Evolution 2019: Comparative Landscape Genetics and Epigenetics in Anolis Lizards

The field of landscape genetics seeks to understand how patterns of genetic diversity vary across a landscape. But an organism’s traits are not just determined by their genome – they are also impacted by processes that affect the way the genome is expressed. The study of such mechanisms (i.e. heritable non-genetically based gene expression) is known as epigenetics, and has become a topic of great interested to evolutionary biologists who aim to understand the processes by which phenotypes change over time and space. Non-genetically based phenotypes can be the targets of selection, can impact the plasticity of traits in different environments, and more.

Understanding the impact of epigenetics on evolutionary processes is difficult, because it is hard to disentangle the genetic and epigenetic effects on phenotypes. Of course, epigenetics are not independent from the underlying genetic code – the genes that are expressed are a part of the genome after all. Thus because populations differ in genetic structure, it is difficult to determine whether differences in phenotypes across populations are driven by genetic changes, or epigenetic changes. To understand the influence of epigenetic changes on phenotypes, it is necessary to “subtract” the effects of the underlying genetic variation.

Ian Wang decided to tackle this problem using a well-studied Anolis species, A. cristatellus. Wang is interested in understanding what factors drive epigenetic patterns; but before understanding the factors involved, it is first necessary to describe the patterns. Wang chose to focus on A. cristatellus because it is distributed widely and throughout various environments on the island of Puerto Rico, and is therefore a good candidate for understanding how populations diverge across geographic regions (i.e. isolation by distance) and in different habitats (i.e. isolation by environment).

Wang and colleagues collected tissues from 8 localities, some of which were located in the xeric southwest, and some of which were located in the mesic interior. He performed RRBS sequencing, which captures information about methylated regions of DNA, and therefore provides information on variation in gene expression across populations (i.e. epigenetic variation). He also performed ddRAD sequencing, which captures information about genetic differences across populations (i.e. genetic variation).

In analyzing these two complementary datasets, Wang found that epigenetic and genetic distances were correlated between populations – that is to say, populations with high genetic divergence also had high epigenetic divergence. Recall that epigenetics are to not wholly independent from genetics, so this result is expected. However, each of these two types of variation – genetic and epigenetic – were also influenced by other factors.

In terms of genetic divergence, geographic distance was the strongest correlate – populations that were close to one another were more similar than populations that were further away. Interestingly, temperature and vegetation also appeared to play a role as well. In terms of epigenetic divergence, genetic distance (as represented by Fst) was the strongest predictor. Interestingly, however, vegetation was also a strong predictor as well. This suggests that on top of the genetic changes that accumulate when populations diverge, additional epigenetic shifts have also occurred, and are likely impacting the populations’ fitness in their respective environments.

These results highlight the importance of considering both genetic and epigenetic changes in studies of adaptive variation. Genomes alone may not explain the whole story! Wang is continuing this research in multiple avenues, including comparing results across species (e.g. comparing results from A. cristatellus to another trunk ground anole, A. cybotes on Hispaniola), and digging deeper into the functions of individual outlier loci from the RRBS sequencing. Looking forward to hearing more about this emerging perspective on adaptation in anoles!