Differential Selection Pressures Research Articles

Detection of differential selection pressure and functional-specific sites in subunits of vertebrate neuronal nicotinic acetylcholine receptors

The nicotinic acetylcholine receptors (nAChR) are made of subunits evolved from a common ancestor. Despite the similarity in their sequences and structures, the properties of these subunits vary significantly. Thus, identifying the evolution features and function-related sites specific to each subunit is essential for understanding the characteristics of the subunits and the receptors assembled by them. In this study, we examined the sequence features of the nine neuronal nAChRs subunits from representative vertebrate species. Analysis revealed that all the subunits were subject to strong purifying selection in evolution, and each was under a unique pattern of selection pressures. At the same time, the functional constraints were not uniform within each subunit, with different domains in the molecule being subject to different selection pressures. We also detected potential positive selection events in the subunits or subunit clusters, and identified the sites might be associated with the function specificity of each subunit. Furthermore, positive selection at some domains might contribute to the diversity of subunit function; for example, the β9 strand might be related to the agonist specificity of α subunit in heteromeric receptor and β4-β5 linker could be involved in Ca2+ permeability. Subunits α7, α4 and β2 subunits possess a strong adaptability in vertebrates. Our results highlighted the importance of tracking functional differentiation in protein sequence underlying functional properties of nAChRs. In summary, our work may provide clues on understanding the diversity and the function specificity of the nAChR subunits, as well as the receptors co-assembled by them. Communicated by Ramaswamy H. Sarma

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.

A quantitative genetics approach to validate lab- versus field-based behavior in novel environments

AbstractConclusions about the adaptive nature of repeatable variation in behavior (i.e., “personality”) are often derived from laboratory-based assays. However, the expression of genetic variation differs between laboratory and field. Laboratory-based behavior might not predict field-based behavior thus, cross-context validation is required. We estimated the cross-context correlation between behavior expressed by wild great tits (Parus major) in established laboratory versus field novel environment assays. Both assays have been used as proxies for “exploration tendency.” Behavior in both contexts had similar repeatability (R = 0.35 vs. 0.37) but differed in heritability (h2 = 0.06 vs. 0.23), implying differences in selection pressures. Unexpectedly, there was no cross-context correlation. Laboratory- and field-based behavior thus reflected expressions of two distinct underlying characters. Post hoc simulations revealed that sampling bias did not explain the lack of correlation. Laboratory-based behavior may reflect fear and exploration, but field-based behavior may reflect escape behavior instead, though other functional interpretations cannot be excluded. Thus, in great tits, activity expressed in laboratory versus field novel environment assays is modulated by multiple quasi-independent characters. The lack of cross-context correlation shown here may also apply to other setups, other repeatable behaviors, and other taxa. Our study thus implies care should be taken in labeling behaviors prior to firm validation studies.

Final report from a registry study of patients with active cancer undergoing ecological staging.

e22501 Background: The host-cancer relationship can be viewed as a set of tumor supportive and inhibitory interactions, that is as an ecosystem. An advantage of such a perspective might include a more dynamic understanding of the selection pressures affecting tumor evolution. If so then a means of detecting and measuring those forces would be of help in understanding that drive and point to potential therapeutic clinical interventions. Towards this goal a registry study of patients with invasive cancer was conducted to examine readily available clinical measures to inform an ecological staging system. Methods: Eligibility for registry participation included age of 18 years or older, active cancer requiring treatment, life expectancy estimated to be at least six months and willingness to provide informed consent for this IRB-approved study. Ecological staging was then conducted at entry assessing 22 separate clinical parameters from history, physical exam and laboratory known to effect tumor biology, grouped into eight profiles and scored using a trichotomization of data, increasing score corresponding to an increase in positive tumor selection. To aggregate data from the profiles, a geometric figure, an octamer, or ecogram, was constructed, vertices representing the net score of each of the eight profiles. We hypothesize that the area bounded by the polygon, ecogram area (EA) would reflect an index of adverse, tumor-supporting ecological influence. Overall survival was determined from time of diagnosis of cancer until time of registry closure. Results: 15 subjects, eight female, seven male, ages 53-84 (median 64) participated in the registry. Complete ecological staging was obtained from all participating subjects, an indication of feasibility for collection of such data in the clinic. Resulting EA ranged 12-fold (0-12.1) across subjects suggesting sensitivity of EA to differences in selection pressures among the participants; ecogram morphology from individual subjects demonstrated unique shapes, an indication of specificity for character of individual tumor ecological landscape. Mean overall survival for participants from time of cancer diagnosis was 265 weeks. For 12 subjects with advanced stage disease, overall survival was inversely related to ecogram area (r = -.45). Conclusions: Ecological staging of cancer from clinical parameters proved feasible in this registry study of patients with active cancer. Ecological information from those parameters when aggregated using a geometric figure, an ecogram, demonstrated both sensitivity and specificity for differences among participants. For those subjects with advanced stage disease, ecogram area was inversely related to overall cancer survival. Ecological staging may be a useful tool in gauging selection pressures affecting cancer evolutionary tendency and of potential benefit to oncologists in forecasting such development.

Maternal Schistosomiasis Hinders B Cell Development Leading to Reduced Humoral Immunity Upon Immunization

Abstract Maternal helminth infections are a global public health concern that correlate with altered infant immune responses to childhood immunizations and infection. A mechanistic understanding of how maternal helminth infection alters the immune responses of offspring is critical to improve childhood vaccine regimens in endemic areas, decrease childhood morbidity, and to understand the consequences of specific defects in long-lived immunity. Our murine model of maternal Schistosoma mansoni infection demonstrated that pups born to mothers chronically infected with Schistosoma mansoni have reduced IL-4 production and B cell expansion. This defect continues following tetanus/diphtheria immunization, resulting in impaired immunity. To determine the origin of this humoral immunity defect, we began investigating lymphoid progenitors. We found an increase in the common lymphoid progenitors (CLPs) in the bone marrow of naïve mice from infected mothers. When immunized with a Tetanus/Diphtheria vaccination, there is a significant reduction in expansion of these progenitors in comparison to age matched controls from uninfected mothers coupled with a decrease in bone marrow B cells. RNA sequencing revealed a defect in stem cell pluripotency signaling pathway. Further analysis post-immunization shows a decrease in immature B cells in the bone marrow of pups from infected mothers, suggesting a more exclusive selection process or differential selective pressure, leading to lower B cell frequencies in the draining lymph node. We hypothesize that altered transcriptional regulation at the progenitor level caused by maternal Schistosomiasis is the mechanistic root of long-lived defects in humoral immunity to foreign antigens.

Agrobacterium-Mediated Capsicum annuum Gene Editing in Two Cultivars, Hot Pepper CM334 and Bell Pepper Dempsey.

Peppers (Capsicum annuum L.) are the most widespread and cultivated species of Solanaceae in subtropical and temperate countries. These vegetables are economically attractive worldwide. Although whole-genome sequences of peppers and genome-editing tools are currently available, the precision editing of peppers is still in its infancy because of the lack of a stable pepper transformation method. Here, we employed three Agrobacterium tumefaciens strains—AGL1, EHA101, and GV3101—to investigate which Agrobacterium strain could be used for pepper transformation. Hot pepper CM334 and bell pepper Dempsey were chosen in this study. Agrobacterium tumefaciens GV3101 induced the highest number of calli in cv. Dempsey. All three strains generated similar numbers of calli for cv. CM334. We optimized a suitable concentration of phosphinothricin (PPT) to select a CRISPR/Cas9 binary vector (pBAtC) for both pepper types. Finally, we screened transformed calli for PPT resistance (1 and 5 mg/L PPT for cv. CM334 and Dempsey, respectively). These selected calli showed different indel frequencies from the non-transformed calli. However, the primary indel pattern was consistent with a 1-bp deletion at the target locus of the C. annuum MLO gene (CaMLO2). These results demonstrate the different sensitivity between cv. CM334 and Dempsey to A. tumefaciens-mediated callus induction, and a differential selection pressure of PPT via pBAtC binary vector.

The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau

Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.

Equal performance but distinct behaviors: sex differences in a novel object recognition task and spatial maze in a highly social cichlid fish.

Sex differences in behavior and cognition can be driven by differential selection pressures from the environment and in the underlying neuromolecular mechanisms of decision-making. The highly social cichlid fish Astatotilapia burtoni exhibits dynamic and complex social hierarchies, yet explicit cognitive testing (outside of social contexts) and investigations of sex differences in cognition have yet to be fully explored. Here we assessed male and female A. burtoni in two cognitive tasks: a novel object recognition task and a spatial task. We hypothesized that males outperform females in a spatial learning task and exhibit more neophilic/exploratory behavior across both tasks. In the present study we find that both sexes prefer the familiar object in a novel object recognition task, but the time at which they exhibit this preference differs between the sexes. Females more frequently learned the spatial task, exhibiting longer decision latencies and quicker error correction, suggesting a potential speed-accuracy tradeoff. Furthermore, the sexes differ in space use in both tasks and in a principal component analysis of the spatial task. A model selection analysis finds that preference, approach, and interaction duration in the novel object recognition task reach a threshold of importance averaged across all models. This work highlights the need to explicitly test for sex differences in cognition to better understand how individuals navigate dynamic social environments.

Human uniqueness? Life history diversity among small-scale societies and chimpanzees.

Humans life histories have been described as "slow", patterned by slow growth, delayed maturity, and long life span. While it is known that human life history diverged from that of a recent common chimpanzee-human ancestor some ~4-8 mya, it is unclear how selection pressures led to these distinct traits. To provide insight, we compare wild chimpanzees and human subsistence societies in order to identify the age-specific vital rates that best explain fitness variation, selection pressures and species divergence. We employ Life Table Response Experiments to quantify vital rate contributions to population growth rate differences. Although widespread in ecology, these methods have not been applied to human populations or to inform differences between humans and chimpanzees. We also estimate correlations between vital rate elasticities and life history traits to investigate differences in selection pressures and test several predictions based on life history theory. Chimpanzees' earlier maturity and higher adult mortality drive species differences in population growth, whereas infant mortality and fertility variation explain differences between human populations. Human fitness is decoupled from longevity by postreproductive survival, while chimpanzees forfeit higher potential lifetime fertility due to adult mortality attrition. Infant survival is often lower among humans, but lost fitness is recouped via short birth spacing and high peak fertility, thereby reducing selection on infant survival. Lastly, longevity and delayed maturity reduce selection on child survival, but among humans, recruitment selection is unexpectedly highest in longer-lived populations, which are also faster-growing due to high fertility. Humans differ from chimpanzees more because of delayed maturity and lower adult mortality than from differences in juvenile mortality or fertility. In both species, high child mortality reflects bet-hedging costs of quality/quantity tradeoffs borne by offspring, with high and variable child mortality likely regulating human population growth over evolutionary history. Positive correlations between survival and fertility among human subsistence populations leads to selection pressures in human subsistence societies that differ from those in modern populations undergoing demographic transition.

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters.

Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n=86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.

Identifying genetic modifiers of APOE in Alzheimer’s disease using evolutionary information and regression analyses

AbstractBackgroundTo date, the APOEɛ4 allele is the best known genetic risk factor of late‐onset Alzheimer’s Disease (AD), while the APOEɛ2 allele is known to protect against AD. However, some APOEɛ4 allele carriers remain AD‐free, and some APOEɛ2 carriers develop dementia.MethodWe focused on the whole‐exome sequences of patients with paradoxical genotype‐phenotype relationships (APOEɛ2 AD carriers and APOEɛ4 healthy individuals) and assessed the predicted impact of coding variants using Evolutionary Action equation. Then, for each gene, we measured the mutational EA burden given its background mutation rate and quantified the deviance in mutational EA burden of a gene against those with similar background mutation rate. We repeated this in the two populations of interest to identify outliers with apparent potential for protective or pathogenic qualities. The predicted modifiers of APOE were tested computationally through statistical analyses as well as experimentally by assessing neuronal dysfunction in a Drosophila AD model.ResultWe found ∼200 genes with differential mutational signatures in the paradoxical patient groups. These genes were differentially expressed in AD brains and shown to include or interact with known AD genes. Nearly half of the fly homologs tested modified motor performance deficits induced by tau or β42, both of which are responsible for pathological hallmarks of AD.ConclusionWe conclude that this method successfully identifies protective or pathogenic nature of genes related to AD and allow for a tractable analysis of specific variants often missed by conventional methods, by quantitatively distinguishing genes under differential selection pressures. Identification of such dependencies and how they interact together would allow better understanding of epistatic relationships in Alzheimer’s disease and provide additional insight into novel drug targets for therapeutic exploration.

Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding.

The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub-genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.

Cryptic sexual dimorphism reveals differing selection pressures on continental islands

AbstractBirds are well known for their sexual dimorphism. But not all forms of dimorphism are the same, and differences in morphology can be so subtle that they are not detected by casual observation. We report that this is the case with the Sulawesi Babbler (Pellorneum celebense), the first reported instance of sexual dimorphism in this species or any of the ground babblers of the South‐East Asian islands. Our finding is based on a combination of morphometric analyses, genetic sexing, and observation of breeding condition. We highlight the utility of unsupervised clustering approaches, widely used in the biomedical literature, for the investigation of sexual dimorphism in ecological and evolutionary contexts. The sexual dimorphism was weaker on the mainland of Sulawesi and stronger on the continental islands of Kabaena, Muna, and Buton. This suggests that different evolutionary pressures have led the species to partition niches differently in these habitats, which separated only recently in geological history. This kind of intraspecific niche partitioning is an intrinsic part of the ecological niche of such species, one we must not miss if we are to fully understand these endlessly fascinating organisms and systems.Abstract in Bahasa Indonesian is available with online material

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome.

Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.

Assessment of between-founder heterogeneity in inbreeding depression for reproductive traits in Baluchi sheep

Magnitude of inbreeding depression could be different among descendants of various founder animals, when recessive genetic composition of a population is unevenly distributed among founder animal genomes. Reproductive records of Baluchi sheep for the litter variables size at birth (LSB), size at weaning (LSW), mean weight/lamb born (LMWLB), mean weight/lamb weaned (LMWLW), total weight at birth/ewe lambing (TLWB) and total weight at weaning/ewe lambing (TLWW) were used to examine heterogeneity in inbreeding depression between founder animals. Pedigree-based inbreeding coefficients were proportioned into components coming from founder animals and Mendellian contribution from non-founder animals. Two approaches were used to assess effects of inbreeding: overall inbreeding coefficients or partial inbreeding of the four main founder animals as possible covariates included in statistical models. Among the traits evaluated, there were effects on LMWLB, LMWLW and TLWW of inbreeding with there being a −8, -48, and −95 g decrease per 1% increase in inbreeding, respectively. Linear regressions of traits on partial inbreeding coefficients due to founder animals were of different magnitudes and ranged between -0.12 and +0.128. Heterogeneous contribution of founder animals to inbreeding depression occurred for LSB, LMWLB, and TLWW. These results indicate there was uneven distribution of recessive genetic composition among genomes of founder animals or differences in selection pressures on unfavorable alleles between different founder lines. The observed variation in founder-specific inbreeding depression indicates a small number of alleles with major effects are contributing to inbreeding depression.

In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB).

The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylumProteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.

Locomotion in Rodents and Small Carnivorans: Are they So Different?

Rodents and carnivorans constitute two diverse clades with variable life habits. To analyze the common ecomorphological aspects of their limbs in relation to their different substrate uses, the shape of humerus and femur was explored using 3-D geometric morphometrics. The principal components and MANOVA analyses show that the shape of the humerus is similarly related to the substrate use and taxonomy, and the shape of the femur is heavily influenced by taxonomic differences. Nevertheless, beneath those differences in the latter, a relation with the proposed ecological categories is also found. The stronger ecomorphological correlation of the humerus with respect to the femur may indicate a differential selective pressure on each limb. This could be reflecting the greater involvement of the forelimb over the hind limb in several activities performed with the limbs such as digging and climbing. The combined analysis of two distantly related groups with diverse ecological characteristics allows a recognition of similar biological patterns hidden under taxonomic differences. Furthermore, the study of morphological similarities and differences underlying taxonomic variability may led to a more profound understanding of the evolution of the locomotor apparatus.

Does facial hair greying in chimpanzees provide a salient progressive cue of aging?

The greying of human head hair is arguably the most salient marker of human aging. In wild mammal populations, greying can change with life history or environmental factors (e.g., sexual maturity in silverback gorillas). Yet, whether humans are unique in our pattern of age-related hair depigmentation is unclear. We examined the relationship between pigmentation loss in facial hair (greying) to age, population, and sex in wild and captive chimpanzees (Pan troglodytes). Digital facial photographs representing three chimpanzee populations (N = 145; ages 1–60 years) were scored for hair greying on a scale of one [~100% pigmented] to six [~0% pigmented]. Our data suggest that chimpanzee head and facial hair generally greys with age prior to mid-life (~30 years old), but afterwards, greying ceases to increase incrementally. Our results highlight that chimpanzee pigmentation likely exhibits substantial variation between populations, and that both 'grey' and pigmented phenotypes exist across various age classes. Thus, chimpanzee facial hair greying is unlikely a progressive indicator of age beyond mid-life, and thus facial greying in chimpanzees seems different from the pattern observed in humans. Whether this reflects neutral differences in senescence, or potential differences in selection pressures (e.g. related to conspecific communication), is unclear and worthy of more detailed examination across populations and taxa.

Avian Metapneumovirus subtype B around Europe: a phylodynamic reconstruction

Avian Metapneumovirus (aMPV) has been recognized as a respiratory pathogen of turkey and chickens for a long time. Recently, a crescent awareness of aMPV, especially subtype B, clinical and economic impact has risen among European researchers and veterinarians. Nevertheless, the knowledge of its epidemiology and evolution is still limited. In the present study, the broadest available collection of partial G gene sequences obtained from European aMPV-B strains was analyzed using different phylodynamic and biostatistical approaches to reconstruct the viral spreading over time and the role of different hosts on its evolution. After aMPV-B introduction, approximatively in 1985 in France, the infection spread was relatively quick, involving the Western and Mediterranean Europe until the end of the 1990s, and then spreading westwards at the beginning of the new millennium, in parallel with an increase of viral population size. In the following period, a wider mixing among aMPV-B strains detected in eastern and western countries could be observed. Most of the within-country genetic heterogeneity was ascribable to single or few introduction events, followed by local circulation. This, combined with the high evolutionary rate herein demonstrated, led to the establishment of genetically and phenotypically different clusters among countries, which could affect the efficacy of natural or vaccine-induced immunity and should be accounted for when planning control measure implementation. On the contrary, while a significant strain exchange was proven among turkey, guinea fowl and chicken, no evidence of differential selective pressures or specific amino-acid mutations was observed, suggesting that no host adaptation is occurring.

The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation

The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. In this study, we generated and analyzed high-quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola), and hexaploid (E. crus-galli) Echinochloa species. Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization, contrary to their significant expansionduring wheat polyploidization, suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. In addition, distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E. crus-galli and bread wheat. Collectively, our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization. The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.