Biology Data Sets

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Now showing 1 - 13 of 13
  • Dataset
    Tag attachment device on a pole (TADpole)
    (Woods Hole Oceanographic Institution, 2024-01-23) Lanagan, Thomas ; Kapit, Jason ; Moore, Michael J.
    To attach satellite-linked telemetry tags to bow-riding and surface swimming large marine vertebrates such as dolphins and sharks, a pole mounted, pneumatically powered tool has been developed. It uses the proven single-pin dorsal fin attachment method.
  • Dataset
    Otolith characterization and integrative species identification of adult mesopelagic fishes from the western North Atlantic Ocean
    (Woods Hole Oceanographic Institution, 2023-08-16) Quigley, Lucinda A. ; Llopiz, Joel K.
    Fish diversity and ecology in the ocean’s mesopelagic zone are understudied compared to other marine regions despite growing interest in harvesting these potential resources. Otoliths can provide a wealth of taxonomic and life history information about fish, which can help fill these knowledge gaps; however, there has been relatively little research to date on the otoliths of mesopelagic species. Here, a species-specific image library was assembled of sagittal otoliths from 70 mesopelagic fishes belonging to 29 families collected in the western North Atlantic Ocean. Images of adult sagittal otoliths from 12 species were documented and photographed for the first time. The fish were identified to species with a combination of morphological characters and DNA barcoding. Regressions between otolith size and fish length are presented for the six species with the largest sample sizes in this study. This otolith image library, coupled with otolith-length and width to fish-length relationships, can be used for prey identification and back-calculation of fish size, making it a valuable tool for studies relating to food webs in the important yet poorly understood mesopelagic zone. In addition, the 44 fish barcodes generated in this study highlight the benefit of using an integrative taxonomic approach to studies of this nature, as well as add to existing public databases that enable cryptic species and metabarcoding analyses of mesopelagic species.
  • Dataset
    Bottlenose dolphin mothers modify signature whistles in the presence of their own calves
    (Woods Hole Oceanographic Institution, 2023-05-22) Sayigh, Laela S. ; El Haddad, Nicole ; Tyack, Peter L. ; Janik, Vincent M. ; Jensen, Frants H. ; Wells, Randall S.
    Human caregivers interacting with children typically modify their speech in ways that promote attention, bonding and language acquisition. Although this “motherese,” or child-directed communication (CDC), occurs in a variety of human cultures, evidence among non-human species is very rare. We looked for its occurrence in a non-human mammalian species with long-term mother-offspring bonds that is capable of vocal production learning, the bottlenose dolphin (Tursiops truncatus). Dolphin signature whistles provide a unique opportunity to test for CDC in non-human animals, because we are able to quantify changes in the same vocalizations produced in the presence or absence of calves. We analyzed recordings made during brief catch-and-release events of wild bottlenose dolphins in waters near Sarasota Bay, Florida, USA, and found that females produced signature whistles with significantly higher maximum frequencies and wider frequency ranges when they were recorded with their own dependent calves vs. not with them. These differences align with the higher fundamental frequencies and wider pitch ranges seen in human CDC. Our results provide the first evidence in a non-human mammal for changes in the same vocalizations when produced in the presence vs. absence of offspring, and thus strongly support convergent evolution of motherese, or child-directed communication, in bottlenose dolphins. CDC may function to enhance attention, bonding and vocal learning in dolphin calves, as it does in human children. Our data add to the growing body of evidence that dolphins provide a powerful animal model for studying the evolution of vocal learning and language.
  • Dataset
    Macrofauna and larvae collected at the Auka hydrothermal vent field in Pescadero Basin in 2017
    (Woods Hole Oceanographic Institution, 2023-01-13) Beaulieu, Stace E. ; Mills, Susan W. ; Fleming, Bethany F. M. ; Angier, Sabine ; Toner, Mary ; Mullineaux, Lauren S.
    This data package provides the sampling locations and identifications for macrofauna and larvae collected at the Auka hydrothermal vent field in Pescadero Basin in 2017 and used in a study by Fleming et al. (2022). This data package contains five tables: paired tables for benthic slurps (sampling metadata and specimen counts), paired tables for plankton slurps (sampling metadata and specimen counts), and one table summarizing benthic and plankton specimens with Barcode of Life Data System (BOLD) Barcode Index Numbers (BINs). The paired data tables are partially aligned to Darwin Core event and occurrence tables for future contribution to the Ocean Biodiversity Information System (OBIS). Records for specimens in BOLD are available through the Global Biodiversity Information Facility (GBIF).
  • Dataset
    Investigating thermal physiology in large whales via aerial infrared thermography
    (Woods Hole Oceanographic Institution, 2021-04-23) Lonati, Gina ; Zitterbart, Daniel ; Miller, Carolyn A. ; Corkeron, Peter ; Murphy, Christin T. ; Moore, Michael J.
    The critically endangered status of North Atlantic right whales (NARWs, Eubalaena glacialis) warrants the development of new, less invasive technology to monitor the health of individuals. Combined with advancements in remotely piloted aircraft systems (RPAS, commonly “drones”), infrared thermography (IRT) is being increasingly used to detect and count marine mammals and study their physiology. We conducted RPAS-based IRT over NARWs in Cape Cod Bay, Massachusetts, USA in 2017 and 2018. Observations demonstrated three particularly useful applications of RPAS-based IRT to study large whales: 1) exploring patterns of cranial heat loss and providing insight into the physiological mechanisms that produce these patterns; 2) tracking subsurface individuals in real-time (depending on the thermal stratification of the water column) using cold surface water anomalies resulting from fluke upstrokes; and 3) detecting natural changes in superficial blood circulation or diagnosing pathology based on hot anomalies on post-cranial body surfaces. These qualitative applications present a new, important opportunity to study and monitor large whales, particularly rare and at-risk species like NARWs. Despite the challenges of using this technology in aquatic environments, the applications of RPAS-based IRT for monitoring the health and behavior of endangered marine mammals, including the collection of quantitative data on thermal physiology, will continue to diversify.
  • Dataset
    Temporal trends and effects of noise on upsweep calls of Eastern South Pacific southern right whales
    (Woods Hole Oceanographic Institution, 2022-03-30) Jacobs, Ellen ; Landea Briones, Rafaela ; Sayigh, Laela S.
    Eastern South Pacific southern right whales (ESPSRW) are a subpopulation of southern right whales (Eubalaena australis) off the coasts of Peru and Chile recognized by the International Union for the Conservation of Nature (IUCN) as critically endangered as a result of heavy whaling efforts in the late 18th to 20th centuries. Most recent population estimates put their numbers around 50 individuals. To test for the efficacy of passive acoustic monitoring of this population, we recorded five months of continuous acoustic data (January 2012-June 2012) off the southwestern tip of Isla de Chiloé. To test for trends in occurrence, we identified a total of 11,313 individual ESPSRW upsweep calls, which have been associated with maintaining contact with conspecifics. Calls increased over the course of the deployment and peaked between April and June, indicating an increase in use of the habitat consistent with the concurrent blue whale migration in the area. A clear diel pattern in which upsweep calls were predominately detected during dusk and night hours was identified, indicating that ESPSRW are likely foraging during daylight hours, as upsweep calls are known to be inversely related to foraging behavior. We also quantified noise levels in the frequency range of their communication (100 Hz third octave) to understand the change in active space whales may be experiencing. We measured noise levels from 90 dB re 1 µPa to 111 dB re 1 µPa (5th and 95th percentile), a 21 dB fluctuation that results in an order-of-magnitude decrease in active space area. We identified sources of high noise at or above the 75th percentile as predominately blue and humpback whale calls (occurring in 71.6% of total sampled minutes) and ship noise (occurring in 69.4% of total sampled minutes). Ship noise was responsible for outliers in excess of 140 dB re 1 µPa. In a population as diminished as ESPSRW, such disruptions of their communication range could result in significant barriers to maintaining contact with conspecifics. Passive acoustic monitoring is a powerful tool for monitoring populations as rarely sighted as ESPSRW. Understanding trends in presence and behavior as well as potential sources of disruption of their calling behavior is vital to determining conservation measures that will be most effective toward helping this critically endangered population.
  • Dataset
    Seasonal trends and diel patterns of downsweep and SEP calls in Chilean blue whales (Balaenoptera musculus)
    (Woods Hole Oceanographic Institution, 2022-01-13) Redaelli, Laura ; Mangia Woods, Sari ; Landea Briones, Rafaela ; Sayigh, Laela S.
    To learn more about occurrence and behavior of a recently discovered population of blue whales, passive acoustic data were collected for 15 consecutive months (January 2012 – April 2013) in the Chiloense ecoregion of southern Chile. Automatic detectors and manual auditing were used to detect blue whale songs (SEP calls) and D calls, which were then analyzed to gain insights into temporal calling patterns. We found a year-round acoustic presence of D calls, with the majority occurring during austral summer (December to April), with several sub-monthly peaks. On the other hand, no SEP calls were found during austral winter. Thus, our results support previous studies documenting austral summer residency of blue whales in the Chiloense ecoregion, although they suggest that some individuals remain in the area year-round, highlighting the importance of the Chiloense ecoregion as blue whale habitat. We also investigated daily occurrence of each call type and found that D calls occurred more frequently during dusk and night hours compared to dawn and day periods, whereas SEP calls did not show any significant diel differences. Overall, these findings contribute to a better understanding of occurrence and behavior of endangered Chilean blue whales, which can enhance our ability to develop conservation strategies in this important southern hemisphere habitat.
  • Dataset
    Reducing effort in the U.S. American lobster (Homarus americanus) fishery to prevent North Atlantic right whale (Eubalaena glacialis) entanglements may support higher profits and long-term sustainability
    (Woods Hole Oceanographic Institution, 2019-11-27) Myers, Hannah J. ; Moore, Michael J.
    Supplemental data for Reducing effort in the U.S. American lobster (Homarus americanus) fishery to prevent North Atlantic right whale (Eubalaena glacialis) entanglements may support higher profits and long-term sustainability. Figure 5: Estimated North Atlantic right whale population, number of calves, observed mortalities and serious injuries, and diagnosed cause of death or serious injury. Diagnosed entanglements have increased significantly since the population has been in decline. Data from Waring et al. 1997, Kraus et al. 2001, Waring et al. 2002, Moore et al. 2004, Waring et al. 2015, Pace et al. 2017, Pettis et al. 2018, Hayes et al. 2018b, and NOAA Northeast Fisheries Science Center (unpublished). Figure 15: Maine and Nova Scotia (NS) Maritimes lobster landings and landings per trap from 1990 to 2017. While NS Maritimes landings per trap mirrored landings growth, Maine landings per trap remained relatively stagnant for the majority of this period. Data from DFO Seafisheries Landings, DFO Atlantic Region Licences, DFO Integrated Fisheries Management Plan for LFAs 27-38 (2011), NMFS Annual Commercial Landings Statistics, and Maine Department of Marine Resources Historical Maine Lobster Landings. Figure 16: Maine lobster landings per trap, number of traps (an upper bound indicated by the number of trap tags sold), and total landings weight from 1986 to 2017. Landings per trap were relatively stagnant except from 2007 to 2013, when landings per trap increased substantially year on year, correlating with a decrease in the number of traps and faster rate of growth in total landings. Data from National Marine Fisheries Service Annual Commercial Landings and Maine Department of Marine Resources Historical Maine Lobster Landings. Figure 18: Annual lobster landings weight, in millions of pounds, for Massachusetts Statistical Reporting Areas (SRAs) 5, 6, 7, 8, and 9 from 1990 to 2017. Vertical line indicates the start of the Massachusetts Restricted Area Trap/Pot Closure in 2015. The Massachusetts Restricted Area Trap/Pot Closure includes all of SRAs 6, 7, 8, and 9, as well as most of SRA 5 and small portions of SRAs 18 and 19. Data from the Massachusetts Division of Marine Fisheries (unpublished). Figure 20: American lobster commercial landings weight standardized to 1990 in the primary Statistical Reporting Areas (SRAs) covered by the Massachusetts Restricted Area (SRAs 5, 6, 7, 8, and 9) and the rest of the state of Massachusetts. The Massachusetts Restricted Area seasonal trap/pot fishery closure took place on February 1st, 2015. Data from Massachusetts Division of Marine Fisheries (unpublished) and National Marine Fisheries Service Annual Commercial Landings Statistics. Figure 21: Lobster landings weight in the Statistical Reporting Areas (SRAs) covered by the Massachusetts Restricted Area (5-9) and to the north (1-4) and south (10-14) from 1990 to 2017. Relative growth in landings in SRAs 5 to 9 was stronger than in neighboring areas since the closure was implemented. Vertical line indicates the start of the three-month closure in 2015. Data from Massachusetts Division of Marine Fisheries (unpublished). Figure 23: Lobster landings value in February, March, and April from Massachusetts Statistical Reporting Areas 5 to 9, 2005 to 2018. Landings value from these areas dropped approximately $94,000 from the period immediately before to the period immediately after the closure was implemented. Vertical line indicates the start of the Massachusetts Restricted Area trap/pot closure in 2015. Landings value calculated by multiplying landings weight for each area by average price for Massachusetts for that month and year. Value is nominal and not adjusted for inflation. Data from Massachusetts Division of Marine Fisheries (unpublished).
  • Dataset
    Animals on the Move and Deep‐Sea Vents: Dataset for Spherical Display Systems
    ( 2019-06-04) Beaulieu, Stace E. ; Brickley, Annette
    This educational package was developed to engage live audiences with datasets displayed on spherical display systems, in particular NOAA’s Science On a Sphere® (SOS; The playlist was designed to show how different animal species - from birds in the air to tubeworms in the deep sea - migrate or disperse to new locations as part of the dynamics and resilience of animal populations on Earth. Datasets are selected to align with the Next Generation Science Standard (NGSS) LS2.C: Ecosystem Dynamics, Functioning, and Resilience. This package includes Version 1 of an SOS Live Program “Animals on the Move: Stories of Migration Over Land and Dispersal Under Sea” that was developed for the Buttonwood Park Zoo in New Bedford, MA, in a project led by the Woods Hole Oceanographic Institution. The datasets in the playlist are relevant to this specific partnership. To help tailor a live program to other local audiences, we provide supplemental documents to aid the selection of datasets aligned with the NGSS. This package also includes Version 2 of NOAA SOS datasets “Deep-Sea Vent Discoveries” and “Deep-Sea Vent Locations”. Locations are provided for all known deep-sea vent fields that were confirmed active by observations at the seafloor at depths greater than 200 m, as of year 2016. The Version 2 Discoveries dataset has the same data as Version 1 for years 1977 - 2005, revised data for 2006 - 2011, and new data for 2012 - 2016. The total number of active confirmed vent fields at water depths > 200 m as of year 2016 was 241, i.e., 28 more than in the previous NOAA SOS datasets (16 discovered in 2012 - 2016, and 12 discovered 2011 or earlier but not in previous NOAA SOS datasets).
  • Dataset
    Supplementary Information: Antibiotic resistance in Vibrio-like bacteria is common on Cape Cod, MA beaches
    ( 2018-10-23) May, Megan K. ; Gast, Rebecca J.
    Antibiotic resistance (AR) is a natural process, enhanced by anthropogenic antibiotic use. Natural environments, like the ocean, act as reservoirs of resistance; but until recently, little research has examined their dynamics. Six beaches on Cape Cod, MA, with varying human impacts, were sampled over one year on nine occasions. Vibrio-like bacteria were isolated from wet sand, dry sand, and water from each beach and tested for sensitivity to five antibiotics (amoxicillin/clavulanic acid, ciprofloxacin, doxycycline, oxytetracycline, and trimethoprim) using the disk diffusion method. 73% of isolates showed resistance to at least one antibiotic, and resistance was persistent over time, space, and sample type. Isolates commonly exhibited trimethoprim, ciprofloxacin, and/or amoxicillin resistance. 16S ribosomal DNA amplicon-based community structure varied along with the dominant operational taxonomic unit (OTU). Permutational multivariate analysis of variance (PERMANOVA) indicate that resistance patterns, prevalence, and bacterial community composition were often related to month of sampling. Seasonal environmental variables also explain AR and community structure data. Distance based linear models (DistLM) using arcGIS land use variables reflecting homogeneity in land use. Estimates of Vibrio-like resistant bacteria range from 57 to 980 cells per ml water, accounting for 0.00057-0.0098% of the total bacteria encountered with beach water contact. These results illustrate that resistance to antibiotics by Vibrio- like bacteria is widespread on local recreational marine beaches. Although these resistant bacteria are a small percentage of the total bacteria, they may represent a potential public health issue through the introduction of resistance genes into human microbiomes during recreation or shellfish consumption.
  • Dataset
    Entanglement is a costly life history stage in large whales
    ( 2016-06-28) van der Hoop, Julie
    Individuals store energy to balance deficits in natural cycles; however, unnatural events can also lead to unbalanced energy budgets. Entanglement in fishing gear is one example of an unnatural but relatively common circumstance that imposes energetic demands of a similar order of magnitude and duration of life history events such as migration and pregnancy in large whales. We present two complementary bioenergetic approaches to estimate the energy associated with entanglement in North Atlantic right whales, and compare these estimates to the natural energetic life history of each individual whale.
  • Software
    Stochastic Dominance Test (MATLAB and R Code)
    ( 2015-02-23) Moberg, Emily A. ; Solow, Andrew R.
    This is a MATLAB function which can be run as a .m file. It takes locational data (x), with associated abundances (ax) at those locations from one time period and locational data (y), with associated abundance (ay) at those locations from a later time period and tests for stochastic dominance of the distribution of the data (y,ay) to that of the data (x,ax). The number of bootstraps are also specified. The same function is also included in the R programming language (R Core Team. (2014) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria.
  • Dataset
    Global viewport to deep-sea vents : dataset for spherical display systems
    ( 2014-09-11) Beaulieu, Stace E. ; Brickley, Annette ; Spargo, Abbey ; Joyce, Katherine ; Silva, Tim ; Patterson, Kathleen ; Madin, Katherine ; Emery, Meredith
    Spherical display systems, including digital globes, are new technologies increasingly used in both informal and formal education to display global datasets. By creating a narrative using multiple datasets, inter‐disciplinary concepts and linkages between Earth systems ‐ lithosphere, hydrosphere, atmosphere, and biosphere ‐ can be conveyed. The Woods Hole Oceanographic Institution, in collaboration with New Bedford Ocean Explorium, invites you to explore the deep sea with the Global Viewport to Deep‐Sea Vents: Dataset for Spherical Display Systems. Our content was developed for public audiences by a team of scientists, educators, and graphic artists. We created new content for digital globes that interweaves imagery obtained by deep‐diving vehicles with global datasets, including a new dataset locating the world's known hydrothermal vents and an animation showing where these vents were discovered every year since the first discovery in 1977. We provide site‐specific movies to show the diversity of geological settings and life at deep‐sea vents. Our two narratives, "Life Without Sunlight" and "Smoke and Fire Underwater,” are provided as compilation movies matched to interactive playlists for docent‐led presentations. Each narrative focuses on a set of Earth Science and Ocean Literacy Principles to educate and excite the public about dynamic geophysical and biological processes and exploration in the deep ocean. In Version 1, we provide datasets, movies, and educational materials prepared for NOAA’s Science on a Sphere® (SOS;, with our two compilation movies also formatted for Magic Planet (