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Swenson JD, Brooks EN, Kacev D, Boyd C, Kinney MJ, Marcy‐Quay B, Sévêque A, Feldheim KA, Komoroske LM. Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments. Ecol Evol 2024; 14:e10854. [PMID: 38327683 PMCID: PMC10847890 DOI: 10.1002/ece3.10854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 01/01/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.
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Affiliation(s)
- John D. Swenson
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
| | - Elizabeth N. Brooks
- Population Dynamics Branch, Northeast Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationWoods HoleMassachusettsUSA
| | - Dovi Kacev
- Marine Biology Research DivisionScripps Institution of OceanographySan DiegoCaliforniaUSA
| | - Charlotte Boyd
- International Union for Conservation of NatureNorth America OfficeWashington DCMarylandUSA
| | - Michael J. Kinney
- NOAA FisheriesPacific Island Fisheries Science CenterHonoluluHawaiiUSA
| | - Benjamin Marcy‐Quay
- Rubenstein Ecosystem Science LaboratoryUniversity of VermontBurlingtonVermontUSA
| | - Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionThe Field MuseumChicagoIllinoisUSA
| | - Lisa M. Komoroske
- Department of Environmental ConservationThe University of Massachusetts AmherstAmherstMassachusettsUSA
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2
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Newton KC, Kacev D, Nilsson SRO, Saettele AL, Golden SA, Sheets L. Lateral line ablation by ototoxic compounds results in distinct rheotaxis profiles in larval zebrafish. Commun Biol 2023; 6:84. [PMID: 36681757 PMCID: PMC9867717 DOI: 10.1038/s42003-023-04449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
The zebrafish lateral line is an established model for hair cell organ damage, yet few studies link mechanistic disruptions to changes in biologically relevant behavior. We used larval zebrafish to determine how damage via ototoxic compounds impact rheotaxis. Larvae were treated with CuSO4 or neomycin to disrupt lateral line function then exposed to water flow stimuli. Their swimming behavior was recorded on video then DeepLabCut and SimBA software were used to track movements and classify rheotaxis behavior, respectively. Lateral line-disrupted fish performed rheotaxis, but they swam greater distances, for shorter durations, and with greater angular variance than controls. Furthermore, spectral decomposition analyses confirmed that lesioned fish exhibited ototoxic compound-specific behavioral profiles with distinct changes in the magnitude, frequency, and cross-correlation between fluctuations in linear and angular movements. Our observations demonstrate that lateral line input is needed for fish to hold their station in flow efficiently and reveals that commonly used lesion methods have unique effects on rheotaxis behavior.
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Affiliation(s)
- Kyle C Newton
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Fisheries, Wildlife and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, Hatfield Marine Science Center, Newport, OR, USA.
| | - Dovi Kacev
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Simon R O Nilsson
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Allison L Saettele
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sam A Golden
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Lavinia Sheets
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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3
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Thompson AR, Ben-Aderet NJ, Bowlin NM, Kacev D, Swalethorp R, Watson W. Putting the Pacific marine heatwave into perspective: The response of larval fish off southern California to unprecedented warming in 2014-2016 relative to the previous 65 years. Glob Chang Biol 2022; 28:1766-1785. [PMID: 34951510 DOI: 10.1111/gcb.16010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/26/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
The 2014-2016 Northeast Pacific marine heatwave (MHW) induced the warmest 3-year period on record in the California Current Ecosystem. We tested whether larval fish assemblage structure, phenology, and diversity dynamics were comparable to past warming events from 1951 to 2013. First, we hypothesized, based on past observations of biological effect of warming, that mesopelagic species with southern distributions relative to southern California and Pacific sardine Sardinops sagax (a coastal pelagic species) would increase during the MHW while northern mesopelagics and northern anchovy Engraulis mordax (coastal pelagic) abundances would decline. Similar to past warming, southern mesopelagics increased and northern mesopelagics decreased. Unexpectedly, however, a common southern mesopelagic, Mexican lampfish Triphoturus mexicanus, was approximately three times more abundant than the previous annual high. Furthermore, whereas sardine abundance did not increase, larval anchovy abundance rose to near-record highs in summer 2016. Second, we hypothesized that fishes would spawn earlier during the MHW. Fishes did not spawn in an earlier season within a year, but five of six southern mesopelagic taxa spawned earlier than typical within winter and spring. Third, we predicted that species richness would increase moderately due to an influx of southern and exodus of northern species. Richness, however, was very high in all seasons and the highest ever during the summer as multiple species with primarily southern distributions were recorded spawning for the first time in southern California. The richness of northern species was also unexpectedly high during the MHW. Northern species likely persisted in the study area because in addition to the warm water, pockets of cold water were consistently present. If, as predicted, conditions similar to the MHW become more common as oceans warm, this unique and largely unexpected combination of fishes may reflect future biological conditions.
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Affiliation(s)
- Andrew R Thompson
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, California, USA
| | - Noah J Ben-Aderet
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, California, USA
- Ocean Protection Council, California Resources Agency, Sacramento, California, USA
| | - Noelle M Bowlin
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, California, USA
| | - Dovi Kacev
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, California, USA
| | - Rasmus Swalethorp
- Scripps Institution of Oceanography, University of California - San Diego, La Jolla, California, USA
| | - William Watson
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, California, USA
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4
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Gold Z, Curd EE, Goodwin KD, Choi ES, Frable BW, Thompson AR, Walker HJ, Burton RS, Kacev D, Martz LD, Barber PH. Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem. Mol Ecol Resour 2021; 21:2546-2564. [PMID: 34235858 DOI: 10.1111/1755-0998.13450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023]
Abstract
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Emma S Choi
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Benjamin W Frable
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Andrew R Thompson
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Harold J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Ronald S Burton
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Dovi Kacev
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Lucas D Martz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
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Lyons K, Kacev D, Mull CG. An inconvenient tooth: Evaluating female choice in multiple paternity using an evolutionarily and ecologically important vertebrate clade. Mol Ecol 2021; 30:1574-1593. [PMID: 33586211 PMCID: PMC8251896 DOI: 10.1111/mec.15844] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/29/2022]
Abstract
Understanding mating systems is a pillar of behavioural ecology, placing the complex interactions between females and males into a reproductive context. The field of multiple paternity, the phenomenon whereby many sires contribute to an individual litter, has traditionally viewed females as passive players in a male–male competitive framework. With the emergence of feminist perspectives in ecological fields, novel alternative mechanisms and evolutionary theories across invertebrate and vertebrate taxa recognize females are active stakeholders in the reproductive process. Despite their evolutionary significance, ecological diversity and myriad reproductive modes, elasmobranch (sharks, skates and rays) research lags behind other fields regarding complex biological processes, such as multiple paternity which is often ascribed to convenience polyandry. Here, we layout hypotheses and resynthesize multiple paternity literature from a female and life history perspective to highlight how alternative mechanisms influence the predominance of multiple paternity across elasmobranchs. We draw upon parallels in other invertebrate and vertebrate taxa to demonstrate how female elasmobranchs can influence multiple paternity outcomes that benefit their reproductive success. Our article challenges dogma that has resulted from years of dismissing the female perspective as important and provides a framework for future advancement using more holistic approaches to studying mating systems.
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Affiliation(s)
| | - Dovi Kacev
- Scripps Institution of Oceanography, San Diego, CA, USA
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6
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Doane MP, Morris MM, Papudeshi B, Allen L, Pande D, Haggerty JM, Johri S, Turnlund AC, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery AJ, Lima LFO, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards RA, Dinsdale EA. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. Microbiome 2020; 8:93. [PMID: 32534596 PMCID: PMC7293782 DOI: 10.1186/s40168-020-00840-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/15/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. RESULTS We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. CONCLUSION Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.
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Affiliation(s)
- Michael P Doane
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Megan M Morris
- Biology Department, San Diego State University, San Diego, CA, USA
- Department Biology, Stanford University, Stanford, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Indiana University, San Diego, Indiana, USA
| | - Lauren Allen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Dnyanada Pande
- Computer Sciences Department, San Diego State University, San Diego, CA, USA
| | - John M Haggerty
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shaili Johri
- Biology Department, San Diego State University, San Diego, CA, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Abigail C Turnlund
- Biology Department, San Diego State University, San Diego, CA, USA
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queens, USA
| | | | - Dovi Kacev
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
| | - Andy Nosal
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA, USA
| | - Deni Ramirez
- Whale Shark Mexico, ConCiencia Mexico AC, La Paz, BC, USA
| | - Kevin Hovel
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Julia Ledbetter
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Alker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Jackeline Avalos
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristi Baker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shruti Bhide
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Emma Billings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Steven Byrum
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Molly Clemens
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | | | - Oscar Gomez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Omar Gutierrez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Selena Hinton
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Donald Kieu
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Angie Kim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rebeca Loaiza
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | - Jordan McGhee
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristine Nguyen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Sabrina Parlan
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Pham
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rosalyn Price-Waldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert A Edwards
- Biology Department, San Diego State University, San Diego, CA, USA
- Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Dinsdale
- Biology Department, San Diego State University, San Diego, CA, USA.
- Viral Information Institute, San Diego State University, San Diego, CA, USA.
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Lyons K, Kacev D, Preti A, Gillett D, Dewar H. Organic contaminants as an ecological tool to explore niche partitioning: a case study using three pelagic shark species. Sci Rep 2019; 9:12080. [PMID: 31427708 PMCID: PMC6700177 DOI: 10.1038/s41598-019-48521-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/06/2019] [Indexed: 11/08/2022] Open
Abstract
Chemical contaminant profiles are linked to an animal's niche, providing a potential tool by which to assess resource partitioning in pelagic species. As proof of concept, we examined contaminant signatures in three species of sharks (Isurus oxyrinchus, Prionace glauca, and Alopias vulpinus) known to overlap in both space and time. Since these sharks comprise a predatory guild within the Southern California Bight (SCB), we predicted that species may partition spatial and dietary resources to limit the extent of competitive exclusion. Indeed, species were distinguishable by both total contaminant loads and their contaminant fingerprint, as random forest analysis found that species could be correctly classified 96% of the time. Our results demonstrate the utility of chemical analyses for ecological studies, and how contaminant tracers can be used in combination with traditional methods to elucidate how species may undergo niche partitioning to reduce competition for overlapping resources within predatory guilds.
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Affiliation(s)
- Kady Lyons
- Georgia Aquarium, 225 Baker Street NW, 30313, Atlanta, Georgia.
| | - Dovi Kacev
- Southwest Fisheries Science Center, La Jolla, California, USA
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Antonella Preti
- Southwest Fisheries Science Center, La Jolla, California, USA
- University of California Santa Cruz, Santa Cruz, California, USA
| | - David Gillett
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Heidi Dewar
- Southwest Fisheries Science Center, La Jolla, California, USA
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Lyons K, Kacev D, Preti A, Gillett D, Dewar H, Kohin S. Species-Specific Characteristics Influence Contaminant Accumulation Trajectories and Signatures Across Ontogeny in Three Pelagic Shark Species. Environ Sci Technol 2019; 53:6997-7006. [PMID: 31090417 DOI: 10.1021/acs.est.8b07355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Factors influencing organic contaminant accumulation in sharks, especially across ontogeny, are not well-known. Contaminant concentrations were measured in three species of sharks (Blue, Shortfin Mako, and Common Thresher) across a range of size classes (neonatal to adult) that vary in their ecological and physiological characteristics. Empirical data was compared to a theoretical framework that predicted the shape of lifetime accumulation curves. We found that a one-size-fits-all accumulation model was not appropriate as species-specific characteristics had a significant effect on contaminant accumulation trajectories. Maternal offloading likely has an important effect on determining neonatal shark contaminant starting points, and trophic ecology and physiology may interact to affect the shape of species' contaminant accumulation curves. Makos were found to have the highest accumulation potential and Blues the lowest, with Threshers being intermediate in accumulation potential. Changes in species' ecology and/or physiology were also reflected in contaminant signature changes over ontogeny. If contaminant concentrations are to be used as a proxy for risk, species-specific characteristics need to be taken into account when estimating contaminant exposure and its potential negative effects on shark health and human consumption safety.
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Affiliation(s)
- Kady Lyons
- Georgia Aquarium , 225 Baker Street NW , Atlanta , Georgia 30313 , United States
| | - Dovi Kacev
- Southwest Fisheries Science Center , La Jolla , California 92037 , United States
- Southern California Coastal Water Research Project , Costa Mesa , California 92626 , United States
| | - Antonella Preti
- Southwest Fisheries Science Center , La Jolla , California 92037 , United States
- University of California Santa Cruz , Santa Cruz , California 95064 , United States
| | - David Gillett
- Southern California Coastal Water Research Project , Costa Mesa , California 92626 , United States
| | - Heidi Dewar
- Southwest Fisheries Science Center , La Jolla , California 92037 , United States
| | - Suzanne Kohin
- Southwest Fisheries Science Center , La Jolla , California 92037 , United States
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Lyons K, Bigman JS, Kacev D, Mull CG, Carlisle AB, Imhoff JL, Anderson JM, Weng KC, Galloway AS, Cave E, Gunn TR, Lowe CG, Brill RW, Bedore CN. Bridging disciplines to advance elasmobranch conservation: applications of physiological ecology. Conserv Physiol 2019; 7:coz011. [PMID: 31110763 PMCID: PMC6519003 DOI: 10.1093/conphys/coz011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/02/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
A strength of physiological ecology is its incorporation of aspects of both species' ecology and physiology; this holistic approach is needed to address current and future anthropogenic stressors affecting elasmobranch fishes that range from overexploitation to the effects of climate change. For example, physiology is one of several key determinants of an organism's ecological niche (along with evolutionary constraints and ecological interactions). The fundamental role of physiology in niche determination led to the development of the field of physiological ecology. This approach considers physiological mechanisms in the context of the environment to understand mechanistic variations that beget ecological trends. Physiological ecology, as an integrative discipline, has recently experienced a resurgence with respect to conservation applications, largely in conjunction with technological advances that extended physiological work from the lab into the natural world. This is of critical importance for species such as elasmobranchs (sharks, skates and rays), which are an especially understudied and threatened group of vertebrates. In 2017, at the American Elasmobranch Society meeting in Austin, Texas, the symposium entitled `Applications of Physiological Ecology in Elasmobranch Research' provided a platform for researchers to showcase work in which ecological questions were examined through a physiological lens. Here, we highlight the research presented at this symposium, which emphasized the strength of linking physiological tools with ecological questions. We also demonstrate the applicability of using physiological ecology research as a method to approach conservation issues, and advocate for a more available framework whereby results are more easily accessible for their implementation into management practices.
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Affiliation(s)
- K Lyons
- Georgia Aquarium, Atlanta, GA, USA
| | - J S Bigman
- Simon Fraser University, Burnaby, Canada
| | - D Kacev
- Southwest Fisheries Science Center, La Jolla, CA, USA
| | - C G Mull
- Simon Fraser University, Burnaby, Canada
| | | | - J L Imhoff
- Florida State University Coastal and Marine Laboratory, St. Teresa, FL, USA
| | - J M Anderson
- University of Hawai`i at Mānoa, Honolulu, HI, USA
| | - K C Weng
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - A S Galloway
- South Carolina Department of Natural Resources, SC, USA
| | - E Cave
- Florida Atlantic University, Boca Raton, FL, USA
| | - T R Gunn
- Georgia Southern University, Statesboro, GA USA
| | - C G Lowe
- California State University Long Beach, Long Beach, CA, USA
| | - R W Brill
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - C N Bedore
- Georgia Southern University, Statesboro, GA USA
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Corrigan S, Lowther AD, Beheregaray LB, Bruce BD, Cliff G, Duffy CA, Foulis A, Francis MP, Goldsworthy SD, Hyde JR, Jabado RW, Kacev D, Marshall L, Mucientes GR, Naylor GJP, Pepperell JG, Queiroz N, White WT, Wintner SP, Rogers PJ. Population Connectivity of the Highly Migratory Shortfin Mako (Isurus oxyrinchus Rafinesque 1810) and Implications for Management in the Southern Hemisphere. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Doane MP, Kacev D, Harrington S, Levi K, Pande D, Vega A, Dinsdale EA. Mitochondrial recovery from shotgun metagenome sequencing enabling phylogenetic analysis of the common thresher shark (Alopias vulpinus). Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Kacev D, Sippel TJ, Kinney MJ, Pardo SA, Mull CG. An Introduction to Modelling Abundance and Life History Parameters in Shark Populations. Adv Mar Biol 2017; 78:45-87. [PMID: 29056143 DOI: 10.1016/bs.amb.2017.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Elasmobranchs play critically important ecological roles throughout the world's oceans, yet in many cases, their slow life histories and interactions with fisheries makes them particularly susceptible to exploitation. Management for these species requires robust scientific input, and mathematical models are the backbone of science-based management. In this chapter, we provide an introductory overview of the use of mathematical models to estimate shark abundance. First, we discuss life history models that are used to understand the basic biology of elasmobranchs. Second, we cover population dynamics models, which are used to make inferences regarding population trend, size, and risk of extinction. Finally, we provide examples of applied models used to assess the status of elasmobranchs in the Northeast Pacific Ocean to guide management for these species. This chapter is not a comprehensive review of quantitative methods, but rather introduces various mathematical tools in fisheries management, with a focus on shark management in the Northeast Pacific Ocean.
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Affiliation(s)
- Dovi Kacev
- Ocean Associates, Inc., Arlington, VA, United States.
| | | | | | - Sebastián A Pardo
- Earth to Ocean Research Group, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher G Mull
- Earth to Ocean Research Group, Simon Fraser University, Burnaby, BC, Canada
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Doane MP, Haggerty JM, Kacev D, Papudeshi B, Dinsdale EA. The skin microbiome of the common thresher shark (Alopias vulpinus) has low taxonomic and gene function β-diversity. Environ Microbiol Rep 2017; 9:357-373. [PMID: 28418094 DOI: 10.1111/1758-2229.12537] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 03/23/2017] [Accepted: 04/03/2017] [Indexed: 05/22/2023]
Abstract
The health of sharks, like all organisms, is linked to their microbiome. At the skin interface, sharks have dermal denticles that protrude above the mucus, which may affect the types of microbes that occur here. We characterized the microbiome from the skin of the common thresher shark (Alopias vulpinus) to investigate the structure and composition of the skin microbiome. On average 618 812 (80.9% ± S.D. 0.44%) reads per metagenomic library contained open reading frames; of those, between 7.6% and 12.8% matched known protein sequences. Genera distinguishing the A. vulpinus microbiome from the water column included, Pseudoalteromonas (12.8% ± 4.7 of sequences), Erythrobacter (5. 3% ± 0.5) and Idiomarina (4.2% ± 1.2) and distinguishing gene pathways included, cobalt, zinc and cadmium resistance (2.2% ± 0.1); iron acquisition (1.2% ± 0.1) and ton/tol transport (1.3% ± 0.08). Taxonomic community overlap (100 - dissimilarity index) was greater in the skin microbiome (77.6), relative to the water column microbiome (70.6) and a reference host-associated microbiome (algae: 71.5). We conclude the A. vulpinus skin microbiome is influenced by filtering processes, including biochemical and biophysical components of the shark skin and result in a structured microbiome.
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Affiliation(s)
- Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Dovi Kacev
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Bhavya Papudeshi
- Department of Computer Sciences, San Diego State University, San Diego, CA, USA
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Abstract
This article documents a case of genetic polyandry in the oceanic and pelagic shortfin mako Isurus oxyrinchus and briefly comments on the implications of this finding.
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Affiliation(s)
- S Corrigan
- Hollings Marine Laboratory, College of Charleston, Charleston, SC 29412, U.S.A
| | - D Kacev
- Department of Biology, San Diego State University, San Diego, CA 92182, U.S.A
| | - J Werry
- Ocean and Coast Research, Main Beach, QLD 4217, Australia
- Griffith Centre for Coastal Management, Griffith University, Southport, QLD 4222, Australia
- Australian Rivers Institute, Griffith Centre for Environment, Griffith University, Southport, QLD 4222, Australia
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Lyons K, Preti A, Madigan DJ, Wells RJD, Blasius ME, Snodgrass OE, Kacev D, Harris JD, Dewar H, Kohin S, MacKenzie K, Lowe CG. Insights into the life history and ecology of a large shortfin mako shark Isurus oxyrinchus captured in southern California. J Fish Biol 2015; 87:200-211. [PMID: 25998058 DOI: 10.1111/jfb.12709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
In June 2013, a record-breaking female Isurus oxyrinchus (total length 373 cm, mass 600 kg) was captured by rod and reel off Huntington Beach, California, where it was subsequently donated to research and provided a rare opportunity to collect the first data for a female I. oxyrinchus of this size. Counts of vertebral band pairs estimate the shark to have been c. 22 years old, depending upon assumptions of band-pair deposition rates, and the distended uteri and spent ovaries indicated that this shark had recently given birth. The stomach contained a c. 4 year-old female California sea lion Zalophus californianus that confirmed the high trophic position of this large I. oxyrinchus, which was corroborated with the high levels of measured contaminants and tissue isotope analyses.
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Affiliation(s)
- K Lyons
- California State University Long Beach, Department of Biological Sciences, 1250 Bellflower Blvd, Long Beach, CA 90840, U.S.A
| | - A Preti
- Ocean Associates, Incorporated, 4007 N Abingdon Street, Arlington, VA 22207, U.S.A
- Fisheries Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA 92037, U.S.A
| | - D J Madigan
- School of Marine and Atmospheric Sciences, Stony Brook University, 105 Dana Hall, Stony Brook, NY 11794-5000, U.S.A
| | - R J D Wells
- Texas A & M University Galveston, Department of Marine Biology, 1001 Texas Clipper Rd, Galveston, TX 775543, U.S.A
| | - M E Blasius
- California State University Long Beach, Department of Biological Sciences, 1250 Bellflower Blvd, Long Beach, CA 90840, U.S.A
| | - O E Snodgrass
- Ocean Associates, Incorporated, 4007 N Abingdon Street, Arlington, VA 22207, U.S.A
- Fisheries Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA 92037, U.S.A
| | - D Kacev
- San Diego State University, Biology Department, 5500 Campanile Dr, San Diego, CA 92182, U.S.A
| | - J D Harris
- National Marine Fisheries Service, Alaska Fisheries Science Center, National Marine Mammal Laboratory, Seattle, WA, U.S.A
| | - H Dewar
- Fisheries Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA 92037, U.S.A
| | - S Kohin
- Fisheries Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA 92037, U.S.A
| | - K MacKenzie
- School of Biological Sciences (Zoology), The University of Aberdeen, Tillydrone Avenue, Aberdeen, Scotland AB24 2TZ, U.K
| | - C G Lowe
- California State University Long Beach, Department of Biological Sciences, 1250 Bellflower Blvd, Long Beach, CA 90840, U.S.A
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