Does developmental plasticity influence speciation?

Lead Research Organisation: University of Southampton
Department Name: School of Ocean and Earth Science

Abstract

Life is a journey. As we grow older, we change. Sometimes we respond in the spur of the moment. Occasionally, an event has long-lasting consequences in spite of any change in circumstance and shapes our outlook far into the future.

This future flexibility, or a lack thereof, also applies to the traits like size and weight that influence our daily risk of death and our reproductive success. Some of these traits retain flexibility throughout life, whereas others can only change in a fixed early window. As humans, we are far more likely to shift weight gain trajectories before six months of age than when older.

Any ability to flexibly adjust traits can boost survival chances in new or changing environments, but also provides the means to innovate and so express new combinations of traits. Flexibility as a means of innovation might promote the divergence of ancestral organisms into new species, but also might not because such flexibility would mean that species can already deal with whatever circumstances they encounter, which would in turn remove the pressure for any innovation to become hardwired into their DNA.

The long timescales over which this hardwiring plays out complicates collection of data. We don't know whether future flexibility or a lack of it is more likely to catalyse change into new species. In this project, we will contribute this increasingly requested data and therefore provide the first evidence if a lifetime of flexibility, or a stubborn refusal to change, influences the emergence of new species.

Planktonic foraminifera are single-celled organisms that live in vast numbers in all the world's oceans. While chemical analysis of their fossil remains has generated a remarkably continuous record of past climate change, each individual also retains a complete record of its size and shape at each stage along its journey through life.

These growth stages can be revealed by state-of-the-art imaging technology, which has sparked a digital revolution in how biologists study life on Earth. To study evolution, we need to study differences among lots of individuals. We need to know how and why these differences change through time. This need to measure lots of individuals means that the current practise of a person pointing and clicking on a computer screen to identify distinct parts is too slow. Computer programmes that provide a faster, more repeatable and less biased way of identifying and analysing such parts are now available, completing the toolkit needed to build big databases.

By bringing together lessons from diverse scientific disciplines, we propose to use the same fossil specimens to collate records of an individual's journey through life and the environment it experienced every step of the way, both of which were changing from day-to-day, millions of years ago.

While the fossil record of planktonic foraminifera provides the necessary timespan and abundance, new computer programmes and imaging technology complete the toolkit jigsaw to investigate for the first time if certain parts of an individual's journey through life are more influential than others in determining the eventual evolutionary destinations of its species.

Our unique, direct link between organism and environment lets us study the dynamic journey through life in the static death of the fossil record. The fundamental limitation to the current ways we study how new species emerge is the lack of repeated samples through time to follow the genesis of novel lifeforms, and explicitly targeting this limitation using state-of-the-art approaches from multiple scientific disciplines means we will deliver a breakthrough in attempts to answer one of the most fundamental of all biological questions: how do differences among individuals make differences among species?

Planned Impact

PISTON takes an unprecedented transdisciplinary approach to investigate how new species form. Species are the foundation of biodiversity. The House of Lords Systematics & Taxonomy review identified biodiversity's critical underpinning of an extensive array of natural environment research ranging from blue skies evolutionary questions, particularly into charismatic "missing links" that reveal how differences among individuals generate differences among species, to applied questions such as ecosystem service provision (i.e., the benefits we derive from natural ecosystems) and global health threat mitigation.

PISTON has been designed as a set of interrelated work packages that will integrate to more than the sum of their individual parts to impact policy, public health, industry and the general public. PISTON investigators are active in all these sectors and will build on and further develop existing relationships and activities.

Members of PISTON have a strong track record of contributing to Intergovernmental Panel on Climate Change (IPCC) reports. Our unprecedented data, focusing on the pivotal link between organism and environment and from the last interval when the world was 2-3 degrees warmer than it is today, can contribute to future IPCC reports in this area. Foster (Contributing Author) and Schmidt (Chapter Lead Author; Co-author of Summary for Policymakers) will co-ordinate impact in this area.

Proprietary versions of WP1 computer vision algorithms have successfully delineated the ball and socket of hip joints as a diagnostic to improve hip replacement therapy, which indicates their potential for wider healthcare benefits for the general public. The PISTON team has considerable experience working with industry (Sinclair with Nikon to develop bespoke biological and medical tools) and the public sector (Nixon on, e.g., automated gait recognition) and will draw on this experience to ensure the open-source PISTON outputs are carefully described, annotated and made accessible in toolbox form to the broadest possible community of end-users.

Taxonomic revisions through refined dating and age control will directly impact foraminiferal specialists in commercial operations, particularly the oil industry. The statistical approaches we propose minimise subjective choices, which adds repeatability and transparency across end-users. We will build on existing networks: Wade (NE/N017900) and Wilson (PI: NE/K007211 and NE/K014137) name PetroStrat, Network Stratigraphic, Shell, RPS Energy and Neftex-Halliburton as Industrial Partners on current awards. Wade will act as Industry Impact Champion (1.5% costed time) to incorporate PISTON data and curate the Mikrotax illustrated online portal. In addition to working with External Advisory Board member Haydon Bailey (Network Stratigraphic) to deliver Industrial impact, we will invite further industrial partners to the second scientific scoping workshop in Year 3 (£2500 budgeted for one UK and one international).

All Research Staff will participate in Public Engagement activities during PISTON in areas of particular appeal to each individual. In particular, we will work with Ellen Dowell, a Science Communicator, interdisciplinary facilitator and current collaborator of PI Ezard (NE/J018163), to run interactive workshops in Einstein's Garden at the Green Man Festival in Year 3 (led by Aze), which we will then run subsequently at exhibitions through applications to the NERC Science Festival, Royal Society Summer School and local science festivals in our regions. These hands-on workshops will let festival-goers see evolution in action and contribute to an animated "flick book" style-film based on the divergence into new species (£3000 budgeted). This film will ensure legacy and impact beyond the festival fence.

Publications

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Description Over the first 18 months of the award, we have recruited a Micropalaeontologist, Chemist and Computer Scientist to the 2 PDRA and 1 RA positions based out of Southampton. In collaboration with Investigators, this team has now developed the high-throughput approaches that allow us to construct the necessary databases required for this complex interdisciplinary project.

Much of this work has been foundational (e.g., RA constructing relational database to hold and query all data; refinement of age models to identify precise dates of divergence; collection of raw sample material from Site 925) and workflow development (e.g., optimal x-ray CT scanning speeds and mounting mechanisms; LA-ICP-MS robotic routes; repeated blasts at different laser strengths). We proposed 7 case studies in the Case for Support and now have unified data sampled and either scanned or queued for the first 2. Preliminary data were presented at the Geological Society of America 2018 Meeting (on 10 of 6300 individuals, statistical tests provided no clarity), with the first presentations of the full multidisciplinary case study data scheduled for ICP Sydney (September 2019). We are on schedule to achieve this and release of a stable beta version of the feature extraction software developed in Computer Science (presentation scheduled for April 10th 2019 at British Machine Vision Association conference on Visual Image Interpretation in Humans and Machines). Development of the Feature Extraction software was the major uncertainty in the timings of the project; it is reassuring that essential 2D features have been collected for machine learning purposes (without prior labelling) and an artificial neural network model (U-Net) trained to predict key internal features for each specimen. The discrepancies between alternative dates from phylogenetic and biostratigraphic methods have been overcome for the current case studies; a shortlist for the next 4 case studies is being investigated.

Over the next 12 months, we plan to publish the first papers from the project (feature extraction software; mathematical modelling of biological changes; also presented at Geological Society of America 2018) and continue to build the momentum of the past six months. With data and protocols now at an appropriately advanced stage of development, we will meet with our External Advisory Board in September to consolidate the move from foundational processes to addressing the environmental objectives.
Exploitation Route Software is currently being developed under proprietary licenses (MATLAB), but is planned to be converted to open-source platforms later.
Sectors Digital/Communication/Information Technologies (including Software),Education,Culture, Heritage, Museums and Collections,Security and Diplomacy

URL https://www.southampton.ac.uk/oes/research/projects/piston-does-developmental-plasticity-influence-speciation.page
 
Description In very early stages of development work with De La Rue for use of high-resolution computed tomographic images to be used in passport and banknote security features. Julian Payne (Creative Director), Andy Sharp (Photographer) and Stuart Rost (Designer) from De La Rue visited in September 2018 to discuss plans, capture images and talk to team members. Unclear of future use at this stage (follow-up meeting in April 2019). Images will become part of a National Trust exhibition on digital nature from May 2019; precise involvement to be clarified and led by University of Bristol component of the award.
First Year Of Impact 2019
Sector Digital/Communication/Information Technologies (including Software),Education,Culture, Heritage, Museums and Collections,Security and Diplomacy
Impact Types Cultural,Societal

 
Description The contribution of plasticity to adaptive divergence: domestication as a model
Amount £473,142 (GBP)
Funding ID NE/S002022/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2021