Heather B. Thakar

Collagen is a vital archaeological material, preserving biochemical signatures that provide insights into past environments, diets, and human–animal interactions. However, diagenetic processes can lead to rapid and often inconspicuous degradation of collagen. Given the variability in collagen preservation and its significance for analyses such as radiocarbon dating, stable isotope analysis, and ZooMS, researchers have developed various prescreening techniques to assess collagen preservation before destructive sampling. In this study, we applied near‐infrared (NIR) spectroscopy to rapidly and nondestructively prescreen collagen preservation using a previously validated partial least squares regression model. To assess its effectiveness, we analyzed 830 bones from the Cooper's Ferry/Nipéhe site, a dodo and Rodrigues solitaire collection, and a collection of ancient to modern bison. NIR spectroscopy demonstrated high effectiveness in identifying samples suitable for radiocarbon dating, with success rates of 80% (4/5) for Cooper's Ferry/Nipéhe and 91% (10/11) for the dodo and Rodrigues solitaire specimens. Additionally, NIR spectroscopy effectively selected bison samples for ZooMS at a lower collagen yield threshold, with a success rate of 92% (34/37). The results demonstrate that NIR spectroscopy is a viable, nondestructive alternative for collagen prescreening in archaeological bone before destructive analyses, minimizing unnecessary destructive sampling of irreplaceable archaeological materials.

Societal Impact Statement: Avocados are a multibillion‐dollar global commodity, but their growing export market pressures local farmers to abandon local fruit tree diversity in favor of commercial cultivar production. Interviews with rural avocado farmers and households from the Southern Mexican Highlands, Pacific Coastal Honduras, and Western Nicaragua, as well as the genetic analysis of their cultivars, highlight the importance of native avocado conservation in sustainable breeding programs. Local Central American avocados serve as hearty rootstocks well‐adapted to their specific climate and grow in symbiosis alongside commercial trees. Landraces are also substantially genetically separated from commercial cultivars, representing a source of genetic diversity in the face of threats to global production such as climate change and pathogens. Summary: The genomes of landrace cultivars offer a unique view into a plant's history of human usage and a fuller understanding of the genetic diversity available for sustainable production. The avocado tree ( Persea americana Mill., family Lauraceae), native to Central and South America, has a complicated history of traditional and commercial production revealed through previous genetic research. We sequenced 50 low‐coverage genomes from avocado landraces grown in home gardens and local farms from Honduras, Nicaragua, and on roadsides in Chiapas, Mexico. We also interviewed local cultivators to document traditional perspectives on native Central American avocado management and biodiversity. Samples collected from Chiapas show evidence for recent hybridization both within and between native and commercial cultivars. In contrast, lowland Nicaraguan and Honduran landraces were substantially differentiated from commercial genomes. Lowland genomes show evidence for ancient episodes of migration from South American avocados detectable only in noncommercial germplasm. Differences in relatedness to commercial avocados between regions are explained by the region's historical involvement in exports to large consumer markets throughout time. Chiapas landraces are closer genetically to commercial avocados than those in lowland Honduras and Nicaragua, as the highlands of Southern Mexico offer a better growth environment for more exportable varieties. Since the humid lowlands are largely unaffected by commercial production, we are able to detect ancient signals of pre‐colonial migration from South America.

Los yacimientos en el oeste de la isla Santa Cruz, que datan entre 7000 y 5300 años, suelen contener llamativas conchas de abulón rojas, a pesar de que los fragmentos de conchas de mejillón son más abundantes. La mayoría de los yacimientos identificados al principio se encontraban en la costa o cerca de ella, pero en los últimos 30 años también se han documentado en lugares tierra adentro que ofrecen la oportunidad de aprender acerca del uso de los recursos alimentarios y la importancia de los recursos alimentarios costeros mientras se vive tierra adentro. Aunque, el muestreo a pequeña escala en algunos de los sitios tierra adentro se llevaron a cabo principalmente con el propósito de obtener muestras para la datación de radiocarbono, más recientemente se han excavado pozos de prueba a mayor escala en cuatro de ellos para obtener muestras lo suficientemente grandes como para evaluar cómo se articulaban los sitios con los sistemas de asentamiento. Los sitios que se encuentran tierra adentro de este período suelen presentar un área pequeña y están ubicados en una variedad de características topográficas. Algunos están enterrados bajo depósitos posteriores y otros pocos poseen estratos asociados que contienen conchas de abulón rojo. Los datos disponibles, aunque aún escasos, indican que pequeñas unidades sociales ocuparon sitios tierra adentro durante algunas semanas o meses seguidos, aparentemente para adquirir y consumir recursos alimenticios vegetales. Se necesitará mayores esfuerzos para localizar e investigar sitios tierra adentro durante el período 7000–5300 AP para crear una idea más clara.

Molecular research suggests that avocados ( Persea americana Mill.) were domesticated multiple times in the Americas. Seed exchange, hybridization, and cloning have played an essential role across their wild distribution from Mexico to South America to create the modern varieties of today. Archaeological sites with well-preserved and directly radiocarbon-dated botanical assemblages are rare, however, so we know very little about the complexities of the domestication process. Here, we define an early locus of avocado domestication using well-dated desiccated and carbonized avocado remains from El Gigante rockshelter in western Honduras spanning the last 11,000 y. Measurements of avocado seeds and rinds show evidence for long-term management resulting in selection for larger, more robust fruits through time that culminated by 2,250 to 2,080 calendar B.P. (cal. B.P.). However, human-directed selection for larger fruits with thicker rinds is evident as early as 7,565 to 7,265 cal. B.P. Seed morphology is similar to P. americana var. guatemalensis and is congruent with genetic data for the development of this variety in both the highlands of Guatemala and Honduras. Increases in seed size and rind thickness through time are consistent with genetic evidence for the enrichment of putative candidate genes for fruit development and ripening in this variety.

This article discusses ethical frameworks for planning and implementing composite research in the United States. Composites, defined here as archaeological materials with multiple genetic sources, include materials such as sediment, coprolites, birch pitch, and dental calculus. Although composites are increasingly used in genetic research, the ethical considerations of their use in ancient DNA studies have not been widely discussed. Here, we consider how composites’ compositions, contexts, and potential to act as proxies can affect research plans and offer an overview of the primary ethical concerns of ancient DNA research. It is our view that ethical principles established for analyses of Ancestral remains and related materials can be used to inform research plans when working with composite evidence. This work also provides a guide to archaeologists unfamiliar with genetics analyses in planning research when using composite evidence from the United States with a focus on collaboration, having a clear research plan, and using lab methods that provide the desired data with minimal destruction. Following the principles discussed in this article and others allows for engaging in composite research while creating and maintaining positive relationships with stakeholders.

Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica. Significance Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently fixed and improved varieties developed away from the influence of wild gene flow. We demonstrate that hybrids of some of these improved varieties were likely reintroduced back to Central America. We hypothesize that this backflow of South American genetic material may have contributed to the development of a more productive staple, which was related to the growth and aggregation of human populations, and the formation of more complex social and political structures regionally.