If you ever are asked to write a book chapter, think about your answer long and hard. When your boss tells you to contribute to a chapter, that’s one thing – you do it. But, if somebody else asks you to do it, realize that writing a book chapter will take up a lot of your time, and it may or may not turn out how you expect. My first experience writing a book chapter left me reconsidering the merits and benefits of writing it to begin with. Of course, my old boss told me to write it, so I did.
The book itself is a neat concept, as most book ideas are. The title of the book is Ecosystems and Biodiversity of the Arabian Gulf – Saudi Arabian Waters: 50 Years of Marine Research and it highlights the contributions to the study of the Arabian Gulf system by the Center for Environment and Water at King Fahd University of Petroleum and Minerals. Parts of it are great, but parts of it are not.
I contributed to two chapters, one that’s not great and another that’s fine.
The two chapters are on Plankton and the Pelagic Environment of the Arabian Gulf.
Here’s the deal. Publishing a book means deadlines. Hard deadlines. Deadlines based on the publisher’s needs and when they can slot printing your book into their schedule. When you are given a deadline by a book publisher, you kinda have to stick to it, or else your chapter may not be published at all. It’ll just get cut by the editor. Deadlines have to be met or else. A rush to meet a deadline on this book put us in a pickle.
I was a co-author on the Plankton chapter. I wrote the section focused on zooplankton and ichthyoplankton and let co-authors handle the portions on nutrients, environmental conditions, phytoplankton, and primary production. The sections that I wrote were thin and needed some extra details to make it better. I knew I needed to rework those sections, and I was hoping that the lead author would give me some pointers. Or, I was hoping to see what the other sections looked like so I knew what direction to take. The problem was that we got hit with a deadline – finish up by the end of the week! Almost everything I wrote was re-written at the last minute by someone else. The Zooplankton section of that chapter still retained some of my text to the point where I recognized a few sentences I wrote. Two or three of those words are mine, yay! The Ichthyoplankton sections was completely redone by someone other than me. That’s why the Ichthyoplankton section is wholly about shrimp. Shrimp are not ichthyoplankton. Ichthyoplankton includes fish eggs and fish larvae, but not shrimp. All the material I wrote about fish larvae in the Arabian Gulf got tossed out, for reasons that are still unclear. I still don’t know if or where my Ichthyoplankton section wound up. Probably, it just got deleted.
The second chapter went better, but the finished product still had some issues because of the rush to make the deadline. I was the lead author on the Pelagic Environment chapter. It was on me to deliver a final product that was solid if not spectacular. There were a few things we wanted to do to flesh out the final product, and, regrettably, we did not have much time to proofread everything. The end result is a book chapter that is short and has a few errors. It’s better than the Plankton chapter, but it still isn’t what I hoped it would be.
Ultimately, I think both chapters contain some good information and are decent enough primers for people interested in the Arabian Gulf, but they turned out quite messy. I refer to some of the chapters in the book, particularly those dealing with the Physical Environment of the Arabian Gulf (with “Physical” written as “Phisical” in the Table of Contents) and some of the fauna chapters, because they contain some good information. The real benefit of the book is the references, which are comprehensive and a good source of primary literature on the Arabian Gulf. If you want a basic overview of the Gulf, the book has some use, but, if you want accuracy and detail, use the references cited within the book to find the good stuff.
I will not say no out of hand to writing another book chapter. I will consider it. But, I will need to be very clear with the editor and/or lead chapter author on expectations and deadlines before I commit. I recommend that you do the same if anyone asks you to work on a book chapter.
Looking for a fun challenge? Got some time to kill? Why not dissect a fish and describe every bone of its skeleton?
Performing this task on the two species in the genus Xiphister was the first chapter of my dissertation.
Let me explain.
My dissertation research focused on the comparative anatomy of a family of marine fish called Stichaeidae. The goal of the dissertation was to reconstruct the evolutionary history of the family, and others thought to be its relatives, by comparing the skeletal anatomy of each genus. There are about 37 genera and 80 some odd species of stichaeids. Where does one begin to make these sorts of comparisons?
The primary literature was a good place to start. There is a lot of great fish anatomy work out there, and it’s possible to piece together a pretty good picture of the skeletal anatomy of most stichaeids just by reading previous publications. A sizable portion of my first year as a student went to familiarizing myself with that literature. I went as far as tracking down copies of the original descriptions of the two species of Xiphister, which both were published in 1858, one of which was in German.
The problem was that after months of research, while I was closer to understanding the anatomy of Stichaeidae, I was not quite where I needed to be. There were lots of discrepancies among publications. Terminology changed. Descriptions contradicted themselves. Some publications missed obvious features or ignored whole portions of the skeleton. Using the literature alone left me educated but confused.
What I really needed to do was pick a stichaeid, dissect it from head to tail, and focus on learning all the details of that particular fish. That species then would become the template for comparison of all the other species. I chose Xiphister for a few reasons. First, we had loads of them in our Nunnally Ichthyology Collection at the Virginia Institute of Marine Science, and we could easily go collect more near Friday Harbor Labs. Second, we had a good size series, meaning I could look at the development of their skeletal system. Third, they have some weird characteristics about their mechanosensory lateral-line system (discussed here) that I wanted to look at in more detail.
I used a combination of clearing and staining, whole fish dissections, and x-rays to look at their anatomy. Then, I pulled apart all of the major bits – the neurocranium, suspensorium and jaws, pectoral girdle, axial skeleton, and the like. Then, I illustrated and described every bone. It was time consuming and meticulous work. It was also incredibly effective at helping me learn the anatomy of a stichaeid.
This deep dive into the anatomy of Xiphister was the first chapter and second peer-reviewed publication from my dissertation (if you don’t count the Xiphister locomotion project that wasn’t technically part of my dissertation). In it, I was able to completely describe the anatomy of this genus, clarify points from the primary literature, and discuss their development. Even better, by working for this intimate knowledge of the anatomy of this genus, I had a basis of comparison for all of the other stichaeids and their relatives that was the main part of my dissertation.
Do you like puzzles? Have you ever thought about fish as super complex puzzles and wondered how they are put together? Let me know in the comments below or on Twitter!
One of the coolest adaptations of bony fishes is their mechanosensory lateral-line system. The lateral-line system is a network of sensory organs, called neuromasts, dispersed across the body. When water moves the hair cells that sit on top of the neuromast, a neuron fires that signals the fish’s brain that water has moved. By having a network of neuromasts across the body, fish receive constant information about the way water moves around them and how they move through water.
Neuromasts come in a few different types. One type is known as superficial neuromasts. These are small neuromasts dispersed across the body surface and are in direct contact with the water around the fish. Another type is called canal neuromasts. These are larger neuromasts that are enclosed in a canal just under the surface of the skin. The canals are open to the environment through a series of pores in special scales, called lateral line scales.
These canals, and the neuromasts inside, they interest me.
Fish tend to have canals on the head, known as cephalic canals, and on the body, known as trunk canals. The exact configuration of cephalic and trunk canals can be diagnostic in species identification. The different patterns of cephalic and trunk canals also have implications on mechanosensory lateral line function. Most fishes have a single lateral line that runs down the side of their body.
Most, but not all.
The family Stichaeidae is one of the few fish families in which some species have multiple trunk canals. The condition is variable across the family. Some stichaeids have no trunk lateral line canal, some have a single canal, some have multiple canals with lots of branches, and some have a complex mesh network of canals. Why all that variation? I haven’t a clue. This question is the main reason I selected Stichaeidae as my family of study for my dissertation.
When I came to the Virginia Institute of Marine Science (VIMS) to work on my dissertation, I joined the lab of Eric Hilton, curator of the Nunnally Ichthyology Collection and expert in fish anatomy. This was perfect because I wanted to learn more about fish anatomy. The problem when I arrived at VIMS was that I didn’t know where to start. I had no clear picture of what it meant to study fish anatomy. There are 35,000 species of fish. How do I pick one or one small group to study in excruciating detail, the kind of detail that would see me sink years of study into that species or group? It turns out that I needed to find a group about which I could ask interesting questions.
Why does the stichaeid genus Xiphister have multiple lateral line canals? Do they do anything? Are all of those canals functional? Easy. Now I had my questions and the start of a dissertation.
The first publication of my dissertation (aside from the Xiphister locomotion project) was this one describing the structure of the lateral-line canals in Xiphister. Both species of this genus actually have four canals that run down the body. The question was – do all of these canals contain neuromasts? That is, are all of the canals functional?
To get at this, I used histology to look at the cellular structure of the canals. I examined thin sections of the head, looking for neuromasts inside the cephalic canals, and several sections of the body, looking for neuromasts in the trunk canals. The results were fascinating, and not at all what I was expecting. The cephalic canal had neuromasts pretty much where you would expect them. There was nothing too exciting there, except to say it probably functions normally. The cool part was in those trunk lateral-line canals.
Only two of the four canals in Xiphister actually contained neuromasts. The other canals on the body were just accessory canals, meaning they could not possibly function as part of the mechanosensory system. Ultimately, I don’t know why Xiphister has extra canals that lack neuromasts, but there are a couple of possibilities. One explanation is that all canals in Xiphister, at some point in evolutionary history, contained neuromasts but two of the canals have subsequently lost them. Another possibility is that canal formation in Xiphister operates independently of neuromasts. This would be interesting, because the current idea behind lateral-line canal formation says that neuromasts are required to start the process of canal formation (it’s a complicated mechanism that postulates all neuromasts start on the surface and the canal neuromasts are enveloped by a tube that forms around them). If the latter situation is true, then that means there is another, unexplained mechanism for canal formation.
This project also allowed me to do some additional cool things. I looked at the support structures of the canals, talked about scale development in Xiphister, and even developed a technique to describe the complexity of lateral-line canal patterns using fractals.
I wish I had more concrete answers about Xiphister and their strange mechanosensory systems, since there are still lots of questions. But, at least we now know more about these weird canals. Some of the things learned from this project will assist broader studies of mechanosensory system evolution and function across all bony fishes, which is pretty cool.
What do you think of fishes' weird mechanosensory system? Let me know in the comments below or on Twitter!
Fish larvae are my jam.
I cut my teeth as a newbie ichthyologist by working as a larval fish taxonomist for an environmental consulting firm. I spent 40 hours per week mostly looking through a microscope and identifying fish larvae collected from the northern Gulf of Mexico. I held that job for three years, and I learned a lot about the taxonomy of the early life history stages of marine fishes. But, after three years, I felt I needed to learn more about the anatomy and ecology of larval fishes, more than what the consulting job was offering. I needed my PhD.
A big reason I made the decision to quit my job and to go study at the Virginia Institute of Marine Science (VIMS) was because my PhD advisor, Eric Hilton, was managing a project monitoring larval fishes moving into Chesapeake Bay. Joining his lab allowed me to do three things. First, Eric is the curator of the Nunnally Ichthyology Collection at VIMS, so I got to learn a thing or two about natural history museums, which was pretty good considering my current position as the Collection's Manager for the Department of Ichthyology at the Natural History Museum of Los Angeles County. Second, Eric is an expert on fish anatomy, so my dissertation project focused on comparative anatomy of fishes. And third, I got to have a leadership role on this project and stay in the world of larval fishes.
For this project (https://www.int-res.com/abstracts/meps/v527/p167-180/), we worked in collaboration with colleagues in Delaware who were doing the same sampling we were doing. Once a week, we would go out at night on an incoming tide and collect triplicate sets of larval fish samples. We also would measure a suite of environmental parameters. By doing this, we had a weekly record of environmental conditions and the larval fish communities in both Chesapeake and Delaware Bays for two full years. That’s a really neat data set and made for a cool comparison. Chesapeake and Delaware Bays are only about 175 kilometers apart, and they are two of the largest estuaries along the Mid Atlantic Bight (MAB). Understanding the diversity and the timing/duration of larval fish entering each bay has big implications for the ecology of the whole MAB.
We found that the two bays transitioned differently throughout the year. Chesapeake Bay featured two seasons: one in summer and another in winter. These seasons were defined in Chesapeake Bay by an abundance of gobies and anchovies in summer, and drums, flounder, and menhaden in winter. Delaware Bay, on the other hand, featured four seasons, corresponding to spring, summer, fall, and winter. Even though the bays are separated by only a short distance, structurally they are quite different.
This project wound up being a cool collaborative experience with several members of Eric’s lab and Tim Targett’s lab in Delaware. Filipe, Eric’s postdoc, handled the heavy lifting on the manuscript preparation, which is great because this project was not directly part of my dissertation research (more on that in future blog posts). Filipe did a lot of the data analyses and writing. My major contribution was to coordinate field sampling at our site in Chesapeake Bay and identify our larvae. Those are the skills I was already pretty good at, so I was more than happy to take on those tasks. By being involved in this research, I got to learn a lot more about the ecology of larval fishes along the MAB, so that was awesome.
Have any cool fish larvae stories? Let me know in the comments below or over on Twitter!
What is the best way to calculate biodiversity in fish communities? Is it to count of the number of species? Is it better to calculate phylogenetic diversity, which is the distance among fishes in a sample across the fish tree of life? What about functional diversity, which is a measure of the ecological role of a species? How does abundance, where some species are super abundant and others are super rare, or biomass, where some species are bigger and take up more space within the community, influence biodiversity?
It turns out there is no one way to calculate biodiversity. Lots of different calculations can be made, and they all take into account different aspects of an organism’s biology, ecology, and evolutionary history.
A big unknown in ecology is understanding how these different biodiversity metrics play out over space and time. Do all biodiversity methods paint the same picture? Which metrics agree with one another, and how do they differ?
In Lefcheck et al. 2014, our biodiversity class at VIMS tackled some of these questions. We analyzed a 10-year data set of Chesapeake Bay Multispecies Monitoring and Assessment Program data and compared several different metrics of biodiversity. We calculated things like Richness, Evenness, Gini-Simpson Diversity, Functional Diversity, Phylogenetic Diversity, and Taxonomic Diversity. Some of these metrics are common and widely used in ecology. Others are used less frequently. We even weighted the species data by abundance and biomass to see what that did to our results. For the big analysis, we compared how all of these different types of biodiversity assessment methods stacked up with each other, what they told us about biodiversity across Chesapeake Bay, and how they held up over multiple seasons.
There was a lot of coding in R. I mostly left this to my classmates. I was happy to help calculate Functional Diversity, which included a trip to the Smithsonian National Museum of Natural History to measure fish proportions, and get gene sequence data for the calculation of Phylogenetic Diversity.
It turns out that, most of the methods we used to calculate diversity gave the same basic patterns. Evenness wasn’t such a good measure, but all of the others compared favorably. Honestly, I was a bit surprised by the results. I assumed that the metrics would agree some or most of the time but fall apart when compared across seasons. The fish community in Chesapeake Bay follows some regular seasonal patterns, and almost every method we used picked up the patterns. There were a few fuzzy areas where the results did not always match up perfectly, but, by and large, several methods gave the same story.
Taxonomic Diversity, Phylogenetic Diversity, and Functional Diversity, which all take into account very different types of data to calculate biodiversity, were nearly redundant. Richness and Gini-Simpson Diversity also performed well. The only metric that was different from the rest was Evenness. The areas where the different metrics failed to match are interesting areas to look at in the future. What is it about those particular spots within Chesapeake Bay that caused the different biodiversity metrics to disagree?
Before this project, I hadn’t thought much about the subtle differences given by different methods used to measure biodiversity. This class offered an opportunity to explore some of those areas. Now, I try to incorporate multiple aspects of biodiversity measurements in my ongoing ecological studies. It’s funny how a single class project can influence the direction of your research moving forward. This is a topic that I would likely never have explored on my own, but, because I had seven other students and two professors who bought into this project, I developed a skill set that I am using today.
What is your favorite biodiversity metric? Let me know in the comments below, by email at firstname.lastname@example.org, or on Twitter!
Not all fishes are confined to the briny waters of the sea. A surprising number of fishes make terrestrial excursions, walking around on land like they own the place. There are gobies that climb waterfalls, fish that hop around mudflats, catfish that walk from pond to pond, and a whole bunch of fishes that can flop around on land in an effort to return to water. The reasons that fish move around on land are numerous and varied. They do it to look for food, escape conditions where the temperature, salinity, oxygen, or moisture content is hazardous to their health, move between locations, or return to water if they get stranded high and dry.
There is a lot of interest in how fish move on land. For some fishes, the ability comes from modifications of the skeleton. Strengthened pectoral- or pelvic-fin girdles. Fin spines or fin rays modified in some unique way. The exact modifications are of keen interest to researchers who study biomechanics, evolutionary biology, and ecology. Other fishes have no apparent modifications and yet still perform well on land.
Welcome to my second published research project: aquatic vs terrestrial locomotion in the rock prickleback - Clardy 2012!
The rock prickleback, Xiphister mucosus, is an intertidal fish that lives high up in the intertidal zone. Unfortunately for the poor rock prickleback, they occasionally get stranded at high tide in pools that dry out. They sometimes need to search for pools of water further down the shore slope. They do not have any obvious, weird adaptations that might help them move on land. Instead, they have elongate bodies and slither, snake-like, across the ground.
This project, part of the Functional Morphology and Ecology of Marine Fishes course at the Friday Harbor Labs in Washington, compared how rock prickleback swam in water and crawled on land. The goal of the project was to compare their locomotion to see if they do anything different between aquatic and terrestrial environments. To test this, I used high-speed video to film rock prickleback swimming in a tank of water and crawling over a bed of gravel. I measured a couple of locomotion parameters to see how efficiently they move.
It turns out that rock prickleback do not use any crazy tricks when they crawl on land. Fundamentally, they use the same mechanics they use in water. The difference is that their movements on land are exaggerated and their overall movement is slower. This works because their elongate bodies are efficient at generating propulsion in water, and they also are efficient at generating force on land. Basically, they coopt their already efficient swimming locomotion onto land.
Frankly, when I finished the project, the results did not feel all that groundbreaking or earth shattering. Rock prickleback don’t have fancy, modified fins, weird pectoral girdles, or other strange features that stand out. They just kinda make do with what they have. It turns out, though, that this is an important observation, and documenting this behavior is useful for researchers studying fish locomotion. I have been quite surprised by how many citations this little study has gotten in other peer-reviewed publications. The interest in this paper from the broader scientific community has far exceeded my expectations. You never know when the broader scientific community may value your small, simple study that produces clear, easy-to-understand results.
Are you a fan of land-loving fishes? Drop a comment below, via email at email@example.com, or on Twitter.
King mackerel, Scomberomorus cavalla, are biological torpedoes, sleek, long, silver bullets that live in nearshore waters of the Gulf of Mexico and US Atlantic coast. They are a popular gamefish throughout their range, known for making impressive first strikes on fish or squid lures. “Smokers”, they are called, for what happens to the gears inside fishing reels when a big one hits. They are feisty fish, and big too, with an IGFA world record of 42 kilos (93 pounds). They are important for recreational fisheries in the southern US, and they also support a substantial commercial fishery.
Management of king mackerel is a bit complicated. First, they are found across two management zones, one in the Gulf and a second in the Atlantic. Second, they are seasonal migrators – they move south when water temperatures cool during fall/winter and north as water temperatures warm again during spring/summer. During winter, both Atlantic and Gulf migratory groups are found in south Florida where they mix around the Florida peninsula. Problematically, they both experience recreational and commercial fishing when they are mixed up. So, what is the effect of these mixed-up fish around Florida for the overall management of the species? It would be helpful if we could determine how many fish from this mixed region were of Gulf and Atlantic migratory-group origin.
Welcome to my Master’s thesis and my first publication, Clardy et al. 2008!
My mission during my thesis was to perform otolith shape analysis on Gulf and Atlantic king mackerel during summer when they are separate, and then do the same for fish collected in winter around the Florida peninsula. The overall goal was to estimate the proportion of Gulf and Atlantic migratory groups to the winter catch in three zones around the Florida peninsula so that management of the species could be improved. Up to that point, the fisheries management approach was a bit arbitrary in assigning all fish from south Florida to either the Gulf or Atlantic depending on the time of the year. If I could determine the pattern of how Gulf and Atlantic fish mixed up in winter, then managers could have a better idea of what to do with the fish caught in south Florida.
Wait. What’s an otolith? And what does their shape have to do with anything?
Otoliths are structures in the inner ear of bony fishes that the fish use for balance, hearing, and orientation. They are composed of calcium carbonate and continuously grow throughout the life of the fish. They wind up being super important for fisheries scientists for a variety of reasons, primarily as a way to age fish. It also turns out that otolith shape is species specific. So, the shape of a king mackerel otolith is different from that of its close relative, the Spanish mackerel, Scomberomorus maculatus. Even better, the shape of otoliths within king mackerel is different between Gulf and Atlantic groups, because Gulf and Atlantic fish have different growth rates. Good news for me.
I performed shape analysis on otoliths from over 1100 mackerel collected from the Gulf and Atlantic. I used a suite of shape analysis metrics, everything from otolith length and width to Fourier analysis. I broke down the fish by year, region, time of year, sex, age, and even left vs right otoliths. Once I calculated the shape of Gulf and Atlantic king mackerel otoliths from summer samples, I broke Florida into three regions and calculated the origin of winter-caught fish around the Florida peninsula.
This analysis was before the days of R, so it was done with a combination of Image Pro, SAS, and a customized program in S-Plus. I melted down a computer estimating the proportion of Gulf and Atlantic fish around Florida in winter. I had to run part of the analysis in batches due to RAM issues; if I tried to run all the data at once, the RAM allocated to S-Plus would fill up, and the computer would crash. I melted down my personal laptop running the analysis due to overheating and had to borrow the lab laptop to finish up.
At the end of the analyses, I had a pretty good estimate of mixing of king mackerel around the Florida peninsula during winter. On the Gulf side of the peninsula, 2/3 of the fish were from the Gulf, at the southern tip of the peninsula, the breakdown was 50/50 Gulf/Atlantic, and on the Atlantic side of the peninsula, 2/3 of the fish were from the Atlantic. These results are a bit intuitive if you think about it. The cool thing was that I was able to put numbers on the estimates and hand that off to the king mackerel management council. It’s the equivalent of showing your work in math class. We published a peer-reviewed manuscript that shows all the gritty details, so managers have a clearer understanding of a complex issue.
King mackerel management is one of the great success stories in US fisheries management. Things were going pretty well before I came along. Catches for both recreational and commercial fishing are in good, stable shape and have been for a few decades. I’m happy that my thesis helped improve management going forward so that the future of king mackerel fishing remains bright.
Have you ever tangled with a Smoker king? Want to know more about otoliths? Drop a comment below, via email at firstname.lastname@example.org, or on Twitter!