USC Dana and David Dornsife College of Letters, Arts & Sciences > Blog

February 10, 2015

Looking for patterns in Catalina Conservancy Diver data

Filed under: Wrigley Institute — Jessica Dutton @ 8:23 am

USC Wrigley Institute

By: Albert Chang

Last May marked the end of four and a half amazing months I spent studying at the Wrigley Institute for Environmental Studies on Catalina Island. Under the USC Environmental Studies (ENST) Program’s Catalina Semester, I became a certified scientific diver and took courses exploring marine and coastal policy, fisheries biology and management, and conservation biology. The semester exposed my classmates and I to field research techniques, real-world issues and applications, and the natural beauty of Catalina. When it was time to return to reality and the stresses of urban life on the mainland, I knew I wanted to continue developing the skills and the knowledge I had attained in the spring.

Fast forward to this recent Fall Semester. My classmate Berenice and I approached Professor David Ginsburg (or DG as we affectionately call him), one of our professors from Catalina, about doing independent ENST 490 Directed Research. We knew we wanted to get involved in research, but we had no idea what. Fortunately, he was already looking at something that had potential and proposed this to us.

Carr Diver

It was an amalgamation of diver survey data – about 20 years worth from the waters of Catalina Island. This data was a survey of Macrocystis pyrifera or Giant Kelp, an integral component to the kelp forest community – these kelp are the foundation of a very diverse ecological community of fishes, invertebrates, mammals, and sea birds. Thus, they represent an important focus of research.

For two decades, the Catalina Conservancy Divers have been counting the number of giant kelp individuals around Catalina Island by looking at the holdfasts, which are the root-like structures of the brown algae that anchors it to a rocky substrate. They also determined which individuals were adults and which ones were juveniles by the length and by the number of stipes: individuals longer than one meter and with at least four stipes were considered adults.

This archive of data is great but there was never any analysis done, which means the dataset is just waiting to be explored and understood. What hidden truths do the data contain? Can we use these surveys to track the growth and decline of giant kelp biomass at Catalina over the last 20 years? Are there other significant patterns waiting to be found? My partner and I decided to take up this project for our independent research, and we began working.

Carr Fish

We started by digging through the literature – who else has done research on kelp biomass? We found numerous sources, but we had to make sure that their methods lined up with the methods of the Catalina divers. Turns out that in 2004, the Catalina dive team changed their survey methods and so we had to divide the data in two. Each set must be analyzed separately and may be comparable to different work by different research groups. The data also needs to be cleaned and organized. Although we’ve been able to clarify many questions and break down many barriers, there is still much work to do. And that is where we are now.

Organizing 20 years worth of data is proving to be quite the challenge, but I’m confident we’ll find something exciting in this pile of numbers. We’re also looking to incorporate GIS mapping and satellite data into the analysis, to connect our information about the kelp to an understanding of the landscape where they lived. And maybe very soon, we’ll get the chance to go out and dive at one of these locations. One site happens to be just around the corner from Big Fisherman’s Cove, outside the Wrigley Marine Science Center. Going there will help us even better understand the places these divers devotedly surveyed for the last 20 years.

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January 13, 2015

What Does the (Island) Fox Say?

Filed under: Graduate,Wrigley Institute — Jessica Dutton @ 8:43 am

USC Wrigley Institute

By: Nicole Adams

Besides being adorable, why should we care about the island fox?

The housecat-sized island fox (Urocyon littoralis) lives on six of the eight Channel Islands, and contributes to the flora and fauna found only on the islands. You may have already heard the story of the island foxes, that they suffered great population declines in the last 25 years. Over a span of three years the northern islands’ fox populations declined 96-99% due to hyperpredation by golden eagles. Simultaneously, on the eastern part of Santa Catalina Island there was a 90% population decrease in one year due to a canine distemper virus outbreak.


The island foxes are active during the day (unlike most canids) and can be seen hanging around the picnic tables at the Wrigley Institute for Environmental Studies.

Fortunately, rigorous captive breeding programs were swiftly and effectively put in place to save the foxes from sure extinction on some of the islands. Island fox estimates as of 2013 show substantial population growth on the islands that underwent declines. Woohoo! A conservation success story! This is great news for the stability of the channel island ecosystem, but should we declare victory and stop worrying about the foxes?

I don’t think so. The number of foxes has definitely increased, but such severe population decreases can have drastic effects on the genetics of a population. Many questions still remain. How much genetic diversity was lost due to these crashes? What genetic diversity was lost? Which genes were changed as a result? These questions are crucial to answer because genetic diversity allows the foxes to adapt to their ever changing environment.

What does the fox genetics say?

In order to discern the differences in genetics pre- and post- population declines, I am comparing historical museum samples collected prior to the population crashes to samples collected after the crashes. I get to use a really cool and unique collection of island fox skins and skeletons collected in the late 1930s from the Los Angeles County Natural History Museum located just across the street from USC. What I have done is collected “crusties” (the official, scientific term for dried bits of remnant tissue) from the skins and skeletons in order to extract their DNA.


An island fox skull from the LA County Natural History collection, which I get “crusties” from to extract historic DNA.

To compare the genetics pre- and post- population crash, I am also using tissue from foxes collected in the past 10 years. Then the exact code of the pre- and post- decline fox DNA will be determined by sequencing.


I use a special filtering workstation to minimize contamination among samples.

What does the fox scat say?

Foxes are continually facing health threats such as from introduced species. Known health concerns in the island fox populations include a number of viruses, bacteria, and fungi that cause diseases. On Catalina, ear mites in the foxes often lead to ear tumors. And a new pathogen, a spiny worm, is currently causing fox fatalities on San Miguel.

It is difficult to know when another outbreak like the one on Santa Catalina Island will occur, what the next pathogen be, or how much genetic diversity will be lost. So it’s important that the fox populations are monitored for the presence of known pathogens and the emergence of new ones. Monitoring for pathogens can be easily done by non-invasive sampling, which attempts to collect useful animal material while causing the least amount of stress on the animal. Therefore, I am monitoring pathogens in fox populations by collecting scat samples, a smelly but non-invasive sampling technique.


A fresh scat sample left for me at the Wrigley Institute that I collected!

I am in the process of getting scat samples from all of the six inhabited islands. I am also working on extracting all available DNA out of the scat sample including that from the fox, bacteria, fungi, and its prey. Then I will sequence common genes that can differentiate among species. Finally, I will compare the sequences from the scat samples to known pathogen sequences and then identify putative pathogens.

The complex population history and the health issues contribute to the need for conservation of the island foxes. I look forward to sharing my results and conclusions and potentially informing the management practice of these curious critters.

Nicole Adams is a Ph.D. student in the lab of Dr. Suzanne Edmands, with the USC Marine and Environmental Biology program. The Edmands group studies evolutionary and population genetics, as well as genetic variation in organisms of concern for conservation and management. 

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