Bayesian analyses of Pacific swordfish (Xiphias gladius L.) genetic differentiation using multilocus single nucleotide polymorphism (SNP) data

Lu, Ching-Ping; Smith, Brad L.; Hinton, Michael G.; Bremer, Jaime R. Alvarado

doi:10.1016/j.jembe.2016.03.010

Cited by 13 publications

(13 citation statements)

References 70 publications

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“…None of the analyses of this study that used neutral loci identified any significant population structure. Homozygosity values mirror those of other pelagic species using similar study designs including yellowfin tuna ( Thunnus albacares, average H e = .24, average H o = .26 using DArTseq‐produced SNPs; Grewe et al, ) and dolphinfish ( Coryphaena hippurus, average H e = .25, average H o = .25 using RADseq‐produced SNPs; Maroso, Franch, Dalla Rovere, Arculeo, & Bargelloni, ), and only slightly below that of swordfish ( Xiphias gladius, average H e = .29 using HRMA methods; Lu, Smith, Hinton, & Alvarado Bremer, ). None of the listed species are mentioned on the IUCN Red List for conservation (Collette, Acer, et al, ; Collette, Acero, Amorim, Bizsel, et al, ; Collette, Acero, Amorim, Boustany, et al, ), or highlighted for concern in Western and Central Pacific Fisheries Commission stock assessments (ISC Billfish WG, ; Tremblay‐Boyer, McKechnie, Pilling, & Hampton, ), implying that albacore should be a similarly robust species.…”

Section: Discussionmentioning

confidence: 60%

Indications of strong adaptive population genetic structure in albacore tuna (Thunnus alalunga) in the southwest and central Pacific Ocean

Anderson

Hampton

Smith

et al. 2019

Ecology and Evolution

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Albacore tuna (Thunnus alalunga) has a distinctly complex life history in which juveniles and adults separate geographically but at times inhabit the same spaces sequentially. The species also migrates long distances and presumably experiences varied regimes of physical stress over a lifetime. There are, therefore, many opportunities for population structure to arise based on stochastic differences or environmental factors that promote local adaptation. However, with the extent of mobility consistently demonstrated by tagged individuals, there is also a strong argument for panmixia within an ocean basin. It is important to confirm such assumptions from a population genetics standpoint for this species in particular because albacore is one of the principal market tuna species that sustains massive global fisheries and yet is also a slow‐growing temperate tuna. Consequently, we used 1,837 neutral SNP loci and 89 loci under potential selection to analyze population genetic structure among five sample groups collected from the western and central South Pacific. We found no evidence to challenge panmixia at neutral loci, but strong indications of structuring at adaptive loci. One population sample, from French Polynesia in 2004, was particularly differentiated. Unfortunately, the current study cannot infer whether the divergence is geographic or temporal, or possibly caused by sample distribution. We encourage future studies to include potentially adaptive loci and to continue fine‐scale observations within an ocean basin, and not to assume genome‐wide panmixia.

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Section: Discussionmentioning

confidence: 60%

Indications of strong adaptive population genetic structure in albacore tuna (Thunnus alalunga) in the southwest and central Pacific Ocean

Anderson

Hampton

Smith

et al. 2019

Ecology and Evolution

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“…Unlike using the full microsatellite dataset, results of the AMOVA using a reduced sample size (n = 101) microsatellite dataset was unable to detect significant differences among groupings assuming a Williams et al (2015a) model, suggesting that the decreased sample size was likely to be affecting the detection of population structure. (Waples 1998, Laconcha et al, 2015, Lu et al, 2016. Similar patterns of genetic structure were observed among SNP's and microsatellite datasets which overall supported the presence of three populations.…”

Section: Stock Model Testingsupporting

confidence: 69%

The global biology, ecology and phylogenetic status of black marlin (Istiompax indica)

Williams¹

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The black marlin [Istiompax indica (Morrow, 1968)] is one of the largest teleost fish and has a continuous distribution throughout tropical waters of the Indo-Pacific. Throughout its range, I. indica has been documented to undertake wide-ranging, transoceanic and transequatorial movements. In coastal waters and on the high seas I. indica may be targeted by commercial and artisanal fisheries, but the majority of the world's landings are as a by-product species of tuna longline and purse seine fisheries. Due to its large size and 'fighting qualities', I. indica is also valued as a prized sport or game fish in recreational fisheries. While considerable effort to understand the level of exploitation of high value species such as the tunas has occurred, the stock status for many other species caught on the high seas such as many sharks, dolphinfish and istiophorid billfishes remain unassessed. This lack of attention is reflected by I. indica being listed as 'Data Deficient' on the International Union for Conservation of Nature Red List. The lack of attention and data available on I. indica extends to biological, ecological, taxonomic and fisheries catch records, which in turn hinders stock assessments and management. This thesis aims to improve the biological and ecological knowledge of I. indica, thereby providing a stronger foundation for assessments and management of stocks globally. PUBLICATIONS DURING CANDIDATURE Peer-reviewed papers and book chaptersA Cohen, D. Spooner and SM. Williams (In Press). Examining the importance of marine transport and transport infrastructure and the initiatives adopted for managing potential impacts whilst enhancing transport services. Moreton Bay and Catchment.

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“…Although monotypic, past work has shown swordfish distribution and population structure to be complex, with structure evident across and within ocean basins (Alvarado Bremer, Hinton, & Greig, ; Reeb, Arcangeli, & Block, ; Smith et al, ). As shown in the Atlantic, swordfish in the Pacific have been proposed to segregate, with several different hypotheses proposed on the delineation and distribution of the different management units (Alvarado Bremer et al, ; Brodziak & Ishimura, ; Hinton et al, ; Lu, Smith, Hinton, & Alvarado Bremer, ; Reeb et al, ; Sosa‐Nishizaki & Shimizu, ).…”

Section: Introductionmentioning

confidence: 99%

“…2006; Reeb, Arcangeli, & Block, 2003;Smith et al, 2015). As shown in the Atlantic, swordfish in the Pacific have been proposed to segregate, with several different hypotheses proposed on the delineation and distribution of the different management units (Alvarado Bremer et al, 2006;Brodziak & Ishimura, 2009;Hinton et al, 2005;Lu, Smith, Hinton, & Alvarado Bremer, 2016;Reeb et al, 2003;Sosa-Nishizaki & Shimizu, 1991).…”

mentioning

confidence: 99%

Insights into the horizontal movements, migration patterns, and stock affiliation of California swordfish

Sepúlveda

Wang

Aalbers

et al. 2020

Fisheries Oceanography

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This study reports on the horizontal movements of swordfish (Xiphias gladius L.) tagged during deep‐set fishery trials off the California coastline. Position estimates from several electronic tag types were used to better understand swordfish stock structure and regional affiliation with current boundary hypotheses used to manage swordfish in the eastern north Pacific. Swordfish were outfitted with (a) satellite‐linked mark–recapture tags (n = 66), (b) electronic data storage tags that were recaptured (n = 16), (c) fin‐mounted Argos transmitters (n = 6), and (d) satellite‐linked archival tags (n = 4). Twenty‐six percent of tagged swordfish reported close to (<225 km) their deployment location within the southern California Bight (SCB). Of the 50 swordfish that moved outside the SCB, 76% exhibited affiliation to the Eastern Pacific Ocean (EPO) management unit, 20% moved into the Western and Central North Pacific (WCNP) and 4% spent time within both the EPO and WCNP boundaries. Mean displacement between deployment and reporting locations was 1,250 ± 1,375 km, with daily rates of movement up to 55 km/day. Seasonal migrations ranged from the equator (0.8°N.132.4°W) to the Hawaiian Islands (17.0°N/154.2°W), with multiple individuals returning to the initial tagging locations the subsequent season. Seasonal site fidelity exhibited by several individuals highlights the importance of the SCB foraging grounds. While no evidence of trans‐equatorial or trans‐Pacific crossing was documented, extensive movements validate the highly migratory nature of California swordfish and support the need for future inclusion of spatial distribution data in management. Findings suggest that SCB swordfish may exhibit a higher level of EPO connectivity than previously proposed.

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Bayesian analyses of Pacific swordfish (Xiphias gladius L.) genetic differentiation using multilocus single nucleotide polymorphism (SNP) data

Cited by 13 publications

References 70 publications

Indications of strong adaptive population genetic structure in albacore tuna (Thunnus alalunga) in the southwest and central Pacific Ocean

Indications of strong adaptive population genetic structure in albacore tuna (Thunnus alalunga) in the southwest and central Pacific Ocean

The global biology, ecology and phylogenetic status of black marlin (Istiompax indica)

Insights into the horizontal movements, migration patterns, and stock affiliation of California swordfish

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