Biology subjects

Thompson, M. J.

Publications and source records attributed to Thompson, M. J..

9 recordsLinked to original sources

bioRxiv2026

Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life

Chromosome number shapes genome organization, recombination, and speciation, yet how fast it evolves across the tree of life has never been measured. We analyzed 63,682 karyotypes across 55 eukaryotic clades and found that dysploidy rates vary by 844-fold, from approximately 0.0008 to 0.7 events per million years. This variation does not follow kingdom boundaries or deep phylogeny; intraclade variance exceeds interclade differences by more than an order of magnitude. Even birds, the textbook example of chromosomal stasis, exceed the global median rate once microchromosome dynamics are resolved. Contrasting the stasis of Odonata with the volatility of Orchidaceae reveals that life history and population structure, rather than deep phylogenetic constraints, govern the tempo of karyotypic change.

evolutionary biology↗

bioRxiv2024

Asynchronous subunit transitions precede acetylcholine receptor activation

Rapid communication at synapses is facilitated by postsynaptic receptors, which convert a chemical signal into an electrical response. In the case of ligand-gated ion channels, agonist binding triggers rapid transition through a series of intermediate states leading to a transient open-pore conformation. These transitions are usually framed in terms of a mechanism where agonist binding and channel activation are separate events. Here, we collect cryo-EM images over a range of agonist concentrations to define structures of the muscle-type nicotinic acetylcholine receptor in unliganded, mono-liganded, and di-liganded states. We show that agonist binding to a single agonist site stabilizes an intermediate state where an entire principal agonist-binding subunit has transitioned to an active-like conformation, while the other unoccupied principal subunit remains inactive, albeit poised for activation. Binding of agonist to the second agonist site fully activates the remaining subunits leading to hydration of the ion pore. Uniting this cryo-EM derived intermediate structure with single-channel recordings leads to a model where individual acetylcholine receptor subunits asynchronously undergo conformational transitions, and thus a sequential activation mechanism that has implications for the entire superfamily of pentameric ligand-gated ion channels.

neuroscience↗

bioRxiv2024

Tit wit: environmental and genetic drivers of cognitive variation along an urbanization gradient

Cognitive abilities can promote acclimation and adaptation to life in cities. However, the genetic versus environmental drivers of cognition have rarely been studied in the wild and there exists a major gap concerning the role of cognition in adaptation to novel urban contexts. To address this, we evaluate cognitive variation in wild great tits (Parus major; N = 393) along an urban gradient, and decipher the genetic basis of this variation using a combination of a common garden experiment, quantitative genetic analyses, and genome-wide association studies. Specifically, we measure inhibitory control abilities which affect how animals respond to novel resources and challenges. We find that wild urban and forest tits do not clearly differ in inhibitory control performance (number of errors or the latency to escape) during a motor detour task; a result that was consistent in birds from urban and forest origins reared in a common garden (N = 73). Cognitive performance was repeatable (R = 0.35 - 0.38) and showed low to moderate heritability in the wild (h2= 0.16 - 0.28 using social and genomic pedigrees). We identified five SNPs that were significantly associated with the number of errors during the task, explaining 21% of the cognitive variation. These SNPs are linked to genes related to serotonergic and dopaminergic systems that are known to play important roles in cognition. Altogether, our study finds limited evidence that inhibitory control abilities have evolved under novel urban contexts, yet reveals a genetic basis of this cognitive trait in great tits.

animal behavior and cognition↗

bioRxiv2024

The city and forest bird flock together in a common garden: genetic and environmental effects drive urban phenotypic divergence

Urban phenotypic divergences are documented across diverse taxa, but the underlying genetic and environmental drivers behind these phenotypic changes are unknown in most wild urban systems. We conduct a common garden experiment using great tit (Parus major) eggs collected along an urbanization gradient to: 1) determine whether documented morphological, physiological, and behavioural shifts in wild urban great tits are maintained in birds from urban and forest origins reared in a common garden (N = 73) and 2) evaluate how different sources of genetic, early maternal investment, and later environmental variation contributed to trait variation in the experiment. In line with the phenotypic divergence in the wild, common garden birds from urban origins had faster breath rates (i.e., higher stress response) and were smaller than birds from forest origins, while wild differences in aggression and exploration were not maintained in the experiment. Differences between individuals (genetic and environmentally induced) explained the most trait variation, while variation among foster nests and captive social groups was limited. Our results provide trait-specific evidence of evolution in an urban species where genetic change likely underlies urban differences in morphology and stress physiology, but that urban behavioural divergences are more strongly driven by plasticity.

evolutionary biology↗

bioRxiv2021

A global meta-analysis reveals more variable life histories in urban birds compared to their non-urban neighbours

Cities pose a major ecological challenge for wildlife worldwide. Phenotypic variation, which can result from underlying genetic variation or plasticity, is an important metric to understand eco-evolutionary responses to environmental change. Recent work suggests that urban populations might have higher levels of phenotypic variation than non-urban counterparts. This prediction, however, has never been tested across species nor over a broad geographical range. Here, we conduct a meta-analysis of the avian literature to compare urban versus non-urban means and variation in phenology (i.e., lay date) and reproductive effort (i.e., clutch size, number of fledglings). First, we show that urban populations reproduce earlier and have smaller broods than non-urban conspecifics. Second, we show that urban populations have higher phenotypic variation in laying date than non-urban populations. This result arises from differences between populations within breeding seasons, conceivably due to higher landscape heterogeneity in urban habitats. These findings reveal a novel effect of urbanisation on animal life-histories with potential implications for species adaptation to urban environments (which will require further investigation). Higher variation in phenology in birds subjected to urban disturbance could result from plastic responses to a heterogeneous environment, or from higher genetic variation in phenology, possibly linked to higher evolutionary potential.

evolutionary biology↗

bioRxiv2021

DNA Methylation Networks Underlying Mammalian Traits

Epigenetics has hitherto been studied and understood largely at the level of individual organisms. Here, we report a multi-faceted investigation of DNA methylation across 11,117 samples from 176 different species. We performed an unbiased clustering of individual cytosines into 55 modules and identified 31 modules related to primary traits including age, species lifespan, sex, adult species weight, tissue type and phylogenetic order. Analysis of the correlation between DNA methylation and species allowed us to construct phyloepigenetic trees for different tissues that parallel the phylogenetic tree. In addition, while some stable cytosines reflect phylogenetic signatures, others relate to age and lifespan, and in many cases responding to anti-aging interventions in mice such as caloric restriction and ablation of growth hormone receptors. Insights uncovered by this investigation have important implications for our understanding of the role of epigenetics in mammalian evolution, aging and lifespan.

evolutionary biology↗

bioRxiv2021

A mammalian methylation array for profiling methylation levels at conserved sequences

Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures 36k CpGs that are well conserved across mammalian species. We designed a set of probes on the array that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.

bioinformatics↗

bioRxiv2020

An epigenetic clock to estimate the age of living beluga whales

IntroductionDNA methylation data facilitate the development of accurate molecular estimators of chronological age, or epigenetic clocks. We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. Methods and ResultsWe used a custom methylation array to measure methylation levels at 37,491 cytosine-guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R2 = 0.92 for the training data; and an R2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross-validation. We applied the epigenetic clock to an independent data set of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. DiscussionThe epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.

developmental biology↗

bioRxiv2018

Do city cachers store less? The effect of urbanization and exploration on spatial memory in individual scatter hoarders

Urbanization has been shown to affect a variety of traits in animals, including their physiology, morphology, and behaviour, but it is less clear how cognitive traits are modified. Urban habitats contain artificially elevated food sources, such as bird feeders, that are known to affect the foraging behaviours of urban animals. As of yet however, it is not known whether urbanization and the abundance of supplemental food during the winter reduce caching behaviours and spatial memory in scatter hoarders. We aimed to examine individual variation in caching and spatial memory between and within urban and rural habitats to determine i) whether urban individuals cache less frequently and perform less accurately on a spatial task, and ii) explore, for the first time in scatter hoarders, whether slower explorers perform more accurately on a spatial task, indicating a speed-accuracy trade-off within individuals. We assessed spatial memory of wild-caught black-capped chickadees (Poecile atricapillus; N = 96) from 14 sites along an urban gradient. While the individuals that cached more food in captivity were all from rural environments, we find no clear evidence that caching intensity and spatial memory accuracy differ along an urban gradient, and find no significant relationship between spatial cognition and exploration of a novel environment within individuals. However, individuals that performed more accurately also tended to cache more frequently, suggesting for the first time that the specialization of spatial memory in scatter hoarders may also occur at the level of the individual in addition to the population and species levels.

animal behavior and cognition↗