DOI: 10.5061/dryad.k0p2ngff8
title: Population size shapes trade-off dilution and adaptation to a marginal niche unconstrained by sympatric habitual conditions

description: How does niche expansion occur when the habitual (high-productivity) and
 marginal (low-productivity) niches are simultaneously available? Without
 spatial structuring, such conditions should impose fitness maintenance in
 the former while adapting to the latter. Hence, adaptation to a given
 marginal niche should be influenced by the identity of the simultaneously
 available habitual niche. This hypothesis remains untested. Similarly, it
 is unknown if larger populations, which can access greater variation and
 undergo more efficient selection, are generally better at niche expansion.
 We tested these hypotheses using a large-scale evolution experiment with
 Escherichia coli. While we observed widespread niche expansion, larger
 populations consistently adapted to a greater extent to both marginal and
 habitual niches. Owing to diverse selection pressures in different
 habitual niches (constant versus fluctuating environments; environmental
 fluctuations varying in both predictability and speed), fitness in
 habitual niches was significantly shaped by their identities.
 Surprisingly, despite this diversity in habitual selection pressures,
 adaptation to the marginal niche was unconstrained by the habitual niche’s
 identity. We show that in terms of fitness, two negatively correlated
 habitual niches can still have positive correlations with the marginal
 niche. This allows the marginal niche to dilute fitness trade-offs across
 habitual niches, thereby allowing costless niche expansion. Our results
 provide fundamental insights into sympatric niche expansion.
description: This data was collected on laboratory populations of <em>E.
 coli</em> subjected to experimental evolution.
description: # Population size shapes trade-off dilution and adaptation to a marginal
 niche unconstrained by sympatric habitual conditions
 The dataset consists of an
 .xlsx file with six tabs, as described below. ## Description of the data
 and file structure We founded E. coli MG1655 populations from a single
 common ancestral clone and cultured them in eight different environmental
 conditions at two distinct population sizes, large (L) and small (S). All
 eight environments offered Acetate as the low productivity carbon source
 that constituted the marginal niche. Out of the eight environments, four
 offered a single distinct high productivity carbon source (constant
 habitual niche) for bacterial growth (one of thymidine (Thy), galactose
 (Gal), sorbitol (Sor) or arabinose (Ara)). In the other four environments,
 the habitual niche (high productivity carbon source) fluctuated over time
 in all combinations of predictable versus unpredictable and fast
 (switching every ~13.3 generations) versus slow (switching every ~40
 generations) fluctuations. We designated these fluctuations in the
 habitual niche as PF (predictable and fast), PS (predictable and slow), UF
 (unpredictable and fast) and US (unpredictable and slow). Taken together,
 a combination of two different population sizes and eight different
 environments gave rise to 16 separate evolutionary regimens (Thy-L, Thy-S,
 Gal-L, Gal-S, Sor-L, Sor-S, Ara-L, Ara-S, PFL, PFS, PSL, PSS, UFL, UFS,
 USL and USS; here L and S refer to large and small population sizes
 respectively). We propagated six independently evolving biological
 replicates of each regimen, making a total of 96 independently evolving
 experimental populations. Each of these 96 populations were assayed in
 five different environments: thymidine (Thy), galactose (Gal), sorbitol
 (Sor) or arabinose (Ara), acetate (Ace). We used the maximum slope of the
 growth curves, calculated over a moving window of ten readings, as the
 measure of fitness. These values were divided by the correspnding mean
 fitnesses of the ancestors in these five environments (data presented in
 the tab "Absolute ancestral growth rate") to obtain the relative
 fitness values. These relative fitness values are presented in the five
 tabs: \- Relative fitness in Ara \- Relative fitness in Gal \- Relative
 fitness in Sor \- Relative fitness in Thy \- Relative fitness in Acetate