Elaboration and degeneration of complex traits: The visual systems of lizards and snakes

Project Information

Evol-Eyes

Grant agreement ID: 703438

DOI

10.3030/703438

Project closed

EC signature date 18 March 2016

Start date 1 October 2016

End date 30 September 2019

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 258 107,40

EU contribution

€ 258 107,40

Coordinated by

UNIVERSITY OF BRISTOL
United Kingdom

Periodic Reporting for period 2 - Evol-Eyes (Elaboration and degeneration of complex traits: The visual systems of lizards and snakes)

Reporting period: 2018-10-01 to 2019-09-30

Summary of the context and overall objectives of the project

How are complex traits lost during evolution, and once lost how can they be regained? Our project addresses these fundamental questions using the exceptionally diverse visual systems of squamate reptiles (snakes and lizards). Specialist nocturnal and burrowing lineages have evolved many times in squamates, offering multiple in- dependent comparisons of taxa that have lost genes in functionally redundant visual pathways. Two groups, snakes and geckos, lost several key visual genes during such ‘sensory bottlenecks’, but both show remarkable re-innovation of eye anatomy and physiology: diurnal snakes inherited incomplete cone (bright-light) photoreceptor and transduction pathways from their nocturnal/burrowing ancestors but have highly sensitive colour vision; geckos are descended from diurnal lizards and lack major components of the rod (low-light) pathway, but secondarily nocturnal species have superb night vision. We will use this powerful comparative framework to 1) thoroughly reconstruct patterns of reduction and loss of visual gene function in squamates that have entered low light environments, and 2) discover the molecular mechanisms that have compensated for ancestral gene losses in exemplar snake and gecko taxa with secondarily evolved visual capabilities. This will yield significant new knowledge of the fundamental processes of gene loss in evolution and provide a paradigmatic case of evolutionary re-innovation following degeneration in complex traits.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Work Package 1 – Exploring the Squamate Visual System [Completed]
Fieldwork was be carried out in South Australia, Western Australia Queensland for target species. During these fieldwork expeditions I collected lizards and snakes with the aim of covering most of ecological diversity and multiple lineages. Fieldwork was done under research permits issued by Australian State governments.
The retinal tissues for each of these lizard and snakes was removed, RNA extracted and sent to NGS sequencing. I currently have sequenced the eye transcriptome of 130 squamates.
Additionally, I collected microspectrophotometry data for 24 animals and electroretinography data for 18 Squamates through collaborators. Further 26 species were studied for retinal anatomy and photoreceptor complement under light and electronic microscopy methods.

1.2.2 Work package 2 – Expanding Taxon Selection [Completed]
I designed a gene-capture probes to sequence genes involved in visual sensory perception, circadian rhythm and genes involved in retinal degeneration (retinopathy diseases) in humans. I collected the samples from the ABTC collection in the South Australia Museum and across other Natural History Museums across the world. Sampling comprises 95% of all squamate lineages, diverse ecologies (nocturnal vs diurnal, subterranean vs above ground, terrestrial vs aquatic). I sequenced the visual genes for 580 species.

1.2.3 Work package 3: Phylogenomic, comparative genomic and transcriptomic analysis [in progress]: Transcriptomes have been assembled and annotated. Gene-captures were also assembled and visual genes identified. Pipelines to analyse genomic and transcriptomic data was designed. Phylogenetic analysis and comparative genomic analysis of vision genes is still underway given the enormous amount of data.


The results of the analysis of the current data, suggests that the visual system of lizards and snakes is a highly diverse shaped by gene-loss, positive selection and polymorphism. The diversity of the visual system in lizards and snakes can be observed in the eye anatomy, retinal structure and diversity in their vision genes.
The results were disseminated in several publications and through presentation at international conferences. The results of this were also disseminated in the results in brief of the cordis website https://cordis.europa.eu/article/id/415770-looking-into-how-complex-eyes-of-lizards-and-snakes-evolved through public engagement activities in Australia and UK and through 2 nature TV shows.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

My project will contribute substantially by combining gene sequence comparisons and expression data for all major visual pathways across multiple independent transitions, spanning recent to relatively ancient divergence timescales. Our multispecies approach will also provide significant empirical data to test model estimates of the timeframes that inactivated genes can lie latent without being irreversibly lost. I have generated substantial genetic data to study the visual system of lizard and snakes, produced data for eye anatomy and physiology. The data is currently being analysed and some publications are published were some are being written and being peer-review.

Left: Dr Bruno Simões doing fieldwork in sea snakes; T-R: Gecko; B-R: Sleepy lizard