Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade.

After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.

The arrival of European colonists to the Americas, beginning in the 15^th century, contributed to the spread of new viruses amongst Indigenous people. This led to massive outbreaks of disease, and millions of deaths that caused an important Native population to collapse. The exact viruses that caused these outbreaks are unknown, but smallpox, measles, and mumps are all suspected. During these times, traders and colonists forcibly enslaved and displaced millions of people mainly from the West Coast of Africa to the Americas. The cruel, unsanitary, and overcrowded conditions on ships transporting these people across the Atlantic contributed to the spread of infectious diseases onboard. Once on land, infectious diseases spread quickly, partly due to the poor conditions that enslaved and ndigenous people were made to endure. Native people were also immunologically naïve to the newly introduced pathogens, making them susceptible to severe or fatal outcomes. The new field of paleovirology may help scientists identify the viruses that were circulating in the first years of colonization and trace how viruses arrived in the Americas. Using next-generation DNA sequencing and other cutting-edge techniques, Guzmán-Solís et al. extracted and enriched viral DNA from skeletal remains dating back to the 16^th century. These remains were found in mass graves that were used to bury epidemic victims at a colonial hospital and chapel in what is now Mexico City. The experiments identified two viruses, human parvovirus B19 and a human hepatitis B virus. These viral genomes were recovered from human remains of first-generation African people in Mexico, as well as an individual who was an Indigenous person. Although the genetic material of these ancient viruses resembled pathogens that originated in Africa, the study did not determine if the victims died from these viruses or another cause. On the other hand, the results indicate that viruses frequently found in modern Africa were circulating in the Americas during the slave trade period of Mexico. Finally, the results provide evidence that colonists who forcibly brought African people to the Americas participated in the introduction of viruses to Mexico. This constant influx of viruses from the old world, led to dramatic declines in the populations of Indigenous people in the Americas.

Estimación del sexo con metacarpos y metatarsos para población mexicana / Estimation of gender from metacarpals and metatarsals in a Mexican population

INTRODUCCIÓN: El objetivo de este estudio fue la obtención de funciones discriminantes para estimación del sexo a partir de mediciones directas en metacarpos y metatarsos para contribuir en la identificación de individuos desconocidos. MATERIAL Y MÉTODOS: Se analizaron métricamente los metacarpos y metatarsos de 112 esqueletos adultos contemporáneos (49 femeninos y 63 masculinos) de la Colección-UNAM del Laboratorio de Antropología Física, Facultad de Medicina, UNAM. Empleando un vernier digital se tomaron 5 medidas (longitud máxima y 4 anchuras) en cada uno de los huesos del metacarpo y del metatarso. RESULTADOS: Se desarrollaron 14 funciones discriminantes para los metacarpos, con porcentajes del 79,5% a 85,3% de asignación sexual correcta, siendo el segundo metacarpo el hueso más dimórfico de la muestra. Para el caso de los metatarsos se obtuvieron 5 funciones que van del 77,8% al 83,2% de certidumbre, siendo el primer metatarso el hueso más dimórfico. De manera general, las anchuras en ambas epífisis fueron las medidas más dimórficas. CONCLUSIONES: Las funciones discriminantes de metacarpos y metatarsos obtenidas presentan, de manera general, porcentajes por encima del 80%, lo cual concuerda con lo reportado para otras poblaciones; por lo tanto, pueden ser utilizadas en contextos forenses para la identificación humana, en restos completos o fragmentados, en el caso de no contar con otro elemento óseo, como la pelvis

INTRODUCTION: The aim of this study was to obtain discriminant functions for estimating gender from direct measurements of the metacarpal and metatarsal bones for identification of unknown individuals. MATERIAL AND METHODS: An analysis was performed on metacarpal and metatarsals bones of 112 adult contemporary skeletons (49 females and 63 males). The sample belongs to the Autonomous University of Mexico (UNAM) Collection from the Physical Anthropology Laboratory, UNAM Faculty of Medicine. Five measurements were taken (maximum length and four widths) of each metacarpal and metatarsal bones employing a digital calliper. RESULTS: Fourteen discriminant functions were developed for metacarpals with percentages from 79.5% to 85.3% of correct gender classification. The second metacarpal was the most dimorphic of the sample. For metatarsals, five discriminant functions were obtained, ranging from 77.8% to 83.2% of certainty. In this case the first metatarsal was the most dimorphic. In general terms, the widths of both epiphyses were the most dimorphic measurements. CONCLUSIONS: The discriminant functions of metacarpal and metatarsal bones obtained are generally above 80%, which is similar to reports from other populations. Therefore, it can be used in forensic contexts for human identification with complete or fragmented remains, in the cases where no other bone element is available, such as the pelvis

Stature estimation formulae for Mexican contemporary population: A sample based study of long bones.

Stature estimation is an important step to create a biological profile for human identification of unknown individuals in forensic anthropological practice, and it is well known that the long bone length is highly correlated with this feature. The purpose of the present study is to develop formulae for height estimation, based on simple linear regression model for humerus, femur and tibia in Mexican contemporary population. Stature was taken in 56 males and 30 female corpses as well as maximum length of three long bones of the limbs after autopsy following the Menéndez et al. (2014) criteria, at the Facultad de Medicina (School of Medicine) of the Universidad Nacional Autónoma de México. Based on this data, equations for each sex and for the three long bones were developed, obtaining a highly significant (p < .001) linear regression models with correlation coefficients of r = 0.820 for female femur and r = 0.855 for male tibia. In this manner, the new formulae provide better and reliable results of stature estimation for the contemporary population of Mexico.

Análisis de funciones discriminantes para la estimación del sexo con la mandíbula en población mexicana / Gender assessment using the mandible in the mexican population

Introducción. El presente trabajo tuvo como objetivos: conocer el grado de dimorfismo sexual entre una población de la Ciudad de México y otra de Hidalgo, México; y el desarrollo de funciones discriminantes para la estimación de sexo por medio de la mandíbula, para identificación humana. Material y métodos. Se analizaron morfométricamente mandíbulas de dos muestras, una procedente de la Ciudad de México (MEX) (Colección-UNAM) y otra de Santa María Xigui, Alfajayucan, Hidalgo, México (XIG). La muestra MEX consistió en 108 mandíbulas (75 masculinos y 33 femeninos) y en la muestra XIG se utilizaron 56 mandíbulas (33 femeninos y 30 masculinos), con una edad media entre 49,2 y 55,1 años. Se tomaron 18 medidas mandibulares y se desarrollaron cuatro funciones discriminantes para estimar el sexo con cada muestra. Resultados. Se observó el mismo patrón de diferenciación en ambas poblaciones, no obstante se presentaron diferencias entre estas, ya que se demostró que existe mayor grado de diferencias sexuales en XIG. Las funciones discriminantes desarrolladas para ambas poblaciones, alcanzaron entre el 76,4 y 84% de clasificación sexual correcta. Conclusiones. La muestra XIG presentó mayor dimorfismo sexual que la muestra MEX, con mandíbulas más alargadas y mentones altos y alargados. Las funciones discriminantes del presente trabajo presentan porcentajes de clasificación mayores a los de las demás propuestas existentes. Y al ser desarrolladas a partir de población contemporánea, pueden ser utilizadas en contextos forenses para identificación humana con restos completos o fragmentados y/o incompletos (AU)

Introduction. The aims of the present study were to determine the level of sexual dimorphism among two populations, one from Mexico City and the other from Hidalgo, Mexico, as well as the development of discriminant functions for gender assessment using the mandible, for human identification. Material and methods. Two samples of mandibles were analysed morphometrically, one from Mexico City (Colección-UNAM) (MEX), and the other from Santa María Xigui, Alfajayucan, Hidalgo, México (XIG). The sample MEX consisted of 108 mandibles (75 male and 33 female), and XIG sample with 56 mandibles (33 female and 30 male), with a mean age between 49.2 to 55.1 years old. Eighteen measurements were taken to create four discriminant functions for gender estimation for each sample. Results. The differentiation pattern among populations (samples) was the same. Nevertheless, there were differences between them, with a higher degree of sexual difference in XIG. The discriminant functions, developed for both populations, achieved a correct classification in between 76.4 and 84%, respectively. Conclusions. The XIG sample showed greater sexual dimorphism than the MEX sample, with longer mandibles and higher and elongated chins. The discriminant functions generated in this study, present higher classification percentages than the other existing proposals. Furthermore, being developed from the contemporary population, they can be used in forensic contexts for human identification, with complete or fragmented/incomplete remains (AU)

Recalibration of the Klales et al. (2012) method of sexing the human innominate for Mexican populations.

OBJECTIVES: The aim of this study was to test the accuracy of the Klales et al. (2012) equation for sex estimation in contemporary Mexican population. MATERIALS AND METHODS: Our investigation was carried out on a sample of 203 left innominates of identified adult skeletons from the UNAM-Collection and the Santa María Xigui Cemetery, in Central Mexico. The Klales' original equation produces a sex bias in sex estimation against males (86-92% accuracy versus 100% accuracy in females). Based on these results, the Klales et al. (2012) method was recalibrated for a new cutt-of-point for sex estimation in contemporary Mexican populations. RESULTS AND DISCUSSION: The results show cross-validated classification accuracy rates as high as 100% after recalibrating the original logistic regression equation. Recalibration improved classification accuracy and eliminated sex bias. This new formula will improve sex estimation for Mexican contemporary populations.

Long bone (humerus, femur, tibia) measuring procedure in cadavers.

In this work, we present a measuring methodology for long bones of the limbs (humerus, femur, and tibia) of human corpses. Measurements of cadaveric height and long bone lengths were conducted on 72 corpses (20 females and 52 males) from the School of Medicine at the National Autonomous University of Mexico. Additionally, these measurements were compared with those taken from dry bones of a subsample of individuals. Our results show marginal differences (TEM% = 0.59) between cadaveric and dry bone measurements, resulting from different osteometric technical procedures. This note outlines the measuring methodology, which will be subsequently used to create regression formulas for stature estimation.

Technical note: geometric morphometrics and sexual dimorphism of the greater sciatic notch in adults from two skeletal collections: the accuracy and reliability of sex classification.

The greater sciatic notch (GSN) is one of the most important and frequently used characteristics for determining the sex of skeletons, but objective assessment of this characteristic is not without its difficulties. We tested the robustness of GSN sex classification on the basis of geometric morphometrics (GM) and support vector machines (SVM), using two different population samples. Using photographs, the shape of the GSN in 229 samples from two assemblages (documented collections of a Euroamerican population from the Maxwell Museum, University of New Mexico, and a Hispanic population from Universidad Nacional Autónoma de México, Mexico City) was segmented automatically and evaluated using six curve representations. The optimal dimensionality for each representation was determined by finding the best sex classification. The classification accuracy of the six curve representations in our study was similar but the highest and concurrently homologous cross-validated accuracy of 92% was achieved for a pooled sample using Fourier coefficient and Legendre polynomial methods. The success rate of our classification was influenced by the number of semilandmarks or coefficients and was only slightly affected by GSN marginal point positions. The intrapopulation variability of the female GSN shape was significantly lower compared with the male variability, possibly as a consequence of the intense selection pressure associated with reproduction. Males were misclassified more often than females. Our results show that by using a suitable GSN curve representation, a GM approach, and SVM analysis, it is possible to obtain a robust separation between the sexes that is stable for a multipopulation sample.

Fibroblast growth factor receptor 1 (FGFR1) variants and craniofacial variation in Amerindians and related populations.

OBJECTIVES: The polymorphic site rs4647905 of the FGFR1 gene was previously associated with a decrease in cephalic index (CI). Here, we evaluate the relationships between genotypes and cephalometric measurements and indices in one Mexican Native and two mestizo Mexican populations using two haplotype-tag SNPs (rs4647905 and rs3213849) that represent >85% of the FGFR1 variability, plus three other SNPs (rs2293971, rs2304000, and rs930828) situated nearby. In addition, we genotyped five South American natives, two European, one African, and one Siberian populations to evaluate their intra and intercontinental population diversity. METHODS: The five SNPs were tested and the craniofacial measurements and indices were collected using standardized procedures. Principal Component Analysis was used to verify individual/population comparisons. Associations were performed through the generalized linear model (GLM), coefficient of determination R(2) and linear regression tests. RESULTS: We found a tendency for a decrease in CI in individuals homozygous for allele rs4647905C, regardless of the population to which they belong, though the effect is more pronounced in mestizo. When the GLM analyses were performed using the absolute/linear cephalometric measurements, a statistically significant association was found between four SNPs and head length in the mestizo population. CONCLUSIONS: FGFR1 polymorphisms, especially rs4647905, can have an important role in the normal human skull variation, primarily due to their influence in head length, which would affect other cephalometric absolute/linear measures as well as indices like CI as a result of the pervasive nature of the morphological integration that characterizes the human skull.

Comparison of methods to determine sex by evaluating the greater sciatic notch: Visual, angular and geometric morphometrics.

Sex estimation is the first step for biological profile reconstruction of an unknown skeleton (archaeological or contemporary) and consequently for positive identification of skeletal remains recovered from forensic settings. Several tools have been developed using different osseous structures. With the intention to provide an objective method comparison, we reported the analysis of three different methods (visual, metric and geometric morphometrics) for sex assessment of the greater sciatic notch. One hundred and thirty pelvic bones (45.4% females and 54.6% males) from the National Autonomous University of Mexico Skeletal Collection pertaining to the contemporary Mexican population were analyzed. We used the ROC-analysis to test between desired false positive thresholds (1-specificity) and expected true positive rates (sensitivity) in order to predict the best approach to sex assessment. The comparison of the area under the ROC-curves shows significant differences among visual and metric methods. At the same time, the analysis suggested that higher morphological variation among the sexes is independent of the methodological approach. The results indicate that the metric (angle), with a high percent of indeterminate cases (34.6%), and visual, with 26.2% of the cases allocated as intermediate cases, were poorly accurate; we cannot recommend these techniques for sexing an unknown specimen. On the other hand, the geometric morphometrics approach improves sex estimation in 82.3% of correctly classified individuals with more than 95% of posterior probability. In addition to the method comparison, the major sexual variation of the greater sciatic notch was determined to be located on its posterior border.