Heterozygote Advantage Research Articles

Convergent selection and evolutionary trade-offs shape social transitions in sweat bees.

Convergent selection and evolutionary trade-offs shape social transitions in sweat bees.

Cranial adaptations of the Night Parrot (Psittaculidae: Pezoporus occidentalis), a cryptic nocturnal bird

ABSTRACT The Night Parrot Pezoporus occidentalis is a critically endangered, elusive, nocturnal bird that is difficult to study in the field. Much is unknown about its biology, including how it navigates at night. A previous investigation of the eye and brain revealed that it likely has poor nocturnal vision, but its other sensory abilities, and overall skull anatomy, have not yet been investigated. This osteological study, based on micro-CT-scans of the holotype, describes and compares the anatomy of the Night Parrot skull, and identifies its possible ecological adaptations. Specialised ear anatomy suggests that the Night Parrot has enhanced acoustic abilities, in contrast with its diurnal congener P. wallicus and the only other nocturnal parrot, the Kakapo Strigops habroptila. The Night Parrot’s uniquely enlarged exoccipital bones may amplify sound, and bilateral ear asymmetry, not identified in any other parrot species, likely enhances its directional hearing, as in many species of owl. Enlarged exoccipitals displace the zygomatic processes and constrain orbit size, suggesting an evolutionary trade-off between hearing and vision. The auditory abilities of the species require deeper investigation, but our anatomical observations indicate that the potential impacts of noise disturbance may warrant consideration in Night Parrot conservation strategies as a precaution.

Exploring the ecosystem services bundles and influencing drivers at different scales in southern Jiangxi, China

Located in the hilly and mountainous central area of the national ecological security strategic pattern (described as “two ecological barriers and three green belts”), southern Jiangxi is an important ecological barrier in southeast China and a pilot area for the national mountains-rivers-forests-farmlands-lakes-grasslands restoration projects. In recent years, the rapid economic development of the southern Jiangxi region and the rapid changes in land use, agricultural intensification, and population urbanization have severely tested this ecosystem on which people depend for their survival. Currently, studies of ecosystems and their interactions from a single spatial perspective have sprung up, but only a few studies have comprehensively analyzed different spatial scales to facilitate the sustainable development of regional ecosystems. Multi-scale studies should be carried out to quantitatively understand the relationship between ecosystem services (ESs) and socio-natural drivers, in an attempt to find a suitable scale to assess regional ESs or to achieve complementary advantages by combining multi-scales so as to conduct hierarchical management of ESs. Therefore, to better understand the interplay between ESs and to achieve the goals of sustainable development, we quantitatively analyzed the evolutionary patterns, trade-offs, and synergies of ESs. In our analysis, we also looked at bundling ESs and their drivers for seven ecosystem services at the township and watershed scales for 2000–2020 in southern Jiangxi. Crop production, meat production, water yield, carbon storage, soil retention, habitat quality, and forest recreation services were specifically quantified, and redundancy analysis was used to explore the influence degree of precipitation, temperature, elevation, slope, GDP, and population density on ESs. The results showed that most ESs have increased in southern Jiangxi, indicating spatial and temporal heterogeneity. The scale effect of trade-off and synergy showed that the spatial variation was similar, but the amplitude of variation was different. Compared with the watershed scale, the overall bundle of ESs in southern Jiangxi is better identified and clustered at the township scale. In addition, Cluster 4 at the township scale and Cluster 3 at the watershed scale can comprehensively identify high-value areas of ecosystem services in the study area. The rapid growth of GDP and population density caused by rapid urbanization were the main driving factors of the difference in ESs between the two scales in southern Jiangxi. Our results provide recommendations for governance and restoration of regional ecosystem services and support for conducting a comprehensive analysis of spatio-temporal evolutionary mechanisms and interactions of ecosystem services at different scales.

Evolutionary trade-offs in osmotic and ionic regulation and expression of gill ion transporter genes in high latitude, cold clime Neotropical crabs from the 'end of the world'.

Osmoregulatory findings on crabs from high Neotropical latitudes are entirely lacking. Seeking to identify the consequences of evolution at low temperature, we examined hyperosmotic/hypo-osmotic and ionic regulation and gill ion transporter gene expression in two sub-Antarctic Eubrachyura from the Beagle Channel, Tierra del Fuego. Despite sharing the same osmotic niche, Acanthocyclus albatrossis tolerates a wider salinity range (2-65‰ S) than Halicarcinus planatus (5-60‰ S); their respective lower and upper critical salinities are 4‰ and 12‰ S, and 63‰ and 50‰ S. Acanthocyclus albatrossis is a weak hyperosmotic regulator, while H. planatus hyperosmoconforms; isosmotic points are 1380 and ∼1340 mOsm kg-1 H2O, respectively. Both crabs hyper/hypo-regulate [Cl-] well with iso-chloride points at 452 and 316 mmol l-1 Cl-, respectively. [Na+] is hyper-regulated at all salinities. mRNA expression of gill Na+/K+-ATPase is salinity sensitive in A. albatrossis, increasing ∼1.9-fold at 5‰ compared with 30‰ S, decreasing at 40-60‰ S. Expression in H. planatus is very low salinity sensitive, increasing ∼4.7-fold over 30‰ S, but decreasing at 50‰ S. V-ATPase expression decreases in A. albatrossis at low and high salinities as in H. planatus. Na+/K+/2Cl- symporter expression in A. albatrossis increases 2.6-fold at 5‰ S, but decreases at 60‰ S versus 30‰ S. Chloride uptake may be mediated by increased Na+/K+/2Cl- expression but Cl- secretion is independent of symporter expression. These unrelated eubrachyurans exhibit similar systemic osmoregulatory characteristics and are better adapted to dilute media; however, the expression of genes underlying ion uptake and secretion shows marked interspecific divergence. Cold clime crabs may limit osmoregulatory energy expenditure by hyper/hypo-regulating hemolymph [Cl-] alone, apportioning resources for other energy-demanding processes.

Evolutionary coexistence in a fluctuating environment by specialization on resource level.

Microbial communities in fluctuating environments, such as oceans or the human gut, contain a wealth of diversity. This diversity contributes to the stability of communities and the functions they have in their hosts and ecosystems. To improve stability and increase production of beneficial compounds, we need to understand the underlying mechanisms causing this diversity. When nutrient levels fluctuate over time, one possibly relevant mechanism is coexistence between specialists on low and specialists on high nutrient levels. The relevance of this process is supported by the observations of coexistence in the laboratory, and by simple models, which show that negative frequency dependence of two such specialists can stabilize coexistence. However, as microbial populations are often large and fast growing, they evolve rapidly. Our aim is to determine what happens when species can evolve; whether evolutionary branching can create diversity or whether evolution will destabilize coexistence. We derive an analytical expression of the invasion fitness in fluctuating environments and use adaptive dynamics techniques to find that evolutionarily stable coexistence requires a special type of trade-off between growth at low and high nutrients. We do not find support for the necessary evolutionary trade-off in data available for the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae on glucose. However, this type of data is scarce and might exist for other species or in different conditions. Moreover, we do find evidence for evolutionarily stable coexistence of the two species together. Since we find this coexistence in the scarce data that are available, we predict that specialization on resource level is a relevant mechanism for species diversity in microbial communities in fluctuating environments in natural settings.

Molecular evolution of extended spectrum beta-lactam resistance.

Multidrug-resistant bacteria reduce the number of available medications that can treat resistant infections. In the United States, nearly 36,000 deaths per year are caused by antibiotic-resistant infections. To stop or slow down the evolution of the resistance, it is crucial to explore and understand the underlying molecular mechanism driving evolution of resistance. Here, utilizing a saturation mutagenesis library of TEM-1 beta lactamase, we systematically investigate resistance conferring mutations and biophysical changes as a result of these mutations. We employ a high-throughput sequencing based fitness assays and atomic scale molecular dynamic simulations. By systematically studying resistance conferring mutations and epistatic interactions between these mutations, we uncover evolutionary patterns and tradeoffs that can be utilized for developing rational antibiotic treatment strategies that can impede evolution of antibiotic resistance.

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice

ABSTRACT Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel “pathometagenomic” approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.

BTG1 mutation yields supercompetitive B cells primed for malignant transformation.

Multicellular life requires altruistic cooperation between cells. The adaptive immune system is a notable exception, wherein germinal center B cells compete vigorously for limiting positive selection signals. Studying primary human lymphomas and developing new mouse models, we found that mutations affecting BTG1 disrupt a critical immune gatekeeper mechanism that strictly limits B cell fitness during antibody affinity maturation. This mechanism converted germinal center B cells into supercompetitors that rapidly outstrip their normal counterparts. This effect was conferred by a small shift in MYC protein induction kinetics but resulted in aggressive invasive lymphomas, which in humans are linked to dire clinical outcomes. Our findings reveal a delicate evolutionary trade-off between natural selection of B cells to provide immunity and potentially dangerous features that recall the more competitive nature of unicellular organisms.

Ras/MAPK signalling intensity defines subclonal fitness in a mouse model of hepatocellular carcinoma.

Quantitative differences in signal transduction are to date an understudied feature of tumour heterogeneity. The MAPK Erk pathway, which is activated in a large proportion of human tumours, is a prototypic example of distinct cell fates being driven by signal intensity. We have used primary hepatocyte precursors transformed with different dosages of an oncogenic form of Ras to model subclonal variations in MAPK signalling. Orthotopic allografts of Ras-transformed cells in immunocompromised mice gave rise to fast-growing aggressive tumours, both at the primary location and in the peritoneal cavity. Fluorescent labelling of cells expressing different oncogene levels, and consequently varying levels of MAPK Erk activation, highlighted the selection processes operating at the two sites of tumour growth. Indeed, significantly higher Ras expression was observed in primary as compared to secondary, metastatic sites, despite the apparent evolutionary trade-off of increased apoptotic death in the liver that correlated with high Ras dosage. Analysis of the immune tumour microenvironment at the two locations suggests that fast peritoneal tumour growth in the immunocompromised setting is abrogated in immunocompetent animals due to efficient antigen presentation by peritoneal dendritic cells. Furthermore, our data indicate that, in contrast to the metastatic-like outgrowth, strong MAPK signalling is required in the primary liver tumours to resist elimination by NK (natural killer) cells. Overall, this study describes a quantitative aspect of tumour heterogeneity and points to a potential vulnerability of a subtype of hepatocellular carcinoma as a function of MAPK Erk signalling intensity.

Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs.

Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.

Digest: Multiple selective pressures drive color diversity in moths.

How are color polymorphisms maintained within populations? De Pasqual et al. (2022) showed that female wood tiger moths (Arctia plantaginis) that were heterozygous for a wing color gene had higher fertility, hatching success, and offspring survival. These findings suggest that the complex interaction between heterozygote advantage and pleiotropic effects maintains color variability through a balance between multiple and competing selective pressures in wild populations.

Hypoxia-resistance heterogeneity in tumours: the impact of geometrical characterization of environmental niches and evolutionary trade-offs. A mathematical approach

In the study of cancer evolution and therapeutic strategies, scientific evidence shows that a key dynamics lies in the tumour-environment interaction. In particular, oxygen concentration plays a central role in the determination of the phenotypic heterogeneity of cancer cell populations, whose qualitative and geometric characteristics are predominant factors in the occurrence of relapses and failure of eradication. We propose a mathematical model able to describe the eco-evolutionary spatial dynamics of tumour cells in their adaptation to hypoxic microenvironments. As a main novelty with respect to the existing literature, we combine a phenotypic indicator reflecting the experimentally-observed metabolic trade-off between the hypoxia-resistance ability and the proliferative potential with a 2d geometric domain, without the constraint of radial symmetry. The model is settled in the mathematical framework of phenotype-structured population dynamics and it is formulated in terms of systems of coupled non-linear integro-differential equations. The computational outcomes demonstrate that hypoxia-induced selection results in a geometric characterization of phenotypic-defined tumour niches that impact on tumour aggressiveness and invasive ability. Furthermore, results show how the knowledge of environmental characteristics provides a predictive advantage on tumour mass development in terms of size, shape, and composition.

Agta hunter-gatherer oral microbiomes are shaped by contact network structure.

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter-gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African BaYaka hunter-gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses and even unrelated friends can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter-gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

Relationships between female size, egg size, clutch size, and hatchling size in Morelet’s crocodile

Resources are limited by the environment in which an individual is found and can be influenced by natural selection. Evolutionary trade-offs in the reptilian reproductive effort literature have focused on optimal egg size. The objective of this study was to test egg size, clutch size, female size and hatching size in Morelet’s Crocodile (Crocodylus moreletii). Thirteen nests, 13 post-oviposition females, and 434 eggs were evaluated, from which 292 (67.2%) neonates hatched. No correlation was found between clutch size and egg size; however, the Gaussian model best explained the relationship between egg volume and mass. The relationship between TL of the female and egg size may be explained in that the size of the egg has a defined limit even when the female continues to increase in TL. Other factors may influence clutch size, such as environmental factors, reproductive adult quality, diet, the of the females, and captive conditions.

Large-scale genomic and transcriptomic profiles of rice hybrids reveal a core mechanism underlying heterosis

BackgroundHeterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and 265 rice varieties from a mini-core collection.ResultsPhenotypic analysis shows that heterosis is dependent on genetic backgrounds and environments. By genome-wide association study of 418 hybrids and their parents, we find that nonadditive QTLs are the main genetic contributors to heterosis. We show that nonadditive QTLs are more sensitive to the genetic background and environment than additive ones. Further simulations and experimental analysis support a novel mechanism, homo-insufficiency under insufficient background (HoIIB), underlying heterosis. We propose heterosis in most cases is not due to heterozygote advantage but homozygote disadvantage under the insufficient genetic background.ConclusionThe HoIIB model elucidates that genetic background insufficiency is the intrinsic mechanism of background dependence, and also the core mechanism of nonadditive effects and heterosis. This model can explain most known hypotheses and phenomena about heterosis, and thus provides a novel theory for hybrid rice breeding in future.

Evolutionary trade-offs associated with copy number variations in resistance alleles in Culex pipiens mosquitoes

Organophosphate and carbamate insecticides have largely been used worldwide to control mosquito populations. As a response, the same amino acid substitution in the ace-1 gene (G119S), conferring resistance to both insecticides, has been selected independently in many mosquito species. In Anopheles gambiae, it has recently been shown that the G119S mutation is actually part of homogeneous duplications that associate multiple resistance copies of the ace-1 gene. In this study, we showed that duplications of resistance copies of the ace-1 gene also exist in the Culex pipiens species complex. The number of copies is variable, and different numbers of copies are associated with different phenotypic trade-offs: we used a combination of bioassays and competition in population cages to show that having more resistance copies conferred higher resistance levels, but was also associated with higher selective disadvantage (or cost) in the absence of insecticide. These results further show the versatility of the genetic architecture of resistance to organophosphate and carbamate insecticides around the ace-1 locus and its role in fine-tuned adaptation to insecticide treatment variations.Graphical

Rapid Phenotypic Convergence towards Collateral Sensitivity in Clinical Isolates of Pseudomonas aeruginosa Presenting Different Genomic Backgrounds.

Collateral sensitivity (CS) is an evolutionary trade-off by which acquisition of resistance to an antibiotic leads to increased susceptibility to another. This Achilles' heel of antibiotic resistance could be exploited to design evolution-based strategies for treating bacterial infections. To date, most studies in the field have focused on the identification of CS patterns in model strains. However, one of the main requirements for the clinical application of this trade-off is that it must be robust and has to emerge in different genomic backgrounds, including preexisting drug-resistant isolates, since infections are frequently caused by pathogens already resistant to antibiotics. Here, we report the first analysis of CS robustness in clinical strains of Pseudomonas aeruginosa presenting different ab initio mutational resistomes. We identified a robust CS pattern associated with short-term evolution in the presence of ciprofloxacin of clinical P. aeruginosa isolates, including representatives of high-risk epidemic clones belonging to sequence type (ST) 111, ST175, and ST244. We observed the acquisition of different ciprofloxacin resistance mutations in strains presenting varied STs and different preexisting mutational resistomes. Importantly, despite these genetic differences, the use of ciprofloxacin led to a robust CS to aztreonam and tobramycin. In addition, we describe the possible application of this evolutionary trade-off to drive P. aeruginosa infections to extinction by using the combination of ciprofloxacin-tobramycin or ciprofloxacin-aztreonam. Our results support the notion that the identification of robust patterns of CS may establish the basis for developing evolution-informed treatment strategies to tackle bacterial infections, including those due to antibiotic-resistant pathogens. IMPORTANCE Collateral sensitivity (CS) is a trade-off of antibiotic resistance evolution that could be exploited to design strategies for treating bacterial infections. Clinical application of CS requires it to robustly emerge in different genomic backgrounds. In this study, we performed an analysis to identify robust patterns of CS associated with the use of ciprofloxacin in clinical isolates of P. aeruginosa presenting different mutational resistomes and including high-risk epidemic clones (ST111, ST175, and ST244). We demonstrate the robustness of CS to tobramycin and aztreonam and the potential application of this evolutionary observation to drive P. aeruginosa infections to extinction. Our results support the notion that the identification of robust CS patterns may establish the basis for developing evolutionary strategies to tackle bacterial infections, including those due to antibiotic-resistant pathogens.

Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal

The major histocompatibility complex (MHC) has been intensively studied for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing variation of microsatellite and diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g., immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely distributed wild mammal.

Simple models for cladoceran species interactions: how competition, predation, and evolutionary trade-offs potentially influence coexistence of Bosminid species

Simple models for cladoceran species interactions: how competition, predation, and evolutionary trade-offs potentially influence coexistence of Bosminid species

Antibiotic Cycling Affects Resistance Evolution Independently of Collateral Sensitivity.

Antibiotic cycling has been proposed as a promising approach to slow down resistance evolution against currently employed antibiotics. It remains unclear, however, to which extent the decreased resistance evolution is the result of collateral sensitivity, an evolutionary trade-off where resistance to one antibiotic enhances the sensitivity to the second, or due to additional effects of the evolved genetic background, in which mutations accumulated during treatment with a first antibiotic alter the emergence and spread of resistance against a second antibiotic via other mechanisms. Also, the influence of antibiotic exposure patterns on the outcome of drug cycling is unknown. Here, we systematically assessed the effects of the evolved genetic background by focusing on the first switch between two antibiotics against Salmonella Typhimurium, with cefotaxime fixed as the first and a broad variety of other drugs as the second antibiotic. By normalizing the antibiotic concentrations to eliminate the effects of collateral sensitivity, we demonstrated a clear contribution of the evolved genetic background beyond collateral sensitivity, which either enhanced or reduced the adaptive potential depending on the specific drug combination. We further demonstrated that the gradient strength with which cefotaxime was applied affected both cefotaxime resistance evolution and adaptation to second antibiotics, an effect that was associated with higher levels of clonal interference and reduced cost of resistance in populations evolved under weaker cefotaxime gradients. Overall, our work highlights that drug cycling can affect resistance evolution independently of collateral sensitivity, in a manner that is contingent on the antibiotic exposure pattern.