About This Project

Welcome to the coolest ecosystem you've never heard of - the anchialine ecosystem! Anchialine habitats are coastal ponds, pools, and caves with underground connections to sea- and fresh waters. They are rare and have tons of endemic organisms, many of which are threatened. We're using environmental DNA (eDNA - DNA found in the water itself) to monitor anchialine shrimps in Hawaii. We will use common species kept in the lab to develop an eDNA toolkit for monitoring rare, endangered species.

Ask the Scientists

What is the context of this research?

Anchialine habitats are rare and understudied worldwide. Hawaii has the largest concentrations of these habitats, where different shrimps are the most conspicuous animals:

We study a common shrimp, Halocaridina rubra, which is both an anchialine and Hawaiian endemic species. However, there are 7 other anchialine shrimp found in Hawaii, many of which are endemics and/or endangered. We know virtually nothing about these species because they're so rare - they have only been observed haphazardly as single individuals in a few specific habitats. Environmental DNA (eDNA) offers a way to learn about these species. We will use lab populations of the common species to develop an eDNA toolkit to study the distribution and genetics of the rare species.

What is the significance of this project?

Much of the anchialine ecosystem is found in the underground waters below the anchialine ponds. The only way to unveil this ecosystem is to use creative tools like eDNA. eDNA has been used previously to study rare and endangered species and basically consists of filtering water from the habitats, extracting DNA from the filter, and then screening for the presence of DNA fragments specific to the species of interest. We can therefore determine whether a species is present without ever actually observing it (for example, if it is underground and not in the ponds themselves). We also know from the common species of shrimp that there can be unique genetic lineages across the islands. We can address this for the rare species by sequencing and analyzing their eDNA.

What are the goals of the project?

We will develop an eDNA toolkit using populations of the H. rubra we already have in the lab. This will include filtering water from our lab aquaria, extracting eDNA from the filters, and screening for H. rubra using a technique called digital PCR:

This will let us to determine best practices.

Using these data, we will then create digital PCR probes for the rare species (8 in total) and filter water from at least 25 anchialine habitats of interest across Hawaii. We will extract and screen eDNA from these habitats for the species of interest to determine their potential ranges and if certain areas warrant special conservation concern.

Finally, we will examine population genetics of the rare species by sequencing their eDNA.