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 email@example.com, 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 firstname.lastname@example.org, 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 email@example.com, or on Twitter!