Biology subjects

Kistler, L.

Publications and source records attributed to Kistler, L..

9 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

A depositional taphonomy model for sedimentary ancient DNA based on biotic profiles of contrasting sedimentation regimes

Sedimentary ancient DNA (sedaDNA) has become an important tool in Quaternary Science, but still little is understood of its taphonomy and whether sedaDNA represents the local vicinity or originates from distant sources. Here we show key insights can be made about the origins of sedaDNA by integrating sedimentological and sedaDNA data into a sediment influx depositional model. We reconstruct contrasting taphonomic regimes of lacustrine, alluvial, terrestrial and permafrost systems. Lacustrine systems show signals of regional catchment sources of sedaDNA, while alluvial, terrestrial and permafrost systems show a greater influence of DNA from the immediate local environment. However, there is a prevalence of mixed ecosystem signals which may span a broad temporal timeframe if sediment reworking has occurred. The ability to distinguish between local and distal sources of sedaDNA is of major importance in the interpretation of taxonomic profiles to reconstruct palaeoenvironments.

ecology↗

bioRxiv2025

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, and selection (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

evolutionary biology↗

bioRxiv2023

Morphometrics and phylogenomics of coca (Erythroxylum spp.) illuminate its reticulate evolution, with implications for taxonomy

South American coca (Erythroxylum coca and E. novogranatense) has been a key-stone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half century, global demand for cocaine has placed this plant in the centre of armed conflict, deforestation, and explosive growth of illegal economies. While national and international agencies progress from a war on drugs policy model towards locally appropriate, data-informed strategies to tackle coca plantations, monitoring their expansion and composition remains essential. The principal means to identify coca plants is leaf morphology, yet the extent to which it is reflected in taxonomy is uncertain. Here, we analyse the consistency of the current naming system of coca and its four closest wild relatives (the coca clade), using morphometrics, phylogenomics, and population genomics. We include the name-bearing type specimens of cocas closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the rounder and more obovate leaves of certain coca varieties could be associated with domestication syndrome of this crop. Our phylogenomic data indicate gene flow involving monophyletic clades of E. gracilipes and the E. coca clade. These results further clarify the evolution of coca and support a taxonomic framework wherein E. gracilipes is retained as a single species. Our findings have implications for the development of cost-effective genotyping methods to effectively discriminate varieties of cultural significance from high-yielding cultivars fuelling the lucrative cocaine market.

plant biology↗

bioRxiv2021

Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus spp.) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

plant biology↗

bioRxiv2020

Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi

No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal subfossil remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.

genomics↗

bioRxiv2020

Multi-proxy evidence for the impact of the Storegga Slide Tsunami on the early Holocene landscapes of the southern North Sea

Doggerland was a land mass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British land mass from the rest of Europe. The Storegga Slide, which triggered a tsunami reflected in sediment deposits in the Northern North Sea, North East coastlines of the British Isles and across the North Atlantic, was a major event during this transgressive phase. The spatial extent of the Storegga tsunami however remains unconfirmed because to date no direct evidence for the event has been recovered from the southern North Sea. We present evidence that Storegga associated deposits occur in the southern North Sea. Palaeo-river systems have been identified using seismic survey in the southwestern North Sea and sedimentary cores extracted to track the Mid Holocene inundation. At the head of one palaeo-river system near the Outer Dowsing Deep, the Southern River, we observed an abrupt and catastrophic inundation stratum. Based on lithostratigraphic, macro and microfossils and sedimentary ancient DNA (sedaDNA) evidence, supported by optical stimulation luminescence (OSL) and radiocarbon dating, we conclude these deposits were a result of the Storegga event. Seismic identification of this stratum to adjacent cores indicated diminished traces of the tsunami, largely removed by subsequent erosional processes. Our results demonstrate the catastrophic impact of Storegga within this area of the Southern North Sea, but indicate that these effects were temporary and likely localized and mitigated by the dense woodland and topography of the area. We conclude clear physical remnants of the wave are likely to be restricted to inland basins and incised river valley systems.

paleontology↗

bioRxiv2018

A domestication history of dynamic adaptation and genomic deterioration in sorghum

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated introgressions. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck but instead suggest a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially on architectural and nutritional domestication traits, and adaptation to the local environment. Later introgression between sorghum races allowed exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration was not focused on the initial stages of domestication but occurred throughout the history of cultivation.

evolutionary biology↗

bioRxiv2017

A new model for ancient DNA decay based on paleogenomic meta-analysis

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time is likely due to a bulk diffusion process, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation.

genomics↗