Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation

A free Plain Language Summary can be found within the Supporting Information of this article. Environmental fluctuations present a fundamental challenge to organisms as changing conditions may result in mismatch between environment and organismal phenotypes. One way which populations persist thrive is through their capacity adapt phenotypes on time frame relevant environmental variation. The ability has become acutely important during current period anthropogenic change climate events have more extreme frequent (Collins et al., 2013), habitats are increasingly disturbed (Fischer & Lindenmayer, 2007; Schweiger 2010; Smith 1999). Adaptive trait shifts typically considered occur two different ways. First, at individual level, phenotypic plasticity allows modify phenotype response an trigger (Bradshaw, 1965). Second, population selection act upon standing genetic (i.e. DNA sequence) variation shift mean values over several generations (Barrett Schluter, 2008). Recently, both environmentally induced modifications (Danchin, Pocheville, Rey, 2019; Rey 2016) non-genetic heritable (Bonduriansky Day, 2018; Jablonka 1995) been proposed additional pathways for rapid adaptation. However, experimental evidence currently lacking establish if, what extent, these sources produce adaptive (Hu Barrett, 2017; Marin 2020; Perez Lehner, 2019). In last 25 years, firmly established dominant process ecologically time-scales 2008; Bolnick 2011). This requires high diversity natural on. processes such range expansions (Eckert Excoffier 2009) colonization metapopulations (De Meester 2002) potential generate low-diversity (So 2015). Additionally, habitat deterioration (Lino Mather 2015; Schlaepfer 2018) introduction invasive species (Allendorf Lundquist, 2003) also small, isolated vulnerable drift erosion. Some with low levels variation, nevertheless, show remarkable maintain performance face (Rollins 2013). Loss especially pronounced clonal where single individuals able populations, yet shown remarkably successful. exemplified by genotype Daphnia pulex Lake Naivasha Kenya 1920s now water bodies along 5,500 km continental transect (Mergeay 2006). Similar successful invasion from small number genotypes observed mollusk (Gomes 2016), plant (Hollingsworth Bailey, 2000; Shi fish (Golani 2007). success sparked great interest possible mechanisms that genotype. While de novo mutations drive responses (e.g. Barrick Lenski, 2013; Chan Hartley 2006; Hoekstra 2006), they long far too infrequent ecological time-scales, when sizes (Hermisson Pennings, 2005). recent suggests novel stressful generation Point transposable element activity positively associated epigenetic features methylation specific genomic sites) often factors Makova Hardison, Miousse Yi Goodisman, 2021). As some variants beneficial, marks elements suggested adaptation Pimpinelli Piacentini, 2016; Stapley Heritable produced other than changes sequences. Non-genetic inheritance (NGI) passed via transmission nutrients, patterns, RNAs or microbiomes) but not sequences Macke 2017). Given NGI it play role Danchin 2011; Day Bonduriansky, 1995; Raz, 2009; O'Dea 2016). Sources NGI, expected action radius limited dispersal cannot move favourable environments chance being exposed similar parents (Beery Francis, Galloway Etterson, Mirouze Paszkowski, These would promote (Verhoeven Preite, 2014) (Rapp Wendel, 2005; Vogt, 2017) (Marin Pérez Prentis fluctuate temporal scale greater (O'Dea An question whether there its extent determine evolutionary respond frequency intensity fluctuation. Previous studies documented differ magnitude direction same stressor Asselman Gillis Walsh, Herman Sultan, although dedicated effort document intraspecific thus largely lacking. Currently, very few empirical examples animals generated despite mechanistic 2017, see Webster 2018). investigated monoclonal stressors pea aphids (Sentis green algae (Kronholm Together, without exhibit mechanisms, epimutations, goal study was experimentally test if absence initial recombination frame. To investigate question, we conducted two-part experiment using microzooplankton Brachionus calyciflorus. first part (further referred ‘exposure experiment’), replicate culturing regime selecting elevated growth rates least 20 either (HP) (LP) phosphorus food. LP food C:P content deviates strongly requirements B. calyciflorus, represents quality comparison HP (Sterner Hessen, 1994; Zhou Declerck, second experiment, performed full factorial common garden experiments successive points, exposure experiment. Using rate fitness measure aimed evaluate (i) occurred, (ii) clones strength (iii) increases duration divergent conditions. We hypotheses occurs consistent local sources; however, response. required elicit response, variant spread population, predict compared freshwater calyciflorus excellent metazoan system because cyclical parthenogenetic asexual offspring apomictic parthenogenesis. such, excluded mechanism responsible When monogonont rotifers reproduce asexually, oocytes undergo maturation production one polar body, no indication synapsis homologous chromosomes (Birky Gilbert, 1971). Thus, under apomixis, prevents inhibiting meiosis I asexually genetically identical itself. ameiotic crossovers (Omilian rarely frames work apomictically reproducing zooplankton (Dukić sexually, avoided maintaining densities (Stelzer Snell, 2003). sexual reproduction does occur, results diapausing embryos easily distinguished eggs (Figure S1). aspect life history offers benefit distinct lines compared. Although previous investigations taken advantage Kielland Walsh 2015), short (Declerck Papakostas, Stelzer, provides added many studied relatively period. maintained cultures Chlamydomonas reinhardtii source rotifer 2L chemostats 23 ± 1℃ dilution 0.33 day−1 WC medium (Kilham 1998). By varying phosphate concentration light created stoichiometric treatments. High (HP, molar 102.3 1.4 SE) were cultured media 65 μmol/L P ≈40 μmol quanta m−2 s−1 continuous light, while (LP, 690 10.9 15 ≈120 µmol light. ensure available directly centrifuged collected re-suspended pellet nutrient-free desired concentration. Carbon suspension estimated converting biovolume (Multisizer 3 Coulter Counter, Beckman Coulter) carbon (Appendix After dilution, vitamin mixture 1998) 1 ml/L. For used clone lines, Clone-7 Clone-128, belonging s.s. complex (Michaloudi hatching had laboratory S2). During initiation stock cultures. density 10 individuals/ml ~1,000 C algal comprised nutrient replete C. room temperature 16:8 (light:dark) cycle. keep identity line intact daily inspections batch removed any sexually large (>100 µm) visible naked eye S3). initiated 8 weeks after founding each hatched. estimate correspond approximately 29–34 S4), less 50 individuals. genotype, five treatments (HP LP) haphazardly allocating wells tissue culture plates ml designated 1,000 entire design consisted 2 × qualities 5 replicates). allowed independent growth. achieve conditions, restarted every 24 hr transferring new vessel fresh satiating concentrations (1,000 C). Selection done haphazard fashion except females bearing embryos. If fewer available, transferred all subset daily, favoured reproductive output, abundant likely transferred. prevented entering require produced, followed 72 hatch (Stelzer, Following transfer, counted remaining calculate realized interval. lasted 55 days. egg resource (Zhou 2018), length 32 S4 details). Throughout incubated 1℃, constant darkness rotation rpm prevent settling. Plate position incubator randomized location effects. persistent signal quality, changed exposure. began day 15, 39, days respectively. suspensions measured performance. Each fully crossed histories = 40 units). unit chosen respective population. units darkness. end 24-hr interval, them suspensions. did select against true including demographic cost reproduction; Montero-Pau 2014). experiments, calculated basis (lnNt − lnN0)/t, N0 Nt represent size start period, t Population ln-transformed prior analysis reduce variance residuals groups. wanted occurred Furthermore, detect immediate increased/decreased saturation response) gradually throughout consist multiple individuals, suggest majority expressing phenotype. Such level indicate induction plastic Sentis Heard Martienssen, 2014; Richards, Wang 2017), possibly combination processes. Alternatively, due tendency accumulate across consecutive generations, progressive increase regulatory (Houri-Ze'evi gradual could reflect mutation epimutation state) distinguish scenarios, constructed piecewise (immediate stability) linear (gradual change) regression model identified best fit Akaike information criterion assumed ΔAIC > 2; (Burnham Anderson, 2004). model, Davies significant difference slopes before breakpoint. breakpoint models better (Table S1), explored trends mixed effects (LMMs) separately. four analyses, treated fixed effect ID random effect. LMM analysis, avoid influence LMM, tested (HP- vs. LP-exposed populations) points since (common two). ‘food history’, ‘common diet’, experiment’ ‘clone’ Individual units) specified longer standardize diet only data fourth sixth corresponding 6–11 9–17 excluding three eliminating maternal 2020) simultaneous 2019) interested patterns concordant adaptation, priori contrasts compare HP- LP-exposure treatment experiments. All statistical analyses selection, contrasts, post-hoc tests R software 4.0.2 (R Core Team, 2020). lme4 package (Bates 2015) segmented (Muggeo, obtained significances type III sums squares car (Fox Weisberg, Kenward–Roger degrees freedom LMM. emmeans (Lenth cases, differences slope increased significantly course 1; Table 1), factor 46% 34% contrast, Clone-128. three-way interactions. differed diets, interaction 2: Diet * EH CG). tended albeit marginally Clone). planned us detail treatment, higher (a LPexp HPexp LP: p 0.030). HP: 0.597). Clone-128 contrasting 1.0; 1.0). interactions seem driven history, well CG, always substantially treatment. 2). Overall, our demonstrate (six generations) limitation parthenogenetically populations. studied. Populations displayed outperformed stable Contrary provided strengthened findings contribute burgeoning set contributor time-scales. serves further understanding how successfully little diversity. Our challenging conventional perspective substantial necessary history. pattern partially ‘home versus away’ (Kawecki Ebert, 2004) difficult explain intra-generational anticipatory (Marshall Uller, 2007) transmitted mothers known research opposite striking adaption environments. hatched entirely discount possibility originated culturing. Under circumstances, accelerated emerged 71 days, therefore time-scale system. Direct multigenerational producing initially uniform limited. artificial disruptive differentiation among fleas (Daphnia) foundress (Andrade Roitberg, Bunting Van Emden, 1980; Gorokhova 2002; Wilhoit Mittler, 1991). So far, aphid Acyrthosiphon pisum, (2018) group report selection. support demonstrating non-arthropod wide organisms. half wide-ranging consequences eco-evolutionary dynamics underlying unknown. Advances molecular techniques recently point multicellular Flynn Ho (Flynn Omilian Xu 2011) previously assumed. Rates sequence altering 10–5 per site negative neutral, beneficial emerge go fixation still hundreds thousands given developed rapidly spontaneous candidate even removal inducing environment. Transgenerationally epimutations systems Danchin, Huneman, Rechavi Remy, generates stress exposure, proliferation, Rebollo Schrader Schmitz, speculative explanation accumulation RNA) Further elucidate Traits enable come costs (Levins, 1968). observe relative traits physiological costs. benign nature masked subtle trade-offs. Intriguingly, LP- HP-adapted Frisch Lemmen consistently parts variety organisms, (Ho Ness (Leung Menezes Seudre clones, larger anticipated. imply genome inclusively (Danchin Wagner, 2010) suggesting subject stability Within-generation within, between, adjacent (Botero intergenerational predicted remain periods, so parental predictive value regarding those will experienced Klironomos Lachmann Jablonka, 1996; Rando Verstrepen, prediction supported (2016) who predation cues lakes regimes varied growing seasons theoretically favour appear (Colicchio Herman, 2020), connecting study, potentially caused stressor. Differences decreased rather garden). contrary expectations, demonstrated positive relationship stress-induced only, instead series observations, power directional gardens differentiated brief anticipated HP-exposure histories. Instead, unable trend. Low frequently (Haileselasie Louette (Roman Darling, long-term understood, (Pérez observation rapid, provide expand variable example, allow tracking akin rescue particularly distance dispersal, encounter originate. novel, benefits empty patches priority 2002). establishment restricted speculated enhance Numerous field correlations divergence (Schrey 2012; Sheldon (Wogan It determined heritable, hint warrant investigation. unprecedented change, understand use adapt. believe underappreciated role, Predicting economic importance interconnected world (Kolar Lodge, 2001). Genetically depauperate resulted failed Hairston 1999) incredibly invasions Mergeay generally unknown why succeed others do (Zenni Nuñez, demonstrates accounting improve invasiveness native display classified ‘high risk’, stricter measures decontamination put place transport vectors originating (Fournier Despite speculation generating (Day responses, animal clear example based mechanism, impact think about seen (Menezes dependent, furthermore, needed insight into genotypic differences, relevance Thus microbes short-lived invertebrates D. pulex, A. pisum calyciflorus). pertinent taxa, wider essential find alternative aid persistence Division Earth Life Sciences (ALW) Netherlands Organization Scientific Research (NWO) NIOO-KNAW Strategic Fund. wish thank Laurens Verhage assistance Wei Zhang allowing make his banks extracted focal Libin supplementary assistance. Cam Hudson constructive comments manuscript. authors conflict declare. K.J.F.V. S.A.J.D. conceived experiment; K.D.L. analysed data; wrote draft contributed revisions. Data Dryad Digital Repository https://doi.org/10.5061/dryad.qrfj6q5h5 (Lemmen Please note: publisher functionality supporting supplied authors. Any queries (other missing content) should directed author