Biology subjects

Baier, F.

Publications and source records attributed to Baier, F..

14 recordsLinked to original sources

bioRxiv2026

Evolution of mutational fitness effects in island populations

The distribution of fitness effects (DFE) quantifies the selective consequences of newly arising mutations. Theoretical and empirical investigations of the DFE suggest that it is highly context-specific, shaped by both intrinsic properties of an organism (e.g., biological complexity) and extrinsic properties of a population (e.g., environment). Despite recent comparisons of the DFE between populations and species, little is known about how this distribution changes over shorter evolutionary timescales. Islands provide a powerful framework for understanding the impact of recent shifts in selection on the DFE, as founding populations often experience abrupt environmental changes. Using whole-genome, population-level sequence data, we investigate how such extreme transitions shape the DFE in two island radiations of Peromyscus mice: white-footed mice (P. leucopus) in Massachusettss Boston Harbor and deer mice (P. maniculatus) in the Gulf Islands of British Columbia. To measure the extent to which the selective effects of mutations have diverged between island and mainland populations, we leverage recent advances that extend DFE inference to multiple populations. By reconstructing the "joint DFE", we estimate both the strength of selection acting on distinct mutational classes and the correlation in mutational fitness effects between populations. We find that mutational fitness effects have diverged between island and mainland populations, despite the relative recency of these radiations. Comparisons between island populations, which reveal higher fitness effect correlations, suggest that this feature of the joint DFE captures broad-scale divergence in the environment populations inhabit. Together, our discoveries provide a rare empirical example of divergent environments shaping genome-wide patterns of fitness-affecting genetic variation in natural populations.

evolutionary biology↗

bioRxiv2026

Viral isolation reveals novel and diverse phages infecting natural stream biofilms

Bacteriophages of environmental bacteria remain underrepresented, lending paucity to phage-biofilm research beyond clinical and model species domains. Here, we present the Alpine Lotic Phage (ALP) collection, curated through an isolation campaign from biofilm-forming bacteria of alpine streams. We obtained 57 phage isolates, which were dereplicated to 28 unique genomes following sequencing. The collection consists of tailed phages infecting 14 bacterial host species with genomes spanning 37 to 363 kb while exhibiting diverse plaque morphologies, depolymerase activity, and distinct impacts on host biofilm architecture. Comparative analyses against public viral genomes and a curated planetary-scale contig database revealed limited sequence similarity, underscoring the novelty of ALP phages. Functional annotation resolved 9 - 54% of predicted genes which encoded viral structural components, nucleotide metabolism functions, anti-defence mechanisms, and auxiliary genes that facilitate viral infection and replication. Together, the ALP collection represents a foundational resource for investigating phage evolution and ecology in natural bacterial communities.

microbiology↗

bioRxiv2026

Low-salt diet induces claudin-3 expression and drives adaptive changes in collecting duct of claudin-3-deficient mice

BackgroundRenal sodium reabsorption occurs via both transcellular and paracellular pathways. Tight junction proteins play a key role in mediating paracellular transport. The collecting duct (CD) is critical for the fine-tuning of Na+ balance and is sensitive to changes in dietary salt intake. A low-sodium diet, which increases endogenous aldosterone secretion, stimulates transcellular sodium transport via epithelial Na+ channels (ENaC) and Na,K-ATPase. We hypothesized that a low-sodium diet also modulates paracellular Na+ permeability by regulating the expression or function of claudin-3, a major tight junction protein in the CD, in order to limit the back-leak of reabsorbed sodium and preserve sodium balance. MethodsWe used in vivo mouse models and cultured mouse CD principal cells (mCCDcl1) to assess aldosterones effects on tight junction proteins. In mCCDcl1 cells, aldosterone-induced changes in claudin-3 expression and localization were evaluated via Western blotting and immunofluorescence, and Ussing chamber assays were used to assess paracellular Na+ and Cl- permeability after modulating claudin-3 expression. Wild-type and claudin-3 knockout mice were fed low (0.01%) or normal (0.18%) sodium diets for seven days. In subsets of low sodium diet mice, spironolactone (a mineralocorticoid receptor antagonist) was administered. ResultsIn mice, a low-sodium diet upregulates renal claudin-3 expression. Concordantly, in vitro studies using mCCDcl1 cells showed that aldosterone treatment increased claudin-3 protein levels and promoted its localization to the lateral membrane. Functional analyses demonstrated that claudin-3 overexpression reduced paracellular permeability to both Na+ and Cl-, while claudin-3 silencing increased it. Claudin-3 knockout mice subjected to a low-sodium diet exhibited compensatory upregulation of the - and {gamma}-subunits of ENaC, alongside increased expression of claudin-4, claudin-8, and claudin-10. This highlights an adaptive response that maintains sodium homeostasis in the absence of claudin-3. Importantly, this compensatory mechanism persists even under spironolactone treatment, suggesting that the adaptation of claudin-3-deficient mice occurs independently of mineralocorticoid receptor activation. ConclusionsOur findings demonstrate that aldosterone enhances claudin-3 expression, reinforcing the paracellular barrier to Na+ and complementing its classical role in transcellular Na+ transport. Under low-sodium conditions, claudin-3-deficient mice adapt through complementary mechanisms aimed at increasing sodium reabsorption via ENaC activation and upregulation of claudin-4 and claudin-8, both barrier-forming claudins that restrict paracellular sodium leakage in the CD. This is associated with increased claudin-10 abundance in the thick ascending limb of Henle, a pore-forming claudin that facilitates paracellular sodium permeability. This study advances our understanding of the complex control of renal sodium handling, revealing adaptive mechanisms in response to low-salt diet and claudin-3 deficiency.

physiology↗

bioRxiv2025

The genomic imprint of chromosomal inversions and demographic history in island populations of deer mice

Populations that colonize islands experience novel selective pressures, fluctuations in size, and changes to their connectivity. Owing to their unique geographic setting, islands can function as natural laboratories in which to examine the interactions between demographic history and natural selection replicated across isolated populations. We used whole genome sequences of wild-caught deer mice (Peromyscus maniculatus) from two islands (Saturna and Pender) and one mainland location (Maple Ridge) in the Gulf Islands region of coastal British Columbia to investigate two primary determinants of genome-wide diversity: chromosomal inversions and non-equilibrium demographic history. We found that segregating inversions produce characteristic, large-scale distortions in allele frequencies and linkage disequilibrium that make it possible to identify and characterize them from short-read sequence data. Patterns of variation within and between karyotypes indicate that six inversion polymorphisms have been maintained by a shared history of balancing selection in both island and mainland populations. Whereas the estimated timing of contemporary population splits is consistent with the isolation of island populations from each other following the Last Glacial Maximum, ancestral island and mainland lineages are inferred to have diverged much earlier. These aspects of demographic history suggest that shared inversions existed long ago in a common ancestor or spread via limited gene flow between ancestral island and mainland lineages. Our results raise the possibility that inversions segregating among Gulf Islands populations are on similar evolutionary trajectories, providing a contrast to previous findings in mainland P. maniculatus and contributing to the emerging portrait of inversion evolution in this species.

evolutionary biology↗

bioRxiv2023

Evolution of gene expression across brain regions in behaviorally divergent deer mice

The evolution of innate behaviors is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. polionotus) - which differ in a range of innate behaviors, including their social system - and their F1 hybrids. We find that most of the variation in gene expression distinguishes subregions, followed by species. Interspecific differential expression (DE) is pervasive (52-59% of expressed genes), whereas the number of DE genes between sexes is modest overall ([~]3%). Interestingly, the identity of DE genes varies considerably across brain regions. Much of this modularity is due to cis-regulatory divergence, and while 43% of genes were consistently assigned to the same gene regulatory class across subregions (e.g., conserved, cis-, or trans-regulatory divergence), a similar number were assigned to two or more different gene regulatory classes. Together, these results highlight the modularity of gene expression differences and divergence in the brain, which may be key to explain how the evolution of brain gene expression can contribute to the astonishing diversity of animal behaviors.

evolutionary biology↗

bioRxiv2023

A direct experimental test of Ohno's hypothesis

Gene duplication drives evolution by providing raw material for proteins with novel functions. The oldest and historically most influential hypothesis about the evolutionary fate and potential of duplicated genes has been proposed by Susumu Ohno in 1970. This hypothesis essentially posits that gene duplication can help genes tolerate new mutations and thus facilitates the evolution of new phenotypes. Competing hypotheses argue that deleterious mutations will usually inactivate gene duplicates too rapidly for Ohnos hypothesis to work. Here, we provide a first direct experimental test of Ohnos hypothesis. Specifically, we evolved one or exactly two copies of a gene encoding a fluorescent protein in Escherichia coli through multiple rounds of mutagenesis and selection. We then analyzed the genotypic and phenotypic evolutionary dynamics of the evolving populations through high-throughput DNA sequencing, biochemical assays, and engineering of selected variants. In support of Ohnos hypothesis, populations carrying two gene copies displayed higher mutational robustness than those carrying a single gene copy. As a consequence, the double-copy populations experienced relaxed purifying selection, evolved higher phenotypic and genetic diversity, carried more mutations and accumulated combinations of key beneficial mutations earlier. However, their phenotypic evolution was not accelerated, possibly because one gene copy rapidly became inactivated by deleterious mutations. Our work provides an experimental platform to test models of evolution by gene duplication, and it supports alternatives to Ohnos hypothesis that point to the importance of gene dosage.

evolutionary biology↗

bioRxiv2023

The neural basis of defensive behaviour evolution in Peromyscus mice

Evading imminent predator threat is critical for survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours is still poorly understood. Here we find that two sister species of deer mice (genus Peromyscus) show different responses to the same looming stimulus: P. maniculatus, which occupy densely vegetated habitats, predominantly dart to escape, while the open field specialist, P. polionotus, pause their movement. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal gray (dPAG) in driving behaviour differs. While dPAG activity scales with running speed and involves both excitatory and inhibitory neurons in P. maniculatus, the dPAG is largely silent in P. polionotus, even when darting is triggered. Moreover, optogenetic activation of excitatory dPAG neurons reliably elicits darting behaviour in P. maniculatus but not P. polionotus. Together, we trace the evolution of species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the complex mammalian brain.

neuroscience↗

bioRxiv2022

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis confounds our understanding of how mutations impact the expression patterns of gene regulatory networks, because such nonlinearities make it difficult to predict the combined phenotypic effects of mutations based on knowledge of the mutations individual effects. This challenge is exacerbated by the dependence of epistasis on the environment, which is particularly germane to gene regulatory networks that interpret signals in space or time. To help fill this knowledge gap, we used the toolkit of synthetic biology to systematically assay the effects of pairwise and triplet combinations of mutant genotypes on the expression pattern of a gene regulatory network expressed in Escherichia coli that interprets an inducer gradient across a spatial domain. We uncovered a preponderance of epistasis in both pairwise and triplet combinations that can switch in magnitude and sign across the inducer gradient to produce a greater diversity of expression pattern phenotypes than would be possible in the absence of such environment-dependent epistasis. We discuss our findings in the context of the evolution of hybrid incompatibilities and evolutionary novelties, arguing that environment-dependent epistasis is likely an important cause of both phenomena in gene regulatory networks.

evolutionary biology↗

bioRxiv2022

Acute Cytomegalovirus Infection Modulates the Intestinal Microbiota and Targets Intestinal Epithelial Cells

Primary and recurrent cytomegalovirus (CMV) infections frequently cause CMV colitis in immunocompromised as well as inflammatory bowel disease (IBD) patients. Additionally, colitis occasionally occurs upon primary CMV infection in patients who are apparently immunocompetent. In both cases, the underlying pathophysiologic mechanisms are largely elusive - in part due to the lack of adequate access to specimens. We employed the mouse cytomegalovirus (MCMV) model to probe into the association between CMV and colitis. During acute primary MCMV infection of immunocompetent mice, the gut microbial composition was affected within the first 5 days post-infection as manifested by an altered ratio of the Firmicutes to Bacteroidetes phyla. Interestingly, these microbial changes incited with high-titer MCMV replication in the colon, mild crypt necrosis and increased colonic pro-inflammatory cytokine levels. Further analyses revealed that murine and human intestinal epithelial cell line as well as primary intestinal crypt cells/ organoids represent direct targets of CMV accompanied by increased cell mortality upon infection. Accordingly, in vivo MCMV infection disrupted the intestinal epithelial barrier and increased apoptosis of intestinal epithelial cells. In summary, our data show that CMV induces colitis in immunocompetent hosts by altering the intestinal homeostasis.

microbiology↗

bioRxiv2019

Secondary environmental variation creates a shifting evolutionary watershed for the methyl- parathion hydrolase enzyme

Enzymes can evolve new catalytic activity when their environments change to present them with novel substrates. Despite this seemingly straightforward relationship, factors other than the direct catalytic target can also impact enzyme adaptation. Here, we characterize the adaptive landscape separating an ancestral dihydrocoumarin hydrolase from a methyl parathion hydrolase descendant under eight different environments supplemented with alternative divalent metals. This variation shifts an evolutionary watershed, causing the outcome of adaptation to depend on the environment in which it occurs. The resultant landscapes also vary in terms both the number and the genotype(s) of \"fitness peaks\" as a result of genotype-by-environment (GxE) interactions and environment-dependent epistasis (GxGxE). This suggests that adaptive landscapes may be fluid and that molecular adaptation is highly contingent not only on obvious factors (such as catalytic targets) but also on less obvious secondary environmental factors that can direct it toward distinct outcomes.

evolutionary biology↗

bioRxiv2019

Behavioural mechanisms underlying the evolution of cooperative burrowing in Peromyscus mice

While some behaviours are largely fixed and invariant, others can respond flexibly to different social contexts. Here, we leverage the unique burrowing behaviour of deer mice (genus Peromyscus) to investigate if and how individuals of three species adapt their behaviour when digging individually versus with partners. First, we find that pairs of mice from monogamous (P. polionotus) but not promiscuous (P. maniculatus, P. leucopus) species cooperatively construct burrows that are approximately twice as long as those dug by individuals and similar in size to burrows found in the wild. However, the length of burrows built by P. polionotus pairs differs: opposite-sex pairs construct longer burrows than same-sex pairs. By designing a novel behavioural assay in which we can observe and measure burrowing behaviour directly, we find that longer burrows are achieved not by changing individual behaviour, but instead because opposite-sex pairs are more socially cohesive and thus more likely to dig simultaneously, which is a more efficient mode of burrow elongation. Thus, across social contexts, individual burrowing behaviour appears largely invariant, even when the resultant burrow from pairs of mice differs from expectation based on individual behaviour, underscoring the fixed nature of burrowing behaviour in Peromyscus mice.

evolutionary biology↗

bioRxiv2018

Higher-order epistatic networks underlie the evolutionary fitness landscape of a xenobiotic- degrading enzyme

Characterizing the adaptive landscapes that encompass the emergence of novel enzyme functions can provide molecular insights into both enzymatic and evolutionary mechanisms. Here, we combine ancestral protein reconstruction with biochemical, structural, and mutational analyses to characterize the functional evolution of methyl-parathion hydrolase (MPH), a xenobiotic organophosphate-degrading enzyme. We identify five mutations that are necessary and sufficient for the evolution of MPH from an ancestral dihydrocoumarin hydrolase. In-depth analyses of the adaptive landscapes encompassing this evolutionary transition revealed that a complex interaction network, defined in part by higher-order epistasis, determined the adaptive pathways that were available. By also characterizing the adaptive landscapes in terms of their functional activity towards three other OP substrates, we reveal that subtle differences in substrate substituents drastically alter the enzymes epistatic network by changing its intramolecular interactions. Our work suggests that the mutations function collectively to enable substrate recognition via subtle structural repositioning.

biochemistry↗

bioRxiv2018

The genetics of morphological and behavioral island traits in deer mice

Animals on islands often exhibit dramatic differences in morphology and behaviour compared to mainland individuals, a phenomenon known as the \"island syndrome\". These differences are thought to be adaptations to island environments, but the extent to which they have a genetic basis or instead represent plastic responses to environmental extremes is often unknown. Here, we revisit a classic case of island syndrome in deer mice (Peromyscus maniculatus) from British Columbia. We first show that Saturna Island mice and those from neighbouring islands are [~]35% ([~]5g) heavier than mainland mice and diverged approximately 10 thousand years ago. We then established laboratory colonies and find that Saturna Island mice are heavier both because they are longer and have disproportionately more lean mass. These trait differences are maintained in second-generation captive-born mice raised in a common environment. In addition, island-mainland hybrids reveal a maternal genetic effect on body weight. Using behavioural testing in the lab, we also find that wild-caught island mice are less aggressive than mainland mice; however, lab-raised mice born to these founders do not differ in aggression. Together, our results reveal that these mice respond differently to environmental conditions on islands - evolving both heritable changes in a morphological trait and also expressing a plastic phenotypic response in a behavioural trait.

evolutionary biology↗

bioRxiv2017

Cryptic genetic variation defines the adaptive evolutionary potential of enzymes

Genetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may also impact the evolutionary potential of proteins, but the molecular basis for this remains unclear. Here we perform comparative directed evolution in which four orthologous metallo-{beta}-lactamases were evolved toward a new function. We found that genetic variation between these enzymes resulted in distinct evolutionary outcomes. The ortholog with the lower initial activity reached a 20-fold higher fitness plateau exclusively via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show that the cryptic molecular properties and conformational variation of residues in the initial genotypes cause epistasis, thereby constraining evolutionary outcomes. Our work highlights that understanding the molecular details relating genetic variation to protein functions is essential to predicting the evolution of proteins.

evolutionary biology↗