Big Ideas

San Francisco Bay Subtidal Habitat Goals Project

I recently learned about the San Francisco Subtidal Habitat Goals Project, a self-stated “Collaborative, Interagency Approach to Protect the Hidden Bay.” The organization is a collaboration between a variety of local and federal agencies and local conservation groups, and is committed to “setting science-based goals for maintaining a healthy, productive, and resilient ecosystem.”

Figure 3-1 from the most recent report from SF Bay Subtidal Habitat Goals Project, illustrating the types of subtidal habitats and processes that are common in subtidal urban environments

Quite a feat for an organization that works on urbanized subtidal environments – the ultimate unknown when it comes to modern marine ecology. I’m most impressed!

I’m particularly impressed because of their open and informed recognition that managing urban subtidal ecosystems is critical despite the limitations of our current understanding. In their own words: “Although a tremendous amount of scientific information is available from research and monitoring in the bay, little of it is useful in making decisions about specific proposals for development or restoration as it relates to subtidal habitat. Part of the reason for this shortfall is that subtidal habitats are usually invisible in the bay’s turbid waters, and most sampling methods cannot provide detailed information about the location and condition of the various habitats. Equally important is the need to learn more about the functions of these habitats, how they respond to environmental change, and how to protect and enhance them.”

I bring up this recent discovery because the organization put out a 200+ page report that is more comprehensive, contemplative, and contemporary in the context of current theoretical ecology than any I’ve ever seen from a governmental/non-profit collaboration of any kind, let alone one focused on urban subtidal ecosystems! In their report, highlighted science goals include identifying the ecosystem services that urban subtidal habitats support, understanding how artificial structures affect estuarine ecosystems, and characterizing the interactions between different urban subtidal habitat types. This is novel stuff! Someone involved is quite up to date on the cutting edge of ecology, and is applying it where it matters.

Not only are the research needs they highlight completely on point, they represent essential areas of study if climate change adaptation efforts are to be planned and implemented in a way that maintains and/or enhances the services that subtidal ecosystems provide to urban populations. Unless we understand how the modifications we make to marine habitats influence fishing, crabbing, the filtering and processing of water-borne pollutants, and various other benefits we receive from subtidal ecosystems, we may lose these benefits as we amour and prepare our shorelines for rising seas.

Figure 6-3 from San Francisco Bay Subtidal Habitat Goals Project’s 2010 report – an impressive flow chart of the relevant effects and considerations when managing urban artificial structures

Indeed, urban subtidal ecosystems globally are understudied and poorly understood.  But the Bay Area has surprised me by being well ahead of the curve. Whether it’s their impressive benthic maps or their honest statements of the limitations of current knowledge, I’m quite glad to know that my hometown is in good hands with the San Francisco Bay Subtidal Habitat Goals Project. Stay tuned to all their endeavors here. And read their full report from 2010 here.

Cheers!

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Big Ideas

Urbanization and evolution

Galapagos finches, drawn by John Gould (1804-1881)

Galapagos finches, drawn by John Gould (1804-1881)

Urbanization may affect many aspects of marine ecosystems, but as ecologists we often ignore the potential evolutionary consequences of urban development. Several years ago now, there was a great study on just this by Andrew Hendry and colleagues in Proceedings of the Royal Society. They studied the most famous of model species for evolution: Darwin’s finches (the ground finch, genus Geospiza).

Specifically, Hendry et al. were studying two morphs (right) of the Medium Ground Finch (Geospiza fortis) on the island of Santa Cruz in Galapagos. The two morphs had different beaks sizes (used for eating different foods), different songs, and tended to mate preferentially within their morph (ie – with other birds that looked like them).

Two finch morphs (Photo by A.P. Hendry, 2014)

By documenting the differences between these two morphs, Hendry and colleagues expected they were in the process of observing a speciation event. But then something strange happened: in areas on the island where there were lots of humans, the morphological differences between the two morphs diminished. In particular, the “bimodal” (distinct large and small) beak sizes of the two morphs fused and beak size became widely variable in more urban locations. Why would this happen? Human activities had made a wider variety of food sources available to the finches (see photo of finch on cereal box). The little birds indulged in the anthropogenic cornucopia urbanization offered, and human food of all shapes and sizes was sure to satiate regardless of one’s beak morphology. Selection against intermediate beak size was thus eliminated, allowing birds of all beak sizes to thrive in urban areas. As Hendry describes it, humans were causing “reverse speciation”.

Galapagos finch on a cereal box (Photo by A.P. Hendry, 2014)

Galapagos finch on a cereal box (Photo by A.P. Hendry, 2014)

This is old news really, as it was published almost a decade ago. Two things have led me to post about it now: (1) I recently came across this blog post by Hendry on eco-evo, which I highly suggest, and (2) Hendry’s findings were featured in Episode 3 of Galapagos, which was made available on YouTube earlier this month. (The episode in its entirety is worth making an evening of! But skip forward to 36:08 if you just want to hear about urban finches).

To my knowledge, there have yet to be any comparable examples documented in the marine environment. Other human activities are known to influence evolutionary traits in marine organisms. For instance, fishing can lead to an earlier age or smaller size at which marine fish become reproductive. But evolutionary consequences from marine urbanization specifically are poorly understood.

With time and further study, we hope to know more!

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This Week In The Lab

Leavin’ on a jet plane

I’m terribly sad to be leaving this beautiful city and a new assemblage of friends and colleagues who I will forever cherish. My time at UNSW has been eye opening in so many ways, from the culture of collaboration in my host lab and department, to the suite of new critters I encountered (link), to the daily evidence of ecology and evolution that abound when one first becomes acquainted with life in the opposite hemisphere (link). My EAPSI host, Emma Johnston, has provided inspiration and ideas that will keep me motivated for much time to come. With luck, that motivation will be matched with interesting findings from the stable isotope and genetics data we’ve collected.

Top: Sydney Opera House as seen while underway to Gore Cove, one of our field sites. Bottom: Side of our SIMS-based research vessel, heading west past the opera house and towards Balmain, another inner-harbor site.

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Background, This Week In The Lab

Niche Theory In Everyday Life

SYDNEY, AUS: In the day to day here, as I commute to work, take the bus around town, and observe, I’m frequently overwhelmed by daily demonstrations of niche theory and convergent evolution in the world around me. The terrestrial flora in Sydney is of an entirely different lineage, primarily of the Myrtoideaen tribe Eucalypteae, than what I know from the Pacific Northwest. Though Eucalypts have long been present on Earth, their radiation in Australia is apparently relatively recent. Eucalypts now make up ¾ of the vegetation on this island continent, and fill nearly every ecological function that I, as a North American, attribute to other trees. For instance, coastal swamplands similar to the cypress swamps of Louisiana and Texas are here inhabited by swamp gum trees, other Eucalyptus spp., and their Myrtoideaen cousins, the paperbark trees. Savanna and temperate grassland habitats that in the US would have scattered oaks, cottonwoods, or willows, are here are inhabited by bimble box and coolibah eucalyptus trees. The Sydney red gum is one of several Eucalypts that plays the role of North American fruit trees, providing food for fruigivores. On my commute home at night, I often get to watch enormous ‘flying foxes’, or Ku-ring-gai bats (Pteropus poliocephalus), indulging in the tree’s nectar.

This, of course, is entirely tangential from my work on man-made alterations to urban shorelines in Sydney Harbour. While I know I should be entirely focused on the project that brought me here, the natural history nerd within has a hard time ignoring what Darwin and many others since found astonishing upon first traveling to the opposite hemisphere: That a similar set of ecological professions (niches) exist everywhere, and who fills them (which species) is heavily influenced by chance.

Post about ancient Eucalyptus from Eliza’s Instagram

Eliza’s instagram

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This Week In The Lab

Next Generation Sequencing – Life Forms of Sydney Harbor

Leonard Nimoy as Spock from Star Trek: The Original Series.

In the original Star Trek, Lieutenant Spock, upon beaming down to a new planet from the Starship Enterprise, would immediately pull out a Tricorder and begin scanning the environment for life forms. Results were instantaneous, providing a comprehensive view of the surrounding ecosystem within seconds.

Though we have yet to fully see such a novel invention on Earth, I’m overwhelmed today by how close we actually are to inventing the Tricoder in real life. I spent the day in lab at the Sydney Institute of Marine Science, extracting DNA from marine sediments and their invertebrate inhabitants. Thanks to support from the IGERT Program on Ocean Change at UW and from the Applied Marine and Estuarine Ecology Lab at UNSW, the genetic material I extracted will be sequenced and matched to a database of known organism sequences, in a process called DNA barcoding.

Eliza looking very serious in her white lab coat

Like DNA extractions of the old school variety, the endeavor required donning a white lab coat, goggles, and gloves, and making sure not to sneeze or shed excessively. Unlike genetic adventures past, the materials needed for the extractions were available in a self-contained kit shipped par avion from Texas — no gels or interpretation of specific sequences was needed, and the entire process for many 10s of samples took only a single work day (20 years ago, comparable work might have been the focus of an entire PhD).

Vials and pipetting tools for the final stage of DNA extractions

I hope results from the day’s genetic escapades will yield helpful information about both the microbial and invertebrate community on manmade and natural shorelines in urban settings, such as Sydney. And I’m thrilled to report there is a chance that by the end of my lifetime, I could be scanning Earth’s ecosystems, Tricoder in hand, with my best interpretation of a female embodiment of Lieutenant Spock.

Tricorder from Star Trek: The Next Generation.

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This Week In The Lab

Hello again from down under

Hello again from down under! Henna Wilckens (intern) and I are deep into processing the sediment samples we collected last month from the bottom of Sydney Harbour. From our temporary work post at the University of New South Wales, we aim to sort through each of the millions of tiny sediment grains in our frozen samples to extract anything that once wriggled, crawled, filtered, or respired. The identity and number of creepy crawly critters in our samples will help us discern whether marine communities adjacent to man-made seawalls and pilings differ from those adjacent to natural rocky shorelines. All of this is part of a project I’m doing as an NSF EAPSI fellow with my Australian host, Dr. Emma Johnston, and post-doctoral researchers in her lab (link to earlier post).

Surprising as it may be, we’ve thus far encountered a number of striking and beautiful organisms within the urban muck.

A carnivorous polychaete worm from Syndey Harbor

Snail from Sydney Harbor

A snail cacophony from Syndey Harbor

Ostracods (tiny shelled crustaceans) from Sydney Harbor

Foraminifera from Sydney Harbor

Single foraminifera

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This Week In The Lab

Gettin’ Dirty in Sydney Harbor

It’s been a week of gettin’ dirty in what must be the world’s most beautiful urban waterway: Sydney Harbor. After several early mornings, a bit of sea time, and some good ole manual labor, I’m happy to say our field work is complete! We’ve collected sediment samples and epilithic (animals that live on rocks) specimens from four sites and are now ready to hit the lab.

Top: Sydney Opera House as seen while underway to Gore Cove, one of our field sites. Bottom: Side of our SIMS-based research vessel, heading west past the opera house and towards Balmain, another inner-harbor site.

We launched out of the Sydney Institute of Marine Science (SIMS), a marine lab in the heart of Sydney Harbour that was established just over a decade ago in a collaboration between four major universities: University of Technology Sydney (UTS), the University of Sydney, Macquarie University, and UNSW. SIMS has provided easy boat access, lab facilities, and much more established means for collecting samples than I’m used to in Seattle. Sample collection didn’t even require trespassing or intertidal bouldering with heavy equipment! It was lovely.

The only downside was learning that Bull Sharks are not just a curse inflicted on the good people of Florida; these aquatic hunters also patrol the waters of Sydney Harbor and also happen to be to source of all my deepest darkest fears (“great whites? tigers? no problem… wait did you say bull sharks?”). So, my usual approach of diving in to collect samples by hand was not going to work. Luckily we were able to deploy tools from the surface to collect samples at the murkiest of our sites. I’m happy to say all samples are now safely stashed in cold storage awaiting analysis, and I still have all my appendages and a beating heart.

Data collection in Sydney Harbour. Left: Deploying the “Van Veen grab” to collect sediment. Right: Transferring a small amount of sediment into tiny vials for DNA extraction, while intern Henna Wilckens deploys the Van Veen grab over the side for another sediment sample.

Stay tuned for more on the wild and beautiful creatures in our samples, and on my adventures in lab as I explore food web relationships in Sydney’s urban marine ecosystems.

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Happenings

Greetings from Down Under

Greetings from down under! I’ve just arrived in Sydney to work with one of my all-time top science heroes, Dr. Emma Johnston, at University of New South Wales (UNSW). It’s all thanks to support from the National Science Foundation and the Australian Academy of Science, through a program they jointly fund called EAPSI – East Asia Pacific Summer Institute.

Twitter post following rocky landing in Sydney

My Twitter post after landing amidst Sydney’s 100-year storm

Of course, it’s not at all summer here in Australia. My approach into Sydney Airport was among the most exciting aviation experiences I can recall due to a 100-year winter storm that was pounding the coast of New South Wales. Upon deplaning, I discovered a usually fair-weather city deep in the throes of winter weather chaos. City buses were rerouted, sirens of emergency vehicles chirped persistently in the distance, and Hassan, my Uber driver, had to turn around on three different occasions to avoid downed power lines.

Of course, my first reaction as a wise American tourist was to instantly flock to the water’s edge to watch. Here was the scene above iconic Bondi Beach in East Sydney:

Zaza Silk (pictured) lost her swimming pool and her mother’s ashes as the sea gobbled up her yard and home. Photo credit – top: © Seven/Sunrise, bottom: Peter Rae.

Harrowing stories from the storm’s victims have since emerged. Storm surge and wave action seized up to 50 horizontal meters of shoreline in a single night in some locations, wreaking havoc for residents and businesses.

Of course, the fact that the sea poses such a risk to coastal communities (both in Australia and around the world) is a small part of why I am here conducting research. I study the artificial structures we build to protect shorelines from seawater inundation, also known as shoreline armoring. As climate change raises sea levels and human populations migrate towards the coasts (Neumann et al. 2015), the need for shoreline armoring is more critical than ever. Yet, we must balance this need with the potential negative consequences of armoring. Previous research suggests that artificial structures such as seawalls and breakwaters alter the composition of marine ecosystems (Bulleri and Chapman 2010). These changes could influence the goods and services that marine ecosystems provide to coastal communities, such as pollution processing and recreational fishing.

Over the next few months, I will work closely with researchers at UNSW to examine how marine trophic (feeding) relationships compare between natural and armored shorelines in Sydney Harbour. Sydney is the epicenter for research on urban marine ecosystems, and researchers here have unparalleled knowledge of the species that live on artificial structures locally. This knowledge will enable me to use stable isotope analysis and next generation sequencing to identify the position of each species in the food chain and its original source of photosynthetic energy. By comparing these characteristics between organisms living on altered and natural shorelines, we will gain insight into how the structure and function of marine communities may be influenced by shoreline armoring.

 

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Sites and Critters

Sea Lions as urban megafauna

Sea Lion pup in restaurant booth (c) Mike Aguilera

Sea Lion pup in restaurant booth (c) Mike Aguilera

The owners of the “Marine Room” restaurant in San Diego were certainly in for a surprise this morning, after an eight-month old sea lion pup found her way into their establishment overnight and decided to set up shop. She was quite obviously grumpy when a marine mammal rescue team arrived to take her away (right). You can read the full story and see the video of her deportation here from the LA Times.

(c) The Cave Store

(c) The Cave Store

Oddly enough, this was not the first strange sea lion encounter in San Diego this year. Back in January, another California Sea Lion pup (left) climbed up 145 steps from the beach below to colonize a gift shop in La Jolla; the desperado allegedly would only vacate the premises upon being bribed with salmon. In addition, this young sea lion decided to hitch a ride with a random paddle boarder near the Coronado Bridge back in October, though no ransom was reported for the high jacking:

If you’re thinking to yourself: ‘Why on Earth are sea lion pups moving into restaurants and gift shops?’ you’re not alone. Representatives from Sea World suggest that high tides and high sea surface temperatures associated with El Niño have reduced the food supply for California Sea Lions. Indeed, coastal areas in the Pacific have experienced abnormally warm temperatures as of late, and a recent paper from Bernardo Shirasago-Germán and colleagues in Mexico highlights that pups and young adults are particularly vulnerable to environmental fluctuations like higher sea surface temperatures. But further science on the matter has yet to hit the primary literature as far as I can tell. While the pup who found her way into the restaurant last night was apparently tiny for her age, it’s not clear to me whether her journey, and that of her gift shop- and paddleboard-invading comrades can be effectively linked to climate-induced food shortages.

(c) Takashi Hososhima

(c) Takashi Hososhima

Marine mammals may well serve as the canary in the coal mine for large-scale ecological changes in the ocean, but perhaps a different species would be a better representative for such an important task… one that’s not inherently so curious and unruly. California Sea Lions have lived and interacted with humans in heavily urban areas for as long as I can remember. When I was a girl, they took over a popular tourist destination in San Francisco and have remained in charge there ever since (left). In Seattle, they do just as they please on the buoys and barges operated by the port (at the top of this post). And when I’m underwater, they generally seem quite keen to make their presence known (below).

Perhaps it’s best to think of them like other urban wildlife, such as raccoons and coyotes – natural in a sense, but there in large part because of their ability to thrive in dense urban centers. This is all conjecture, of course, as much work would be needed to confirm whether California Sea Lions are indeed the type of generalist consumer the has adapted to urban life. Just something to ponder next time a sea lion wanders into your neighborhood coffee shop or corner market.

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Sites and Critters

Winter is coming

Winter is coming… well, it’s here really. January is a time of change and rebirth for many species in the seasonal seas of the Pacific Northwest. Perhaps this is true for none more so than the Giant Pacific Octopus, Enteroctopus dofleini. As the largest known octopus species in the world, these graceful giants are prominent inhabitants of Seattle’s underwater environment and serve as a captivating icon of local marine ecosystems for many Seattleites.

Despite their considerable size, Giant Pacific Octopus are thought to live only 3 years on average. And they’re semelparous… meaning they reproduce only once before they die. In their final year of life, the male presents a spermatophore to the female using a special tentacle called a hectocotylus. She carries the spermatophore around delicately for some time. Then, as winter descends, she establishes her clutch of fertilized eggs in the safety of her den. For months, she works tirelessly to keep them clean and protect them from predators. She doesn’t eat or leave their side. They remain her focus for the remainder of her life. With luck, she’ll survive to see the eggs hatch and her offspring swim off into the great blue world that awaits.

In the video below, you’ll see fertilized octopus eggs in a den we found last year under a fiberglass boat that was resting on the seafloor at a depth of about 50ft (in south Seattle). My video skills are admittedly horrific. Though the mother’s body isn’t visible in its entirety, you’ll see her flush the eggs with the end of her tentacle repeatedly (if you look very closely).

However, for a very sweet and far better visual exploration of an octomom’s final days, see the beautiful video by Drew Collins (below):

 

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