Exploiting sociogenomics datasets for understanding phenotypic plasticity

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences

Abstract

Determining how biological diversity is generated from the most basic building blocks of life (i.e. the genes) is fundamental to our understanding and sustainable stewardship of the environment and its biodiversity. It is also fundamental for revealing how biological complexity arises and is maintained during the evolution of life.
In a rapidly changing global environment it is not just genetic variation between individuals in a population that will prove essential to their long-term survival; behavioural flexibility is also likely to be crucial to survival, as it permits an organism to respond rapidly to environmental change. Such behavioural plasticity is mediated at the level of the genes; genes respond to environmental cues, changing their expression, resulting in changes in the types and quantities of proteins produced. This affects the behaviour of cells, and ultimately, of the organism as a whole. Our understanding of the fundamental molecular processes which govern interactions between genome and environment is currently limited, especially for wild organisms in ecologically meaningful contexts.
Biology is entering the 'omics era, where data on the broad-scale molecular processes underlying phenotype flexibility, adaptation and resilience can be easily produced. Until recently, these datasets were limited to a few lab-based organisms. Advances in molecular technologies means we can now ask these questions of any organism in natural populations. This potential is of immeasurable benefit to the environmental sciences, where organisms need to be studied in meaningful ecological contexts. However, currently, our ability to generate such 'omics data far out-strips our capacity to analyse and interpret it. This proposal requests modest resources to exploit existing genomic datasets on ecologically important organisms, to address long-standing questions in biology and simultaneously develop informatics skills and resources for ecologists.
Social insects are a powerful model system for testing ecological and evolutionary questions, and understanding how their cooperative societies function may give insights into our own. Social insects also constitute a vast proportion of the insect pollinators on whom we depend for assuring global food security, but who are currently facing global population declines. Within an insect society, all individuals share the same genome, which is translated into many different physical and / or behavioural forms (namely, queen and worker castes). Which caste an individual becomes depends on its environment (e.g. nutritional, social, ecological). In species with small colonies and simple social organisation (e.g. Polistes paper wasps), individuals show incredible ability to switch between castes in rapid response to changes in their environment. They are therefore excellent organisms for understanding how phenotypic diversity and adaptability are generated at the level of the genes. Yet, these simple insect societies remain relatively understudied from a molecular perspective.
We propose to exploit existing datasets to probe the genomic basis of behavioural phenotypes in a range of social insect species. We explore to what extent similar phenotypes are underlain by genes shared across all species ('conserved genes'), or genes that are specific to a particular species ('novel genes'). We will provide a first analysis of the relationship between gene expression and protein production in social insects, allowing us to identify the genes involved in regulating phenotypic change. We will share our learning and results with other researchers and putative stakeholders through a workshop, where the broader value of gene-level research in ecology, conservation and environmental sustainability will be explored. Thus, we hope that this project will nurture innovative and long-term collaborations between computational scientists and ecologist both locally and in the wider scientific community.

Planned Impact

The short-term impact of this proposal will be primarily academic (see Academic Beneficiaries). However, the long-term benefits are likely to influence indirectly a number of sectors, contribute to the UK's economic and intellectual competitiveness and enhance society's health and wellbeing.

Public and private sectors will benefit through the development of computational and informatics skills in the postgraduate and professional work force. This project will contribute to UK economy by developing essential informatic, numeracy and analytical skills for the environmental sector. Equipped with these skills, the PhD student will be a national asset, both for the academic sector (should she choose to carry on in academia), and the non-academic sector, e.g. policy, government, NGOs. Informatics and computational competency, as developed in this project, are essential for ensuring economic growth and future intellectual posterity in the UK, and world sustainability. This fits within NERC's skills framework, to promote and develop mathematical and computational skills among postgraduates and professionals for the environmental sector.

The public, health and medical communities will benefit from an enhanced understanding of how genes and their interaction with the environment produce diversity in the natural world. There are many parallels between animal societies and our own, and social insect research has provided valuable insights into this. For example, social insects resolve conflicts with neighbours and use division of labour to enhance social group performance and cohesion. The general public broadly understands genetic inheritance (e.g. in disease etc), but the interaction between genes and the environment, and how a genomes' responsiveness determines adaptation and plasticity at the whole organism level, remains less well appreciated by the public. Charismatic whole organisms, like bees, wasps and ants, that the public come across in their everyday lives, are tractable study systems that the public can relate to. Public awareness of these animals is relatively high, especially given the recent interest and concern over the decline of bee populations. Our work will serve as an educational springboard for enriching public awareness and understanding of the link from genes to phenotypes.

Policy makers, conservation practitioners and stakeholders will benefit from the enhanced understanding of economically and ecologically important organisms in the molecular processes by which they respond and adapt to their environment. Our project will also help raise awareness of how 'omics approaches may contribute to future evidence-based policy-making that is essential for protecting tomorrow's biodiversity and environmental sustainability. Adaptation occurs at the molecular level through changes in gene expression, protein production, and cell signalling thresholds, which in turn affects an organism's behaviour, life history and ultimately, reproductive success. The importance of understanding genomic patterns and processes in managing and sustainably exploiting ecosystems is not fully appreciated by policy makers and conservation practitioners. In the long-term, the basic science that our collaborations will produce have the potential to influence the choices made by conservation stakeholders in stimulating investment in evidence-based science on the importance of gene-level information in conservation, and developing innovative approaches to understanding species' decline. It will also contribute to generating a model informatics framework for quantifying genomic value of biodiversity. Finally, 'omics projects on non-model organisms always hold some bio-prospecting potential, which may deliver unexpected economic or societal benefits beyond our original, scientific goals.

Publications

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Patalano S (2015) Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. in Proceedings of the National Academy of Sciences of the United States of America

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Sumner S (2014) The importance of genomic novelty in social evolution. in Molecular ecology

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Wyatt, C. (2013) Exploiting sociogenomics datasets to understand social behavior. in iEOS2014 Omics Annual Conference

 
Description This project established bioinformatics pipelines for proteomic and transcriptomics analyses on social insects. It helped reveal the genes under pinning plastic behaviours.
Exploitation Route Pipelines will make other similar studies more feasible for non specialists
Sectors Education

 
Description 25Genomes Sanger/Wellcome Trust I'm a Scientist (winner; 2017). 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Proposer for the genome sequencing of the asian hornet as part of the 25 Genomes Sanger/Wellcome Trust I'm a Scientist competition. Online chats with school children; promotion of hornet via websites. Winner.
Year(s) Of Engagement Activity 2017
URL http://www.sanger.ac.uk/science/collaboration/25-genomes-25-years
 
Description Invited speaker at Cheltenham Science Festival on wasps 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I was one of three invited speakers on a session about why we should appreciate wasps.
The attracted huge media interest, and resulted in a cascade of invitations to give media interviews, write articles, TV appearances.

e.g.
http://metro.co.uk/2016/06/14/heres-what-to-do-if-youre-attacked-by-a-wasp-5944974/
http://www.itv.com/news/2016-06-10/experts-create-a-buzz-as-they-reveal-why-we-should-love-wasps/
http://www.telegraph.co.uk/news/2016/06/10/catch-the-first-wasp-to-avoid-an-attack-by-whole-swarm-scientist/
Year(s) Of Engagement Activity 2016
URL http://www.cheltenhamfestivals.com/science/whats-on/2016/whats-the-point-of-wasps/
 
Description Sumner S & Brock R (2016) In defence of wasps. The Conversation. 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Invited article for The conversation on the ecosystem value of wasps. The article was then re-published multiiple times, globally. eg.
http://www.independent.co.uk/environment/in-defence-of-wasps-why-squashing-them-comes-with-a-sting-in-the-tale-a7144306.html
Year(s) Of Engagement Activity 2016
URL http://theconversation.com/in-defence-of-wasps-why-squashing-them-comes-with-a-sting-in-the-tale-607...