Research Overview
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My research focuses on developing quantitative tools to predict the life history, distribution and abundance, and conservation status of species. Most of the tools I build focus on melding natural history, formal models of ecological processes, and modern big data approaches. Current research projects include dynamic ocean management in the Central Pacific, integrated Bayesian life history models, and pelagic shark community assembly.
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DISTRIBUTION MODELING
Distribution modeling is a key step in defining species-habitat relationships and resolving higher order dynamics such as drivers of abundance, community membership, biodiversity patterns, and ecosystem structure. As such, I perennially return to distribution modeling to take advantage of the advancements, contribute to advancing modeling components, and applying these models to new taxa. Below are a few of my past and ongoing projects.
(Above) An example distribution map for one of the shark species that is caught as bycatch in the Hawaii-based tuna and swordfish pelagic longline fisheries. Warmer colors indicate a higher probability of bycatch.
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Ensemble Random Forests — How can distribution models be built when there are exceptionally few locations where a species is detected? Recent work with the NOAA PIFSC and WPRFMC has lead to the development of the Ensemble Random Forest algorithm to tackle datasets with rare and ultra-rare presences but a host of absences. This machine-learning approach is an intuitive extension to the Random Forests algorithm and has very high performance at predicting where the species is present. Published in Endangered Species Research. This model has been used to model the distribution of rare cetacean species in the Mariana Archipelago and is published in Frontiers in Marine Science.
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Benthic-oriented species -- With marine species associated with structure, it can be difficult to model their fine-scale habitat associates because tradition environmental covariates have little influence (e.g. sea surface temperature or chlorophyll-a) or have poor resolution (e.g. bathymetry). Recent work with the Red Snapper has led to the development of a big-data, high-resolution predictive distribution model for the whole Gulf of Mexico. With this model, I developed camera-based sampling designs for an independent population assessment. Further research will be looking at how the availability and quality of Red Snapper habitat influences angler catch rates.
(Above) The distribution of Red Snapper in the Gulf of Mexico (< 100 m in depth). Warmer colors indicate a higher probability of presence (not abundance). Multiple datasets from NOAA SEFSC, NOAA NOP, FWC FWRI, and NOAA SEAMAP were used to build the Random Forests predictive model that made the above map.
(Above) The September distribution of Basking Sharks in the Bay of Fundy. Sharks are concentrated near Grand Manan Island but have started exiting the Bay and heading south into the Gulf of Maine.
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Basking Sharks -- The Bay of Fundy is a hyper-productive gyre system in the Northwest Atlantic and has some of the strongest tidal swings in the world. Intense phytoplankton blooms are grazed heavily by Calanus finmarchicus copepods which, as the bloom wanes, diapause in the deep-waters of the bay, Grand Manan Basin. These sinking, resting copepods form a thick layer of prey that Basking Sharks travel from the warm-waters of the Caribbean to consume. My master's research was concerned with resolving the spatial dynamics of Basking Sharks within the Bay of Fundy over the course of their visiting season (June - October). A maximum entropy distribution model was used to determine the spatial patterns from 23 years of presence-only locations. You can hear more about this research with an interview I did with CBC's Paul Castle in 2013 (on the left).
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FLORIDA LAKES
Most of my PhD research was conducted in four picturesque north Florida lakes located on BJ Bar Ranch. Unlike many Florida lakes, these lakes were relatively deep (23, 20, 19, and 8 feet in maximum depth) and weakly stratified in the winter months. Two of these lakes were augmented by small and large brush piles in nearshore and offshore habitats and all the lakes were monitored before and after the augmentation. The Florida Bass population was tracked in a mark-recapture study as well as the piscine and testudine community was monitored using cameras for a year and half post-augmentation. With over 400 field days on the BJ Bar Ranch, it was hard not to deeply appreciate the opportunity to immerse myself into these rich freshwater habitats as well as be grateful for the access provided by the landowners and funding by FWC FWRI.
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Florida Bass Mark-Recapture — As part of my PhD, I was interested in how the Florida Bass population might respond to habitat augmentation. I took advantage of many students before me tagging individuals with Floy (see the yellow tags in the top video) and PIT tags to track the abundance of Florida Bass in lakes with and without the augmentation. I used day and night electrofishing (see the bottom video) as well as angling to mark new fish and recapture previously tagged individuals with the help of many friends, technicians, and volunteers. I found very little effect on Florida Bass population dynamics following augmentation in the time frame of my study. This was not terribly surprising as the brush piles did little to increase primary productivity in the systems and, thus, did not alleviate the density-dependent bottleneck on young-of-the-year fish.
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Lake Community Dynamics — The most laborious and enjoyable component of the Florida Lake research was conducting camera monitoring of each lake in areas with and without brush piles. With 642 camera surveys completed, 18 terabytes of video, and 9, 575 fish observed, there was a lot to analyze. In my dissertation, I was primarily concerned with changes in the hyper-local community throughout each lake. I observed that brush piles were strong habitat filters overall with the effect exacerbated in the speciose lake. Larger-bodied taxa were more likely to occupy brush piles than small body fish though fry and age-0 Florida Bass as well as Bluegill fry did occupy the brush piles following spawning season for the respective species. For the analysis, I extended a multilevel occupancy model to a multi-species variant.
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ELASMOBRANCH LIFE HISTORY
Elasmobranchs are priority conservation concern worldwide. A lack of life history information is a key stumbling block for assessing data-deficient species of sharks, skates, and rays. One key component of life history is the age-growth relationship which can be used to infer maturity, longevity, and mortality. Many suggestions have been made on how to best approach age-growth analytics in elasmobranchs but there is a lack of a unified approach that can handle the variety of issues common to aging elasmobranchs. I have been working on a series of papers defining a new integrated life history model to tackle this critical gap in elasmobranch conservation. These papers have included a variety of taxa that have helped refine the culminating framework and have opened opportunities to work with international elasmobranch biologists.
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Brazilian Guitarfish — Led by Dr. Fabio Caltabellotta, I developed a Bayesian age-growth model for Pseudobatos horkelii, Pseudobatos percellens, and Zapteryx brevirostris in southern Brazil. The resulting model was used to estimate age and growth parameters for these three priority guitarfish species listed as Critically Endangered, Near Threatened, and Vulnerable by the International Union for the Conservation of Nature. Now published: doi: 10.1111/jfb.14123
(Above) Bowtie sections of guitarfish vertebrae for the three Brazilian guitarfish species showing off the classic banding patterns left behind by annual growth spurts. (Left) Age-growth relationships for three Brazilian Guitarfish species. Age is on the x-axis in units of years and growth is on the y-axis in units of centimeters of total length.
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Brazilian Electric Ray — Led by Dr. Fernanda Rolim, a postdoc at Universidade Estadual Paulista in São Paolo, Brazil, I extended the Brazilian guitarfish model to estimate two-dimensional growth of Narcine brasiliensis, the Brazilian Electric Ray, in southern Brazil. The joint estimation of length-weight and age-growth parameters was added along with derivations of age at maturity, longevity, and mortality at age. A significant component was incorporating uncertainty in size at birth into the von Bertalanffy growth model.
Now published: doi: 10.1111/jfb.14378 |
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(Above) Silhouettes of Goblin Sharks through the ages. (top) 1898 in the description of the species by David Starr Jordan. (top middle) 1904 by King Bragança of Portugal. (top bottom) 1909 by Hussakof and the renaming of Mitsukurina to Scapanorhynchus for a time. (bottom) 1981 by Cadenat and Blache in Requins de Méditerranée et d' Atlantique.
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Goblin Shark — Led by myself and Dr. Fabio Caltabellotta, we estimated the first age-growth relationship for Goblin Sharks (Mitsukurina owstoni), one of the largest deepwater sharks. Fabio developed a method to highlight the classic banding pattern that allowed an age reading on a specimen caught in Brazil in 2008. I developed a Bayesian age-growth model that used back-calculated lengths at age from this specimen, data on maximum male sizes, and data on size at birth to estimate the first age-growth parameters for the species. We are excited to age more specimens in the future. Now published: doi.org/10.1071/MF19370
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FISHERIES MANAGEMENT
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Protected Species Bycatch — As part of a collaboration with the NOAA Pacific Islands Fisheries Science Center, NOAA Pacific Islands Regional Office, and the Western Pacific Regional Fisheries Management Council, I have worked to help model the trajectory of two populations of protected sea turtle species: western Pacific Leatherbacks and north Pacific Loggerheads. This species are caught incidentally on the Hawai'i and American Samoa pelagic longline fisheries. Using a Bayesian population trend estimation and a "take" model with demographic and fishery stochasticity, we estimated negligible impacts of the Hawai'i shallow-set, deep-set, and the American Samoa longline fishery on the two populations. Unfortunately, other external threats are negatively impacting the trend of western Pacific Leatherbacks, which are likely to go extinct before the end of the century. Our findings are published in two NOAA Technical Memorandum: TM-PIFSC-95 & TM-PIFSC-101.
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DYNAMIC OCEAN MANAGEMENT
Central North Pacific — My ongoing research builds dynamic ocean management tools for the Central North Pacific in collaboration with the NOAA Pacific Island Fisheries Science Center and Western Pacific Regional Fisheries Management Council. The two primary pelagic fisheries are the Hawaii-based Bigeye Tuna and Swordfish using longlines. Protected sea turtle, cetacean, seabird, and shark species are infrequently encountered by the fisheries but, due to their conservation status, each interaction is a potential cause for concern. But with the moving target of pelagic species, it can be difficult to effectively maintain sustainable fisheries alongside protected pelagic species.
Dynamic Ocean Management seeks to solve this by using risk maps or dynamically closed spatial areas to reduce bycatch. My research is exploring the effects on bycatch rates by building dynamic ocean management products then using management strategy evaluation to simulate how fishers might respond and evaluate the performance of the tools.
Dynamic Ocean Management seeks to solve this by using risk maps or dynamically closed spatial areas to reduce bycatch. My research is exploring the effects on bycatch rates by building dynamic ocean management products then using management strategy evaluation to simulate how fishers might respond and evaluate the performance of the tools.
PELAGIC BIODIVERSITY
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Pelagic species are often circumglobal, spanning most of the planet's oceans, resulting in pelagic megafaunal communities assembling from recombinations of mostly the same species. Some of my current research explores the governing assembly dynamics of these combinatorial communities. The aim of this research is to determine the influence of niche overlap and environmental drivers on community assembly. Initial research has been funded by the University of Florida Biodiversity Institute and is focused on dimensions of pelagic shark biodiversity.
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A key aspect of shark morphology is differences in teeth. As part of exploring pelagic shark biodiversity, I am leading research on shark crown photogrammetry to explore how crown morphological differences might explain community structure. (Above) Silhouettes of shark teeth crowns (4 lower, 4 upper, left to right) for seven shark species.
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MANAGEMENT
STRATEGY EVALUATION
STRATEGY EVALUATION
Red Snapper — Part of my postdoctoral research was building a management strategy evaluation model for Gulf of Mexico Red Snapper then actualizing the model into a decision support tool. The process involves translating the SEDAR 52 stock assessment into a spatialized model for the whole gulf. The decision support tool is being designed in RShiny. Dr. Fabio Caltabellotta lead the RShiny design while I built out the modeling backend. The tool was hosted for stakeholders to engage with and play management optimization game.
COLLABORATIONS
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Solving collaborative analytical challenges can be immensely fulfilling and bring solutions to diverse, interdisciplinary research problems.
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I have a variety of ongoing collaborations with a wide variety of researchers spanning multiple disciplines. Some exciting developments have been two recent manuscripts. One, on modeling the physical maturity using vertebrae fusing of the Common Bottlenose Dolphin (Tursiops tursiops) in the intensely monitored Sarasota Bay population. A second was an analysis of nanomaterial plating types on cellular growth. Both opportunities resulted in development and application of Bayesian techniques to take advantage of the way the data was collected. Ongoing projects include Everglades Stormwater Treatment Area phosphorous dynamics and morphological differences between Common Bottlenose Dolphin ecotypes. In the past, I have collaborated on assessing environmental drivers of Black Crappie (Pomoxis nigromaculatus) growth with Dr. Bryan Matthias, on algal bloom dynamics of Lake Okeechobee with the late Dr. Karl Havens, and on pine rockland plant community phylogenetic structure.
PAST PROJECTS
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Basking Sharks as ocean loggers — Before, during, and after my master's research on the vertical movement of Basking Sharks, 13 sharks were tagged in the Bay of Fundy with time-depth recorders. In addition, these biotelemetry tags recorded ocean temperature. Led by Dr. Heather Koopman and Dr. Andrew Westgate, I performed an analysis exploring how temperatures in the Bay of Fundy had increased from 2008 to 2012 before falling again in 2013. What was particularly concerning, was this warming was throughout the entire water column and indicated extreme changes in the Bay of Fundy over this time frame. Anecdotally, the extra warm summer of 2012 was incredibly different than year's past with warm-water species moving into the bay in large numbers, such as Blue Sharks, Great White Sharks, Sperm Whales, and Ocean Sunfish. In turn, it was a hard year to find classic Bay of Fundy denizens such as North Atlantic Right Whales and Basking Sharks. Fortunately, over a banter week in late August we managed to tag three sharks and saw over 30.
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American Lobster fecundity — My undergraduate thesis contributed to a larger overall investigation of the reproductive investment of American Lobsters (Homarus americanus) in the Bay of Fundy. We measured fecundity (number of eggs), egg energy content, lipid content, and fatty acid profiles. My part was determining the egg energy content which I did using a bomb calorimeter. This scientific instrument injects pure oxygen into a canister containing a sample of lobster eggs and ignites a fire using a small cotton thread. The resulting burn raises the temperature ever so slightly in the surrounding water bath which is measured precisely and converted to calories. Our results, published in 2015, showed that fecundity was declining in American Lobsters from 2008 to 2013 and that very large lobsters were likely undergoing reproductive senescence, investing less into reproduction than smaller lobsters.
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Reproductive energetics of Blue Crabs -- Between my undergraduate and master's projects, I worked on exploring correlates of reproductive investment, egg energy content, lipid content, fatty acid profiles, and zoea size, in Blue Crabs (Callinectes sapidus). We found none of the investment measurements correlated with female size and, instead, found environmental factors to likely be responsible for the variation in reproductive investment. Our results were published in 2013 in the Journal of Crustacean Biology.
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PUBLICATIONS
- McCullough J.L.K., Wren J.L.K., Oleson E.M., Allen A.N., Siders Z.A. & Norris E.S. (2021). An Acoustic Survey of Beaked Whales and Kogia spp. in the Mariana Archipelago Using Drifting Recorders. Frontiers in Marine Science. https://doi.org/10.3389/fmars.2021.664292
- Trotta L.B., Siders Z.A., Sessa E.B., Baiser B. (2021) The role of phylogenetic scale in Darwin's naturalization conundrum in the critically imperiled pine rockland ecosystem. Diversity and Distributions. onlinelibrary.wiley.com/doi/10.1111/ddi.13220
- Siders Z.A., Ducharme-Barth N., Carvalho F., Kobayashi D., Martin S., Raynor J., Jones T.T., Ahrens R.N.M. (2020) Ensemble Random Forests as a tool to model rare occurrences. Endangered Species Research. doi.org/10.3354/esr01060
- Siders Z.A., Havens K.E. (2020) Revisiting the Total Maximum Daily Load Total Phosphorous Goal in Lake Okeechobee. Hydrobiologia. doi.org/10.1007/s10750-020-04406-8
- Caltabellotta F.P.†, Siders Z.A.†, Cailliet G.M., Motta F., Gadig O.B.F. Preliminary age and growth of the deep-water Goblin Shark Mitsukurina owstoni (Jordan, 1898). Marine and Freshwater Research. doi.org/10.1071/MF19370
- Hazelkorn R.A., Wells R.S., Siders Z.A., DeLynn R., Lovewell G.N. (2020) Physical maturity in common bottlenose dolphins (Tursiops truncatus) from Sarasota Bay, FL. Marine Mammal Science. doi.org/10.1111/mms.12733
- Siders Z.A., Allen M.S., Walters C.J., Ahrens R.N.M. (2020) Density-dependent prey behaviors and mutable predator foraging modes induce Allee effects and variability in prey mortality rates. Freshwater Biology. doi:10.1111/fwb.13577
- Rolim F.A.†, Siders Z.A.†, Caltabelotta F.P.†, Rotundo M.M., Vaske-Júnior T. (2020) Growth and derived life history characteristics of the Brazilian electric ray Narcine brasiliensis. Journal of Fish Biology. doi: 10.1111/jfb.14378
- Martin S.†, Siders Z.A.†, Eguchi T., Langseth B., Yau A., Baker J., Ahrens R.N.M., Jones T.T. (2020) Update to Assessing the Population-level Impacts of North Pacific Loggerhead and Western Pacific Leatherback Turtle Interactions, inclusion of the Hawaii-based Deep-set and American Samoa-based Longline Fisheries. NOAA Technical Memorandum NMFS-PIFSC-101. Honolulu, Hawaii, USA. doi: 10.25923/pnf2-2q77
- Mobini S., Kuliasha C.A., Siders Z.A., Bohmann N., Jamal S-M, Judy J.W., Schmidt C.E., Brennan A.B. (2020) Microtopographical patterns on the surface of neural implants promote different responses in Fibroblasts and Schwann cells. Journal of Biomedical Materials Research Part A. doi:10.1002/jbm.a.37007
- Martin S., Siders Z.A., Eguchi T., Langseth B., Yau A., Baker J., Ahrens R.N.M., Jones T.T. (2020) Assessing the population level impacts of North Pacific Loggerhead and western Pacific Leatherback interactions in the Hawaii-based shallow set fishery. NOAA Technical Memorandum NMFS-PIFSC-95. Honolulu, Hawaii, USA. doi:10.25923/ydp1-f891
- Caltabellotta F.P., Siders Z.A., Murie D.J., Motta F.S., Cailliet G.M., Gadig O.B.F. (2019) Age and growth of three endemic threatened guitarfishes (Pseudobatos horkelii, Pseudobatos percellens and Zapteryx brevirostris) in the Western South Atlantic (Chondrichthyes, Rhinopristiformes). Journal of Fish Biology. doi: 10.1111/jfb.14123
- Matthias B.G., Ahrens R.N.M., Allen M.S., Tuten T., Siders Z.A., Wilson K.L. (2018) Understanding the effects of density and environmental variability on the process of fish growth. Fisheries Research. 198. 209-219. doi: 10.1016/j.fishres.2017.08.018
- Lynch A.J., Cooke S.J., …, Siders Z.A., Taylor W.W., Youn S. (2017) Grand challenges in the management and conservation of North American inland fish and fisheries. Fisheries. 42(2): 115-124. doi: 10.1080/03632415.2017.1259945
- Koopman H.N., Westgate A.J., Siders Z.A. (2015) Declining fecundity and factors affecting embryo quality in the American lobster (Homarus americanus) from the Bay of Fundy. CJAFS. 72: 353-363. doi: 10.1139/cjfas-2014-0277
- Koopman H.N., Westgate A.W., Siders Z.A., Cahoon L.B. (2014) Rapid sub-surface ocean warming in the Bay of Fundy as measured by free-swimming basking sharks. Oceanography 2: 14-16. doi: 10.5670/oceanog.2014.32
- Westgate A.W., Koopman H.N., Siders Z.A., Wong S.N.P., Ronconi R.A. (2014) Population density and abundance of basking sharks in the lower Bay of Fundy, Canada. Endangered Species Research. 23: 177-185. doi:10.3354/esr00567
- Siders Z.A., Westgate A.J., Johnston D.J., Murison L.M., Koopman H.N. (2013) Seasonal variation in the spatial distribution of basking sharks (Cetorhinus maximus) in the lower Bay of Fundy, Canada. PLoS ONE 8(12): e82074. doi:10.1371/journal.pone.0082074
- Koopman H.N., Siders Z.A. (2013) Variations in egg quality in blue crabs, Callinectes sapidus, from North Carolina: does female size matter? Journal of Crustacean Biology. 33. 481-487. doi: 10.1163/1937240X-00002152