Biology subjects

Kapp, J. D.

Publications and source records attributed to Kapp, J. D..

8 recordsLinked to original sources

bioRxiv2026

The DNA Legacy of Thomas Jefferson

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 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.

genomics↗

bioRxiv2026

First Plant sedaDNA assemblage from California reveals ecological stability throughout 10,000 years of human presence at Lake Elsinore

As we face the sixth mass extinction, understanding how ecosystems have persisted--or collapsed--through millennia of changing climates and human activity is critical for preventing biodiversity loss. We bolstered the past 24,000 years of plant and mammal records using targeted capture of ancient sedimentary DNA (sedaDNA) from Southern Californias Lake Elsinore, a cultural center for the Payomkawichum (Luiseno), Cahuilla, and other Peoples. Our sedaDNA approach generated a diverse dataset that included 18 plant orders not previously documented from Lake Elsinore. We paired these records with local measurements and paleo evidence of fire regimes, climate, demographic history, and ethnobotanical knowledge. We find that ecological stability persisted for 10,000 years of continuous human presence, reflecting ecosystem resilience through major climatic shifts, altered fire regimes, and varying intensities of Indigenous land use. SedaDNA revealed increased availability of food, medicinal, and utilitarian plant taxa during this period of botanical stability, shedding light on ancient fire-environment-human interactions that can inform contemporary management strategies.

paleontology↗

bioRxiv2025

Paleogenomic insight into the collapse, recovery, and management of American bison

American bison were pushed to the brink of extinction by the 20th century. This bottleneck and the fragmented nature of remnant populations pose challenges to their resilience, as does human-facilitated admixture between bison subspecies and with cattle. To contextualize current diversity, we sequenced 115 ancient and 45 modern bison genomes from across North America dating back within the last [~]20,000 years. Past bison populations were highly connected, in contrast to structured modern herds. Modern wood bison carry plains bison ancestry from 1920s translocations, while many bison lack cattle ancestry that has previously been believed to be ubiquitous. Our findings reveal the legacy of human impacts on bison in the context of modern conservation and highlight the applicability of ancient DNA for guiding wildlife restoration.

evolutionary biology↗

bioRxiv2025

Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

Predicting the genetic consequences of population decline is a major problem in conservation genomics. Time lags following demographic bottlenecks can delay genomic erosion and make it difficult to determine a populations current and future risk, especially when pre-bottleneck genomic baselines are unavailable. Black abalone (Haliotis cracherodii) suffered a severe disease bottleneck in the 1980s, resulting in an estimated 99% population decline. However, recent work found surprisingly high genetic diversity and little population structure in current black abalone populations, raising questions of whether genomic erosion has been delayed. To investigate this, we applied ancient DNA methods to pre-bottleneck abalone shells, generating 59 whole genomes including one 34-fold coverage genome from a 1,500-year-old specimen. These data show that heterozygosity, runs of homozygosity, genetic load and population structure remained stable up to and following the bottleneck. Simulations reveal that this stability is consistent with even severe bottleneck scenarios because too few generations have lapsed since the decline. Projections suggest that future genomic erosion may be avoided even in limited recovery scenarios. Following the bottleneck we observe widespread balancing selection at genes with immune function, along with parallel increases of two inversions on separate chromosomes that are in linkage disequilibrium, where the disease bottleneck was most severe. Altogether, these findings explain why genomic change has thus far been limited, outline recovery scenarios that minimize genomic erosion, and identify loci likely that may harbor adaptive variation key to the success of future black abalone populations.

evolutionary biology↗

bioRxiv2024

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species recovery.

evolutionary biology↗

bioRxiv2021

A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data. Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern. Nonetheless, given what is known from well-studied circulating variants of concern, it seems unlikely that the lineage could pose larger concerns for human health than many already globally distributed lineages. Our work highlights a need for rapid turnaround time from sequence generation to submission and improved sequence quality control that removes submission bias. We identify promising paths toward this goal.

genomics↗

bioRxiv2018

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny.

Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery within the {small tilde}0.5 million years (Ma) time range3. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older biomolecular information4, though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae5-7 using {small tilde}1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)8. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Mercks rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

evolutionary biology↗

bioRxiv2017

A new genus of horse from Pleistocene North America

The extinct \"New World stilt-legged\", or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event.

paleontology↗