The field of paleogenomics (the study of ancient genomes) is rapidly advancing, with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a 2017 article by Kennett et al., “Archaeogenomic evidence reveals prehistoric matrilineal dynasty,” that brings to light several ethical issues that should be addressed in paleogenomics research. The study helps elucidate the matrilineal relationships in ancient Chacoan society through ancient DNA analysis. However, we, as Indigenous researchers and allies, raise ethical concerns with the study's scientific conclusions that can be problematic for Native American communities: (1) the lack of tribal consultation, (2) the use of culturally insensitive descriptions, and (3) the potential impact on marginalized groups. Further, we explore the limitations of the Native American Graves Protection and Repatriation Act, which addresses repatriation but not research, because clear ethical guidelines have not been established for research involving Native American ancestors, especially those deemed “culturally unaffiliated.” Multiple studies of “culturally unaffiliated” remains have been initiated recently, so it is imperative that researchers consider the ethical ramifications of paleogenomics research. Past research indiscretions have created a history of mistrust and exploitation in many Native American communities. To promote ethical engagement of Native American communities in research, we therefore suggest careful attention to ethical considerations, strong tribal consultation requirements, and greater collaborations among museums, federal agencies, researchers, scientific journals, and granting agencies.

The major histocompatibility complex is directly involved in the immune response, and thus the genes coding for its proteins are useful markers for the study of genetic diversity, susceptibility to disease (autoimmunity and infections), transplant medicine, and pharmacogenetics, among others. The polymorphism of the system also allows researchers to use it as a proxy for population genetics analysis, such as genetic admixture and genetic structure. In order to determine the immunogenetic characteristics of a sample from the northern part of Mexico City and to use them to analyze the genetic differentiation from other admixed populations, including those from previous studies of Mexico City population, we analyzed molecular typing results of donors and patients from the Histocompatibility Laboratory of the Central Blood Bank of the Centro Médico Nacional La Raza selected according to their geographic origin. HLA-A, -B, -DRB1, and -DQB1 alleles were typed by polymerase chain reaction with sequence-specific primers. Allelic and haplotype frequencies, as well as population genetics parameters, were obtained by maximum likelihood methods. The most frequent haplotypes found were HLA-A^*02/-B^*39/-DRB1^*04/-DQB1^*03:02P, HLA-A^*02/-B^*35/-DRB1^*04/-DQB1^*03:02P, HLA-A^*68/-B^*39/-DRB1^*04/-DQB1^*03:02P, and HLA-A^*02/-B^*35/-DRB1^*08/-DQB1^*04. Importantly, the second most frequent haplotype found in our sample (HLA-A^*02/-B^*35/-DRB1^*04/-DQB1^*03:02P) has not been previously reported in any mixedancestry populations from Mexico but is commonly encountered in Native American human groups, which can reflect the impact of migration dynamics in the genetic conformation of the northern part of Mexico City, and the limitations of previous studies with regard to the genetic diversity of the analyzed groups. Differences found in haplotype frequencies demonstrated that large urban conglomerates cannot be analyzed as one homogeneous entity but, rather, should be understood as a set of structures in which social, political, and economical factors influence their genesis and dynamics.

The indigenous Mazahua and Otomi have inhabited the same localities in Estado de México since pre-Columbian times. Their languages, Mazahua and Otomi, belong to the Oto-Manguean linguistic family, and although they share cultural traditions and a regional history that suggest close genetic relationships and common ancestry, the historical records concerning their origin are confusing. To understand the biological relationships between Mazahua and Otomi, we analyzed mitochondrial DNA (mtDNA) genetic variation. We identified the mtDNA haplogroups by restriction fragment length polymorphism typing and sequenced hypervariable region 1 of the mtDNA control region in 141 Mazahua and 100 Otomi. These results showed that Otomi exhibit a higher frequency of haplogroup A than B, whereas Mazahua exhibit the opposite pattern. In the Otomi EM population the most frequent subhaplogroups are, in order of frequency, A2, B2, and C1, whereas in the Mazahua 1 population they are B2, D1, and A2. The most frequent haplotypes (Ht) of haplogroups A and B are Ht2 (A) and Ht58 (B2g1) in Mazahua 1 and Ht8 (A2), Ht22 (A2ao1), and Ht53 (B2c2b) in Otomi EM. The genetic differences between the Mazahua 1 and Otomi EM suggest a distant shared ancestry and a moderate degree of maternal admixture that has not obscured the difference of their mtDNA patterns. These unexpected results suggest the Mazahua and Otomi probably descend from the same group but separated very early and admixed with other Mesoamerican populations before their arrival in Central Mexico. The historical evidence of conflicting relations between the Mazahua and Otomi and the almost nonexistence of marriage between them could be responsible for maintaining only a moderate degree of maternal admixture.

In this study, we evaluated the extent to which regional history has shaped the social identity nomenclature in New Mexicans of Spanish-speaking descent (NMSD). We asked 507 NMSD to list the social-identity terms they used to describe themselves and their parents, and we examined the correspondence between these choices and family ties to the region, birthplace, and continental ancestry. NMSD frequently identified using the regional terms “Nuevomexicano/a” (15%) and “Spanish” (12%). These individuals reported family ties to the region that predate New Mexican statehood. They and their parents were frequently born in New Mexico, frequently chose the other of the two terms as a secondary descriptor, and frequently ascribed one of the two terms to their parents. About 10% of NMSD identified as “Mexican American” and “Mexican.” About 25% of these individuals, and more than half of their parents, were born in Mexico. They also frequently chose the other of the two terms as a secondary descriptor and frequently ascribed one of the two terms to their parents. Compared to NMSD who identified as “Mexican” and “Mexican American,” individuals who identified as “Nuevomexicano/a” and “Spanish” had higher European ancestry and lower Native American and African ancestry. Our results also suggest that the term “Hispanic,” frequently chosen as both a primary and secondary social identity term by NMSD, may, as it continues to rise in prominence, mask more deeply rooted and potential socially relevant aspects of social identity in New Mexico. More broadly, these results indicate that regional history influences social identity nomenclatures in ways that are potentially incompatible with US Office of Management and Budget standards. This incompatibility may adversely affect the ability of researchers in the social sciences to assess the causes of social inequality and health disparities in individuals of Spanish-speaking descent in different regions of the United States. We argue that future studies would benefit from more fine-grained, region-specific analyses of social identity.

Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history. We analyzed six data sets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), Control plus cytochrome b (cytb), and cytb plus 12S plus 16S. The amount of information in each data set was estimated employing several site-by-site and haplotype-based statistics, distances among sequences, neighbor-joining trees, distances among the estimated trees, Bayesian skyline plots, and phylogenetic informativeness profiles. The different mtDNA data sets have different amounts of information to reconstruct demographic events and phylogenetic trees with confidence. Whereas HVRI is not suitable for phylogenetic reconstruction of ancient clades, this region, as well as the Control data set, displays information for the demographic reconstruction during the Holocene period, probably because of the high rate of mutation of these regions. As expected, the Complete mtDNA and Coding data sets, displaying slower rates of mutation, present suitable information to estimate the founding subhaplogroups that populated South America and for the reconstruction of ancient demographic events. Our results point out the importance of evaluating the utility of different DNA regions to respond to different questions and problems in the human population studies, mainly considering the time scale of the phenomenon and the informativeness of the molecular region in a particular geographical area.