Biosystems, Journal Year: 2024, Volume and Issue: 237, P. 105154 - 105154
Published: Feb. 10, 2024
Language: Английский
Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(10)
Published: April 9, 2024
The vast diversity of life on earth is the result evolutionary processes that acted over billions years. Historically it was assumed adaptation and origin new species required long periods time. However, now well established to environments can occur rapidly sometimes even within a few generations. We define here rapid as selective process, which allows population or substantially improve its average fitness in short time scale tens generations, typically hundred years for annual species. More precisely, occurs through natural selection acting phenotype (and ultimately underlying genetic variants) therefore encompasses both ecological (demographic abundance inter-specific interactions given habitat community) (genetic drift, mutation, recombination, gene flow selection) (Hairston et al., 2005; Kokko 2017). occurrence speed thus determined by feedback between (eco-evo) processes. A large body literature documents examples eco-evo feedbacks driving especially consequences human activities, with damaging agriculture (e.g. invasion crop pests pathogens resistant fungicides) (Fisher 2022), medicine parasite resistance drugs/antibiotics) (Birkholtz 2022; Zhang 2022) and/or ecosystems invasive emergent diseases) 2012). Indeed, underpins species' habitats, coevolution hosts their parasites, fluctuating due fast environmental change human-altered environments. Deciphering mechanisms critical current rate global loss biodiversity forecast potential promote ad hoc conservation measures prevent emergence novel unwanted pathogens. This research endeavour entails two major questions bridging mechanisms: What are sources variation evolution? Which evolutionary, factors enable (hasten) constrain (slow down) In this special issue 'Rapid adaptation: Potential constraints' we address these presenting developments theory concerning evolution combination empirical investigations evolving systems from all kingdoms life. Two percolate studies presented here. first central question whether predominately reliant small changes allele frequencies standing at many loci (polygenic adaptation) effect mutations arising either de novo entering migration. second important topic identification investigation such demographic parameters size), genetic/genomic architecture, life-history traits heterogeneity. To provide answers questions, grouped contributions three main topical parts. First, start simple case occurring genes phenotypic effects, spread 'selective sweep' mechanism. mode positive generates fixation advantageous alleles be very short. theoretical investigate how trait, sweepstake reproduction (i.e. variance offspring production) common fish, invertebrates fungi, one hand hasten beneficial but other make less likely (Eldon & Stephan, 2023; Korfmann 2023). (invasion) habitats strong then genomics fall webworm (FWW; Dai 2023) hairfin anchovy (Setipinna tenuifilis) (Liu Finally, review summarises findings genomic role transposable elements (TEs) determining dynamics TEs resulting mutational play an fungal mildew pathogen Blumeria cereal crops evade fungicides (Kusch Conversely, part, focus evidence via quantitative (polygenic) constraints. papers core assumptions underpinning slowing down polygenic traits: existence (metabolic) trade-offs (Hashemi Laitinen Nikoloski, effects epistatic recombination (Li Three further reveal architecture determine brown anole (Anolis sagrei) (Bock 2023), Italian wall lizard (Podarcis siculus) (Sabolić during domestication yeast (Saccharomyces cerevisiae) (Raas Dutheil, Third, response feedbacks, feature antagonistic sexes parasites). present range generating coevolution/fluctuating controlled set-ups using generation Fluctuating chiefly characterised under across whole genome documented analysed Drosophila melanogaster (Glaser-Schmitt poplars (Saubin Furthermore, host–parasite also coincide affects sizes time, turn has available (Le Pennec dissecting environment co-adaptation (Goehlich Hernandez Strong adaptive sweeps selected (typically generation). finite populations, changing biotic abiotic probability action initial frequency possible linkage neighbouring genes. waiting mutation inversely proportional rate, latter being, example, high bacteria viruses. contrast, most eukaryotic multi-cellular exhibit lower rates (on order 10−9 up 10−7 per site generation) smaller effective than viruses, meaning fuel limited comparison. Rapid more originate existing variation, advantage becoming after conditions. These predictions arise, allele, characterise sweep, obtained standard models genetics: Moran Wright–Fisher (Charlesworth Charlesworth, 2010). Both conceptualise modelling stochastic distribution produced parental integrate Mendelian rules heredity character transmission. rely binomial numbers parent assumption variance. marine (fish, crustaceans), humans crops, so-called sweepstakes production number (fecundity phase) only fraction may survive next (viability phase). contribution, al. (2023) generalising conceptualising different phases life-cycle reproducing Note distinction unimportant production, fecundity viability yields similar results model. Using simulations, efficiency unlinked locus (with coefficient), thus, since have distinguishable 2018). mean is, expected, function size, increases stronger when parents. From biological point view, means do produce same possibly reproductive variance, rare multiple mutant show excess mutations. Second, magnifies drift increasing neutral decreasing alleles. (as neutral) shortened reproduction. An interesting result, contrast classic mentioned above, probabilities times intermediate weak display synergistic selection, namely types reinforce another disproportionally decrease fixation, increase strengths selection. Eldon Stephan recent based model, before they impact random highly fecund haploid diploid populations coefficient. For influence dominance studied. authors assume experience recurrent (random) bottlenecks. As (2023), sweepstakes, individual recruitment success skewed, huge contributed individuals any generation. computer dissect single joint bottlenecks (selective sweeps). Population enhance fixation. modulated Sweepstakes facilitate adaptation, defined (conditioned fixation), while general decreased events Measuring accurately unusual life-cycles crucial predict potential, considering humans, wild plants, livestock, economically (fishes, molluscs crustaceans). implications highlighted above differ genetics models, relevant management domesticated/cultivated additional threat climate change. extensive discussion model system, Atlantic cod, genome-wide polymorphism data available, assessed. addition issue. Liu indeed tenuifilis), ecologically pelagic fish spans broad latitudinal gradient along marginal seas Northwest Pacific. They generate reference S. tenuifilis PacBio reads high-resolution chromosome conformation capture (Hi-C) technology assembly 798.38 Mb anchored onto 24 pseudo-chromosomes. annotate 22,019 genes, accounting 95.27% predicted protein-coding When comparing Clupeiformes related species, fusion fission found chromosomal collinearity analysis. Based data, used restriction site-associated DNA sequencing (RADseq) sample 173 study structuring groups were Chinese coast, albeit differentiation appears rather weak. redundancy analysis, identify candidate functional putatively exhibiting footprints suggesting bioclimatic variables, sea surface temperature, spatially varying tenuifilis. general, however, still preliminary disentangling forces testing adaptation. Another deals FWW, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), native North-America mainland China (Dai introduction event 40 ago involved severe bottleneck subsequent divergence into groups. there footprint following invasion. ddRADseq 265 (covering approximately 4% yielding 59,261 SNPs), genetically separated western eastern event. Further, correlate spatial SNPs geographical five climatic variables. together, proportion explained factors, explain (than ones) separately. SNP outliers group relatively precipitation temperature-related total 64, 117 71 might desiccation temperature annotated responsive Further annotation associated lipase biosynthesis found, potentially relate group. hints invertebrate retain adapt heterogeneous despite bottleneck) strengthen, directional promoting local 2018, future precise estimates would need perform depth search severely impede ability detect (Korfmann 2016). Kusch long- short-term powdery fungi (Erysiphaceae) plants. globally distributed plant 10,000 hosts. highlight overcome immunity, evolve fungicide broaden host range. mutations, hybridisation (between strains species). It noticeable TEs, 50% 85% genome, plays key acquisition traits. closely diversified patterns ongoing transposon activity. uniformly genomes, variable lacking obvious regions conserved space. variability (and/or functions), picked neofunctionalisation virulence factors. Such be, secreted effector proteins, undermine immune system infection. cereals like barley wheat, some effectors recognised receptors encoded copy part TEs. providing (Sánchez-Vallet 2018; Tellier 2014). underpin arms race (Bergelson 2001; Woolhouse 2002) (Brown Tellier, 2011; Möller Stukenbrock, 2017; continuum ranging above) each size (Barghi 2020; depends coefficients (Jain 2017a; John 2020). presence become shift optimum. Moreover, scheme, combinations environments, introducing notion habitats. Trade-offs traits, coded sets arise constraints imposed physicochemical laws sessile cannot choose growth, limitation resource allocation metabolism, responses (Hörger 2013). Hashemi metabolic levels. systematic approaches various exist kinetic properties enzymes, reactions, pathways networks. Extending notions objectives organism, communities. describe mathematical conceptual framework constraint-based modelling. black box Y-model classically describing allocation. conclude directions knowledge manipulate level organisms microbial accompanying Nikoloski measure basis. With progress omics datasets, interest molecular basis trade-offs. what are, measured architecture. classification definitions quantification, dependence experimental designs used. Typically, compare quantify correlations. yet not generalised overlap pathways. highlighting trade-offs, been discover nucleotide variability. Understanding importance biologists understand applications breeding. perspective, Li contribution way recombining populations. Their work step forward beyond usual free Vladar Barton, 2014; Jain 2017b). prediction requires defining quantifying additive among simultaneously segregating variants, difficult experimentally theoretically. use simulations landscapes tuneable ruggedness. mostly slows landscapes. Interestingly, had greater chance reach epistasis if landscape ruggedness high. words, broken apart frequency. tracked path direct pairwise weaker expected. Therefore, (rapid) rugged lead spurious signals generated epistasis. Bock provides slow introduced south-eastern United States, region much colder Caribbean thermal physiology 30 find cline tolerance. cold spots (more half genome) maintain long-range disequilibrium tolerance previously identified. suggest constraining parts anoles, Sabolić founding siculus), 35 island Adriatic Sea, exhibits already diet morphological, behavioural, physiological Combining experimental, approaches, several trait preponderant plasticity shifts. third Raas Dutheil investigates Saccharomyces cerevisiae domesticated coalescent analyses, compared infer distributions (ωa) non-adaptive (ωna) non-synonymous substitutions Overall, though higher There predominance background Hill–Robertson interference, indicated being negatively correlated ωna positively ωa. ωa artefact size. residue solvent exposure, supporting sites. Taken comparison demonstrates protein evolution. ever pressures. direction fluctuations, parasites (Bell, 2010; 2002). Depending strength balancing long-term maintenance (Devi Jain, MacPherson 2021; years, insect melanogaster, undergoes generations year, fluctuations thought (Bergland Wittmann 2017) often driven form temporally sexually Fluctuation observed linked loci, demonstrated Glaser-Schmitt example regulatory D. fezzik gene. Polymorphism maintained extended period. observations regular intervals period 7 demonstrating significant differences derived collections sexes. discuss allelic alone Instead, demonstrate repeated span temporal needed our understanding magnitude deciphering occur, assess fluctuates aforementioned drive sizes. demography referred feedback. dependency particularly where vary greatly interaction epidemiological (Frickel Gokhale 2013; Živković 2019). studying viruses (bacteriophages phages) bacterial study, virus (infectivity/virulence) genotypes phenotypes lytic phages. phages have, treatments, coevolved phytopathogen Pseudomonas syringae, treatments repeatedly passaged unchanging (ancestral) strain P. syringae. those constant host, encoding phage tail-associated proteins. All evolved share outcomes expansion replicate Nevertheless, virulence, translates reduced correlation genotypic composition infectivity profile. coevolving ancestral does tail proteins patterns, faster infectivity/virulence. systems, co-demography (Märkle Retel 2019; turn, inference Saubin develop Approximate Bayesian Computation (ABC) couples individual-based disentangle overcomes cultivars introduction. method tuned rust pathogen, Melansporina larici-populina, poplar landscape. accuracy statistical framework, incomplete series samples. apply ABC set microsatellite markers fungus samples overcoming able estimate deployed occurred. inferred values fit estimates. shows improved trajectories subject Eco-evo cause accompanied frequent (during expected reduce amount co-evolution Le contrasting affect levels grow 12 unicellular, asexually algae (Chlorella variabilis) regimes: (1) growth (2) external (3) exposure (4) virus–algae interaction. Whole algal performed 50 Higher (nucleotide) jointly experienced separated. exceeds that, contrary expectations, co-adapting another. co-adaptation, considered environment. outcome GxG pathogens, examined cells infected filamentous, non-lethal fitness: phage-encoded accessory fitness, viral particles energetically costly bacteria. If costs outweigh benefits resistance, return shorten epidemics. depending conditions, fitness. bacterium Vibrio alginolyticus filamentous salinity levels: ambient, reduction ambient. acquire super infection exclusion (SIE) cost. Over SIE taken fitter mutants (surface receptor mutants). replacement Goehlich suboptimal slower, evolution, longer frequently exposed conditions regimes, seen prevalence experiments exemplify depend pervasiveness epidemics resistance/infectivity/virulence, (co-evolutionary dynamics) host–pathogen unique blend widespread links scales set-up shape defines possibility addition, hastened slowed Effective epigenetic) novelty themselves co-evolutionary events. finally note covered specific epigenetic features Future efforts AT wrote manuscript support KH, WS ES. reviewed approved final manuscript. declare no conflicts interest. Data sharing applicable article created analyzed study.
Language: Английский
Citations
3
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(3)
Published: Jan. 21, 2024
Abstract Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high‐level model complexity recently been developed, the advancement tree sequence recording now allows simulations to merge efficiency genealogical insight coalescent with flexibility forward simulations. However, frameworks utilizing these features have not yet compared benchmarked. Here, we evaluate various workflows using simulator msprime SLiM , assess resource determine an optimal framework. Three aspects were evaluated: (1) burn‐in, establish equilibrium level neutral diversity in population; (2) simulation, which temporally fluctuating selection is acting; (3) final computation summary statistics. We provide typical memory time requirements each step. find that fastest framework, combination recording, increases speed by over twenty times classical without although it does require six more memory. Overall, efficient can lead substantial improvement when modelling scenarios—although framework ultimately depends on available computational resources.
Language: Английский
Citations
2
Biosystems, Journal Year: 2024, Volume and Issue: 237, P. 105154 - 105154
Published: Feb. 10, 2024
Language: Английский
Citations
1