From egg-laying to live-bearing: Unravelling the genetics of a major evolutionary transition

Lead Research Organisation: University of Glasgow
Department Name: College of Medical, Veterinary &Life Sci

Abstract

The process of reproduction is incredibly complex. From attracting the right mate, being genetically compatibility, and incubating a baby, there are many steps that must all work in concert. Each step is under stark natural selection because if unsuccessful then an individual's genes are not passed to the next generation. Tinkering with this process sees like tempting a Darwinian dead-end. So how can major, transformative changes in reproductive process happen during evolution?
The evolution of live-bearing (viviparity) from egg-laying (oviparity) in animals is an example of such a transformation, which has profound and wide-ranging consequences for a species. Yet live-bearing has evolved many times independently, in fishes, amphibians, early in the origin of therian mammals, and more than 100 times in reptiles.
Usually there is no opportunity to watch how changes from egg-laying to live-bearing happen because they occurred deep in the evolutionary past. Lizards are are an exception as some species have evolved live-bearing quite recently. Most species are completely either egg-laying or live-bearing: eggs are incubated for a relatively short time and then laid with a thick, calcified shell (oviparity) or babies are nurtured in the uterus until fully developed and then born covered with only a thin membrane (viviparity). The genetic basis of live-bearing is not known in any vertebrate.
The recent revolution in genomic sequencing technologies is allowing evolutionary biologists to address questions never before possible. One of these is the extent to which similar, complex adaptations have evolved from the same genetic bases across lineages. This issue is pivotal to understand how, and at what rate, natural selection shapes genomes so animals can adapt to their environment. Despite the 300 million years of evolutionary distance between reptiles and mammals, the basic structures, physiology, and molecular mechanisms of pregnancy are comparable between lizards and mammals, so the answer is relevant beyond just reptiles. The first step is to identify the genetic basis of live-bearing in a single species.
Europe's common lizard (Zootoca vivipara) has the remarkable attribute of both reproductive modes within one species. The reproductive modes are genetically fixed and egg-layer and live-bearers are found in different geographic areas, except in one part of the Alps where oviparous and viviparous individuals come into contact and interbreed. This hybrid zone offers a unique and amazing 'natural experiment' where the genetics of reproductive traits can be studied.
This project will be the first to identify the genetic mechanisms of reproductive mode To do so we will focus on the common lizard. Our objectives are to:
(1) Characterise the genetic basis of reproductive mode and its traits shown by mothers, such as eggshell structure and the developmental stage at which embryos are laid as eggs or born as fully developed neonates. This is done by an experiment in the hybrid zone;
(2) Quantify how oviparous individuals' and viviparous individuals' genomes mix through hybridization, and locate the genetic variations that are under strong natural selection in either reproductive mode;
(3) Resolve the phylogenetic tree of the entire species complex and determine the timing and order of changes in reproductive style. Surprisingly, there is some evidence that reversals back to oviparity might occur in common lizards, but the evidence has not been well supported. Our genomic experiments will identify if multiple independent origins of viviparity, or a reversal to oviparity, have occurred in the species' history. We will identify whether those transitions involve the same genetic mechanism each time.
This research will examine for the first time the genetic architecture of reproductive mode, with direct relevance to biodiversity adaptation and reproductive biology.

Planned Impact

BENEFICIARIES OF THIS RESEARCH
Academia: A major research goal of evolutionary biology is to link adaptive phenotypes with the breadth of genetic variation found in nature. This research will contribute new knowledge to the question of how different reproductive modes evolve and will aim to significantly advance our understanding of evolution. The results of this research will be relevant and beneficial to the academic community in the UK and internationally.
Training: 'Omics skills enhance the economic and scientific competitiveness of UK researchers.
Biodiversity conservation: Biodiversity conservation science as a field will benefit from this research, which is the first genomic analysis of the common lizard and will include information about an important wild population.
Agriculture: The eggshell is a prominent model for biomineralization because of its importance for avian reproduction and the commercial sectors' interest in improving eggshell quality and safety.
General public: Many members of the general public have a fascination about biodiversity, herpetology, and animal reproductive biology and so will be very interested in the results of this research. Glasgow in particular is home to an engaged citizenship with regard to natural history, herpetology, and science, both for local groups (e.g. Glasgow Natural History, Glasgow Herpetology) and regional groups with local chapters (e.g. National Trust for Scotland, FrogLife, British Herpetology Society).
Corporate collaborators: Chivas Brothers Ltd in Dumbarton is a nearby business with global trade links, and which is committed to 'preserving the environment 'and 'promoting sustainable agriculture'. They recognise the value of this research project for UK biodiversity and conservation and are keen to affiliate with the research team (especially MB).
Given the early stage of this research project, the full societal and economic benefits of this research project may not come clear until later in the research programme.

MEANS OF BENEFITING
The economic and societal impacts of our research project will reach out to, or draw from, the beneficiaries in the following manners:
Influencing Public Policy: Conservation priorities, legislation and policy will be impacted by the genetic, evolutionary and ecological results. The common lizard is a UK Biodiversity Action Plan Priority (BAP) and the UK has international obligations for protecting the species (http://jncc.defra.gov.uk/); UK BAP and Amphibian and Reptile Conservation (ARC) both propose that research at the landscape scale is required for this species. The current project will provide estimates of genome-wide genetic diversity and its relevance to reproduction - an important benchmark for future analyses nationally and internationally. Conserving biodiversity has important benefits to society as a whole by contributing to a healthy and resilient natural world.
Commercial, Economic and Industry: Poultry scientists and stakeholders involved in the poultry industry will benefit from this study as the results will a) inform our understanding of the unique status of the avian egg in the evolution of the vertebrate reproduction, b) brings us closer to understanding the genetic control of key eggshell quality traits in a range of species (including chickens, turkeys, ducks and quail), and c) bring poultry breeding companies closer to adopting a genome-wide approach in selecting for improved eggshell quality and efficiency of production. Our involvement with Chivas Brothers will provide the corporation with links to non-profit scientific research through which they can evidence their corporate ethic of responsibility to environment and community.
Academia and training: Science is in the midst of a revolution in genetics, facilitated by major advances in DNA and RNA sequencing technology. Academic advancements in this field, outputs, and training, are of major benefit to the UK's scientific competitiveness.
 
Description The study published in Molecular Phylogenetics and Evolution (2018), led by Hans Recknagel, used high resolution genomics of 200,000 loci informed by our new high quality genome (Yurchenko et al. 2019) to resolve the phylogeny of the Zootoca vivipara species complex - or the Eurasian common lizard. This lizard species has egg-laying and live-bearing lineages but it has not been at all clear how and in what order the different reproductive modes evolved from the oviparous ancestry. Our topology is consistent with a single origin of viviparity from oviparity, and then a re-evolution of viviparity. While this remains to be assessed with more detailed experiments, ours is the most robust and data-rich tackling of this long-standing question and for which there has not been sufficient resolution to infer reversal.
Exploitation Route This work will stimulate an increased focus on the developmental and genetic mechanisms of reproductive mode and reversal.
Sectors Environment,Culture, Heritage, Museums and Collections

URL https://elmerlab.blogspot.com/2017/12/coverage-in-new-scientist.html
 
Description This project is novel because this is the first genetically defined example of a phylogenetic reversal to egg-laying from live-bearing, which is contentious in the reproductive physiology research community and therefore has the potential to be paradigm changing. Because of this, our study on the phylogenomic pattern of a reversal (Recknagel, Kamenos and Elmer 2018 Molecular Phylogenetics and Evolution) garnered popular interest and was covered by a full page news story in The New Scientist (9 Dec 2017) print and online, a periodical that reaches nearly 1 million scientist and non-scientist readers per week. The research project involved the use of museum collections and new collections from this project. The project engages well with the general public and nature enthusiasts. Therefore the PDRA and PI's team have previously given several talks about lizards to children at a rural village near our field site in Austria. This occurs approximately twice a summer and has throughout the award and targets education for children and appreciation of natural heritage, for locals and tourists. The field team was even covered in the local newspaper (https://www.meinbezirk.at/hermagor/c-lokales/koennten-menschen-eines-tages-wieder-eier-legen_a1847599).
First Year Of Impact 2017
Sector Education,Environment,Leisure Activities, including Sports, Recreation and Tourism,Culture, Heritage, Museums and Collections
Impact Types Cultural,Societal

 
Description NERC Biomolecular Analysis Facility Pilot Grant
Amount £5,600 (GBP)
Funding ID NBAF1018 
Organisation Natural Environment Research Council 
Department NERC Biomolecular Analysis Facility (NBAF)
Sector Public
Country United Kingdom
Start 11/2016 
End 03/2017
 
Title High quality reference genome of Zootoca vivipara 
Description We have developed and now freely share the first lacertid reference genome, for Zootoca vivipara (model species of the research grant). This is a very high quality genome with low proportion of gaps (<3%), chromosome-level assembly, oriented, and annotated. 
Type Of Material Biological samples 
Year Produced 2019 
Provided To Others? Yes  
Impact Before its release but when its development was known, we were contacted by researchers in France (CNRS, Julien Cote) with a request for using the reference genome. The Genome 10K Vertebrate Genomes Project is assessing whether to include this in their project as the lacertid representative. 
URL https://doi.org/10.1101/520528
 
Description Blog posts about research updates 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact All research activities such as outreach activities, papers published, achievement, and conference presentations given are shared publicly via a blog. This receives overall >1000 hits per year and most research posts between 20 and 100 views. This is a window into our activities that is particularly valuable for undergraduate students within Glasgow looking for labs for internships or honours projects and also for external academics and students. It is also for example how other academics learn about new techniques and resources from our group and contact me about them, for example common lizard reference genome.
Year(s) Of Engagement Activity 2016,2017,2018,2019
URL http://elmerlab.blogspot.co.uk/
 
Description Interview for international magazine 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact I was interviewed by The New Scientist, who contacted me because of our preprint posted on bioRxiv and which was later published as Recknagel et al. (2018) Molecular Phylogenetics and Evolution. The telephone interview then contributed to a substantial article published online and in print in the 9 Dec edition. The New Scientist reaches more than 1 million people. The journalist asked that we keep in touch about major findings in the future.
Year(s) Of Engagement Activity 2017
URL https://elmerlab.blogspot.com/2017/12/coverage-in-new-scientist.html
 
Description Interview for regional newspaper 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact PDRA and the field research team were interviewed for a piece in the local newspaper about the interesting lizards and natural heritage in the geographic area where we do much of our field collections. This generated questions and discussion with the paper and interest from the local community.
Year(s) Of Engagement Activity 2018
URL https://www.meinbezirk.at/hermagor/c-lokales/koennten-menschen-eines-tages-wieder-eier-legen_a184759...
 
Description Invited presentation to Glasgow University Earth Sciences Society 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact I was invited to present on a panel on the topic "How geological events affect evolution" together with a geologist. The primary audience was geography undergraduate students aiming to gain better understanding of the relationship between biodiversity and geology. They reported interest in the subject and sought additional discussion about research prospects and career decisions.
Year(s) Of Engagement Activity 2019
 
Description Invited seminar speaker 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact PI Elmer was invited as seminar speaker to the Department of Ecology and Evolutionary Biology, Univ. Bern Switzerland 28 March 2018. The audience was approximately 30 undergraduates, graduate students, postdocs, and faculty. The audience learned about reproductive mode evolution and ecology, and gained new knowledge about the field.
Year(s) Of Engagement Activity 2018
 
Description Outreach to children on evolution and biodiversity at field site 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The field team (led by PDRA) provide information and educational activities for children at the campsite where much of the field research is based from (Alpenferienpark Reisach). This reaches 5-10 children at a time and is held at least twice per field season. The team teaches about reproductive mode differences, evolution, and the natural heritage and herpetological biodiversity that is native to the area. Children and their parents report increased knowledge and interest.
Year(s) Of Engagement Activity 2017,2018