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Although ethical reforms in biological anthropology have gained ground in recent years, there is still a scarcity of ethical standards for work involving historical documented collections (HDCs) at US museums and universities. These collections of deceased individuals were created in the late 19th to mid‐20th centuries under anatomy laws that targeted socially marginalized communities and allowed for the dissection of these individuals without their consent. Due to the extensive information associated with the individuals and made available to researchers, these collections have served as foundational resources for theory and methods development in biological anthropology into the 21st century. Recognizing the need for ethical guidelines for research, teaching and training, community engagement, and curation involving HDCs, we held a workshop called "Ethical Futures for Curation, Research, and Teaching in Biological Anthropology" on November 15–17, 2021. Here we summarize the conversations and major points of consensus among the workshop participants on these topics in order to advance these ethical considerations more broadly across the field. [ABSTRACT FROM AUTHOR]

The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.

The article focuses on the significance of studying human skeletons, dental plaque, and biomolecules to uncover hidden aspects of the past, particularly through paleogenomics. Topics include how molecular analyses reveal historical interactions between humans and their environment, the application of these findings to modern health issues and disease prevention, and the advancement of new therapeutic approaches through interdisciplinary research.

The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record—a long-term archive of human–animal–environmental interactions—has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence. [ABSTRACT FROM AUTHOR]

Keywords: archeology; baselines; cities; community science; museums; paleontology; urban ecology; paleoecology EN archeology baselines cities community science museums paleontology urban ecology paleoecology 1 5 5 12/01/22 20221201 NES 221201 A fundamental challenge for 21st century conservation is to develop goals that are meaningful and attainable in a world shaped by anthropogenic change (Kareiva & Marvier, [10]). These separate data sources can be used to understand the deep-time natural history, recent human history, or current ecology of urban landscapes in isolated conservation contexts. This narrow view downplays conservation efforts in urban areas and limits the ability of cities to support biodiversity; decreases access to ecosystem services for many people; and facilitates actions that result in environmental injustices. Archeology, baselines, cities, museums, paleontology, urban ecology, paleoecology, community science. [Extracted from the article]

A multimethod archaeometry study (zooarchaeological, isotopic, ancient DNA, paleobotanical, and radiocarbon dating) of a spider monkey sacrificed in the ceremonial center of Teotihuacan, Mexico (1 to 550 CE) is interpreted as a diplomatic gift exchange with neighboring Maya. Not only does this spider monkey provide the earliest known instance of primate translocation and captivity in Mesoamerica, it helps date incipient modes of interregional diplomacy between two major powers during Early Classic Mesoamerica: Teotihuacan and the Maya. Details of human–primate interaction include age at capture and transport (before ~3 y of age), captive duration (over 2 y), anthropogenic diet (staple was maize, though secondary resources unique to anthropogenic diet including arrowroot and chili pepper were also found), context of sacrifice (tethered and associated with complete golden eagle and an array of other statecrafts), and general site context (including presence of Maya vessels and Maya-style murals). The timing of the spider monkey’s sacrifice (250 to 300 CE) and its life history suggest a reconsideration of epigraphically attested militaristic involvement of Teotihuacan at certain Maya sites. We propose that a period of more multilateral and fluid ritual exchange with Maya dignitaries preceded the Teotihuacan state’s eventual ascent to prominence. [ABSTRACT FROM AUTHOR]

Objectives: Natural history collections are often thought to represent environments in a pristine natural state—free from human intervention—the so‐called "wild." In this study, we aim to assess the level of human influence represented by natural history collections of wild‐collected primates over 120 years at the Smithsonian Institution's National Museum of Natural History (NMNH). Materials and Methods: Our sample consisted of 875 catarrhine primate specimens in NMNH collections, representing 13 genera collected in 39 countries from 1882 to 2004. Using archival and accession information we determined the approximate locations from which specimens were collected. We then plotted location coordinates onto publicly available anthrome maps created by Ellis et al. (Global Ecology and Biogeography, 2010, 19, 589), which delineate terrestrial biomes of human population density and land use worldwide since the 1700s. Results: We found that among primates collected from their native ranges, 92% were from an environment that had some level of human impact, suggesting that the majority of presumed wild‐collected primate specimens lived in an environment influenced by humans during their lifetimes. Discussion: The degree to which human‐modified environments may have impacted the lives of primates currently held in museum collections has been historically ignored, implicating unforeseen consequences for collection‐based research. While unique effects related to commensalism with humans remain understudied, effects currently attributed to natural phenomena may, in fact, be related to anthropogenic pressures on unmanaged populations of primates. [ABSTRACT FROM AUTHOR]

We synthesize how the tools of molecular anthropology, integrated with analyses of skeletal material, can provide direct insights into the context-specific experiences of racial structural violence in the past. Our work—which is emblematic of how biological anthropologists are increasingly interested in exploring the embodied effects of structural and race-based violence—reveals how anthropology can illuminate past lived experiences that are otherwise invisible or inscrutable. This kind of integrative research is exposing the legacies of structural violence in producing anatomical collections and the embodied effects of structural violence evident within individuals in those collections. [ABSTRACT FROM AUTHOR]

Atlas occipitalization (AO) is a spinal anomaly, characterized by the fusion of the first cervical vertebra and occipital bone, with a complex etiology that can arise from congenital and environmental causes. AO has been reported in three regions of pre-Hispanic Peru in skeletal remains with artificial cranial modification (ACM), which involves the use of compression devices to permanently alter cranial shape and may have affected the fusion of the atlas and occipital bone. The aims of this study were to gain insights into AO's etiology by testing correlations between AO and ACM presence/type and geographic region as well as to characterize morphological variation associated with AO. We investigated the geographic distribution of AO and its potential relationship to ACM in a large sample of human crania from eight coastal and highland regions of pre-Hispanic Peru, held at the Smithsonian's National Museum of Natural History (n = 608, 1300–1500 CE). Eleven cases of AO were observed in three coastal regions—including two previously unreported regions—at an overall frequency of 1.8%. The frequency of AO did not differ significantly between crania with and without ACM, in general or by type, suggesting that ACM is not an etiological factor that influences AO in this sample. AO was observed at a significantly higher rate in the southern coastal region of Arequipa than in any other region. Genetic, dietary, and epidemiological conditions are evaluated as factors possibly shaping the geographic distribution of AO along the central and southern coasts of Peru. [ABSTRACT FROM AUTHOR]

During the last 10 years, we have learned a great deal about the potential for a coastal peopling of the Americas and the importance of marine resources in early economies. Despite research at a growing number of terminal Pleistocene archaeological sites on the Pacific Coast of the Americas, however, important questions remain about the lifeways of early Paleocoastal peoples. Research at CA-SRI-26, a roughly 11,700 year old site on California's Santa Rosa Island, provides new data on Paleoindian technologies, subsistence strategies, and seasonality in an insular maritime setting. Buried beneath approximately two meters of alluvium, much of the site has been lost to erosion, but its remnants have produced chipped stone artifacts (crescents and Channel Island Amol and Channel Island Barbed points) diagnostic of early island Paleocoastal components. The bones of waterfowl and seabirds, fish, and marine mammals, along with small amounts of shellfish document a diverse subsistence strategy. These data support a relatively brief occupation during the wetter "winter" season (late fall to early spring), in an upland location several km from the open coast. When placed in the context of other Paleocoastal sites on the Channel Islands, CA-SRI-26 demonstrates diverse maritime subsistence strategies and a mix of seasonal and more sustained year-round island occupations. Our results add to knowledge about a distinctive island Paleocoastal culture that appears to be related to Western Stemmed Tradition sites widely scattered across western North America. [ABSTRACT FROM AUTHOR]

Objectives: To describe and interpret previously unreported marks on the dry cranium of an adult chimpanzee (Pan troglodytesverus) from Côte d'Ivoire at the Smithsonian's National Museum of Natural History (USNM 450071). Materials and Methods: All marks on the cranium were documented and assessed through physical examination of the specimen, photography, micro‐computed tomography (micro‐CT), and 3D laser scanning. Pits and punctures were measured with digital calipers for comparison with published carnivore tooth mark measurements. Results: The cranium shows perimortem or postmortem damage to the temporal, occipital, and maxillary regions that is not recent. Size and color variation in the marks suggest two damage events, possibly involving chewing by different animals, at least one of which was a large‐bodied mammal. The 22 tooth pits and punctures (0.89–8.75 mm in maximum length and 0.88–6.63 mm in breadth) overlap in size with those inflicted by wild leopards, the most significant predators of common chimpanzees due to their largely overlapping ecological distributions. Conclusions: Based on qualitative and quantitative evidence, we conclude that leopards are the most likely cause of the most prominent marks on the cranium. However, we cannot rule out the additional possibility of other chimpanzees, although there are no published studies of chimpanzee tooth marks for direct comparison. This study is the most extensive documentation to date of a modern adult chimpanzee skull exhibiting tooth marks by a large mammal, thus providing new evidence to help identify and interpret other events of predation and scavenging of large‐bodied apes in the modern and fossil records. [ABSTRACT FROM AUTHOR]

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts. [ABSTRACT FROM AUTHOR]

Objectives: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host‐associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. Methods: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well‐preserved human and dog paleofeces from Mexico (~1,300 BP). Results: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA. Conclusions: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies. [ABSTRACT FROM AUTHOR]

Objectives: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing. Results: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples. [ABSTRACT FROM AUTHOR]

Rats and mice are among the most successful mammals on earth, with some of these species thriving in and around human settlements or areas disturbed by human activities. Here, we present morphological, taphonomic, and chronological data on two mice (Peromyscus nesodytes [extinct] and P. maniculatus [extant]) from a trans-Holocene sequence at Daisy Cave, San Miguel Island, California. We explore the colonization history of each species, species abundance through time, taphonomic history, and the causes and timing of the extinction of P. nesodytes. P. maniculatus were probably introduced by humans to San Miguel Island ~11,000 years ago, 1000 years earlier than previous estimates, and P. nesodytes does not occur in Daisy Cave deposits after ~8000 years ago, some 7000 years earlier than reported at adjacent Cave of the Chimneys. Island P. maniculatus form a distinct morphological group from all other North American subspecies. These data highlight the importance of morphological analyses of archaeological and subfossil rodent specimens for understanding the evolution and natural history of island endemic species and their interactions with humans. [ABSTRACT FROM AUTHOR]

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules. [ABSTRACT FROM AUTHOR]

The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations. [ABSTRACT FROM AUTHOR]

ABSTRACT Objectives Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Results Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox ( Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA ( RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. [ABSTRACT FROM AUTHOR]