Conservation Transcriptomics of Ambystomatid Salamanders and Their Polyploid Hybrids

Amphibians are declining worldwide, in part due to Batrachochytridium dendrobatidis (Bd), a pandemic chytrid fungal disease. This disease affects salamanders more than initially thought, but several gaps in knowledge hinder response to this and other disease threats. Current demographic information for salamanders is lacking. Without an efficient means of surveying salamander populations, it is difficult to monitor or respond to these declines. Additionally, little is known about how salamanders respond to chytrid fungus, a major contributor to amphibian decline. This is particularly worrisome in the Great Lakes Region, as it is home to a cryptic polyploid complex that makes up the majority of many salamander communities. These polyploids may be particularly susceptible to disease, but little is known about vertebrate response to polyploidy.

In this doctoral dissertation, I address these gaps in salamander conservation. First I developed eDNA markers that allows for quick, non-invasive identification of laboratory and field samples without the need for technical or taxonomic expertise. I used this method to identify cryptic polyploid and diploid salamanders of the genus Ambystoma. These salamanders were used in a transcriptomic study on the functional response of salamanders to Bd. I was able to sequence, assemble, annotate, and analyze three salamander transcriptomes using this data. I characterized the immune response of one of these salamanders to Bd, finding links to wound healing pathways characteristic of salamanders and generally much quicker response time to chytrid challenge than is observed in frogs. Additionally, I investigated the expression patterns of polyploid salamanders in comparison to the parental taxa in normal and disease conditions. I found that different genomic copies within the polyploids maintain their own regulation patterns under normal conditions, but are disrupted in disease conditions. This may indicate an increase susceptibility to chytrid in the highly common salamander polyploids and other vertebrate polyploids.

What follows are an introductory chapter, three data chapters, and a conclusion where I offer my concluding remarks on the utility of these chapters and the future importance of such analyses in conservation genomics, particularly in light of recently discovery of a more pathogenic chyrid fungus, Batrachochytridium salamandervorans.