Logan Kistler

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

Abstract The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a 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 may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.

Cultigen Chenopods in the Americas: A Hemispherical Perspective

In this chapter, we summarize recent contributions made by archaeologists and researchers in other disciplines toward understanding the many factors involved in the domestication of Chenopodium berlandieri in North America and Chenopodium quinoa in South America. We focus on studies of seed morphology and molecular genetics, which have aided in clarifying the trajectories of domestication for both species. The comparison of these trajectories allows us to examine the similarities and differences in the evolutionary, economic, social, and political processes that contributed not only to their domestication but the roles they played in the later agricultural and sociopolitical systems in their respective regions. The eastern North American cultigen chenopod eventually lost its role as a key component of pre-Columbian agricultural systems, whereas quinoa flourished in the Andes and has attained global super-food status today. Still, both of these crops constituted food that was central to and inseparable from considerations of identity, status, ritual, exchange, and sociopolitical life. An appreciation of chenopods as important foods in each region allows us to reflect upon their diverse evolutionary pathways and the significance of individual foods and broader cuisines within regional histories.

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.

A re-evaluation of the domestication bottleneck from archaeogenomic evidence

Domesticated crops show a reduced level of diversity that is commonly attributed to the “domestication bottleneck”; a drastic reduction in the population size associated with subsampling the wild progenitor species and the imposition of selection pressures associated with the domestication syndrome. A prediction of the domestication bottleneck is a sharp decline in genetic diversity early in the domestication process. Surprisingly, archaeological genomes of three major annual crops do not indicate that such a drop in diversity occurred early in the domestication process. In light of this observation, we revisit the general assumption of the domestication bottleneck concept in our current understanding of the evolutionary process of domestication.

Archaeogenomics and Crop Adaptation

The genetic history of domestic plants is complex, protracted, and unique to often very specific factors including location, human intent, and the wider environment. In addition to well-addressed questions of domestication syndrome, and conscious versus unconscious selection, the issue of domestication poses a plethora of more nuanced questions, in particular regarding plants’ abilities to adapt to new environments, and the genomic scars those forced changes leave behind. Ancient DNA from archaeobotanical remains offers a window through which we are now beginning to unravel these histories, in a large part through the technical advances in sequencing technologies and theoretical advances in genome evolution. In this chapter, we will explore how plant archaeogenomics is characterized in a large part by plasticity, of genome size, genome activity, and transposable elements, through specific mechanisms including introgression, mutation load, and stress response. We will also examine the various substrates from which invaluable information can be recovered, by no means limited to DNA from seeds.

SONiCS: PCR stutter noise correction in genome-scale microsatellites

Motivation Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymerase Chain Reaction (PCR) cycle numbers needed for target capture experiments create genotyping noise through polymerase slippage known as PCR stutter. Results We developed SONiCS-Stutter mONte Carlo Simulation-a solution for stutter correction based on dense forward simulations of PCR and capture experimental conditions. To test SONiCS, we genotyped a 2499-marker STR panel in 22 humpback dolphins (Sousa sahulensis) using target capture, and generated capillary-based genotypes to validate five of these markers. In these 110 comparisons, SONiCS showed a 99.1% accuracy rate and a 98.2% genotyping success rate, miscalling a single allele in a marker with low sequence coverage and rejecting another as un-callable. Availability and implementation Source code and documentation for SONiCS is freely available at https://github.com/kzkedzierska/sonics. Raw read data used in experimental validation of SONiCS have been deposited in the Sequence Read Archive under accession number SRP135756. Supplementary information Supplementary data are available at Bioinformatics online.

Do aye-ayes echolocate? Studying convergent genomic evolution in a primate auditory specialist

Several taxonomically distinct mammalian groups – certain microbats and cetaceans (e.g. dolphins) – share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a derived auditory processing system. Aye-ayes tap rapidly along the surfaces of dead trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation. Here we investigated whether there are signals of genomic convergence between aye-ayes and known mammalian echolocators. We developed a computational pipeline (BEAT: Basic Exon Assembly Tool) that produces consensus sequences for regions of interest from shotgun genomic sequencing data for non-model organisms without requiring de novo genome assembly. We reconstructed complete coding region sequences for the seven convergent echolocating bat-dolphin genes for aye-ayes and another lemur. Sequences were compared in a phylogenetic framework to those of bat and dolphin echolocators and appropriate non-echolocating outgroups. Our analysis reaffirms the existence of amino acid convergence at these loci among echolocating bats and dolphins; we also detected unexpected signals of convergence between echolocating bats and both mice and elephants. However, we observed no significant signal of amino acid convergence between aye-ayes and echolocating bats and dolphins; our results thus suggest that aye-aye tap-foraging auditory adaptations represent distinct evolutionary innovations. These results are also consistent with a developing consensus that convergent behavioral ecology is not necessarily a reliable guide to convergent molecular evolution.