Differential Selection Pressures Research Articles

How the Structure of Signaling Regulation Evolves: Insights from an Evolutionary Model.

To remain responsive to environmental changes, signaling pathways attenuate their activity with negative feedback loops (NFLs), where proteins produced upon stimulation downregulate the response. NFLs function both upstream of signaling to reduce input and downstream to reduce output. Unlike upstream NFLs, downstream NFLs directly regulate gene expression without the involvement of intermediate proteins. Thus, we hypothesized that downstream NFLs evolve under more stringent selection than upstream NFLs. Indeed, genes encoding downstream NFLs exhibit a slower evolutionary rate than upstream genes. Such differences in selective pressures could result in the robust evolution of downstream NFLs while making the evolution of upstream NFLs more sensitive to changes in signaling proteins and stimuli. Here, we test these assumptions within the context of immune signaling. Our minimal model of immune signaling predicts robust evolution of downstream NFLs to changes in model parameters. This is consistent with their critical role in regulating signaling and the conservative rate of evolution. Furthermore, we show that the number of signaling steps needed to activate a downstream NFL is influenced by the cost of signaling. Our model predicts that upstream NFLs are more likely to evolve under a shorter half-life of signaling proteins, absence of host-pathogen co-evolution, and a high infection rate. Although it has been proposed that NFLs evolve to reduce the cost of signaling, we show that a high cost does not necessarily predict the evolution of upstream NFLs. The insights from our model have broad implications for understanding the evolution of regulatory mechanisms across signaling pathways.

Bacterial microbiome and their assembly processing in two sympatric desert rodents (Dipus sagitta and Meriones meridianus) from different geographic sources

Abstract The microbiome of mammals has profound effects on host fitness, but the process, which drives the assembly and shift of mammalian microbiome remains poorly understood. To explore the patterns of small mammal microbial communities across host species and geographical sites and measure the relative contributions of different processes in driving assembly patterns, 2 sympatric desert rodent species (Dipus sagitta and Meriones meridianus) were sampled from 2 geographically distant regions, which differed in the environment, followed by 16S rRNA gene sequencing. The microbiomes differed significantly between D. sagitta and M. meridianus, and linear mixed modeling (LMM) analysis revealed that microbial diversity was mostly affected by species rather than the environment. For each rodent species, the microbiome diversity and structure differed across geographical regions, with individuals from lower rainfall environments exhibiting greater diversity. The null modeling results suggested dispersal limitation and ecological drift rather than differential selective pressures acting on the microbiome. In addition, each group had a different core genus, suggesting that the taxonomic composition of the microbiome was shaped most strongly by stochastic processes. Our results suggest that variation in the microbiome between hosts, both within and among geographic rodent populations, is driven by bacterial dispersal and ecological drift rather than by differential selective pressures. These results elucidated the diversity patterns and assembly processes of bacterial microbiomes in small desert mammals. Deciphering the processes shaping the assembly of the microbial community is a premise for better understanding how the environment-host-microbe interactions of mammals are established and maintained, particularly in the context of increased environmental disturbances and global changes.

Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska.

In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.

On the wings of dragons: Wing morphometric differences in the sexually dichromatic common whitetail skimmer dragonfly, Plathemis lydia (Odonata: Libellulidae).

Sexual dimorphism is common throughout the animal kingdom, leading to sex-specific phenotypic differences. The common whitetail skimmer dragonfly, Plathemis lydia (Drury, 1773), is sexually dichromatic, where males of this species display a conspicuous white abdomen and females display a dark brown abdomen. Differences in abdomen conspicuousness between male and female P. lydia are likely attributed to differences in selective pressure where males use their white conspicuous abdomen during male-male territorial chases. We hypothesized that male P. lydia would exhibit wing morphology adaptations to better offset the costs of predation and territoriality and that these adaptations would differ from females. We used field-collected images to quantify differences in body length, wing length, wing area, wing shape, and wing loading between male and female P. lydia. Our results show that male P. lydia have significantly shorter fore and hind wings relative to body size with a higher wing loading when compared to females. We also found that male P. lydia have narrower and pointier fore and hind wings compared to females. These results are consistent with the idea that males are adapted for faster flight, specifically higher acceleration capacity, and higher agility whereas females are adapted for higher maneuverability.

Variant Analysis of XDR Salmonella Typhi Strains Using Global Alignment Tool Kit in South Asian Region

Objective: To concisely compare genomic profiles of XDR Salmonella Typhi isolates from Lahore withantimicrobial-resistant Salmonella Typhi isolates from other developing nations.Study Design: Comparative analysis of whole genome sequences.Place and Duration of Study: The study was conducted from December 2020 to September 2021 at KauserAbdulla Malik (KAM) School Life Sciences, Forman Christian College University, Lahore, Pakistan.Methods: The Galaxy pipeline was run to obtain detailed information at the nucleotide level regardingmutations that lead to the emergence of XDR strains. Whole genome sequences were analyzed to compare thegenomes of selected three developing nations.Results: The Pakistani isolates had a significantly higher mutation rate, higher proportion of modifiers, andsilent mutations as compared to isolates of Bangladesh and India.Conclusion: Cases of Salmonella Typhi XDR are rapidly rising in Asian countries such as Pakistan, Bangladesh,and India emphasizing the need to analyze and compare its genome with relevant strains. Our study highlightsthe unique profile of the Lahore (Pakistan) isolate with the highest mutation rate suggesting the potentialregional differences in selective pressure. Further spotlights the necessity to elucidate the functionalconsequences of the identified mutations in S. Typhi isolates. How to cite this: Niaz M, Mumtaz Z, Ahmed M, Ahmad S, Ali A, Yousaf MZ. Variant Analysis of XDR Salmonella Typhi Strains Using Global Alignment Tool Kit in South Asian Region. Life and Science. 2024; 5(2): 244-250. doi: http://doi.org/10.37185/LnS.1.1.432

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.

Successional changes in bacterial phyllosphere communities are plant-host species dependent.

Leaf surface microbiomes have the potential to influence agricultural and ecosystem productivity. We assessed their stability by determining composition, functional resistance, and resilience. Resistance is the degree to which communities remain unchanged as a result of disturbance, and resilience is the ability of a community to recover to pre-disturbance conditions. By understanding the mechanisms of community assembly and how they relate to the resistance and resilience of microbial communities under common environmental stresses such as drought, we can better understand how communities will adapt to a changing environment and how we can promote healthy agricultural microbiomes. In this study, phyllosphere compositional stability was highly related to plant host species phylogeny and, to a lesser extent, known stress tolerances. Phyllosphere community assembly and stability are a result of complex interactions of ecological processes that are differentially imposed by host species.

Abstract B058: Deconvoluting the intra-tumour heterogeneity and subclonal evolution of CDK4/6 inhibitor resistance in ER+ breast cancer

Abstract Subclonal heterogeneity and evolution are characteristics of breast cancer (BC), that play a key role in tumour development, progression, and resistance to current therapies. Preliminary single-cell sequencing studies suggest that subclonal heterogeneity drives therapy response in aggressive BC. Here, we sought to identify whether pre-existing transcriptomically defined cell subpopulations underpin resistance to CDK4/6 inhibitors (CDK4/6i) in ER+ BC, and to identify the distinct or shared resistance mechanisms between different CDK4/6i currently used in the clinic. ER+ BC cell lines, MCF7 and T47D, were infected with a lentiviral barcode library and were long-term exposed to DMSO or CDK4/6i (Abemaciclib or Palbociclib) until drug resistance was achieved. CDK4/6i resistant or DMSO cell lines were then subjected to DNA sequencing for the detection of barcodes coupled with single-cell transcriptomic and barcode sequencing, whole exome sequencing and G1/S cell cycle checkpoint analysis at a protein level. Single-cell lineage tracing identified that resistance to both CDK4/6i in MCF7 cells was stochastic, while in T47D cells, resistance to both CDK4/6i was conserved across all biological replicates. In all cell models, abemaciclib exerted a stronger selective pressure than palbociclib. Detection of barcodes from dead cells highlighted differential selective pressures of the drugs during resistance generation and upon resistance emergence. Single-cell transcriptomic sequencing identified shared and differential mechanisms of resistance between cell lines and specific CDK4/6i, suggestive of different subclonal, non-genetic mechanisms driving resistance. Some of these subclones were pre-defined (i.e. shared transcriptomic features with parental cells), whereas other resistant subclones were demarked by acquisition of pathway up-regulation. For instance, RB1 expression was abolished in the entire palbociclib-resistant T47D population, with copy number loss, indicating RB1 as a genetic driver of resistance. No evidence of RB1 loss was observed in MCF7 palbociclib-resistant clonal population, however a subclonal cluster was identified with loss of RB1 expression. Interestingly, abemaciclib-resistant MCF7 cells had lost RB1 protein expression, suggesting differential non-genetic mechanisms of resistance to CDK4/6i in MCF7 cells. Through single-cell lineage tracing, we have identified that resistance to CDK4/6i can be stochastic or conserved according to the cell model. Additionally, single-cell transcriptomic sequencing identified that in some cell models, cells that have the ability to become resistant are pre-existing, suggesting transcriptomic and epigenomic mechanisms of resistance, where cells exhibit drug-tolerant or drug-induced persistent properties. Citation Format: Ioanna Mavrommati, Fatemeh Ahmadi Moughari, Shefali Thakur, Yu Zhang, Lesley-Ann Martin, Syed Haider, Rachael Natrajan. Deconvoluting the intra-tumour heterogeneity and subclonal evolution of CDK4/6 inhibitor resistance in ER+ breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B058.

Ecologically mediated differences in electric organ discharge drive evolution in a sodium channel gene in South American electric fishes.

Active electroreception-the ability to detect objects and communicate with conspecifics via the detection and generation of electric organ discharges (EODs)-has evolved convergently in several fish lineages. South American electric fishes (Gymnotiformes) are a highly species-rich group, possibly in part due to evolution of an electric organ (EO) that can produce diverse EODs. Neofunctionalization of a voltage-gated sodium channel gene accompanied the evolution of electrogenic tissue from muscle and resulted in a novel gene (scn4aa) uniquely expressed in the EO. Here, we investigate the link between variation in scn4aa and differences in EOD waveform. We combine gymnotiform scn4aa sequences encoding the C-terminus of the Nav1.4a protein, with biogeographic data and EOD recordings to test whether physiological transitions among EOD types accompany differential selection pressures on scn4aa. We found positive selection on scn4aa coincided with shifts in EOD types. Species that evolved in the absence of predators, which likely selected for reduced EOD complexity, exhibited increased scn4aa evolutionary rates. We model mutations in the protein that may underlie changes in protein function and discuss our findings in the context of gymnotiform signalling ecology. Together, this work sheds light on the selective forces underpinning major evolutionary transitions in electric signal production.

Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha.

Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.

Bacteria colonization in tumor microenvironment creates a favorable niche for immunogenic chemotherapy

The tumor microenvironment (TME) presents differential selective pressure (DSP) that favors the growth of cancer cells, and monovalent therapy is often inadequate in reversing the cancer cell dominance in the TME. In this work, we introduce bacteria as a foreign species to the TME and explore combinatorial treatment strategies to alter DSP for tumor eradication. We show that cancer-selective chemotherapeutic agents and fasting can provide a strong selection pressure against tumor growth in the presence of bacteria. Moreover, we show that an immunogenic drug (oxaliplatin), but not a non-immunogenic one (5-FU), synergizes with the bacteria to activate both the innate and adaptive immunity in the TME, resulting in complete tumor remission and a sustained anti-tumor immunological memory in mice. The combination of oxaliplatin and bacteria greatly enhances the co-stimulatory and antigen-presenting molecules on antigen-presenting cells, which in turn bridge the cytotoxic T cells for cancer-cell killing. Our findings indicate that rational combination of bacterial therapy and immunogenic chemotherapy can promote anticancer immunity against the immunosuppressive TME.

Stochastic processes and changes in evolutionary rate are associated with diversification in a lineage of tropical hard pines (Pinus)

The study of the patterns of polymorphism and molecular evolution among closely related species is key to understanding the evolutionary forces involved in the diversification of lineages. This point is a big challenge in species with slow evolutionary rates, long life cycles, and ancient, shared polymorphisms such as conifers. Under the premise of divergence in a stepwise migration process, we expect clinal geographical patterns of purifying selection efficiency, and genetic structure related to latitude or longitude. If migration is accompanied by changes in the environment, we could further expect a role of positive selection in driving species divergence. Here, we infer patterns of polymorphism, efficiency of purifying selection, and molecular evolution using a dataset of 161 nuclear genes (∼71 Kb) in a lineage of hard pines from North America, the Caribbean, Mexico, and Central America presumed to have migrated from North America toward lower latitudes with tropical conditions. Under the premise of differences in selective pressures, we also look for possible signals of positive selection. To test our hypothesis, first we estimated different indices to infer patterns of polymorphism and efficiency of purifying selection (Ka, Ks, Ka/Ks, dN, dS, dN/dS, and dxy) and compared these metrics across five clades. Also, we investigated possible clinal patterns in these indices and morphological traits (needle length and cone length). Then we inferred genetic structure and environmental differences among species to test for possible signals of positive selection using phylogenetic methods in specific clades. We found differences among clades using Ka, Ks, and Ka/Ks with a relaxation of purifying selection, especially in the Elliotti and Patula clades. We also found environmental differences related to geographic distance, and among clades suggesting differences in selective pressures. The indices Ks, dxy, and needle length had relationships with geography but not ovulate cone length. Finally, we found that most analyzed genes are under purifying selection, but there was an exception of faster evolutionary rate in some pine species, suggesting the possible action of positive selection in divergence. Our study indicated that stochastic processes have played a key role in the diversification of the group, with a possible input of positive selection in pines from Mexico and Central America.

Isolating a culture of son preference among Armenian, Georgian and Azeri Parents in Soviet-era Russia.

A basic hypothesis is that cultural evolutionary processes sustain differences between groups, these differences have evolutionary relevance and they would not otherwise occur in a system without cultural transmission. The empirical challenge is that groups vary for many reasons, and isolating the causal effects of culture often requires appropriate data and a quasi-experimental approach to analysis. We address this challenge with historical data from the final Soviet census of 1989, and our analysis is an example of the epidemiological approach to identifying cultural variation. We find that the fertility decisions of Armenian, Georgian and Azeri parents living in Soviet-era Russia were significantly more son-biased than those of other ethnic groups in Russia. This bias for sons took the form of differential stopping rules; families with sons stopped having children sooner than families without sons. This finding suggests that the increase in sex ratios at birth in the Caucasus, which began in the 1990s, reflects a cultural preference for sons that predates the end of the Soviet Union. This result also supports one of the key hypotheses of gene-culture coevolution, namely that cultural evolutionary processes can support group-level differences in selection pressures that would not otherwise occur in a system without culture.

Genogeographic technologies of a population biobank as a tool for assessing selection effects (using the example of pharmacogenetic biomarkers of cardiovascular diseases)

Significant differences between the gene pools of Russian peoples require the development of ethno- regional adapted pharmacogenetic tests and the identification of priority regions for their implementation.Aim. To develop a genogeographic technology to identify selection effects using the example of biomarkers that are significant for pharmacotherapy of patients with cardiovascular diseases (CVD), using a population biobank and the Pharmacogenetics of Populations of Russia and Adjacent Countries database.Material and methods. Deoxyribonucleic acid (DNA) samples from the Biobank of Northern Eurasia from 20 metapopulations of the indigenous population of the European Russia were studied using two following data sets: 24 pharmacogenetic markers of CVDs (3170 samples); 1 276 191 polymorphic DNA markers of the autosomal genome (1293 samples). For each data set, estimates of interpopulation variability in the gene pool are provided — the difference between these estimates characterizes the selection pressure on each of the 24 CVD biomarkers. A genogeographic atlas has been created, the maps of which demonstrate the selection pressure on each biomarker according to the degree of deviation from the selective- neutral variability of the gene pool.Results. Twenty-four CVD biomarkers are divided into three following classes: those close to selective- neutral variability, those subject to stabilizing and differentiating selection. For each of the 24 CVD biomarkers, genogeographic maps were created that reveal selection effects in each of the 20 metapopulations. Most maps have identified populations that are under differential selection pressure and therefore a priority for the implementation of ethno- regionally adapted pharmacogenetic protocols.Conclusion. Pharmacogenetic markers and populations under differential selection require the development of ethno- regionally adapted pharmacogenetic tests. The created cartographic atlas of selection can serve as the basis for pharmacogenetic studies carried out using genogeographic methods.

Wide divergence of fungal communities inhabiting rocks and soils in a hyper-arid Antarctic desert.

Highly simplified microbial communities colonise rocks and soils of continental Antarctica ice-free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen-forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.

Phenotypic plasticity of a generalist fish species resident to lotic environments: Insights from the Great Lakes region.

Fish morphology is incredibly plastic and local/resident morphology can be influenced by factors including habitat, predation, resource availability, and water velocity. Through analysis of body shape using geometric morphometrics, we describe the degree of phenotypic plasticity within a generalist fish species resident to low-order tributaries of Green Bay and Lake Michigan. We predicted that isolated populations of creek chub (Semotilus atromaculatus) would display plastic responses in body shape due to differences in selective pressures imposed by stream environments. We show that body shape of creek chub was significantly different between streams which are considered to be isolated populations, and while we expected body shape variation to remain constant between study years, we found that shape was not fixed and changed over time in the same manner among focal streams. The diversity of creek chub diet and degree of agricultural land use in the watershed were significant predictors of body morphology. The effect of resource availability and land use within the watershed demonstrates how selective pressures influence phenotypes at the population level. Our study provides insight into morphological changes of stream fish populations, which may be important in the context of changing ecosystems and novel conditions.

FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses

Many gene families are shared across the tree of life between distantly related species because of horizontal gene transfers (HGTs). However, the frequency of HGTs varies strongly between gene families and biotic realms suggesting differential selection pressures and functional bias. One gene family with a wide distribution are FIC-domain containing enzymes (FicDs). FicDs catalyze AMPylation, a post-translational protein modification consisting in the addition of adenosine monophosphate to accessible residues of target proteins. Beside the well-known conservation of FicDs in deuterostomes, we report the presence of a conserved FicD gene ortholog in a large number of protostomes and microbial eukaryotes. We also reported additional FicD gene copies in the genomes of some rotifers, parasitic worms and bivalves. A few dsDNA viruses of these invertebrates, including White spot syndrome virus, Cherax quadricarinatus iridovirus, Ostreid herpesvirus-1 and the beetle nudivirus, carry copies of FicDs, with phylogenetic analysis suggesting a common origin of these FicD copies and the duplicated FicDs of their invertebrate hosts. HGTs and gene duplications possibly mediated by endogenous viruses or genetic mobile elements seem to have contributed to the transfer of AMPylation ability from bacteria and eukaryotes to pathogenic viruses, where this pathway could have been hijacked to promote viral infection.

Pseudogenization of the Hair-Related Genes PADI3 and S100A3 in Cetaceans and Hippopotamus amphibius.

Hair-related genes in mammals play important roles in the development and maintenance of hair and other keratinous structures in mammals. The peptidyl arginine deiminase 3 (PADI3) gene encodes an enzyme that catalyzes the conversion of arginine residues to citrulline. The S100 calcium binding protein A3 (S100A3) gene encodes a protein that is highly expressed in the hair cuticle and contains arginine residues that are converted to citrullines by PADI enzymes. In this study, we investigated the pseudogenization events of PADI3 and S100A3 in cetaceans and Hippopotamus amphibius. We found that PADI3 underwent three independent pseudogenization events during cetacean evolution, in baleen whales, toothed cetaceans other than Physeter catodon, and P. catodon. Notably, the entire PADI3 gene is absent in the baleen whales. Pseudogenization of S100A3 occurred independently in cetaceans and H. amphibius. Interestingly, we found that in cetaceans S100A3 underwent pseudogenization before PADI3, suggesting that differential selection pressures were acting on the two genes. Our findings provide valuable insights into the molecular evolution of these genes in cetaceans and hippopotamuses, highlighting their importance for understanding the evolution of hair-related genes.

Convergence in sympatric swallowtail butterflies reveals ecological interactions as a key driver of worldwide trait diversification

Ecological interactions can promote phenotypic diversification in sympatric species. While competition can enhance trait divergence, other ecological interactions may promote convergence in sympatric species. Within butterflies, evolutionary convergences in wing color patterns have been reported between distantly related species, especially in females of palatable species, where mimetic color patterns are promoted by predator communities shared with defended species living in sympatry. Wing color patterns are also often involved in species recognition in butterflies, and divergence in this trait has been reported in closely related species living in sympatry as a result of reproductive character displacement. Here, we investigate the effect of sympatry between species on the convergence vs. divergence of their wing color patterns in relation to phylogenetic distance, focusing on the iconic swallowtail butterflies (family Papilionidae). We developed an unsupervised machine learning-based method to estimate phenotypic distances among wing color patterns of 337 species, enabling us to finely quantify morphological diversity at the global scale among species and allowing us to compute pairwise phenotypic distances between sympatric and allopatric species pairs. We found phenotypic convergence in sympatry, stronger among distantly related species, while divergence was weaker and restricted to closely related males. The convergence was stronger among females than males, suggesting that differential selective pressures acting on the two sexes drove sexual dimorphism. Our results highlight the significant effect of ecological interactions driven by predation pressures on trait diversification in Papilionidae and provide evidence for the interaction between phylogenetic proximity and ecological interactions in sympatry, acting on macroevolutionary patterns of phenotypic diversification.