Lillie lab: Our research

Sand lizards occur in fragmented populations across Sweden, with varying population sizes and degrees of isolation, and face significant threats from habitat degradation and land use change. Here, we apply a low-coverage whole genome sequencing approach to the conservation genomics of Swedish sand lizard populations, from Dalarna to Skåne. We reveal strong population structure among populations, likely reflecting prolonged fragmentation and isolation. Genetic diversity in populations declined with increasing latitude, likely reflecting the historical northward expansion process and the subsequent population fragmentation and isolation. This project was lead by Dr Mette Lillie, in collaboration with Prof. Mats Olsson (University of Gothenburg), Dr Patrik Rödin Mörch and Prof. Jacob Höglund (Uppsala University), Dr Sven-Åke Berglind (Länsstyrelsen Värmland) and Prof. Erik Wapstra (University of Tasmania).

Sand lizard populations in Sweden are small and isolated with limited gene flow, which is particularly evident in populations on the west coast. Here, signs of inbreeding were observed, including deformities and reduced hatching success. Approximately 25 years ago, a new population was established on an isolated island via cross-breeding of several Swedish sand lizard populations, which alleviated the morphological and physiological inbreeding effects.

In this project, we study the genetic consequences of population cross-breeding using ultra-low coverage (~2x) whole-genome sequencing data of the cross-bred population and the main founder population. Our results indicate that cross-breeding has substantially improved genetic diversity throughout the genome and appears to have stabilized the population demographics, while the founder population’s trajectory continued towards population contraction. This project is being lead by postdoc Dr Seraina Bracamonte.

Parasites have a strong impact on the health of their host and reduce its fitness and survival. In combination with additional stressors, parasites can pose a substantial threat to species of conservation concern. However, parasites themselves are sensitive to host demographics, which may benefit some species while driving others to extinction. The aim of this project is to characterize and quantify blood parasite infections in several Swedish sand lizard populations with varying levels of genetic diversity. This project is being lead by postdoc Dr Seraina Bracamonte.

Transposable Elements (TEs) are DNA sequences that can move independently inside eukaryotic genomes using self-coded enzymes. TEs can play important roles in shaping genome evolution, regulating gene expression, and contributing to genetic diversity, disease, and adaptation. To date, TE studies have been biased towards mammals and birds, while reptiles remain under-studied.

In this research program, we are studying the evolutionary history of TEs in the Swedish sand lizard, Lacerta agilis, and other members of the family Lacertidae, comparing repeat landscapes and recent expansions of retrotransposon families. This project is being lead by postdoc Dr Malavi Sengupta.

Global climate change is predicted to have significant impacts on infectious disease dynamics, increasing the prevalence, distribution and intensity of disease. Resistance will rely heavily on the variation present at genes related to immune function that will enable host populations to adaptation to these changing pathogenic challenges. These changes to infectious disease dynamics are heightened in ectotherms, where climate warming will also impact critical physiological processes that directly depend on the thermal environment. Even more so in egg-laying (oviparous) ectotherms, where sensitive early developmental stages can be significantly impacted by environmental stressors. We know precious little about how climate warming will impact disease dynamics in ectotherms. With a significant proportion of the Earth’s vertebrates (fishes, lizards, amphibians) and all invertebrates being ectothermic, there is a critical need to increase our understanding.

This research program seeks to characterise the sand lizard immune response using RNAseq and methylation sequencing to investigate changes in gene expression. We are investigating how warming incubation temperatures affect methylation patterns across the genome, with particular focus on immune genes.

This research program is funded by The Swedish Research Council (Vetenskapsrådet) and being lead by doctoral student, Joshua Hufton.