Strong Selective Pressure Research Articles

Linking pathogen-microbiome-host interactions to explain amphibian population dynamics.

Symbiotic interactions can determine the evolutionary trajectories of host species, influencing genetic variation through selection and changes in demography. In the context of strong selective pressures such as those imposed by infectious diseases, symbionts providing defences could contribute to increase host fitness upon pathogen emergence. Here, we generated genome-wide data of an amphibian species to find evidence of evolutionary pressures driven by two skin symbionts: a batrachochytrid fungal pathogen and an antifungal bacterium. Using demographic modelling, we found evidence of decreased effective population size, probably due to pathogen infections. Additionally, we investigated host genetic associations with infection status, antifungal bacterium abundance and overall microbiome diversity using structural equation models. We uncovered relatively lower nucleotide diversity in infected frogs and potential heterozygote advantage to recruit the candidate beneficial symbiont and fight infections. Our models indicate that environmental conditions have indirect effects on symbiont abundance through both host body traits and microbiome diversity. Likewise, we uncovered a potential offsetting effect among host heterozygosity-fitness correlations, plausibly pointing to different ecological and evolutionary processes among the three species due to dynamic interactions. Our findings revealed that evolutionary pressures not only arise from the pathogen but also from the candidate beneficial symbiont, and both interactions shape the genetics of the host. Our results advance knowledge about multipartite symbiotic relationships and provide a framework to model ecological and evolutionary dynamics in wild populations. Finally, our study approach can be applied to inform conservation actions such as bioaugmentation strategies for other imperilled amphibians affected by infectious diseases.

Somatic mutations during rapid clonal domestication of Populus alba var. pyramidalis.

For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short-time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10-9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.

Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.).

BackgroundDNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet.MethodsUsing the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns.ResultsFifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.

Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate.

Although mate choice is expected to favor partners with advantageous genetic properties, the relative importance of genome‐wide characteristics, such as overall heterozygosity or kinship, versus specific loci, is unknown. To disentangle genome‐wide and locus‐specific targets of mate choice, we must first understand congruence in global and local variation within the same individual. This study compares genetic diversity, both absolute and relative to other individuals (i.e., complementarity), assessed across the genome to that found at the major histocompatibility complex (MHC), a hyper‐variable gene family integral to immune system function and implicated in mate choice across species. Using DNA from 22 captive olive baboons (Papio anubis), we conducted double digest restriction site‐associated DNA sequencing to estimate genome‐wide heterozygosity and kinship, and sequenced two class I and two class II MHC loci. We found that genome‐wide diversity was not associated with MHC diversity, and that diversity at class I MHC loci was not correlated with diversity at class II loci. Additionally, kinship was a significant predictor of the number of MHC alleles shared between dyads at class II loci. Our results provide further evidence of the strong selective pressures maintaining genetic diversity at the MHC in comparison to other randomly selected sites throughout the genome. Furthermore, our results indicate that class II MHC disassortative mate choice may mediate inbreeding avoidance in this population. Our study suggests that mate choice favoring genome‐wide genetic diversity is not always synonymous with mate choice favoring MHC diversity, and highlights the importance of controlling for kinship when investigating MHC‐associated mate choice.

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Genetic diversity of modern lines of hybrid pigs based on variations in mitochondrial DNA sequence

Unique Evolution of Antiviral Tetherin in Bats.

ABSTRACTBats are recognized as important reservoirs of viruses deadly to other mammals, including humans. These infections are typically nonpathogenic in bats, raising questions about host response differences that might exist between bats and other mammals. Tetherin is a restriction factor which inhibits the release of a diverse range of viruses from host cells, including retroviruses, coronaviruses, filoviruses, and paramyxoviruses, some of which are deadly to humans and transmitted by bats. Here, we characterize the tetherin genes from 27 bat species, revealing that they have evolved under strong selective pressure, and that fruit bats and vesper bats express unique structural variants of the tetherin protein. Tetherin was widely and variably expressed across fruit bat tissue types and upregulated in spleen tissue when stimulated with Toll-like receptor agonists. The expression of two computationally predicted splice isoforms of fruit bat tetherin was verified. We identified an additional third unique splice isoform which includes a C-terminal region that is not homologous to known mammalian tetherin variants but was functionally capable of restricting the release of filoviral virus-like particles. We also report that vesper bats possess and express at least five tetherin genes, including structural variants, more than any other mammal reported to date. These findings support the hypothesis of differential antiviral gene evolution in bats relative to other mammals.IMPORTANCE Bats are an important host of various viruses which are deadly to humans and other mammals but do not cause outward signs of illness in bats. Furthering our understanding of the unique features of the immune system of bats will shed light on how they tolerate viral infections, potentially informing novel antiviral strategies in humans and other animals. This study examines the antiviral protein tetherin, which prevents viral particles from escaping their host cell. Analysis of tetherin from 27 bat species reveals that it is under strong evolutionary pressure, and we show that multiple bat species have evolved to possess more tetherin genes than other mammals, some of which encode structurally unique tetherins capable of activity against different viral particles. These data suggest that bat tetherin plays a potentially broad and important role in the management of viral infections in bats.

Serpentine Adaptation of Ligustrum japonicum Thunb. (Oleaceae) Based on Morphological and Anatomical Approaches

Serpentine soils consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient content in drought-prone, patchily distributed substrates; therefore, they are one of the most challenging settings for plant life. In this study, a comparative study was conducted using serpentine and inland populations of Ligustrum japonicum Thunb. (Oleaceae) to determine morphological and anatomical differences between the same species growing in the serpentine and inland areas. Longitudinal leaf sections indicated that serpentine populations had slightly thicker leaves than inland populations, contributing to the increased heights of adaxial and abaxial epidermal cells and palisade and spongy tissues. Moreover, the serpentine population had smaller stomata than the inland populations. These results suggest that the strong selective pressure under serpentine soil conditions could force leaves to restore water and avoid excessive transpiration.

Predatory cue use in flush responses of a colonial nesting seabird during polar bear foraging

Nest predation is a primary cause of reproductive failure in birds; thus, predators apply strong selective pressure on nesting behaviour, especially risk assessment behaviours during predator encounters at nests. Prey's risk assessments are not static; rather, dynamic risk assessment theory predicts that prey assess risk in real-time and update it according to changes in cues posed by the predator(s). We used drone videography to film nest-flushing behaviours of common eiders, Somateria mollissima, in response to foraging polar bears, Ursus maritimus, on East Bay Island (Nunavut, Canada). We assessed how cue use influenced flushing behaviour and nest fate in a path analysis using 200 observations of 193 eiders in 2017. Our most supported model found that more direct angles of visual gaze and travel angle by polar bears resulted in conspicuous nest flushes by eiders (β = −0.236 ± 0.059), whereas the presence of herring gulls, Larus argentatus, resulted in more discrete flushes of hens walking from their nests (β = −0.181 ± 0.059). Shorter flush initiation distances between eiders and approaching bears resulted in greater nest predation by polar bears (β = −0.203 ± 0.076). We found no support that an eider's visibility from the nest influenced any component of flushing behaviour. We suggest that during encounters with bears, eiders are capable of assessing risk and making appropriate behavioural decisions to reduce the chances of nest loss. However, as the colony experienced heavy predation by bears in 2017, behavioural responses alone appear to be insufficient to mitigate polar bear predation at the population level.

Community‐wide trait adaptation, but not plasticity, explains ant community structure in extreme environments

Abstract Quantifying trait–environment associations can help elucidate the processes underpinning the structure of species assemblages. However, most work has focused on trait variation across rather than within species, meaning that processes operating at the intraspecific levels cannot be detected. Incorporating intraspecific trait variation in community‐wide analyses can provide valuable insights about the role of morphological adaptation and plasticity on species persistence and the composition of ecological communities. Here, we assessed geographical variation in the direction (i.e. adaptation) and strength of selection, and the magnitude of plasticity, by examining community‐wide trait variation in ant communities along an environmental gradient spanning 9° latitude in Quebec, Canada. Specifically, we measured 9 morphological traits related to foraging strategies, resource use and thermal regulation at 20 locations across temperate and boreal forests. We then examined how the mean and variance of these traits varied along temperature and precipitation gradients. Moreover, we examined how these trait–environment relationships varied across levels of organization, from individual workers (intraspecific) to colonies (intraspecific) and species (interspecific). We observed changes in mean trait values along environmental gradients, but very little change in variance. Specifically, we observed a decrease in the mean length of antennae and an increase in the mean eye length from mild (warm and wet) to more extreme environments (cold and dry). These shifts in trait means were mostly coordinated across organizational levels (i.e. worker, colony and species). We also observed a general increase in trait variance from mild to extreme environments, but only at the species level. Our findings suggest that stressful environmental conditions exert a strong selection pressure on ant morphology causing shifts in optimal trait values. These adaptations may enable persistence at the northern edge of the boreal forest and therefore influence the composition of these ant communities. Specifically, ants with large eyes and short antennae are overrepresented at the transition zone between the boreal forest and the tundra, possibly representing an adaptation to these more open habitats. Our study demonstrates that combining spatial and community‐wide intraspecific functional trait data provides a promising way forward to gain new insights on trait adaptations and processes underpinning community structure along environmental gradients. Read the free Plain Language Summary for this article on the Journal blog.

More time for aliens? Performance shifts lead to increased activity time budgets propelling invasion success

In the Grinnellian niche concept, the realized niche and potential distribution is characterized as an interplay among the fundamental niche, biotic interactions and geographic accessibility. Climate is one of the main drivers for this concept and is essential to predict a taxon’s distribution. Mechanistic approaches can be useful tools, which use fitness-related aspects like locomotor performance and critical thermal limits to predict the potential distribution of an organism. These mechanistic approaches allow the inclusion key ecological processes like local adaptation and can account for thermal performance traits of different life-history stages. The African Clawed Frog, Xenopus laevis, is a highly invasive species occurring on five continents. The French population is of special interest due to an ongoing expansion for 40 years and a broad base of knowledge. We hypothesize that (1) the French population exhibits increased activity time in the invasive European range that could be devoted to fitness-relevant activity and (2) tadpoles may have less activity time available than adult frogs from the same range. We investigate how thermal performance traits translate into activity time budgets and how local adaptation and differences in the thermal responses of life-history stages may boost the European Xenopus invasion. We use a mechanistic approach based on generalized additive mixed models, where thermal performance curves were used to predict the hours of activity and to compare the potential activity time budgets for two life-history stages of native and invasive populations. Our results show that adult French frogs have more activity time available in Europe compared to South African frogs, which might be an advantage in searching for prey or escaping from predators. However, French tadpoles do not have more activity time in Europe compared to the native South African populations suggesting that tadpoles do not suffer the same strong selective pressure as adult frogs.

S5.4b Genomic variation structure in clinical isolate collections alters benefits of association screening: a study of Cryptococcus neoformans var. grubii in Colombia

S5.4 Free oral paper session, September 22, 2022, 3:00 PM - 4:30 PMObjectiveRecent genome-wide genotype-phenotype association studies (GWAS) of sets of clinical fungal isolates have reported problems resulting from strong phylogenetic clustering (apparent quasi-clonal population structure, difficulties in localizing association signals on chromosomes). We wished to directly investigate such difficulties, for whole-genome sequence data, and corresponding phenotypic data we had generated.MethodsOur recently released Illumina read sequences (Bioproject PRJNA669191) for 29 clinical Colombian isolate genomes of Cryptococcus neoformans var. grubii (28 VNI and 1 VNII as outgroup)12 were assembled and aligned to the annotated H99 VNI reference genome. Single nucleotide polymorphisms (SNPs) were called for the VNI alignment. MLST types, phenotypes, and source metadata of the same isolates12 were integrated with the genomic data. Analyses were interpreted in the light of published literature.ResultsThe 28 VNI isolates were assigned an order considering MLST classification and whole-genome phylogenetic distances. Most SNPs were biallelic, allowing straightforward barcoding: each of the 28 isolates was given a bar if it had the minor allele. Barcode profiles (SNP state vectors) were found repeated numerous times within genes and across entire chromosomes, indicating that neither fine nor ‘rough’ mapping of associations would succeed, except where flagged genes had already been characterized by relevant molecular biology experiments. The same repetitiveness can allow amplicons of individual MLST loci to tag and inform on variation present in other loci in the genome. The gene for the capsule-associated protein CAP59 and its promoter region illustrate such implications at a small (genic) scale.ConclusionsMost associations of phenotypes with fungal genomes from modestly sampled clinical isolate populations cannot be localized to one or a few regions in a genome. This problem is less restrictive in human GWAS studies or (possibly) in studies of recombining fungi sampled from the environment3. It limits the benefits for molecular etiologic understanding that one might expect from GWAS of isolates obtained in clinical contexts, where key fungal phenotypes can be under stronger selection pressure. Explanatory power may be low if one compares just MLST types or phylogenetic clusters4 or examines only variation within individual MLST types. More informative results may be gained by restricting the genomic search space a priori to a subset of genes that are likely to be related to a phenotype, and then zooming in to individual SNPs that are known/suspected to affect protein structure/function1 or influence transcription/translation of the gene. Where the modes of regulation of a key gene are still not completely characterized despite decades of research, such as in CAP59, the presence of a phenotypically monitored, lone SNP in a strategic position within an almost SNP-less region can give potentially precious hints where otherwise none exist; we illustrate this strategy of SNP-focused local exploration for the promoter/enhancer and currently used MLST amplicon of CAP59.Sources:Vélez N, Vega-Vela N, et al. (2022), J Fungi 8(3):245.Vélez N, Monteoliva L, et al. (2022). J Fungi 8(1):57.Whiston E, Taylor JW (2015). G3 6(2):235-244.Felsenstein J (2008). Am Nat. 171(6):713-725.

S9.3d Antivirulence drug discovery to disarm Candida albicans with metabolites from myxobacteria.

S9.3 Drug resistance in emerging pathogenic fungi, September 23, 2022, 4:45 PM - 6:15 PM Candida albicans is an opportunistic fungal pathogen. While nearly 40%-60% of humans are colonized harmlessly by C. albicans, prolonged use of antibiotics or an immune-compromised status can lead to mucosal or deadly systemic candidiasis (Kumamoto et al., 2020). There are only three classes of antifungals available to physicians to treat and prevent severe Candidiasis. These drugs, which include polyenes, echinocandins, and azoles, protect the host by killing or inhibiting growth of C. albicans, thereby exerting a strong selective pressure toward drug resistance. Antivirulence drugs, by contrast, target virulence traits of pathogens without affecting their growth, making drug resistance less likely to evolve. We seek to discover novel antivirulence compounds against C. albicans that keep it at, or return it to, its baseline commensal state even under conditions that support pathogenicity. Bacteria have evolved a large repository of metabolites that can inhibit and modulate the behavior of other organisms in their environment. Clades like the predatory myxobacteria are untapped for potential antifungal and antivirulence drug discovery (Vij et al., 2021). We here screened ≈ 2800 crude extracts from myxobacteria in an in situ C. albicans-mammalian epithelial cell infection model. Typically, when oral epithelial cells (TR146) are infected by C. albicans, the fungus proliferates, forms hyphae, and invades and damages the monolayer. In our assay, we estimate the damage to epithelial cells by released lactate dehydrogenase. We also note changes to the growth and morphology of the fungus. Based on these readouts we assign antivirulence and antifungal ranks to each extract, and confirm top-ranked hits with an independent propidium iodide-based assay for host cell damage, and a colorimetric assay of fungal metabolic activity. We found that several of the top-ranked antifungal extracts also showed effects on a multi-drug resistant strain of C. auris. Using an established pipeline, we identified several of the antifungal and antivirulent bioactive components in these extracts. After scaling the production of promising lead compounds, we will test their drugability on clinical Candida spp. strains, and identify their mode of action using large-scale Candida spp. knock-out libraries and multi-omics approaches. Our tested extracts are likely to contain new classes of non-toxic antifungals that can potentially treat infections by multi-drug resistant fungi. We identified and confirmed several myxobacteria extracts that protected mammalian epithelial cells without severely affecting the fungus’ growth, which are, therefore, considered antivirulent.SourcesKumamoto, C.A., Gresnigt, M.S., Hube, B., 2020. The gut, the bad and the harmless: Candida albicans as a commensal and opportunistic pathogen in the intestine. Curr. Opin. Microbiol. 56, 7–15. https://doi.org/10.1016/j.mib.2020.05.006Vij, R., Hube, B., Brunke, S., 2021. Uncharted territories in the discovery of antifungal and antivirulence natural products from bacteria. Comput. Struct. Biotechnol. J. 19, 1244–1252. https://doi.org/10.1016/j.csbj.2021.02.003

Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens

Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes — dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 — requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.

Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer

Mutations in the TERT promoter represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants is unknown. In seven cancer types, we identify duplications of wildtype sequence within the core promoter region of TERT that have strikingly similar features including an ETS motif, the duplication length and insertion site. The duplications recruit a GABP tetramer by virtue of the native ETS motif and its precisely spaced duplicated counterpart, activate the promoter and are clonal in a TERT expressing multifocal glioblastoma. We conclude that recurrent TERT promoter duplications are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.

The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola.

Effectors are secreted by plant-associated microorganisms to modify the host cell physiology. As effectors, the Necrosis- and Ethylene-inducing peptide 1-like proteins (NLPs) are involded in the early phases of plant infection and may trigger host immune responses. Corynespora cassiicola is a polyphagous plant pathogen that causes target spot on many agriculturally important crops. Using genome assembly, gene prediction, and proteome annotation tools, we retrieved 135 NLP-encoding genes from proteomes of 44 isolates. We explored the evolutionary history of NLPs using Bayesian phylogeny, gene genealogies, and selection analyses. We accessed the expression profiles of the NLP genes during the early phase of C. cassiicola-soybean interaction. Three NLP putative-effector genes (Cc_NLP1.1, Cc_NLP1.2A, and Cc_NLP1.2B) were maintained in the genomes of all isolates tested. An NLP putative-non-effector gene (Cc_NLP1.3) was found in three isolates that had been originally obtained from soybean. Putative-effector NLPs were under different selective constraints: Cc_NLP1.1 was under stronger selective pressure, while Cc_NLP1.2A was under a more relaxed constraint. Meanwhile, Cc_NLP1.2B likely evolved under either positive or balancing selection. Despite highly divergent, the putative-effector NLPs maintain conserved the residues necessary to trigger plant immune responses, suggesting they are potentially functional. Only the Cc_NLP1.1 putative-effector gene was significantly expressed at the early hours of soybean colonization, while Cc_NLP1.2A and Cc_NLP1.2B showed much lower levels of gene expression.

Fractional factorial experimental design for optimizing volatile fatty acids from anaerobic fermentation of municipal sludge: Microbial community and activity investigation

Volatile fatty acids (VFAs) production from municipal sludge is a promising venture for resource recovery while ensuring wastewater treatment plants' ecological and economic sustainability. This study used a fractional factorial design (FFD) and response surface methodology (RSM) to optimize VFAs production from municipal sludge in semi-continuous flow acid fermenters (AFs) based on four critical parameters (i.e., sludge retention time (SRT), sludge composition, pH, and temperature) interactively and individually. To ascribe the mechanisms to VFAs production dynamics, non-methanogenic microbial activity assays and microbial community composition linked to the VFAs yields were explored. FFD and RSM successfully optimized VFAs production in the AFs, and a second-order polynomial model with an R-squared of 0.83 was derived. Optimal model conditions for VFAs production were 3-days SRT, 45 °C, pH 8.1, and 0.92 sludge composition (VS/TS ratio). Under these conditions, the model predicted a 3.47-fold increase in VFAs production, close to the experimental value of 3.48. AFs at pH of 8.1 and varying temperatures harbored the highest proportion of fermentative bacteria, mainly Clostridia, and lowest community diversity, indicating strong selective pressure for VFAs-producing populations. Furthermore, the microbial activities assays provided quantitative functional information linked to the microbial communities in each AF configuration consistent with VFAs production.

Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer.

The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. Bacteria deploy SIM when faced with DNA double-strand breaks in the presence of conditions that elicit an SOS response. SIM employs DinB, the evolutionary precursor to human trans-lesion synthesis (TLS) error-prone polymerases, and results in mutations concentrated around DNA double-strand breaks with an abundance that decays with distance. We performed a quantitative study on single nucleotide variant calls for whole-genome sequencing data from 1950 tumors, non-inherited mutations from 129 normal samples, and acquired mutations in 3 cell line models of stress-induced adaptive mutation. We introduce statistical methods to identify mutational clusters, quantify their shapes and tease out the potential mechanism that produced them. Our results show that mutations in both normal and cancer samples are indeed clustered and have shapes indicative of SIM. Clusters in normal samples occur more often in the same genomic location across samples than in cancer suggesting loss of regulation over the mutational process during carcinogenesis. Additionally, the signatures of TLS contribute the most to mutational cluster formation in both patient samples as well as experimental models of SIM. Furthermore, a measure of cluster shape heterogeneity was associated with cancer patient survival with a hazard ratio of 5.744 (Cox Proportional Hazard Regression, 95% CI: 1.824–18.09). Our results support the conclusion that the ancient and evolutionary-conserved adaptive mutation response found in bacteria is a source of genomic instability in cancer. Biological adaptation through SIM might explain the ability of tumors to evolve in the face of strong selective pressures such as treatment and suggests that the conventional ‘hit it hard’ approaches to therapy could prove themselves counterproductive.

Sexual size dimorphism and male reproductive traits vary across populations of a tropical rainforest dung beetle species (Onthophagus babirussa).

Sexual size dimorphism (SSD) arises when natural selection and sexual selection act differently on males and females. Male‐biased SSD is rarer in insects and usually indicates strong sexual selection pressure on male body size in a species. Patterns of SSD can also vary between populations of species that are exposed to different environmental conditions, such as differing resource availability and diversity. Here, we investigate intraspecific variation in SSD as well as relative investment in precopulatory (horn length) and postcopulatory traits (sperm length and testes weight) in a tropical rainforest dung beetle Onthophagus babirussa across Singapore and Peninsular Malaysia. Overall, three out of four populations displayed significant male‐biased SSD, and SSD was greater in populations with smaller overall body size. Average male body size was similar across all populations while female body size was significantly smaller in Singapore, suggesting that the pronounced SSD may also be due to stronger sexual selection on male body size in Singapore populations. All populations showed significant investment in horns as a weapon likely used in male‐male competition, while postcopulatory traits showed no clear scaling relationship with body size, suggesting a higher priority on precopulatory sexual traits in the mating system of this species.

The call of the wild: a challenge to reveal the natural history of birds on the Tibetan plateau

<p indent="0mm">Knowledge on the natural history of organisms is the bedrock upon which ecology and evolutionary biology stand, and contributes to natural conservation, public health and human culture. With an average elevation of more than <sc>4000 m</sc> and a territory of <sc>2500000 km²,</sc> the Tibetan plateau is the highest and largest highland on earth. The extreme environments in the plateau have imposed strong selective pressures on the evolution of organisms’ life histories, leading to the biodiversity hotpots with global conservation concern. Of more than 700 bird species inhabiting the plateau, 90% are unknown with respect to natural history. Without such data, many important scientific and conservative questions cannot be fully understood. Chinese ornithologists are encouraged to full up the knowledge gap.

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

BackgroundPhages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.ResultsWe corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.ConclusionsOur findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.DbLYqYwr-FU-DxBRk3MVnLVideo