Biology subjects

Fleischer, R. C.

Publications and source records attributed to Fleischer, R. C..

5 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↗

bioRxiv2025

President Roosevelt's lions reveal a century of population fragmentation in Africa's largest carnivore

Over the past century, lion (Panthera leo) populations across Africa have experienced rapid and severe declines. Despite this, East Africa is considered a modern-day lion stronghold. Here, we use whole-genome sequencing of both recent and historical lion populations, primarily collected during the Smithsonians Roosevelt East African (1909-1911) and Rainey (1911-1912) Expeditions, to investigate changes in population structure, connectivity, and diversity over the last [~]100 years in East Africa. We find a clear signal of population fragmentation when comparing historical (1896-1946) and recent (1990-present) lion populations. Our analyses reveal genetic distinctions between remaining lion populations in Kenya and Tanzania and document loss of genetic diversity over time including reduced heterozygosity and the accumulation of runs of homozygosity. We detect a severe bottleneck in both Kenya and Tanzania approximately 25 generations ago, coinciding with a severe rinderpest outbreak in the region that is known to have decimated bovid and ultimately carnivore populations in the area. Nevertheless, modern lions in East Africa still exhibit overall high levels of diversity and low levels of inbreeding. Our results provide direct evidence of the effects of increasing habitat fragmentation and the significance of temporal data for contextualizing current patterns of population connectivity and diversity.

evolutionary biology↗

bioRxiv2024

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error rates in sequence data and uncertainty in the fossil record. Here, we directly estimate de novo germline mutation rates for all extant members of Panthera, as well as the closely related outgroup Neofelis nebulosa, using pedigrees. We use a previously validated pipeline (RatesTools) to calculate mutation rate for each species and subsequently explore the impacts of the novel rates on historic effective population size estimates in each of these charismatic felids of conservation concern. Importantly, we find that the choice of reference genome, the data type and coverage, and the individual all impact estimates of the mutation rate. Despite these stochastic effects, we inferred that base pair mutation rates for all species fell between 0.5 and 1.4e-08 per generation per base pair (mean 0.81e-08 {+/-} 0.35-08 across Pantherinae). Our results provide a cautionary view on inter-species mutation rate comparisons, given the error associated with the reference genome choice and sequencing depth of coverage of the individuals.

evolutionary biology↗

bioRxiv2022

Re-assessing niche partitioning in MacArthur's Warblers: foraging behavior, morphology, and diet metabarcoding in a phylogenetic context

Due in large part to MacArthurs classic 1958 paper, wood-warblers (Parulidae) are ecological icons, textbook protagonists of a story of competition and niche partitioning. As the story goes, subtle differences in foraging behavior are the principal means by which these nearly morphologically indistinguishable species are able to co-occur and avoid extinction. Yet, MacArthurs study was in fact quite limited in scale, and he said little about the relevance of evolution to the study system. Here, we reassess MacArthurs conclusions across an expanded set of syntopic warbler species in a forest in northern New York. We combine morphometrics, quantitative foraging data, and fecal metabarcoding--a direct measure of warbler diet--to study competition and niche partitioning in an evolutionary framework. We find close and kinematically realistic relationships between morphology and foraging behavior, but little connection between warbler ecomorphology and the 2,882 invertebrate taxa detected in their diets. Instead, diet remains phylogenetically conserved--closely related warblers eat similar suites of invertebrates, regardless of where they forage. Finally, we present evidence that these species not only partition niche space in the present day, but that competition has shaped their behaviors over evolutionary time. MacArthur (1958) may have drawn a few incorrect inferences, but his overall conclusion that evolved differences in foraging position, driven by competition among close relatives, does indeed appear to be a key reason these warblers can occur in such close sympatry.

evolutionary biology↗

bioRxiv2022

Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum

Culex quinquefasciatus, the mosquito vector of avian malaria in Hawai{square}i, became established in the islands in the 1820s and the deadly effects of malaria on endemic bird species have been documented for many decades. To evaluate the gene expression response of the mosquito to the parasite, we let the offspring of wild-collected Hawaiian Cx. quinquefasciatus feed on a domestic canary infected with Plasmodium relictum GRW4 freshly isolated from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. We sequenced the individual transcriptomes of five infected and three uninfected individual mosquitoes at three different stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands. Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor. Overall, the gene expression response of Hawaiian Culex exposed to a Plasmodium infection intensity that occur naturally in Hawaii was low, but more pronounced during ookinete invasion. The low fitness costs often documented in Culex infected with avian Plasmodium likely reflect the relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism.

microbiology↗