Human Biology最新文献

{"title":"Typicality and Predictive Distributions in Discriminant Function Analysis","authors":"L. Konigsberg, S. Frankenberg","doi":"10.13110/humanbiology.90.1.01","DOIUrl":"https://doi.org/10.13110/humanbiology.90.1.01","url":null,"abstract":"abstract While discriminant function analysis is an inherently Bayesian method, researchers attempting to estimate ancestry in human skeletal samples often follow discriminant function analysis with the calculation of frequentist-based typicalities for assigning group membership. Such an approach is problematic because it fails to account for admixture and for variation in why individuals may be classified as outliers or nonmembers of particular groups. This article presents an argument and methodology for employing a fully Bayesian approach in discriminant function analysis applied to cases of ancestry estimation. The approach requires adding the calculation, or estimation, of predictive distributions as the final step in ancestry-focused discriminant analyses. The methods for a fully Bayesian multivariate discriminant analysis are illustrated using craniometrics from identified population samples within the Howells published data. The article also presents ways to visualize predictive distributions calculated in more than three dimensions, explains the limitations of typicality measures, and suggests an analytical route for future studies of ancestry and admixture based in discriminant function analysis.","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"1 1","pages":"31 - 44"},"PeriodicalIF":0.0,"publicationDate":"2018-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88778515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population Identifiability from Forensic Genetic Markers: Ancestry Variation in Latin America.","authors":"Cris E Hughes,&nbsp;Bridget F B Algee-Hewitt,&nbsp;Lyle W Konigsberg","doi":"10.13110/humanbiology.90.3.03","DOIUrl":"https://doi.org/10.13110/humanbiology.90.3.03","url":null,"abstract":"<p><p>The Combined DNA Index System (CODIS) loci comprise a standard microsatellite marker set widely used for distinguishing among individuals in forensic DNA identity testing for medicolegal casework in the United States and in other countries. In anthropological genetic research, CODIS markers have become an important tool for uses extending beyond case investigations to quantify ancestry proportions, reveals patterns of admixture, and trace population histories. These investigations are especially prevalent in studies of Latin American population structure. Nevertheless, the accuracy of the ancestry estimates computed from the CODIS loci for highly admixed Latino populations has not been formally tested. Longstanding arguments have been made that small ancestry panels, including the CODIS loci specifically, are not suitable for ancestry inference in admixed populations, due to high heterozygosity and limited number of loci used. Recent studies on ancestry inference using the CODIS loci suggest that these do confer more information of population-level identifiability than recognized in forensic genetic scholarship and by the medicolegal community. Here, we formally test the ability of CODIS and CODIS-proxy (e.g., high-heterozygosity and individual-identifiability loci) marker panels to accurately estimate admixture proportions of individuals, including a sample of Latinos with a wide range of ancestry proportions. Using the same individuals to make direct comparisons of the outcomes, the authors produced ancestry estimates from (a) a small CODIS/CODIS-proxy locus panel and (b) a robust and validated microsatellite ancestry-informative panel. They found evidence (e.g., ρ = 0.80-0.88) that supports the use of CODIS/ CODIS-proxy loci to capture the general ancestry estimation trends of a sample. This finding is in line with results of studies using CODIS on Latin American populations: the ancestry estimations generated by CODIS present trends supported by documented population histories (e.g., colonialism and population movements) and microevolutionary events (e.g., gene flow) in Latin America. However, this study also highlights the limitations of CODIS for making individual-level inferences of ancestry: the associated estimates for an acceptable level of statistical confidence (95%) are too broad to make any nuanced inferences regarding an individual's actual ancestry composition.</p>","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 3","pages":"161-175"},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38949312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oxygen and Hydrogen Isotopes in Human Hair and Tap Water: Modeling Relationships in a Modern Mexican Population.","authors":"Chelsey A Juarez,&nbsp;Robin Ramey,&nbsp;David T Flaherty,&nbsp;Belinda S Akpa","doi":"10.13110/humanbiology.90.3.04","DOIUrl":"https://doi.org/10.13110/humanbiology.90.3.04","url":null,"abstract":"<p><p>This study investigated the relationship between ¹⁸O and ²H isotopes in samples of Mexican hair and drinking water. The purpose of this study was twofold: to quantify the relationship between isotopes in Mexican hair and tap water, in order to understand the impact of water stress and differing socioeconomic status on accurate predictions of drinking water; and to determine whether currently existing semimechanistic models can accurately represent the relationship between hair and tap water. This study used a subset of paired samples of human hair (<i>n</i> = 62) and tap water (<i>n</i> = 76). Isotope values in tap water ranged from -11.4‰ to -4.3‰ and -79.1‰ to -22.5‰, and in hair from +9.5‰ to +16.1‰ and -90.8‰ to -53.7‰, for δ¹⁸O and δ²H, respectively. The most depleted δ¹⁸O and δ²H hair values came from individuals in the state of Morelos. For modern Mexican populations, positive correlations between isotopes in hair and water were not significant, with correlation coefficients <i>r</i> = 0.61 (<i>p</i> = 0.05) and <i>r</i> = 0.60 (<i>p</i> = 0.06) for ¹⁸O and ²H, respectively. Error-in-variables regression yielded linear fits that were somewhat better for ²H relative to ¹⁸O: δ¹⁸O_h = 0.183 [±0.132] δ¹⁸O_tw + 15.7 [±0.9]‰ (<i>r</i>² = 0.23); δ²H_h = 0.181 [±0.076] δ²H_tw - 64.0 [±3.0]‰ (<i>r</i>² = 0.34). In short, data from this Mexican population did not exhibit the strong relationships between isotope values of ¹⁸O and ²H in tap water and hair that have been characteristic of other populations studied to date. Given the economic stratification of this region and the poor correlation between hair and water samples, the authors considered the possibility that <i>l</i>, the fraction of the diet derived from local sources, and <i>f_s</i>, the fraction of nonexchangeable H in keratin that was fixed in vivo, are local rather than global parameters for this population. The authors estimated different values of <i>l</i> and <i>f_s</i> for each location. Given the anticipated importance of the nonlocal dietary contribution, they treated the isotopic content of nonlocal food and the offset parameters for predicting isotopes in locally derived food as tuning parameters and compared the results with parameters based on the American supermarket diet. They found that, although O and H isotopes in water and hair maintained similar geographic distributions, O and H isotopes in tap water explained only a small part of the variation observed in hair samples. Compared to the standard American supermarket diet, the Mexican estimates for nonlocal diet and local diet offsets predicted regional distributions of <i>l</i> and <i>f_s</i> that cleanly segregated urban areas from rural towns.</p>","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 3","pages":"197-211"},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38949314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2018 Outstanding Trainee Presentations in Anthropological Genetics Awards Announced.","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 1","pages":"83-84"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36641564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2018 Outstanding Trainee Presentations in Anthropological Genetics Awards Announced","authors":"","doi":"10.13110/humanbiology.90.1.0083","DOIUrl":"https://doi.org/10.13110/humanbiology.90.1.0083","url":null,"abstract":"","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"22 1","pages":"83 - 84"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84219243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Survey and Insights into Unmanned Aerial-Vehicle-Based Detection and Documentation of Clandestine Graves and Human Remains.","authors":"Bryce Murray,&nbsp;Derek T Anderson,&nbsp;Daniel J Wescott,&nbsp;Robert Moorhead,&nbsp;Melissa F Anderson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Numerous biological and archaeological studies have demonstrated the legitimacy of remote sensing in anthropology. This article focuses on detecting and documenting terrestrial clandestine graves and surface remains (CGSR) of humans using unmanned aerial vehicles (UAVs), sensors, and automatic processing algorithms. CGSR is a problem of complex decision making under uncertainty that requires the identification and intelligent reasoning about direct evidence of human remains and their environmental fingerprints. As such, it is as much an engineering and geospatial problem as it is an anthropology problem. This article is an effort to survey existing work across disciplines and to provide insights and recommendations to assist future research. To support our claims, preliminary experiments were performed at the Forensic Anthropological Research Facility at Texas State University using UAVs, hyperspectral imaging, thermal imaging, and structure from motion. Prior work, our experience, and preliminary results indicate that both great potential and extreme challenges face remote sensing of CGSR.</p>","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 1","pages":"45-61"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36641566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New Approaches to Juvenile Age Estimation in Forensics: Application of Transition Analysis via the Shackelford et al. Method to a Diverse Modern Subadult Sample.","authors":"Kelly R Kamnikar,&nbsp;Nicholas P Herrmann,&nbsp;Amber M Plemons","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each \"stage\" and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited application to modern humans. We use this same method on a subadult test sample (n = 201), representing modern individuals that may become part of the forensic record. We assess the probability coverage of the Shackelford et al. method derived from MFH standards as it applies to all available dentition. Results indicate promise: the age range at 90% and 95% confidence levels includes the chronological age of almost every individual tested. The maximum likelihood age estimates underestimate age by 0.5-2.5 years for individuals 0-15 years of age and by >2.5 years for individuals 16-18 years of age, as previously shown. In an attempt to refine the method, we adjusted the numerical parameters underlying the stages for developing teeth based on a combined modern reference sample (n = 1,964) and tested these revised parameters using the same test sample. The estimated ages from the modified method differ from the original Shackelford et al. methodology by underestimating age to a lesser degree. The modified method does include mean age-at-attainment values for earlier stages of several teeth, allowing for the calculation of narrower confidence intervals. While this study highlights areas of future research in refining dental developmental aging by transition analysis, it also demonstrates that the Shackelford et al. method is applicable and accurate when aging modern subadults in forensic work.</p>","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 1","pages":"11-30"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36641565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thinking Computationally about Forensics: Anthropological Perspectives on Advancements in Technologies, Data, and Algorithms.","authors":"Bridget F B Algee-Hewitt,&nbsp;Jieun Kim,&nbsp;Cris E Hughes","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 1","pages":"5-10"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36641571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thinking Computationally about Forensics: Anthropological Perspectives on Advancements in Technologies, Data, and Algorithms","authors":"Bridget F. B. Algee‐Hewitt, Jieun Kim, Cris E. Hughes","doi":"10.13110/humanbiology.90.1.04","DOIUrl":"https://doi.org/10.13110/humanbiology.90.1.04","url":null,"abstract":"abstract:Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less afffected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each \"stage\" and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited application to modern humans. We use this same method on a subadult test sample (n = 201), representing modern individuals that may become part of the forensic record. We assess the probability coverage of the Shackelford et al. method derived from MFH standards as it applies to all available dentition. Results indicate promise: the age range at 90% and 95% confidence levels includes the chronological age of almost every individual tested. The maximum likelihood age estimates underestimate age by 0.5–2.5 years for individuals 0–15 years of age and by >2.5 years for individuals 16–18 years of age, as previously shown. In an attempt to refine the method, we adjusted the numerical parameters underlying the stages for developing teeth based on a combined modern reference sample (n = 1,964) and tested these revised parameters using the same test sample. The estimated ages from the modified method difffer from the original Shackelford et al. methodology by underestimating age to a lesser degree. The modified method does include mean age-at-attainment values for earlier stages of several teeth, allowing for the calculation of narrower confidence intervals. While this study highlights areas of future research in refining dental developmental aging by transition analysis, it also demonstrates that the Shackelford et al. method is applicable and accurate when aging modern subadults in forensic work.","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"102 1","pages":"10 - 5"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80636129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Typicality and Predictive Distributions in Discriminant Function Analysis.","authors":"Lyle W Konigsberg,&nbsp;Susan R Frankenberg","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>While discriminant function analysis is an inherently Bayesian method, researchers attempting to estimate ancestry in human skeletal samples often follow discriminant function analysis with the calculation of frequentist-based typicalities for assigning group membership. Such an approach is problematic because it fails to account for admixture and for variation in why individuals may be classified as outliers or nonmembers of particular groups. This article presents an argument and methodology for employing a fully Bayesian approach in discriminant function analysis applied to cases of ancestry estimation. The approach requires adding the calculation, or estimation, of predictive distributions as the final step in ancestry-focused discriminant analyses. The methods for a fully Bayesian multivariate discriminant analysis are illustrated using craniometrics from identified population samples within the Howells published data. The article also presents ways to visualize predictive distributions calculated in more than three dimensions, explains the limitations of typicality measures, and suggests an analytical route for future studies of ancestry and admixture based in discriminant function analysis.</p>","PeriodicalId":13053,"journal":{"name":"Human Biology","volume":"90 1","pages":"31-44"},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36641563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}