The roles of gene duplications in the dynamics of evolutionary conflicts.

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.

High parasite diversity maintained after an alga-virus coevolutionary arms race.

Arms race dynamics are a common outcome of host-parasite coevolution. While they can theoretically be maintained indefinitely, realistic arms races are expected to be finite. Once an arms race has ended, for example due to the evolution of a generalist-resistant host, the system may transition into coevolutionary dynamics that favour long-term diversity. In microbial experiments, host-parasite arms races often transition into a stable coexistence of generalist-resistant hosts, (semi-)susceptible hosts, and parasites. While long-term host diversity is implicit in these cases, parasite diversity is usually overlooked. In this study, we examined parasite diversity after the end of an experimental arms race between a unicellular alga (Chlorella variabilis) and its lytic virus (PBCV-1). First, we isolated virus genotypes from multiple time points from two replicate microcosms. A time-shift experiment confirmed that the virus isolates had escalating host ranges, i.e., that arms races had occurred. We then examined the phenotypic and genetic diversity of virus isolates from the post-arms race phase. Post-arms race virus isolates had diverse host ranges, survival probabilities, and growth rates; they also clustered into distinct genetic groups. Importantly, host range diversity was maintained throughout the post-arms race phase, and the frequency of host range phenotypes fluctuated over time. We hypothesize that this dynamic polymorphism was maintained by a combination of fluctuating selection and demographic stochasticity. Together with previous work in prokaryotic systems, our results link experimental observations of arms races to natural observations of long-term host and parasite diversity.

Red-on-Yellow Queen: Bio-Layer Interferometry Reveals Functional Diversity Within Micrurus Venoms and Toxin Resistance in Prey Species.

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.

Both nuclear and cytoplasmic polymorphisms are involved in genetic conflicts over male fertility in the gynodioecious snail, Physa acuta.

Gynodioecy, the coexistence of hermaphrodites with females, often reflects conflicts between cytoplasmic male sterility (CMS) genes and nuclear genes restoring male fertility. CMS is frequent in plants and has been recently discovered in one animal: the freshwater snail, Physa acuta. In this system, CMS was linked to a single divergent mitochondrial genome (D), devoid of apparent nuclear restoration. Our study uncovers a second, novel CMS-associated mitogenome (K) in Physa acuta, demonstrating an extraordinary acceleration of molecular evolution throughout the entire K mitochondrial genome, akin to the previously observed pattern in D. This suggests a pervasive occurrence of accelerated evolution in both CMS-associated lineages. Through a 17-generation introgression experiment, we further show that nuclear polymorphisms in K-mitogenome individuals contribute to the restoration of male function in natural populations. Our results underscore shared characteristics in gynodioecy between plants and animals, emphasizing the presence of multiple CMS mitotypes and cytonuclear conflicts. This reaffirms the pivotal role of mitochondria in influencing male function and in generating genomic conflicts that impact reproductive processes in animals.

Host size matters for reproduction: Evolution of spawning preference and female reproductive phenotypes in mussel-symbiotic freshwater bitterling fishes.

Bitterling fishes evolve an idiosyncratic symbiosis with freshwater mussels, in which they are obligated to spawn in the gills of mussels for reproduction. In recent years, freshwater mussel populations have been drastically diminishing, due to accelerating anthropogenic impacts, which can be large threats to the risk of bitterling's extinction cascade (i.e. 'coextinction'). The host mussel size may be an important factor driving the adaptation and evolution of bitterling's reproductive phenotypes. Here we examined the host size preference and morphological adaptation of female bitterling to the host size from 17 localities at the Han River in Korea. Using our developed molecular-based species identification for bitterling's eggs/larvae inside the mussels, we further determined the spawning patterns of seven bitterling species. Mean length of spawned mussels (N = 453) was significantly larger than that of unspawned mussels (N = 1814), suggesting that bitterling prefers to use larger hosts as a spawning ground. Spawning probability was clearly greater as mussel size increases. Results of our reciprocal transplant experiments do provide some evidence supporting the 'bitterling's larger host preference' hypothesis. Interspecific competition appeared to be intense as two fish species often spawned eggs in the same mussel individuals simultaneously. Longer ovipositor and more elongated egg may evolve in females of Tanakia signifer in response to larger host environments. The observed bitterling's spawning preference for large-sized mussels may evolve perhaps because of the fitness advantage in relation to the offspring survival. Our findings further inform on the development of effective conservation and management strategy for the endangered bitterling fishes.

Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics.

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.

The successive emergence of ERVL-MaLRs in primates.

Although the ERVL-mammalian-apparent LTR retrotransposons (MaLRs) are the fourth largest family of transposable elements in the human genome, their evolutionary history and relationship have not been thoroughly studied. In this study, through RepeatMasker annotations of some representative species and construction of phylogenetic tree by sequence similarity, all primate-specific MaLR members are found to descend from MLT1A1 retrotransposon. Comparative genomic analysis, transposition-in-transposition inference, and sequence feature comparisons consistently show that each MaLR member evolved from its predecessor successively and had a limited activity period during primate evolution. Accordingly, a novel MaLR member was discovered as successor of MSTB1 in Tarsiiformes. At last, the identification of candidate precursor and intermediate THE1A elements provides further evidence for the previously proposed arms race model between ZNF430/ZNF100 and THE1B/THE1A. Taken together, this study sheds light on the evolutionary history of MaLRs and can serve as a foundation for future research on their interactions with zinc finger genes, gene regulation, and human health implications.

Fitness Trade-Offs between Phage and Antibiotic Sensitivity in Phage-Resistant Variants: Molecular Action and Insights into Clinical Applications for Phage Therapy.

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.

An Eocene insect could hear conspecific ultrasounds and bat echolocation.

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.

Brood parasitism and egg recognition in three bunting hosts of the cuckoos.

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.

Acoustic camouflage increases with body size and changes with bat echolocation frequency range in a community of nocturnally active Lepidoptera.

Body size is an important trait in predator-prey dynamics as it is often linked to detection, as well as the success of capture or escape. Larger prey, for example, often runs higher risk of detection by their predators, which imposes stronger selection on their anti-predator traits compared to smaller prey. Nocturnal Lepidoptera (moths) vary strongly in body size, which has consequences for their predation risk, as bigger moths return stronger echoes for echolocating bats. To compensate for increased predation risk, larger moths are therefore expected to have improved anti-predator defences. Moths are covered by different types of scales, which for a few species are known to absorb ultrasound, thus providing acoustic camouflage. Here, we assessed whether moths differ in their acoustic camouflage in a size-dependent way by focusing on their body scales and the different frequency ranges used by bats. We used a sonar head to measure 3D echo scans of a total of 111 moth specimens across 58 species, from eight different families of Lepidoptera. We scanned all the specimens and related their echo-acoustic target strength to various body size measurements. Next, we removed the scales covering the thorax and abdomen and scanned a subset of specimens again to assess the sound absorptive properties of these scales. Comparing intact specimens with descaled specimens, we found almost all species to absorb ultrasound, reducing detection risk on average by 8%. Furthermore, the sound absorptive capacities of body scales increased with body size suggesting that larger species benefit more from acoustic camouflage. The size-dependent effect of camouflage was in particular pronounced for the higher frequencies (above 29 kHz), with moth species belonging to large-bodied families consequently demonstrating similar target strengths compared to species from small-bodied families. Finally, we found the families to differ in frequency range that provided the largest reduction in detection risk, which may be related to differences in predation pressure and predator communities of these families. In general, our findings have important implications for predator-prey interactions across eco-evolutionary timescales and may suggest that acoustic camouflage played a role in body size evolution of nocturnally active Lepidoptera.

Stealth echolocation in aerial hawking bats reflects a substrate gleaning ancestry.

Predator-prey co-evolution can escalate into an evolutionary arms race.1 Examples of insect countermeasures to bat echolocation are well-known,2 but presumptive direct counter strategies in bats to insect anti-bat tactics are rare. The emission of very low-intensity calls by the hawking Barbastella barbastellus to circumvent high-frequency moth hearing is the most convincing countermeasure known.2,3 However, we demonstrate that stealth echolocation did not evolve through a high-intensity aerial hawking ancestor becoming quiet as previously hypothesized2,3,4 but from a gleaning ancestor transitioning into an obligate aerial hawker. Our ancestral state reconstructions show that the Plecotini ancestor likely gleaned prey using low-intensity calls typical of gleaning bats and that this ability-and associated traits-was subsequently lost in the barbastelle lineage. Barbastelles did not, however, revert to the oral, high-intensity call emission that other hawking bats use but retained the low-intensity nasal emission of closely related gleaning plecotines despite an extremely limited echolocation range. We further show that barbastelles continue to emit low-intensity calls even under adverse noise conditions and do not broaden the echolocation beam during the terminal buzz, unlike other vespertilionids attacking airborne prey.5,6 Together, our results suggest that barbastelles' echolocation is subject to morphological constraints prohibiting higher call amplitudes and beam broadening in the terminal buzz. We suggest that an abundance of eared prey allowed the co-opting and maintenance of low-intensity, nasal echolocation in today's obligate hawking barbastelle and that this unique foraging behavior7 persists because barbastelles remain a rare, acoustically inconspicuous predator to eared moths. VIDEO ABSTRACT.

Calibrated microphone array recordings reveal that a gleaning bat emits low-intensity echolocation calls even in open-space habitat.

Echolocating bats use ultrasound for orientation and prey capture in darkness. Ultrasound is strongly attenuated in air. Consequently, aerial-hawking bats generally emit very intense echolocation calls to maximize detection range. However, call levels vary more than tenfold (>20 dB) between species and are tightly linked to the foraging strategy. The brown long-eared bat (Plecotus auritus) is a primarily gleaning, low-amplitude species that may occasionally hawk airborne prey. We used state-of-the-art calibrated acoustic 3D-localization and automated call analysis to measure P. auritus' source levels. Plecotus auritus emits echolocation calls of low amplitude (92 dB rmsSPL re. 20 µPa at 10 cm) even while flying in open-space. While P. auritus thus probably benefits from delayed evasive manoeuvres of eared insects, we propose that low-amplitude echolocation did not evolve as an adaptive countermeasure, but is limited by morphological constraints.

Multi-Species Host Use by the Parasitoid Fly Ormia lineifrons.

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.

Pathogen protein modularity enables elaborate mimicry of a host phosphatase.

Pathogens produce diverse effector proteins to manipulate host cellular processes. However, how functional diversity is generated in an effector repertoire is poorly understood. Many effectors in the devastating plant pathogen Phytophthora contain tandem repeats of the "(L)WY" motif, which are structurally conserved but variable in sequences. Here, we discovered a functional module formed by a specific (L)WY-LWY combination in multiple Phytophthora effectors, which efficiently recruits the serine/threonine protein phosphatase 2A (PP2A) core enzyme in plant hosts. Crystal structure of an effector-PP2A complex shows that the (L)WY-LWY module enables hijacking of the host PP2A core enzyme to form functional holoenzymes. While sharing the PP2A-interacting module at the amino terminus, these effectors possess divergent C-terminal LWY units and regulate distinct sets of phosphoproteins in the host. Our results highlight the appropriation of an essential host phosphatase through molecular mimicry by pathogens and diversification promoted by protein modularity in an effector repertoire.

A billion years arms-race between viruses, virophages, and eukaryotes.

Bamfordviruses are arguably the most diverse group of viruses infecting eukaryotes. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses, Mavericks and Polinton-like viruses. Two main hypotheses for their origins have been proposed: the 'nuclear-escape' and 'virophage-first' hypotheses. The nuclear-escape hypothesis proposes an endogenous, Maverick-like ancestor which escaped from the nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the virophage-first hypothesis proposes that NCLDVs coevolved with protovirophages; Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the nucleus at a later stage. Here, we test the predictions made by both models and consider alternative evolutionary scenarios. We use a data set of the four core virion proteins sampled across the diversity of the lineage, together with Bayesian and maximum-likelihood hypothesis-testing methods, and estimate rooted phylogenies. We find strong evidence that adenoviruses and NCLDVs are not sister groups, and that Mavericks and Mavirus acquired the rve-integrase independently. We also found strong support for a monophyletic group of virophages (family Lavidaviridae) and a most likely root placed between virophages and the other lineages. Our observations support alternatives to the nuclear-escape scenario and a billion years evolutionary arms-race between virophages and NCLDVs.

Eggshell composition and surface properties of avian brood-parasitic species compared with non-parasitic species.

The eggs of avian obligate brood-parasitic species have multiple adaptations to deceive hosts and optimize development in host nests. While the structure and composition of the eggshell in all birds is essential for embryo growth and protection from external threats, parasitic eggs may face specific challenges such as high microbial loads, rapid laying and ejection by the host parents. We set out to assess whether eggshells of avian brood-parasitic species have either (i) specialized structural properties, to meet the demands of a brood-parasitic strategy or (ii) similar structural properties to eggs of their hosts, due to the similar nest environment. We measured the surface topography (roughness), wettability (how well surfaces repel water) and calcium content of eggshells of a phylogenetically and geographically diverse range of brood-parasitic species (representing four of the seven independent lineages of avian brood-parasitic species), their hosts and close relatives of the parasites. These components of the eggshell structure have been demonstrated previously to influence such factors as the risk of microbial infection and overall shell strength. Within a phylogenetically controlled framework, we found no overall significant differences in eggshell roughness, wettability and calcium content between (i) parasitic and non-parasitic species, or (ii) parasitic species and their hosts. Both the wettability and calcium content of the eggs from brood-parasitic species were not more similar to those of their hosts' eggs than expected by chance. By contrast, the mean surface roughness of the eggs of brood-parasitic species was more similar to that of their hosts' eggs than expected by chance, suggesting brood-parasitic species may have evolved to lay eggs that match the host nest environment for this trait. The lack of significant overall differences between parasitic and non-parasitic species, including hosts, in the traits we measured, suggests that phylogenetic signal, as well as general adaptations to the nest environment and for embryo development, outweigh any influence of a parasitic lifestyle on these eggshell properties.

Horizontal gene transfer from plant to whitefly.

The recent discovery of the horizontal transfer of a toxin-neutralizing gene from plant to whitefly (Bemisia tabaci), a polyphagous insect, sparked a new area of study. In this forum, we discuss some potential biotechnological applications of this newly discovered knowledge in the coevolutionary arms race between plants and whitefly.

Pangenomic analysis reveals plant NAD+ manipulation as an important virulence activity of bacterial pathogen effectors.

Nicotinamide adenine dinucleotide (NAD+) has emerged as a key component in prokaryotic and eukaryotic immune systems. The recent discovery that Toll/interleukin-1 receptor (TIR) proteins function as NAD+ hydrolases (NADase) links NAD+-derived small molecules with immune signaling. We investigated pathogen manipulation of host NAD+ metabolism as a virulence strategy. Using the pangenome of the model bacterial pathogen Pseudomonas syringae, we conducted a structure-based similarity search from 35,000 orthogroups for type III effectors (T3Es) with potential NADase activity. Thirteen T3Es, including five newly identified candidates, were identified that possess domain(s) characteristic of seven NAD+-hydrolyzing enzyme families. Most Pseudomonas syringae strains that depend on the type III secretion system to cause disease, encode at least one NAD+-manipulating T3E, and many have several. We experimentally confirmed the type III-dependent secretion of a novel T3E, named HopBY, which shows structural similarity to both TIR and adenosine diphosphate ribose (ADPR) cyclase. Homologs of HopBY were predicted to be type VI effectors in diverse bacterial species, indicating potential recruitment of this activity by microbial proteins secreted during various interspecies interactions. HopBY efficiently hydrolyzes NAD+ and specifically produces 2'cADPR, which can also be produced by TIR immune receptors of plants and by other bacteria. Intriguingly, this effector promoted bacterial virulence, indicating that 2'cADPR may not be the signaling molecule that directly initiates immunity. This study highlights a host-pathogen battleground centered around NAD+ metabolism and provides insight into the NAD+-derived molecules involved in plant immunity.