning of the 17(th) century that first contacts were made with European settlers. Subsequently, tuberculosis spread throughout Yakutia, and the evolution of tuberculosis frequencies can be tracked until the 19(th) century. This study took a multidisciplinary approach, examining historical and paleo-epidemiological data to understand the impact of tuberculosis on ancient Yakut population. In addition, molecular identification of the ancient tuberculosis strain was realized to elucidate the natural history and host-pathogen co-evolution of human tuberculosis that was present in this population. This was achieved by the molecular detection of the IS6110 sequence and SNP genotyping by the SNaPshot technique. Results demonstrated that the strain belongs to cluster PGG2-SCG-5, evocating a European origin. Our study suggests that the Yakut population may have been shaped by selection pressures, exerted by several illnesses, including tuberculosis, over several centuries. This confirms the validity and necessity of using a multidisciplinary approach to understand the natural history of Mycobacterium tuberculosis infection and disease.

Human evolution in Siberia: from frozen bodies to ancient DNA.

BACKGROUND: The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. the precise origin of paternal lineages and the admixture rate with indigenous populations). This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia). RESULTS: High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population. CONCLUSION: We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baïkal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today.

"OpenLAB": A 2-hour PCR-based practical for high school students.

The Strasbourg University PhD school in Life and Health Sciences launched an initiative called "OpenLAB." This project was developed in an effort to help high school teenagers understand theoretical and abstract concepts in genetics. A second objective of this program is to help students in defining their future orientation and to attract them to biology. The general idea is a 2-hour PCR-based practical that is developed around a fictitious criminal investigation. The practical is taught by PhD graduate students who bring all the required reagents and modern equipment into the classroom. Running the PCR provides free time dedicated to discussions with students about their future plans after the high school diploma. A specific website and a powerpoint presentation were developed to provide appropriate scientific information. Starting on a modest scale in Strasbourg in December 2008, "OpenLAB" was rapidly and well received all around, visiting 53 classes spread over a 200 km area in Alsace until May 2009. It permitted interactions with almost one thousand students in their last year of high school, with the prospect to visit 20% more classes this school year. Our experience, along with feedback from students and their teachers, suggests that it is possible to reach out to many students and have a strong impact with a rather limited budget.

Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis.

In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry. To our knowledge, this study reports for the first time the multiplexed typing of autosomal SNPs on aged and degraded DNA. By providing valuable information on pigment traits of an individual and allowing individual biogeographical ancestry estimation, autosomal SNP typing can improve ancient DNA studies and aid human identification in some forensic casework situations when used to complement conventional molecular markers.

Ancient DNA provides new insights into the history of south Siberian Kurgan people.

To help unravel some of the early Eurasian steppe migration movements, we determined the Y-chromosomal and mitochondrial haplotypes and haplogroups of 26 ancient human specimens from the Krasnoyarsk area dated from between the middle of the second millennium BC. to the fourth century AD. In order to go further in the search of the geographic origin and physical traits of these south Siberian specimens, we also typed phenotype-informative single nucleotide polymorphisms. Our autosomal, Y-chromosomal and mitochondrial DNA analyses reveal that whereas few specimens seem to be related matrilineally or patrilineally, nearly all subjects belong to haplogroup R1a1-M17 which is thought to mark the eastward migration of the early Indo-Europeans. Our results also confirm that at the Bronze and Iron Ages, south Siberia was a region of overwhelmingly predominant European settlement, suggesting an eastward migration of Kurgan people across the Russo-Kazakh steppe. Finally, our data indicate that at the Bronze and Iron Age timeframe, south Siberians were blue (or green)-eyed, fair-skinned and light-haired people and that they might have played a role in the early development of the Tarim Basin civilization. To the best of our knowledge, no equivalent molecular analysis has been undertaken so far.