Levi Y. Raskin, Maja Šešelj, Bárbara D. Bitarello, Sofia Stroustrup, Jacky K. Li, John Huelsenbeck
{"title":"Principal Components Analysis Fails to Recover Phylogenetic Structure in Hominins","authors":"Levi Y. Raskin, Maja Šešelj, Bárbara D. Bitarello, Sofia Stroustrup, Jacky K. Li, John Huelsenbeck","doi":"10.1002/ajpa.70306","DOIUrl":"10.1002/ajpa.70306","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Objectives</h3>\u0000 \u0000 <p>Paleoanthropologists often utilize geometric morphometrics and principal components analysis (PCA) to interpret shape variation within the hominin fossil record. It is common practice to interpret proximity in principal components (PC) space among taxa as indicative of not just morphological but also phylogenetic affinity. This interpretation, however, has not been directly evaluated for hominins.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Materials and Methods</h3>\u0000 \u0000 <p>First, we inferred the posterior distribution of hominin phylogenetic trees and subsampled trees from this distribution. On these phylogenies, we simulated 2D and 3D geometric morphometric datasets and traditional morphological datasets, containing traits analogous to measurements of size or length, with varying numbers of landmarks or traits and evolutionary rates. On each dataset, we conducted a PCA and used neighbor-joining to infer evolutionary relationships from the PC scores of each taxon. We measured the difference between the PCA tree and sampled tree with subtree pruning and regrafting distance and Robinson-Foulds distance.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>PCA trees inferred from traditional morphometric data were identical to the sampled tree in 0.11% of datasets when we only considered PC axes 1 and 2, and in 2.9% of datasets when we considered all axes. No PCA tree inferred from any of the 2,400,000 shape datasets was identical to the sampled tree, regardless of the number of axes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Phylogenetic interpretations of the hominin fossil record based on proximity in PC space are inherently flawed and likely to be erroneous. Arguments in the hominin systematics literature based on PCA, whether implied or explicit, should therefore be reevaluated using phylogenetically informed alternatives.</p>\u0000 </section>\u0000 </div>","PeriodicalId":29759,"journal":{"name":"American Journal of Biological Anthropology","volume":"190 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148362388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leela McKinnon, Eric C. Shattuck, Igor Martín Ramos Herrera, René Cristobal Crocker Sagastume, Quetzabel de la Cruz, Paritemai González Torrez, Thankam Sunil, David R. Samson
{"title":"The Effect of Migration on Perceived Safety and Sleep Quality: An Analysis From Rural and Urban Indigenous Wixárika Communities in Jalisco, Mexico\u0000 El efecto de la migración en la seguridad percibida y la calidad del sueño: un análisis en comunidades indígenas Wixaritari rurales y urbanas en Jalisco, México","authors":"Leela McKinnon, Eric C. Shattuck, Igor Martín Ramos Herrera, René Cristobal Crocker Sagastume, Quetzabel de la Cruz, Paritemai González Torrez, Thankam Sunil, David R. Samson","doi":"10.1002/ajpa.70307","DOIUrl":"10.1002/ajpa.70307","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Objectives</h3>\u0000 \u0000 <p>This study explores how perceived safety influences sleep quality among Wixárika individuals in Mexico. We compared the sleep quality of those living in a rural town in northern Jalisco with those living in the Guadalajara Metropolitan Area (GMA). We aimed to assess differences in perceived safety, model its association with sleep outcomes, and test for gendered effects.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Sleep was measured using actigraphy and surveys. Perceived neighborhood safety (PNS) was measured with survey items. Sleep outcomes included efficiency, fragmentation, wake after sleep onset (WASO), self-rated quality, and daytime dysfunction. Analyses used Mann–Whitney <i>U</i> tests, linear mixed effects models, and logistic regression.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our sample included 127 participants. In the rural location (<i>n</i> = 61), the mean age was 38.02 years (SD = 12.18, range = 18–65), with 72.13% comprised of women. In the GMA, the mean age was 29.59 years (SD = 8.43, range = 18–57), of whom 65.15% were women. PNS was significantly higher in the rural town than in the GMA. Gender moderated the association between PNS and sleep quality, with women showing improved sleep quality with greater PNS. Poorer mental health predicted lower sleep quality in rural participants and greater odds of daytime dysfunction in urban participants.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>In our analyses, living in urban contexts is associated with reduced perceived safety, which interacts with gender to shape sleep. Women's sleep appears to be particularly sensitive to perceived safety, reflecting broader intersecting vulnerabilities and health inequities faced by Indigenous migrant women. Policies addressing housing and neighborhood safety, alongside culturally grounded supports, may improve sleep health in these communities.</p>\u0000 </section>\u0000 </div>","PeriodicalId":29759,"journal":{"name":"American Journal of Biological Anthropology","volume":"190 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ajpa.70307","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148362411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}