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Sexual dimorphism and heightened conditional expression in a sexually selected weapon in the Asian rhinoceros beetle.

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TLDR
RNAseq analysis is used to build on recent work exploring mechanisms in the exaggerated weapons of beetles, by examining patterns of differential gene expression in exaggerated and non‐exaggerated traits in the Asian rhinoceros beetle, Trypoxylus dichotomus, to suggest that sexually dimorphic expression of weaponry involves large‐scale changes in gene expression, relative to other traits, while nutrition‐driven changes inGene expression in these same weapons are less pronounced.
Abstract
Among the most dramatic examples of sexual selection are the weapons used in battles between rival males over access to females. As with ornaments of female choice, the most "exaggerated" sexually selected weapons vary from male to male more widely than other body parts (hypervariability), and their growth tends to be more sensitive to nutritional state or physiological condition compared with growth of other body parts ("heightened" conditional expression). Here, we use RNAseq analysis to build on recent work exploring these mechanisms in the exaggerated weapons of beetles, by examining patterns of differential gene expression in exaggerated (head and thorax horns) and non-exaggerated (wings, genitalia) traits in the Asian rhinoceros beetle, Trypoxylus dichotomus. Our results suggest that sexually dimorphic expression of weaponry involves large-scale changes in gene expression, relative to other traits, while nutrition-driven changes in gene expression in these same weapons are less pronounced. However, although fewer genes overall were differentially expressed in high- vs. low-nutrition individuals, the number of differentially expressed genes varied predictably according to a trait's degree of condition dependence (head horn > thorax horn > wings > genitalia). Finally, we observed a high degree of similarity in direction of effects (vectors) for subsets of differentially expressed genes across both sexually dimorphic and nutritionally responsive growth. Our results are consistent with a common set of mechanisms governing sexual size dimorphism and condition dependence.

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Population differences in the strength of sexual selection match relative weapon size in the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae)†.

TL;DR: Observations of local habitat conditions and breeding ecology point to shifts in the relative abundance of feeding territories as the most likely cause of population differences in selection on male weapon size in this species.
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The development of body and organ shape

TL;DR: This review discusses the methods of characterizing body and organ shape, the developmental programs thought to underlie each, highlight when and how the mechanisms regulating body andorgan shape might overlap, and provides the perspective on future avenues of research.
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Recent advances in understanding the mechanisms of sexually dimorphic plasticity: insights from beetle weapons and future directions.

TL;DR: The advent of next-generation -omics technologies has allowed researchers to decipher the common and diverged mechanisms of sexually dimorphic plasticity and expand investigations beyond the foundation laid by studies utilizing beetle weapons.
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Changes in gene expression during female reproductive development in a color polymorphic insect

TL;DR: The results suggest that long‐term sexual conflict does not only maintain this polymorphism, but has also modulated the evolution of gene expression profiles during color development of these sympatric female morphs.
References
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Journal Article

R: A language and environment for statistical computing.

R Core Team
- 01 Jan 2014 - 
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
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Basic Local Alignment Search Tool

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Controlling the false discovery rate: a practical and powerful approach to multiple testing

TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
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Trimmomatic: a flexible trimmer for Illumina sequence data

TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
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