“Thus organisms and environments are both causes and effects

in a coevolutionary process.”

—Richard C. Lewontin in The Triple Helix: Gene, Organism, and Environment.

Friday, April 5, 2019

Deep inside the forest

Imagine you are a bird soaring over the top of a dense redwood forest. As you effortlessly glide on the wind, your gaze turns to the thick canopy below you—treetops of monotonous shades of green and brown. The canopy, still and silent from your perspective, is itself not very diverse; coastal redwoods dominate as the main tree species. But at a bird’s eye perspective, much is missed. Beneath the tops of these quiet giants are rich communities of plants, animals, and fungi that could not exist on their own.
Foundation species, like the trees in a forest, are species that provide essential habitat for others (Dayton 1972; Ellison et al. 2005). We call habitats formed by foundation species biogenic habitats because they are structured by living organisms. They provide shelter and food and support diverse communities. We have all been in a forest and know how much the climate changes—if you have ever hiked in Henry Cowell Redwoods State Park, for example, you know how much darker, cooler, and more humid it is deep among the trees. But there are smaller biogenic habitats we can’t hike through, and, like a bird flying high, we view only from above unless we make an effort to learn more. One such habitat is coastal mussel beds.
If you’re a resident of the central Californian coast, you’ve probably hiked down a bluff and explored the wave-swept rocky shores. Most likely, you perused the dense beds of mussels until you found a sea star, urchin, or in the very low zone, an octopus. But the mussel beds themselves are full of colorful and exciting life, supporting hundreds of species (Suchanek 1992; Lohse 1993; Lafferty & Suchanek 2016)! Here is a description of some of my favorite mussel bed species found on and within the bed.
In the mid to high intertidal zone, you can find several types of striped or checkered snails. Some of these snails eat the lichens and algae growing over the mussels, and others eat the mussels themselves. My personal favorite is called a unicorn snail, named after the single horn (also called a tooth) on the edge of its shell that it uses to open its hard-shelled prey.

Acanthinucella spirata, the unicorn snail, also eats mussels and barnacles but uses its single tooth (also known as a horn, like a unicorn; see it in the upper right) to puncture its prey. Photo credit Dave Cowles from inverts.wallawalla.edu

Littorina scutulata, the checkered snail, about 1 cm long. It eats lichens and microalgae and is also found above the mussel beds in the high zone. Photo credit Gina Contolini

Nucella ostrina, a dogwhelk, eats mussels and barnacles by drilling a hole into their shells. This individual has its proboscis extended into a hole it made in the mussel on the right. Photo credit Gina Contolini

The mid-zone mussel bed is also home to a large, colorful worm called a pile worm (Nereis spp.). Its tough skin is iridescent and often turquoise, and it has sharp, retractable jaws it uses to attack its prey. Though there is a species of Neries native to Californian shores (Nereis grubei), a nonnative species has been introduced when fishermen discarded it as unused bait. Worms are particularly dependent on mussel beds because the beds trap sediment in which the worms live (Kanter 1977).

A particularly colorful pile worm Nereis grubei about 5 cm long. Photo credit Gary McDonald

Peanut worms (e.g. Phascolosoma agassizii) that live in the sediments at the bottom of the mussel bed. Photo credit Gina Contolini

There are also many species of algae that grow on mussels. My personal favorite is Nemalion helminthoides which is a slimy, rubbery alga aptly named sea noodles.

Nemalion helminthoides, the sea noodle, growing on a mussel bed. Photo credit Gina Contolini

In addition to algae, some animals live on the mussels themselves. In order to do this, they need to be firmly cemented on. Many species of worms have done this by forming calcareous tubes to live in. If you look closely, some mussels have hard white dots or lines on their shells or sometimes hard rows of sand. These are the homes of different species of worms that have given up a mobile life for the safety of a hard tubular home. There is even a species of snail that has made a similar life choice and lives in a long tube rather than a spiral shell, though these snails are not often found on mussels.

The whitish growths on these mussels are calcareous tube worms Serpula columbiana. When underwater, they filter feed with a colorful tentacle array. The tube snail Serpulorbis squamigerus looks very similar to these worms. Photo credit Gina Contolini

Just like a forest, mussel beds create biogenic habitat that provides a home for hundreds of species. Many intertidal species require hard surfaces to live on, and mussel beds increase available colonizable surfaces five to thirty times that of bare rock (Suchanek 1992). The species above were just some of my favorites that I’ve found during my research, but there are also dozens more species of small worms, arthropods, and molluscs that live in mussel beds in California. So next time you are out on the rocky shores, don’t just breeze over the top of the canopy. Look on and within it (keeping it intact, of course) and see if you can find anything new!

Photos of a small section of mussel bed before and after removing mussels. Sediment and shells are trapped under the mussels, and many organisms live in and among the debris. Mussels were removed under CDFW Scientific Collecting Permit #13169. Photo credit Gina Contolini

Literature cited
Dayton PK 1972. Toward an understanding of community resilience and the potential effects of enrichments to the benthos at McMurdo Sound, Antarctica. In: Parker BC (Ed). Proceedings of the colloquium on conservation problems in Antarctica. Lawrence, KS: Allen Press
Ellison AM, Bank MS, Clinton BD, Colburn EA, Elliott K, Ford CR, Foster DR, Kloeppel BD, Knoepp JD, Lovett GM, Mohan J, Orwig DA, Rodenhouse NL, Sobczak W V, Stinson KA, Stone JK, Swan CM, Thompson J, Holle B Von, Webster JR (2005) Loss of foundation species: consequences for the structure and dynamics of forested ecosystems. Front Ecol Environ 3:479–486
Kanter RG (1977) Structure and Diversity in Mytilus californianus (Mollusca: Bivalvia) Communities. University of Southern California
Lafferty KD, Suchanek TH (2016) Revisiting Paine’s 1966 sea star removal experiment, the most-cited empirical article in the American Naturalist. Am Nat 188:365–378
Lohse DP (1993) The importance of secondary substratum in a rocky intertidal community. J Exp Mar Bio Ecol 166:1–17
Suchanek TH (1992) Extreme biodiversity in the marine environment: mussel bed communities of Mytilus Californianus. Northwest Environ J 8:150–152

Tuesday, April 2, 2019

Radio interview

A few months ago, a fellow grad student interviewed me about my research. Now, the interview will be on the radio on a local Santa Cruz station! The station is 90.7 fm. It will air Wednesday, April 3 at 3:55 pm and Friday April 5 at 6:40 am. You can also listen online at KSQD.org.

Helpful tips for R

There are always new things to learn in R that totally change how you use it. Then there are those things that are super frustrating but the solutions elude you for years. Here is my list of those things.

  • Problem: Can't remember the syntax for basic functions in several useful packages
    • Solution: R cheatsheets [link]
  • Problem: Can't use dates like a number line
    • Solution: package "lubridate" (there's a cheatsheet for it, too)
  • Problem: Can't specify limits to date axis in ggplot.
    • Solution: use "scale_x_date" instead of "scale_x_continuous"
  • Problem: It takes so much time to constantly update figures and tables into my manuscript.
    • Solution: Rmarkdown [link]. It knits together your writing and your code so your figures and tables are automatically updated.
  • Problem: Plots in base don't have x and y axes touching.
    • Solution: Within the plot() command, use xaxs='i', yaxs='i'
  • Problem: It's hard to summarize a lot of data when you need it split up in certain groups.
    • Solution: function ddply(). You tell it what your groups are, then you can specify what functions you want it to perform on any other variable and it will do this and split it up by your groups into a nice dataframe.
  • Problem: I want to use many TRUE/FALSE criteria to select certain rows of data.
    • Solution: use the syntax %in% and then a vector of criteria to tell R you are looking for items that match anything in your vector. Example: plot.com[which(plot.com$plot%in%c('A03','A04','B03','B04','NC01','NC06')),]
      looks for all values of plot.com where plot is A03 or A04 or B03, etc. You can also specify a vector object with the criteria you're trying to match, such as plot.com[which(plot.com$plot%in%my.plot.criteria),] where my.plot.criteria is a vector with the plots you want to specify.

Monday, December 3, 2018

Coastal Gastropod Reproduction: an Animated Cartoon

Dr. Tom Carefoot, a retired faculty member of the University of British Columbia, made an animated cartoon about reproductive strategies of two types of coastal gastropods. This is just one of the features of his amazing website, A Snail's Odyssey. Enjoy!

Dr. Carefoot also shares a short history of the word dogwhelk. I have always wondered why the word "dog" is part of the name of this type of gastropod. Here is his commentary:

The word “whelk” has appeared in many different forms over the ages and has an obscure origin. The Oxford English Dictionary notes that the “unetymological” spelling of wh-elk (as opposed to such earlier names as “wiloc”, “wyloc”, “wylke”, and “welke”) commenced in the 15th C. The term “dog” whelk is used commonly in Britain and elsewhere in reference to Nucella spp., for no obvious reason that would relate to a snail. However, as we also have “dog shark”, “dog rose”, “dog violet”, and “dog wood”, perhaps it refers to something that is common or familiar, like our 4-legged companions.

Thursday, October 4, 2018

Field experiment finished!

After 40 weeks, my field experiment examining how dogwhelk predation affects mussel bed communities is finished! I collected the experimental mussel beds and cleaned up the equipment in the beginning of August.




This is a video of the tide washing over my experimental cages.



After August, low tides are during the night, which is why I decided to end it then. It's a very good thing I did, because two weeks later during the next spring tide, this washed up!

This is a spotter boat—one that locates schools of squid at night so other fishermen can catch them—that has run aground on the reef.

It was about 100 ft. away from where my experiment was and probably would have ruined the whole thing, which would have been a HUGE loss for me; I honestly might not have been able to graduate this year if my experiment was still out there when this happened.

Over the course of a few days, the waves tore up the boat and left it in pieces. A salvage crew eventually came down and lifted up the pieces with a crane.

Now that that's all cleaned up and done, I have started measuring the mussel samples and I'm eager to get results!

Thursday, July 19, 2018

Field experiment observations

I'm about to wrap up my field experiment finally! Now that lots of mussels are drilled and empty, thanks to my dogwhelks, I've noticed many lined shore crabs that like to live inside them. I'm not sure if this will be a real result or if it's just a fun observation, but either way, it's cute.

We also found many of these gelatinous, salp-looking creatures in my cages this week. I don't know what they are, but they look really weird!

Pachygrapsus crab hiding in an empty mussel shell. I suspect larger empty mussels 
support more Pachygrapsus. Could this be an interesting result of my experiment?

Unknown gelatinous creature or substance found in my experimental mussel beds.

Monday, July 16, 2018

Field experiment interview

Here I explain some of the details of my field experiment in the mussel beds. Huge thanks to Laura Shields, a former Science Communications student at UCSC for putting this together.