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bioRxiv2022

Random and natural non-coding RNA have similar structural motif patterns but can be distinguished by bulge, loop, and bond counts

An important question in evolutionary biology is whether and in what ways genotype-phenotype (GP) map biases can influence evolutionary trajectories. Untangling the relative roles of natural selection and biases (and other factors) in shaping phenotypes can be difficult. Because RNA secondary structure (SS) can be analysed in detail mathematically and computationally, is biologically relevant, and a wealth of bioinformatic data is available, it offers a good model system for studying the role of bias. For quite short RNA (length L [≤] 126), it has recently been shown that natural and random RNA are structurally very similar, suggesting that bias strongly constrains evolutionary dynamics. Here we extend these results with emphasis on much larger RNA with length up to 3000 nucleotides. By examining both abstract shapes and structural motif frequencies (ie the numbers of helices, bonds, bulges, junctions, and loops), we find that large natural and random structures are also very similar, especially when contrasted to typical structures sampled from the space of all possible RNA structures. Our motif frequency study yields another result, that the frequencies of different motifs can be used in machine learning algorithms to classify random and natural RNA with quite high accuracy, especially for longer RNA (eg ROC AUC 0.86 for L = 1000). The most important motifs for classification are found to be the number of bulges, loops, and bonds. This finding may be useful in using SS to detect candidates for functional RNA within junk DNA regions.

evolutionary biology↗

bioRxiv2023

Stochasticity explains non-genetic inheritance of lifespan and apparent trade-offs between reproduction and ageing

Stochastic effects are central to the biology and demography of ageing. Genetically identical individuals do not all die at the exact same time but show a distribution of lifespan. Although such effects are appreciated, any cascading effects from stochastic effects of ageing are underappreciated. We show here that genetically identical female flies (Drosophila melanogaster) that live long, produce longer lived daughters. In line with previous work, we also find that daughters born to older mothers are shorter lived, also termed the Lansing effect. We further show that longer-lived flies produce less offspring, suggesting an apparent trade-off due to stochastic effects alone. We explain these effects using an extension of the reliability theory of ageing by dichotomising ageing physiology in reproduction and lifespan supporting units. These simple models reproduce non-genetic inheritance of lifespan, the Lansing effect and trade-offs between reproduction and lifespan. Our work implies that if non-genetic inheritance of lifespan is widespread it explains the generally low heritability of this trait. Furthermore, trade-offs between performance, e.g. reproduction, and lifespan may be less widespread than predicted by evolutionary biology of ageing, stemming from stochasticity rather than differential investment. Anti-ageing treatments therefore come without any unintended costs to other physiology, a perceived risk that limits translation of these treatments to humans.

evolutionary biology↗

bioRxiv2023

A rugged yet easily navigable fitness landscape of antibiotic resistance

A fitness landscape is a biological analogue of a physical landscape, in which each genotype occupies a location whose elevation corresponds to fitness. Theoretical models predict that rugged fitness landscapes with multiple peaks should impair Darwinian evolution, because natural selection prevents evolving populations from traversing the valleys that lie between peaks. Experimental tests of this prediction are very limited. Here we combine CRISPR-Cas9 genome editing and deep sequencing to map the fitness landscape of more than 260000 genotypes of the E. coli folA gene in an environment harboring the antibiotic trimethoprim. The folA gene encodes the key metabolic enzyme dihydrofolate reductase (DHFR), which is also a target of this antibiotic. With 514 mostly low fitness peaks, the DHFR fitness landscape is rugged. Despite this ruggedness, its highest fitness peaks are easily accessible to evolving populations. Fitness-increasing paths to high fitness peaks are abundant, and individual peaks have large basins of attractions. The basins of different peaks overlap, which renders the outcome of adaptive evolution highly contingent on chance events. In sum, ruggedness need not be an obstacle to Darwinian evolution but can reduce its predictability. If true in general, evolutionary biology and other fields of sciences in which landscapes play an important role may have to re-appraise the complexity of optimization problems on realistic landscapes.

evolutionary biology↗

bioRxiv2025

Behavioral and phenotypic constraint belie deep genomic divergence and seasonal adaptation in a widespread desert lizard

Cryptic species offer opportunities to reveal the mechanisms that constrain phenotypic divergence during speciation. We integrated whole-genome sequencing, morphological, micro- and macro-climatic, and behavioral data to investigate divergence across a well- documented genetic break in the desert-adapted side-blotched lizard, Uta stansburiana, on the Baja California peninsula. Despite deep genomic differentiation, clades show remarkable similarity in morphology, habitat use, and thermal biology. Nearly all genetic differentiation (87%) is explained by isolation by distance and seasonal variation in precipitation, with almost no effect of temperature. Behavioral thermoregulation and changes in activity time accommodate strong macro- and micro-climatic differences, buffering against selection that would otherwise drive morphological and physiological divergence. In contrast, genomic signatures of selection and divergence in genes associated with the nervous system, sensory perception, and biomolecule metabolism indicate adaptation to differences in rainfall seasonality. The results show behavioral flexibility can constrain phenotypic divergence, yielding cryptic species-level genetic divergence despite strong eco-climatic disparities and selection pressures. More broadly, this study shows how rigorous statistical integration of multiple data types can disentangle competing eco- climatic drivers that can decouple phenotype from genotype during speciation. SignificanceUnderstanding why deep genetic divergence occurs without phenotypic differentiation is a longstanding challenge in evolutionary biology. By statistically integrating genomic, morphological, climatic, and behavioral data, we test the mechanisms controlling differentiation within a natural lizard system in a geo-climatically diverse setting. Results show that isolation by distance and adaptation to precipitation seasonality drive nearly all genomic differentiation. Behavioral adjustment to strong thermal variation buffers against selection pressure otherwise expected to cause divergence in morphology, thermal biology, and habitat use. This work demonstrates how rigorous integrative analyses can tease apart ecological and neutral factors controlling genomic divergence, providing rare insight into causal mechanisms driving speciation while constraining phenotypic divergence.

evolutionary biology↗

bioRxiv2023

The evolution of morphological castes under decoupled control

Eusociality, where units that previously reproduced independently function as one entity, is of major interest in evolutionary biology. Obligate eusociality is characterised by morphologically differentiated castes and reduced conflict. We explore conditions under which morphological castes may arise in the Hymenoptera and factors constraining their evolution. Control over offspring morphology and behaviour seem likely to be decoupled. Provisioners (queens and workers) can influence offspring morphology directly through the nutrition they provide, while adult offspring control their own behaviour. Provisioners may, however, influence worker behaviour indirectly if offspring modify their behaviour in response to their morphology. If manipulation underlies helping, we should not see helping evolve before specialised worker morphology, yet empirical observations suggest that behavioural castes precede morphological castes. We use evolutionary invasion analyses to show how the evolution of a morphologically differentiated worker caste depends on the prior presence of a behavioural caste: specialist worker morphology will be mismatched with behaviour unless some offspring already choose to work. A mothers certainty about her offsprings behaviour is also critical - less certainty results in greater mismatch. We show how baseline worker productivity can affect the likelihood of a morphological trait being favoured by natural selection. We then show how under a decoupled control scenario, morphologically differentiated castes should be less and less likely to be lost as they become more specialised. We also suggest that for eusociality to be evolutionarily irreversible, workers must be unable to functionally replace reproductives and reproductives must be unable to reproduce without help from workers.

evolutionary biology↗

bioRxiv2023

Effects of phylogenetic variation on prioritization of species for conservation

Many questions in evolutionary biology require the specification of a phylogeny for downstream phylogenetic analyses. However, with the increasingly widespread availability of genomic data, phylogenetic studies are often confronted with conflicting signal in the form of genomic heterogeneity and incongruence between gene trees and the species tree. This raises the question of determining what data and phylogeny should be used in downstream analyses, and to what extent the choice of phylogeny (e.g., gene trees versus species trees) impacts the analyses and their outcomes. In this paper, we study this question in the realm of phylogenetic diversity indices, which provide ways to prioritize species for conservation based on their relative evolutionary isolation on a phylogeny, and are thus one example of downstream phylogenetic analyses. We use the Fair Proportion (FP) index, also known as the evolutionary distinctiveness score, and explore the variability in species rankings based on gene trees as compared to the species tree for several empirical data sets. Our results indicate that prioritization rankings among species vary greatly depending on the underlying phylogeny, suggesting that the choice of phylogeny is a major influence in assessing phylogenetic diversity in a conservation setting. While we use phylogenetic diversity conservation as an example, we suspect that other types of downstream phylogenetic analyses such as ancestral state reconstruction are similarly affected by genomic heterogeneity and incongruence. Our aim is thus to raise awareness of this issue and inspire new research on which evolutionary information (species trees, gene trees, or a combination of both) should form the basis for analyses in these settings.

evolutionary biology↗

bioRxiv2026

Eco-evolutionary feedbacks generate bistability in population persistence under gradual environmental change

Understanding how populations persist in gradually deteriorating environments through evolution is a central question in ecology and evolutionary biology. Previous studies have primarily focused on identifying the critical rate of environmental change beyond which extinction is certain. However, the existence of a viable equilibrium when the rate is below the threshold does not guarantee that a population can survive the transient dynamics to reach it. Using a quantitative genetic model that explicitly incorporates feedback among population size, genetic variance, and mean trait evolution, we show that population persistence can exhibit bistability when the rate of environmental change is below the extinction threshold. Specifically, extinction still occurs if the initial population size and genetic variance fall below a critical level. The initial state also influences the eco-evolutionary dynamics, such that a temporary increase or decline in population size and/or genetic variance does not necessarily predict the ultimate fate of the population. Therefore, in addition to estimating the critical rate of environmental change for extinction, characterizing current population size, genetic variation, and the degree of maladaptation may improve predictions of extinction risk in deteriorating environments.

evolutionary biology↗

bioRxiv2016

A Central Limit Theorem for Punctuated Equilibrium

Current evolutionary biology models usually assume that a phenotype undergoes gradual change. This is in stark contrast to biological intuition, which indicates that change can also be punctuated-the phenotype can jump. Such a jump can especially occur at speciation, i.e. dramatic change occurs that drives the species apart. Here we derive a Central Limit Theorem for punctuated equilibrium. We show that, if adaptation is fast, for weak convergence to hold, dramatic change has to be a rare event.\n\nAMS subject classification: 60F05, 60J70, 60J85, 62P10, 92B99

Evolutionary Biology↗

bioRxiv2025

Phylogram instead of chronogram when assessing the neutral evolution of a trait

Comparative analyses of trait evolution aim to uncover the different evolutionary forces shaping phenotypic diversity among species. This is typically done by fitting various evolutionary models to observed trait changes along a species tree. For instance, under neutral evolution, trait values are modelled as changing randomly along the branches of the tree. In contrast, for a trait under selection, species are typically assumed to track an optimal trait value, which itself may shift along the tree. Here, rather than relying on alternative models to discriminate among evolutionary scenarios, we focus on the underlying species tree, and specifically the units in which its branch lengths are measured. Species trees are usually represented as chronograms, with branch lengths proportional to time. The rationale is that time correlates with trait changes through its connection to the number of generations. However, since the generation time of species can also vary along the phylogenetic tree, we argue that chronograms introduces biases. In contrast, phylograms with branch lengths in units of sequence divergence will account for the effect of changing generation time. In this study, we develop a method to test whether a phylogram provides a better fit than a chronogram for modelling trait evolution. We show using simulations that, for a trait evolving neutrally, the fit of a random evolution model has more support on a phylogram than on a chronogram. However, comparing models and testing different scenarios of selection using a phylogram leads to incorrect predictions. Given these results, we argue that we should use phylograms instead of chronograms when assessing the neutral evolution of a trait. Nevertheless, we support the fact that we should generally continue to use chronograms to model selection acting on a quantitative trait. Lay summaryWhen we look at different species, we can see that some traits are different between them. For example, the brain size of different primate and human lineages varies. The question we ask is: does the time that passed explain the differences in their traits? Or are genetic differences between species better at explaining the differences? The standard in evolutionary biology is to use time to explain differences in traits. However, if the trait is not under natural selection and instead is changing due to accumulating mutations, the genetic differences between species instead of time should best explain the differences in traits. As a result, we argue that using both genetic differences and species divergence time simultaneously provides a better understanding of how traits evolve across species.

evolutionary biology↗

bioRxiv2026

Lineage-specific positive selection on stress-response genes in wild wheat relatives

Understanding how crop wild relatives (CWR) adapt to diverse environments is important both for evolutionary biology and for the development of climate-resilient agriculture. CWR represent an important reservoir of adaptive variation that can be exploited for future crop improvement. To investigate how natural selection has shaped adaptation in these species, we analysed whole-transcriptome data from four diploid wild wheat relatives with contrasting mating systems: the outcrossing species Aegilops speltoides and Aegilops mutica, and the selfing species Aegilops tauschii and Triticum urartu. We combined the imputed McDonald--Kreitman test (MKT) with lineage-specific estimates of divergence obtained from branch-specific models of molecular evolution. This framework reduces biases caused by slightly deleterious mutations and enables adaptive substitutions to be assigned to individual evolutionary lineages. We detected marked differences among species in the prevalence of positive selection. Evidence of adaptive evolution was concentrated in the outcrossing species, whereas few positively selected genes were identified in the selfing species. Comparisons between standard and branch-specific MKT approaches showed that some signals initially inferred as shared among species were reassigned to individual lineages when divergence was estimated on a branch-specific basis, emphasizing the importance of accurately localizing adaptive substitutions. Functional annotation revealed several candidate genes containing domains associated with abiotic and biotic stress responses. Our study provides a framework for detecting positive selection in wild wheat relatives and identifies candidate genes that may contribute to adaptation and represent valuable targets for future functional analyses and wheat improvement programs.

evolutionary biology↗

bioRxiv2023

Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data

The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell data set of eye cells from five distantly-related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.

evolutionary biology↗

bioRxiv2019

Evolutionary dynamics of the trypsin superfamily and the origins of novel secretory cell function in the internalized ectoderm of the sea anemone Nematostella vectensis

Understanding the drivers of morphological diversity is a persistent challenge in evolutionary biology. Here, we investigate functional diversification of secretory cells in the sea anemone Nematostella vectensis to understand the mechanisms promoting cellular specialization across animals. We demonstrate regionalized expression of gland cell subtypes in the internal ectoderm of N. vectensis and show that adult gland cell identity is acquired very early in development. A phylogenetic survey of trypsins across animals suggests this gene family has undergone numerous expansions. We reveal unexpected diversity in trypsin protein structure and show that trypsin diversity arose through independent acquisitions of non-trypsin domains. Finally, we show that trypsin diversification in N. vectensis was effected through a combination of tandem duplication, exon shuffling, and retrotransposition. Together we reveal that numerous evolutionary mechanisms drove trypsin duplication and divergence during the morphological specialization of cell types and suggest the secretory cell phenotype is highly adaptable as a vehicle for novel secretory products.

evolutionary biology↗

bioRxiv2026

On repeatability and directionality of collateral effects of drug resistance evolution

Drug resistance evolution is hindering the treatment of various diseases. One possible solution could be exploiting trade-offs in resistance to different, existing drugs. Collateral sensitivity means that resistance to one drug increases susceptibility to another. Contrarily, cross-resistance means that resistance to one drug implies resistance to another. These two collateral effects are, however, not always repeatable, nor are they always independent of drug order, i.e. bidirectional. Understanding what drives repeatability and directionality would help define the clinical applicability of collateral sensitivity and avoid cross-resistance. Nevertheless, the genetic and evolutionary mechanisms causing non-repeatability and unidirectionality patterns are not yet fully understood. In this study, we aim to define which drug concentrations, population dynamics, and genetic architectures cause these patterns of collateral effects. We describe the fewest loci and conditions needed for repeatable and non-repeatable, uni- or bidirectional cross-resistance and collateral sensitivity to occur. We show that increasing drug concentration narrows the set of possible adaptive genotypes and thereby increases repeatability. As for selection regimes, clonal interference can explain unidirectional cross-resistance and can increase repeatability, whereas a strong selection, weak mutation regime increases non-repeatability. Overall, we show how non-repeatability and unidirectionality of collateral effects are not properties solely of a drug pair but also of the selection regime: drug dose and population dynamics. Further studies, combining extensive mathematical modelling with measurements of full dose-response curves for drug pairs with known patterns of collateral effects, are needed to shed more light on this problem. 1 Significance statementPredicting the evolution of multidrug resistance is one of the most pressing challenges in modern evolutionary biology and medicine. On the other hand, exploiting "collateral sensitivity" (where resistance to one drug increases susceptibility to another) is a promising direction for sustainable therapies. Collateral effects are often unpredictable and may depend on the order of drug administration (asymmetry), which hinders their clinical applications. While research traditionally treats collateral effects and their patterns as fixed properties of specific drug pairs, we demonstrate how they are fundamentally shaped by the selection environment.

evolutionary biology↗

bioRxiv2021

Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.

evolutionary biology↗

bioRxiv2025

Classification of Urticaceae based on morphology and phylogenetic inference

The Urticaceae (ca. 2600 species) were first formally recognized by Jussieu in the 18th century and last comprehensively monographed by Weddell in the 19th century. Since Weddells work, family delimitation has been modified and many genera described in a fragmented manner. Over the past two decades, numerous molecular studies have supported the inclusion of Cecropiaceae within Urticaceae and identified paraphyly in several genera, notably Laportea, Urera, Boehmeria, Parietaria, Pellionia, and Pouzolzia. However, few studies have translated these molecular insights into a revised taxonomy. This study aimed to provide a robust, updated classification for Urticaceae by: a) increasing taxon and genomic locus sampling through the integration of newly generated sequence data with previously published datasets; and b) incorporating morphological data to support a revised delimitation of tribes and genera, and to establish a new linear sequence for the family. We also sought to identify remaining taxonomic challenges. Using Sanger and Angiosperms353 sequence data, we constructed a phylogenetic framework for 57 out of 59 currently accepted genera. We also assessed the phylogenetic informativeness of 57 morphological characters by mapping them onto the phylogeny. Our analyses support the delimitation of 61 monophyletic genera and an infrafamilial classification comprising seven tribes, two of which we describe as new: Myriocarpeae and Leukosykeae. We provide a revised linear sequence for the family. Our classification reinstates several names previously treated as synonyms (Fleurya, Leptocnide, Margarocarpus, Polychroa, Scepocarpus, Sceptrocnide), places several genera in synonymy (Hemistylus and Rousselia under Pouzolzia; Hesperocnide under Urtica; Gesnouinia and Soleirolia under Parietaria), and proposes the recognition of two new genera, Muimar gen. nov. and Pouzolziella gen. nov., to accommodate Boehmeria nivea and Pouzolzia australis, respectively. Mapping morphological characters onto the phylogeny indicates that while most states are homoplastic at the family level, their combination is valuable for recognizing genera. Geographic character mapping suggests a high degree of spatial conservatism at the genus rank. Our dated ultrametric tree suggests an origin for Urticaceae in Indomalaya during the mid-Cretaceous, followed by establishment in the Laurasian boreotropical flora and subsequent dispersal to the neotropics and Africa. Once classified within an evolutionary framework we believe that the Urticaceae represent a valuable study system in evolutionary biology for investigating transitions across biomes, the drivers of floral trait evolution, and intrinsic speciation mechanisms. New tribes: --Leukosykeae, Myriocarpeae New genera: --Muimar, Pouzolziella

evolutionary biology↗

bioRxiv2023

Saturated Transposon Analysis in Yeast as a One-step Method to Quantify the Fitness Effects of Gene Disruptions on a Genome-Wide Scale

Transposon insertion site sequencing (TIS) is an extremely powerful tool that has greatly advanced our knowledge of functional genomics. However, studies using TIS often focus on gene essentiality and neglect possibly interesting but subtle differences in the importance of genes for fitness. As shown by other studies, expanding of the analysis of TIS data to allow a quantitative estimate of fitness has important application in genetics and evolutionary biology. Here, we present a method to estimate the fitness of gene disruption mutants on a quantitative level using data obtained from a TIS screen developed for the yeast Saccharomyces cerevisiae called SATAY. We show that using the average read count per transposon insertion site provides a metric for fitness that is robust across biological and technical replicate experiments. Importantly, the ability to resolve differences between gene disruption mutants with low fitness depends crucially on the inclusion of insertion sites that are not observed in the sequencing data to estimate the mean. While our method provides reproducible results between replicate SATAY datasets, the obtained fitness distribution differs substantially from those obtained using other techniques. It remains unclear whether these inconsistencies are due to biological or technical differences between the methods. Finally, we give suggestions for modifications of the SATAY procedure that could improve the resolution of the fitness estimates. Our analysis indicates that increasing the sequencing depth does very little to reduce the uncertainty in the estimates, while replacing the PCR amplification with methods that avoid or reduce the number of amplification cycles will likely be most effective in reducing noise.

evolutionary biology↗

bioRxiv2024

Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae

What constraints govern the evolution of gene expression patterns across development remains a fundamental question of evolutionary biology. The advent of single-cell sequencing opens the possibility of learning these constraints by systematically profiling homologous cells across different organisms. The nematode C. elegans is a well-studied model for embryonic development, and its invariant lineage that is conserved with other Caenorhabditis species makes it an ideal model to directly compare gene expression between homologous progenitor and terminal cell types across evolution. We have measured the spatiotemporal divergence of gene expression across embryogenesis by collecting, annotating, and comparing the transcriptomes of homologous embryonic progenitors and terminal cell types, using a dataset comprising >200,000 C. elegans cells and >190,000 C. briggsae cells. We find a high level of similarity in gene expression programs between the species despite tens of millions of years of evolutionary divergence, consistent with their conserved developmental lineages. Even still, thousands of genes show divergence in their cell-type specific expression patterns, and these are enriched for categories involved in environmental response and behavior. Comparing the degree of expression conservation across cell types reveals that certain cell types such as neurons, have diverged more than others such as the intestine and body wall muscle. Taken together, this work identifies likely constraints on the evolution of developmental gene expression and provides a powerful resource for addressing diverse evolutionary questions.

evolutionary biology↗

bioRxiv2024

The divergent responses of salinity generalists to hyposaline stress provide insights into the colonization of freshwaters by diatoms

Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the evolutionary genetic underpinnings behind habitat transitions is therefore a central question in evolutionary biology. We used time-resolved transcriptomics to contrast the hyposalinity stress responses of two ecologically important diatoms: Skeletonema marinoi has a deep marine ancestry but recently invaded brackish waters, whereas Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. S. marinoi is less adept at mitigating even mild salinity stress compared to C. cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long-term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage-specific environmental responses in phytoplankton have likely shaped marine-freshwater transitions on evolutionary timescales and, on contemporary timescales, will likely determine which lineages survive and adapt to changing ocean conditions.

evolutionary biology↗