Developmental decoupling of alternative phenotypes: insights from the transcriptomes of horn-polyphenic beetles
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PROVIDER: PRJNA131045 | ENA |
REPOSITORIES: ENA
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Project description:Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the metaphor of developmental “decoupling,” where alternate morphs result from evolutionarily independent developmental pathways. We test this assumption through a microarray study that explores differences in gene expression between alternate morphs relative to differences between sexes, a classic example of developmental decoupling. We then examine whether morph-biased genes are less conserved, relative to morph-shared genes, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with spectacular sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are somewhat developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined. We compared gene expression in three focal epidermal tissues (head, prothorax, legs) relative to a "control" tissue (dorsal abdominal epidermis) without any outgrowths. We also surveyed gene expression in the brain, relative to ganglionic neural tissue. We compared such patterns of gene expression between two male morphs (horned, fighter and hornless, sneaker males) and between males and females. We focused our array analyses (N = 48 arrays) on Onthophagus taurus (the species for which the array was designed), but also ran 19 arrays on thoracic tissue of Onthophagus nigriventris, a species which expresses thoracic horns as adults (O. taurus expresses head horns). Finally, we included a small subset of arrays (N = 4) directly hybridizing head epidermis tissue of O. taurus male morphs to validate our overall estimates of morph-biased expression. For more detail, refer to Snell-Rood et al. 2010, Evolution.
2010-09-15 | E-GEOD-23425 | biostudies-arrayexpress
Project description:Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the metaphor of developmental “decoupling,” where alternate morphs result from evolutionarily independent developmental pathways. We test this assumption through a microarray study that explores differences in gene expression between alternate morphs relative to differences between sexes, a classic example of developmental decoupling. We then examine whether morph-biased genes are less conserved, relative to morph-shared genes, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with spectacular sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are somewhat developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined.
2010-09-15 | GSE23425 | GEO
Project description:Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the hypothesis of developmental decoupling, where alternate morphs result from evolutionarily independent developmental pathways. We address this assumption through a microarray study that tests whether differences in gene expression between alternate morphs are as divergent as those between sexes, a classic example of developmental decoupling. We then examine whether genes with morph-biased expression are less conserved than genes with shared expression between morphs, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with impressive sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are to some extent developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined.
| S-EPMC3010270 | biostudies-literature
Project description:This series examines gene expression patterns in the head horns, thoracic horns, and legs of the horned beetles Onthophagus taurus. Expression in each of these tissues was compared to that in common non-appendage reference - abdominal epithelium. The series consists of three pair-wise comparisons: head horn versus abdominal epithelium, thoracic horn versus abdominal epithelium and legs versus abdominal epithelium. Each tissue sample was obtained by pooling tissue dissected from four pupae. Samples compared on the same array were derived from tissues dissected from the same four animals. Five independent biological replicates were performed for each comparison with dye flips (three in one direction and two in the opposite direction).
2010-05-18 | E-GEOD-13616 | biostudies-arrayexpress
Project description:The general morphology of the insect head has remained relatively unchanged through more than 400 million years of evolution. Yet throughout this period this same region has also become a hotspot for evolutionary novelty, yielding structures such as the eyestalks of stalk-eyed flies or the cephalic horns of dung beetles. How novelty can be integrated within ancient complex traits without disrupting the function and formation of that trait is a foundational, yet largely unresolved question in developmental and evolutionary biology. Here, we approached this question by performing unique, head compartment specific RNAseq using the heads of Onthophagus taurus beetles, which bear impressive posterior horns in males. We sequenced the transcriptomes in horned males and hornless females from six distinct head compartments covering two major axes of patterning: anterior to posterior (AP) and medial to lateral (ML). Our results provide evidence of differential compartmentalization of the head along both AP and ML axes, and reveal striking parallels between morphological and transcriptomic complexity – that is, head regions with more complex morphologies, such as the posterior region, are more transcriptionally intricate compared to morphologically homogenous regions, such as the anterior of the head. Our findings support the hypothesis that the integration of novel traits within ancestral trait complexes may require the recruitment of additional genes and pathways into the networks instructing within and among compartment development. However, sexual dimorphism in posterior horn development was not paralleled by a corresponding sexual dimorphism in transcriptional complexity, instead hornless females exhibited approximately the same diversity of differentially expressed genes across posterior head compartments than did horn-bearing males.
2020-01-01 | GSE136677 | GEO
Project description:The dorsal horn of the spinal cord transforms incoming somatosensory information and transmits it supraspinally to generate sensory perception, including pain and itch. Recent research using mouse Cre-driver lines has implicated specific populations of dorsal horn neurons in the transmission of different types of pain. In parallel, human genome-wide association studies (GWAS) have identified dozens of loci confidently associated with the genetic predisposition to chronic pain. The ability to connect controlled experiments in rodent models with human genetic studies could provide a platform for translational research, but the cell type heterogeneity of the dorsal horn and the complex genetic architecture of chronic pain have created challenges in bridging that gap. Here, we apply a variety of single cell genomic technologies and a comparative genomic analysis to identify conserved dorsal horn neuron subtypes whose open chromatin regions show enrichment for genetic variants associated with human chronic pain phenotypes. To achieve this, we first use single nucleus RNA-Seq and fluorescence in situ hybridization in Rhesus macaque to create a more detailed map of primate dorsal horn neuron subtypes. These were integrated with publicly available human and mouse single nucleus RNA-Seq datasets to create a multi-modal cross species atlas. Then, for the mouse dorsal horn, we combined single nucleus RNA-Seq, spatial transcriptomics, and single nucleus ATAC-Seq to infer spatial and epigenomic profiles of conserved dorsal horn neuron subtypes. Finally, we compared our conserved cell-type open chromatin resource to chronic pain GWAS and found that open chromatin regions of specific dorsal horn neuron subtypes showed enrichment for a variety of human chronic pain phenotypes. Our results provide a foundation to further explore how conserved dorsal horn neuron subtypes influence the transmission of pain signals.
2024-08-01 | GSE253951 | GEO
Project description:The dorsal horn of the spinal cord transforms incoming somatosensory information and transmits it supraspinally to generate sensory perception, including pain and itch. Recent research using mouse Cre-driver lines has implicated specific populations of dorsal horn neurons in the transmission of different types of pain. In parallel, human genome-wide association studies (GWAS) have identified dozens of loci confidently associated with the genetic predisposition to chronic pain. The ability to connect controlled experiments in rodent models with human genetic studies could provide a platform for translational research, but the cell type heterogeneity of the dorsal horn and the complex genetic architecture of chronic pain have created challenges in bridging that gap. Here, we apply a variety of single cell genomic technologies and a comparative genomic analysis to identify conserved dorsal horn neuron subtypes whose open chromatin regions show enrichment for genetic variants associated with human chronic pain phenotypes. To achieve this, we first use single nucleus RNA-Seq and fluorescence in situ hybridization in Rhesus macaque to create a more detailed map of primate dorsal horn neuron subtypes. These were integrated with publicly available human and mouse single nucleus RNA-Seq datasets to create a multi-modal cross species atlas. Then, for the mouse dorsal horn, we combined single nucleus RNA-Seq, spatial transcriptomics, and single nucleus ATAC-Seq to infer spatial and epigenomic profiles of conserved dorsal horn neuron subtypes. Finally, we compared our conserved cell-type open chromatin resource to chronic pain GWAS and found that open chromatin regions of specific dorsal horn neuron subtypes showed enrichment for a variety of human chronic pain phenotypes. Our results provide a foundation to further explore how conserved dorsal horn neuron subtypes influence the transmission of pain signals.
2024-08-01 | GSE253953 | GEO
Project description:The dorsal horn of the spinal cord transforms incoming somatosensory information and transmits it supraspinally to generate sensory perception, including pain and itch. Recent research using mouse Cre-driver lines has implicated specific populations of dorsal horn neurons in the transmission of different types of pain. In parallel, human genome-wide association studies (GWAS) have identified dozens of loci confidently associated with the genetic predisposition to chronic pain. The ability to connect controlled experiments in rodent models with human genetic studies could provide a platform for translational research, but the cell type heterogeneity of the dorsal horn and the complex genetic architecture of chronic pain have created challenges in bridging that gap. Here, we apply a variety of single cell genomic technologies and a comparative genomic analysis to identify conserved dorsal horn neuron subtypes whose open chromatin regions show enrichment for genetic variants associated with human chronic pain phenotypes. To achieve this, we first use single nucleus RNA-Seq and fluorescence in situ hybridization in Rhesus macaque to create a more detailed map of primate dorsal horn neuron subtypes. These were integrated with publicly available human and mouse single nucleus RNA-Seq datasets to create a multi-modal cross species atlas. Then, for the mouse dorsal horn, we combined single nucleus RNA-Seq, spatial transcriptomics, and single nucleus ATAC-Seq to infer spatial and epigenomic profiles of conserved dorsal horn neuron subtypes. Finally, we compared our conserved cell-type open chromatin resource to chronic pain GWAS and found that open chromatin regions of specific dorsal horn neuron subtypes showed enrichment for a variety of human chronic pain phenotypes. Our results provide a foundation to further explore how conserved dorsal horn neuron subtypes influence the transmission of pain signals.
2024-08-01 | GSE253952 | GEO
Project description:We report the temporal dynamics of differential gene expression between primed and unprimed beetles infected with the entomopathogen Bt
2017-02-28 | GSE95387 | GEO