Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource

Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river shark found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis, and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeted sampling in nurseries and juvenile aggregations should be included in the genomic toolbox of threatened species management.

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“…samples processed twice from DNA library preparation to SNP calling) to optimize its algorithm parameters (Grewe et al . ).…”

Section: Methodsmentioning

confidence: 97%

“…The protocol used in this study mostly followed that described by Grewe et al . (), except that to generate more markers, two complexity reduction methods were used, PstI‐SphI and PstI‐NspI, instead of one. The SNP calling was performed with DArT PLD's proprietary software DArTsoft14.…”

Section: Methodsmentioning

confidence: 99%

Inferring contemporary and historical genetic connectivity from juveniles

et al. 2016

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“…Current technology allows geneticists to measure thousands of markers for a single animal at a cost that is feasible for research and management (see Davey et al., ; Ovenden et al., ). For populations of marine animals, this means researchers now have unprecedented potential to characterize stock structure (e.g., Grewe et al., ; Nielsen et al., ; Riccioni et al., ). The implications of this for sustainable exploitation are immediate: Better information about stocks helps to ensure that stocks are maintained into the future.…”

Section: Introductionmentioning

confidence: 99%

Reliably discriminating stock structure with genetic markers: Mixture models with robust and fast computation

Foster

Feutry

Grewe

et al. 2018

Molecular Ecology Resources

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Delineating naturally occurring and self-sustaining subpopulations (stocks) of a species is an important task, especially for species harvested from the wild. Despite its central importance to natural resource management, analytical methods used to delineate stocks are often, and increasingly, borrowed from superficially similar analytical tasks in human genetics even though models specifically for stock identification have been previously developed. Unfortunately, the analytical tasks in resource management and human genetics are not identical-questions about humans are typically aimed at inferring ancestry (often referred to as "admixture") rather than breeding stocks. In this article, we argue, and show through simulation experiments and an analysis of yellowfin tuna data, that ancestral analysis methods are not always appropriate for stock delineation. In this work, we advocate a variant of a previously introduced and simpler model that identifies stocks directly. We also highlight that the computational aspects of the analysis, irrespective of the model, are difficult. We introduce some alternative computational methods and quantitatively compare these methods to each other and to established methods. We also present a method for quantifying uncertainty in model parameters and in assignment probabilities. In doing so, we demonstrate that point estimates can be misleading. One of the computational strategies presented here, based on an expectation-maximization algorithm with judiciously chosen starting values, is robust and has a modest computational cost.

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“…In marine ecosystems, physical barriers to gene flow are few. Marine species that could potentially form panmictic populations due to their incredible mobility show behavioural constraints to gene flow, for example in whales (Baker et al., ), sharks (Blower et al., ; Portnoy, McDowell, Heist, Musick, & Graves, ) and tuna (Grewe et al., ). In particular, seabirds provide an interesting model in which to examine evolutionary genetics and the relationship between dispersal and gene flow, due to the dichotomy between their huge potential for dispersal coupled with their reluctance to disperse, driven by a strong instinct for philopatry (Friesen, Burg, & McCoy, ; Steeves, Anderson, & Friesen, ).…”

Section: Introductionmentioning

confidence: 99%

Widespread gene flow between oceans in a pelagic seabird species complex

et al. 2017

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Global-scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well-studied example of a mixed-species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (Pterodroma neglecta and Pterodroma heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between-species hybridization occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans were demonstrated between the species in this complex. Analysis of migration rates estimated using bayesass revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, structure analysis revealed gene flow between species of the Atlantic and Pacific oceans, with potential three-way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that interspecific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariiform species on a global scale, demonstrating the need for consideration of widespread migration and hybridization in the conservation of threatened seabirds.

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Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource

Cited by 96 publications

References 46 publications

Inferring contemporary and historical genetic connectivity from juveniles

Inferring contemporary and historical genetic connectivity from juveniles

Reliably discriminating stock structure with genetic markers: Mixture models with robust and fast computation

Widespread gene flow between oceans in a pelagic seabird species complex

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