Biology subjects

Boyer, S.

Publications and source records attributed to Boyer, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Threat imminence and estimates of agency dictate proactive and reactive defensive behaviors in active place avoidance

Defensive survival behaviors are shaped by both danger attributes and internal physiological states. Well-characterized defensive responses depend not only on whether danger is potential or perceived, but also on its spatial and or temporal proximity. The relationship between danger imminence and defensive behaviors is referred to as the threat imminence continuum, which provides a conceptual framework bridging ecology and behavioral neuroscience. Although this theoretical framework is gaining momentum, another much less explored danger attribute is the extent to which the environment may be controllable. Most paradigms assessing defensive behaviors rely on conditioned stimuli as danger warning-signals in stable environments that hamper the study of environment controllability and its impact on defensive behaviors. To address this question, we repurposed the active place avoidance (APA) paradigm combined with supervised machine learning to characterize multivariate exploratory and defensive behaviors in male and female mice. One important benefit of APA is that it allows the study of active avoidance when the platform is rotating as well as deliberative avoidance when the platform is immobile. As such, APA is very well suited to test the impact of environment controllability on the expression of defensive behaviors. Using this unified preparation, we systematically compared quantitative danger attributes (punishment intensity, behavioral agency) across danger states (absence, presence and omission of punishment) and learning experience (early and late learning stages), while considering sex as a biological variable. Our results demonstrate that defensive behaviors depend on punishment intensity in a sex-dependent manner in APA. Defensive responses can be classified as proactive (risk assessment) or reactive (freezing, escape) in APA. Their response probability depends on behavioral agency, is mutually exclusive and depends on danger spatial proximity. Acute treatment with norepinephrine transporter blocker selectively increases reactive defensive behaviors while sparing proactive defensive behavior. Collectively, these results provide experimental evidence that environmental stability calibrate proactive and reactive defensive behaviors whose neural correlates may be divergent.

animal behavior and cognition↗

bioRxiv2026

Genetic erosion and projected habitat loss in the protected Alpine moth Actias isabellae galliaegloria (Lepidoptera: Saturniidae)

O_LIMontane and specialist insects are particularly vulnerable to habitat loss and climate change. The Spanish Moon Moth (Actias isabellae), a rare and protected species, hosts an isolated Alpine population (subspecies galliaegloria) whose conservation status remains unclear. C_LIO_LIWe combined Restriction-site Associated DNA sequencing (RADseq) and Ecological Niche Modelling (ENM) to assess its genetic diversity, population structure, and environmental vulnerability. C_LIO_LIGenomic analyses revealed extremely low genetic diversity and inbreeding in the Alpine subspecies, consistent with a historical bottleneck, reducing adaptive potential. C_LIO_LISpecies distribution models predict a major contraction of suitable habitat by 2050 due to rising temperatures and declines in its primary host, Scots pine (Pinus sylvestris). C_LIO_LIThese findings highlight the compounded risks posed by genetic impoverishment and habitat loss, emphasizing the urgent need for targeted conservation measures. C_LIO_LIOur study demonstrates the value of integrating genomic and ecological approaches to evaluate extinction risk and guide management strategies for montane specialist insects under rapid environmental change. C_LI

evolutionary biology↗

bioRxiv2025

Climate-driven specialisation in plant-pollinator networks peaks outside the tropics

Pollination is a key ecological process sustaining biodiversity and food security, yet global patterns of plant-pollinator specialisation have remained unresolved. Using the largest global dataset of quantitative networks (>3,400 networks, >110,000 interactions), we show that the latitudinal specialisation gradient (LSG) exists, but it is non-linear, hemispherically asymmetric, and strongly taxon-dependent. Network-level and pollinator specialisation were lowest in the tropics and peaked at northern mid-latitudes, whereas plants tended to become more specialised toward higher latitudes. Climate consistently outperformed latitude, species richness, and environmental productivity as a predictor of these patterns. Specialisation declined with increasing temperature, rose with moderate rainfall before declining at the wettest sites, and increased with temperature seasonality, but plants and pollinators responded differently to these drivers. Functional groups diverged strongly: ectothermic insects were most specialised in cooler, seasonal climates, while birds showed weaker links to latitude but reduced specialisation in wetter regions. These findings demonstrate that climate, rather than latitude or species richness, structures global variation in specialisation. Because warmer and less seasonal climates promote generalisation, climate change is likely to disrupt the most specialised pollination systems, unevenly across taxa and regions, with important consequences for biodiversity and ecosystem stability.

ecology↗

bioRxiv2025

Spatio-temporal factors shape mosquito virome diversity and composition in a host and virus phylogeny-dependent manner

Beyond the arboviruses they transmit to humans and animals, mosquitoes harbour diverse viral communities that shape infection and immunity dynamics. Understanding how these communities shift within mosquito populations across time and space has important implications for how we anticipate and manage arboviral disease epidemics. Here, we examined the viromes of rural and sylvatic mosquito species sampled longitudinally across two years from countries representing South America, Africa, and Southeast Asian geographies to quantify the relative contributions of host and ecological factors in shaping their virome dynamics. We found that virus diversity and virome composition are strongly influenced by host phylogeny and spatial factors and show limited temporal variation. By examining virus similarity networks across mosquito species and biogeographies, we observed frequent instances of within- and cross-genus Culex-Anopheles virus sharing in Madagascar. Taken together, these findings inform the development and implementation strategies of any virome-based vector control technology and raise new evolutionary questions on how host generalism shapes the spatial prevalence of viruses and their potential for disease emergence.

microbiology↗

bioRxiv2025

Discovery of a Novel Coltivirus in a Newly Identified Bat Bug Species (Heteroptera: Cimicidae) in Cambodia

Bats and their ectoparasites are significant reservoirs and potential vectors of emerging zoonotic pathogens, yet the viral diversity within bat-associated arthropods remains poorly characterized. This study reports the identification of a novel coltivirus (order Reovirales), provisionally designated Stricticimex coltivirus (SCCV), in a newly described bat bug species, Stricticimex phnomsampovensis, collected from cave-dwelling wrinkle-lipped free-tailed bats (Mops plicatus) in Cambodia. Metagenomic sequencing and phylogenetic analysis revealed that SCCV clusters within the Coltivirus genus, showing closest similarity to Tai Forest Reovirus (TFRV) previously isolated from African bats. SCCV was detected in 18.4% of examined bat bugs and successfully isolated in VeroE6 cells, with replication confirmed in multiple mammalian cell lines. The discovery of SCCV extends the known diversity and geographic range of Coltivirus and highlights bat ectoparasites as overlooked hosts of potentially zoonotic viruses. These findings underscore the importance of integrated One Health surveillance targeting both bats and their ectoparasites to better assess the risk of pathogen spillover in biodiverse regions with high human-animal contact. Author SummaryIn this study, we identify a novel Coltivirus, named Stricticimex coltivirus (SCCV), in a newly described bat bug species collected from cave-dwelling bats in Cambodia. Using metagenomic sequencing and phylogenetic analysis, we find that SCCV is closely related to Tai Forest Reovirus, previously identified in African bats. We successfully isolated the virus in mammalian cell lines, suggesting potential to infect vertebrate hosts. This discovery not only expands the known diversity of Coltiviruses, but also underscores the role of bat ectoparasites as underexplored reservoirs of potentially zoonotic viruses. Our findings emphasize the importance of integrated One Health surveillance efforts targeting both bats and their ectoparasites to better assess the risk of virus spillover in regions where human and wildlife habitats overlap.

microbiology↗

bioRxiv2023

Offline RL for generative design of protein binders

Offline Reinforcement Learning (RL) offers a compelling avenue for solving RL problems without the need for interactions with an environment, which may be expensive or unsafe. While online RL methods have found success in various domains, such as de novo Structure-Based Drug Discovery (SBDD), they struggle when it comes to optimizing essential properties derived from protein-ligand docking. The high computational cost associated with the docking process makes it impractical for online RL, which typically requires hundreds of thousands of interactions during learning. In this study, we propose the application of offline RL to address the bottleneck posed by the docking process, leveraging RLs capability to optimize non-differentiable properties. Our preliminary investigation focuses on using offline RL to conditionally generate drugs with improved docking and chemical properties.

bioinformatics↗

bioRxiv2023

Mimicking of tau hyperphosphorylation in GABAergic motoneurons of C. elegans induces severe peripheral and neuronal alterations

In several neurodegenerative diseases including Alzheimers disease (AD), tau, a microtubule-associated protein (MAP) enriched in the axon, becomes hyperphosphorylated, detaches from microtubules, redistributes to the somato-dendritic compartment and self-aggregates. The mechanisms leading to neuronal dysfunction and death by tau pathology remain to be fully elucidated. C. elegans has been successfully used by several groups including ours to identify mechanisms involved in neurodegeneration. We generated three strains, one overexpressing wild-type human tau (WT Tau), one a tau mutant mimicking hyperphosphorylation (hyperP Tau) and one preventing phosphorylation (hypoP Tau) in GABA motor neurons. A significant reduction of body size and egg laying was noted in these tau strains. Starting at day 1, we found that the worms overexpressing hyperP Tau were smaller than the N2 control strain and the worms either overexpressing WT Tau or hypoP Tau. Starting at day 5, the worms overexpressing WT Tau were smaller than control and the worms overexpressing hypoP Tau. Egg laying was reduced in both hyperP Tau and WT Tau worms. Survival was only decreased in WT Tau worms. Motility deficits were also observed. For age-dependent paralysis, a difference was noted between control and hyperP Tau. Swimming activity and speed were increased in hypoP Tau and decreased in hyperP Tau strains. Axonal integrity was altered in all tau strains. In the case of synaptic activity, at day 1, it was increased in the hypoP Tau strain and decreased in the hyperP Tau one. Collectively, our data revealed that overexpression of tau exerted neuronal and peripheral defects indicating that tau dysfunction could affect cell-cell communication.

neuroscience↗

bioRxiv2023

Environmental variables and species traits as drivers of wild bee pollination in intensive agroecosystems -a metabarcoding approach

Wild bees are known to be efficient pollinators of wild plants and cultivated crops and they are essential ecosystem service providers. However, wild bee populations have been suffering from significant declines in the last decades mainly due to the use of agrochemicals. Within this framework, we aimed to characterize wild bees pollination spectrum (i.e. the community of pollinated flowering plants) in intensive agroecosystems, and describe the environmental variables and wild bee species traits influencing the pollination. To do this, we conducted metabarcoding analyses of pollen loads from wild bees collected in sunflower crops in the French region of Nouvelle-Aquitaine. Our study revealed that wild bees visited flowering plants corresponding to 231 different Operational Taxonomic Units, classified in 38 families of which Asteraceae, Brassicaceae and Apiaceae were the most visited and more than 90% of the visited taxa turned out to be wild flowers. We also analysed the potential effect of environmental variables and wild bee species traits in governing their choice of pollinated plants. The community composition of pollinated plants varied depending on the flowering stages of the sunflower and the farming system. Our results also show that pollination niche breadth (alpha diversity) varied depending on the flowering stages of the sunflower but was not different between organic and conventional farming systems. Regarding wild bee species traits, the community composition of pollinated plants varied in relation to wild bees body sizes and, sociality levels. Our results are consistent with previous studies, suggesting that solitary bees are more specialists when it comes to flower selection than social bees, which are more generalist. The metabarcoding of pollen loads enabled us to draw a global picture of plant-wild bee interactions in an intensive agroecosystem. Our findings support the hypothesis that a higher diversity of weeds may increase wild bee diversity in intensive agroecosystems.

ecology↗

bioRxiv2022

pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex mosquitoes worldwide

Mosquitoes represent the most important pathogen vectors and are responsible for the spread of a wide variety of poorly treatable diseases. Wolbachia are obligate intracellular bacteria that are widely distributed among arthropods and collectively represents one of the most promising solutions for vector control. In particular, Wolbachia has been shown to limit the transmission of pathogens, and to dramatically affect the reproductive behavior of their host through its phage WO. While much research has focused on deciphering and exploring the biocontrol applications of these WO-related phenotypes, the extent and potential impact of the Wolbachia mobilome remain poorly appreciated. Notably, several Wolbachia plasmids, carrying WO-like genes and Insertion Sequences (IS), thus possibly interrelated to other genetic units of the endosymbiont, have been recently discovered. Here we investigated the diversity and biogeography of the first described plasmid of Wolbachia in Culex pipiens (pWCP) in several islands and continental countries around the world--including Cambodia, Guadeloupe, Martinique, Thailand, and Mexico--together with mosquito strains from colonies that evolved for 2 to 30 years in the laboratory. Together with earlier observation, our results show that pWCP is omnipresent and strikingly conserved among Wolbachia populations within mosquitoes from distant geographies and environmental conditions. These data suggest a critical role for the plasmid in Wolbachia ecology and evolution, and the potential of a great tool for the further genetic dissection or potential manipulation of the endosymbiont.

microbiology↗

bioRxiv2022

The estrous cycle modulates early-life adversity effects on mouse avoidance behavior through progesterone signaling

Early-life adversity (ELA) predisposes individuals to develop neuropsychiatric conditions, which are more prevalent in women than men. Efforts to model this sex difference in rodents have produced mixed results, with some studies paradoxically showing stronger phenotypes in males than females. Since changes in reproductive hormone levels can increase the likelihood of anxiety disorders in women, we examined the effects of ELA on adult female mice across the estrous cycle. We found that during diestrus, when the ratio of progesterone to estrogen is relatively high, ELA mice exhibit increased avoidance behavior, altered activity levels in specific contexts, and increased theta oscillation power in the ventral hippocampus. Ovariectomy, which eliminates circulating estrogen but not progesterone, unexpectedly preserved some of the effects present in diestrus ELA mice. Progesterone receptor antagonism in diestrus normalized avoidance behavior in ELA mice, while treatment with a negative allosteric modulator of the progesterone metabolite allopregnanolone promoted avoidance behavior in control mice. These results suggest that altered progesterone and allopregnanolone signaling during diestrus increases avoidance behavior in ELA mice

neuroscience↗

bioRxiv2022

Genetic and microbial diversity of the invasive mosquito vector species Culex tritaeniorhynchus across its extensive inter-continental geographic range

Culex (Cx.) tritaeniorhynchus is a mosquito species with an extensive and expanding inter-continental geographic distribution, currently reported in over 50 countries, across Asia, Africa, the Middle East, Europe and now Australia. It is an important vector of medical and veterinary concern, capable of transmitting multiple arboviruses which cause significant morbidity and mortality in human and animal populations. In regions endemic for Japanese encephalitis virus (JEV) in Asia, Cx. tritaeniorhynchus is considered the major vector and this species has also been shown to contribute to the transmission of several other significant zoonotic arboviruses, including Rift Valley fever virus and West Nile virus. Significant variation in vectorial capacity can occur between different vector populations. Obtaining knowledge of a species from across its geographic range is crucial to understanding its significance for pathogen transmission across diverse environments and localities. Vectorial capacity can be influenced by factors including the mosquito genetic background, composition of the microbiota associated with the mosquito and the co-infection of human or animal pathogens. In addition to enhancing information on vector surveillance and potential risks for pathogen transmission, determining the genetic and microbial diversity of distinct populations of a vector species is also critical for the development and application of effective control strategies. In this study, multiple geographically dispersed populations of Cx. tritaeniorhynchus from countries within Europe, Africa, Eurasia and Asia were sampled. Molecular analysis demonstrated a high level of genetic and microbial diversity within and between populations, including genetic divergence in the mosquito CO1 gene, as well as diverse microbiomes identified by 16S rRNA gene amplicon sequencing. Evidence for the detection of the endosymbiotic bacteria Wolbachia in some populations was confirmed using Wolbachia-specific PCR detection and sequencing of Wolbachia MLST genes; in addition to PCR-based detection of insect-specific viruses. Laboratory vector competence showed Cx. tritaeniorhynchus from a Greek population are likely to be competent vectors of JEV. This study expands understanding of the diversity of Cx. tritaeniorhynchus across its inter-continental range, highlights the need for a greater focus on this invasive vector species and helps to inform potential future directions for development of vector control strategies.

genetics↗

bioRxiv2022

Decoding rRNA Sequences for Improved Metagenomics in Sylvatic Mosquito Species

As mosquito-borne virus epidemics are often preceded by undetected spillover events, surveillance and virus discovery studies in non-urban mosquitoes informs pre-emptive and responsive public health measures. RNA-seq metagenomics is a popular methodology but it is constrained by overabundant rRNA. The lack of reference sequences for most mosquito species is a major impediment against physical and computational removal of rRNA reads. We describe a strategy to assemble novel rRNA sequences from mosquito specimens, producing an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). We also evaluate the utility of rRNA sequences as molecular barcodes relative to the mitochondrial cytochrome c oxidase I (COI) gene. We show that rRNA sequences can be used for species identification when COI sequences are ambiguous or unavailable, revealing evolutionary relationships concordant with contemporary mosquito systematics. This expansion of the rRNA reference library improves mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader species range and streamlined species identification by rRNA barcoding. In addition, rRNA barcodes could serve as an additional tool for mosquito taxonomy and phylogeny.

bioinformatics↗

bioRxiv2021

dynamAedes: a unified modelling framework for invasive Aedes mosquitoes

O_LIMosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers for their invasive species traits and efficient capacity of transmitting viruses affecting humans. Some of these species were brought outside their native range by human activities such as trade and tourism, and colonised new regions thanks to a unique combination of eco-physiological traits. C_LIO_LIConsidering mosquito physiological and behavioural traits to understand and predict the spatial and temporal population dynamics is thus a crucial step to develop strategies to mitigate the local densities of invasive Aedes populations. C_LIO_LIHere, we synthesised the life cycle of four invasive Aedes species (Ae. aegypti, Ae. albopictus, Ae. japonicus and Ae. koreicus) in a single multi-scale stochastic modelling framework which we coded in the R package dynamAedes. We designed a stage-based and time-discrete stochastic model driven by temperature, photo-period and inter-specific larval competition that can be applied to three different spatial scales: punctual, local and regional. These spatial scales consider different degrees of spatial complexity and data availability, by accounting for both active and passive dispersal of mosquito species as well as for the heterogeneity of the input temperature data. C_LIO_LIOur overarching aim was to provide a flexible, open-source and user-friendly tool rooted in the most updated knowledge on species biology which could be applied to the management of invasive Aedes populations as well as for more theoretical ecological inquiries. C_LI

ecology↗

bioRxiv2021

Development of a multi-primer metabarcoding approach to understand trophic interactions in agroecosystems

Knowing which arthropod and plant resources are used by generalist predators in agroecosystems is important to understand trophic interactions and the precise ecological role of each predatory species. To achieve this objective, molecular approaches, such as the use of high-throughput sequencing (HTS) platforms are key. This study develops a multi-primer metabarcoding approach and explores its suitability for the screening of the most common trophic interactions of two predatory species of arthropod with contrasted morphology, Rhagonycha fulva (Coleoptera: Cantharidae) and Anthocoris nemoralis (Hemiptera: Anthocoridae) collected in an organic peach crop. To save time and cost in this metabarcoding approach, we first evaluated the effect of two different predator-pool sizes (10 and 23 individuals of the same species), as well as the performance of using one or two primer pairs in the same library. Our results show that the analysis of 23 individuals together with the use of two primer pairs in the same library optimizes the HTS analysis. With these best-performing conditions, we analyzed whole bodies of field-collected predators as well as the washing solutions used to clean the insect bodies. Results showed that we were able to identify both, gut content (i.e. diet) as well as external pollen load (i.e. on the insects body), respectively. This study also demonstrates the need of washing predatory insects prior to HTS analysis when the target species have a considerable size and hairy structures. This metabarcoding approach has a high potential for the study of trophic links in agriculture, revealing both expected and unexpected trophic relationships.

ecology↗

bioRxiv2020

Investigating spatiotemporal variation in the diet of Westland Petrel through metabarcoding, a non-invasive technique

As top predators, seabirds can be indirectly impacted by climate variability and commercial fishing activities through changes in marine communities. However, high mobility and foraging behaviour enables seabirds to exploit prey distributed patchily in time and space. This capacity to adapt to environmental change can be described through the study of their diet. Traditionally, the diet of seabirds is assessed through the morphological identification of prey remains in regurgitates. This sampling method is invasive for the bird and limited in terms of taxonomic resolution. However, the recent progress in DNA-based approaches is now providing a non-invasive means to more comprehensively and accurately characterize animal diets. Here, we used a non-invasive metabarcoding approach to characterize the diet of the Westland petrel (Procellaria westlandica), which is an endangered burrowing species, endemic to the South Island of New Zealand. We collected 99 fresh faecal samples at two different seasons and in two different sub-colonies. Our aims were to describe the diet of the Westland petrel, investigate seasonal and spatial variation in the petrels diet, and assess potential impacts of the New Zealand fishery industry. We found that amphipods were the most common prey, followed by cephalopods and fish. Our results could be the result of natural foraging behaviour, but also suggest a close link between the composition of prey items and New Zealands commercial fishing activities. In particular, the high abundance of amphipods could be the result of Westland petrels feeding on discarded fisheries waste (fish guts). Our results also showed significant differences in diet between seasons (before hatching vs chick-rearing season) and between sampling sites (two sub-colonies 1.5 km apart), indicating plasticity in the foraging strategy of the Westland petrel. Due to its non-invasive nature, metabarcoding of faecal samples can be applied to large numbers of samples to help describe dietary variation in seabirds and indicate their ecological requirements. In our example, dietary DNA (dDNA) provided valuable information regarding the dietary preferences of an iconic species in New Zealands unique biodiversity. dDNA can thus inform the conservation of endangered or at-risk species that have elusive foraging behaviours.

ecology↗

bioRxiv2020

A novel assay for tracking carboxylesterase gene amplifications conferring organophosphate resistance in the mosquito Aedes aegypti: from experimental evolution to field application

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterise a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100 Kb amplification spanning at least five carboxylesterase genes at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number polymorphism among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-colour multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector.

evolutionary biology↗

bioRxiv2019

A new high-throughput tool to screen mosquito-borne viruses in Zika virus endemic/epidemic areas

Mosquitoes are vectors of arboviruses affecting animal and human health. Arboviruses circulate primarily within an enzootic cycle and recurrent spillovers contribute to the emergence of human-adapted viruses able to initiate an urban cycle involving anthropophilic mosquitoes. The increasing volume of travel and trade offers multiple opportunities for arbovirus introduction in new regions. This scenario has been exemplified recently with the Zika pandemic. To incriminate a mosquito as vector of a pathogen, several criteria are required such as the detection of natural infections in mosquitoes. In this study, we used a high-throughput chip based on the BioMarkTM Dynamic arrays system capable of detecting 64 arboviruses in a single experiment. A total of 17,958 mosquitoes collected in Zika-endemic/epidemic countries (Brazil, French Guiana, Guadeloupe, Suriname, Senegal, and Cambodia) were analyzed. Here we show that this new tool can detect endemic and epidemic viruses in different mosquito species in an epidemic context. Thus, this fast and low-cost method can be suggested as a novel epidemiological surveillance tool to identify circulating arboviruses.

molecular biology↗

bioRxiv2019

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment

The environmental conditions of microorganisms habitats may fluctuate in unpredictable ways, such as changes in temperature, carbon source, pH, and salinity to name a few. Environmental heterogeneity presents a challenge to microorganisms, as they have to adapt not only to be fit under a specific condition, but they must also be robust across many conditions and be able to deal with the switch between conditions itself. While experimental evolution has been used to gain insight into the adaptive process, this has largely been in either unvarying or consistently varying conditions. In cases where changing environments have been investigated, relatively little is known about how such environments influence the dynamics of the adaptive process itself, as well as the genetic and phenotypic outcomes. We designed a systematic series of evolution experiments where we used two growth conditions that have differing timescales of adaptation and varied the rate of switching between them. We used lineage tracking to follow adaptation, and whole genome sequenced adaptive clones from each of the experiments. We find that both the switch rate and the order of the conditions influences adaptation, and that switching can both speed up and slow down adaptation, depending on those parameters. We also find different adaptive outcomes, at both the genetic and phenotypic levels, even when populations spent the same amount of total time in the two different conditions, but the order and/or switch rate differed. Thus, in a variable environment adaptation depends not only on the nature of the conditions and phenotypes under selection, but also on the complexity of the manner in which those conditions are combined to result in a given dynamic environment.

evolutionary biology↗