Biology subjects

Tisthammer, K. H.

Publications and source records attributed to Tisthammer, K. H..

3 recordsLinked to original sources

bioRxiv2025

Evidence of positive polygenic selection following a series of environmental and demographic disasters in Pacific herring

The causes and consequences of population collapse and recovery are difficult to discern and therefore predict because historical data are often sparse, and environmental drivers may interact in complex ways. Yet the influence of environmental change can imprint in contemporary and historic DNA sequences, thereby offering clues about drivers of population dynamics. The Prince William Sound (PWS) stock of Pacific herring famously collapsed in the early 1990s following the Exxon Valdez oil spill (EVOS), yet the causes of the collapse and reasons for a persistent lack of recovery are controversial. Three seasons after the spill, the PWS population declined precipitously, coincident with repeated disease outbreaks, and has remained small across the three decades since. We use population genetics as a forensic tool to gain insight into the causes and consequences of the collapse. We tracked genome-wide genetic variation across time, spanning the period immediately after the spill but preceding the collapse (1991) and across three subsequent decades to 2017. We compared genetic change through time between the PWS population and two reference Alaska populations. We detected high genetic differentiation between the Bering Sea and the Gulf of Alaska, and relatively small but significant genetic structure within the Gulf of Alaska. No loss of genome-wide genetic diversity was observed in the PWS population after the collapse. We did not detect any evidence for selective sweeps at individual loci. However, using sensitive temporal covariance methods, we detected significant signatures of positive polygenic adaptation in the PWS population but not in either of the reference populations. Gene functional enrichment analysis is consistent with selection acting on immune function and pathways that regulate crude oil developmental toxicity in the period following the spill and collapse. This suggests that environmental perturbations unique to the PWS region, including oil spills and disease outbreaks, affected the fitness of resident fish, and shifted their population genetic trajectory.

evolutionary biology↗

bioRxiv2020

Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus

Like many viruses, Hepatitis C Virus (HCV) has a high nutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts, are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes. Author SummaryUnderstanding how viruses evolve within patients is important for combatting viral diseases, yet studying viruses within patients is difficult. Laboratory experiments are often used to understand the evolution of viruses, in place of assessing the evolution in natural populations (patients), but the dynamics will be different. In this study, we aimed to understand the within-patient evolution of Hepatitis C virus, which is an RNA virus that replicates and mutates extremely quickly, by taking advantage of high-throughput next generation sequencing. Here, we describe the evolutionary patterns of Hepatitis C virus from 195 patients: We analyzed mutation frequencies and estimated how costly each mutation was. We also assessed what factors made a mutation more costly, including the costs associated with drug resistance mutations. We were able to create a genome-wide fitness map of within-patient mutations in Hepatitis C virus which proves that, with technological advances, we can deepen our understanding of within-patient viral evolution, which can contribute to develop better treatments and vaccines.

evolutionary biology↗

bioRxiv2019

Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawai i. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04 [~] 0.19, P < 0.001), but no significant isolation by distance between islands. In contrast, a third site with a less impacted nearshore site showed no significant structure. Strikingly, corals from the two impacted nearshore sites on different islands over 100km apart with similar environmentally stressful conditions were genetically closer (FST[~] 0, P = 0.733) than those within a single location less than 2 km apart (FST= 0.041[~]0.079, P < 0.01). Our results suggest that ecological boundaries appear to play a strong role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow may be explained by disruptive selection across contrasting habitats.

genetics↗