Nicholas Holmes Scientific Portfolio

Our laboratory seeks to answer the following question: Is plastic pollution driving an evolutionary response in green sea turtles (Chelonia mydas) by selecting for genes that help them differentiate between their natural prey and plastic debris? This study will investigate whether populations in high-pollution areas show genomic signatures of recent natural selection. Green sea turtles are an ideal species for this research. They have a global distribution, which allows for a direct comparison between populations experiencing high plastic mortality and those in more pristine environments. The availability of historical museum specimens will enable us to establish a genetic baseline from before the global plastic boom.

To answer our question, we will use whole-genome resequencing (WGS). We selected this technique because it provides the most comprehensive data, which will be essential when searching for unknown adaptive genes in a non-model organism (Ellegren, 2014). Alternative methods, such as RADseq, only sample a fraction of the genome and could easily miss the specific loci under selection. WGS provides the high-resolution data needed to scan the entire genome for signatures of selective sweeps, which are regions of reduced genetic diversity that indicate recent natural selection (Luikart et al., 2019).

We will compare the genomes of turtles from high-pollution areas, low-pollution areas, and historical specimens. We expect to find strong signatures of selection in the high-pollution population around genes related to sensory systems, such as vision or chemosensation. These results would provide the first evidence of rapid, human-driven evolution in this species. This study will not be able to prove that the turtles’ diet has changed, but it can identify the genes under selection. That would require follow-up ecological studies.

References

Ellegren, H. (2014). Genome sequencing and population genomics in non-model organisms. Trends in Ecology & Evolution, 1(29), 51-63. 10.1016/j.tree.2013.09.008

Luikart, G., Kardos, M., Hand, B. K., Rajora, O. P., Aitken, S. N., & Hohenlohe, P. A. (2019). Population genomics: Advancing understanding of nature. In O. P. Rajora (Ed.), Population genomics: Concepts, approaches and applications (pp. 3–79). Springer Nature Switzerland AG.