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Radical shifts in reproductive systems result in radical changes in selective pressures acting on reproductive traits. Nematode Caenorhabditis elegans constitutes one of rare model systems where such shifts can be experimentally induced, providing an opportunity for studying the evolution of reproductive phenotypes in real time. Evolutionary history of predominantly selfing reproduction in has led to degeneration of traits involved outcrossing, making it inefficient. Here, we introduced obligatory outcrossing into isogenic lines of C. elegans and allowed replicate populations to evolve under the new reproductive system. We predicted that they should evolve higher outcrossing efficiency, leading to increased fitness relative to unevolved ancestors. To test this prediction, we assayed fitness of both ancestral and evolved outcrossing populations. To control for the potentially confounding effect of adaptation to laboratory conditions, we also assayed populations with wild-type (selfing) reproductive system. In five experimental blocks, we measured competitive fitness of 12 evolved populations (6 outcrossing, 6 selfing) after ca. 95 generations of evolution, along with their respective ancestors. On average, we found that fitness increased by 0.72 SD (± 0.3 CI) in outcrossing and by 0.52 (± 0.35 CI) in selfing populations, suggesting further adaptation to laboratory conditions in both types. Contrary to predictions, fitness increase was not significantly higher in outcrossing populations, suggesting no detectable adaptation to the changed reproductive system. Importantly, the results for individual populations varied strongly between experimental blocks, in some cases even differing in effect direction. This emphasises the importance of experimental replication in avoiding reporting false findings.

Epistaza jest to zjawisko interakcji pomiędzy genami, w której fenotyp jednego genu jest zależny od obecności innego genu/genów. Epistaza powoduje, że określenie fenotypu na podstawie pojedynczych mutacji staje się niemożliwe, na skutek nieliniowego współdziałania genów. W poniższym artykule opisujemy rodzaje epistazy, metody jej badania oraz jej znaczenie dla procesów ewolucyjnych. Przybliżamy czytelnikom pojęcie epistazy wyższego rzędu (pomiędzy więcej niż dwoma genami) oraz pokrótce wprowadzamy zagadnienie praktycznego znaczenia epistazy dla człowieka.

Age-specific differences in individual performance are reported in a number of taxa and are particularly well documented in humans. However, such data are generally lacking for birds, the taxon showing exceptionally long life in relation to body size. Here, we studied differences in vertical flight performance among three distinctive age classes (0.5-, 2- and 4.5-year-old birds) in laboratory-kept zebra finches, Taeniopygia guttata . We found that take-off flight speed differed significantly between the age classes with the oldest birds being ca. 10% slower than the youngest birds. Age classes also differed significantly in flight motivation, with old birds tending to be less motivated to fly than young ones. Thus, the age-specific decline in flight performance is clearly visible in zebra finches. In a broader perspective, poorer flight performance may impair foraging efficiency, social interactions and, most importantly, take-off speed when escaping predators. This may help elucidate age-specific decline in reproductive and survival rates commonly observed in natural populations.

Body condition indices are widely used by ecologists, but many indices are used without empirical validation. To test the validity of a variety of indices, we compared how well a broad range of body condition indices predicted body fat mass, percent body fat and residual fat mass in mice Mus musculus. We also compared the performance of these condition indices with the multiple regression of several morphometric variables on body fat mass, percent body fat and residual fat mass. In our study population, two ratio based condition indices – body mass/body length and log body mass/log body length – predicted body fat mass as well as or better than other ratio and residual indices of condition in females. In males one ratio based condition index (log body mass/log body length) and one residual index (residuals from a regression of pelvic circumference on body length) were best at predicting body fat mass. All indices were better at estimating body fat mass, and residual fat mass than at estimating percent body fat. The predictions of body fat were much better for females than for males. Multiple regressions incorporating pelvic circumference (i.e. girth at the iliac crests) were the best predictors of body fat mass, residual fat mass, and percent body fat, and these multiple regressions were better than any of the condition indices. We recommend 1) that condition be precisely defined, 2) that predictors of condition be empirically validated, 3) that pelvic circumference be considered as a potential predictor of fat content, and 4) that, in general, multiple regression be considered as an alternative to condition indices.

Background Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. Methods In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Results Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. Conclusions We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0508-4) contains supplementary material, which is available to authorized users.

The maintenance of males and outcrossing is widespread, despite considerable costs of males. By enabling recombination between distinct genotypes, outcrossing may be advantageous during adaptation to a novel environments and if so, it should be selected for under environmental challenge. However, a given environmental change may influence fitness of male, female, and hermaphrodite or asexual individuals differently, and hence the relationship between reproductive system and dynamics of adaptation to novel conditions may not be driven solely by the level of outcrossing and recombination. This has important implications for studies investigating the evolution of reproductive modes in the context of environmental changes, and for the extent to which their findings can be generalized. Here, we useCaenorhabditis elegans– a free-living nematode species in which hermaphrodites (capable of selfing but not cross-fertilizing each other) coexist with males (capable of fertilizing hermaphrodites) – to investigate the response of wild type as well as obligatorily outcrossing and obligatorily selfing lines to stressfully increased ambient temperature. We found that thermal stress affects fitness of outcrossers much more drastically than that of selfers. This shows that apart from the potential for recombination, the selective pressures imposed by the same environmental change can differ between populations expressing different reproductive systems and affect their adaptive potential.

The maintenance of males and outcrossing is widespread, despite considerable costs of males. By enabling recombination between distinct genotypes, outcrossing may be advantageous during adaptation to novel environments and if so, it should be selected for under environmental challenge. However, a given environmental change may influence fitness of male, female, and hermaphrodite or asexual individuals differently, and hence the relationship between reproductive system and dynamics of adaptation to novel conditions may not be driven solely by the level of outcrossing and recombination. This has important implications for studies investigating the evolution of reproductive modes in the context of environmental changes, and for the extent to which their findings can be generalized. Here, we use Caenorhabditis elegans—a free-living nematode species in which hermaphrodites (capable of selfing but not cross-fertilizing each other) coexist with males (capable of fertilizing hermaphrodites)—to investigate the response of wild type as well as obligatorily outcrossing and obligatorily selfing lines to stressfully increased ambient temperature. We found that thermal stress affects fitness of outcrossers much more drastically than that of selfers. This shows that apart from the potential for recombination, the selective pressures imposed by the same environmental change can differ between populations expressing different reproductive systems and affect their adaptive potential.

Morphometric estimates of body condition are widely used by ornithologists, but which estimates work best is a matter of debate. We review morphometric approaches (body mass, ratio and residual condition indices, predictive regression models, fat scoring, and abdominal profiles) for estimating body condition (defined as fat mass) in birds. We describe the strengths and weaknesses of each approach. Across diverse indices and species (~200 estimates total), the mean r 2 relating condition indices to mass of body fat was 0.55, and 64% of the r 2 values were greater than 0.50. But despite their generally good performance, condition indices sometimes perform poorly (i.e., r 2 is low). The data indicate that: (1) no single index was clearly best, (2) on average body mass alone, fat scores, and predictive multiple regression equations explained slightly more than 50% of the variation in fat content, (3) on average, ratio and residual indices explained slightly less than 50% of the variation in fat content, and (4) body mass alone, a variable that can be easily and reliably measured, is as good or nearly as good an indicator of fat content as any other condition index. We recommend that: (1) morphometric indicators of condition be empirically validated, (2) researchers publish their body composition data in sufficient detail that they can be used in future analyses exploring the relative merits of different condition indices, and (3) multiple regression directly on measured traits be used instead of condition indices whenever the condition index is not empirically validated.

Basal metabolic rate (BMR) is a fundamental energetic trait and has been measured in hundreds of birds and mammals. Nevertheless, little is known about the consistency of the population-average BMR or its repeatability at the level of individual variation. Here, we report that average mass-independent BMR did not differ between two generations of bank voles or between two trials separated by one month. Individual differences in BMR were highly repeatable across the one month interval: the coefficient of intraclass correlation was 0.70 for absolute log-transformed values and 0.56 for mass-independent values. Thus, BMR can be a meaningful measure of an individual physiological characteristic and can be used to test hypotheses concerning relationships between BMR and other traits. On the other hand, mass-independent BMR did not differ significantly across families, and the coefficient of intraclass correlation for full sibs did not differ from zero, which suggests that heritability of BMR in voles is not high.

Metabolic rates are correlated with many aspects of ecology, but how selection on different aspects of metabolic rates affects their mutual evolution is poorly understood. Using laboratory mice, we artificially selected for high maximal mass-independent metabolic rate (MMR) without direct selection on mass-independent basal metabolic rate (BMR). Then we tested for responses to selection in MMR and correlated responses to selection in BMR. In other lines, we antagonistically selected for mice with a combination of high mass-independent MMR and low mass-independent BMR. All selection protocols and data analyses included body mass as a covariate, so effects of selection on the metabolic rates are mass adjusted (that is, independent of effects of body mass). The selection lasted eight generations. Compared with controls, MMR was significantly higher (11.2%) in lines selected for increased MMR, and BMR was slightly, but not significantly, higher (2.5%). Compared with controls, MMR was significantly higher (5.3%) in antagonistically selected lines, and BMR was slightly, but not significantly, lower (4.2%). Analysis of breeding values revealed no positive genetic trend for elevated BMR in high-MMR lines. A weak positive genetic correlation was detected between MMR and BMR. That weak positive genetic correlation supports the aerobic capacity model for the evolution of endothermy in the sense that it fails to falsify a key model assumption. Overall, the results suggest that at least in these mice there is significant capacity for independent evolution of metabolic traits. Whether that is true in the ancestral animals that evolved endothermy remains an important but unanswered question.

Fast and quantitative analysis of animal phenotypes is one of the major challenges of current biology. Here we report the WormGender open-source software, which is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements. We further demonstrated the usage of WormGender by quantifying the high incidence of male (him) phenotype in 27 mutant strains. Mutants of nine genes (brc-1, C30G12.6, cep-1, coh-3, him-3, him-5, him-8, skr-1, unc-86) showed significant him phenotype. The WormGender is written in Java and can be installed and run on both Windows and Mac platforms. The source code is freely available together with a user manual and sample data at http://www.QuantWorm.org/. The source code and sample data are also available at http://dx.doi.org/10.6084/m9.figshare.1541248.

Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans . Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein Gαq, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the γ isoform of phospholipase C as a component in the Gαq pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.

The genetic variances and covariances of traits must be known to predict how they may respond to selection and how covariances among them might affect their evolutionary trajectories. We used the animal model to estimate the genetic variances and covariances of basal metabolic rate (BMR) and maximal metabolic rate (MMR) in a genetically heterogeneous stock of laboratory mice. Narrow-sense heritability (h2) was approximately 0.38 ± 0.08 for body mass, 0.26 ± 0.08 for whole-animal BMR, 0.24 ± 0.07 for whole-animal MMR, 0.19 ± 0.07 for mass-independent BMR, and 0.16 ± 0.06 for mass-independent MMR. Allh2estimates were significantly different from zero. The phenotypic correlation of whole animal BMR and MMR was 0.56 ± 0.02, and the corresponding genetic correlation was 0.79 ± 0.12. The phenotypic correlation of mass-independent BMR and MMR was 0.13 ± 0.03, and the corresponding genetic correlation was 0.72 ± 0.03. The genetic correlations of metabolic rates were significantly different from zero, but not significantly different from one. A key assumption of the aerobic capacity model for the evolution of endothermy is that BMR and MMR are linked. The estimated genetic correlation between BMR and MMR is consistent with that assumption, but the genetic correlation is not so high as to preclude independent evolution of BMR and MMR.

Basal metabolic rate (BMR), commonly used as a measure of the cost of living, is highly variable among species, and sources of the variation are subject to an enduring debate among comparative biologists. One of the hypotheses links the variation in BMR with diversity of food habits and life-history traits. We test this hypothesis by asking how BMR of a particular species, the bank vole Myodes (=Clethrionomys) glareolus, would change under selection for high growth rate (measured as a postweaning body mass change; MD(PW)) and the ability to cope with a low-quality herbivorous diet (measured as body mass change during a four-day test; MD(LQD)). We show that both of the traits are heritable in the narrow sense (MD(PW): h(2)= 0.30; MD(LQD): h(2)= 0.19), and are genetically correlated with mass-independent BMR (additive genetic correlation, r(A)= 0.28 for MD(PW) and 0.37 for MD(LQD)). Thus, both of the traits could change in response to a selection, and the selection would also result in a correlated evolution of the level of metabolism. The results are consistent with the hypothesis that a part of the interspecific variation in BMR evolved in response to selection for life-history and ecological traits such as food habits.

According to the aerobic capacity model, endothermy in birds and mammals evolved as a correlated response to selection for an ability of sustained locomotor activity, rather than in a response to direct selection for thermoregulatory capabilities. A key assumption of the model is that aerobic capacity is functionally linked to basal metabolic rate (BMR). The assumption has been tested in several studies at the level of phenotypic variation among individuals or species, but none has provided a clear answer whether the traits are genetically correlated. Here we present results of a genetic analysis based on measurements of the basal and the maximum swim- and cold-induced oxygen consumption in about 1000 bank voles from six generations of a laboratory colony, reared from animals captured in the field. Narrow sense heritability (h2) was about 0.5 for body mass, about 0.4 for mass-independent basal and maximum metabolic rates, and about 0.3 for factorial aerobic scopes. Dominance genetic and common environmental (= maternal) effects were not significant. Additive genetic correlation between BMR and the swim-induced aerobic capacity was high and positive, whereas correlation resulting from specific-environmental effects was negative. However, BMR was not genetically correlated with the cold-induced aerobic capacity. The results are consistent with the aerobic capacity model of the evolution of endothermy in birds and mammals.

According to the aerobic capacity model, endothermy in birds and mammals evolved as a correlated response to selection for an ability of sustained locomotor activity, rather than in a response to direct selection for thermoregulatory capabilities. A key assumption of the model is that aerobic capacity is functionally linked to basal metabolic rate (BMR). The assumption has been tested in several studies at the level of phenotypic variation among individuals or species, but none has provided a clear answer whether the traits are genetically correlated. Here we present results of a genetic analysis based on measurements of the basal and the maximum swim- and cold-induced oxygen consumption in about 1000 bank voles from six generations of a laboratory colony, reared from animals captured in the field. Narrow sense heritability (h2) was about 0.5 for body mass, about 0.4 for mass-independent basal and maximum metabolic rates, and about 0.3 for factorial aerobic scopes. Dominance genetic and common environmental (= maternal) effects were not significant. Additive genetic correlation between BMR and the swim-induced aerobic capacity was high and positive, whereas correlation resulting from specific-environmental effects was negative. However, BMR was not genetically correlated with the cold-induced aerobic capacity. The results are consistent with the aerobic capacity model of the evolution of endothermy in birds and mammals.