Olfactory kin recognition in a songbird

Volatile organic compounds in preen oil and feathers - a review

For a long time birds were assumed to be anosmic or at best microsmatic, with olfaction a poorly understood and seldom investigated part of avian physiology. The full viability of avian olfaction was first discovered through its functions in navigation and foraging. Subsequently, researchers have investigated the role of olfaction in different social and non-social contexts, including reproduction, kin recognition, predator avoidance, navigation and foraging. In parallel to the recognition of the importance of olfaction for avian social behaviour, there have been advances in the techniques and methods available for the sampling and analysis of trace volatiles and odourants, leading to insights into the chemistry underlying chemical communication in birds. This review provides (i) an overview of the current state of knowledge regarding the volatile chemical composition of preen oil and feathers, its phylogenetic coverage, chemical signatures and their potential functions, and (ii) a discussion of current methods used for the isolation and detection of volatiles. Finally, lines for future research are proposed.

No sex difference in preen oil chemical composition during incubation in Kentish plovers

Preen oil, the secretion from the uropygial gland of birds, may have a specific function in incubation. Consistent with this, during incubation, the chemical composition of preen oil is more likely to differ between sexes in species where only one sex incubates than in species where both sexes incubate. In this study, we tested the generality of this apparent difference, by investigating sex differences in the preen oil composition of a shorebird species, the Kentish plover (Anarhynchus, formerly Charadrius, alexandrinus). As both sexes incubate in this species, we predicted the absence of sex differences in preen oil composition during incubation. In the field, we sampled preen oil from nine females and 11 males during incubation, which we analysed with gas chromatography-mass spectrometry (GC-MS). Consistent with predictions, we found no sex difference in preen oil composition, neither in beta diversity (Bray-Curtis dissimilarities) nor in alpha diversity (Shannon index and number of substances). Based on these results, we cannot conclude whether preen oil has a function during incubation in Kentish plovers. Still, we discuss hypothetical roles, such as olfactory crypsis, protection against ectoparasites or olfactory intraspecific communication, which remain to be tested.

Highly diverse cuticular hydrocarbon profiles but no evidence for aggression towards non-kin in the ambrosia beetle Xyleborinus saxesenii

Animal societies use nestmate recognition to protect against social cheaters and parasites. In most social insect societies, individuals recognize and exclude any non-nestmates and the roles of cuticular hydrocarbons as recognition cues are well documented. Some ambrosia beetles live in cooperatively breeding societies with farmed fungus cultures that are challenging to establish, but of very high value once established. Hence, social cheaters that sneak into a nest without paying the costs of nest foundation may be selected. Therefore, nestmate recognition is also expected to exist in ambrosia beetles, but so far nobody has investigated this behavior and its underlying mechanisms. Here we studied the ability for nestmate recognition in the cooperatively breeding ambrosia beetle Xyleborinus saxesenii, combining behavioural observations and cuticular hydrocarbon analyses. Laboratory nests of X. saxesenii were exposed to foreign adult females from the same population, another population and another species. Survival as well as the behaviours of the foreign female were observed. The behaviours of the receiving individuals were also observed. We expected that increasing genetic distance would cause increasing distance in chemical profiles and increasing levels of behavioural exclusion and possibly mortality. Chemical profiles differed between populations and appeared as variable as in other highly social insects. However, we found only very little evidence for the behavioural exclusion of foreign individuals. Interpopulation donors left nests at a higher rate than control donors, but neither their behaviours nor the behaviours of receiver individuals within the nest showed any response to the foreign individual in either of the treatments. These results suggest that cuticular hydrocarbon profiles might be used for communication and nestmate recognition, but that behavioural exclusion of non-nestmates is either absent in X. saxesenii or that agonistic encounters are so rare or subtle that they could not be detected by our method. Additional studies are needed to investigate this further.

Chemical Profiles Differ between Communal Breeding Groups in a Highly Social Bird

AbstractGregarious species must distinguish group members from nongroup members. Olfaction is important for group recognition in social insects and mammals but rarely studied in birds, despite birds using olfaction in social contexts from species discrimination to kin recognition. Olfactory group recognition requires that groups have a signature odor, so we tested for preen oil and feather chemical similarity in group-living smooth-billed anis (Crotophaga ani). Physiology affects body chemistry, so we also tested for an effect of egg-laying competition, as a proxy for reproductive status, on female chemical similarity. Finally, the fermentation hypothesis for chemical recognition posits that host-associated microbes affect host odor, so we tested for covariation between chemicals and microbiota. Group members were more chemically similar across both body regions. We found no chemical differences between sexes, but females in groups with less egg-laying competition had more similar preen oil, suggesting that preen oil contains information about reproductive status. There was no overall covariation between chemicals and microbes; instead, subsets of microbes could mediate olfactory cues in birds. Preen oil and feather chemicals showed little overlap and may contain different information. This is the first demonstration of group chemical signatures in birds, a finding of particular interest given that smooth-billed anis live in nonkin breeding groups. Behavioral experiments are needed to test whether anis can distinguish group members from nongroup members using odor cues.

No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.

Sensory Mechanisms of Parent-Offspring Recognition in Fishes, Amphibians, and Reptiles

Parental care is important for offspring survival and success. Recognition of offspring by parents is critical to ensure parents direct care behaviors at related offspring and minimize energy lost by caring for unrelated young. Offspring recognition of parents prevents possible aggressive interactions between young and unrelated adults and allows offspring to direct begging behaviors toward the correct adult. Despite its importance and widespread nature, much of the current research has focused on a small range of species, particularly mammals and birds. We review the existing literature on the sensory mechanisms of parent-offspring recognition in fishes, amphibians, and reptiles. Within these groups, there is diversity in the presence and strategies for parent-offspring recognition. Future studies should continue to identify these mechanisms, as well as the neural and endocrine underpinnings in non-model organisms to expand our knowledge of this behavior and inform our understanding of the evolution of parent-offspring recognition.

Changes in the Amount and Distribution of Soil Nutrients and Neighbours Have Differential Impacts on Root and Shoot Architecture in Wheat (Triticum aestivum)

Plants exhibit differential behaviours through changes in biomass development and distribution in response to environmental cues, which may impact crops uniquely. We conducted a mesocosm experiment in pots to determine the root and shoot behavioural responses of wheat, T. aestivum. Plants were grown in homogeneous or heterogeneous and heavily or lightly fertilized soil, and alone or with a neighbour of the same or different genetic identity (cultivars: CDC Titanium, Carberry, Glenn, Go Early, and Lillian). Contrary to predictions, wheat did not alter relative reproductive effort in the presence of neighbours, more nutrients, or homogenous soil. Above and below ground, the plants' tendency to use potentially shared space exhibited high levels of plasticity. Above ground, they generally avoided shared, central aerial space when grown with neighbours. Unexpectedly, nutrient amount and distribution also impacted shoots; plants that grew in fertile or homogenous environments increased shared space use. Below ground, plants grown with related neighbours indicated no difference in neighbour avoidance. Those in homogenous soil produced relatively even roots, and plants in heterogeneous treatments produced more roots in nutrient patches. Additionally, less fertile soil resulted in pot-level decreases in root foraging precision. Our findings illustrate that explicit coordination between above- and belowground biomass in wheat may not exist.

Fifty shades of greenbeard: robust evolution of altruism based on similarity of complex phenotypes

We study the evolution of altruistic behaviour under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently similar to themselves in a multidimensional phenotype space. We find the generic maintenance of robust altruism when phenotypes are multidimensional. Selection for altruism is driven by the coevolution of individual strategy and phenotype; altruism levels shape the distribution of individuals in phenotype space. Low donation rates induce a phenotype distribution that renders the population vulnerable to the invasion of altruists, whereas high donation rates prime a population for cheater invasion, resulting in cyclic dynamics that maintain substantial levels of altruism. Altruism is therefore robust to invasion by cheaters in the long term in this model. Furthermore, the shape of the phenotype distribution in high phenotypic dimension allows altruists to better resist the invasion by cheaters, and as a result the amount of donation increases with increasing phenotype dimension. We also generalize previous results in the regime of weak selection to two competing strategies in continuous phenotype space, and show that success under weak selection is crucial to success under strong selection in our model. Our results support the viability of a simple similarity-based mechanism for altruism in a well-mixed population.

Social network analysis reveals context-dependent kin relationships in wild sulphur-crested cockatoos Cacatua galerita

A preference to associate with kin facilitates inclusive fitness benefits, and increased tolerance or cooperation between kin may be an added benefit of group living. Many species exhibit preferred associations with kin; however, it is often hard to disentangle active preferences from passive overlap, for example caused by limited dispersal or inheritance of social position. Many parrots exhibit social systems consisting of pair-bonded individuals foraging in variably sized fission-fusion flocks within larger communal roosts of hundreds of individuals. Previous work has shown that, despite these fission-fusion dynamics, individuals can exhibit long-term preferred foraging associations outside their pair bonds. Yet the underlying drivers of these social preferences remain largely unknown. In this study, we use a network approach to examine the influence of kinship on social associations and interactions in wild, communally roosting sulphur-crested cockatoos, Cacatua galerita. We recorded roost co-membership, social associations and interactions in 561 individually marked birds across three neighbouring roosts. We then collected genetic samples from 205 cockatoos, and conducted a relationship analysis to construct a kinship network. Finally, we tested correlations between kinship and four social networks: association, affiliative, low-intensity aggression and high-intensity aggression. Our result showed that while roosting groups were clearly defined, they showed little genetic differentiation or kin structuring. Between roost movement was high, with juveniles, especially females, repeatedly moving between roosts. Both within roosting communities, and when visiting different roosts, individuals preferentially associated with kin. Supporting this, individuals were also more likely to allopreen kin. However, contrary to expectation, individuals preferred to direct aggression towards kin, with this effect only observed when individuals shared roost membership. By measuring social networks within and between large roosting groups, we could remove potential effects of passive spatial overlap on kin structuring. Our study reveals that sulphur-crested cockatoos actively prefer to associate with kin, both within and between roosting groups. By examining this across different interaction types, we further demonstrate that sulphur-crested cockatoos exhibit behavioural and context-dependent interaction rules towards kin. Our results help reveal the drivers of social association in this species, while adding to the evidence for social complexity in parrots.

Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese

Geese are herbivorous birds that play an essential role in the agricultural economy. We construct the chromosome-level genome of a Chinese indigenous goose (the Xingguo gray goose, XGG; Anser cygnoides) and analyze the adaptation of fat storage capacity in the goose liver during the evolution of Anatidae. Genomic resequencing of 994 geese is used to investigate the genetic relationships of geese, which supports the dual origin of geese (Anser cygnoides and Anser anser). Chinese indigenous geese show higher genetic diversity than European geese, and a scientific conservation program can be established to preserve genetic variation for each breed. We also find that a 14-bp insertion in endothelin receptor B subtype 2 (EDNRB2) that determines the white plumage of Chinese domestic geese is a natural mutation, and the linkaged alleles rapidly increase in frequency as a result of genetic hitchhiking, leading to the formation of completely different haplotypes of white geese under strong artificial selection. These genomic resources and our findings will facilitate marker-assisted breeding of geese and provide a foundation for further research on geese genetics and evolution.

GSK-3β Inhibition in Birds Affects Social Behavior and Increases Motor Activity

Glycogen synthase kinase-3 (GSK-3) is a highly conserved serine/threonine protein kinase that plays a central role in a wide variety of cellular processes, cognition and behaviour. In a previous study we showed that its α and β isozymes are highly conserved in vertebrates, however the α gene is missing in birds. This selective loss offers a unique opportunity to study the role of GSK-3β independently. Accordingly, in the present study we aimed to investigate the role of GSK-3β in social behaviour, motivation, and motor activity in zebra finches (Taeniopygia guttata). We did that by selective inhibition of GSK-3β and by using tests that were specifically designed in our laboratory. Our results show that GSK-3β inhibition: 1) Affected social recognition, because the treated birds tended to move closer towards a stranger, unlike the control birds that stood closer to a familiar bird. 2) Caused the treated birds to spend more time in the more middle parts of the cage compared to controls, a behaviour that might indicate anxiety. 3) As the experiment progressed, the treated birds took less time to make a decision where to stand in the cage compared to controls, suggesting an effect on decision-making. 4) Increased in the motor activity of the treated birds compared to the controls, which can be regarded as hyperactivity. 5) Caused the treated birds to pass through a barrier in order to join their flock members faster compared to controls, and regardless of the increase in the level of difficulty, possibly suggesting increased motivation. Our study calls for further investigation, because GSK-3 is well acknowledged as a central player in regulating mood behaviour, cognitive functions, and neuronal viability. Therefore, studying its impact on normal behaviour as we did in the current study, unlike most studies that were done in diseases models, can advance our understanding regarding GSK-3 various roles and can contribute to the discovery and development of effective treatments to repair cognition and behaviour.

A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl

Background

The dazzling phenotypic characteristics of male Indian peafowl (Pavo cristatus) are attractive both to the female of the species and to humans. However, little is known about the evolution of the phenotype and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl.

Results

A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362×), and contig and scaffold N50 were up to 6.2 and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, and skeletal and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that PMEL was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl.

Conclusions

This study provides an Indian peafowl genome of high quality, as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution. Furthermore, the discovery of the genetic mechanism for the development of leucism plumage is both a breakthrough in the exploration of peafowl plumage and also offers clues and directions for further investigations of the avian plumage coloration and artificial breeding in peafowl.

Olfactory camouflage and communication in birds

Smell is a sensory modality that is rarely considered in birds, but evidence is mounting that olfaction is an important aspect of avian behaviour and ecology. The uropygial gland produces an odoriferous secretion (preen oil) that can differ seasonally and between the sexes. These differences are hypothesized to function in olfactory camouflage, i.e. minimizing detection by nest predators (olfactory crypsis hypothesis), and/or intraspecific olfactory communication, particularly during breeding (sex semiochemical hypothesis). However, evidence for seasonal and sex differences in preen oil is mixed, with some studies finding differences and others not, and direct evidence for the putative function(s) of seasonal variation and sex differences in preen oil remains limited. We conducted a systematic review of the evidence for such changes in preen oil chemical composition, finding seasonal differences in 95% of species (57/60 species in 35 studies) and sex differences in 47% of species (28/59 species in 46 studies). We then conducted phylogenetic comparative analyses using data from 59 bird species to evaluate evidence for both the olfactory crypsis and sex semiochemical hypotheses. Seasonal differences were more likely in the incubating than non-incubating sex in ground-nesting species, but were equally likely regardless of incubation strategy in non-ground-nesting species. This result supports the olfactory crypsis hypothesis, if ground nesters are more vulnerable to olfactorily searching predators than non-ground nesters. Sex differences were more likely in species with uniparental than biparental incubation and during breeding than non-breeding, consistent with both the olfactory crypsis and sex semiochemical hypotheses. At present, the data do not allow us to disentangle these two hypotheses, but we provide recommendations that will enable researchers to do so.

Mate Choice, Sex Roles and Sexual Cognition: Neuronal Prerequisites Supporting Cognitive Mate Choice

Across taxa, mate choice is a highly selective process involving both intra- and intersexual selection processes aiming to pass on one’s genes, making mate choice a pivotal tool of sexual selection. Individuals adapt mate choice behavior dynamically in response to environmental and social changes. These changes are perceived sensorily and integrated on a neuronal level, which ultimately leads to an adequate behavioral response. Along with perception and prior to an appropriate behavioral response, the choosing sex has (1) to recognize and discriminate between the prospective mates and (2) to be able to assess and compare their performance in order to make an informed decision. To do so, cognitive processes allow for the simultaneous processing of multiple information from the (in-) animate environment as well as from a variety of both sexual and social (but non-sexual) conspecific cues. Although many behavioral aspects of cognition on one side and of mate choice displays on the other are well understood, the interplay of neuronal mechanisms governing both determinants, i.e., governing cognitive mate choice have been described only vaguely. This review aimed to throw a spotlight on neuronal prerequisites, networks and processes supporting the interaction between mate choice, sex roles and sexual cognition, hence, supporting cognitive mate choice. How does neuronal activity differ between males and females regarding social cognition? Does sex or the respective sex role within the prevailing mating system mirror at a neuronal level? How does cognitive competence affect mate choice? Conversely, how does mate choice affect the cognitive abilities of both sexes? Benefitting from studies using different neuroanatomical techniques such as neuronal activity markers, differential coexpression or candidate gene analyses, modulatory effects of neurotransmitters and hormones, or imaging techniques such as fMRI, there is ample evidence pointing to a reflection of sex and the respective sex role at the neuronal level, at least in individual brain regions. Moreover, this review aims to summarize evidence for cognitive abilities influencing mate choice and vice versa. At the same time, new questions arise centering the complex relationship between neurobiology, cognition and mate choice, which we will perhaps be able to answer with new experimental techniques.

Olfactory detection of trace amounts of plant volatiles is correlated with testosterone in a passerine bird

In response to damage by insects, plants release herbivore-induced plant volatiles (HIPVs) into the air. Insectivorous birds exploit these cues and, consequently, reduce the damages inflicted to the plants. However, little is known about whether they solely use HIPVs as foraging cues, or if they also use them to modulate traits linked to reproduction. As caterpillars are the primary food source required for insectivorous birds to raise offspring, their ability to locate and predict future peaks in caterpillar biomass using olfaction is likely to be advantageous. Therefore, we tested whether an insectivorous songbird that naturally inhabits oak dominated forests can be trained to detect early spring infestation by hatchling caterpillars, at a time when oaks begin bursting, and birds prepare to breed. Tree buds were either infested with caterpillars or left as a control and visually obscured in a Y-Maze choice test. Additionally, we measured testosterone and 17β-estradiol as they influence olfactory perception in mammals and are linked to reproduction in vertebrates. After being trained to associate the presence of HIPVs with that of food, blue tits spent more time with, were more active around, and more frequently chose to first visit the infested trees, showing that blue tits can smell caterpillar activity. Males with higher testosterone spent more time around infested trees, suggesting that foraging behavior during the pre-breeding season is linked with a major reproductive signal. There was no relationship between foraging and estradiol in females. These results are an important foundation for further investigation of the role of hormones in avian olfaction and how smell may be useful for making breeding decisions that could improve reproductive success.

Meadow voles differentiate between scents of different sources

Scent marks are an important means of transmitting information between rodents, and they can be produced from several body sources. Previous studies have shown that scents from multiple sources can convey the same information; female meadow voles, for example, have three scent sources that communicate sex. However, possessing three separate sources that convey the same information is likely costly due to the metabolic energy required to produce these signals and the increased chance that eavesdropping individuals may intercept information present in these signals. In this study, we investigated if these scent sources could communicate other information, in addition to scent donor sex, by determining if male meadow voles could distinguish scent marks taken from different sources of a single female scent donor. This was accomplished with a habituation-test method, that allowed us to compare how male meadow voles differently investigate scent from a familiar and novel source of a female scent donor. Male meadow voles could distinguish between faeces and urine scent marks of a female, but could only distinguish mouth from urine and faeces scent marks when first familiarized with mouth scent marks. Our findings suggest that mouth, urine, and faeces scent marks of female meadow voles produce both redundant and distinct information. The overlap in information between scent marks produced from separate sources may be needed to provide social context, which allows receiving individuals to accurately weigh the tradeoffs associated with responding to an olfactory cue. While this overlap in information remains costly, this cost may be minimized by the different fade-out times of scent marks from distinct body sources, which may limit the amount of time information in a scent mark is available to a time period where this information is socially relevant.

Cooperatively breeding banded mongooses do not avoid inbreeding through familiarity-based kin recognition

Abstract

In species that live in family groups, such as cooperative breeders, inbreeding is usually avoided through the recognition of familiar kin. For example, individuals may avoid mating with conspecifics encountered regularly in infancy, as these likely include parents, siblings, and closely related alloparents. Other mechanisms have also been reported, albeit rarely; for example, individuals may compare their own phenotype to that of others, with close matches representing likely relatives (“phenotype matching”). However, determinants of the primary inbreeding avoidance mechanisms used by a given species remain poorly understood. We use 24 years of life history and genetic data to investigate inbreeding avoidance in wild cooperatively breeding banded mongooses (Mungos mungo). We find that inbreeding avoidance occurs within social groups but is far from maximised (mean pedigree relatedness between 351 breeding pairs = 0.144). Unusually for a group-living vertebrate, we find no evidence that females avoid breeding with males with which they are familiar in early life. This is probably explained by communal breeding; females give birth in tight synchrony and pups are cared for communally, thus reducing the reliability of familiarity-based proxies of relatedness. We also found little evidence that inbreeding is avoided by preferentially breeding with males of specific age classes. Instead, females may exploit as-yet unknown proxies of relatedness, for example, through phenotype matching, or may employ postcopulatory inbreeding avoidance mechanisms. Investigation of species with unusual breeding systems helps to identify constraints against inbreeding avoidance and contributes to our understanding of the distribution of inbreeding across species.

Significance statement

Choosing the right mate is never easy, but it may be particularly difficult for banded mongooses. In most social animals, individuals avoid mating with those that were familiar to them as infants, as these are likely to be relatives. However, we show that this rule does not work in banded mongooses. Here, the offspring of several mothers are raised in large communal litters by their social group, and parents seem unable to identify or direct care towards their own pups. This may make it difficult to recognise relatives based on their level of familiarity and is likely to explain why banded mongooses frequently inbreed. Nevertheless, inbreeding is lower than expected if mates are chosen at random, suggesting that alternative pre- or post-copulatory inbreeding avoidance mechanisms are used.

A larval aggregation pheromone as foraging cue for insectivorous birds

Although birds have traditionally been considered anosmic, increasing evidence indicates that olfaction plays an important role in the foraging behaviours of insectivorous birds. Recent studies have shown that birds can exploit herbivore-induced plant volatiles and sexual pheromones of adult insects to locate their prey. Many insectivorous birds prey on immature insects, providing relevant ecosystem services as pest regulators in natural and agricultural ecosystems. We asked whether birds could rely on chemical cues emitted by the immature stages of insects to prey on them. To address this question, we performed field experiments to evaluate if insectivorous birds can detect the aggregation pheromone produced by the larvae of the carpenter worm, Chilecomadia valdiviana. Groups of five artificial larvae were placed in branches of 72 adult trees in a remnant fragment of a sclerophyllous forest in central Chile. Each grouping of larvae contained a rubber septum loaded with either larval pheromone as treatment or solvent alone as control. We found that the number of larvae damaged by bird pecks was significantly higher in groups with dispensers containing the larval extract than in control groups. Our results show that birds can rely on immature insect-derived chemical cues used for larvae aggregation to prey on them.

Highly contiguous genomes improve the understanding of avian olfactory receptor repertoires

Third generation (long read-based) sequencing technologies are reshaping our understanding of genome structure and function. One of the most persistent challenges in genome biology has been confidently reconstructing radiations of complex gene families. Olfactory receptors (ORs) represent just such a gene family with upwards of 1000s of receptors in some mammalian taxa. Whereas in birds olfaction was historically an overlooked sensory modality, new studies have revealed an important role for smell. Chromosome-level assemblies for birds allow a new opportunity to characterize patterns of OR diversity among major bird lineages. Previous studies of short read (second-generation) genome assemblies have associated OR gene family size with avian ecology, but such conclusions could be premature if new assembly methods reshape our understanding of avian OR evolution. Here we provide a fundamental characterization of OR repertoires in five recent genome assemblies, including the most recent assembly of golden-collared manakin (Manacus vitellinus). We find that short read-based assemblies systematically undercount the avian-specific gamma-c OR subfamily, a subfamily that comprises over 65% of avian OR diversity. Therefore, in contrast to previous studies we find a high diversity of gamma-c ORs across the avian tree of life. Building on these findings, ongoing sequencing efforts and improved genome assemblies will clarify the relationship between OR diversity and avian ecology.

Evolutionary history of mental glands in turtles reveals a single origin in an aquatic ancestor and recurrent losses independent of macrohabitat

Despite the relevance of chemical communication in vertebrates, comparative examinations of macroevolutionary trends in chemical signaling systems are scarce. Many turtle and tortoise species are reliant on chemical signals to communicate in aquatic and terrestrial macrohabitats, and many of these species possess specialized integumentary organs, termed mental glands (MGs), involved in the production of chemosignals. We inferred the evolutionary history of MGs and tested the impact of macrohabitat on their evolution. Inference of ancestral states along a time-calibrated phylogeny revealed a single origin in the ancestor of the subclade Testudinoidea. Thus, MGs represent homologous structures in all descending lineages. We also inferred multiple independent losses of MGs in both terrestrial and aquatic clades. Although MGs first appeared in an aquatic turtle (the testudinoid ancestor), macrohabitat seems to have had little effect on MG presence or absence in descendants. Instead, we find clade-specific evolutionary trends, with some clades showing increased gland size and morphological complexity, whereas others exhibiting reduction or MG loss. In sister clades inhabiting similar ecological niches, contrasting patterns (loss vs. maintenance) may occur. We conclude that the multiple losses of MGs in turtle clades have not been influenced by macrohabitat and that other factors have affected MG evolution.

Nestling odour modulates behavioural response in male, but not in female zebra finches

Studies investigating parent offspring recognition in birds led to the conclusion that offspring recognition is absent at the early nestling stage. Especially male songbirds were often assumed to be unable to discriminate between own and foreign offspring. However, olfactory offspring recognition in birds has not been taken into account as yet, probably because particularly songbirds have for a long time been assumed anosmic. This study aimed to test whether offspring might be recognised via smell. We presented zebra finch (Taeniopygia guttata) parents either the odour of their own or that of foreign nestlings and investigated whether the odour presentation resulted in a change in the number of head saccades, i.e. the rapid horizontal turning of the head, with which birds scan their environment and which can be used as a proxy of arousal. Our experiment indicates that male zebra finches, in contrast to females, differentiate between their own and foreign offspring based on odour cues, as indicated by a significant differences in the change of head saccadic movements between males receiving the own chick odour and males receiving the odour of a foreign chick. Thus, it provides behavioural evidence for olfactory offspring recognition in male zebra finches and also the existence of appropriate phenotypic odour cues of the offspring. The question why females do not show any sign of behavioural response remains open, but it might be likely that females use other signatures for offspring recognition.

Female-Based Patterns and Social Function in Avian Chemical Communication

Much of the growing interest in avian chemical signals has focused on the role of kin recognition or mate attraction, often with an emphasis on males, with uropygial gland secretions perhaps providing information about an individual's identity and quality. Yet, data collected to date suggest sexual dimorphism in uropygial glands and secretions are often emphasized in female, rather than in male birds. That is, when a sexual difference occurs (often during the breeding season only), it is the female that typically exhibits one of three patterns: (1) a larger uropygial gland, (2) a greater abundance of volatile or semi-volatile preen oil compounds and/or (3) greater diversity of preen oil compounds or associated microbes. These patterns fit a majority of birds studied to date (23 of 30 chemically dimorphic species exhibit a female emphasis). Multiple species that do not fit are confounded by a lack of data for seasonal effects or proper quantitative measures of chemical compounds. We propose several social functions for these secretions in female-based patterns, similar to those reported in mammals, but which are largely unstudied in birds. These include: (1) intersexual advertisement of female receptivity or quality, including priming effects on male physiology, (2) intrasexual competition, including scent marking and reproductive suppression or (3) parental behaviors, such as parent-offspring recognition and chemical protection of eggs and nestlings. Revisiting the gaps of chemical studies to quantify the existence of female social chemosignals and any fitness benefit(s) during breeding are potentially fruitful but overlooked areas of future research.

Insectivorous birds can see and smell systemically herbivore-induced pines

Several studies have shown that insectivorous birds are attracted to herbivore-damaged trees even when they cannot see or smell the actual herbivores or their feces. However, it often remained an open question whether birds are attracted by herbivore-induced changes in leaf odor or in leaf light reflectance or by both types of changes. Our study addressed this question by investigating the response of great tits (Parus major) and blue tits (Cyanistes caeruleus) to Scots pine (Pinus sylvestris) damaged by pine sawfly larvae (Diprion pini). We released the birds individually to a study booth, where they were simultaneously offered a systemically herbivore-induced and a noninfested control pine branch. In the first experiment, the birds could see the branches, but could not smell them, because each branch was kept inside a transparent, airtight cylinder. In the second experiment, the birds could smell the branches, but could not see them, because each branch was placed inside a nontransparent cylinder with a mesh lid. The results show that the birds were more attracted to the herbivore-induced branch in both experiments. Hence, either type of the tested cues, the herbivore-induced visual plant cue alone as well as the olfactory cues per se, is attractive to the birds.

Individual Chemical Profiles in the Leach's Storm-Petrel

Avian chemical communication, once largely overlooked, is a growing field that has revealed the important role that olfaction plays in the social lives of some birds. Leach's storm-petrels (Oceanodroma leucorhoa) have a remarkable sense of smell and a strong, musky scent. This long-lived, monogamous seabird relies on olfaction for nest relocation and foraging, but whether they use scent for communication is less well studied. They are nocturnally active at the breeding colony and yet successfully reunite with their mate despite poor night-vision, indicating an important role for non-visual communication. We investigated the chemical profiles of Leach's storm-petrels to determine whether there is socially relevant information encoded in their plumage odor. To capture the compounds comprising their strong scent, we developed a method to study the compounds present in the air surrounding their feathers using headspace stir bar sorptive extraction coupled with gas chromatography-mass spectrometry. We collected feathers from Leach's storm-petrels breeding on Bon Portage Island in Nova Scotia, Canada in both 2015 and 2016. Our method detected 142 commonly occurring compounds. We found interannual differences in chemical profiles between the two sampling years. Males and females had similar chemical profiles, while individuals had distinct chemical signatures across the two years. These findings suggest that the scent of the Leach's storm-petrel provides sociochemical information that could facilitate olfactory recognition of individuals and may inform mate choice decisions.

Mechanisms of recognition in birds and social Hymenoptera: from detection to information processing

In this opinion piece, we briefly review our knowledge of the mechanisms underlying auditory individual recognition in birds and chemical nest-mate recognition in social Hymenoptera. We argue that even though detection and perception of recognition cues are well studied in social Hymenoptera, the neural mechanisms remain a black box. We compare our knowledge of these insect systems with that of the well-studied avian 'song control system'. We suggest that future studies on recognition should focus on the hypothesis of a distributed template instead of trying to locate the seat of the template as recent results do not seem to point in that direction. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

Helping decisions and kin recognition in long-tailed tits: is call similarity used to direct help towards kin?

Most cooperative breeders live in discrete family groups, but in a minority, breeding populations comprise extended social networks of conspecifics that vary in relatedness. Selection for effective kin recognition may be expected for more related individuals in such kin neighbourhoods to maximize indirect fitness. Using a long-term social pedigree, molecular genetics, field observations and acoustic analyses, we examine how vocal similarity affects helping decisions in the long-tailed tit Aegithalos caudatus. Long-tailed tits are cooperative breeders in which help is typically redirected by males that have failed in their own breeding attempts towards the offspring of male relatives living within kin neighbourhoods. We identify a positive correlation between call similarity and kinship, suggesting that vocal cues offer a plausible mechanism for kin discrimination. Furthermore, we show that failed breeders choose to help males with calls more similar to their own. However, although helpers fine-tune their provisioning rates according to how closely related they are to recipients, their effort was not correlated with their vocal similarity to helped breeders. We conclude that although vocalizations are an important part of the recognition system of long-tailed tits, discrimination is likely to be based on prior association and may involve a combination of vocal and non-vocal cues. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

No evidence for kin recognition in a passerine bird

Theory predicts that individuals behave altruistically towards their relatives. Hence, some form of kin recognition is useful for individuals to optimize their behavior. In species that display bi-parental care and are subject to extra-pair matings, kin recognition theoretically can allow cuckolded fathers to reduce their parental investment, and thus optimize their fitness. Whether this is possible remains unclear in birds. This study investigates whether males provide differential parental care depending on relatedness, as a proxy to recognizing chicks in their nest as kin or not. We cross-fostered House sparrow (Passer domesticus) chicks after hatching, and then expected that fathers would show a decrease in their parental efforts when tending to a clutch of unrelated offspring. House sparrow males are able to adjust their parental care to the identity of their partner, making them an ideal study species. However, there was no significant effect of relatedness on provisioning rates. This suggests that sparrows may not be capable of kin recognition, or at least do not display kin discrimination despite its apparent evolutionary advantage.

Olfaction in raptors

Raptors from the orders Accipitriformes and Falconiformes have been considered to rely principally on vision. Historically, this assumption has led scientists to discount any possible sense of smell in these birds, until work on cathartid vultures indicated that these species at least rely on olfaction to find carrion. In this review I provide evidence that raptors in general have functional olfactory systems that they may use in a range of different contexts. Anatomical studies show that raptors have well-developed olfactory bulbs that are within the range of other bird species. Furthermore, all raptors studied have multiple functional olfactory genes, with, for instance, 283 olfactory genes in the Oriental honey buzzard, Pernis orientalis, of which 81.5% are functional. It has also been shown that some raptors species may functionally use olfactory cues to forage and, potentially, for communication. While further research is required, the available evidence suggests that olfaction may be a more important sensory modality in these birds than previously thought.

Experimental evidence that symbiotic bacteria produce chemical cues in a songbird

Symbiotic microbes that inhabit animal scent glands can produce volatile compounds used as chemical signals by the host animal. Though several studies have demonstrated correlations between scent gland bacterial community structure and host animal odour profiles, none have systematically demonstrated a causal relationship. In birds, volatile compounds in preen oil secreted by the uropygial gland serve as chemical cues and signals. Here, we tested whether manipulating the uropygial gland microbial community affects chemical profiles in the dark-eyed junco (Junco hyemalis). We found an effect of antibiotic treatment targeting the uropygial gland on both bacterial and volatile profiles. In a second experiment, we cultured bacteria from junco preen oil, and found that all of the cultivars produced at least one volatile compound common in junco preen oil, and that most cultivars produced multiple preen oil volatiles. In both experiments, we identified experimentally generated patterns in specific volatile compounds previously shown to predict junco reproductive success. Together, our data provide experimental support for the hypothesis that symbiotic bacteria produce behaviourally relevant volatile compounds within avian chemical cues and signals.

Conspecific olfactory preferences and interspecific divergence in odor cues in a chickadee hybrid zone

Understanding how mating cues promote reproductive isolation upon secondary contact is important in describing the speciation process in animals. Divergent chemical cues have been shown to act in reproductive isolation across many animal taxa. However, such cues have been overlooked in avian speciation, particularly in passerines, in favor of more traditional signals such as song and plumage. Here, we aim to test the potential for odor to act as a mate choice cue, and therefore contribute to premating reproductive isolation between the black-capped (Poecile atricapillus) and Carolina chickadee (P. carolinensis) in eastern Pennsylvania hybrid zone populations. Using gas chromatography-mass spectrometry, we document significant species differences in uropygial gland oil chemistry, especially in the ratio of ester to nonester compounds. We also show significant preferences for conspecific over heterospecific odor cues in wild chickadees using a Y-maze design. Our results suggest that odor may be an overlooked but important mating cue in these chickadees, potentially promoting premating reproductive isolation. We further discuss several promising avenues for future research in songbird olfactory communication and speciation.

Presence of kin-biased social associations in a lizard with no parental care: the eastern water dragon (Intellagama lesueurii)

Numerous studies have observed kin-biased social associations in a variety of species. Many of these studies have focused on species exhibiting parental care, which may facilitate the transmission of the social environment from parents to offspring. This becomes problematic when disentangling whether kin-biased associations are driven by kin recognition, or are a product of transmission of the social environment during ontogeny, or a combination of both. Studying kin-biased associations in systems that lack parental care may aid in addressing this issue. Furthermore, when studying kin-biased social associations, it is important to differentiate whether these originate from preferential choice or occur randomly as a result of habitat use or limited dispersal. Here, we combined high-resolution single-nucleotide polymorphism data with a long-term behavioral data set of a reptile with no parental care to demonstrate that eastern water dragons (Intellagama lesueurii) bias their nonrandom social associations toward their kin. In particular, we found that although the overall social network was not linked to genetic relatedness, individuals associated with kin more than expected given availability in space and also biased social preferences toward kin. This result opens important opportunities for the study of kinship-driven associations without the confounding effect of vertical transmission of social environments. Furthermore, we present a robust multiple-step approach for determining whether kin-biased social associations are a result of active social decisions or random encounters resulting from habitat use and dispersal patterns.

Brood parasitism, relatedness and sociality: a kinship role in female reproductive tactics

Conspecific brood parasitism (CBP) is a reproductive tactic in which parasitic females lay eggs in nests of other females of the same species that then raise the joint brood. Parasites benefit by increased reproduction, without costs of parental care for the parasitic eggs. CBP occurs in many egg-laying animals, among birds most often in species with large clutches and self-feeding young: two major factors facilitating successful parasitism. CBP is particularly common in waterfowl (Anatidae), a group with female-biased natal philopatry and locally related females. Theory suggests that relatedness between host and parasite can lead to inclusive fitness benefits for both, but if host costs are high, parasites should instead target unrelated females. Pairwise relatedness (r) in host-parasite (h-p) pairs of females has been estimated using molecular genetic methods in seven waterfowl (10 studies). In many h-p pairs, the two females were unrelated (with low r, near the local population mean). However, close relatives (r = 0.5) were over-represented in h-p pairs, which in all 10 studies had higher mean relatedness than other females. In one species where this was studied, h-p relatedness was higher than between nesting close neighbours, and hosts parasitized by non-relatives aggressively rejected other females. In another species, birth nest-mates (mother-daughters, sisters) associated in the breeding area as adults, and became h-p pairs more often than expected by chance. These and other results point to recognition of birth nest-mates and perhaps other close relatives. For small to medium host clutch sizes, addition of a few parasitic eggs need not reduce host offspring success. Estimates in two species suggest that hosts can then gain inclusive fitness if parasitized by relatives. Other evidence of female cooperation is incubation by old eider Somateria mollissima females of clutches laid by their relatives, and merging and joint care of broods of young. Merging females tended to be more closely related. Eiders associate with kin in many situations, and in some geese and swans, related females may associate over many years. Recent genetic evidence shows that also New World quails (Odontophoridae) have female-biased natal philopatry, CBP and brood merging, inviting further study and comparison with waterfowl. Kin-related parasitism also occurs in some insects, with revealing parallels and differences compared to birds. In hemipteran bugs, receiving extra eggs is beneficial for hosts by diluting offspring predation. In eggplant lace bugs Gargaphia solani, host and parasite are closely related, and kin selection favours egg donation to related females. Further studies of kinship in CBP, brood merging and other contexts can test if some of these species are socially more advanced than presently known.

Pigeon odor varies with experimental exposure to trace metal pollution

Trace metals are chemical pollutants that have well-known noxious effects on wildlife and that are current major environmental issues in urban habitats. Previous studies have demonstrated their negative (e.g. lead) or positive (e.g. zinc) effects on body condition, immunity and reproductive success. Because of their effects on condition, trace metals are likely to influence the production of condition-dependent ornaments. The last decade has revealed that bird odors, like mammal odors, can convey information on individual quality and might be used as secondary sexual ornaments. Here, we used solid-phase microextraction headspace sampling with gas chromatography-mass spectrometry to investigate whether plumage scent varied with experimental supplementation in lead and/or zinc in feral pigeons. Zinc supplementation (alone or in combination with lead) changed the proportion of several volatiles, including an increase in the proportion of hydroxy-esters. The production of these esters, that most likely originate from preen gland secretions, may be costly and might thus be reduced by stress induced by zinc deficiency. Although lead is known to negatively impact pigeon condition, it did not statistically affect feather scent, despite most of the volatiles that increased with zinc exposure tended to be decreased in lead-supplemented pigeons. Further studies should evaluate the functions of plumage volatiles to predict how trace metals can impact bird fitness.

No evidence for prezygotic postcopulatory avoidance of kin despite high inbreeding depression

Offspring resulting from mating among close relatives can suffer from impaired fitness through the expression of recessive alleles with deleterious effects. Postcopulatory sperm selection (a prezygotic mechanism of cryptic female choice) has been suggested to be an effective way to avoid inbreeding. To investigate whether postcopulatory female choice allows the avoidance of fertilization by close kin, we performed artificial inseminations in a promiscuous bird, the houbara bustard (Chlamydotis undulata undulata). Females were inseminated with a mix of sperm from triads of males, each constituted of a male genetically unrelated to the female, a first cousin and a half-sibling. When counting the number of eggs sired by unrelated males, cousins or half-siblings, we found a significant deviation from the expected random distribution, with more eggs sired by unrelated males. However, offspring sired by cousins, and especially by half-siblings suffered from high prehatching mortality, suggesting that the observed paternity skew towards unrelated males might reflect differential offspring mortality rather than sperm selection. In agreement with this hypothesis, within-triad siring success was similar for the three parental relatedness categories, but the relationship between siring and hatching success differed across categories. In clutches with high hatching success, unrelated males had the highest success while in clutches with high failure rate, half-siblings had the highest success. Offspring sired by half-siblings also suffered from reduced growth rate during the first three months and higher posthatching mortality. Hence, despite substantial fitness costs associated with fertilization by close relatives, females do not seem to select sperm of unrelated males.

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing

An animals' body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host's body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host's genotype.

GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies

Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, there is growing interest in the use of gas chromatography (GC) to investigate the chemical basis of eco-evolutionary interactions. Both GC-MS (mass spectrometry) and FID (flame ionization detection) are commonly used to characterise the chemical composition of biological samples such as skin swabs. The resulting chromatograms comprise peaks that are separated according to their retention times and which represent different substances. Across chromatograms of different samples, homologous substances are expected to elute at similar retention times. However, random and often unavoidable experimental variation introduces noise, making the alignment of homologous peaks challenging, particularly with GC-FID data where mass spectral data are lacking. Here we present GCalignR, a user-friendly R package for aligning GC-FID data based on retention times. The package was developed specifically for ecological and evolutionary studies that seek to investigate similarity patterns across multiple and often highly variable biological samples, for example representing different sexes, age classes or reproductive stages. The package also implements dynamic visualisations to facilitate inspection and fine-tuning of the resulting alignments and can be integrated within a broader workflow in R to facilitate downstream multivariate analyses. We demonstrate an example workflow using empirical data from Antarctic fur seals and explore the impact of user-defined parameter values by calculating alignment error rates for multiple datasets. The resulting alignments had low error rates for most of the explored parameter space and we could also show that GCalignR performed equally well or better than other available software. We hope that GCalignR will help to simplify the processing of chemical datasets and improve the standardization and reproducibility of chemical analyses in studies of animal chemical communication and related fields.

Can house sparrows recognize familiar or kin-related individuals by scent?

In the last decades, higher attention has been paid to olfactory perception in birds. As a consequence, a handful of avian species have been discovered to use olfaction in different contexts. Nevertheless, we still have a very limited knowledge about the use of odor cues in avian social life, particularly, in the case of songbirds. Here, we investigate if female house sparrows Passer domesticus show any preference for the odor of kin and nonkin conspecifics and we also test a possible role of familiarity based on male scent in female choice. We performed the experiment with captive birds twice, during the nonbreeding and breeding seasons. Our results show that female house sparrows strongly avoided the odor of unrelated familiar (UF) males, both in the breeding and nonbreeding seasons. Our results suggest recognition for olfactory stimuli related to familiarity and kinship. We suggest that avoidance for UF males is associated with previous experience in this species. Also, we provided further evidence to the use of olfaction in passerine species by using a new experimental setup.

Insectivorous birds eavesdrop on the pheromones of their prey

Chemical cues play a fundamental role in mate attraction and mate choice. Lepidopteran females, such as the winter moth (Operophtera brumata), emit pheromones to attract males in the reproductive period. However, these chemical cues could also be eavesdropped by predators. To our knowledge, no studies have examined whether birds can detect pheromones of their prey. O. brumata adults are part of the winter diet of some insectivorous tit species, such as the great tit (Parus major) and blue tit (Cyanistes caeruleus). We performed a field experiment aimed to disentangle whether insectivorous birds can exploit the pheromones emitted by their prey for prey location. We placed artificial larvae and a dispenser on branches of Pyrenean oak trees (Quercus pyrenaica). In half of the trees we placed an O. brumata pheromone dispenser and in the other half we placed a control dispenser. We measured the predation rate of birds on artificial larvae. Our results show that more trees had larvae with signs of avian predation when they contained an O. brumata pheromone than when they contained a control dispenser. Furthermore, the proportion of artificial larvae with signs of avian predation was greater in trees that contained the pheromone than in control trees. Our results indicate that insectivorous birds can exploit the pheromones emitted by moth females to attract males, as a method of prey detection. These results highlight the potential use of insectivorous birds in the biological control of insect pests.

Songbird chemical signals reflect uropygial gland androgen sensitivity and predict aggression: implications for the role of the periphery in chemosignaling

Chemical signals can provide useful information to potential mates and rivals. The production mechanisms of these signals are poorly understood in birds, despite emerging evidence that volatile compounds from preen oil may serve as chemosignals. Steroid hormones, including testosterone (T), may influence the production of these signals, yet variation in circulating T only partly accounts for this variation. We hypothesized that odor is a T-mediated signal of an individual's phenotype, regulated in part by androgen sensitivity in the uropygial gland. We quantified natural variation in chemosignals, T, uropygial gland androgen sensitivity, and aggressive behavior in dark-eyed juncos (Junco hyemalis). The interaction between circulating T and androgen receptor transcript abundance significantly correlated with volatile concentrations in male, but not female, preen oil. In both sexes, odorant variables correlated with aggressive response to an intruder. Our results suggest that preen oil volatiles could function as signals of aggressive intent, and, at least in males, may be regulated by local androgen receptor signaling in the uropygial gland. Because these behavioral and chemical traits have been linked with reproductive success, local regulation of androgen sensitivity in the periphery has the potential to be a target of selection in the evolution of avian olfactory signaling.