Find research datasets worth reusing

opencc-zeroFeb 2022View details →

Maintenance of phenotypic plasticity is linked to oxidative stress in spadefoot toad larvae

Phenotypic plasticity allows organisms to improve the match between their phenotype and heterogeneous environments. Theoretical models have argued that costs of maintaining the sensory and response machinery necessary for adaptive phenotypic plasticity are important determinants to the evolution of plasticity. Despite recurrent arguments invoking putative metabolic costs associated with maintenance of cellular machinery, no studies have yet attempted to quantify it from a molecular standpoint. Here we experimentally examine physiological differences across genotypes (sibships) of spadefoot toad larvae with different degrees of plasticity in response to predator cues. We observed marked differences across sibships in developmental, growth and morphological responses to predators, and tested whether increased plasticity was associated with oxidative stress or immune suppression. We observed that more plastic sibships experienced higher antioxidant enzymatic activity when reared in the absence of predator cues, i.e. not expressing their plastic responses. The degree of plasticity was also associated with higher lipid peroxidation and slightly greater granulocyte-to-lymphocyte ratio. Higher antioxidant activity in highly plastic sibships suggests that maintenance of phenotypic plasticity may be linked to energy demanding metabolic processes. Our findings suggest that having the potential to produce plastic responses may incur oxidative and immunological costs. In the long term, such maintenance costs may erode individual fitness and even constrain the evolution of plasticity. To our knowledge, this is the first empirical evidence indicating the existence of a physiological cost to the maintenance of phenotypic plasticity.

opencc-zeroFeb 2022View details →

Phenotype evaluation rawdata of Acinetobacter baumannii harboring chromosomal parallel mutations or an evolved plasmid

OXA-23 is the predominant carbapenemase in carbapenem-resistant Acinetobacter baumannnii. The co-evolutionary dynamics of A. baumannii and OXA-23-encoding plasmids are poorly understood. Here, we transformed A. baumannnii ATCC 17978 with pAZJ221, a blaOXA-23-containing plasmid from a clinical A. baumannnii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub-inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time-points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of blaOXA-23 in pAZJ221, interfering allele dynamics, and chromosomal locus-level parallelism were observed. To characterize genotype-to-phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3'→5') GMP-metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the causal effects of these mutations on fitness costs and plasmid kinetics, the evolved plasmid containing two copies of blaOXA-23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of blaOXA-23 contributed to host fitness under carbapenem pressure but imposed a burden on the host in antibiotic-free media relative to the unevolved pAZJ221. Overall, our study provides a framework for the co-evolution of A. baumannii and a clinical blaOXA-23-containing plasmid, involving early blaOXA-23 duplication followed by chromosomal adaptations.

opencc-by-4.0Feb 2022View details →

Genetic and phenotypic diversity of banana-infecting Fusarium strains

Genetic and phenotypic diversity of banana-infecting Fusarium strains. Dataset1 contains molecular diagnosis and pathogenicity assays of Fusarium isolates. Dataset2 describes the sequenced isolates used in the study.

opencc-by-4.0Mar 2022View details →

hlb-1 behavioural phenotype dataset and associated metadata

This deposition contains the supporting dataset for the article:  'Bi-allelic loss-of-function variants in PPFIBP1 cause a neurodevelopmental disorder with microcephaly, epilepsy and periventricular calcifications'

opencc-zeroMar 2022View details →

Phenotype data for: Pleiotropic and non-redundant effects of an auxin importer in Setaria and maize

Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of Spp1 under its native promoter showed that the SPP1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

opencc-zeroMar 2022View details →

Meta-analysis of phenotypic plasticity in response to thermal treatments in invertebrates

Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity—particularly in traits with modest-to-low cross-sex genetic correlations— typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception—cold resistance—is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.

opencc-zeroMar 2022View details →

Epigenetics underpins phenotypic plasticity of protandrous sex change in fish

Phenotypic plasticity is an important driver of species resilience. Often mediated by epigenetic changes, phenotypic plasticity enables individual genotypes to express variable phenotypes in response to environmental change. Barramundi (Lates calcarifer) is a protandrous (male-first) sequential hermaphrodite that exhibit plasticity in length-at-sex change between geographic regions. This plasticity is likely to be mediated by changes in DNA methylation (DNAm), a well-studied epigenetic modification. However, region-specific relationships between length, sex and DNAm in sequential hermaphrodites were previously unreported. To investigate these relationships, here we compare DNAm in four conserved vertebrate sex-determining genes in male and female barramundi of differing lengths from three regions of northern Australia. Despite a strong association between increasing length and male-to-female sex change, the data reveal that DNAm becomes more sex-specific (rather than more female-specific) with length. Significant differences in DNAm between males and females of similar lengths suggest that female-specific DNAm arises rapidly during sex change, rather than gradually with growth. The findings also reveal that region-specific differences in length-at-sex change are accompanied by differences in DNAm, and were concurrent with variability in remotely sensed sea temperature and salinity. Together, these findings provide the first in situ evidence for epigenetically and environmentally mediated sex change in a protandrous hermaphrodite, and offer significant insight into the molecular and ecological processes governing the marked and unique plasticity of sex in fish.

Data from: Competitive consequences determined by phenotypic but not genetic distance: a study with asexual Daphnia genotypes

1. How evolutionary relatedness influences the strength of competitive interactions among genetically isolated populations has been a long-standing interest in ecology. Darwin's "Competition Relatedness Hypothesis (CRH)" states that, since closely related species should compete more strongly, they are less likely to coexist, while Herbert's "Bimodal Competition Hypothesis (BCH)" predicts that competitive exclusion is less likely to occur when the competing species are genetically close or distant. 2. To test these hypotheses, we experimentally examined the difference in the competitive ability and life tables of fecundity and survivorship among four different genotypes of asexual Daphnia cf. pulex that diverged from a single ancestral genotype. 3. The experiments showed that the competitive consequences differed depending on the pairing of the competing genotypes, and that the degree of the competitive exclusion was lower when the competing genotypes were genetically closer to each other. These results partially supported the BCH but not the CRH at all. More importantly, the degree of competitive exclusion was better predicted by the phenotypic rather than genetic distances between the competing genotypes. 4. The life table experiments revealed that competitively inferior genotypes had higher early reproduction rates, but survival rates decreased with age and thus body size, probably a result of selection by predation pressures found in nature. 5. These results indicate that competitive superiority is highly dependent on selection pressures that given organisms have been evolutionally subjected to, and, that genetic similarity is not necessarily an appropriate measure for predicting the completive exclusion on an ecological time scale. To predict competitive relationships among the organisms, it is essential to comprehend their phenotypic differences rather than simply knowing their genetic or phylogenetic relationships.

High MHC diversity confers no advantage for phenotypic quality and reproductive performance in a wild bird

Genes of the major histocompatibility complex (MHC) encode antigen binding molecules and are an integral part of the acquired immune response of vertebrates. In general, high individual MHC diversity is expected to increase fitness by broadening the spectrum of pathogens recognized by the immune system, in accordance with the heterozygote advantage mechanism. On the other hand, the optimality hypothesis assumes that individuals with optimal (intermediate), rather than maximum diversity of the MHC will achieve the highest fitness because of inherent costs associated with expressing diverse MHC alleles. Here, we tested for associations between individual diversity of the MHC class I and class II genes (binding antigens of intra- and extra-cellular pathogens, respectively) and a range of fitness-related traits (condition, ornament expression and reproduction) in an urban population of the Eurasian coot Fulica atra. Contrary to our expectation, we found that high within-individual allelic diversity of MHC genes (both class I and II) was associated with poorer condition (lower blood haemoglobin concentrations), weaker expression of the putative ornament (smaller frontal shield), later onset of breeding and smaller clutches. An analysis of functional MHC allele clusters (supertypes) provided further support for negative associations of MHC diversity with phenotypic quality and reproductive performance, but most of these relationships could not be explained by the presence of specific maladaptive supertypes. Finally, we found little empirical support for the optimality hypothesis in the Eurasian coot. Our results suggest that the costs of high MHC diversity outweighed any benefits associated with broad MHC repertoire, which could be driven by depauperate pathogen diversity in an urban landscape. To the best of our knowledge, this is one of the first studies providing consistent evidence for negative associations of MHC diversity with a range of fitness-related traits in a natural avian population.

Mutation, selection, and the prevalence of the C. elegans heat-sensitive mortal germline phenotype

C. elegans strains with the heat-sensitive mortal germline (Mrt) phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of C. elegans' tolerance. Mrt is transgenerationally-heritable, and proximately under epigenetic control. Previous studies have suggested that Mrt presents a relatively large mutational target, and that Mrt is not uncommon in natural populations of C. elegans. The Mrt phenotype is not monolithic. Some strains exhibit a strong Mrt phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the Mrt phenotype, and (2) quantify the frequency of Mrt in a collection of 95 wild isolates. Over the course of ~16,000 meioses, we detected one mutation to a strong Mrt phenotype, resulting in a point estimate of the mutation rate UMrt≈ 6 10-5/genome/generation. We detected no mutations to a weak Mrt phenotype. 6/95 wild isolates have a strong Mrt phenotype, and although quantification of the weak Mrt phenotype is inexact, the weak Mrt phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong Mrt phenotype ≈0.1%, similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak Mrt variants in nature combined with the low mutation rate suggests that Mrt may be maintained by balancing selection.

A test of frequency dependent selection in the evolution of a generalist phenotype

A solitary population of consumers frequently evolves to the middle of a resource gradient and an intermediate mean phenotype compared to a sympatric pair of competing species that diverge to either side via character displacement. The forces governing the distribution of phenotypes in these allopatric populations, however, are little investigated. Theory predicts that the intermediate mean phenotype of the generalist should be maintained by negative frequency dependent selection, whereby alternate extreme phenotypes are favored because they experience reduced competition for resources when rare. However, the theory makes assumptions that are not always met, and alternative explanations for an intermediate phenotype are possible. We provide a test of this prediction in a mesocosm experiment using threespine stickleback that are ecologically and phenotypically intermediate between the more specialized stickleback species that occur in pairs. We manipulated the frequency distribution of phenotypes in two treatments and then measured effects on a focal intermediate population. We found a slight frequency-dependent effect on survival in the predicted direction but not on individual growth rates. This result suggests that frequency dependent selection might be a relatively weak force across the range of phenotypes within an intermediate population and we suggest several general reasons why this might be so. We propose that allopatric populations might often be maintained at an intermediate phenotype instead by stabilizing or fluctuating directional selection.

opennotspecifiedApr 2022View details →

Figure 3 in Automatic identification of bird females using egg phenotype

Figure 3. Correlation between spectral (A), pattern/luminance (B) and shape (C) distances, respectively and genetic distances. Individual phenotypic distances of average eggs laid by nine genotyped common cuckoo females: spectral (D), pattern/luminance (E) and shape (F) distances.

opennotspecifiedApr 2022View details →

Figure 1 in Automatic identification of bird females using egg phenotype

Figure 1. Values for individual eggs on the two most important PC variables (according to the random forest model), grouped by cuckoo female ID based on the genetic assignment. PCA2 pattern variable indicates egg skew and PC2 spectra variable indicates blueness/greenness of eggs (for details, see Table 2).

opennotspecifiedApr 2022View details →

Figure 2 in Automatic identification of bird females using egg phenotype

Figure 2. Phenotypic distances of nine average eggs laid by nine genotyped common cuckoo females (A) and their genetic distances (B). Thicker green lines denote higher phenotypic and genetic similarity. Correlation between phenotypic and genetic distances (C).

Data for: Anti-predator phenotype in crucian carp altered by a psychoactive drug

Predator-inducible defences constitute a widespread form of adaptive phenotypic plasticity, and such defences have recently been suggested linked with the neuroendocrine system. The neuroendocrine system is a target of endocrine disruptors, such as psychoactive pharmaceuticals, which are common aquatic contaminants. We hypothesized that exposure to an antidepressant pollutant, fluoxetine, influences the physiological stress response in our model species, crucian carp, affecting its behavioural and morphological responses to predation threat. We examined short- and long-term effects of fluoxetine and predator exposure on behaviour and morphology in crucian carp. 17 days of exposure to a high dose of fluoxetine (100 µg L-1), resulted in a shyer phenotype, regardless of the presence/absence of a pike predator, but this effect disappeared after long-term exposure. Fluoxetine effects on morphological plasticity was context dependent as a low dose (1 µg L-1) only influenced crucian carp body shape in pike presence. A high dose of fluoxetine strongly influenced body shape regardless of predator treatment. Our results highlight that environmental pollution by pharmaceuticals could disrupt physiological regulation of ecologically important inducible defences.

opencc-by-4.0May 2021View details →

Comorbid-phenome prediction and phenotype risk scores enhance gene discovery for generalized anxiety disorder and posttraumatic stress disorder

GWAS summary statistics. See ReadMe for column descriptions.

Thoroughbred horse inbreeding measures and racing phenotypes

We quantified inbreeding based on runs of homozygosity (ROH) using 297K SNP genotypes from 6,128 horses born in Europe and Australia, of which 13.2% were unraced.

A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation, and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.

Data for: Phenotypic senescence in a natural insect population

Senescence seems to be universal in living organisms and plays a major role in life-history strategies. Phenotypic senescence, the decline of body condition and/or performance with age, is a largely understudied component of senescence in natural insect populations, although it would be important to understand how and why insects age under natural conditions. We aimed (i) to investigate how body mass and thorax width change with age in a natural population of the univoltine Clouded Apollo butterfly (Parnassius mnemosyne, Lepidoptera: Papilionidae) and (ii) to assess the relationship of this change with sex and wing length. We studied a population between 2014 and 2020 using mark-recapture during the whole flight period each year. Repeated measurements of body mass and thorax width and single measurements of wing length were performed on marked individuals. We analysed body mass and thorax width change with age (days since marking), wing length and the date of the first capture. Both body mass and thorax width declined non-linearly with age. Individuals appearing earlier in the flight period had significantly higher initial body mass and thorax width and their body mass declined faster than later ones. Initial body sizes of females were higher, but males' body sizes decreased slower. Initial thorax width showed higher annual variation than body mass. To our best knowledge, this is the first study that revealed phenotypic senescence in a natural butterfly population, using in vivo measurements. We found sexual differences in the rate of phenotypic senescence. Despite the annual variation of initial body sizes, the rate of senescence did not vary considerably across the years.