Papers by Thomas Farrugia
1354 Evolutionary Responses to Climate Change Skelly
DAVID K. SKELLY,∗†‡‡ LIANA N. JOSEPH,‡ HUGH P. POSSINGHAM,‡ L. KEALOHA FREIDENBURG,∗† THOMAS J. F... more DAVID K. SKELLY,∗†‡‡ LIANA N. JOSEPH,‡ HUGH P. POSSINGHAM,‡ L. KEALOHA FREIDENBURG,∗† THOMAS J. FARRUGIA,§ MICHAEL T. KINNISON,∗∗ AND ANDREW P. HENDRY§ ∗School of Forestry & Environmental Studies, Yale University, New Haven, CT 06511, U.S.A. †Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, U.S.A. ‡School of Integrative Biology, University of Queensland, St Lucia, QLD 4072, Australia §Department of Biology, McGill University, Montreal H3A 2K6, Canada ∗∗Department of Biological Sciences, University of Maine, Orono, ME 04469, U.S.A.
Diving into the vertical dimension of elasmobranch movement ecology
Science Advances
Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand thei... more Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need t...
Journal of Experimental Marine Biology and Ecology, 2011
It is thought that some elasmobranchs use shallow temperate estuaries during warmer months becaus... more It is thought that some elasmobranchs use shallow temperate estuaries during warmer months because these habitats may provide thermal physiological advantages. However, extensive loss and degradation of southern California bays and estuaries has reduced coastal species access to estuarine habitats. While restoration of southern California estuaries has increased over the last two decades, little is known about the recovery of ecological function. Top predators are thought to be important indicators of restoration of ecological function in many ecosystems, including estuarine habitats. In this study, abundance surveys and acoustic telemetry were employed to examine how gray smooth-hound sharks (GSH) use the newly restored Full Tidal Basin (FTB) of Bolsa Chica. GSH were most abundant inside the FTB during the spring and summer, and numbers decreased during the winter. Over 83% of all individuals (n = 336) caught were immature juveniles and were most abundant when water temperatures were between 20 and 22°C. Sharks fitted with acoustic transmitters (n = 22) were continuously detected for 6-153 days (August 2008-December 2009). Forays into coastal waters were uncommon until individuals left for the season. GSH selected warmer habitats within the middle FTB; however, they also exhibited diel movements along the basin. GSH were most often found associated with mud and eelgrass at night, presumably for feeding. Since its restoration, population and behavioral data suggest that the FTB may provide juvenile GSH with a suitable seasonal environment for feeding and growth.
Scientific Data, 2022
Species occurrence records are vital data streams in marine conservation with a wide range of imp... more Species occurrence records are vital data streams in marine conservation with a wide range of important applications. From 2001–2020, the Monterey Bay Aquarium led an international research collaboration to understand the life cycle, ecology, and behavior of white sharks (Carcharodon carcharias) in the southern California Current. The collaboration was devoted to tagging juveniles with animal-borne sensors, also known as biologging. Here we report the full data records from 59 pop-up archival (PAT) and 20 smart position and temperature transmitting (SPOT) tags that variously recorded pressure, temperature, and light-level data, and computed depth and geolocations for 63 individuals. Whether transmitted or from recovered devices, raw data files from successful deployments (n = 70) were auto-ingested from the manufacturer into the United States (US) Animal Telemetry Network’s (ATN) Data Assembly Center (DAC). There they have attributed a full suite of metadata, visualized within their...
IUCN Red List of Threatened Species: Shovelnose Guitarfish
Skates are common bottom -dwelling fishes and valuable non target species in Gulf of Alaska fishe... more Skates are common bottom -dwelling fishes and valuable non target species in Gulf of Alaska fisheries. Although there is little demand for skates in the United States, markets in Europe and Asia are fueling desires for additional fishing opportunities on skates in Alaska. Management agencies, however, have been hesitant to allow increased harvests due to the lack of information on the ecology and population dynamics of skates, and the bioeconomics of skate fisheries. Specifically focusing on the two most commonly landed skate species in the Gulf of Alaska (GOA), the big skate (Beringraja binoculata) and the longnose skate (Raja rhina), I conducted an interdisciplinary project to address these knowledge gaps. First, I advanced our understanding of the movement patterns and habitat use of skates by satellite tagging big skates in the GOA. The results show that big skates can, and likely frequently do, travel long distances, cross management boundaries within the GOA, and spend more ti...
Basin-scale reproductive segregation of Pacific halibut (Hippoglossus stenolepis )
Fisheries Management and Ecology
First use of satellite tags to examine movement and habitat use of big skates Beringraja binoculata in the Gulf of Alaska
Marine Ecology Progress Series, 2016
IUCN Red List of Threatened Species: Aleutian Skate
Interannual Nearshore Habitat Use of Young of the Year White Sharks Off Southern California
Frontiers in Marine Science
Young-of-the-year (YOY) and juvenile-stage white sharks may use southern California nearshore bea... more Young-of-the-year (YOY) and juvenile-stage white sharks may use southern California nearshore beach habitats more extensively than previously known, within meters of some of the most heavily used beaches in the world. Such knowledge forms a critical component of species management and conservation plans, in addition to public safety and risk mitigation planning. We used data derived from a combination of satellite tag locations (13 animals over 3 years) and passive acoustic monitoring (34 animals over 8 years) to examine the occurrence, relative abundance, and residency patterns of YOY white sharks in southern California waters. Our results suggest that southern California contains spatiotemporally dynamic centers of primary nursery habitat. Tagged YOY white sharks formed loose aggregations at “hotspot” locations that were interannually variable, where individuals exhibited temporal fidelity, higher levels of residency, and spatially restricted movements, with multiple YOY individua...
Straddling the line: high potential impact on vulnerable marine ecosystems by bottom-set longline fishing in unregulated areas beyond national jurisdiction
ICES Journal of Marine Science
Impacts of Patagonian toothfish bottom-set longline fishing on vulnerable marine ecosystems (VMEs... more Impacts of Patagonian toothfish bottom-set longline fishing on vulnerable marine ecosystems (VMEs) are examined in a licenced fishery and adjacent areas beyond national jurisdiction (ABNJ) lacking fishery management. VME taxa distributions were predicted using MaxEnt and compared to fishing footprints of ABNJ and licenced fleets. The ABNJ fishery footprint was almost twice as large as in licenced waters. Whilst the footprint of low fishing effort (0.0–3.4 h km−2) was similar between areas, footprints of medium (3.4–10.2 h km−2) and high (10.2–45.3 h km−2) fishing effort were 4 and 13 times greater, respectively, in ABNJ. Percent overlap of licenced fishing distribution on VME indicator taxa groups was low (6.45–9.82%) compared to the considerably higher (32.62–61.99%) percentage fishing overlap on VME indicator distribution in ABNJ. Our results show that, despite the main area of VME indicator taxa being found within jurisdictional waters, there are important VME habitats on the adj...
Does Estuary Restoration Design Alter the Fine Scale Movements of Gray Smoothhounds (Mustelus californicus) in Southern California?
Bulletin, Southern California Academy of Sciences
Movement Patterns, Spatially Explicit Stock Assessment and Bioeconomic Model for Two Alaskan Skate Species
Using Vemco VPS Acoustic Telemetry Techniques to Quantify Fine-Scale, Long-Term Movement Patterns of Estuarine and Coastal Fishes
Coastal elasmobranchs such as the shovelnose guitarfish (Rhinobatos productus) seasonally use bay... more Coastal elasmobranchs such as the shovelnose guitarfish (Rhinobatos productus) seasonally use bays and estuaries for mating, pupping and feeding. However, many human-populated coastal areas have been developed, making them unavailable to coastal fish populations. The Full Tidal Basin (FTB) of the Bolsa Chica Ecological Reserve, California, USA, was completed in 2006, with the aim to restore lost estuarine habitat in southern California. Monthly abundance surveys conducted inside the FTB between June 2008 and September 2009 showed that shovelnose guitarfish were present throughout the year. Over 96% of the individuals caught were juveniles and these were most abundant in waters between 208C and 248C. Concurrently, 23 shovelnose guitarfish were fitted with coded acoustic transmitters and continuously tracked within the FTB for 16 months. Telemetry data showed individuals remained inside the FTB for, on average, 73.9 days (range 15-172 days), and made few movements between the FTB and the ocean. Tagged individuals disproportionately used mud habitats and waters at temperatures of 228C, both of which are more common in the FTB than the neighbouring coastal ocean. The present study examined the structure and functionality of a restored estuary and suggests that the FTB is important habitat for a benthic predator, a promising result three years after restoration.
An approach to describe depth-specific periodic behavior in Pacific halibut (Hippoglossus stenolepis)
Journal of Sea Research, 2015
ABSTRACT Correspondence between patterns of occupied depth and environmental cycles, called “dept... more ABSTRACT Correspondence between patterns of occupied depth and environmental cycles, called “depth-specific periodic behavior”, has been used to inform management of several flatfishes. However, little is known about depth-specific periodic behavior of Pacific halibut (Hippoglossus stenolepis), an important species in recreational, commercial and subsistence fisheries in the eastern North Pacific Ocean. To evaluate depth-specific periodic behavior of Pacific halibut, an approach was developed in which depth data from electronic tags were used to produce four types of complementary plots, including two-dimensional time series of depth, activity level derived from differencing adjacent depth recordings, periodograms, and wavelet transform coefficients. From a visual examination of the plots, daily depth-specific periodic behavior types, including diel, tidal, spawning, semi-lunar and lunar, were assigned to 37 individual Pacific halibut. Overall, the approach used in this study was useful for describing relatively short term depth-specific periodic behavior, but was less informative for understanding relatively long term behavioral patterns. The results suggest that patterns in occupied depth may be related to seasonal activities of Pacific halibut. Specifically, during the summer feeding season, fish most commonly behaved periodically on a diel scale or inactively laid on the seafloor, which was manifested as tidal periodicity as the height of the water column fluctuated above the fish. Both active swimming and inactivity on the seafloor may be related to different foraging strategies. During fall and spring migratory periods and the winter spawning season, no periodicity in depth-specific behavior was most common, which may correspond to directed movement over irregular bathymetry between feeding and spawning locations or to reproductive behaviors. Evidence of an additional reproductive behavior, spawning rises off the seafloor, was also observed during the winter spawning season. This approach for understanding the periodicity of occupied depth of Pacific halibut provides additional insight into the behavior of this iconic species. This knowledge perhaps may be used in the future to inform this species' management, such as refining estimates of susceptibility to capture and examining timing of movement among regulatory areas.
Nutritional content, mercury, and trace element analyses of two skate (Rajidae) species in the Gulf of Alaska
Journal of Food Composition and Analysis, 2015
Ocean Engineering, 2013
Quantifying the fine-scale movement patterns and habitat use of active fishes has historically be... more Quantifying the fine-scale movement patterns and habitat use of active fishes has historically been challenging due to their scope of movement or the labor intensive nature of actively tracking potentially wide-ranging species. This project focuses on improving the localization accuracy and temporal resolution of an acoustically tagged fish by filtering the position measurements received from an acoustic receiver array. Using the k-means clustering algorithm, data sets are broken into groups which have similar fish speeds and yaw rates to yield a discrete number of movement behaviors characterized by the mean and standard deviation of speed and yaw. Next, a Particle Filter state estimator is proposed, in which position and speed state estimates of particles are used to calculate the most likely motion behavior, which in turn is used as a first order motion model to propagate the particle's fish state estimates forward in time. These predicted particle states are compared with the position measurements and then resampled as done with most Particle Filters. Offline processing of a shovelnose guitarfish (Rhinobatos productus) data set shows that the estimation of the fish's location is improved during periods of time when no measurements could be obtained when compared with two common filtering approaches.
Molecular Ecology, 2008
Human activities can expose populations to dramatic environmental perturbations, which may then p... more Human activities can expose populations to dramatic environmental perturbations, which may then precipitate adaptive phenotypic change. We ask whether or not phenotypic changes associated with human-disturbed (anthropogenic) contexts are greater than those associated with more 'natural' contexts. Our meta-analysis is based on more than 3000 rates of phenotypic change in 68 'systems', each representing a given species in a particular geographical area. We find that rates of phenotypic change are greater in anthropogenic contexts than in natural contexts. This difference may be influenced by phenotypic plasticity-because it was evident for studies of wild-caught individuals (which integrate both genetic and plastic effects) but not for common-garden or quantitative genetic studies (which minimize plastic effects). We also find that phenotypic changes in response to disturbance can be remarkably abrupt, perhaps again because of plasticity. In short, humans are an important agent driving phenotypic change in contemporary populations. Although these changes sometimes have a genetic basis, our analyses suggest a particularly important contribution from phenotypic plasticity.
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Papers by Thomas Farrugia