Genes involved in damage response caused by UV radiation in Ecuadorian population of different altitude regions

Ecuador has various regions at different altitudes. It is known that at high altitudes, organisms experience multiple stressors, including exposure to ultraviolet (UV) radiation. The UV radiation exposure increases when getting closer to the Equator line. Consequently, cities in the Ecuadorian inter-Andean region and located at 2,800-3,000 m above sea level (masl) are exposed to UV levels approximately 40% higher than those of the lowlands. UV light is a carcinogen that causes mutations, DNA damage and cellular apoptosis. However, the XPC, XPD and XPG genes encode proteins that repair DNA caused by UV radiation. The aim of this study was to evaluate the distribution of three polymorphisms (rs2228001, rs13181 and rs17655) involved in the response to the damage caused by UV radiation in the Ecuadorian populations of high and low altitudes, and thus, correlate the ancestral proportions of these populations. Results showed that the behavior of both groups located at different altitudes is similar. The ancestry of these groups exhibited that the Native American component prevails, and the European and African component varies.     

Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an admixed population from the Brazilian Amazon

Allelic frequencies of 48 informative insert-delete (INDEL) loci were obtained from a sample set of 130 unrelated individuals living in Macapá, a city located in the northern Amazon region, in Brazil. The values of heterozygosity (H), polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), matching probability (MP) and typical paternity index (TPI) were calculated and showed the forensic efficiency of these genetic markers. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 50%, 21% and 29%. Comparing these allele frequencies with those of other Brazilian populations and the parental populations, statistically significant distances were found. The interpopulation genetic distance (F_ST coefficients) to the present database ranged from F_ST = 0.0431 (p < 0.00001) between Macapá and Belém to F_ST = 0.266 (p < 0.00001) between Macapá and the Native American group.     

Differentiating among racial/ethnic groups and its implications for understanding juvenile justice decision making

Both theory and research have been refined to gain a better understanding of when race and ethnicity matter in justice proceedings. In the present research, this line of inquiry was continued by differentiating among minority youth to assess the extent being African American, Native American, and Asian American influenced juvenile justice decision making and how these effects compared to one another and Whites. Utilizing an interpretation of the symbolic threat thesis that emphasizes stereotyping, the authors anticipated Native Americans to be responded to more severely than African Americans, followed by Asian Americans who were anticipated to be responded to more like Whites. The results indicated partial support for these expectations.     

Y chromosome microsatellite genetic variation in two Native American populations from Argentina: Population stratification and mutation data

Two Native American populations from North and northwest regions of Argentina (Toba and Colla) were analyzed for 17 Y chromosome short tandem repeat loci (Y-STRs), namely, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1. Over 357 allele transfers, two one-step mutations could be detected at DYS456 and GATA H4.1 loci. A new 16.1 ‘micro-variant’ allele was observed for DYS385, characterized by an insertion at the fifth GAAA repeat. We also observed two alleles at the DYS448 locus in three samples (two from Toba and one from Colla). A total of 34 and 16 different haplotypes were detected for Toba and Colla, respectively, the former with a haplotype diversity value of 0.9769 ± 0.01, whereas 0.9497 ± 0.02 for the latter. Significant population differences were observed between Colla and Toba, at least in part, due to a more prevalent European input in the Colla. In agreement with this observation is the fact that the genetic distances between Colla and Iberian populations are lower than those observed between Iberian and any other Native American population. The results of multiscaling dimensional analysis and genetic distances (Rst) among Native American population samples also reflect this fact. The data show the existence of clear population stratification in the Argentina, a fact that should be taken into account in forensic casework.     

Distribution of Y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala

In this study, a sample of 225 Guatemalan males, comprising 115 Mestizo-Guatemalan and 110 Mayan-Guatemalan, was typed for 17 Y-short tandem repeats (STRs) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). The haplotype diversity (H = 1) and discrimination capacity (96.86%) were calculated. Analysis of molecular variance (AMOVA) demonstrated a low but significant interpopulation differentiation when compared with the results obtained when we confront the Mestizo and Mayan populations with the European populations.Furthermore, the genetic variability and differences among the American, African, Asian, and European populations were analyzed with the software Statistica 9.1. In addition, the genetic distances were also calculated using other published data. Reynolds and Slatkińs genetic distance was visualized using the multidimensional scaling (MDS) analysis. All the analysis performed locates the Mayan population next to the Native American population, while Guatemalan-Mestizo population was found to be between these populations and the European population, similar to other Mestizo one.The implementation of the estimation of individual ancestry proportions of the whole population sample showed the presence of two well-differentiated population groups.     

Divergent genetic strata in five Bahamian islands

Based on historical records, the genetic landscape of the Bahamian archipelago is presumed to be complex and to exhibit island-specific characteristics, yet the genetic composition of the island chain, which could corroborate or refute these past accounts, remains poorly defined. As such, the current investigation was undertaken to genetically characterize 5 Bahamian populations representing the Northwest (Grand Bahama and Abaco) and Central (Eleuthera, Exuma and Long Island) Bahamas across the 15 autosomal Identifiler loci routinely employed in forensic analyses. Altogether, our findings suggest that Bahamians are a genetically heterogeneous group, with each island sampled receiving differential contributions from African, European, East Asian and Native American sources. Even though the strongest genetic signal in all 5 collections emanates from continental Africa, inter-island differentiation is noted in both the Structure and admixture analyses. The presence of alleles not in common among the 5 insular populations also signals genetic heterogeneity among the islands of the archipelago. This is especially the case when considering the Long Island population, which exhibits statistically significant genetic differences in relation to the other Bahamian collections and the New World groups of African descent (Afro-American and Afro-Caribbean) in the G-test pair-wise comparisons, even after application of the Bonferroni adjustment.     

The impact of family indifference on delinquency among American Indian youth: A test of general strain theory

Native American (NA) youth's delinquency is one of the major problems that have been overlooked by criminal justice researchers and practitioners. To examine if negative family environment influences their delinquency with the mediating effect of negative emotion, this study analyzed structural equation modeling based on the General Strain Theory (GST). Using data regarding NA adolescents, this study found much evidence supporting GST. The results of the model with anger showed that anger was a mediating variable between family indifferences and delinquency, and the model with depression indicated that family indifferences increased delinquency through depression. However, some results in the model with anger and depression were not in accordance with GST hypothesis.     

The paternal heritage of self-declared Ecuadorian indigenous people

The present study aimed to characterize the paternal genetic composition of the Ecuadorian indigenous population. To investigate a possible matting bias, AIM-InDels were also analyzed. The population sample of 54 self-declared Ecuadorian indigenous presented a high haplotype diversity. A major proportion of the male lineages belong to Native American haplogroups. Although from self-declared indigenous, the studied population sample presented a low genetic distance with a sample of admixed individuals from Ecuador.     

Experimental long-distance haplotyping of OCA2-HERC2 variants

The regulatory HERC2 SNP, rs12913832, is strongly associated with blue and brown eye colour. However, eye colour in heterozygous rs12913832 individuals is observed to vary greatly. Missense mutations in OCA2, such as rs1800407 and rs74653330, are associated with lighter eye colour in some but not all heterozygous rs12913832 individuals. Determining the physical linkage of these variants might help to further explain eye colour variation. So far, experimental haplotyping of these variants has been challenging because the genomic distance between them (∼ 135 kb) exceeds the fragment lengths produced by commonly used DNA isolation kits. The aim for this study was to explore novel methods for long distance haplotyping to assess associations between OCA2-HERC2 haplotypes and eye colour. DNA was isolated from frozen blood samples collected from Norwegians that are known to be heterozygous for both HERC2 rs12913832 and OCA2 SNPs, either rs1800407 (n = 23) or rs74653330 (n = 17), using the newly commercially available Monarch® HMW (heigh molecular weight) DNA Extraction Kit (New England BioLabs_inc). We successfully isolated DNA fragments up to 210 kb, which were long enough to haplotype OCA2-HERC2 loci by droplet digital PCR (ddPCR). Three haplotypes were observed in the study population: rs12913832:A-rs1800407:T in 22/23 individuals, rs12913832:A-rs1800407:C in 1/23 individuals and rs12913832:A-rs74653330:T in 16/16 individuals. As expected, all individuals with the rs12913832:A-rs74653330:T haplotype had intermediate to blue eye colour. However, the rs12913832:A-rs1800407:T haplotype was observed in both blue and brown-eyed individuals, suggesting more research is needed.     

Analysis of genetic polymorphisms associated with the presence of freckles for phenotypic prediction

The prediction of externally visible characteristics (EVCs) is a commonly used practice by the forensic sciences as an important resource in the investigation of criminal cases in which the identity of perpetrators or victims is unknown or even to recognize decomposed cadavers. With this purpose, genetic markers associated with pigmentation traits have been widely studied by forensic scientists and, nowadays, it is possible to predict phenotypic characteristics such as hair, eyes and skin colour, as well as the presence of skin freckles by analysing single nucleotide polymorphisms (SNPs). In this study, we analysed the association of six SNPs located in pigmentation genes to the presence of freckles in individuals from the Brazilian population for forensic DNA phenotyping. The study was based within the context of a larger project on a population sample of 534 adult Brazilians of both sexes and different skin colours. DNA was extracted from peripheral blood and genotyped using the TaqMan® OpenArray® Real-Time PCR System (ThermoFischer Scientific) technique. Statistical analyses were carried out with the R software (version 4.0.2). As for the results obtained, three SNPs were shown to be statistically associated to the freckling, rs12203592, rs1800404 and rs222847, with CT, AG and AA genotypes being the main contributors, respectively. Variables such as sex of the individuals and skin colour were found to also contribute to the manifestation of this pigmentation trait. Further statistical analyses will be carried out to evaluate the possibility of using the SNPs in this study for phenotyping prediction of the Brazilian population, improving existing DNA phenotyping models in forensic sciences.     

The postmortem fate of Pat Gregory: a disinterred Native American

In late June 1990, the Mono County Sheriffs Department in Bridgeport, CA contacted the Physical Anthropology Human Identification Laboratory (PAHIL) at California State University, Chico to seek assistance in the identification of a recently discovered skull. To assist with possible identification, the cranium received a classic physical anthropological/morphological analysis to suggest the decedent's sex, age at death, ancestral affiliation, and uniqueness. It was concluded the cranium was that of an older male, and someone with mixed ancestry, probably Native American/White. Suggested uniquenesses were an eroded and greasy texture, with adhering white sand, evidence of healed antemortem nasal fractures, and a bifid left occipital condyle. The cranium was confiscated from a man suspected of vandalizing a Native American cemetery just south of the community of Lee Vining. The cemetery was established in the mid-1800's by local Native American tribes. Although ownership of the land was disputed by the US Forest Service (the Inyo National Forest), and the Los Angeles Department of Water and Power (LADWP), county authorities claimed that because the incident involved the desecration of a cemetery and human remains, it was a legal issue, and therefore, the Sheriff's Department had jurisdiction over the case if not the land. The suspect pled guilty to the possession of Native American remains but claimed not to have desecrated a grave. Over the next year and a half, members of the Native American community representing various tribes sought the return of the cranium, while also seeking assurance that it belonged to the vandalized grave. While county, US Forest Service, and LADWP officials continued to argue over whom had jurisdiction of the remains the superior court judge ordered the county to pay for any analysis necessary to determine if the cranium belonged to the decedent in question. This report addresses the conclusions of that analysis and the disposition of the case. Furthermore, the report addresses the forensic value to Native Americans of the continued study of a wide variety of human skeletal remains.     

Identification of Arrhythmogenic Right Ventricular Cardiomyopathy‐Causing Gene Mutations in Young Sudden Unexpected Death Autopsy Cases

Arrhythmogenic right ventricular cardiomyopathy (ARVC) results in an increased risk of sudden death. We sought mutations of desmoglein‐2 (DSG2), desmoplakin (DSP), and plakophilin‐2 (PKP2) in 15 cases of sudden death whose causes of death could not be determined at autopsy. In three victims, mutations were identified in DSP. Two of these mutations were novel; one had previously been reported in a patient with ARVC that had been diagnosed clinically. Histological findings were not typical of ARVC; however, it was notable that these mutations were present in three of 15 cases, a relatively high proportion. The causal relationship between the mutations and ARVC is unclear, but the mutations might have been associated with faulty desmosomal proteins resulting in fatal arrhythmia. Combining information gathered by the traditional means of gross and histological examination with postmortem genetic analysis of young victims would assist in identifying their cause of death.     

Microsatellite autosomal genotyping data in four indigenous populations from El Salvador

Fifteen microsatellite loci (D3S1358, TH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, vWA, D8S1179, TPOX, and FGA) have been genotyped in four indigenous populations from El Salvador (Central America), namely, Conchagua, Izalco, Panchimalco, and San Alejo. Here we have obtained values for several indices of forensic interest for these population samples. Population differentiation test showed no significant statistical differences between these four populations, and an AMOVA test indicates that most of the genetic variation (approximately 100%) occurs within individuals. Population pairwise genetic comparisons with other population samples seem to indicate the existence of a major Native American component in the populations from El Salvador.     

Misclassifications of Hispanics Using Fordisc 3.1: Comparing Cranial Morphology in Asian and Hispanic Populations

It has been brought to the attention of the authors of Fordisc 3.1 that Hispanic samples will often misclassify as Japanese when Asian population samples are included. This study examined this problem in an effort to better document the occurrence and deduce possible causes via comparative analyses. Asian and Hispanic samples were first compared utilizing the existing samples from the University of Tennessee's Forensic Data Bank. Additional modern Japanese, Thai, and Korean samples collected by the first author that have previously not been utilized in analyses were subsequently included. Results of this study confirm frequent rates of misclassification among Hispanic and Japanese groups. Furthermore, a close morphological relationship is identified through further group comparisons and the addition of data used in conjunction with Fordisc samples. Similarities identified among Hispanic and Japanese crania may stem from similar population histories reflected in ancestral Native American and East Asian populations.     

A Quantitative Assessment of Zygomatic Projection for Ancestry Estimation

Anterior zygomatic projection (ZP) is historically referenced as a useful trait in ancestry estimation, particularly when differentiating between Native Americans and U.S. Whites and Blacks. However, methods of assessing ZP vary, are susceptible to multiple interpretations, and have not been quantitatively validated. This study uses 228 3D surface scans of U.S. Whites, U.S. Blacks, and Native Americans to quantitatively test the ZP methods published by Rhine in 1990 (Skeletal attribution of race: methods for forensic anthropology, Albuquerque, NM, Maxwell Museum of Anthropology, 1990) and Bass in 1995 (Human osteology: a laboratory and field manual, Columbia, MO: Missouri Archaeological Society, 1995). Two ZP angles and two distances, representing method interpretations, were collected and analyzed via ANOVA and discriminant function analyses. Although significant ancestry differences were found across all variables, only the Bass inferior zygomatic distance successfully differentiated the pooled Native American group from pooled U.S. Whites/Blacks (73.7% correct). Arctic Native Americans, displaying the most projecting zygomas, are driving group differences. Significant overlap in measurement distributions were observed between groups in all variables, indicating limited forensic utility.     

Review of the Literature on Risk and Protective Factors of Offending Among Native Americans

Abstract

The social and economic conditions faced by much of the Native American population, as well as the history and treatment of Native Americans in our society, create many risk factors for criminal offending. At the same time, however, the cultures, traditions, and spiritualities of Native American tribes likely provide unique protective factors against offending in light of these risks. While these issues, especially drug and alcohol abuse, have received considerable attention by a handful of scholars, the level of research on risk and protective factors of offending have not, although recent research and funding decisions are beginning to make this topic a priority. This paper provides a brief review of the literature on risk and protective factors among Native Americans, highlighting some of the major factors likely to receive the most research attention over the next several years.     

Population Genomics and Research Ethics with Socially Identifable Groups

In this paper, the author questions whether the research ethics guidelines and procedures are robust enough to protect groups when conducting genetics research with socially identifiable populations, particularly with Native American groups. The author argues for a change in the federal guidelines in substance and procedures of conducting genetic research with socially identifiable groups.     

Allele frequency data for 15 autosomal strs and ancestral proportions using aims-indels in the shuar ethnic group from Ecuador

The ethnic group Shuar is located in Ecuador. To identify their genetic composition, 46 ancestry-informative insertion deletion markers (AIM-INDELs) were used. Also, characterization of 15 tandem repeats (STRs) in the AmpFISTR Identifiler Kit were applied. Forensic parameters showed a matching probability of 0.1535, a power of discrimination of 0.8465, a polymorphism information content of 0.6584, probability of exclusion of 0.415 and a typical paternity index of 1.78. The Shuar are not influenced by admixture population events, being a Native American group 98.7%, along with a genetic diversity of 0.699346+/-0.356964.