Relaxed selection in the wild

Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals

Cetaceans have evolved unique limb structures, such as flippers, due to genetic changes during their transition to aquatic life. However, the full understanding of the genetic and evolutionary mechanisms behind these changes is still developing. By examining 25 limb-related protein-coding genes across various mammalian species, we compared genetic changes between aquatic mammals, like whales, and other mammals with unique limb structures such as bats, rodents and elephants. Our findings revealed significant modifications in limb-related genes, including variations in the Hox, GDF5 and Evx genes. Notably, a relaxed selection in several key genes was observed, suggesting a lifting of developmental constraints, which might have facilitated the emergence of morphological innovations in cetacean limb morphology. We also uncovered non-synonymous changes, insertions and deletions in these genes, particularly in the polyalanine tract of HOXD13, which are distinctive to cetaceans or convergent with other aquatic mammals. These genetic variations correlated with the diverse and specialized limb structures observed in cetaceans, indicating a complex interplay of relaxed selection and specific mutations in mammalian limb evolution.

Acoustic recognition of predators by mantled howler monkeys (Alouatta palliata): A playback experiment with naïve and experienced subjects

OBJECTIVES

When the production of antipredator behaviors is costly, prey is expected to stop displaying such behaviors and lose the ability to recognize extirpated predators. However, the loss or maintenance of predator recognition abilities is conditional on the eco-evolutionary context of prey. Here, we examined the behavioral responses of naïve and experienced mantled howler monkeys (Alouatta palliata) to simulated acoustic cues from natural predators.

METHODS

We studied experienced individuals in the Uxpanapa Valley and naïve individuals in Los Tuxtlas (Veracruz, México). Jaguars (Panthera onca) and harpy eagles (Harpia harpyja), the main predators of howler monkeys, are extant in the Uxpanapa Valley but have been extirpated in Los Tuxtlas for approximately 70 and 45 years, respectively. We exposed six naïve and six experienced groups to playbacks of acoustic stimuli from the two predators and a non-predator control species (plain chachalacas, Ortalis vetula), and recorded the latency, frequency, and duration of antipredation behaviors (n = 127 trials).

RESULTS

In contrast with experienced mantled howler monkeys, naïve subjects did not respond to trials from harpy eagles. However, response patterns were generally similar between naïve and experienced individuals when exposed to jaguar stimuli.

DISCUSSION

Our findings suggest that naïve mantled howler monkeys do not recognize harpy eagle calls, but they respond to jaguar calls in a manner consistent with experienced individuals. These results illustrate how different mechanisms for the recognition of extirpated predators operate within a single species according to evolutionary and ecological experience.

Impact of feralization on evolutionary trajectories in the genomes of feral cat island populations

Feralization is the process of domesticated animals returning to the wild and it is considered the counterpart of domestication. Molecular genetic changes are well documented in domesticated organisms but understudied in feral populations. In this study, the genetic differentiation between domestic and feral cats was inferred by analysing whole-genome sequencing data of two geographically distant feral cat island populations, Dirk Hartog Island (Australia) and Kaho'olawe (Hawaii) as well as domestic cats and European wildcats. The study investigated population structure, genetic differentiation, genetic diversity, highly differentiated genes, and recombination rates. Genetic structure analyses linked both feral cat populations to North American domestic and European cat populations. Recombination rates in feral cats were lower than in domestic cats but higher than in wildcats. For Australian and Hawaiian feral cats, 105 and 94 highly differentiated genes compared to domestic cats respectively, were identified. Annotated genes had similar functions, with almost 30% of the divergent genes related to nervous system development in both feral groups. Twenty mutually highly differentiated genes were found in both feral populations. Evolution of highly differentiated genes was likely driven by specific demographic histories, the relaxation of the selective pressures associated with domestication, and adaptation to novel environments to a minor extent. Random drift was the prevailing force driving highly divergent regions, with relaxed selection in feral populations also playing a significant role in differentiation from domestic cats. The study demonstrates that feralization is an independent process that brings feral cats on a unique evolutionary trajectory.

Turbinal bones are still one of the last frontiers of the tetrapod skull: hypotheses, challenges and perspectives

Turbinals are bony or cartilaginous structures that are present in the nasal cavity of most tetrapods. They are involved in key functions such as olfaction, heat, and moisture conservation, as well as protection of the respiratory tract. Despite recent studies that challenged long-standing hypotheses about their physiological and genomic correlation, turbinals remain largely unexplored, particularly for non-mammalian species. Herein, we review and synthesise the current knowledge of turbinals using an integrative approach that includes comparative anatomy, physiology, histology and genomics. In addition, we provide synonyms and correspondences of tetrapod turbinals from about 80 publications. This work represents a first step towards drawing hypotheses of homology for the whole clade, and provides a strong basis to develop new research avenues.

Lipid Metabolism in Parasitoids and Parasitized Hosts

Parasitoids have an exceptional lifestyle where juvenile development is spent on or in a single host insect, but the adults are free-living. Unlike parasites, parasitoids kill the host. How parasitoids use such a limiting resource, particularly lipids, can affect chances to survive and reproduce. In part 1, we describe the parasitoid lifestyle, including typical developmental strategies. Lipid metabolism in parasitoids has been of interest to researchers since the 1960s and continues to fascinate ecologists, evolutionists, physiologists, and entomologists alike. One reason of this interest is that the majority of parasitoids do not accumulate triacylglycerols as adults. Early research revealed that some parasitoid larvae mimic the fatty acid composition of the host, which may result from a lack of de novo triacylglycerol synthesis. More recent work has focused on the evolution of lack of adult triacylglycerol accumulation and consequences for life history traits. In part 2 of this chapter, we discuss research efforts on lipid metabolism in parasitoids from the 1960s onwards. Parasitoids are also master manipulators of host physiology, including lipid metabolism, having evolved a range of mechanisms to affect the release, synthesis, transport, and take-up of lipids from the host. We lay out the effects of parasitism on host physiology in part 3 of this chapter.

Sustained predation pressure may prevent the loss of anti-predator traits from havened populations

Conservation havens free of invasive predators are increasingly relied upon for fauna conservation, although havened populations can lose anti-predator traits, likely making them less suitable for life 'beyond the fence'. Sustaining low levels of mammalian predator pressure inside havens may prevent the loss of anti-predator traits from havened populations. We opportunistically compared behavioural and morphological anti-predator traits between four woylie (Bettongia penicillata ogilbyi) populations- one haven isolated from all mammalian predators, one haven containing a native mammalian predator (chuditch; Dasyurus geoffroii), and their respective non-havened counterparts (each containing both chuditch and invasive predators). Havened woylies existing without mammalian predators were smaller (shorter hindfeet, smaller body weight) and less reactive (consumed more food from fox-treated and control feeding stations, less agitated during human handling) than a non-havened reference population. However, in the haven containing chuditch, we found no difference in behaviour or morphology compared to the adjacent non-havened population. Across populations, anti-predator responses tended to appear stronger at sites with higher predator activity, suggestive of an adaptive response across a gradient of predation pressure. Our findings suggest that maintaining mammalian predation pressure in conservation havens could be effective for preventing or slowing the loss of anti-predator traits from these populations.

The Roles of Drift and Selection on Short Stamen Loss in Arabidopsis thaliana along an Elevational Gradient in the Spanish Pyrenees

Traits that have lost function sometimes persist through evolutionary time. These traits may be maintained by a lack of standing genetic variation for the trait, if selection against the trait is weak relative to drift, or if they have a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in the Spanish Pyrenees. We found a cline in short stamen number from retention of short stamens in high elevation populations to incomplete loss in low elevation populations. We did not find evidence that limited genetic variation constrains the loss of short stamens at high elevations nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in the Spanish Pyrenees that are different from loci associated with variation in short stamen number across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms maintaining an elevational cline in short stamen number but did identify different genetic loci underlying the variation in short stamen along similar phenotypic clines.

Genomic signatures associated with recurrent scale loss in cyprinid fish

Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.

Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (i) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (ii) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected-and more pleiotropic-genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.

Genomic and phenotypic signatures of bacteriophage coevolution with the phytopathogen Pseudomonas syringae

The rate and trajectory of evolution in an obligate parasite is critically dependent on those of its host(s). Adaptation to a genetically homogeneous host population should theoretically result in specialization, while adaptation to an evolving host population (i.e., coevolution) can result in various outcomes including diversification, range expansion, and/or local adaptation. For viruses of bacteria (bacteriophages, or phages), our understanding of how evolutionary history of the bacterial host(s) impacts viral genotypic and phenotypic evolution is currently limited. In this study, we used whole genome sequencing and two different metrics of phage impacts to compare the genotypes and phenotypes of lytic phages that had either coevolved with or were repeatedly passaged on an unchanging (ancestral) strain of the phytopathogen Pseudomonas syringae. Genomes of coevolved phages had more mutations than those of phages passaged on a constant host, and most mutations were in genes encoding phage tail-associated proteins. Phages from both passaging treatments shared some phenotypic outcomes, including range expansion and divergence across replicate populations, but coevolved phages were more efficient at reducing population growth (particularly of sympatric coevolved hosts). Genotypic similarity correlated with infectivity profile similarity in coevolved phages, but not in phages passaged on the ancestral host. Overall, while adaptation to either host type (coevolving or ancestral) led to divergence in phage tail proteins and infectivity patterns, coevolution led to more rapid molecular changes that increased bacterial killing efficiency and had more predictable effects on infectivity range. Together, these results underscore the important role of hosts in driving viral evolution and in shaping the genotype-phenotype relationship.

Dynamics of evolutionary succession and coordination between opposite adaptations in cuckoo hosts under antagonistic coevolution

Adaptations are driven by specific natural selection pressures throughout biological evolution. However, these cannot inherently align with future shifts in selection dynamics, thus manifesting in opposing directions. We performed field experiments on cuckoo hosts to investigate the coexistence and conflict between two evolutionarily successive but opposing behavioral adaptations-egg retrieval and rejection. Our findings provide key insights. (1) Egg rejection against brood parasites in hosts reshapes egg retrieval to flexible reactions-retrieval, ignoring, or outright rejection of foreign eggs outside the nest cup, departing from instinctual retrieval. (2) Parasitism pressure and egg mimicry by parasites remarkably alter the proportions of the three host reactions. Host species with higher parasitism pressure exhibit frequent and rapid rejection of non-mimetic foreign eggs and reduced ignoring or retrieval responses. Conversely, heightened egg mimicry enhances retrieval behaviors while diminishing ignoring responses. (3) Cuckoos employ consistent mechanisms for rejecting foreign eggs inside or outside the nest cup. Direct rejection of eggs outside the nest cup shows that rejection precedes retrieval, indicating prioritization of specific adaptation over instinct. (4) Cuckoo hosts navigate the conflict between the intentions and motivations associated with egg rejection and retrieval by ignoring foreign eggs, a specific outcome of the rejection-retrieval tradeoff.

Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch Macquaria australasica, which over 3 years (2017-2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome-wide genotypes were used to assess individual ancestry, heterozygosity, short-term effective population size and identify parent-offspring and full-sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half-sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low-flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.

Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant

Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.

Evolutionary Analysis of Cnidaria Small Cysteine-Rich Proteins (SCRiPs), an Enigmatic Neurotoxin Family from Stony Corals and Sea Anemones (Anthozoa: Hexacorallia)

Cnidarians (corals, sea anemones, and jellyfish) produce toxins that play central roles in key ecological processes, including predation, defense, and competition, being the oldest extant venomous animal lineage. Cnidaria small cysteine-rich proteins (SCRiPs) were the first family of neurotoxins detected in stony corals, one of the ocean's most crucial foundation species. Yet, their molecular evolution remains poorly understood. Moreover, the lack of a clear classification system has hindered the establishment of an accurate and phylogenetically informed nomenclature. In this study, we extensively surveyed 117 genomes and 103 transcriptomes of cnidarians to identify orthologous SCRiP gene sequences. We annotated a total of 168 novel putative SCRiPs from over 36 species of stony corals and 12 species of sea anemones. Phylogenetic reconstruction identified four distinct SCRiP subfamilies, according to strict discrimination criteria based on well-supported monophyly with a high percentage of nucleotide and amino acids' identity. Although there is a high prevalence of purifying selection for most SCRiP subfamilies, with few positively selected sites detected, a subset of Acroporidae sequences is influenced by diversifying positive selection, suggesting potential neofunctionalizations related to the fine-tuning of toxin potency. We propose a new nomenclature classification system relying on the phylogenetic distribution and evolution of SCRiPs across Anthozoa, which will further assist future proteomic and functional research efforts.

Floral morph variation mediated by clonal growth and pollinator functional groups of Limonium otolepis in a heterostylous fragmented population

Abstract. Heterostyly, a genetic style polymorphism, is linked to symmetric pollen transfer, vital for its maintenance. Clonal growth typically impacts sexual reproduction by influencing pollen transfer. However, the floral morph variation remains poorly understood under the combined effects of pollinators and clonal growth in heterostyly characterized by negative frequency-dependent selection and disassortative mating. We estimated morph ratios, ramets per genet and heterostylous syndrome and quantified legitimate pollen transfer via clonal growth, pollinators and reciprocal herkogamy between floral morphs in Limonium otolepis, a fragmented population composed of five subpopulations in the desert environment of northwestern China, with small flower and large floral morph variation. All subpopulations but one exhibited pollen-stigma morphology dimorphism. The compatibility between mating types with different pollen-stigma morphologies remained consistent regardless of reciprocal herkogamy. Biased ratios and ramets per genet of the two mating types with distinct pollen-stigma morphologies caused asymmetric pollen flow and varying fruit sets in all subpopulations. Short-tongued insects were the primary pollinators due to small flower sizes. However, pollen-feeding Syrphidae sp. triggered asymmetry in pollen flow between high and low sex organs, with short-styled morphs having lower stigma pollen depositions and greater variation. Clonal growth amplified this variation by reducing intermorph pollen transfer. All in all, pollinators and clonal growth jointly drive floral morph variation. H-morphs with the same stigma-anther position and self-incompatibility, which mitigate the disadvantages of sunken low sex organs with differing from the classical homostyly, might arise from long- and short-styled morphs through a 'relaxed selection'. This study is the first to uncover the occurrence of the H-morph and its associated influencing factors in a distylous plant featuring clonal growth, small flowers and a fragmented population.

Developmental temperature, more than long-term evolution, defines thermal tolerance in an estuarine copepod

Climate change is resulting in increasing ocean temperatures and salinity variability, particularly in estuarine environments. Tolerance of temperature and salinity change interact and thus may impact organismal resilience. Populations can respond to multiple stressors in the short-term (i.e., plasticity) or over longer timescales (i.e., adaptation). However, little is known about the short- or long-term effects of elevated temperature on the tolerance of acute temperature and salinity changes. Here, we characterized the response of the near-shore and estuarine copepod, Acartia tonsa, to temperature and salinity stress. Copepods originated from one of two sets of replicated >40 generation-old temperature-adapted lines: ambient (AM, 18°C) and ocean warming (OW, 22°C). Copepods from these lines were subjected to one and three generations at the reciprocal temperature. Copepods from all treatments were then assessed for differences in acute temperature and salinity tolerance. Development (one generation), three generations, and >40 generations of warming increased thermal tolerance compared to Ambient conditions, with development in OW resulting in equal thermal tolerance to three and >40 generations of OW. Strikingly, developmental OW and >40 generations of OW had no effect on low salinity tolerance relative to ambient. By contrast, when environmental salinity was reduced first, copepods had lower thermal tolerances. These results highlight the critical role for plasticity in the copepod climate response and suggest that salinity variability may reduce copepod tolerance to subsequent warming.

Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance

Aquatic mammals (marine and freshwater species) share significant and similar adaptations, enabling them to tolerate hypoxia during regular breath-hold diving. Despite the established importance of HIF1A, a master regulator in the molecular mechanism of hypoxia response, and other associated genes, their role in the evolutionary adaptation of aquatic mammals is not fully understood. In this study, we investigated this topic by employing a candidate gene approach to analyze 11 critical genes involved in the HIF1A signaling pathway in aquatic mammals. Our gene analyses included evaluating positive and negative selection, relaxation or constriction of selection, and molecular convergence compared to other terrestrial mammals, including subterranean mammals. Evidence of selection suggested a significant role of negative selection, as well as relaxation of the selective regime in cetaceans for most of these genes. We found that the glutamine 68 variant in the HIF3α protein is unique to cetaceans and initial evaluations indicated a destabilizing effect on protein structure. However, further analyses are necessary to evaluate its functional impact and adaptive relevance in this taxon.

Reduced social function in experimentally evolved Dictyostelium discoideum implies selection for social conflict in nature

Many microbes interact with one another, but the difficulty of directly observing these interactions in nature makes interpreting their adaptive value complicated. The social amoeba Dictyostelium discoideum forms aggregates wherein some cells are sacrificed for the benefit of others. Within chimaeric aggregates containing multiple unrelated lineages, cheaters can gain an advantage by undercontributing, but the extent to which wild D. discoideum has adapted to cheat is not fully clear. In this study, we experimentally evolved D. discoideum in an environment where there were no selective pressures to cheat or resist cheating in chimaeras. Dictyostelium discoideum lines grown in this environment evolved reduced competitiveness within chimaeric aggregates and reduced ability to migrate during the slug stage. By contrast, we did not observe a reduction in cell number, a trait for which selection was not relaxed. The observed loss of traits that our laboratory conditions had made irrelevant suggests that these traits were adaptations driven and maintained by selective pressures D. discoideum faces in its natural environment. Our results suggest that D. discoideum faces social conflict in nature, and illustrate a general approach that could be applied to searching for social or non-social adaptations in other microbes.

Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events

Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.

DO Toxic Invasive Prey Become a Toxin Source for Native Consumers?

Toxic organisms can become food that potentially harms consumers. When these organisms become invasive species, the harm often turns to a serious threat that disrupts native ecosystems. On the other hand, there are consumers that can exploit toxic organisms for food and sequester intact toxins from them for the consumers' own chemical defense. Therefore, it can be expected that toxic invasive prey can become a toxin source for native consumers. Here, we focused on the relationship between toads, which are one of the major toxic invasive organisms and possess bufadienolides (BDs), and Rhabdophis snakes, which sequester BDs from toads. On Sado Island, Japan, R. tigrinus is native, but no toads had inhabited this island until Bufo japonicus formosus was introduced as a domestic invasive species in 1963 and 1964. At present, invasive toads are distributed only in the southwestern part of the island. We collected a total of 25 and 24 R. tigrinus from areas allopatric and sympatric with toads, respectively. Then, we investigated the possession of BDs and the BD profile of these snakes. We found that only R. tigrinus sympatric with toads possessed BDs, whereas all snakes allopatric with toads lacked BDs. Based on the characteristics of the BD profile, the toxin source was identified as B. j. formosus. Our findings show that a new case of impact caused by toxic invasive species, i.e., "toxin supply to native consumers from invasive prey", could occur.

Overcoming the phantoms of the past: Influence of predatory stimuli on the antipredator behavior of island pitvipers

The reduction of predation is a potentially important factor for the evolution of the traits of an island animal species. By relaxed selection, insular animals tend to lose their antipredator behaviors. A monophyletic group of pitvipers (genus Bothrops) in southeastern Brazil, which have high genetic affinity and dwell on the mainland and adjacent islands, provide an appropriate setting to study the evolution of antipredator behavior and how different predatory stimuli can influence this behavior. The mainland Bothrops jararaca has several terrestrial and aerial predators, whereas B. insularis and B. alcatraz, restricted to two small islands, Queimada Grande and Alcatrazes, respectively, have a smaller range of aerial predators. Terrestrial predators are absent on Queimada Grande, but one potential snake predator occurs on Alcatrazes. We observed that the defensive repertoire of island snakes has not been lost, but they display different frequencies of some antipredator behaviors. The type of predatory stimuli (terrestrial and aerial) influenced the defensive response. Bothrops insularis most often used the escape strategies, especially against terrestrial predatory stimuli. Bothrops alcatraz displayed the highest rate of strike for both terrestrial and aerial stimuli. Our results indicate that even though relaxed selection may occur in island environments as compared to mainland environments, these pitvipers still retain their antipredator behaviors but with different response degrees to the two predator types.

Bioenergetic Effects of Polycyclic Aromatic Hydrocarbon Resistance Manifest Later in Life in Offspring of Fundulus heteroclitus from the Elizabeth River

Shifts in key physiological processes can confer resistance to chemical pollutants. However, these adaptations may come with certain trade-offs, such as altered energy metabolic processes, as evident in Atlantic killifish (Fundulus heteroclitus) in Virginia's Elizabeth River (ER) that have evolved resistance to polycyclic aromatic hydrocarbons (PAHs). We seek to understand the bioenergetic costs of PAH resistance among subpopulations of Atlantic killifish with differing contamination levels in order to examine how these changes manifest across multiple life stages and how these costs might be exacerbated by additional stressors. Bioenergetics data revealed differences in metabolic rates between offspring of PAH-resistant fish and reference fish were absent or minimal in both the embryo and larval stages but pronounced at the juvenile life stage, suggesting that bioenergetic changes in pollution-adapted killifish manifest later in life. We also provide evidence that killifish from remediated sites are more sensitive to PAH exposure than killifish from nonremediated sites, suggesting loss of PAH tolerance following relaxed selection. Collectively, our data suggest that the fitness consequences associated with evolved resistance to anthropogenic stressors may manifest differently over time and depend on the magnitude of the selection pressure. This information can be valuable in effective risk and remediation assessments as well as in broadening our understanding of species responses to environmental change.

Macroevolution of sexually selected weapons: weapon evolution in chameleons

The evolution of sexually selected traits is a major topic in evolutionary biology. However, large-scale evolutionary patterns in these traits remain understudied, especially those traits used in male-male competition (weapons sensu lato). Here, we analyze weapon evolution in chamaeleonid lizards, both within and between the sexes. Chameleons are an outstanding model system because of their morphological diversity (including 11 weapon types among ~220 species) and a large-scale time-calibrated phylogeny. We analyze these 11 traits among 165 species using phylogenetic methods, addressing many questions for the first time in any group. We find that all 11 weapons have each evolved multiple times and that weapon origins are generally more frequent than their losses. We find that almost all weapons have each persisted for >30 million years (and some for >65 million years). Across chameleon phylogeny, we identify both hotspots for weapon evolution (up to 10 types present per species) and coldspots (all weapons absent, many through loss). These hotspots are significantly associated with larger male body size, but are only weakly related to sexual-size dimorphism. We also find that weapon evolution is strongly correlated between males and females. Overall, these results provide a baseline for understanding large-scale patterns of weapon evolution within clades.

Rural selection drives the evolution of an urban-rural cline in coat color in gray squirrels

Phenotypic differences between urban and rural populations are well-documented, but the evolutionary processes driving trait variation along urbanization gradients are often unclear. We combined spatial data on abundance, trait variation, and measurements of fitness to understand cline structure and test for natural selection on heritable coat color morphs (melanic, gray) of eastern gray squirrels (Sciurus carolinensis) along an urbanization gradient. Population surveys using remote cameras and visual counts at 76 sites along the urbanization gradient revealed a significant cline in melanism, decreasing from 48% in the city center to <5% in rural woodlands. Among 76 squirrels translocated to test for phenotypic selection, survival was lower for the melanic than gray morph in rural woodlands, whereas there was no difference in survival between color morphs in the city. These results suggest the urban-rural cline in melanism is explained by natural selection favoring the gray morph in rural woodlands combined with relaxed selection in the city. Our study illustrates how trait variation between urban and rural populations can emerge from selection primarily in rural populations rather than adaptation to novel features of the urban environment.

Phytochemical Cue for the Fitness Costs of Herbicide-Resistant Weeds

Despite increasing knowledge of the fitness costs of viability and fecundity involved in the herbicide-resistant weeds, relatively little is known about the linkage between herbicide resistance costs and phytochemical cues in weed species and biotypes. This study demonstrated relative fitness and phytochemical responses in six herbicide-resistant weeds and their susceptible counterparts. There were significant differences in the parameters of viability (growth and photosynthesis), fecundity fitness (flowering and seed biomass) and a ubiquitous phytochemical (-)-loliolide levels between herbicide-resistant weeds and their susceptible counterparts. Fitness costs occurred in herbicide-resistant Digitaria sanguinalis and Leptochloa chinensis but they were not observed in herbicide-resistant Alopecurus japonicas, Eleusine indica, Ammannia arenaria, and Echinochloa crus-galli. Correlation analysis indicated that the morphological characteristics of resistant and susceptible weeds were negatively correlated with (-)-loliolide concentration, but positively correlated with lipid peroxidation malondialdehyde and total phenol contents. Principal component analysis showed that the lower the (-)-loliolide concentration, the stronger the adaptability in E. crus-galli and E. indica. Therefore, not all herbicide-resistant weeds have fitness costs, but the findings showed several examples of resistance leading to improved fitness even in the absence of herbicides. In particular, (-)-loliolide may act as a phytochemical cue to explain the fitness cost of herbicide-resistant weeds by regulating vitality and fecundity.

Bacterial-fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species

Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacterium Staphylococcus xylosus. We evolved S. xylosus for 450 generations alone or in co-culture with one of three microbes: the yeast Debaryomyces hansenii, the bacterium Brevibacterium aurantiacum, and the mold Penicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution. The yeast D. hansenii strongly promoted diversification of S. xylosus. By the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations of S. xylosus grown alone, with B. aurantiacum, or with P. solitum did not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments identified numerous unique mutations in the operons for the SigB, Agr, and WalRK global regulators, but only in the D. hansenii treatment. Phenotyping and RNA-seq experiments highlighted altered pigment and biofilm production, spreading, stress tolerance, and metabolism of S. xylosus mutants. Fitness experiments revealed antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeast had strong negative fitness effects in other biotic environments. This work demonstrates that bacterial-fungal interactions can have long-term evolutionary consequences within multispecies microbiomes by facilitating the evolution of strain diversity.

Acquired predator recognition via epidermal alarm cues but not dietary alarm cues by isolated pupfish

We tested whether Shoshone pupfish Cyprinodon nevadensis shoshone and Amargosa River pupfish C. n. amargosae respond behaviourally to conspecific chemical alarm cues released when epidermal tissue is damaged by a predator. We found that both subspecies reduced activity and vertical position in the water column in response to alarm cues. We then tested if pupfish can use alarm cue to acquire recognition of a novel predator. We trained pupfish with (1) water + odour of largemouth bass fed a diet of earthworms, (2) alarm cues from skin extract (epidermal alarm cues) + odour of bass fed a diet of earthworms, or (3) water + odour of bass fed a diet of pupfish (dietary alarm cues). Pupfish responded to epidermal alarm cues but not to dietary alarm cues. Pupfish were retested with the odour of bass that were fed an earthworm diet. Pupfish that had previously received epidermal alarm cues reduced vertical position and activity relative to the other two treatments. This is the first demonstration of acquired recognition of a novel predator by a pupfish, the first report of partial predator naiveté, and opens the possibility of predator-recognition training as a tool for management and conservation of endangered desert fishes.

Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum

The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.

Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression

Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.

Patterns in antipredator armature reduction and maintenance in isolated spring populations of an amphipod crustacean

Organisms colonizing new habitats can undergo adaptive change due to novel selective landscapes encountered in the new environment. Examples in nature where the development of the same traits has repeatedly occurred on multiple independent occasions upon colonizing a novel habitat represent instances of parallel evolution. Here we test whether the colonization of spring habitat by the principally lacustrine amphipod crustacean Pallaseopsis quadrispinosa has resulted in parallel evolution in armature traits using empirical data on morphology and mitochondrial DNA and through a breeding experiment. Analysis of mtDNA CO1 sequences shows that the spring populations share no common history and have evolved in isolation from each other and from their neighbouring lake populations since deglaciation approximately 12,000 years ago and are now fixed for different haplogroups. Dorsal spines and lateral projections were absent or less developed in all spring populations than in lake populations. Variation in armature development also could be explained by predator presence as populations with fish predators exhibited more developed spines than those without fish. In a laboratory breeding experiment, hybrid Spring × Lake F1 offspring had intermediate development of armature compared to offspring of Lake × Lake and Spring × Spring matings. The results support the hypothesis that armature reduction has independently evolved on multiple occasions in P. quadrispinosa. Recent research has questioned the degree to which parallel evolution actually explains variance in traits. Taking into account the predation regime, sexual dimorphism and mineral composition of the trait, a more precise understanding of the factors influencing parallel evolution emerges.

The evolutionary demise of a social interaction: experimentally induced loss of traits involved in the supply and demand of care

Phenotypic plasticity enables animals to adjust their behavior flexibly to their social environment-sometimes through the expression of adaptive traits that have not been exhibited for several generations. We investigated how long social adaptations can usefully persist when they are not routinely expressed, by using experimental evolution to document the loss of social traits associated with the supply and demand of parental care. We allowed populations of burying beetles Nicrophorus vespilloides to evolve in two different social environments for 48 generations in the lab. In "Full Care" populations, traits associated with the supply and demand of parental care were expressed at every generation, whereas in "No Care" populations we prevented expression of these traits experimentally. We then revived trait expression in the No Care populations at generations 24, 43, and 48 by allowing parents to supply post-hatching care and compared these social traits with those expressed by the Full Care populations. We found that offspring demands for care and male provision of care in the No Care populations were lost sooner than female provision of care. We suggest that this reflects differences in the strength of selection for the expression of alternative traits in offspring, males and females, which can enhance fitness when post-hatching care is disrupted.

Selection-driven trait loss in independently evolved cavefish populations

Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.

Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

Time constraints may pace the ontogeny of movement behaviour

During early development, juvenile animals need to acquire a diverse behavioural repertoire to interact with their environment. The ontogeny of animal behaviour, is paced by the motivation to improve, e.g. internal clocks, and limited by external constraints, e.g. weather conditions. We here evaluate how naive Egyptian vultures (Neophron percnopterus) improve in locomotor performance, measured as daily maximum displacement, prior to their first migration under three different time constraint regimes: we compared wild hatched vultures, migrating one month after fledging, with captive-hatched vultures, released in spring four months or in winter nine months before migration. We found that the time until migration paced the development of movement behaviour: wild birds rapidly increased displacement distances within the first two weeks after fledging, while spring and winter released vultures delayed movement increases by two and four months, respectively. Under relaxed time constraints captive-hatched vultures displayed diverse functional forms of performance enhancements and therefore great variability in individual ontogeny of movement behaviour. While weather conditions in winter could limit flight movements, some birds indeed moved immediately after their release, indicating that weather may not be limiting. Our findings promote the idea that relaxed ecological constraints could uncover hidden phenotypic flexibility in ontogeny, which could present a greater potential for adaptability under environmental change than currently expected.

Convergent and complementary selection shaped gains and losses of eusociality in sweat bees

Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two pleiotropic proteins that bind and transport juvenile hormone (JH)-a key regulator of insect development and reproduction. We find that one of these proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behaviour and suggest that eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral developmental hormone may have been co-opted during one of life's major transitions. More broadly, our results highlight how evolutionary trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.

Signalling on islands: the case of Lilford’s wall lizard (Podarcis lilfordi gigliolii) from Dragonera

Studies of the effects of insularity on animal signals are scarce, particularly in lizards. Here, we use Lilford’s wall lizard from Dragonera (Podarcis lilfordi gigliolii) to ask how island conditions have affected its repertoire of social signals, focusing on two visual signals shared by many Podarcis species: ultraviolet (UV)–blue-reflecting ventrolateral colour patches and visual displays. We examined whether the number or spectral characteristics of the UV–blue patches are associated with traits related to individual quality. We also used visual models to assess visual conspicuousness and to measure sexual dichromatism. We did not observe foot shakes or any other visual displays usually found in continental Podarcis. We found that none of the UV–blue patch variables covaried with morphometric variables indicative of fighting ability or body condition in males, suggesting that this coloration does not signal individual quality. We also found very little sexual dichromatism. In particular, the UV–blue patches of females seem over-expressed and more similar to those of males than those of continental Podarcis. Ancestral state reconstruction reveals that the lack of sexual dimorphism in the UV–blue patches is a derived condition for P. lilfordi gigliolii and other Podarcis living on small islands. Our results thus show a pattern of reduced social signalling in P. lilfordi gigliolii relative to mainland Podarcis, with some signals being lost or under-expressed (visual displays) and others losing their signalling function (UV–blue patches). We hypothesize that these changes are attributable to the high population density of P. lilfordi gigliolii, which discourages territorial behaviour and promotes extreme social tolerance, making most social signals unnecessary. More work will be needed to determine whether this is a common pattern in lizards inhabiting small and densely populated islands.

Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria

Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

The role of vital dietary biomolecules in eco-evo-devo dynamics

The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization.

Age-dependent genetic variation in aggression

Understanding the extent to which behavioural variance is underlain by genotypic, environmental and genotype-by-environment effects is important for predicting how behavioural traits might respond to selection and evolve. How behaviour varies both within and among individuals can change across ontogeny, leading to differences in the relative contribution of genetic and environmental effects to phenotypic variation across ages. We investigated among-individual and among-genotype variation in aggression across ontogeny by measuring, twice as juveniles and twice as adults, both approaches and attacks against a three-dimensional-printed model opponent in eight individuals from each of eight genotypes (N = 64). Aggression was only significantly repeatable and heritabile in juveniles. Additionally, how aggression changed between juvenile and adult life-history stages varied significantly among individuals and genotypes. These results suggest that juvenile aggression is likely to evolve more rapidly via natural selection than adult aggression and that the trajectory of behavioural change across the lifespan has the potential to evolve. Determining when genetic variation explains (or does not explain) behavioural variation can further our understanding of key life-history stages during which selection might drive the strongest or swiftest evolutionary response.

Facultative Endosymbiont Serratia symbiotica Inhibits the Apterization of Pea Aphid To Enhance Its Spread

Aphids display wing polyphenism, and the mother can produce a wingless morph for reproduction and a winged morph for dispersal. It is believed that the wingless morph is an adaptive status under favorable conditions and is determined prenatally. In this study, we have found that winged nymphs of the pea aphid, Acyrthosiphon pisum, can change from winged to wingless during normal development. Our results showed that winged nymphs could become the wingless morph by apterization in response to changes from stressful to favorable conditions. The acquired wingless aphids had higher fecundity than the winged morph. However, this process of regression from winged to wingless morph was inhibited by Serratia symbiotica. The existence of the symbiont did not affect the body mass and fecundity of adult aphids, but it increased the body weight of nymphs and temporally increased the quantity of a primary symbiont, Buchnera aphidicola. Our results showed that despite temporal improvement of living conditions causing the induction of apterization of winged nymphs, the inhibition effect of S. symbiotica on this process was activated simultaneously. This finding, for the first time, reveals that the wingless morph can be changed postnatally, which explains a novel regulating mechanism of wing polyphenism driven by external abiotic stimuli and internal biotic regulation together in aphids. IMPORTANCE Wing polyphenism is an important adaptative response to environmental changes for aphids. Endosymbionts are widespread in aphids and also confer the ability to withstand unfavorable conditions. However, little is known about whether endosymbionts are involved in the wing polyphenism. In this study, we report a new finding that winged nymphs of the pea aphid could turn into adults without wings or wing-related structures through apterization when winged nymphs escaped from stressful to favorable environments. Further analysis revealed that the facultative symbiont S. symbiotica could prevent the temporal determination of the host in wing suppression by inhibiting apterization, to enhance its spread. Our findings provide a novel angle to understanding the wing polyphenism regulation of aphids.

Heightened immune surveillance in Drosophila melanogaster populations selected for faster development and extended longevity

Maximization of life-history traits is under constraints due to both, limitations of resource acquisition and the restricted pathways of resource allocation. Drosophila melanogaster has served as an excellent model organism to not only unravel various trade-offs among life history traits but also numerous aspects of host immune response. Drosophila larvae are semi-aquatic that live, feed and excrete inside the food source-often over-ripe fruits and vegetables that are rich in both commensal and pathogenic microbiota that can impact the larval survival. In this study, we have used six populations of D. melanogaster, three of which are selected for faster pre-adult development and extended adult longevity, and their three ancestral controls, to explore the impact of selection on the basal immune activity in the larval stage. The larvae from selected populations had nearly significantly upregulated plasmatocyte density, significantly higher percent phagocytosis, phagocytic index and higher transcript levels of Tep3, eater and NimC1. Selected populations also had significantly upregulated crystal cell number along with higher transcript of PPO2. Out of seven tested AMPs level, Drosomycin was significantly upregulated in selected populations while Drosocin was significantly higher in control populations. ROS levels were comparable in the selected and control populations. Our results strongly suggest that enhanced basal immune activity during larval stage manages the faster development and could be responsible for comparable larval survival of selected and control populations.

How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus

The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.

Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin

The eco-evolutionary history of penguins is characterised by shifting from temperate to cold environments. Breeding in Antarctica, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, more ecologically similar to its sister species, the King penguin, is still an open question. As the Antarctic colonisation likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the relative quantification of the genomic signatures of selection, unique to each sister species, could answer this question. Applying phylogeny-based selection tests on 7651 orthologous genes, we identified a more pervasive selection shift in the Emperor penguin than in the King penguin, supporting the hypothesis that its extreme cold adaptation is a derived state. Furthermore, among candidate genes under selection, four (TRPM8, LEPR, CRB1, and SFI1) were identified before in other cold-adapted homeotherms, like the woolly Mammoth, while other 161 genes can be assigned to biological functions relevant to cold adaptation identified in previous studies. Location and structural effects of TRPM8 substitutions in Emperor and King penguin lineages support their functional role with putative divergent effects on thermal adaptation. We conclude that extreme cold adaptation in the Emperor penguin largely involved unique genetic options which, however, affect metabolic and physiological traits common to other cold-adapted homeotherms.

Evidence for stronger discrimination between conspecific and heterospecific mating partners in sexual vs. asexual female freshwater snails

Once-useful traits that no longer contribute to fitness tend to decay over time. Here, we address whether the expression of mating-related traits that increase the fitness of sexually reproducing individuals but are likely less useful or even costly to asexual counterparts seems to exhibit decay in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail characterized by repeated transitions from sexual to asexual reproduction. The frequent coexistence of sexual and asexual lineages makes P. antipodarum an excellent model for the study of mating-related trait loss. Under the presumption (inherent in the Biological Species Concept) that failure to discriminate between conspecific and heterospecific mating partners represents a poor mate choice, we used a mating choice assay including sexual and asexual P. antipodarum females and conspecific (presumed better choice) vs. heterospecific (presumed worse choice) males to evaluate the loss of behavioral traits related to sexual reproduction. We found that sexual females engaged in mating behaviors with conspecific mating partners more frequently and for a greater duration than with heterospecific mating partners. By contrast, asexual females mated at similar frequency and duration as sexual females, but did not mate more often or for longer duration with conspecific vs. heterospecific males. While further confirmation will require inclusion of a more diverse array of sexual and asexual lineages, these results are consistent with a scenario where selection acting to maintain effective mate discrimination in asexual P. antipodarum is weak or ineffective relative to sexual females and, thus, where asexual reproduction is associated with the evolutionary decay of mating-related traits in this system.

Endosymbiotic selective pressure at the origin of eukaryotic cell biology

The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.