Courtney A Hofman

Courtney A Hofman
University of Oklahoma | ou · Department of Anthropology

Doctor of Philosophy

About

68
Publications
15,747
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1,036
Citations
Additional affiliations
August 2009 - July 2015
University of Maryland, College Park
Position
  • PhD Student

Publications

Publications (68)
Article
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Historical ecology has revolutionized our understanding of fisheries and cultural landscapes, demonstrating the value of historical data for evaluating the past, present, and future of Earth’s ecosystems. Despite several important studies, Indigenous fisheries generally receive less attention from scholars and managers than the 17th–20th century ca...
Article
The places in which people live and spend time are steeped in history, memory, and meaning from the intersection of daily life, environmental interactions, cultural practices, and ritual. Geologic features, plants, animals, and ecosystems merge with these cultural histories, forming critical parts of the landscape and areas of “high cultural salien...
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Archaeologists have long emphasized the importance of large-scale excavations and multi-year or even decades-long projects at a single site or site complex. Here, we highlight archaeological field strategies, termed coring, profiling, and trenching (CPT), that rely on relatively small-scale excavations or the collection of new samples from intact d...
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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...
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In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600-3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity wi...
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We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 7...
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The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late...
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Sturgeon (Acipenser spp.) have long been an important resource for people living in several parts of the world, including the Northwest Coast of North America. Two sturgeon species occur on the Oregon Coast, white (A. transmontanus) and green (A. medirostris), but morphological similarities between the species have generally prevented osteological...
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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...
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A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, w...
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Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter ( Enhydra lutris ) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon se...
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Dental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of physical, chemical, and molecular means. Recently, studies have attempted to reconstruct diet from archaeological dental calculus using archaeogenetic techniques. While dental calculus may provide a...
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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...
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An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interd...
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Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a sou...
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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 micros...
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Objectives: To describe and interpret previously unreported marks on the dry cranium of an adult chimpanzee (Pan troglodytes verus) 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, ph...
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The shells of marine mollusks represent promising metagenomic archives of the past, adding to bones, teeth, hairs, and environmental samples most commonly examined in ancient DNA research. Seminal work has established that DNA recovery from marine mollusk shells depends on their microstructure, preservation and disease state, and that authentic anc...
Preprint
Full-text available
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 micros...
Preprint
Abstract. The shells of marine mollusks represent promising metagenomic archives of the past, adding to bones, teeth, hairs, and environmental samples most commonly examined in ancient DNA research. Seminal work has established that DNA recovery from marine mollusks depends on their shell microstructure, preservation and disease state, and that aut...
Article
Full-text available
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 c...
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Background: Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming 'higher' termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of...
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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 re...
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The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation dataset...
Preprint
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Palaeogenomic investigation of 50,000 years of the human oral microbiome in the Iberian Mediterranean
Preprint
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The peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from...
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Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calcu...
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Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically...
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Biological invasions are one of the great threats to Earth’s ecosystems and biodiversity in the Anthropocene. However, species introductions and invasions extend deep into the human past, with the translocation of both wild and domestic species around the world. Here, we review the human translocation of wild plants and animals to the world’s islan...
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The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previ...
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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...
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The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal intro...
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Understanding how human activities have influenced the foraging ecology of wildlife is important as our planet faces ongoing and impending habitat and climatic change. We review the canine surrogacy approach (CSA)—a tool for comparing human, dog, and other canid diets in the past—and apply CSA to investigate possible ancient human resource provisio...
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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...
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Estuaries around the world are in a state of decline following decades or more of overfishing, pollution, and climate change. Oysters (Ostreidae), ecosystem engineers in many estuaries, influence water quality, construct habitat, and provide food for humans and wildlife. In North America's Chesapeake Bay, once-thriving eastern oyster (Crassostrea v...
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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 analysi...
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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...
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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 7 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 yield...
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There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relat...
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Island endemics are typically differentiated from their mainland progenitors in behavior, morphology, and genetics, often resulting from long-term evolutionary change. To examine mechanisms for the origins of island endemism, we present a phylogeographic analysis of whole mitochondrial genomes from the endangered island fox (Urocyon littoralis), en...
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Historical ecology is becoming an important focus in conservation biology and offers a promising tool to help guide ecosystem management. Here, we integrate data from multiple disciplines to illuminate the past, present, and future of biodiversity on California's Channel Islands, an archipelago that has undergone a wide range of land-use and ecolog...
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Domesticated dogs (Canis familiaris) are an important human companion around the world and have long been a focus of archaeological research. Osteometric analysis of six dogs from a Late Holocene Chumash village on Santa Rosa Island, California indicates that adults, juvenile/young adults, and a puppy were present. Similar to dogs on other Channel...