A.V. Bushuev

Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca)

The pied flycatcher is one of the most phenotypically variable bird species in Europe. The geographic variation in phenotypes has often been attributed to spatial variation in selection regimes that is associated with the presence or absence of the congeneric collared flycatcher. Spatial variation in phenotypes could however also be generated by spatially restricted gene flow and genetic drift. We examined the genetic population structure of pied flycatchers across the breeding range and applied the phenotypic QST (PST)–FST approach to detect indirect signals of divergent selection on dorsal plumage colouration in pied flycatcher males. Allelic frequencies at neutral markers were found to significantly differ among populations breeding in central and southern Europe whereas northerly breeding pied flycatchers were found to be one apparently panmictic group of individuals. Pairwise differences between phenotypic (PST) and neutral genetic distances (FST) were positively correlated after removing the most differentiated Spanish and Swiss populations from the analysis, suggesting that genetic drift may have contributed to the observed phenotypic differentiation in some parts of the pied flycatcher breeding range. Differentiation in dorsal plumage colouration however greatly exceeded that observed at neutral genetic markers, which indicates that the observed pattern of phenotypic differentiation is unlikely to be solely maintained by restricted gene flow and genetic drift.

Archiving primary data: solutions for long-term studies

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.

Evolutionary signals of selection on cognition from the great tit genome and methylome

For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.

OpinionArchiving Primary Data: Solutions for Long-Term Studies

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.

Candidate genes for colour and vision exhibit signals of selection across the pied flycatcher (Ficedula hypoleuca) breeding range

The role of natural selection in shaping adaptive trait differentiation in natural populations has long been recognized. Determining its molecular basis, however, remains a challenge. Here, we search for signals of selection in candidate genes for colour and its perception in a passerine bird. Pied flycatcher plumage varies geographically in both its structural and pigment-based properties. Both characteristics appear to be shaped by selection. A single-locus outlier test revealed 2 of 14 loci to show significantly elevated signals of divergence. The first of these, the follistatin gene, is expressed in the developing feather bud and is found in pathways with genes that determine the structure of feathers and may thus be important in generating variation in structural colouration. The second is a gene potentially underlying the ability to detect this variation: SWS1 opsin. These two loci were most differentiated in two Spanish pied flycatcher populations, which are also among the populations that have the highest UV reflectance. The follistatin and SWS1 opsin genes thus provide strong candidates for future investigations on the molecular basis of adaptively significant traits and their co-evolution.

Estimation of heritability and repeatability of resting metabolic rate in birds by the example of free-living pied flycatchers Ficedula hypoleuca (Aves: Passeriformes)

Repeatability of a trait estimated over long time intervals and its heritability make it possible to assess whether it can serve as an individual characteristic and be subject to selection. Heritability and repeatability of energetic traits are still poorly studied in birds. The most important physiological characteristic of the homoiotherms is the minimal level of energy expenditure, referred to as the resting metabolic rate (RMR), which, in the absence of the expenditure for biomass growth, does not exceed the basal metabolic rate (BMR). We have estimated the BMR repeatability in adult free-living pied flycatchers in Moscow-region (55°44′ N, 36°51′ E; 1992–2008) and Tomsk (56°20′ N, 84°56′ E; 2008–2009) populations over intervals of 40 days to 3 years. In the Moscow-region pied flycatcher population, the BMR repeatability recorded during the same period of the reproductive season was τ = 0.34 ± 0.10 for a 1-year interval (n = 80), τ = 0.60 ± 0.15 for a 2-year interval (n = 19), and τ = 0.85 ± 0.13 for a 3-year interval (n = 6). In the Tomsk population, the BMR repeatability for the 1-year interval was τ = 0.49 ± 0.11 (n = 50). The repeatability of a trait is a measure of its constancy in time and specifies the upper limit of its heritability. RMR heritability was assessed in cross-fostering experiments in the Moscow-region free-living pied flycatcher population in 2003–2005. The RMRs of chicks and BMRs of their biological fathers displayed a positive correlation, whereas no correlation was found between the RMRs of chicks and their foster fathers. The RMR heritability value was h2 = 0.43 ± 0.17 (n = 210). The obtained estimates for repeatability and heritability of fundamental energetic traits in pied fly-catcher are rather high for a physiological trait and suggest the existence of evolutionary stable diversity of the avian population in the BMR.

Solutions for archiving data in long-term studies – a reply to Whitlock et al

In our recent paper [1], we discussed some potential undesirable consequences of public data archiving (PDA) with specific reference to long-term studies and proposed solutions to manage these issues. We reaffirm our commitment to data sharing and collaboration, both of which have been common and fruitful practices supported for many decades by researchers involved in long-term studies. We acknowledge the potential benefits of PDA (e.g., [2]), but believe that several potential negative consequences for science have been underestimated [1] (see also 3 and 4). The objective of our recent paper [1] was to define practices to simultaneously maximize the benefits and minimize the potential unwanted consequences of PDA.

Specific immunity and polymorphism of breeding plumage in pied flycatcher (Ficedula hypoleuca) males (Aves: Passeriformes)

The relationship between the type of melanin-based plumage colouration and the strength of experimentally induced immune response was studied using as an example a pied flycatcher population from the Moscow region. The breeding plumage of pied flycatcher males exhibits the full spectrum of transitions from contrasting black-and-white to cryptic brownish, the latter being very similar to the colouration of females. In spite of numerous studies, the nature of this polymorphism still remains vague. Unlike many other avian species with monocyclic breeding, a considerable fraction of pied flycatchers overlaps two energy-consuming productive processes, breeding and moult, over the whole species range. During the main experimental treatment we activated the humoral immunity of free-living males in chick-rearing period by injection of nonpathogenic multifactorial antigen (sheep red blood cells, SRBC) and estimated the strength of the immune responses after repeated captures in 6–8 days. In addition, after each capture we evaluated the numbers of leucocytes (WBC), heterophil to lymphocyte ratios (H/L) and measured night time basal metabolic rates (BMR). Non-moulting males of different colour types showed the same immune responses. Among moulting birds, the strength of the immune response was significantly higher in pale males (morphs 4–7 by Drost’s scale) than in bright males with rich melanin-based colouration (morphs 2–3). This difference resulted from two opposite processes. During moulting, pale males heightened the antibody titer after immunization, while bright males tended to reduce the strength of immune response. Possibly such an asymmetry in immunocompetence at the first stage of moult reflects the different life strategies of pied flycatcher males—conspicuous birds less commonly overlap breeding with moult than cryptic ones.

Immunocompetence and reproductive characteristics of Campbell’s dwarf hamster males selected for low and high humoral immune response on sheep red blood cells (SRBC): Testing the immunocompetence handicap hypothesis

Characteristics of innate (nonspecific) and acquired T-cell immunity, resting metabolic rate, hormonal and reproductive status, morphological traits of maturation and aggressive behavior were studied in two sample groups of Campbell’s dwarf hamster males (Phodopus campbelli Thomas, 1905) selected in three generations for high and low humoral immune response to sheep red blood cells (SRBC). The groups of males with low and high immune responses (LIR and HIR, respectively) to SRBC did not differ statistically in the intensity of delayed-type hypersensitivity cutaneous response to phytohemagglutinin (T-cell immunity test), the activity of the peroxidase-endogenous hydrogen peroxide system of neutrophils (characteristic of the innate immunity state), the white blood cell counts, the resting metabolic rate, body weight, anogenital distance at the age two months, testosterone level in the blood before immunization and at the peak of secondary immune response to SRBC, or the blood cortisol level in response to social conflict (encountering). LIR males had a significantly higher background blood cortisol level and were less aggressive (reaction to the stranger male). The midventral sebaceous gland was less developed in them at the age of two months. We observed no differences in the time of first litter birth after uniting LIR and HIR males in pairs with intact females; however, females in pairs with LIR males had smaller numbers of pups in the litter. The results of comparison do not favor the immunocompetence handicap hypothesis, which assumes the existence of a trade-off between the immunocompetence and reproductive effort.

Resting metabolic rate, stress, testosterone, and induced immune response in spring- and fall-born males of Campbell’s dwarf hamsters: maintenance in long-day conditions

We have studied morphological and physiological traits of equally aged young males of Campbell’s dwarf hamster (Phodopus campbelli Thomas, 1905) born at the end of summer (fall males) and winter (spring males) in a vivarium with a constant 14-hour day length (LD 14: 10). Animals were removed from parental cages at the age of one month, kept in isolation in the same lighting conditions, and tested at the age of 2 to 3.5 months. Spring males had a higher resting metabolic rate, a higher body mass in the middle of the experiment, bigger testes and seminal vesicles, higher blood testosterone levels, and a stronger T-cell immune response to phytohemagglutinin injected intradermally than fall males. They did not differ significantly from fall males in basal blood cortisol levels or in antibody production in response to the sheep red blood cells (SRBC) antigen challenge, but they showed lower adrenocortical response to a social stressor and to an adrenocorticotropic hormone. A general linear model analysis showed that the blood cortisol level after a 10 min encounter of males in the open arena and the resting metabolic rate were the only factors significantly influencing humoral immune response to SRBC. In the general linear model including the intensity of T-cell immune response or basal testosterone level as dependent variables, birth season was the only factor causing a significant effect.