There is no fitness but fitness,and the lineage is its bearer

Inclusive fitness has been the cornerstone of social evolution theory for more than a half-century and has matured as a mathematical theory in the past 20 years. Yet surprisingly for a theory so central to an entire field, some of its connections to evolutionary theory more broadly remain contentious or underappreciated. In this paper, we aim to emphasize the connection between inclusive fitness and modern evolutionary theory through the following fact: inclusive fitness is simply classical Darwinian fitness, averaged over social, environmental and demographic states that members of a gene lineage experience. Therefore, inclusive fitness is neither a generalization of classical fitness, nor does it belong exclusively to the individual. Rather, the lineage perspective emphasizes that evolutionary success is determined by the effect of selection on all biological and environmental contexts that a lineage may experience. We argue that this understanding of inclusive fitness based on gene lineages provides the most illuminating and accurate picture and avoids pitfalls in interpretation and empirical applications of inclusive fitness theory.     

Quasi-independence, fitness, and advantageousness

I argue that the idea of ‘quasi-independence’ [Lewontin, R. C. (1978). Adaptation. Scientific American, 239(3), 212–230] cannot be understood without attending to the distinction between fitness and advantageousness [Sober, E. (1993). Philosophy of biology. Boulder: Westview Press]. Natural selection increases the frequency of fitter traits, not necessarily of advantageous ones. A positive correlation between an advantageous trait and a disadvantageous one may prevent the advantageous trait from evolving. The quasi-independence criterion is aimed at specifying the conditions under which advantageous traits will evolve by natural selection in this type of situation. Contrary to what others have argued [Sterelny, K. (1992). Evolutionary explanations of human behavior. Australian Journal of Philosophy, 70(2), 156–172, and Sterelny, K., &; Griffiths, P. (1999). Sex and death. Chicago: University of Chicago Press], these conditions must involve a precise quantitative measure of (a) the extent to which advantageous traits are beneficial, and (b) the degree to which they are correlated with other traits. Driscoll (2004) [Driscoll, C. (2004). Can behaviors be adaptations? Philosophy of Science, 71, 16–35] recognizes the need for such a measure, but I argue that she does not provide the correct formulation. The account of quasi-independence that I offer clarifies this point.     

A further note on the estimation of a fitness function from two samples taken from a popolation

A modification is proposed for the moments method for estimating a fitness function that was discussed in an earlier paper (Manly , 1976b). This modification ensures that fitness estimates are always positive. The theory has been worked out for a fitness function of any number of variables and a computer program has been written to carry out the iterative calculations needed for estimation.     

Beneficial fitness effects are not exponential for two viruses

The distribution of fitness effects for beneficial mutations is of paramount importance in determining the outcome of adaptation. It is generally assumed that fitness effects of beneficial mutations follow an exponential distribution, for example, in theoretical treatments of quantitative genetics, clonal interference, experimental evolution, and the adaptation of DNA sequences. This assumption has been justified by the statistical theory of extreme values, because the fitnesses conferred by beneficial mutations should represent samples from the extreme right tail of the fitness distribution. Yet in extreme value theory, there are three different limiting forms for right tails of distributions, and the exponential describes only those of distributions in the Gumbel domain of attraction. Using beneficial mutations from two viruses, we show for the first time that the Gumbel domain can be rejected in favor of a distribution with a right-truncated tail, thus providing evidence for an upper bound on fitness effects. Our data also violate the common assumption that small-effect beneficial mutations greatly outnumber those of large effect, as they are consistent with a uniform distribution of beneficial effects.     

Fame is a bubble,but not for some

Brilliant, acerbic, not given to suffer much of anybody gladly, let alone fools, Francis Crick had enormous influence that was due to his style and high scientific standards.     

Environmental variation is directly responsible for short- but not long-term variation in forest-atmosphere carbon exchange

Tower‐based eddy covariance measurements of forest‐atmosphere carbon dioxide (CO₂) exchange from many sites around the world indicate that there is considerable year‐to‐year variation in net ecosystem exchange (NEE). Here, we use a statistical modeling approach to partition the interannual variability in NEE (and its component fluxes, ecosystem respiration, R_eco, and gross photosynthesis, P_gross) into two main effects: variation in environmental drivers (air and soil temperature, solar radiation, vapor pressure deficit, and soil water content) and variation in the biotic response to this environmental forcing (as characterized by the model parameters). The model is applied to a 9‐year data set from the Howland AmeriFlux site, a spruce‐dominated forest in Maine, USA. Gap‐filled flux measurements at this site indicate that the forest has been sequestering, on average, 190 g C m⁻² yr⁻¹, with a range from 130 to 270 g C m⁻² yr⁻¹. Our fitted model predicts somewhat more uptake (mean 270 g C m⁻² yr⁻¹), but interannual variation is similar, and wavelet variance analyses indicate good agreement between tower measurements and model predictions across a wide range of timescales (hours to years). Associated with the interannual variation in NEE are clear differences among years in model parameters for both R_eco and P_gross. Analysis of model predictions suggests that, at the annual time step, about 40% of the variance in modeled NEE can be attributed to variation in environmental drivers, and 55% to variation in the biotic response to this forcing. As model predictions are aggregated at longer timescales (from individual days to months to calendar year), variation in environmental drivers becomes progressively less important, and variation in the biotic response becomes progressively more important, in determining the modeled flux. There is a strong negative correlation between modeled annual P_gross and R_eco (r=−0.93, P≤0.001); two possible explanations for this correlation are discussed. The correlation promotes homeostasis of NEE: the interannual variation in modeled NEE is substantially less than that for either P_gross or R_eco     

Fame,fortune, and fitness at the Academy Awards

People across many societies routinely participate in physical or intellectual competitions in the absence of immediate substantial monetary or other apparent material rewards. But increased fame and social status associated with awards, such as the “Oscars”, need not be necessarily and solely a cultural construct unrelated to natural selection. Rather, prizes might be badges of honor if they are also honest indicators of evolutionary fitness. Analyses of reported reproductive success data, from a survey of well-known female and male actors, followed previously reported patterns of biological fitness in this sample of a human population. In addition, the numbers of Academy Awards received for acting were positively associated with reported numbers of biological children for both genders. The association of increased fitness with more awards received was statistically consistent even when considering that this subset of the population conformed to the Bateman effect in human reproduction: male actors had a more positive correlation than females between cumulative numbers of married partners and overall numbers of children. Honest signals of reproductive quality that are displayed by both sexes are expected to occur in humans and other species with costly biparental care and mutual mate choice.     

Hyaloraphidium curvatum is not a green alga, but a lower fungus; Amoebidium parasiticum is not a fungus, but a member of the DRIPs

The unicellular heterotrophic protist Hyaloraphidium is classified with a family of green algae, the Ankistrodesmaceae. The only species that exists in pure culture and that is available for taxonomic studies is H. curvatum. Comparative 18S ribosomal RNA sequence analyses showed that H. curvatum belongs to the fungi rather than to the algae. Within the fungi, H. curvatum preferentially clustered with Chytridiomycetes. Unlike Chytridiomycetes, H. curvatum propagates by autosporulation, and the presence of flagella has never been reported. Transmission electron microscopy indicated that H. curvatum in some respects resembles Chytridiomycetes, but no elements of a flagellar apparatus were detected. The habitus of H. curvatum is unlike that of other fungi except the trichomycete Amoebidium parasiticum. The cell wall sugar composition of H. curvatum was unique, but to some extent resembled that of A. parasiticum. However, H. curvatum and A. parasiticum are not closely related to each other according to 18S rRNA sequence data. Moreover, A. parasiticum clustered with protistan animals, the Mesomycetozoa (DRIPs). Combined molecular, ultrastructural and chemical data do not allow assignment of H. curvatum to any recognized clade of fungi. This suggests that H. curvatum may represent an independent evolutionary lineage within the fungi.     

Physiological,but not fitness,effects of two interacting haemoparasitic infections in a wild rodent

In contrast to the conditions in most laboratory studies, wild animals are routinely challenged by multiple infections simultaneously, and these infections can interact in complex ways. This means that the impact of a parasite on its host’s physiology and fitness cannot be fully assessed in isolation, and requires consideration of the interactions with other co-infections. Here we examine the impact of two common blood parasites in the field vole (Microtus agrestis): Babesia microti and Bartonella spp., both of which have zoonotic potential. We collected longitudinal and cross-sectional data from four populations of individually tagged wild field voles. This included data on biometrics, life history, ectoparasite counts, presence/absence of microparasites, immune markers and, for a subset of voles, more detailed physiological and immunological measurements. This allowed us to monitor infections over time and to estimate components of survival and fecundity. We confirm, as reported previously, that B. microti has a preventative effect on infection with Bartonella spp., but that the reverse is not true. We observed gross splenomegaly following B. microti infection, and an increase in IL-10 production together with some weight loss following Bartonella spp. infection. However, these animals appeared otherwise healthy and we detected no impact of infection on survival or fecundity due to the two haemoparasite taxa. This is particularly remarkable in the case of B. microti which induces apparently drastic long-term changes to spleen sizes, but without major adverse effects. Our work sheds light on the ecologies of these important zoonotic agents, and more generally on the influence that interactions among multiple parasites have on their hosts in the wild.     

The SOS response increases bacterial fitness,but not evolvability,under a sublethal dose of antibiotic

Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.     

Cathepsin L, but not cathepsin B, is a potential kininogenase

Although papain-like enzymes are strongly inhibited by their natural tight-binding inhibitors of the cystatin superfamily, cathepsins B and L may still retain some residual proteolytic activity toward Z-Phe-Arg-AMC in the presence of an excess of kininogen. This activity is abolished by adding E-64 or chicken cystatin. Cathepsins B and L show a single band of gelatinolytic activity when subjected to gelatin-SDS-PAGE. Adding high Mr kininogen, low Mr kininogen, T-kininogen, or chicken cystatin to cathepsin L results in additional intense bands of enzyme activity corresponding to the protease-inhibitor complexes. Cathepsin B does not produce these additional bands. This gelatinolytic activity was inhibited by E-64, but not by EDTA, PMSF or Pefabloc. Cathepsin L also specifically generated kinins from high and low molecular weight kininogens in vitro, but cathepsin B did not. T-kininogen did not release any immunoreactive kinins when complexed with cathepsin L, as previously observed using tissue kallikreins. The ability of cathepsin L to generate vasoactive peptides raises the question of the physiological significance of this mechanism during inflammation.     

Immune activation is inversely related to, but does not cause variation in androgen levels in a cichlid fish species

Studies on birds and mammals indicate that sexual traits may signal superior health because active immunity, like inflammatory responses to infections, is suppressive to the production of androgens that facilitate the expression of these traits. Here we test this possible pathway for honest signaling in a teleost species, Sarotherodon galilaeus, by activating the immune system with sheep red blood cells (SRBC), which is a non-pathogenic T- and B-cell stimulating antigen. Two weeks after the start of treatment adult males injected with SRBC showed a significant increase in antibody production in comparison with control males. The variation in specific antibody production was negatively related with variation in both testosterone and 11-ketotestosterone levels. This suggests that investment in immune protection is incompatible with increased activity of the hypothalamic-pituitary-gonadal axis. However, opposite to our expectation no difference in androgen levels was found between placebo and SRBC treatment suggesting that immune activation did not cause androgen suppression in our studied species.     

Surface carbohydrate composition of a tapeworm in its consecutive intermediate hosts: individual variation and fitness consequences

Carbohydrates on parasite surfaces have been shown to play an important role in host–parasite coevolution, mediating host non-self recognition and parasite camouflage. Parasites that switch hosts can change their surface molecules to remain undetected by the diverse immune systems of their different hosts. However, the question of individual variation in surface sugar composition and its relation to infectivity, virulence, immune evasion and growth of a parasite in its different hosts is as yet largely unexplored. We studied such fitness consequences of variation in surface sugars in a sympatric host–parasite system consisting of the cestode Schistocephalus solidus and its intermediate hosts, a copepod and the three-spined stickleback. Using lectins to analyse the sugar composition, we show that the tapeworm changes its surface according to the invertebrate or vertebrate host. Importantly, sugar composition seems to be genetically variable, as shown by differences among tapeworm sibships. These differences are related to variation in parasite fitness in its second intermediate host, i.e. infectivity and growth. Surface sugar composition may thus be a proximate correlate of the evolutionarily relevant variability in infectivity and virulence of parasites in different hosts.     

The X chromosome is a hot spot for sexually antagonistic fitness variation

Sexually antagonistic alleles are selected discordantly between the sexes. Experimental evidence indicates that sexually antagonistic fitness variation is abundant in the genome of Drosophila melanogaster. Theory predicts that the X chromosome will be enriched with this type of variation. To test this prediction in D. melanogaster, we sampled, and cytogenetically cloned, 20 X chromosomes and compared their fitness variation to genome-wide levels. At the juvenile stage, in which gender roles are most similar, the X chromosome made no detectable contribution to genome-wide fitness variation. At the adult stage, in which gender roles diverge, the X chromosome was estimated to harbour 45% of the genome-wide fitness variation and 97% of the genome-wide sexually antagonistic variation. This genomic structure has important implications for the process of sexual selection because X-linked sexually antagonistic variation contributes to negative intersexual heritability for fitness, i.e. high-fitness males (females) produce, on average, low-fitness daughters (sons).     

On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices

Statistical and biochemical studies have revealed non-random patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslation errors and point mutations, since it is known that when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, using altered forms of the fitness functions used in the prior studies, we have optimized the parameters involved in the calculation of the error minimizing property of the genetic code so that the genetic code outscores the random codes as much as possible. This work also compares two prominent matrices, the Mutation Matrix and Point Accepted Mutations 74-100 (PAM(74-100)). It has been resulted that the hypothetical properties of the coevolution theory of the genetic code are already considered in PAM(74-100), giving more evidence on the existence of bias towards the genetic code in this matrix. Furthermore, our results indicate that PAM(74-100) is biased towards the single base mistranslation occurrences in second codon position as well as the frequency of amino acids. Thus PAM(74-100) is not a suitable substitution matrix for the studies conducted on the evolution of the genetic code.     

Matricaria chamomilla is not a hyperaccumulator, but tolerant to cadmium stress

The influence of low (3 μM) and high (60 and 120 μM) cadmium (Cd) concentrations were studied on selected aspects of metabolism in 4-week-old chamomile (Matricaria chamomilla L.) plants. After 10 days’ exposure, dry mass accumulation and nitrogen content were not significantly altered under any of the levels of Cd. However, there was a significant decline in chlorophyll and water content in the leaves. Among coumarin-related compounds, herniarin was not affected by Cd, while its precursors (Z)- and (E)-2-β-d-glucopyranosyloxy-4-methoxycinnamic acids (GMCAs) increased significantly at all the levels of Cd tested. Cd did not have any effect on umbelliferone, a stress metabolite of chamomile. Lipid peroxidation was also not affected by even 120 μM Cd. Cd accumulation was approximately seven- (60 μM Cd treatment) to eleven- (120 μM Cd treatment) fold higher in the roots than that in the leaves. At high concentrations, it stimulated potassium leakage from the roots, while at the lowest concentration it could stimulate potassium uptake. The results supported the hypothesis that metabolism was altered only slightly under high Cd stress, indicating that chamomile is tolerant to this metal. Preferential Cd accumulation in the roots indicated that chamomile could not be classified as a hyperaccumulator and, therefore, it is unsuitable for phytoremediation.     

ATP-NGF-complex, but not NGF, is the neuroprotective ligand

We have shown previously that nerve growth factor (NGF) requires only low nanomolar ATP concentrations in the cell culture medium to protect cortical rat neurons (CRN) from cellular damage induced by staurosporine (STS). We have also demonstrated before that NGF and other growth factors form stable non-covalent complexes with ATP. Here we demonstrated that 8N₁ATP–NGF, but not NGF, protected CRN against damage. The photo-reactive ATP derivative 8N₃ATP was incubated with NGF and was trapped in its position by UV irradiation forming a covalent bond. The cross-link with a molar ratio of 1:1 (8N₁ATP:NGF) was confirmed by mass spectrometry. Circular dichroism experiments revealed that 8N₁ATP altered the secondary structure of NGF in the same way as ATP did. Covalently bound 8N₁ATP–NGF was shown to be stable in the presence of the ATP-hydrolyzing enzyme alkaline phosphatase while the non-covalent ATP–NGF-complex dissociated with the removal of free ATP from the solution. 8N₁ATP–NGF protected CRN against damage by STS independently of free ATP in the culture medium. These results suggest that the ATP–NGF-complex, but not NGF, is the active ligand.     

Drinking,but not feeding,is opiate-sensitive in hamsters

The long-lasting opiate antagonist, naltrexone (NTX), was examined for its effects on various types of consummatory behavior in male golden hamsters and rats. Rat, but not hamster, 24 hr food and water intakes were significantly decreased by four daily NTX (10.0 mg/kg) injections. Hamsters displayed a minimal night to day feeding ratio compared to rats. hamsters increased food intake following insulin (50 U/kg) administration, but not after 24 hr food deprivation (FD) or 2-deoxy-D-glucose (2-DG; 800 mg/kg) injections. NTX (1.0 and 10 mg/kg) had no effect on feeding, but markedly attenuated hamster drinking induced by 48 hr water deprivation or hypertonic saline injection. Dexamethasone (DEX), a glucocorticoid which depletes pituitary β-endorphin and produces anorexia in rats, had no effect on daily hamster intake. Since the normal feeding profile of the hamster is similar to that of naloxone and DEX-treated rats, hamsters appear to lack an opiate-sensitive feeding system. In contrast, stimulated drinking behavior of hamsters operates through an opiate-sensitive mechanism. Thus, there are marked species differences concerning the involvement of endogenous opioids is consummatory behavior.     

Wealth, status, and fitness: a historical study of Norwegians in variable environments

Wealth and status covary with lifetime reproductive success in preindustrial human populations. Local ecology is likely to modify this association, but details of this presumed relationship are not yet known. We sought to determine whether local ecology modifies the relationship between status and fitness (number of grandchildren). Our approach to the problem was to measure variation in fitness relative to status (landless or with land) and to local ecology (inland versus coastal communities). We also analyzed life history traits that might explain observed variations in fitness. Our results confirm previous findings that both status (landless=9.9 vs. with land=16.5) and ecology (inland=12.3 vs. coast=14.1) affect the number of grandchildren produced by a female in pre-industrial society. We also found that the differences in number of children between the status groups were less pronounced on the coast (landless=12.0 vs. with land=16.1) than inland (landless=7.8 vs. with land=16.8). Our findings are novel because they suggest that the fitness consequences of human status may depend on details of local ecology. We discuss four different mechanisms that could account for these fitness differences: (1) differential reproductive rate of mothers, (2) differential marriage rate of children (3) differential survival rate of children, and (4) different social practices (breastfeeding, inheritance of property and diet).     

Sublancin is not a lantibiotic but an S-linked glycopeptide

Sublancin is shown to be an S-linked glycopeptide containing a glucose attached to a cysteine residue, establishing a new post-translational modification. The activity of the S-glycosyl transferase was reconstituted in vitro, and the enzyme is shown to have relaxed substrate specificity, allowing the preparation of analogs of sublancin. Glycosylation is essential for its antimicrobial activity.