Fitness of evolving bacterial populations is contingent on deep and shallow history but only shallow history creates predictable patterns.

Long-term evolution experiments have tested the importance of genetic and environmental factors in influencing evolutionary outcomes. Differences in phylogenetic history, recent adaptation to distinct environments and chance events, all influence the fitness of a population. However, the interplay of these factors on a population's evolutionary potential remains relatively unexplored. We tracked the outcome of 2000 generations of evolution of four natural isolates of Escherichia coli bacteria that were engineered to also create differences in shallow history by adding previously identified mutations selected in a separate long-term experiment. Replicate populations started from each progenitor evolved in four environments. We found that deep and shallow phylogenetic histories both contributed significantly to differences in evolved fitness, though by different amounts in different selection environments. With one exception, chance effects were not significant. Whereas the effect of deep history did not follow any detectable pattern, effects of shallow history followed a pattern of diminishing returns whereby fitter ancestors had smaller fitness increases. These results are consistent with adaptive evolution being contingent on the interaction of several evolutionary forces but demonstrate that the nature of these interactions is not fixed and may not be predictable even when the role of chance is small.

Environment changes epistasis to alter trade-offs along alternative evolutionary paths.

The fitness effect of a mutation can depend on both its genetic background, known as epistasis, and the prevailing external environment. Many examples of these dependencies are known, but few studies consider both aspects in combination, especially as they affect mutations that have been selected together. We examine interactions between five coevolved mutations in eight diverse environments. We find that mutations are, on average, beneficial across environments, but that there is high variation in their fitness effects, including many examples of mutations conferring a cost in some, but not other, genetic background-environment combinations. Indeed, even when global interaction trends are accounted for, specific local mutation interactions are common and differed across environments. One consequence of this dependence is that the range of trade-offs in genotype fitness across selected and alternative environments are contingent on the particular evolutionary path followed over the mutation landscape. Finally, although specific interactions were common, there was a consistent pattern of diminishing returns epistasis whereby mutation effects were less beneficial when added to genotypes of higher fitness. Our results underline that specific mutation effects are highly dependent on the combination of genetic and external environments, and support a general relationship between a genotype's current fitness and its potential to increase in fitness.

Effect of Substrate and Bacterial Zeta Potential on Adhesion of Mycobacterium smegmatis.

Bacterial adhesion is described as a multistep process of interactions between microbes and the substrate, beginning with reversible contact, followed by irreversible adhesion. We explore the influence of substrate zeta potential on adhesion of Mycobacterium smegmatis, a nonpathogenic bacterial model for tuberculosis-causing Mycobacterium tuberculosis and a common foulant of reverse osmosis filtration systems. Substrates having a range of zeta potentials were prepared by coating silica with the polycation, poly(diallyldimethyl ammonium chloride) (pDADMAC), by adjusting the pH of alumina, a pH-responsive material, and by coating silica with a hydrophobic self-assembled monolayer coating of octadecyltrichlorosilane. Our observations using these surfaces demonstrated that adhesion of M. smegmatis increased significantly by more than 200% on the silica-pDADMAC system and more than 300% on alumina substrates, as zeta potential became less negative, and that the variation of pH did not affect adhesion on alumina surfaces. Live and heat-killed bacteria were studied to investigate the contribution of biological response to adhesion with respect to zeta potential. While approximately 60% fewer heat-killed M. smegmatis adhered to pDADMAC-coated silica substrates, the trend of significantly increasing adhesion with less negative zeta potential was still observed. These results show the influence of zeta potential on adhesion of M. smegmatis, which is a separate process from that of the biological response. Across the range of substrate surface chemistries, hydrophobicities, and zeta potentials tested, adhesion of M. smegmatis can primarily be controlled by zeta potential. The bacterial zeta potential was not changed by the various experimental conditions and was -28.3 ± 2.4 mV.

Biological Response of and Blood Plasma Protein Adsorption on Silver-Doped Hydroxyapatite.

Hydroxyapatite (HAP) is an extensively used orthopedic biomaterial because of its high biocompatibility and osteoconductivity. Implant-related infection is a major cause of orthopedic device failure. Previous research showed that silver-doped hydroxyapatite nanoparticles (Ag-HAP NPs) have prominent antimicrobial activity, but their biocompatibility and plasma protein response remained unexplored. Here we investigated the effects of synthesis conditions on Ag-HAP NP antimicrobial (E. coli and S. epidermidis) activity, biocompatibility, and the adsorption of two blood plasma proteins, human serum albumin (HSA) and fibrinogen (Fib). It was found that synthesis pH affected the Ag content of Ag-HAP NPs and subsequent Ag+ release from the NPs in solution. This, in turn, affected antimicrobial efficiency and cytotoxicity to murine preosteoblast cells (MC3T3-E1). More HSA than Fib was adsorbed on a molar basis. The conformation of HSA changed drastically from predominantly α-helix and minor ß-sheet content in solution to greater ß-sheet than α-helix content when adsorbed. Correspondingly, the melting temperature Tm of HSA changed significantly from 76 °C in solution to ∼65-66 °C when adsorbed. Fib exhibited a modest decrease in α-helix content while the ß-sheet content increased modestly upon adsorption and its Tm remained unchanged at ∼60 °C. These differences in behavior of HSA and Fib are ascribed to the much smaller size of HSA, which allows a greater molecular packing density on the surface, which induces greater conformational changes. The protein adsorption behavior on Ag-HAP was similar to that on pure HAP. Thus, we show that Ag-HAP NPs have antimicrobial activity without deleterious effects on biocompatibility and blood plasma protein adsorption.

Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness.

The effect of a mutation depends on its interaction with the genetic background in which it is assessed. Studies in experimental systems have demonstrated that such interactions are common among beneficial mutations and often follow a pattern consistent with declining evolvability of more fit genotypes. However, these studies generally examine the consequences of interactions between a small number of focal mutations. It is not clear, therefore, that findings can be extrapolated to natural populations, where new mutations may be transferred between genetically divergent backgrounds. We build on work that examined interactions between four beneficial mutations selected in a laboratory-evolved population of Escherichia coli to test how they interact with the genomes of diverse natural isolates of the same species. We find that the fitness effect of transferred mutations depends weakly on the genetic and ecological similarity of recipient strains relative to the donor strain in which the mutations were selected. By contrast, mutation effects were strongly inversely correlated to the initial fitness of the recipient strain. That is, there was a pattern of diminishing returns whereby fit strains benefited proportionally less from an added mutation. Our results strengthen the view that the fitness of a strain can be a major determinant of its ability to adapt. They also support a role for barriers of transmission, rather than differential selection of transferred DNA, as an explanation of observed phylogenetically determined patterns of restricted recombination among E. coli strains.

The environment affects epistatic interactions to alter the topology of an empirical fitness landscape.

The fitness effect of mutations can be influenced by their interactions with the environment, other mutations, or both. Previously, we constructed 32 ( = 25) genotypes that comprise all possible combinations of the first five beneficial mutations to fix in a laboratory-evolved population of Escherichia coli. We found that (i) all five mutations were beneficial for the background on which they occurred; (ii) interactions between mutations drove a diminishing returns type epistasis, whereby epistasis became increasingly antagonistic as the expected fitness of a genotype increased; and (iii) the adaptive landscape revealed by the mutation combinations was smooth, having a single global fitness peak. Here we examine how the environment influences epistasis by determining the interactions between the same mutations in two alternative environments, selected from among 1,920 screened environments, that produced the largest increase or decrease in fitness of the most derived genotype. Some general features of the interactions were consistent: mutations tended to remain beneficial and the overall pattern of epistasis was of diminishing returns. Other features depended on the environment; in particular, several mutations were deleterious when added to specific genotypes, indicating the presence of antagonistic interactions that were absent in the original selection environment. Antagonism was not caused by consistent pleiotropic effects of individual mutations but rather by changing interactions between mutations. Our results demonstrate that understanding adaptation in changing environments will require consideration of the combined effect of epistasis and pleiotropy across environments.

The influence of ontogenetic dietary fluctuations on zebrafish size and swimming performance.

Phenotypic flexibility is critical in determining fitness. As conditions change during ontogeny, continued responsiveness is necessary to meet the demands of the environment. Studies have shown that subsequent ontogenetic periods of development can interact with one another and shape developmental outcomes. The role genetic variation within populations plays in shaping these outcomes remains unclear. Four full-sib families of zebrafish Danio rerio were raised under for dietary regimes: high food rations for 60 days (HH), low food rations for 60 days (LL), high food rations for 30 days followed by low food rations for 30 (HL), and low food rations for 30 days followed by high food rations for 30 (LH). While the low ration diet significantly reduced body length at 30 days, diet was no longer a significant factor at day 60. Only family level variation influenced body length. Furthermore, there was significant family level variation in the manner in which swimming performance responded to fluctuating dietary conditions. Some families increased swimming performance in response to dietary change, while others did not. These results suggest that plastic responsiveness to subsequent environmental changes can be trait specific and vary significantly within populations.

The role of thermal niche selection in maintenance of a colour polymorphism in redback salamanders (Plethodon cinereus).

BACKGROUND: In eastern North America two common colour morphs exist in most populations of redback salamanders (Plethodon cinereus). Previous studies have indicated that the different morphs may be adapted to different thermal niches and the morphological variation has been linked to standard metabolic rate at 15 degrees C in one population of P. cinereus. It has therefore been hypothesized that a correlated response to selection on metabolic rate across thermal niches maintains the colour polymorphism in P. cinereus. This study tests that hypothesis. RESULTS: We found that the two colour morphs do sometimes differ in their maintenance metabolic rate (MMR) profiles, but that the pattern is not consistent across populations or seasons. We also found that when MMR profiles differ between morphs those differences do not indicate that distinct niches exist. Field censuses showed that the two colour morphs are sometimes found at different substrate temperatures and that this difference is also dependent on census location and season. CONCLUSION: While these morphs sometimes differ in their maintenance energy expenditures, the differences in MMR profile in this study are not consistent with maintenance of the polymorphism via a simple correlated response to selection across multiple niches. When present, differences in MMR profile do not indicate the existence of multiple thermal niches that consistently mirror colour polymorphism. We suggest that while a relationship between colour morph and thermal niche selection appears to exist it is neither simple nor consistent.

Cardiovascular system in larval zebrafish responds to developmental hypoxia in a family specific manner.

BACKGROUND: Genetic and environmental variation are both known to influence development. Evolution of a developmental response that is optimized to the environment (adaptive plasticity) requires the existence of genetic variation for that developmental response. In complex traits composed of integrated sets of subsidiary traits, the adaptive process may be slowed by the existence of multiple possible integrated responses. This study tests for family (sibship) specific differences in plastic response to hypoxia in an integrated set of cardiovascular traits in zebrafish. RESULTS: Cardiac output, which is the integrated product of several subsidiary traits, varied highly significantly between families, and families differed significantly in the degree and direction of response to developmental oxygen level. The cardiac output response to oxygen environment was entirely family specific with no significant overall trend due to oxygen level. Constituent physiological variables that contribute to cardiac output all showed significant family specific response to hypoxia. Traits that were not directly related to cardiac output, such as arterial and venous diameter, and red blood cell velocities did not respond to hypoxia in a family specific manner. CONCLUSION: Zebrafish families vary in their plastic response to hypoxia. Genetic variation in plastic response to hypoxia may therefore provide the basic ingredient for adaptation to a variable environment. Considerable variation in the degree of familial response to hypoxia exists between different cardiovascular traits that may contribute to cardiac output. It is possible that the integration of several subsidiary traits into cardiac output allows the maintenance of genetic variance in cardiac response.

Pervasive RNA editing among hornwort rbcL transcripts except Leiosporoceros.

RNA editing affecting chloroplast and mitochondrial genomes has been identified in all major clades of land plants. The frequency of edited sites varies greatly between lineages but hornworts represent an extreme in propensity for editing in both their chloroplast and mitochondrial genomes. cDNA sequences from seven taxonomically diverse hornwort rbcL sequences combined with a survey of 13 additional DNA sequences for potential edited sites demonstrate the presence of 62 edited sites and predict a minimum of 10 additional sites. These 72 total edited sites represent 43 C-to-U and 28 U-to-C nucleotide conversions, with 1 site exhibiting editing in both directions. With one exception, all taxa are heavily edited, with each having from 20 to 34 edited sites. However, a single sample, Leiosporoceros, is shown to lack edited sites. Phylogenetic reconstruction of hornworts results in ambiguous resolution of Leiosporoceros depending on whether edited sites are maintained or eliminated from the analyses. Depending on the inferred relationship of Leiosporoceros to the hornworts, at least two explanations for the origin and maintenance of pervasive editing in hornworts are possible. The absence of edited sites in Leiosporoceros could represent either the absence or a low level of editing ability in the common ancestor of hornworts, as represented by Leiosporoceros, or the loss of editing sites in this lineage after the primary diversification events in the group.

A SIMULATION OF WRIGHT'S SHIFTING-BALANCE PROCESS: MIGRATION AND THE THREE PHASES.

Wright partitioned the shifting-balance process into three phases. Phase one is the shift of a deme within a population to the domain of a higher adaptive peak from that of the historical peak. Phase two is mass selection within a deme towards that higher peak. Phase three is the conversion of additional demes to the higher peak. The migration rate between demes is critical for the existence of phases one and three. Phase one requires small effective population sizes, hence low migration rates. Phase three is optimal under high migration rates that spread the most-fit genotype from deme to deme. Thus, a population-wide peak shift requires intermediate levels of migration. By altering the rates of phases one and three, migration affects the predominant direction of mass selection within a population. This study examines the degree to which migration, through its effects on phases one and three, determines the probability of a simulated population arriving at its genotypic optimum after 12,000 generations. These simulations reveal that there is a range of migration rates for which an entire population might be expected to shift to a higher peak. Below m = 0.001 peak shifts occur frequently (phases I and II) but are not successfully exported out of subpopulations (phase III), and above 0.01 peak shifts within demes (phase I and II), required to initiate phase III, become increasingly uncommon. Because it is unlikely that real populations will have uniform migration rates from generation to generation, the probable effects of varying migration rates on broadening the range of conditions producing peak shifts are discussed.