Courtney A. Hofman

Allegations that Thomas Jefferson fathered the children of the enslaved Sally Hemings emerged in the context of U.S. presidential politics in the late 1700s and early 1800s and entailed strongly contested denials and affirmations by family members, biographers, and historians ever since. Previous analysis of Y chromosome markers in contemporary members of the Jefferson and Hemings patrilines was consistent with the paternity hypothesis but rejected by those who pointed out that, absent Jefferson’s DNA and its direct comparison to the DNA of possible descendants, other Jefferson males could have fathered Sally Hemings’ children. In this study, we developed an innovative technique to recover DNA from multiple rootless hair samples in a museum collection whose provenance, mitochondrial genomes, Y chromosome markers, and identity to each other indicate that these hairs and the DNA from them are from Thomas Jefferson. Using these DNA data, we find clear evidence of Thomas Jefferson ancestry in descendants of both his wife Martha Wayles Jefferson and Sally Hemings. We measured the amount of identical-by-descent DNA shared between Thomas Jefferson and his known and putative descendants. We find that the amount of shared Jefferson DNA is more likely under the model of direct Thomas Jefferson paternity than other proposed scenarios.

Objectives: Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452–1485). Materials and Methods: Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of nearly 400 million reads. The metagenomic data were taxonomically profiled and compared to new and previously published dental calculus metagenomes from England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Sequencing data were de novo assembled, and metagenome‐assembled genomes assigned to the genus Tannerella were investigated for phylogenetic relatedness and virulence. Putative dietary DNA was assessed for authenticity. Results: The dental calculus of King Richard III was well‐preserved and yielded an exceptionally high quantity of DNA. Oral microbiome species diversity fell within the range previously observed among other northern European populations, suggesting that a royal lifestyle and a rich diet did not substantially impact his oral microbiota. The reconstructed Tannerella genomes contained many virulence factors found today among oral Tannerella species. No putative dietary DNA could be authenticated. Discussion: The dental calculus of King Richard III produced one of the richest ancient oral metagenomes published to date, yet the species diversity was indistinguishable from that of commoners living in northern Europe over the last 7000 years. Insufficient plant and animal DNA were recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA even when exceptionally well‐preserved.

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.

Convergence provides strong evidence for adaptation, reflecting similar responses to recurring selection pressures. Waterfowl (order Anseriformes) have repeatedly evolved morphotypes putatively correlated with foraging ecology (e.g., dabbler, grazer, diver), making them an ideal model for testing hypotheses of adaptive evolution. Here, we estimated the most robust time-calibrated phylogenetic tree for the waterfowl to date and quantified the shape of the skull, femur, tibiotarsus, and tarsometatarsus of 118 extant waterfowl species using geometric morphometrics. Multivariate generalized evolutionary models provide strong support for convergent phenotypic evolution across lineages that share dietary characteristics. We recovered a significant relationship between the evolution of diet and foraging behavior and the evolution of skull shape. We found a stronger correlation between the evolution of foraging behavior and the evolution of hindlimb shape, but diet evolution was also significantly related to hindlimb shape. Derived terrestrial and diving lineages consistently showed greater rates of phenotypic evolution than surface swimming and wading lineages. We also find evidence for integration between the hindlimb elements and the skull. These results suggest that the morphological diversity of waterfowl is largely explained by adaptive evolution in response to different foraging ecologies.

Metagenomic investigation of archaeological dental calculus has provided insights into the changing oral health, disease, and diet of past human societies, but little is known about the oral microbiota of exceptionally high-status individuals, whose diet and lifestyle sharply differed from the general population. Here we analyze the dental calculus metagenome of King Richard III of England (1452-1485) and compare it to new and previously published dental calculus metagenomes from predominantly non-elite contexts in England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Deep sequencing and de novo assembly enabled the investigation of metagenome-assembled genomes (MAGs) from periopathogens within the genus Tannerella . DNA preservation within the dental calculus of King Richard III was found to be exceptional, yielding an extraordinarily well-preserved oral microbiota. Oral microbiome species diversity fell within the range previously observed among other northern European populations over the past 7,000 years, suggesting that a royal lifestyle and a rich diet did not substantially shift his oral microbiome composition. Reconstructed Tannerella genomes contained many virulence factors found today among periopathogens, including Tannerella forsythia . Insufficient plant and animal DNA was recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA for dietary reconstruction, even when well-preserved. The dental calculus of King Richard III has produced one of the richest and best preserved ancient oral metagenomes studied to date and contributes to understanding the ecology and evolution of the human oral microbiome.

People have influenced Earth’s biodiversity for millennia, including numerous introductions of domestic and wild species to islands. Here, we explore the origins and ecology of the Santa Catalina Island ground squirrel (SCIGS; Otospermophilus beecheyi nesioticus ), one of only five endemic terrestrial mammals found on California’s Santa Catalina Island. We synthesized all records of archaeological/palaeontological SCIGS, conducted radiocarbon dating and stable isotope analysis of the potentially earliest SCIGS remains and performed genetic analysis of modern SCIGS. Squirrels were not identified in island palaeontological deposits, but at least 12 island archaeological sites contain SCIGS bones, including some that are butchered or burned. All directly dated SCIGS bones are Late Holocene in age and younger than approximately 1290 cal BP. The first mitochondrial genome for modern Otospermophilus beecheyi and 15 modern SCIGS mitogenomes document at least one introduction of squirrels. Stable isotope data indicate variable SCIGS diets and potential subsidies from marine environments to terrestrial plants consumed by some individuals. We cannot rule out a natural overwater dispersal, but the earliest SCIGS remains post-date the earliest evidence for people by several millennia and, along with other lines of evidence, support a human-assisted translocation of squirrels during the Late Holocene. These data illustrate the important role of Indigenous people in shaping and enhancing island biodiversity and ecology around the world.

Convergence provides strong evidence for adaptive evolution as it reflects shared adaptive responses to the same selection pressures. The waterfowl (order Anseriformes) are an ideal group in which to study convergent evolution as they have repeatedly evolved morphotypes putatively correlated with diet (i.e., dabbler, grazer, diver). Here, we construct the most robust evolutionary hypothesis to date for waterfowl and reveal widespread morphological convergence across the order. We quantified the shape of the skull and hindlimb elements (femur, tibiotarsus, and tarsometatarsus) of 118 species of extant waterfowl using geometric morphometrics. Multivariate generalized evolutionary models provide strong support for a relationship between dietary ecology and skull shape, and evidence for convergent evolution across lineages that share dietary niches. Foraging behavior better explained the evolution of hindlimb shape, but diet still contributed significantly. We also find preliminary evidence for integration across all three measured hindlimb elements with each other and with the skull. We demonstrate that dietary ecology drives morphological convergence within waterfowl, that this convergent evolution involves multiple integrated skeletal structures, and that morphological changes are associated with shifts in the rate of phenotypic evolution.