Evolutionary conflicts occur when there is antagonistic selection between different individuals of the same or different species, life stages or between levels of biological organization. Remarkably, conflicts can occur within species or within genomes. In the dynamics of evolutionary conflicts, gene duplications can play a major role because they can bring very specific changes to the genome: changes in protein dose, the generation of novel paralogues with different functions or expression patterns or the evolution of small antisense RNAs. As we describe here, by having those effects, gene duplication might spark evolutionary conflict or fuel arms race dynamics that takes place during conflicts. Interestingly, gene duplication can also contribute to the resolution of a within-locus evolutionary conflict by partitioning the functions of the gene that is under an evolutionary trade-off. In this review, we focus on intraspecific conflicts, including sexual conflict and illustrate the various roles of gene duplications with a compilation of examples. These examples reveal the level of complexity and the differences in the patterns of gene duplications within genomes under different conflicts. These examples also reveal the gene ontologies involved in conflict and the genomic location of the elements of the conflict. The examples provide a blueprint for the direct study of these conflicts or the exploration of the presence of similar conflicts in other lineages.

Snakes in the family Elapidae largely produce venoms rich in three-finger toxins (3FTx) that bind to the α 1 subunit of nicotinic acetylcholine receptors (nAChRs), impeding ion channel activity. These neurotoxins immobilize the prey by disrupting muscle contraction. Coral snakes of the genus Micrurus are specialist predators who produce many 3FTx, making them an interesting system for examining the coevolution of these toxins and their targets in prey animals. We used a bio-layer interferometry technique to measure the binding interaction between 15 Micrurus venoms and 12 taxon-specific mimotopes designed to resemble the orthosteric binding region of the muscular nAChR subunit. We found that Micrurus venoms vary greatly in their potency on this assay and that this variation follows phylogenetic patterns rather than previously reported patterns of venom composition. The long-tailed Micrurus tend to have greater binding to nAChR orthosteric sites than their short-tailed relatives and we conclude this is the likely ancestral state. The repeated loss of this activity may be due to the evolution of 3FTx that bind to other regions of the nAChR. We also observed variations in the potency of the venoms depending on the taxon of the target mimotope. Rather than a pattern of prey-specificity, we found that mimotopes modeled after snake nAChRs are less susceptible to Micrurus venoms and that this resistance is partly due to a characteristic tryptophan → serine mutation within the orthosteric site in all snake mimotopes. This resistance may be part of a Red Queen arms race between coral snakes and their prey.

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Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, while potential hosts are expected to evade parasitism by building more concealed nests that are difficult for parasites to enter and in which to lay eggs. We used phylogenetically informed comparative analyses, a global database of the world\'s brood parasites, their host species, and the design of avian host and non-host nests (approx. 6200 bird species) to examine first, whether parasites preferentially target host species that build open nests and, second, whether host species that build enclosed nests are more likely to be targeted by specialist parasites. We found that species building more accessible nests are more likely to serve as hosts, while host species with some of the more inaccessible nests are targeted by more specialist brood parasites. Furthermore, evolutionary-transition analyses demonstrate that host species building enclosed nests frequently evolve to become non-hosts. We conclude that nest architecture and the accessibility of nests for parasitism represent a critical stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.

Hearing has evolved independently many times in the animal kingdom and is prominent in various insects and vertebrates for conspecific communication and predator detection. Among insects, katydid (Orthoptera: Tettigoniidae) ears are unique, as they have evolved outer, middle, and inner ear components, analogous in their biophysical principles to the mammalian ear. The katydid ear consists of two paired tympana located in each foreleg. These tympana receive sound externally on the tympanum surface (usually via pinnae) or internally via an ear canal (EC). The EC functions to capture conspecific calls and low frequencies, while the pinnae passively amplify higher-frequency ultrasounds including bat echolocation. Together, these outer ear components provide enhanced hearing sensitivity across a dynamic range of over 100 kHz. However, despite a growing understanding of the biophysics and function of the katydid ear, its precise emergence and evolutionary history remains elusive. Here, using microcomputed tomography (μCT) scanning, we recovered geometries of the outer ear components and wings of an exceptionally well-preserved katydid fossilized in Baltic amber (∼44 million years [Ma]). Using numerical and theoretical modeling of the wings, we show that this species was communicating at a peak frequency of 31.62 (± 2.27) kHz, and we demonstrate that the ear was biophysically tuned to this signal and to providing hearing at higher-frequency ultrasounds (>80 kHz), likely for enhanced predator detection. The results indicate that the evolution of the unique ear of the katydid, with its broadband ultrasonic sensitivity and analogous biophysical properties to the ears of mammals, emerged in the Eocene.

In recent decades, phage therapy has been overshadowed by the widespread use of antibiotics in Western countries. However, it has been revitalized as a powerful approach due to the increasing prevalence of antimicrobial-resistant bacteria. Although bacterial resistance to phages has been reported in clinical cases, recent studies on the fitness trade-offs between phage and antibiotic resistance have revealed new avenues in the field of phage therapy. This strategy aims to restore the antibiotic susceptibility of antimicrobial-resistant bacteria, even if phage-resistant variants develop. Here, we summarize the basic virological properties of phages and their applications within the context of antimicrobial resistance. In addition, we review the occurrence of phage resistance in clinical cases, and examine fitness trade-offs between phage and antibiotic sensitivity, exploring the potential of an evolutionary fitness cost as a countermeasure against phage resistance in therapy. Finally, we discuss future strategies and directions for phage-based therapy from the aspect of fitness trade-offs. This approach is expected to provide robust options when combined with antibiotics in this era of phage \'re\'-discovery.

Comparative studies of egg recognition and rejection between various sympatric hosts provide insight into the coevolutionary history of the hosts and parasites, as well as the degree of antagonism between the species. Although buntings are widely considered to be a suitable host taxon for cuckoos, there has been relatively little research on this example of parasitism and host antiparasitic behaviour. Here we provided the first report on brood parasitism and egg recognition in three sympatric ground-nesting bunting hosts of the common cuckoo (Cuculus canorus), namely the yellow-throated bunting (Emberiza elegans), south rock bunting (E. yunnanensis), and crested bunting (E. lathami). The results show that for the five breeding seasons during 2018-2022, the parasitism rate by common cuckoos was 0.87% and 0.45% in yellow-throated buntings and south rock buntings, respectively, whereas the parasitism rate by an unidentified parasite was 4% during 2018-2023 in the crested bunting. The rejection rates of the three bunting hosts for blue non-mimetic eggs were 89.3%, 88.9%, and 100% for yellow-throated buntings, south rock buntings, and crested buntings, respectively. The rejection rates for red non-mimetic eggs by yellow-throated buntings and south rock buntings were lower at 76.9% and 82.4%, respectively. All three sympatric bunting hosts examined had high levels of egg recognition and egg rejection, suggesting that it may have been subjected to high parasitic history and that egg recognition ability was retained after the loss of parasitism, which needs to be further verified by future experiments.

Antagonistic species relationships such as parasitoid/host interactions lead to evolutionary arms races between species. Many parasitoids use more than one host species, requiring the parasitoid to adapt to multiple hosts, sometimes being the leader or the follower in the evolutionary back-and-forth between species. Thus, multi-species interactions are dynamic and show temporary evolutionary outcomes at a given point in time. We investigated the interactions of the multivoltine parasitoid fly Ormia lineifrons that uses different katydid hosts for each of its fly generations sequentially over time. We hypothesized that this fly is adapted to utilizing all hosts equally well for the population to persist. We quantified and compared the fly\'s development in each of the four Neoconocephalus hosts. Cumulative parasitism rates ranged between ~14% and 73%, but parasitoid load and development time did not differ across host species. Yet, pupal size was lowest for flies using N. velox as a host compared to N. triops and other host species. Successful development from pupa to adult fly differed across host species, with flies emerging from N. triops displaying a significantly lower development success rate than those emerging from N. velox and the other two hosts. Interestingly, N. triops and N. velox did not differ in size and were smaller than N. robustus and N. nebrascensis hosts. Thus, O. lineifrons utilized all hosts but displayed especially low ability to develop in N. triops, potentially due to differences in the nutritional status of the host. In the multi-species interactions between the fly and its hosts, the poor use of N. triops may currently affect the fly\'s evolution the most. Similarities and differences across host utilization and their evolutionary background are discussed.

In seasonal environments, competition among males can drive males to emerge before females. Females, simultaneously, should avoid emerging at times after sufficient male availability. We show that the consequent sexual conflict over timing traits can produce arms races toward ever earlier emergence, if low mate-search efficiency or sperm limitation elevate the latter risk for females. In reality, however, arms races over timing cannot proceed indefinitely as this ignores the relevant ecological context for phenology: the temporal niche of resource availability for offspring development. We model the interaction of natural and sexual selection to predict the sexual conflict load, i.e., the loss of population fitness caused by sexual conflict. We show that selection to avoid matelessness can exacerbate another problem of maladaptation: a temporal mismatch between the organism (e.g., insect) and its resource (e.g., host plant). Load frequently associates with protandry if males can mate multiply, yet lack of multiple mating does not imply zero load. A temporal mismatch can still evolve, where both sexes emerge and mate suboptimally early with respect to the seasonal resource peak, because monogamy does not guarantee that every individual finds one mate, and selection favors early individuals in mate-finding contexts.

Activation-induced cytidine deaminase/apolipoprotein B mRNA editing catalytic polypeptide-like (AID/APOBEC) proteins are cytosine deaminases implicated in diverse biological functions. APOBEC1 (A1) proteins have long been thought to regulate lipid metabolism, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. Endogenous retroviruses (ERVs) document past retroviral infections and are ubiquitous within the vertebrate genomes. Here, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in ERVs, and interrogate the evolutionary arms race between A1 genes and ERVs across vertebrate species. We find that A1 genes are widely present in tetrapods, recurrently amplified and lost in certain lineages, suggesting that A1 genes might have originated during the early evolution of tetrapods. A1-mediated mutation footprints can be detected in ERVs across tetrapods. Moreover, A1 genes appear to have experienced episodic positive selection in many tetrapod lineages. Taken together, we propose that a long-running arms race between A1 genes and retroviruses might have persisted throughout the evolutionary course of tetrapods. IMPORTANCE APOBEC3 (A3) genes have been thought to function in defense against retroviruses, whereas the evolutionary significance of A1 proteins in antiviral defense remains largely obscure. In this study, we identify the A1 gene repertoire, characterize the A1-mediated mutation footprints in endogenous retroviruses (ERVs), and explore the evolutionary arms race between A1 genes and ERVs across vertebrate species. We found A1 proteins originated during the early evolution of tetrapods, and detected the footprints of A1-induced hypermutations in retroviral fossils. A1 genes appear to have experienced pervasive positive selection in tetrapods. Our study indicates a long-running arms race between A1 genes and retroviruses taking place throughout the evolutionary course of tetrapods.