Over a year and a half after finishing my PhD, all of my work is now published! Academic publishing typically takes forever, due to rounds of peer review and fiddly logistics and extremely high costs—but more on the silly world of contemporary academic publishing in another post. Today, I'm going to summarize what I wrote about in my dissertation.
Where I got my PhD the requirement is that a dissertation has at least three components that are substantial enough to become academic papers. I wrote three chapters, each of which has now gotten published. They are all open-access, so you should be able to freely download the PDFs! The absolute shortest summary is that I asked three questions:
- Where are there waves in protected bays, and what makes them? (paper 1, 2023)
- How do those waves cause erosion/retreat at the edge of a salt marsh? (paper 2, 2024)
- When a salt marsh erodes from waves, where does the mud go? (paper 3, 2025)
I wrote the first paper after doing field work in Tomales Bay, California, with John Largier at U.C. Davis Bodega Marine Lab. He's a coastal oceanographer who has worked in Tomales Bay for decades and he knew the system well. The project began by trying to understand the beaches in the bay, but evolved into a study on the waves.
Beaches, prototypical, are built by waves. Waves have enough energy to move sand around, so they pile it up in places where there is enough sediment supply and enough wave energy, creating beaches. Tomales Bay is a very long, skinny bay (it's created by the San Andreas fault line), making for ostensibly very protected waters—yet there are lots of beaches. This is the interesting question we started from.
It's easy to see Tomales Bay's linear nature from the sky. Sorry for the crummy figure: I've lost my Adobe access as I switch institutions.
Tomales Bay's linear structure makes it a great natural laboratory: there's a clear gradient from its mouth to the ocean going up-bay to the marshes at Point Reyes Station (on the right end of the bay in the image above). The dominant direction from which both wind and swells come is the northwest, which means winds and waves enter the bay and go straight down its main axis! What I found, from a sensor deployment, was that the ocean wave (swell) influence is strongest close to the mouth of the bay, and the influence of wind waves (chop)—i.e. waves created inside the bay—get stronger the deeper up-bay you go. And, interestingly, both swell and chop are modulated by the tidal depth in the bay (which is quite shallow—often just a 1-3 meters deep), but in slightly different ways. Wave fields of shallow and protected bays are actually relatively understudied, compared with the open ocean where people love geeking out about how storms make big waves that are relevant to global shipping and sailing industries. So while hat I found isn't exactly groundbreaking, it hadn't been documented before, and it has ramifications on what kinds of beaches are made by what kinds of waves across the bay.
Figure from my Paper 2! Black arrow in Panel B indicates dominant warm-weather (sea breeze) wind direction.
Paper 2 brings us to San Francisco Bay, where I worked with the U.S. Geological Survey's Jessie Lacy who spent most of her career tracking marshes and sediment around San Francisco Bay. We studied Whale's Tail Marsh, a small (<1 square kilometer) marsh on the eastern shore of South San Francisco Bay. This means the marsh is downwind of the dominant winds over the bay—which blow mostly from the west/northwest, at the widest part of South San Francisco Bay. Lots of wind over a wide stretch of water mean that this marsh is exposed to some of the biggest waves possible inside the bay (I think). The marsh is shrinking quickly as waves cut away at its shoreline, often retreating >1 m/year. I showed, using aerial imagery and 3D models of the marsh, that this rate is quite heterogeneous in time and space over one specific year: almost all of the retreat happened in the spring and summer (the windy seasons, where the sea breeze is very strong) and almost none in the fall and winter. Also, some parts of the marsh eroded quickly and some barely at all over the study year—but over longer time periods (like the past decade), the retreat was spatially homogeneous. Again, not really surprising, but almost nobody had quantified marsh-edge retreat at sub-annual or within a single site timescales before.
For paper 3 I continued to write about the study of Whale's Tail Marsh (note, I've written about it previously in Gnamma), now using sensors that me and the Geological Survey's team installed over our study year. When the edge of the marsh erodes, where does the sediment go? Sediment is a pretty in-demand resource in San Francisco Bay: delivery has changed a lot since pre-colonial times, lots of the accessible sediment is polluted, but there is growing demand to use it for habitat restoration projects. So, knowing how it moves between the marshes—which are focal points for water quality and bird/fish habitat—and the rest of the bay is crucial.
From Accelerated and Decelerated Landscapes by Bretty Milligan.
I found that quite a bit of the sediment lost from edge erosion seems to stay around, either accumulating in the mudflats or getting piled on top of the marsh by the tides. The mud that ends up on the marsh tends to be very close to the edge, of either the bay or the creek that goes up into the marsh, which suggests how the marsh evolves as a 3-dimensional form: with little tiny mud "levees" close to the bay and the creek and shallow depressions in-between. We kept track of sediment movement and deposition with sensors that quantify water velocity and the sediment carried by the water, as well as with tiles that let the sediment deposit on top (so we could weigh it).
My sediment budget of the marsh and its back-marsh system (in blue). Numbers are daily masses of sediment, but generated from annualized volumes.
With all these data, I was able to roughly close the "sediment budget" of the marsh. Nobody, to my knowledge, had ever done this before!? (People do sediment budgets of rivers all the time, though, or at more regional scales, but not ever of a single marsh.) It's really data-intensive to do this, given the complexity of tidal marshes with three-dimensional flows and subtle amounts of deposition, but the Geological Survey has amazing tools and capacity, and we showed it could be done. The marsh is actually net gaining sediment, even while it shrinks laterally, so it is getting taller and taller. Unfortunately, this steepening makes its edge to the bay even more unstable and prone to erosion from waves, so this process has been called "marsh cannibalization." Even a marsh with a positive sediment budget may not be stable.
And that's the three papers! This work has generated a lot of questions for me, around the mechanics of shallow-water wind waves, how sediment gets trapped in specific parts of the marsh, the importance (or not!) of extreme events like storms and king tides, as well as the necessity of giving marshes enough space to grow and shrink: Whale's Tail is hemmed-in by levees, leading it to just shrink, shrink, shrink.
Some of the most fun of this science, to me, is figuring out all of the methods, which inevitably get buried in the details. How do you effectively handle wave spectra with lots of boat wakes? How can I reasonably combine errors from different processing steps of the 3D marsh model into a single number? How homogeneous is the sediment across the marsh, or do I need to assume it varies a lot? Some points like these are in the papers, but many of them are not, relegated to my crappy memory or some folder on a hard drive that now lives in the back of my closet. If I continue in a research career, I may be able to uncork these data again to keep asking more questions: the U.S. Geological Survey takes its data collection seriously, and data publications (like this) are done to very high standards; I believe there is a lot more that can be squeezed out of the aerial imagery and sensor data that I worked with. (Maybe less so in Tomales Bay, but the questions about genesis and maintenance of beaches in estuaries and bays remain). I'm so thankful for the mentors I had—John, Jessie, and my advisor Mark—who made it all seem fun and valuable to keep going, which I now still believe, on my own.
It's dizzying to see five years of work become three PDFs, but that's how the process goes: condensing many open-ended ideas and workflows and discussions into a hard-baked puck for others to read and benefit from. If you give the papers a read, please let me know any thoughts or questions!
Lastly, I have turned on paid subscriptions for Gnamma! You can modify your subscription via the Buttondown interface. I will keep it free in general but if you are a big fan, consider giving $5/month, which helps me prioritize more writing, and more thoughtful writing: a post every two weeks, or maybe every month for chunkier ones. I'm really excited to give this a shot and raise the stakes on my writing!
Watching the waves chop away at the marsh,
Lukas