Biology subjects

Parsons, K.

Publications and source records attributed to Parsons, K..

6 recordsLinked to original sources

bioRxiv2026

Energetic misfires: Hybridization drives transgressive expression in metabolic pathways in thermally divergent Icelandic stickleback

Climate change is causing rapid changes to freshwater environments, driving selection for phenotypes that can cope with altered thermal conditions, while also changing developmental environments. This may promote local adaptation, migration to new habitats, and/or phenotypic plasticity. Climate change may also increase hybridization rates between locally adapted phenotypes, as populations migrate and spatially mix in new ways. Consequently, these conditions may facilitate the production of variation, including both adaptive and maladaptive outcomes. To examine this, we leveraged threespine stickleback (Gasterosteus aculeatus) that have locally adapted to either geothermally warmed or ambient environments in Iceland. We tested the effects of hybridization between thermal ecotypes on gene expression using a common garden experiment, where pure-strain ecotypes and their hybrids were reared under 12{degrees}C and 18{degrees}C. We performed RNA-seq on brain and liver to assess 1) ecotype divergence, 2) plasticity, and 3) the effects of hybridization and inheritance patterns. We identified a low degree of expression divergence between locally adapted ecotypes, despite a high degree of plasticity across rearing environments. Hybrid ecotypes were highly divergent from both geothermal and ambient ecotypes and exhibited transgressive expression under both rearing temperatures. Transgressive expression disrupted gene networks extensively, with broader effects at 18{degrees}C than at 12{degrees}C, primarily associated with metabolism and mitochondrial function. Hybridization between locally adapted thermal ecotypes appears to largely disrupt genes associated with energy balance and metabolic function. While demonstrating mechanisms underlying the rapid evolution of reproductive isolation, these findings also provide insights for how populations may cope or fail within a warming world.

evolutionary biology↗

bioRxiv2025

Modeling cetacean eDNA distribution along the Washington coast using metabarcoding from opportunistic samples and generalized additive models

Effective cetacean conservation depends on robust monitoring, yet traditional visual and passive-acoustic surveys have constraints. We evaluated environmental DNA (eDNA) metabarcoding coupled with species distribution modeling (SDM) as a tool to study habitat use of cetaceans along the Washington State coast, USA. Seawater was collected at the surface and at a 50 m depth from 43 sites (86 samples) during the 2019 U.S.-Canada Integrated Ecosystem & Acoustic-Trawl Survey. A partial section of the mitochondrial control region was amplified with cetacean - specific primers, sequenced on an Illumina MiSeq, and taxonomically assigned with a curated reference database. Nine species were detected; we modelled the three most frequent: Pacific white-sided dolphin (Lagenorhynchus obliquidens) (10 detections), humpback whale (Megaptera novaeangliae) (8 detections), and Rissos dolphin (Grampus griseus) (6 detections). Binomial generalized additive models related presence-absence to bathymetry, distance to shore, longitude, slope, and sea-surface temperature; model performance was assessed with stratified five-fold cross-validation. SDMs explained 17-51% of null deviance and presented high specificity ([≥] 0.80). The Pacific white-sided dolphin showed the highest eDNA presence probabilities offshore, beyond the shelf break. Humpback whale eDNA presence probabilities showed hotspots along the shelf break with secondary high-probability patches in near-shore waters. Rissos dolphin eDNA presence probabilities were elevated in offshore zones characterized by steep bathymetric gradients, particularly northwest of the sampled transect. These spatial patterns are consistent with historical visual-acoustic records, suggesting that eDNA-informed SDMs can capture cetacean habitat use. This proof of concept indicates that combining eDNA detections with flexible SDMs could provide a cost-effective, non-invasive complement to conventional surveys and may offer a scalable pathway for marine-mammal monitoring and spatial planning.

genomics↗

bioRxiv2025

Parallel adaptation to geothermally-warmed habitats due to common structural variation and functional developmental pathways

Climate change is causing rapid increases in temperature which drives genomic changes tied to adaptation. However, predicting the outcomes of climate change presents challenges as the anticipated conditions have yet to be experienced by natural populations. Modelling and lab experiments suggest that natural populations will experience shifts in life history, physiology, phenology, and ecology, but the underlying genomic mechanisms involved are unknown. However, some contemporary natural populations experience habitat warming through geothermal activity and can provide valuable insights into evolutionary responses. Geothermally warmed habitats should impose strong selection on ectotherms compared to ambient habitats as they increase metabolic demands, alter developmental processes, and offer novel ecological conditions. We leveraged Icelandic threespine sticklebacks (Gasterosteus aculeatus) from populations that have adaptively diverged along a geothermal/ambient habitat axis. We obtained 173,485 single nucleotide polymorphisms (SNPs) across four independent instances of population divergence using whole genome sequencing. While the majority of genomic differentiation between geothermal/ambient ecotypes was non-parallel, the MAPK signalling pathway appeared across all ecotype pairs. We also identified a putative inversion located on chromosome XXI which appears to drive parallel genomic differentiation between geothermal and ambient ecotypes. Candidate genes within the putative inversion correspond to metabolic adaptations, including regulation of appetite and fat content. Appetite level showed strong heritable divergence between ecotypes, while the rate of weight loss during starvation and fat levels differed between ecotypes. Overall, both polygenic adaptation and parallel structural variation appeared to be key genomic mechanisms for adaptation to geothermally warmed environments. While allelic divergence was largely unique across populations, it resulted in similar functional phenotypic outcomes. Thus, structural and allelic variation both operate to facilitate adaptation to warming environments. Therefore, while management from a genomic perspective will play a role in mitigating the effects of climate change, this study suggests that consideration of functional molecular pathways will be key to conservation but with precise changes being difficult to predict due to the highly polygenic nature of thermal adaptation.

evolutionary biology↗

bioRxiv2024

The diverse diet of southern Alaska resident killer whales changes across spatiotemporally distinct foraging aggregations

Top predators influence ecological communities in part through the prey they consume, which they often track through cycles of seasonal and geographic abundance. Killer whales are top predators in the marine ecosystem. In the North Pacific, they have diverged into three distinct lineages with different diets, of which the fish-eating type is most abundant. In this study, we examine the diet of the southern Alaska resident killer whale population across three major foraging aggregations. We take advantage of two unique sampling methods to reveal strong spatiotemporal patterns in diet from May through September. Chinook, chum, and coho salmon were each dominant in different locations and times, with substantial dietary contributions from Pacific halibut, arrowtooth flounder, and sablefish. The diverse, location-specific, and seasonal nature of the feeding habits of this marine top predator highlights the importance of diet sampling across broad spatiotemporal and population-level scales.

ecology↗

bioRxiv2022

Toward Quantitative Metabarcoding

Amplicon-sequence data from environmental DNA (eDNA) and microbiome studies provides important information for ecology, conservation, management, and health. At present, amplicon-sequencing studies - known also as metabarcoding studies, in which the primary data consist of targeted, amplified fragments of DNA sequenced from many taxa in a mixture - struggle to link genetic observations to underlying biology in a quantitative way, but many applications require quantitative information about the taxa or systems under scrutiny. As metabarcoding studies proliferate in ecology following decades of microbial and microbiome work using similar techniques, it becomes more important to develop ways ot make them quantitative to ensure that their conclusions are adequately supported. Here we link previously disparate sets of techniques for making such data quantitative, showing that the underlying PCR mechanism explains observed patterns of amplicon data in a general way. By modeling the process through which amplicon-sequence data arises, rather than transforming the data post-hoc, we show how to estimate the starting DNA proportions from a mixture of many taxa. We illustrate how to calibrate the model using mock communities and apply the approach to simulated data and a series of empirical examples. Our approach opens the door to improve the use of metabarcoding data in a wide range of applications in ecology, public health, and related fields.

ecology↗

bioRxiv2019

Temperature preference does not evolve in sticklebacks despite multigenerational exposure to elevated temperatures

Given the threat of climate change to biodiversity, a growing number of studies are investigating the potential for organisms to adapt to rising temperatures. Earlier work has predicted that physiological adaptation to climate change will be accompanied by a shift in temperature preferences, but empirical evidence for this is lacking. Here, we test whether exposure to different thermal environments has led to changes in preferred temperatures in the wild. Our study takes advantage of a natural experiment in Iceland, where freshwater populations of threespine sticklebacks (Gasterosteus aculeatus) are found in waters warmed by geothermal activity year-round (warm habitats), adjacent to populations in ambient-temperature lakes (cold habitats). We used a shuttle-box approach to measure temperature preferences of wild-caught sticklebacks from three warm-cold population pairs. Our prediction was that fish from warm habitats would prefer higher water temperatures than those from cold habitats. We found no support for this, as fish from both warm and cold habitats had an average preferred temperature of 13{degrees}C. Thus, our results challenge the assumption that there will be a shift in ectotherm temperature preferences in response to climate change. In addition, since warm-habitat fish can persist at relatively high temperatures despite a lower temperature preference, this suggests that preferred temperature alone may be a poor indicator of a populations adaptive potential to a novel thermal environment.

evolutionary biology↗