Relating quantitative variation within a behavior to variation in transcription

The Updated Genome of the Burying Beetle Nicrophorus vespilloides, a Model Species for Evolutionary and Genetic Studies of Parental Care

Understanding the evolution of social behavior requires establishing links between genomes and social phenotypes. High quality genomic resources from a diverse set of social species are required for both broad scale comparative genomic analyses and targeted functional genomic experiments and are therefore crucial for this goal. Here, we report on an updated genome for the burying beetle Nicrophorus vespilloides, an evolutionary and genomic model species for social behavior and parental care. The new assembly used PacBio sequencing reads and long read assemblers. This version of the genome greatly improves the continuity of the assembly and added new annotations, particularly lncRNA's. These updates will allow this resource to continue to be useful for newer functional genomic techniques. This improved assembly will also keep N. vespilloides a valuable comparative genomic resource. Updating genomic resources will continue to allow the field to make discoveries about the evolution of complex phenotypes, such as parental care.

Revisiting the ecology and evolution of burying beetle behavior (Staphylinidae: Silphinae)

Investigating fundamental processes in biology requires the ability to ground broad questions in species-specific natural history. This is particularly true in the study of behavior because an organism's experience of the environment will influence the expression of behavior and the opportunity for selection. Here, we provide a review of the natural history and behavior of burying beetles of the genus Nicrophorus to provide the groundwork for comparative work that showcases their remarkable behavioral and ecological diversity. Burying beetles have long fascinated scientists because of their well-developed parenting behavior, exhibiting extended post-hatching care of offspring that varies extensively within and across taxa. Despite the burgeoning success of burying beetles as a model system for the study of behavioral evolution, there has not been a review of their behavior, ecology, and evolution in over 25 years. To address this gap, we leverage a developing community of researchers who have contributed to a detailed knowledge of burying beetles to highlight the utility of Nicrophorus for investigating the causes and consequences of social and behavioral evolution.

Neurogenomic landscape associated with status-dependent cooperative behaviour

The neurogenomic mechanisms mediating male-male reproductive cooperative behaviours remain unknown. We leveraged extensive transcriptomic and behavioural data on a neotropical bird species (Pipra filicauda) that performs cooperative courtship displays to understand these mechanisms. In this species, the cooperative display is modulated by testosterone, which promotes cooperation in non-territorial birds, but suppresses cooperation in territory holders. We sought to understand the neurogenomic underpinnings of three related traits: social status, cooperative display behaviour and testosterone phenotype. To do this, we profiled gene expression in 10 brain nuclei spanning the social decision-making network (SDMN), and two key endocrine tissues that regulate social behaviour. We associated gene expression with each bird's behavioural and endocrine profile derived from 3 years of repeated measures taken from free-living birds in the Ecuadorian Amazon. We found distinct landscapes of constitutive gene expression were associated with social status, testosterone phenotype and cooperation, reflecting the modular organization and engagement of neuroendocrine tissues. Sex-steroid and neuropeptide signalling appeared to be important in mediating status-specific relationships between testosterone and cooperation, suggesting shared regulatory mechanisms with male aggressive and sexual behaviours. We also identified differentially regulated genes involved in cellular activity and synaptic potentiation, suggesting multiple mechanisms underpin these genomic states. Finally, we identified SDMN-wide gene expression differences between territorial and floater males that could form the basis of 'status-specific' neurophysiological phenotypes, potentially mediated by testosterone and growth hormone. Overall, our findings provide new, systems-level insights into the mechanisms of cooperative behaviour and suggest that differences in neurogenomic state are the basis for individual differences in social behaviour.

Insect homolog of oxytocin/vasopressin associated with parenting of males but not females in a subsocial beetle

Parental care is thought to evolve through modification of behavioral precursors, which predicts that mechanistic changes occur in the genes underlying those traits. The duplicated gene system of oxytocin/vasopressin has been broadly co-opted across vertebrates to influence parenting, from a preduplication ancestral role in water balance. It remains unclear whether co-option of these genes for parenting is limited to vertebrates. Here, we experimentally tested for associations between inotocin gene expression and water balance, parental acceptance of offspring, and active parenting in the subsocial beetle Nicrophorus orbicollis, to test whether this single-copy homolog of the oxytocin/vasopressin system has similarly been co-opted for parental care in a species with elaborate parenting. As expected, inotocin was associated with water balance in both sexes. Inotocin expression increased around sexual maturation in both males and females, although more clearly in males. Finally, inotocin expression was not associated with acceptance of larvae, but was associated with a transition to male but not female parenting. Moreover, level of offspring provisioning behavior and gene expression were positively correlated in males but uncorrelated in females. Our results suggest a broad co-option of this system for parenting that may have existed prior to gene duplication.

takeout gene expression is associated with temporal kin recognition

A key component of parental care is avoiding killing and eating one's own offspring. Many organisms commit infanticide but switch to parental care when their own offspring are expected, known as temporal kin recognition. It is unclear why such types of indirect kin recognition are so common across taxa. One possibility is that temporal kin recognition may evolve through alteration of simple mechanisms, such as co-opting mechanisms that influence the regulation of timing and feeding in other contexts. Here, we determine whether takeout, a gene implicated in coordinating feeding, influences temporal kin recognition in Nicrophorus orbicollis. We found that takeout expression was not associated with non-parental feeding changes resulting from hunger, or a general transition to the full parental care repertoire. However, beetles that accepted and provided care to their offspring had a higher takeout expression than beetles that committed infanticide. Together, these data support the idea that the evolution of temporal kin recognition may be enabled by co-option of mechanisms that integrate feeding behaviour in other contexts.

Gene expression underlying parenting and being parented shows limited plasticity in response to different ambient temperatures

Flexible interactions between parents and offspring are essential for buffering families against variable, unpredictable, and challenging environmental conditions. In the subsocial carrion beetle, Nicrophorus orbicollis, mid-summer temperatures impose steep fitness costs on parents and offspring but do not elicit behavioural plasticity in parents. Here, we ask if plasticity of gene expression underpins this behavioural stability or facilitates independent compensation by larvae. To test this, we characterized gene expression of parents and offspring before and during active parenting under benign (20°C) and stressful (24°C) temperatures to identify genes of parents and offspring associated with thermal response, parenting/being parented, and gene expression plasticity associated with behavioural stability of parental care. The main effects of thermal and social condition each shaped patterns of gene expression in females, males, and larvae. In addition, we implicated 79 genes in females as "buffering" parental behaviour across environments. The majority of these underwent significant changes in expression in actively parenting mothers at the benign temperature, but not at the stressful temperature. Our results suggest that neither genetic programmes for parenting nor their effects on offspring gene expression are fundamentally different under stressful conditions, and that behavioural stability is associated primarily with the maintenance of existing genetic programmes rather than replacement or supplementation. Thus, while selection for compensatory gene expression could expand the range of thermal conditions parents will tolerate, without expanding the toolkit of genes involved selection is unlikely to lead to adaptive changes of function.

Juvenile hormone functions as a metabolic rate accelerator in bumble bees (Bombus terrestris)

Juvenile hormone (JH) is a modulator of many physiological transitions in insects, including molting, metamorphosis, diapause, and reproduction. These processes often include metabolic changes. Here we show that JH accelerates metabolic rate in bumble bees (Bombus terrestris). We reduced JH levels in worker bumble bees by removing their corpora allata (allatectomy) and elevated JH levels in queens through a topical application of JH-III. Natural and high JH levels increased the metabolic rate in both workers and queens and triggered an increased protein turnover rate. Following the treatments, JH also caused an increase in food consumption and a reduction in lipid levels and flight muscle mass of queens, and a reduction in lipids levels in workers. Furthermore, the topical application of a JH analog to queens prior to their diapause caused a decline in their survival of diapause. These findings support the hypothesis that JH acts as a metabolic rate accelerator, initiating a resource shift in bumble bees, and thereby reducing diapause survival in queens. Based on previous studies on JH we suggest that, additional to its behavioral or physiological effects, JH's function as an accelerator of metabolic processes is conserved across different life stages and insect species.

Survey of neurotransmitter receptor gene expression into and out of parental care in the burying beetle Nicrophorus vespilloides

Understanding the genetic influences of traits of nonmodel organisms is crucial to understanding how novel traits arise. Do new traits require new genes or are old genes repurposed? How predictable is this process? Here, we examine this question for gene expression influencing parenting behavior in a beetle, Nicrophorus vespilloides. Parental care, produced from many individual behaviors, should be influenced by changes of expression of multiple genes, and one suggestion is that the genes can be predicted based on knowledge of behavior expected to be precursors to parental care, such as aggression, resource defense, and mating on a resource. Thus, testing gene expression during parental care allows us to test expectations of this "precursor hypothesis" for multiple genes and traits. We tested for changes of the expression of serotonin, octopamine/tyramine, and dopamine receptors, as well as one glutamate receptor, predicting that these gene families would be differentially expressed during social interactions with offspring and associated resource defense. We found that serotonin receptors were strongly associated with social and aggression behavioral transitions. Octopamine receptors produced a complex picture of gene expression over a reproductive cycle. Dopamine was not associated with the behavioral transitions sampled here, while the glutamate receptor was most consistent with a behavioral change of resource defense/aggression. Our results generate new hypotheses, refine candidate lists for further studies, and inform the genetic mechanisms that are co-opted during the evolution of parent-offspring interactions, a likely evolutionary path for many lineages that become fully social. The precursor hypothesis, while not perfect, does provide a starting point for identifying candidate genes.

Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae)

Nicrophorus is a genus of beetles that bury and transform small vertebrate carcasses into a brood ball coated with their oral and anal secretions to prevent decay and that will serve as a food source for their young. Nicrophorus pustulatus is an unusual species with the ability to overtake brood of other burying beetles and whose secretions, unlike other Nicrophorus species, has been reported not to exhibit antimicrobial properties. This work aims to better understand how the presence or absence of a food source influences the expression of genes involved in the feeding process of N. pustulatus. To achieve that, total RNA was extracted from pooled samples of salivary gland tissue from N. pustulatus and sequenced using an Illumina platform. The resulting reads were used to assemble a de novo transcriptome using Trinity. Duplicates with more than 95% similarity were removed to obtain a "unigene" set. Annotation of the unigene set was done using the Trinotate pipeline. Transcript abundance was determined using Kallisto and differential gene expression analysis was performed using edgeR. A total of 651 genes were found to be differentially expressed, including 390 upregulated and 261 downregulated genes in fed insects compared to starved. Several genes upregulated in fed beetles are associated with the insect immune response and detoxification processes with only one transcript encoding for the antimicrobial peptide (AMP) defensin. These results confirm that N. pustulatus does not upregulate the production of genes encoding AMPs during feeding. This study provides a snapshot of the changes in gene expression in the salivary glands of N. pustulatus following feeding while providing a well described transcriptome for the further analysis of this unique burying beetle.

Analysis across diverse fish species highlights no conserved transcriptome signature for proactive behaviour

Background

Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome regulation. In this study, using three fish species (zebrafish; Danio rerio, Atlantic salmon; Salmo salar and European sea bass; Dicentrarchus labrax), we firstly address whether personality-specific mRNA transcript abundances are transferrable across distantly-related fish species and secondly whether a proactive transcriptome signature is conserved across all three species.

Results

Previous zebrafish transcriptome data was used as a foundation to produce a curated list of mRNA transcripts related to animal personality across all three species. mRNA transcript copy numbers for selected gene targets show that differential mRNA transcript abundance in the brain appears to be partially conserved across species relative to personality type. Secondly, we performed RNA-Seq using whole brains from S. salar and D. labrax scoring positively for both behavioural and molecular assays for proactive behaviour. We further enriched this dataset by incorporating a zebrafish brain transcriptome dataset specific to the proactive phenotype. Our results indicate that cross-species molecular signatures related to proactive behaviour are functionally conserved where shared functional pathways suggest that evolutionary convergence may be more important than individual mRNAs.

Conclusions

Our data supports the proposition that highly polygenic clusters of genes, with small additive effects, likely support the underpinning molecular variation related to the animal personalities in the fish used in this study. The polygenic nature of the proactive brain transcriptome across all three species questions the existence of specific molecular signatures for proactive behaviour, at least at the granularity of specific regulatory gene modules, level of genes, gene networks and molecular functions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07317-z.

Developments in Amphibian Parental Care Research: History, Present Advances, and Future Perspectives

Despite rising interest among scientists for over two centuries, parental care behavior has not been as thoroughly studied in amphibians as it has in other taxa. The first reports of amphibian parental care date from the early 18th century, when Maria Sibylla Merian went on a field expedition in Suriname and reported frog metamorphs emerging from their mother's dorsal skin. Reports of this and other parental behaviors in amphibians remained descriptive for decades, often as side notes during expeditions with another purpose. However, since the 1980s, experimental approaches have proliferated, providing detailed knowledge about the adaptive value of observed behaviors. Today, we recognize more than 30 types of parental care in amphibians, but most studies focus on just a few families and have favored anurans over urodeles and caecilians. Here, we provide a synthesis of the last three centuries of parental care research in the three orders comprising the amphibians. We draw attention to the progress from the very first descriptions to the most recent experimental studies, and highlight the importance of natural history observations as a source of new hypotheses and necessary context to interpret experimental findings. We encourage amphibian parental care researchers to diversify their study systems to allow for a more comprehensive perspective of the behaviors that amphibians exhibit. Finally, we uncover knowledge gaps and suggest new avenues of research using a variety of disciplines and approaches that will allow us to better understand the function and evolution of parental care behaviors in this diverse group of animals.

Functional genomics of parental care of insects

Parental care was likely the first step most lineages made towards sociality. However, the molecular mechanisms that generate parental care are not broadly characterized. Insects are important as an evolutionary independent group from classic models of parental care, such as, house mice. They provide an opportunity to test the generality of our understanding. With this review, I survey the functional genomics of parental care of insects, summarize several recent advances in the broader framework for studying and understanding parental care, and finish with suggested priorities for further research. Although there are too few studies to draw definitive conclusions, I argue that natural selection appears to be rewiring existing gene networks to produce parental care, that the epigenetic mechanisms influencing parental care are not well understood, and, as an interesting early consensus, that genes strongly associated with carer/offspring interactions appear biased towards proteins that are secreted. I summarize the studies that have functionally validate candidate genes and highlight the increasing need to perform this work. I finish with arguments for both conceptual and practical changes moving forward. I argue that future work can increase the use of predictive frameworks, broaden its definition of conservation of mechanism to gene networks rather than single genes, and increase the use of more established comparative methods. I further highlight the practical considerations of standardizing analyses and reporting, increasing the sampling of both carers and offspring, better characterizing gene regulatory networks, better characterizing taxonomically restricted genes and any consistent role they have underpinning parental care, and using factorial designs to disentangle the influence of multiple variables on the expression of parental care.

Parental Care, Destabilizing Selection, and the Evolution of Tetrapod Endothermy

Parental care has evolved convergently an extraordinary number of times among tetrapods that reproduce terrestrially, suggesting strong positive selection for this behavior in the terrestrial environment. This review speculates that destabilizing selection on parental care, and especially embryo incubation, drove the convergent evolution of many tetrapod traits, including endothermy.

Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life

Offspring of species with facultative family life are able to live with and without parents (i.e. to adjust to extreme changes in their social environment). While these adjustments are well understood on a phenotypic level, their genetic underpinnings remain surprisingly understudied. Investigating gene expression changes in response to parental absence may elucidate the genetic constraints driving evolutionary transitions between solitary and family life. Here, we manipulated maternal presence to observe gene expression changes in the fat body of juvenile European earwigs, an insect with facultative family life. Because parents typically protect offspring against pathogens, expression changes were recorded in pathogen-free and pathogen-exposed environments. We found that manipulating maternal presence changed the expression of 154 genes, including several metabolism and growth-related genes, and that this change depended on pathogen presence. Specifically, localization and cell transporter genes were downregulated in maternal absence without pathogens but upregulated with pathogens. At least one immunity gene (pathogenesis-related protein 5) was affected by pathogen exposure regardless of maternal presence. Overall, our findings explicate how offspring adjust to parental deprivation on a molecular level and reveal that such adjustments heavily depend on pathogens in the environment. This emphasizes the central role of pathogens in family life evolution.

From phenotype to genotype: the precursor hypothesis predicts genetic influences that facilitate transitions in social behavior

Parental care is expected to be one of the key evolutionary precursors to advanced social behavior. This suggests that there could be common genetic underpinnings to both parental care and sociality. However, little is known of the genetics underlying care. Here, we suggest that ethological predictions of behavioral precursors to care along with a genetic toolkit for behavior provide testable hypotheses and a defined approach to investigating genetics of sociality. We call this the 'precursor hypothesis'.

Changes of gene expression but not cytosine methylation are associated with male parental care reflecting behavioural state, social context and individual flexibility

Behaviour is often a front line response to changing environments. Recent studies show behavioural changes are associated with changes of gene expression; however, these studies have primarily focused on discrete behavioural states. We build on these studies by addressing additional contexts that produce qualitatively similar behavioural changes. We measured levels of gene expression and cytosine methylation, which is hypothesized to regulate the transcriptional architecture of behavioural transitions, within the brain during male parental care of the burying beetle Nicrophorus vespilloides in a factorial design. Male parenting is a suitably plastic behaviour because although male N. vespilloides typically do not provide direct care (i.e. feed offspring) when females are present, levels of feeding by a male equivalent to the female can be induced by removing the female. We examined three different factors: behavioural state (caring versus non-caring), social context (with or without a female mate) and individual flexibility (if a male switched to direct care after his mate was removed). The greatest number of differentially expressed genes were associated with behavioural state, followed by social context and individual flexibility. Cytosine methylation was not associated with changes of gene expression in any of the factors. Our results suggest a hierarchical association between gene expression and the different factors, but that this process is not controlled by cytosine methylation. Our results further suggest that the extent a behaviour is transient plays an underappreciated role in determining its underpinning molecular mechanisms.

Predictable gene expression related to behavioral variation in parenting

Differential gene expression has been associated with transitions between behavioral states for a wide variety of organisms and behaviors. Heterochrony, genetic toolkits, and predictable pathways underlying behavioral transitions have been hypothesized to explain the relationship between transcription and behavioral changes. Less studied is how variation in transcription is related to variation within a behavior, and if the genes that are associated with this variation are predictable. Here, we adopt an evolutionary systems biology perspective to address 2 hypotheses relating differential expression to changes within and between behavior. We predicted fewer genes will be associated with variation within a behavior than with transitions between states, and the genes underlying variation within a behavior will represent a narrower set of biological functions. We tested for associations with parenting variation within a state with a set of genes known a priori to be differentially expressed (DE) between parenting states in the burying beetle Nicrophorus vespilloides. As predicted, we found that far fewer genes are DE related to variation within parenting. Moreover, these were not randomly distributed among categories or pathways in the gene set we tested and primarily involved genes associated with neurotransmission. We suggest that this means candidate genes will be easier to identify for associations within a behavior, as descriptions of behavioral state may include more than a single phenotype.

Back to the roots: the importance of using simple insect societies to understand the molecular basis of complex social life

The evolutionary trajectories toward insect eusociality come in two broad forms. In species like wasps, bees, and ants, the first helpers remained at the nest primarily to help with brood care. In species like aphids and termites, on the other hand, nest defense was initially the primary ecological driving force. To better understand the molecular basis of these two alternative evolutionary trajectories, it is therefore important to study the mechanistic basis of brood care and nest defense behavior. So far, most studies have compared morphologically distinct castes in advanced eusocial species of ants, bees, wasps, and termites. However, the interpretation of such comparisons is limited by multiple confounding factors and the fact that castes are typically fixed and cannot be manipulated at the adult stage. In this review, we argue that conducting molecular studies of brood care and nest defense in simpler, more flexible insect societies may complement studies of advanced eusocial insects and provide avenues toward more functional analyses. We review the available literature and propose candidate study systems for future molecular investigations of brood care and nest defense in social insects.

Juvenile hormone and parental care in subsocial insects: implications for the role of juvenile hormone in the evolution of sociality

Juvenile hormone (JH) has both gonadotropic and non-gonadotropic roles in eusocial insects. There is controversy over whether the non-gonadotropic role is novel, related specifically to social evolution, or is a second conserved role. Study of subsocial insects suggests that when JH is non-gonadotropic, the specific associations of high JH, low vitellogenin, suppressed ovarian development and elevated metabolism may parallel those in workers of eusocial insects. This suggests that a more fundamental understanding of JH in insect biology is required.