Molecular determinants of protein evolvability

The plethora of biological functions that sustain life is rooted in the remarkable evolvability of proteins. An emerging view highlights the importance of a protein's initial state in dictating evolutionary success. A deeper comprehension of the mechanisms that govern the evolvability of these initial states can provide invaluable insights into protein evolution. In this review, we describe several molecular determinants of protein evolvability, unveiled by experimental evolution and ancestral sequence reconstruction studies. We further discuss how genetic variation and epistasis can promote or constrain functional innovation and suggest putative underlying mechanisms. By establishing a clear framework for these determinants, we provide potential indicators enabling the forecast of suitable evolutionary starting points and delineate molecular mechanisms in need of deeper exploration.

A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.

Criminal behavior and contingency

Although their perspectives and approaches vary, existing criminological theories are all based on the deterministic optimism that the crucial causes of criminal behavior must exist and can be uncovered. However, no key factor can fully explain the causes of criminal behavior. All factors that directly affect the occurrence of criminal behavior are important, and contingency is always at work. More feasible crime prevention and control measures can be proposed only considering the contingency factor. The aim of this study is to point out the limitations of the deterministic view of existing criminological theories that explain the causes of crime after knowing the results, and simultaneously to propose the contingency model with viable alternative solutions.

Conceptual and empirical bridges between micro- and macroevolution

Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.

Germline-encoded specificities and the predictability of the B cell response

Antibodies result from the competition of B cell lineages evolving under selection for improved antigen recognition, a process known as affinity maturation. High-affinity antibodies to pathogens such as HIV, influenza, and SARS-CoV-2 are frequently reported to arise from B cells whose receptors, the precursors to antibodies, are encoded by particular immunoglobulin alleles. This raises the possibility that the presence of particular germline alleles in the B cell repertoire is a major determinant of the quality of the antibody response. Alternatively, initial differences in germline alleles' propensities to form high-affinity receptors might be overcome by chance events during affinity maturation. We first investigate these scenarios in simulations: when germline-encoded fitness differences are large relative to the rate and effect size variation of somatic mutations, the same germline alleles persistently dominate the response of different individuals. In contrast, if germline-encoded advantages can be easily overcome by subsequent mutations, allele usage becomes increasingly divergent over time, a pattern we then observe in mice experimentally infected with influenza virus. We investigated whether affinity maturation might nonetheless strongly select for particular amino acid motifs across diverse genetic backgrounds, but we found no evidence of convergence to similar CDR3 sequences or amino acid substitutions. These results suggest that although germline-encoded specificities can lead to similar immune responses between individuals, diverse evolutionary routes to high affinity limit the genetic predictability of responses to infection and vaccination.

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.

Speciation and development

Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.

Mutation bias and the predictability of evolution

Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Impact of population size on early adaptation in rugged fitness landscapes

Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases with population size, we find that the height of the first fitness peak encountered when starting from a random genotype displays various behaviours versus population size, even among small and simple rugged landscapes. We show that the accessibility of the different fitness peaks is key to determining whether this height overall increases or decreases with population size. Furthermore, there is often a finite population size that maximizes the height of the first fitness peak encountered when starting from a random genotype. This holds across various classes of model rugged landscapes with sparse peaks, and in some experimental and experimentally inspired ones. Thus, early adaptation in rugged fitness landscapes can be more efficient and predictable for relatively small population sizes than in the large-size limit.

This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.

Evolutionary repeatability of emergent properties of ecological communities

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Rediversification Following Ecotype Isolation Reveals Hidden Adaptive Potential

Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about if communities can regenerate ecological diversity following species removal or extinction, and how the rediversified communities would compare to the original ones. Here we show that simple two-ecotype communities from the E. coli Long Term Evolution Experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different compared to the original community in ways relevant to the mechanism of ecotype coexistence, for example in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, but with unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.

The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems

This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions─the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources─whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.

Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature

Precision medicine offers remarkable potential for the treatment of cancer, but is largely focused on tumors that harbor actionable mutations. Gene expression signatures can expand the scope of precision medicine by predicting response to traditional (cytotoxic) chemotherapy agents without relying on changes in mutational status. We present a new signature extraction method, inspired by the principle of convergent phenotypes, which states that tumors with disparate genetic backgrounds may evolve similar phenotypes independently. This evolutionary-informed method can be utilized to produce consensus signatures predictive of response to over 200 chemotherapeutic drugs found in the Genomics of Drug Sensitivity in Cancer (GDSC) Database. Here, we demonstrate its use by extracting the Cisplatin Response Signature (CisSig). We show that this signature can predict cisplatin response within carcinoma-based cell lines from the GDSC database, and expression of the signatures aligns with clinical trends seen in independent datasets of tumor samples from The Cancer Genome Atlas (TCGA) and Total Cancer Care (TCC) database. Finally, we demonstrate preliminary validation of CisSig for use in muscle-invasive bladder cancer, predicting overall survival in a small cohort of patients who undergo cisplatin-containing chemotherapy. This methodology can be used to produce robust signatures that, with further clinical validation, may be used for the prediction of traditional chemotherapeutic response, dramatically increasing the reach of personalized medicine in cancer.

Systems biology as a framework to understand the physiological and endocrine bases of behavior and its evolution-From concepts to a case study in birds

Organismal behavior, with its tremendous complexity and diversity, is generated by numerous physiological systems acting in coordination. Understanding how these systems evolve to support differences in behavior within and among species is a longstanding goal in biology that has captured the imagination of researchers who work on a multitude of taxa, including humans. Of particular importance are the physiological determinants of behavioral evolution, which are sometimes overlooked because we lack a robust conceptual framework to study mechanisms underlying adaptation and diversification of behavior. Here, we discuss a framework for such an analysis that applies a "systems view" to our understanding of behavioral control. This approach involves linking separate models that consider behavior and physiology as their own networks into a singular vertically integrated behavioral control system. In doing so, hormones commonly stand out as the links, or edges, among nodes within this system. To ground our discussion, we focus on studies of manakins (Pipridae), a family of Neotropical birds. These species have numerous physiological and endocrine specializations that support their elaborate reproductive displays. As a result, manakins provide a useful example to help imagine and visualize the way systems concepts can inform our appreciation of behavioral evolution. In particular, manakins help clarify how connectedness among physiological systems-which is maintained through endocrine signaling-potentiate and/or constrain the evolution of complex behavior to yield behavioral differences across taxa. Ultimately, we hope this review will continue to stimulate thought, discussion, and the emergence of research focused on integrated phenotypes in behavioral ecology and endocrinology.

Stability in gene expression and body-plan development leads to evolutionary conservation

BACKGROUND

Phenotypic evolution is mainly explained by selection for phenotypic variation arising from factors including mutation and environmental noise. Recent theoretical and experimental studies have suggested that phenotypes with greater developmental stability tend to have a constant phenotype and gene expression level within a particular genetic and environmental condition, and this positively correlates with stronger evolutionary conservation, even after the accumulation of genetic changes. This could reflect a novel mechanism that contributes to evolutionary conservation; however, it remains unclear whether developmental stability is the cause, or whether at least it contributes to their evolutionary conservation. Here, using Japanese medaka lines, we tested experimentally whether developmental stages and gene expression levels with greater stability led to their evolutionary conservation.

RESULTS

We first measured the stability of each gene expression level and developmental stage (defined here as the whole embryonic transcriptome) in the inbred F0 medaka population. We then measured their evolutionary conservation in the F3 generation by crossing the F0 line with the distantly related Japanese medaka line (Teradomori), followed by two rounds of intra-generational crossings. The results indicated that the genes and developmental stages that had smaller variations in the F0 generation showed lower diversity in the hybrid F3 generation, which implies a causal relationship between stability and evolutionary conservation.

CONCLUSIONS

These findings suggest that the stability in phenotypes, including the developmental stages and gene expression levels, leads to their evolutionary conservation; this most likely occurs due to their low potential to generate phenotypic variation. In addition, since the highly stable developmental stages match with the body-plan-establishment stage, it also implies that the developmental stability potentially contributed to the strict conservation of animal body plan.

High level of novelty under the hood of convergent evolution

Little is known about the extent to which species use homologous regulatory architectures to achieve phenotypic convergence. By characterizing chromatin accessibility and gene expression in developing wing tissues, we compared the regulatory architecture of convergence between a pair of mimetic butterfly species. Although a handful of color pattern genes are known to be involved in their convergence, our data suggest that different mutational paths underlie the integration of these genes into wing pattern development. This is supported by a large fraction of accessible chromatin being exclusive to each species, including the de novo lineage-specific evolution of a modular optix enhancer. These findings may be explained by a high level of developmental drift and evolutionary contingency that occurs during the independent evolution of mimicry.

Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in 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 the RNA secondary structure (SS) can be analyzed in detail mathematically and computationally, is biologically relevant, and a wealth of bioinformatic data are 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 types are structurally very similar, suggesting that bias strongly constrains evolutionary dynamics. Here, we extend these results with emphasis on much larger RNA with lengths up to 3000 nucleotides. By examining both abstract shapes and structural motif frequencies (i.e., the number 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 spaces of all possible RNA structures. Our motif frequency study yields another result, where the frequencies of different motifs can be used in machine learning algorithms to classify random and natural RNA with high accuracy, especially for longer RNA (e.g., ROC AUC 0.86 for L = 1000). The most important motifs for classification are 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 contingency in lingulid brachiopods across mass extinctions

Morphology usually serves as an effective proxy for functional ecology,^1,2,3,4,5 and evaluating morphological, anatomical, and ecological changes permits a deeper understanding of the nature of diversification and macroevolution.^{5,6,7,8,9,10,11,12} Lingulid (order Lingulida) brachiopods are both diverse and abundant during the early Palaeozoic but decrease in diversity over time, with only a few genera of linguloids and discinoids present in modern marine ecosystems, resulting in them frequently being referred to as "living fossils."^13,14,15 The dynamics that drove this decline remain uncertain, and it has not been determined if there is an associated decline in morphological and ecological diversity. Here, we apply geometric morphometrics to reconstruct global morphospace occupation for lingulid brachiopods through the Phanerozoic, with results showing that maximum morphospace occupation was reached by the Early Ordovician. At this time of peak diversity, linguloids with a sub-rectangular shell shape already possessed several evolutionary features, such as the rearrangement of mantle canals and reduction of the pseudointerarea, common to all modern infaunal forms. The end Ordovician mass extinction has a differential effect on linguloids, disproportionally wiping out those forms with a rounded shell shape, while forms with sub-rectangular shells survived both the end Ordovician and the Permian-Triassic mass extinctions, leaving a fauna predominantly composed of infaunal forms. For discinoids, both morphospace occupation and epibenthic life strategies remain consistent through the Phanerozoic. Morphospace occupation over time, when considered using anatomical and ecological analyses, suggests that the limited morphological and ecological diversity of modern lingulid brachiopods reflects evolutionary contingency rather than deterministic processes.

Experimental approaches to study evolutionary cell biology using yeasts

The past century has witnessed tremendous advances in understanding how cells function. Nevertheless, how cellular processes have evolved is still poorly understood. Many studies have highlighted surprising molecular diversity in how cells from diverse species execute the same processes, and advances in comparative genomics are likely to reveal much more molecular diversity than was believed possible until recently. Extant cells remain therefore the product of an evolutionary history that we vastly ignore. Evolutionary cell biology has emerged as a discipline aiming to address this knowledge gap by combining evolutionary, molecular, and cellular biology thinking. Recent studies have shown how even essential molecular processes, such as DNA replication, can undergo fast adaptive evolution under certain laboratory conditions. These developments open new lines of research where the evolution of cellular processes can be investigated experimentally. Yeasts naturally find themselves at the forefront of this research line. Not only do they allow the observation of fast evolutionary adaptation, but they also provide numerous genomic, synthetic, and cellular biology tools already developed by a large community. Here we propose that yeasts can serve as an "evolutionary cell lab" to test hypotheses, principles, and ideas in evolutionary cell biology. We discuss various experimental approaches available for this purpose, and how biology at large can benefit from them.

Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.

Molecular parallelism in the evolution of a master sex-determining role for the anti-Mullerian hormone receptor 2 gene (amhr2) in Midas cichlids

The evolution of sex chromosomes and their differentiation from autosomes is a major event during genome evolution that happened many times in several lineages. The repeated evolution and lability of sex-determination mechanisms in fishes makes this a well-suited system to test for general patterns in evolution. According to current theory, differentiation is triggered by the suppression of recombination following the evolution of a new master sex-determining gene. However, the molecular mechanisms that establish recombination suppression are known from few examples, owing to the intrinsic difficulties of assembling sex-determining regions (SDRs). The development of forward-genetics and long-read sequencing have generated a wealth of data questioning central aspects of the current theory. Here, we demonstrate that sex in Midas cichlids is determined by an XY system, and identify and assemble the SDR by combining forward-genetics, long-read sequencing and optical mapping. We show how long-reads aid in the detection of artefacts in genotype-phenotype mapping that arise from incomplete genome assemblies. The male-specific region is restricted to a 100-kb segment on chromosome 4 that harbours transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 gene, which has evolved master sex-determining functions repeatedly. Our data suggest that amhr2Y originated by an interchromosomal translocation from chromosome 20 to 4 pre-dating the split of Midas and Flier cichlids. In the latter, it is pseudogenized and translocated to another chromosome. Duplication of anti-Mullerian genes is a common route to establishing new sex determiners, highlighting the role of molecular parallelism in the evolution of sex determination.

Genomic responses to parallel temperature gradients in the eelgrass Zostera marina in adjacent bays

The extent of parallel genomic responses to similar selective pressures depends on a complex array of environmental, demographic, and evolutionary forces. Laboratory experiments with replicated selective pressures yield mixed outcomes under controlled conditions and our understanding of genomic parallelism in the wild is limited to a few well-established systems. Here, we examine genomic signals of selection in the eelgrass Zostera marina across temperature gradients in adjacent embayments. Although we find many genomic regions with signals of selection within each bay there is very little overlap in signals of selection at the SNP level, despite most polymorphisms being shared across bays. We do find overlap at the gene level, potentially suggesting multiple mutational pathways to the same phenotype. Using polygenic models we find that some sets of candidate SNPs are able to predict temperature across both bays, suggesting that small but parallel shifts in allele frequencies may be missed by independent genome scans. Together, these results highlight the continuous rather than binary nature of parallel evolution in polygenic traits and the complexity of evolutionary predictability.

Multiple pathways to herbivory underpinned deep divergences in ornithischian evolution

The extent to which evolution is deterministic is a key question in biology,^{1,2,3,4,5,6,7,8,9} with intensive debate on how adaptation^{6,10,11,12,13} and constraints^14,15,16 might canalize solutions to ecological challenges.^4,5,6 Alternatively, unique adaptations^1,9,17 and phylogenetic contingency^1,3,18 may render evolution fundamentally unpredictable.³ Information from the fossil record is critical to this debate,^1,2,11 but performance data for extinct taxa are limited.⁷ This knowledge gap is significant, as general morphology may be a poor predictor of biomechanical performance.^17,19,20 High-fiber herbivory originated multiple times within ornithischian dinosaurs,²¹ making them an ideal clade for investigating evolutionary responses to similar ecological pressures.²² However, previous biomechanical modeling studies on ornithischian crania^17,23,24,25 have not compared early-diverging taxa spanning independent acquisitions of herbivory. Here, we perform finite-element analysis on the skull of five early-diverging members of the major ornithischian clades to characterize morphofunctional pathways to herbivory. Results reveal limited functional convergence among ornithischian clades, with each instead achieving comparable performance, in terms of reconstructed patterns and magnitudes of functionally induced stress, through different adaptations of the feeding apparatus. Thyreophorans compensated for plesiomorphic low performance through increased absolute size, heterodontosaurids expanded jaw adductor muscle volume, ornithopods increased jaw system efficiency, and ceratopsians combined these approaches. These distinct solutions to the challenges of herbivory within Ornithischia underpinned the success of this diverse clade. Furthermore, the resolution of multiple solutions to equivalent problems within a single clade through macroevolutionary time demonstrates that phenotypic evolution is not necessarily predictable, instead arising from the interplay of adaptation, innovation, contingency, and constraints.^{1,2,3,7,8,9,18}.

Evolution: Mix-and-match adaptations in plant-eating dinosaurs

Ornithischian dinosaurs were primary consumers in Mesozoic ecosystems, their evolution intricately linked to challenges of a plant-heavy diet. Whether phenotypic similarities among different ornithischian lineages imply a common functional solution to herbivory is unclear. New research suggests that they evolved herbivory via multiple biomechanical pathways.

Evolution of the glomerulus in a marine environment and its implications for renal function in terrestrial vertebrates

Nearly a century ago, Homer Smith proposed that the glomerulus evolved to meet the challenge of excretion of water in freshwater vertebrates. This hypothesis has been repeatedly restated in the nephrology and renal physiology literature, even though we now know that vertebrates evolved and diversified in marine (saltwater) environments. A more likely explanation is that the vertebrate glomerulus evolved from the meta-nephridium of marine invertebrates, with the driving force for ultrafiltration being facilitated by the apposition of the filtration barrier to the vasculature (in vertebrates) rather than the coelom (in invertebrates) and the development of a true heart and the more complex vertebrate vascular system. In turn, glomerular filtration aided individual regulation of divalent ions like magnesium, calcium, and sulfate compatible with the function of cardiac and skeletal muscle required for mobile predators. The metabolic cost, imposed by reabsorption of the small amounts of sodium required to drive secretion of these over-abundant divalent ions, was small. This innovation, developed in a salt-water environment, provided a preadaptation for life in freshwater, in which the glomerulus was co-opted to facilitate water excretion, albeit with the additional metabolic demand imposed by the need to reabsorb the majority of filtered sodium. The evolution of the glomerulus in saltwater also provided preadaptation for terrestrial life, where the imperative is conservation of both water and electrolytes. The historical contingencies of this scenario may explain why the mammalian kidney is so metabolically inefficient, with ∼80% of oxygen consumption being used to drive reabsorption of filtered sodium.

Teleonomy: Revisiting a Proposed Conceptual Replacement for Teleology

The concept of teleonomy has been attracting renewed attention recently. This is based on the idea that teleonomy provides a useful conceptual replacement for teleology, and even that it constitutes an indispensable resource for thinking biologically about purposes. However, both these claims are open to question. We review the history of teleological thinking from Greek antiquity to the modern period to illuminate the tensions and ambiguities that emerged when forms of teleological reasoning interacted with major developments in biological thought. This sets the stage for an examination of Pittendrigh's (Adaptation, natural selection, and behavior. In: Roe A, Simpson GG (eds) Behavior and evolution. Yale University Press, New Haven, pp 390-416, 1958) introduction of "teleonomy" and its early uptake in the work of prominent biologists. We then explore why teleonomy subsequently foundered and consider whether the term may yet have significance for discussions of goal-directedness in evolutionary biology and philosophy of science. This involves clarifying the relationship between teleonomy and teleological explanation, as well as asking how the concept of teleonomy impinges on research at the frontiers of evolutionary theory.

Climate adaptation and vulnerability of foundation species in a global change hotspot

Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.

Supply-driven evolution: Mutation bias and trait-fitness distributions can drive macro-evolutionary dynamics

Many well-documented macro-evolutionary phenomena still challenge current evolutionary theory. Examples include long-term evolutionary trends, major transitions in evolution, conservation of certain biological features such as hox genes, and the episodic creation of new taxa. Here, we present a framework that may explain these phenomena. We do so by introducing a probabilistic relationship between trait value and reproductive fitness. This integration allows mutation bias to become a robust driver of long-term evolutionary trends against environmental bias, in a way that is consistent with all current evolutionary theories. In cases where mutation bias is strong, such as when detrimental mutations are more common than beneficial mutations, a regime called “supply-driven” evolution can arise. This regime can explain the irreversible persistence of higher structural hierarchies, which happens in the major transitions in evolution. We further generalize this result in the long-term dynamics of phenotype spaces. We show how mutations that open new phenotype spaces can become frozen in time. At the same time, new possibilities may be observed as a burst in the creation of new taxa.

Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies

Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

Convergent evolution of the annual life history syndrome from perennial ancestors

Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.

Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community

Species interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this question in a community of yeast Saccharomyces cerevisiae and alga Chlamydomonas reinhardtii that have a net commensal relationship that results from a balance between competitive and mutualistic interactions. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular those that increase and reduce the yields of both species. The presence of the alga does not change which mutations are adaptive in yeast (that is, there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favour yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of the alga, adaptative mutations contending for fixation in yeast are more likely to enhance the mutualism, even though cooperativity is not directly favoured by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.

Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis

Cases of parallel or recurrent gene fusions in evolution as well as in genetic disease and cancer are difficult to explain, because unlike point mutations, they can require the repetition of a similar configuration of multiple breakpoints rather than the repetition of a single point mutation. The used-together-fused-together hypothesis holds that genes that are used together repeatedly and persistently in a specific context are more likely to undergo fusion mutation in the course of evolution for mechanistic reasons. This hypothesis offers to explain gene fusion in both evolution and disease under one umbrella. Using bioinformatic data, we tested this hypothesis against alternatives, including that all gene pairs can fuse by random mutation, but among pairs thus fused, those that had interacted previously are more likely to be favored by selection. Results show that across multiple measures of gene interaction, human genes whose orthologs are fused in one or more species are more likely to interact with each other than random pairs of genes of the same genomic distance between pair members; that an overlap exists between genes that fused in the course of evolution in non-human species and genes that undergo fusion in human cancers; and that across six primate species studied, fusions predominate over fissions and exhibit substantial evolutionary parallelism. Together, these results support the used-together-fused-together hypothesis over its alternatives. Multiple implications are discussed, including the relevance of mutational mechanisms to the evolution of genome organization, to the distribution of fitness effects of mutation, to evolutionary parallelism and more.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11692-022-09579-9.

The Inverse Krogh Principle: All Organisms Are Worthy of Study

AbstractKrogh's principle states, "For such a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied." The downside of picking a question first and then finding an ideal organism on which to study it is that it will inevitably leave many organisms neglected. Here, we promote the inverse Krogh principle: all organisms are worthy of study. The inverse Krogh principle and the Krogh principle are not opposites. Rather, the inverse Krogh principle emphasizes a different starting point for research: start with a biological unit, such as an organism, clade, or specific organism trait, then seek or create tractable research questions. Even the hardest-to-study species have research questions that can be asked of them: Where does it fall within the tree of life? What resources does it need to survive and reproduce? How does it differ from close relatives? Does it have unique adaptations? The Krogh and inverse Krogh approaches are complementary, and many research programs naturally include both. Other considerations for picking a study species include extreme species, species informative for phylogenetic analyses, and the creation of models when a suitable species does not exist. The inverse Krogh principle also has pitfalls. A scientist that picks the organism first might choose a research question not really suited to the organism, and funding agencies rarely fund organism-centered grant proposals. The inverse Krogh principle does not call for all organisms to receive the same amount of research attention. As knowledge continues to accumulate, some organisms-models-will inevitably have more known about them than others. Rather, it urges a broader search across organismal diversity to find sources of inspiration for research questions and the motivation needed to pursue them.

Analysis of the evolution of resistance to multiple antibiotics enables prediction of the Escherichia coli phenotype-based fitness landscape

The fitness landscape represents the complex relationship between genotype or phenotype and fitness under a given environment, the structure of which allows the explanation and prediction of evolutionary trajectories. Although previous studies have constructed fitness landscapes by comprehensively studying the mutations in specific genes, the high dimensionality of genotypic changes prevents us from developing a fitness landscape capable of predicting evolution for the whole cell. Herein, we address this problem by inferring the phenotype-based fitness landscape for antibiotic resistance evolution by quantifying the multidimensional phenotypic changes, i.e., time-series data of resistance for eight different drugs. We show that different peaks of the landscape correspond to different drug resistance mechanisms, thus supporting the validity of the inferred phenotype-fitness landscape. We further discuss how inferred phenotype-fitness landscapes could contribute to the prediction and control of evolution. This approach bridges the gap between phenotypic/genotypic changes and fitness while contributing to a better understanding of drug resistance evolution.

Open problems in mathematical biology

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the extent to which our hypotheses agree with reality. But doing so in a systematic way is becoming increasingly challenging as our hypotheses become more detailed, and our data becomes more complex. Mathematical methods are therefore gaining in importance across the life- and biomedical sciences. Mathematical models allow us to test our understanding, make testable predictions about future behaviour, and gain insights into how we can control the behaviour of biological systems. It has been argued that mathematical methods can be of great benefit to biologists to make sense of data. But mathematics and mathematicians are set to benefit equally from considering the often bewildering complexity inherent to living systems. Here we present a small selection of open problems and challenges in mathematical biology. We have chosen these open problems because they are of both biological and mathematical interest.

Laplace's demon in biology: Models of evolutionary prediction

Our ability to predict natural phenomena can be limited by incomplete information. This issue is exemplified by "Laplace's demon," an imaginary creature proposed in the 18th century, who knew everything about everything, and thus could predict the full nature of the universe forward or backward in time. Quantum mechanics, among other things, has cast doubt on the possibility of Laplace's demon in the full sense, but the idea still serves as a useful metaphor for thinking about the extent to which prediction is limited by incomplete information on deterministic processes versus random factors. Here, we use simple analytical models and computer simulations to illustrate how data limits can be captured in a Bayesian framework, and how they influence our ability to predict evolution. We show how uncertainty in measurements of natural selection, or low predictability of external environmental factors affecting selection, can greatly reduce predictive power, often swamping the influence of intrinsic randomness caused by genetic drift. Thus, more accurate knowledge concerning the causes and action of natural selection is key to improving prediction. Fortunately, our analyses and simulations show quantitatively that reasonable improvements in data quantity and quality can meaningfully increase predictability.

Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects

Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental and phenotypic data with Bayesian modelling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (that is, habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

In Silico Analysis of Tetrodotoxin Binding in Voltage-Gated Sodium Ion Channels from Toxin-Resistant Animal Lineages

Multiple animal species have evolved resistance to the neurotoxin tetrodotoxin (TTX) through changes in voltage-gated sodium ion channels (VGSCs). Amino acid substitutions in TTX-resistant lineages appear to be positionally convergent with changes in homologous residues associated with reductions in TTX block. We used homology modeling coupled with docking simulations to test whether positionally convergent substitutions generate functional convergence at the level of TTX–channel interactions. We found little evidence that amino acids at convergent positions generated similar patterns among TTX-resistant animal lineages across several metrics, including number of polar contacts, polar contact position, and estimates of binding energy. Though binding energy values calculated for TTX docking were reduced for some TTX-resistant channels, not all TTX-resistant channels and not all of our analyses returned reduced binding energy values for TTX-resistant channels. Our results do not support a simple model of toxin resistance where a reduced number of bonds between TTX and the channel protein prevents blocking. Rather models that incorporate flexibility and movement of the protein overall may better describe how homologous substitutions in the channel cause changes in TTX block.

Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species

Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (Monarcha castaneiventris) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira M. c. megarhynchus has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA/SC) M. c. ugiensis is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the MC1R pigmentation gene are associated with melanism on SA/SC, while ASIP, an antagonistic ligand of MC1R, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. MC1R shows evidence of a recent, strong, soft selective sweep. The region including ASIP shows more complex signatures; however, we find evidence for sweeps in mutations near ASIP, which are comparatively older than those on MC1R and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies.

Chestnut-bellied Monarchs (Monarcha castaneiventris ugiensis) from two archipelagos in the Solomon Islands have evolved entirely black plumage from a chestnut ancestor (Monarcha castaneiventris megarhynchus), a phenomenon known as island melanism. We obtain and analyze whole genome sequences using traditional summary statistics and new methods that combine inference of the ancestral recombination graph with machine learning. We find multiple lines of evidence for independent selective sweeps on the MC1R and ASIP genes, a receptor/ligand pair which regulates the production of melanin. Melanism on each archipelago is mediated by mutations in one of these two genes. Mutations in and around MC1R underwent a recent soft sweep experiencing strong selection on the islands of Santa Ana and Santa Catalina, whereas selection was also strong but comparatively older for ASIP on the island of Ugi. We show how melanism originated under positive selection on independent molecular targets, evolving convergently in taxa where coloration mediates reproductive isolation.

Evolutionary endocrinology and the problem of Darwin's tangled bank

Like Darwin's tangled bank of biodiversity, the endocrine mechanisms that give rise to phenotypic diversity also exhibit nearly endless forms. This tangled bank of mechanistic diversity can prove problematic as we seek general principles on the role of endocrine mechanisms in phenotypic evolution. A key unresolved question is therefore: to what degree are specific endocrine mechanisms re-used to bring about replicated phenotypic evolution? Related areas of inquiry are booming in molecular ecology, but behavioral traits are underrepresented in this literature. Here, I leverage the rich comparative tradition in evolutionary endocrinology to evaluate whether and how certain mechanisms may be repeated hotspots of behavioral evolutionary change. At one extreme, mechanisms may be parallel, such that evolution repeatedly uses the same gene or pathway to arrive at multiple independent (or, convergent) origins of a particular behavioral trait. At the other extreme, the building blocks of behavior may be unique, such that outwardly similar phenotypes are generated via lineage-specific mechanisms. This review synthesizes existing case studies, phylogenetic analyses, and experimental evolutionary research on mechanistic parallelism in animal behavior. These examples show that the endocrine building blocks of behavior have some elements of parallelism across replicated evolutionary events. However, support for parallelism is variable among studies, at least some of which relates to the level of complexity at which we consider sameness (i.e. pathway vs. gene level). Moving forward, we need continued experimentation and better testing of neutral models to understand whether, how - and critically, why - mechanism A is used in one lineage and mechanism B is used in another. We also need continued growth of large-scale comparative analyses, especially those that can evaluate which endocrine parameters are more or less likely to undergo parallel evolution alongside specific behavioral traits. These efforts will ultimately deepen understanding of how and why hormone-mediated behaviors are constructed the way that they are.

Rapid-cycling Brassica rapa evolves even earlier flowering under experimental drought

PREMISE

Changes in climate can impose selection on populations and may lead to rapid evolution. One such climatic stress is drought, which plant populations may respond to with escape (rapid growth and early flowering) or avoidance (slow growth and efficient water-use). However, it is unclear if drought escape would be a viable strategy for populations that already flower early from prior selection.

METHODS

In an experimental evolution study, we subjected rapid-cycling Brassica rapa (RCBr), which was previously selected for early flowering, to four generations of experimental drought or watered conditions. We then grew ancestral and descendant populations concurrently under drought and watered conditions to assess evolution, plasticity, and adaptation.

RESULTS

The RCBr populations that evolved under drought had earlier flowering and lower water-use efficiency than the populations that evolved under watered conditions, indicating evolutionary divergence. The drought descendants also had a trend of earlier flowering compared to ancestors, indicating evolution. Evolution of earlier flowering under drought followed the direction of selection and increased fitness and was consistent with studies in natural and experimental populations of this species, suggesting adaptive evolution.

CONCLUSIONS

We found rapid adaptive evolution of drought escape in RCBr and little evidence for constraints on flowering time evolution, even though RCBr already flowers extremely early. Our results suggest that some populations may harbor sufficient genetic variation for evolution even after strong selection has occurred. Our study also illustrates the utility of combining artificial selection, experimental evolution, and the resurrection approach to study the evolution of functional traits.

A road map for in vivo evolution experiments with blood-borne parasitic microbes

Laboratory experiments in which blood-borne parasitic microbes evolve in their animal hosts offer an opportunity to study parasite evolution and adaptation in real time and under natural settings. The main challenge of these experiments is to establish a protocol that is both practical over multiple passages and accurately reflects natural transmission scenarios and mechanisms. We provide a guide to the steps that should be considered when designing such a protocol, and we demonstrate its use via a case study. We highlight the importance of choosing suitable ancestral genotypes, treatments, number of replicates per treatment, types of negative controls, dependent variables, covariates, and the timing of checkpoints for the experimental design. We also recommend specific preliminary experiments to determine effective methods for parasite quantification, transmission, and preservation. Although these methodological considerations are technical, they also often have conceptual implications. To this end, we encourage other researchers to design and conduct in vivo evolution experiments with blood-borne parasitic microbes, despite the challenges that the work entails.

Local and global ordering dynamics in multistate voter models

We investigate the time evolution of the density of active links and of the entropy of the distribution of agents among opinions in multistate voter models with all-to-all interaction and on uncorrelated networks. Individual realizations undergo a sequence of eliminations of opinions until consensus is reached. After each elimination the population remains in a metastable state. The density of active links and the entropy in these states varies from realization to realization. Making some simple assumptions we are able to analytically calculate the average density of active links and the average entropy in each of these states. We also show that, averaged over realizations, the density of active links decays exponentially, with a timescale set by the size and geometry of the graph, but independent of the initial number of opinion states. The decay of the average entropy is exponential only at long times when there are at most two opinions left in the population. Finally, we show how metastable states comprising only a subset of opinions can be artificially engineered by introducing precisely one zealot in each of the prevailing opinions.

A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?

Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean F_ST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's D_NS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (d_XY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.

The landscape of transcriptional and translational changes over 22 years of bacterial adaptation

Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here, we use the Escherichia coli long-term evolution experiment (LTEE) as a model to address this challenge. To understand how different genomic changes could lead to parallel fitness gains, we characterize the landscape of transcriptional and translational changes across 12 replicate populations evolving in parallel for 50,000 generations. By quantifying absolute changes in mRNA abundances, we show that not only do all evolved lines have more mRNAs but that this increase in mRNA abundance scales with cell size. We also find that despite few shared mutations at the genetic level, clones from replicate populations in the LTEE are remarkably similar in their gene expression patterns at both the transcriptional and translational levels. Furthermore, we show that the majority of the expression changes are due to changes at the transcriptional level with very few translational changes. Finally, we show how mutations in transcriptional regulators lead to consistent and parallel changes in the expression levels of downstream genes. These results deepen our understanding of the molecular mechanisms underlying complex adaptations and provide insights into the repeatability of evolution.

Emerging Research Topics in the Vibrionaceae and the Squid-Vibrio Symbiosis

The Vibrionaceae encompasses a cosmopolitan group that is mostly aquatic and possesses tremendous metabolic and genetic diversity. Given the importance of this taxon, it deserves continued and deeper research in a multitude of areas. This review outlines emerging topics of interest within the Vibrionaceae. Moreover, previously understudied research areas are highlighted that merit further exploration, including affiliations with marine plants (seagrasses), microbial predators, intracellular niches, and resistance to heavy metal toxicity. Agarases, phototrophy, phage shock protein response, and microbial experimental evolution are also fields discussed. The squid-Vibrio symbiosis is a stellar model system, which can be a useful guiding light on deeper expeditions and voyages traversing these "seas of interest". Where appropriate, the squid-Vibrio mutualism is mentioned in how it has or could facilitate the illumination of these various subjects. Additional research is warranted on the topics specified herein, since they have critical relevance for biomedical science, pharmaceuticals, and health care. There are also practical applications in agriculture, zymology, food science, and culinary use. The tractability of microbial experimental evolution is explained. Examples are given of how microbial selection studies can be used to examine the roles of chance, contingency, and determinism (natural selection) in shaping Earth's natural history.

Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns

Long-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.

Evolutionary history and strength of selection determine the rate of antibiotic resistance adaptation

Bacterial adaptation to stressful environments often produces evolutionary constraints whereby increases in resistance are associated with reduced fitness in a different environment. The exploitation of this resistance-cost trade-off has been proposed as the basis of rational antimicrobial treatment strategies designed to limit the evolution of drug resistance in bacterial pathogens. Recent theoretical, laboratory, and clinical studies have shown that fluctuating selection can maintain drug efficacy and even restore drug susceptibility, but can also increase the rate of adaptation and promote cross-resistance to other antibiotics. In this paper, we combine mathematical modeling, experimental evolution, and whole-genome sequencing to follow evolutionary trajectories towards β-lactam resistance under fluctuating selective conditions. Our experimental model system consists of eight populations of Escherichia coli K12 evolving in parallel to a serial dilution protocol designed to dynamically control the strength of selection for resistance. We implemented adaptive ramps with mild and strong selection, resulting in evolved populations with similar levels of resistance, but with different evolutionary dynamics and diverging genotypic profiles. We found that mutations that emerged under strong selection are unstable in the absence of selection, in contrast to resistance mutations previously selected in the mild selection regime that were stably maintained in drug-free environments and positively selected for when antibiotics were reintroduced. Altogether, our population dynamics model and the phenotypic and genomic analysis of the evolved populations show that the rate of resistance adaptation is contingent upon the strength of selection, but also on evolutionary constraints imposed by prior drug exposures.