The genomic signature of social interactions regulating honey bee caste development
Svjetlana Vojvodic, Brian R Johnson, Brock Harpur, Clement Kent, Amro Zayed, Kirk E Anderson, Timothy Linksvayer
doi: http://dx.doi.org/10.1101/012385

Social evolution theory posits the existence of genes expressed in one individual that affect the traits and fitness of social partners. The archetypal example of reproductive altruism, honey bee reproductive caste, involves strict social regulation of larval caste fate by care-giving nurses. However, the contribution of nurse-expressed genes, which are prime socially-acting candidate genes, to the caste developmental program and to caste evolution remains mostly unknown. We experimentally induced new queen production by removing the current colony queen, and we used RNA sequencing to study the gene expression profiles of both developing larvae and their care-giving nurses before and after queen removal. By comparing the gene expression profiles between both queen-destined larvae and their nurses to worker-destined larvae and their nurses in queen-present and queen-absent conditions, we identified larval and nurse genes associated with larval caste development and with queen presence. Of 950 differentially-expressed genes associated with larval caste development, 82% were expressed in larvae and 18% were expressed in nurses. Behavioral and physiological evidence suggests that nurses may specialize in the short term feeding queen- versus worker-destined larvae. Estimated selection coefficients indicated that both nurse and larval genes associated with caste are rapidly evolving, especially those genes associated with worker development. Of the 1863 differentially-expressed genes associated with queen presence, 90% were expressed in nurses. Altogether, our results suggest that socially-acting genes play important roles in both the expression and evolution of socially-influenced traits like caste.

Evaluating intra- and inter-individual variation in the human placental transcriptome
David A Hughes, Martin Kircher, Zhisong He, Song Guo, Genevieve L Fairbrother, Carlos S Moreno, Philipp Khaitovich, Mark Stoneking
doi: http://dx.doi.org/10.1101/012468

Background: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. Results: We estimate that on average, 33.2%, 58.9% and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling and metabolism. Many biological traits demonstrated correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome (65% of expressed genes) exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection (26%), directional selection (4.9%), or diversifying selection (4.8%). Conclusion: We apportion placental gene expression variation into individual, population and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

Local and systemic gene expression responses to a white syndrome-like disease in a reef building coral, Acropora hyacinthus.

Rachel M Wright, Galina V Aglyamova, Eli Meyer, Mikhail V Matz
doi: http://dx.doi.org/10.1101/012211

Background Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting white syndrome-like symptoms, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals: visibly affected and apparently healthy tissues. Results Tag-based RNA-Seq followed by weighted gene co-expression network analysis identified groups of co-regulated differentially expressed genes between all disease states (diseased, ahead of the lesion, and healthy). Most of the differentially expressed genes were found between tissues at the lesions and asymptomatic (healthy and ahead of the lesion) tissues. These genes were related to innate immunity, oxidative stress responses, lipid metabolism, and calcification. Network analysis also revealed groups of genes regulated specifically in the tissues from diseased colonies that were not yet showing obvious symptoms of disease, indicating a systemic response to infection. Conclusions These observations suggest that tissues ahead of the lesion of disease progression exist in a transitional state between health and lesion appearance. Alternatively, these gene expression profiles capture physiological differences between colonies with varying disease susceptibilities.