Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

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.

Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals.

The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

Shifts in subsistence type and its impact on the human skull's morphological integration.

OBJECTIVE: Here we evaluate morphological integration patterns and magnitudes in different skull regions to detect if shifts in morphological integration are correlated to the appearance of more processed (softer) diets. METHODS: To do so, three transitional populations were analyzed, including samples from groups that inhabited the same geographical region and for which the evidence shows that major changes occurred in their subsistence mode. Ninety three-dimensional landmarks were digitized on 357 skulls and used as the raw data to develop geometric morphometric analyses. The landmark coordinates were divided into several different regions of biomechanical interest, following a three-level hierarchically nested scheme: the whole skull, further subdivided into neurocranium (divided into the vault and basicranium), the facial (divided into the lower and upper facial), and the masticatory apparatus (divided into alveolar, temporal, and temporo-mandibular joint). RESULTS: Our results indicate that the morphological integration and variability patterns significantly vary across skull regions but are maintained across the transitions. The alveolar border and the lower facial are the regions manifesting greater value of morphological integration and variability, while the upper facial, the temporo-mandibular joint, and the basicranium are highly integrated and poorly variable. CONCLUSIONS: The transition to softer diets increased morphological variation across cranial regions that are more exposed to masticatory strains effects.

Facial asymmetry and genetic ancestry in Latin American admixed populations.

Fluctuating and directional asymmetry are aspects of morphological variation widely used to infer environmental and genetic factors affecting facial phenotypes. However, the genetic basis and environmental determinants of both asymmetry types is far from being completely known. The analysis of facial asymmetries in admixed individuals can be of help to characterize the impact of a genome's heterozygosity on the developmental basis of both fluctuating and directional asymmetries. Here we characterize the association between genetic ancestry and individual asymmetry on a sample of Latin-American admixed populations. To do so, three-dimensional (3D) facial shape attributes were explored on a sample of 4,104 volunteers aged between 18 and 85 years. Individual ancestry and heterozygosity was estimated using more than 730,000 genome-wide markers. Multivariate techniques applied to geometric morphometric data were used to evaluate the magnitude and significance of directional and fluctuating asymmetry (FA), as well as correlations and multiple regressions aimed to estimate the relationship between facial FA scores and heterozygosity and a set of covariates. Results indicate that directional and FA are both significant, the former being the strongest expression of asymmetry in this sample. In addition, our analyses suggest that there are some specific patterns of facial asymmetries characterizing the different ancestry groups. Finally, we find that more heterozygous individuals exhibit lower levels of asymmetry. Our results highlight the importance of including ancestry-admixture estimators, especially when the analyses are aimed to compare levels of asymmetries on groups differing on socioeconomic levels, as a proxy to estimate developmental noise.

Cultural diversification promotes rapid phenotypic evolution in Xavánte Indians.

Shifts in social structure and cultural practices can potentially promote unusual combinations of allele frequencies that drive the evolution of genetic and phenotypic novelties during human evolution. These cultural practices act in combination with geographical and linguistic barriers and can promote faster evolutionary changes shaped by gene-culture interactions. However, specific cases indicative of this interaction are scarce. Here we show that quantitative genetic parameters obtained from cephalometric data taken on 1,203 individuals analyzed in combination with genetic, climatic, social, and life-history data belonging to six South Amerindian populations are compatible with a scenario of rapid genetic and phenotypic evolution, probably mediated by cultural shifts. We found that the Xavánte experienced a remarkable pace of evolution: the rate of morphological change is far greater than expected for its time of split from their sister group, the Kayapó, which occurred around 1,500 y ago. We also suggest that this rapid differentiation was possible because of strong social-organization differences. Our results demonstrate how human groups deriving from a recent common ancestor can experience variable paces of phenotypic divergence, probably as a response to different cultural or social determinants. We suggest that assembling composite databases involving cultural and biological data will be of key importance to unravel cases of evolution modulated by the cultural environment.

FGFR1 signaling is associated with the magnitude of morphological integration in human head shape.

OBJECTIVES: The head can be used as a model to study complex phenotypes controlled simultaneously by morphological integration (MI) due to common factors, and modular patterns caused by local factors affecting the development and functional demands of specific structures. The fibroblast growth factor and receptor system (FGF/FGFR) participates in cell communication and pattern formation in osseous tissues, among others, and there is compelling evidence from mouse model studies suggesting a role of the FGF/FGFR pathway as a covariance-generating signaling process in head development. Here we use human data to test if specific genetic variants of another gene of this pathway, the FGFR1 gene, can be associated with differences in the integration of the head. METHODS: We explored whether and how three specific variants on FGFR1, previously associated with human cephalic index, influence the pattern and level of head integration of one Native American and one admixed group from Mexico. MI, measured as the intensity of covariation among head traits, was assessed using data from three-dimensional head landmark coordinates taken on 176 individuals. RESULTS: Individuals carrying the derived allele of the rs4647905:G>C polymorphism present significantly greater levels of head MI, especially in facial structures and on the shape space where the modular portion of the covariation is explicitly removed. CONCLUSIONS: Since FGFR genes present nonconservative and tissue-specific splicing sites, they may have some effect on protein structure and performance likely involved in developmental processes responsible for the magnitude and pattern of MI in the human head.

Early Colonial Diet in El Japón, Xochimilco, Mexico: Examining dietary continuity through stable isotope analysis of bone collagen and bioapatite.

OBJECTIVES: Early colonial documents from central Mesoamerica detail raising and planting of European livestock and crops alongside native ones. The extent to which Indigenous people, especially of the rural commoner class, consumed newly introduced foods is less known. This gap in knowledge is addressed through stable isotope analysis and comparison to published archaeological botanical, human, and faunal data. MATERIALS AND METHODS: Stable isotope analysis of bone collagen and bioapatite is applied to 74 skeletal samples of Indigenous human remains representing Colonial period individuals from El Japón-a farming hamlet in the Xochimilco area-to provide insight into long-term individual dietary practices in the context of a rapidly transforming Mesoamerican world. RESULTS: Carbon isotope ratios in collagen (δ13Ccollagen) average -8.10/00 VPDB (SD 0.55), while δ15N averages 8.90/00 AIR (SD 0.50). δ13Cbioapatite averages -2.90/00 VPDB (SD 0.60). Modest increase in carbon isotopic diversity is observed among more recent males from El Japón when compared to earlier males and females. DISCUSSION: Based on the isotopic results, it is estimated that the individuals of El Japón consumed maize or other C4 plants as a central source of carbohydrates. Dietary protein was largely supplied through domestic maize-fed fauna but potentially supplemented by wild terrestrial and aquatic fauna and fowl. Similarity in skeletal isotopic composition between precontact Mesoamericans from other sites and El Japón individuals of both earlier and later stratigraphy is interpreted as continuity in local diets and foodways despite potentially available European alternatives. Colonial taxation demands on preexisting agricultural regimes may have incentivized maize production, thus indirectly contributing to the maize-centered aspect of local foodways.

OBJETIVOS: Los textos de la época colonial temprana del centro de México documentan la producción de cultivos y ganado europeo a la par de los productos agropecuarios nativos. La magnitud a la cuál las comunidades indígenas consumieron estos productos se conoce con menos certeza en especial dentro de los asentamientos rurales. En este trabajo, se analiza la variabilidad de datos de isótopos estables en el sitio El Japón, Xochimilco y los resultados se comparan con respecto al sexo biológico y la cronología; así como también con datos publicados de muestras humanas y faunísticas. MATERIALES Y MÉTODOS: Se aplican los estudios de isotopos estables en colágeno y bioapatita a 74 muestras esqueléticas de El Japón de la época colonial temprana, una aldea agrícola del área de Xochimilco, con tal de abordar las practicas dietéticas en el contexto de un mundo Mesoamericano en transformación tras el contacto europeo. RESULTADOS: Los isótopos estables de carbono en colágeno (δ13Ccollagen) producen un promedio de −8.10/00 VPDB (DE 0.55), mientras tanto los isótopos estables de nitrógeno en el mismo tejido producen un promedio de 8.90/00 AIR (DE 0.50). Los isótopos estables de carbono en la bioapatita (δ13Cbioapatite) producen un promedio de −2.90/00 VPDB (DE 0.60). Se observa un incremento mínimo en la diversidad isotópica entre los individuos de sexo masculino en comparación a los individuos de sexo femenino de la etapa temprana y tardía del sitio. DISCUSIÓN: Con base en los resultados isotópicos, y con base en comparación a muestras humanas de contextos arqueológicos europeos y norteamericanos se estima que los individuos de El Japón consumieron maíz u otros cultivos tipo C4 como fuentes principales de carbohidratos. Las fuentes de proteína dietética posiblemente fueron fauna alimentada con maíz, pero también se pudieron haber suplementado con alimentos silvestres incluyendo aves silvestres, y fauna terrestre o acuática. La similitud en variación isotópica entre sitios mesoamericanos que preceden el contacto europeo y El Japón de ambas etapas (temprana y tardía) se interpretan como persistencia en fuentes de alimentación y tradiciones culinarias a pesar de las posibles alternativas europeas. Las demandas tributarias coloniales sobre la producción agrícola chinampera pudiesen haber contribuido indirectamente a la continuidad del maíz como fuente alimenticia principal.

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.

Neanderthal introgression in SCN9A impacts mechanical pain sensitivity.

The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.

Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape.

We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.

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.

Prediction of eye, hair and skin colour in Latin Americans.

Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.

A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.

To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico.

The 'red complex' is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T.forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia.

We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD12, a gene recently associated with skin pigmentation in Africans. We show that the frequency of the derived allele at Y182H is significantly correlated with lower solar radiation intensity in East Asia and infer that MFSD12 was under selection in East Asians, probably after their split from Europeans.

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.

Developmental pathways inferred from modularity, morphological integration and fluctuating asymmetry patterns in the human face.

Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds. To do so, 4104 individuals were analyzed using 3D photogrammetry reconstructions and a set of 34 facial landmarks placed on each individual. We found a pattern of modularity and integration that is conserved across sub-samples differing in their genomic ancestry background. Specifically, a signal of modularity based on functional demands and organization of the face is regularly observed across the whole sample. Our results shed more light on previous evidence obtained from Genome Wide Association Studies performed on the same samples, indicating the action of different genomic regions contributing to the expression of the nose and mouth facial phenotypes. Our results also indicate that large samples including phenotypic and genomic metadata enable a better understanding of the developmental and genetic architecture of craniofacial phenotypes.

Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance.

Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample.