Developmental regulation and evolution of scaling: novel insights through the study of Onthophagus beetles

Histone deacetylases regulate organ-specific growth in a horned beetle

BACKGROUND

Nutrient availability is among the most widespread means by which environmental variability affects developmental outcomes. Because almost all cells within an individual organism share the same genome, structure-specific growth responses must result from changes in gene regulation. Earlier work suggested that histone deacetylases (HDACs) may serve as epigenetic regulators linking nutritional conditions to trait-specific development. Here we expand on this work by assessing the function of diverse HDACs in the structure-specific growth of both sex-shared and sex-specific traits including evolutionarily novel structures in the horned dung beetle Onthophagus taurus.

RESULTS

We identified five HDAC members whose downregulation yielded highly variable mortality depending on which HDAC member was targeted. We then show that HDAC1, 3, and 4 operate in both a gene- and trait-specific manner in the regulation of nutrition-responsiveness of appendage size and shape. Specifically, HDAC 1, 3, or 4 knockdown diminished wing size similarly while leg development was differentially affected by RNAi targeting HDAC3 and HDAC4. In addition, depletion of HDAC3 transcript resulted in a more rounded shape of genitalia at the pupal stage and decreased the length of adult aedeagus across all body sizes. Most importantly, we find that HDAC3 and HDAC4 pattern the morphology and regulate the scaling of evolutionarily novel head and thoracic horns as a function of nutritional variation.

CONCLUSION

Collectively, our results suggest that both functional overlap and division of labor among HDAC members contribute to morphological diversification of both conventional and recently evolved appendages. More generally, our work raises the possibility that HDAC-mediated scaling relationships and their evolution may underpin morphological diversification within and across insect species broadly.

Utilizing geometric morphometrics to investigate gene function during organ growth: Insights through the study of beetle horn shape allometry

Static allometry is a major component of morphological variation. Much of the literature on the development of allometry investigates how functional perturbations of diverse pathways affect the relationship between trait size and body size. Often, this is done with the explicit objective to identify developmental mechanisms that enable the sensing of organ size and the regulation of relative growth. However, changes in relative trait size can also be brought about by a range of other distinctly different developmental processes, such as changes in patterning or tissue folding, yet standard univariate biometric approaches are usually unable to distinguish among alternative explanations. Here, we utilize geometric morphometrics to investigate the degree to which functional genetic manipulations known to affect the size of dung beetle horns also recapitulate the effect of horn shape allometry. We reasoned that the knockdown phenotypes of pathways governing relative growth should closely resemble shape variation induced by natural allometric variation. In contrast, we predicted that if genes primarily affect alternative developmental processes, knockdown effects should align poorly with shape allometry. We find that the knockdown effects of several genes (e.g., doublesex, Foxo) indeed closely aligned with shape allometry, indicating that their corresponding pathways may indeed function primarily in the regulation of relative trait growth. In contrast, other knockdown effects (e.g., Distal-less, dachs) failed to align with allometry, implicating these pathways in potentially scaling-independent processes. Our findings moderate the interpretation of studies focusing on trait length and highlight the usefulness of multivariate approaches to study allometry and phenotypic plasticity.

Genetic variation of morphological scaling in Drosophila melanogaster

Morphological scaling relationships between the sizes of individual traits and the body captures the characteristic shape of a species, and their evolution is the primary mechanism of morphological diversification. However, we have almost no knowledge of the genetic variation of scaling, which is critical if we are to understand how scaling evolves. Here we explore the genetics of population scaling relationships (scaling relationships fit to multiple genetically-distinct individuals in a population) by describing the distribution of individual scaling relationships (genotype-specific scaling relationships that are unseen or cryptic). These individual scaling relationships harbor the genetic variation in the developmental mechanisms that regulate trait growth relative to body growth, and theoretical studies suggest that their distribution dictates how the population scaling relationship will respond to selection. Using variation in nutrition to generate size variation within 197 isogenic lineages of Drosophila melanogaster, we reveal extensive variation in the slopes of the wing-body and leg-body individual scaling relationships among genotypes. This variation reflects variation in the nutritionally-induced size plasticity of the wing, leg, and body. Surprisingly, we find that variation in the slope of individual scaling relationships primarily results from variation in nutritionally-induced plasticity of body size, not leg or wing size. These data allow us to predict how different selection regimes affect scaling in Drosophila, and is the first step in identifying the genetic targets of such selection. More generally, our approach provides a framework for understanding the genetic variation of scaling, an important prerequisite to explaining how selection changes scaling and morphology.

Developmental bias in the evolution and plasticity of beetle horn shape

The degree to which developmental systems bias the phenotypic effects of environmental and genetic variation, and how these biases affect evolution, is subject to much debate. Here, we assess whether developmental variability in beetle horn shape aligns with the phenotypic effects of plasticity and evolutionary divergence, yielding three salient results. First, we find that most pathways previously shown to regulate horn length also affect shape. Second, we find that the phenotypic effects of manipulating divergent developmental pathways are correlated with each other as well as multivariate fluctuating asymmetry-a measure of developmental variability. Third, these effects further aligned with thermal plasticity, population differences and macroevolutionary divergence between sister taxa and more distantly related species. Collectively, our results support the hypothesis that changes in horn shape-whether brought about by environmentally plastic responses, functional manipulations or evolutionary divergences-converge along 'developmental lines of least resistance', i.e. are biased by the developmental system underpinning horn shape.

Continuous phenotypic modulation explains male horn allometry in three dung beetle species

Many dung beetle species show male horn polyphenism, the ability of males to develop into distinct phenotypes without intermediate forms as a response to the larval growth environment. While males with long (majors) and rudimentary (minor) horn have been widely reported in literature, little is known about the existence of individuals with intermediate horn length. Here we investigate the occurrence of intermediates in natural populations of three dung beetle species (Onthophagus furcatus, Copris lunaris and C. hispanus). We analysed the body size-horn length relationship using linear, exponential, and sigmoidal models with different error structures. We inferred the number of individuals in the minor, intermediate, and major groups by combining changepoint analysis and simulation from fitted allometric models. The sigmoidal equation was a better descriptor of the body size-horn length relationship than linear or exponential equations in all the three studied species. Our results indicated that the number of intermediates equals or exceeds the number of minor and major males. This work provides evidence that, at least in the studied species, males with intermediate horn length exist in natural populations. For similar cases we therefore suggest that continuous phenotypic modulation rather than discrete polyphenism can explain variation in male horn allometry.

The growth factor BMP11 is required for the development and evolution of a male exaggerated weapon and its associated fighting behavior in a water strider

Exaggerated sexually selected traits, often carried by males, are characterized by the evolution of hyperallometry, resulting in their disproportionate growth relative to the rest of the body among individuals of the same population. While the evolution of allometry has attracted much attention for centuries, our understanding of the developmental genetic mechanisms underlying its emergence remains fragmented. Here we conduct comparative transcriptomics of the legs followed by an RNA interference (RNAi) screen to identify genes that play a role in the hyperallometric growth of the third legs in the males of the water strider Microvelia longipes. We demonstrate that a broadly expressed growth factor, Bone Morphogenetic Protein 11 (BMP11, also known as Growth Differentiation Factor 11), regulates leg allometries through increasing the allometric slope and mean body size in males. In contrast, BMP11 RNAi reduced mean body size but did not affect slope either in the females of M. longipes or in the males and females of other closely related Microvelia species. Furthermore, our data show that a tissue-specific factor, Ultrabithorax (Ubx), increases intercept without affecting mean body size. This indicates a genetic correlation between mean body size and variation in allometric slope, but not intercept. Strikingly, males treated with BMP11 RNAi exhibited a severe reduction in fighting frequency compared to both controls and Ubx RNAi-treated males. Therefore, male body size, the exaggerated weapon, and the intense fighting behavior associated with it are genetically correlated in M. longipes. Our results support a possible role of pleiotropy in the evolution of allometric slope.

Evolution of multivariate wing allometry in schizophoran flies (Diptera: Schizophora)

The proximate and ultimate mechanisms underlying scaling relationships as well as their evolutionary consequences remain an enigmatic issue in evolutionary biology. Here, I investigate the evolution of wing allometries in the Schizophora, a group of higher Diptera that radiated about 65 million years ago, by studying static allometries in five species using multivariate approaches. Despite the vast ecological diversity observed in contemporary members of the Schizophora and independent evolutionary histories throughout most of the Cenozoic, size-related changes represent a major contributor to overall variation in wing shape, both within and among species. Static allometries differ between species and sexes, yet multivariate allometries are correlated across species, suggesting a shared developmental programme underlying size-dependent phenotypic plasticity. Static allometries within species also correlate with evolutionary divergence across 33 different families (belonging to 11 of 13 superfamilies) of the Schizophora. This again points towards a general developmental, genetic or evolutionary mechanism that canalizes or maintains the covariation between shape and size in spite of rapid ecological and morphological diversification during the Cenozoic. I discuss the putative roles of developmental constraints and natural selection in the evolution of wing allometry in the Schizophora.

Integrating evolutionarily novel horns within the deeply conserved insect head

BACKGROUND

How novel traits integrate within ancient trait complexes without compromising ancestral functions is a foundational challenge in evo-devo. The insect head represents an ancient body region patterned by a deeply conserved developmental genetic network, yet at the same time constitutes a hot spot for morphological innovation. However, the mechanisms that facilitate the repeated emergence, integration, and diversification of morphological novelties within this body region are virtually unknown. Using horned Onthophagus beetles, we investigated the mechanisms that instruct the development of the dorsal adult head and the formation and integration of head horns, one of the most elaborate classes of secondary sexual weapons in the animal kingdom.

RESULTS

Using region-specific RNAseq and gene knockdowns, we (i) show that the head is compartmentalized along multiple axes, (ii) identify striking parallels between morphological and transcriptional complexity across regions, yet (iii) fail to identify a horn-forming gene module. Instead, (iv) our results support that sex-biased regulation of a shared transcriptional repertoire underpins the formation of horned and hornless heads. Furthermore, (v) we show that embryonic head patterning genes frequently maintain expression within the dorsal head well into late post-embryonic development, thereby possibly facilitating the repurposing of such genes within novel developmental contexts. Lastly, (vi) we identify novel functions for several genes including three embryonic head patterning genes in the integration of both posterior and anterior head horns.

CONCLUSIONS

Our results illuminate how the adult insect head is patterned and suggest mechanisms capable of integrating novel traits within ancient trait complexes in a sex- and species-specific manner. More generally, our work underscores how significant morphological innovation in developmental evolution need not require the recruitment of new genes, pathways, or gene networks but instead may be scaffolded by pre-existing developmental machinery.

Serotonin differentially affects morph-specific behavior in divergent populations of a horned beetle

Associations between animal weapons and corresponding aggressive behaviors are among the most characteristic features of species, yet at the same time their co-expression is itself often strongly dependent on context, such as male condition or population ecology. Yet the mechanisms that modulate associations between aggression, morphology, and biological context remain poorly understood. The biogenic amine serotonin has been shown to regulate a wide range of aggressive and morph-specific behaviors in diverse insect species. However, the extent to which serotonin may coordinate the expression of behavior with morphology across biological contexts remains unclear. In this study, we pharmacologically increased serotonin biosynthesis in males of the polyphenic beetle, Onthophagus taurus, and assessed how this manipulation affects both aggressive and non-aggressive behaviors in alternative fighter and sneaker morphs, as well as in males derived from two rapidly diverging populations characterized by disparate levels of competition for mates. We find (i) that enhancing serotonin biosynthesis increases most measures of aggressive behaviors, but influences only a subset of nonaggressive behaviors, (ii) that similar serotonin-mediated behavioral changes manifest in both morphs within populations more often than just a single morph, and (iii) that males derived from the two focal populations have diverged in their behavioral responsiveness to serotonin up-regulation. Collectively, our study suggests that serotonin signaling plays a critical role in the regulation of male behavior and its evolution, including in the context of rapid, short-term population divergence.

Evolution of, and via, Developmental Plasticity: Insights through the Study of Scaling Relationships

Scaling relationships emerge from differential growth of body parts relative to each other. As such, scaling relationships are at least in part the product of developmental plasticity. While some of the developmental genetic mechanisms underlying scaling relationships are starting to be elucidated, how these mechanisms evolve and give rise to the enormous diversity of allometric scaling observed in nature is less understood. Furthermore, developmental plasticity has itself been proposed as a mechanism that facilitates adaptation and diversification, yet its role in the developmental evolution of scaling relationships remains largely unknown. In this review, we first explore how the mechanisms of scaling relationships have evolved. We primarily focus on insect development and review how pathway components and pathway interactions have evolved across taxa to regulate scaling relationships across diverse traits. We then discuss the potential role of developmental plasticity in the evolution of scaling relationships. Specifically, we address the potential role of allometric plasticity and cryptic genetic variation in allometry in facilitating divergence via genetic accommodation. Collectively, in this article, we aim to bring together two aspects of developmental plasticity: the mechanistic underpinnings of scaling relationships and their evolution, and the potential role that plasticity plays in the evolutionary diversification of scaling relationships.

Transcriptomic changes during caste development through social interactions in the termite Zootermopsis nevadensis

One of the most striking examples of phenotypic plasticity is the different phenotypes (i.e., castes) within a same nest of social insects. Castes usually derive from a single genotype initially by receiving social cues among individuals during development. Specific gene expression changes may be involved in caste differentiation, and thus, the regulatory mechanism of these changes should be clarified in order to understand social maintenance and evolution. The damp-wood termite Zootermopsis nevadensis is one of the most important model termite species, due to not only the availability of genomic, transcriptomic, and epigenomic information but also evidence that soldier- and worker-destined individuals can be identified in natural conditions. Given that the nutritional intakes via social interactions are crucial for caste differentiation in this species, there is a possibility that transcriptomic changes are influenced by the nutritional difference among these individuals. Here, whole body RNA-seq analysis of 3rd-instar larvae with biological replications and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were conducted. We found the drastic expression differences during caste developments between soldier- and worker-destined individuals. The results indicated that there are several key signaling pathways responsible for caste formations, which are involved in developments and social interactions. Particularly, the nutritional sensitive signaling was upregulated in soldier-destined individuals, while some metabolic pathways were identified in worker-destined individuals. These bioinformatic data obtained should be utilized to examine the molecular mechanisms of caste determination in social insects.

The (ongoing) problem of relative growth

Differential growth, the phenomenon where parts of the body grow at different rates, is necessary to generate the complex morphologies of most multicellular organisms. Despite this central importance, how differential growth is regulated remains largely unknown. Recent discoveries, particularly in insects, have started to uncover the molecular-genetic and physiological mechanisms that coordinate growth among different tissues throughout the body and regulate relative growth. These discoveries suggest that growth is coordinated by a network of signals that emanate from growing tissues and central endocrine organs. Here we review these findings and discuss their implications for understanding the regulation of relative growth and the evolution of morphology.

Asymmetric interactions between doublesex and tissue- and sex-specific target genes mediate sexual dimorphism in beetles

Sexual dimorphisms fuel significant intraspecific variation and evolutionary diversification. Yet the developmental-genetic mechanisms underlying sex-specific development remain poorly understood. Here, we focus on the conserved sex-determination gene doublesex (dsx) and the mechanisms by which it mediates sex-specific development in a horned beetle species by combining systemic dsx knockdown, high-throughput sequencing of diverse tissues and a genome-wide analysis of Dsx-binding sites. We find that Dsx regulates sex-biased expression predominantly in males, that Dsx's target repertoires are highly sex- and tissue-specific and that Dsx can exercise its regulatory role via two distinct mechanisms: as a sex-specific modulator by regulating strictly sex-specific targets, or as a switch by regulating the same genes in males and females in opposite directions. More generally, our results suggest Dsx can rapidly acquire new target gene repertoires to accommodate evolutionarily novel traits, evidenced by the large and unique repertoire identified in head horns, a recent morphological innovation.