An improved method for predicting the accuracy of genetic stock identification

Anderson, Eric C.; Waples, Robin S.; Kalinowski, Steven T.

doi:10.1139/f08-049

Cited by 221 publications

(281 citation statements)

References 27 publications

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“…Sacramento and Chipps Island trawls are considered two high-priority locations for genetic monitoring of SRWRC for four reasons: (1) Although this monitoring review focuses primarily on advances for SRWRC, the resolution of the current genetic baseline provides high-precision identification of both ESA-listed salmon runs in the Central Valley (i.e., SRWRC and wild spring-run Chinook from Deer, Mill, and Butte creeks; Banks et al 2000;Seeb et al 2007;Anderson et al 2008;Banks et al 2014;Clemento et al 2014). However, there are challenges in distinguishing the late-fall run from fall run, and in identifying wild Feather River spring-run Chinook Salmon, because of introgression with fall-run Chinook Salmon (Clemento et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

Johnson¹,

Windell²,

Brandes³

et al. 2017

SFEWS

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A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life stages that span broad geographic regions. Quantitative metrics (e.g., abundance, movement, survival, life history diversity, and condition) at multiple life stages are needed to inform how management actions (e.g., hatcheries, harvest, hydrology, and habitat restoration) influence salmon population dynamics. The existing monitoring network for endangered Sacramento River winterrun Chinook Salmon (SRWRC, Oncorhynchus tshawytscha) in California's Central Valley was compared to conceptual models developed for each life stage and geographic region of the life cycle to identify relevant SRWRC metrics. We concluded that the current monitoring network was insufficient to diagnose when (life stage) and where (geographic domain) chronic or episodic reductions in SRWRC cohorts occur, precluding within-and among-year comparisons. The strongest quantitative data exist in the Upper Sacramento River, where abundance estimates are generated for adult spawners and emigrating juveniles. However, once SRWRC leave the upper river, our knowledge of their identity,

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Section: Discussionmentioning

confidence: 99%

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

Johnson¹,

Windell²,

Brandes³

et al. 2017

SFEWS

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“…To determine whether juveniles could be assigned to their population of origin, mixture analysis was performed by means of the conditional maximum likelihood approach of ONCOR (Anderson et al 2008). Confidence intervals (CIs) of mixture proportions were determined through 10 000 bootstraps.…”

Section: Methodsmentioning

confidence: 99%

“…The accuracy of the genetic stock identification was assessed through self-assignment of adult individuals to their respective populations by using the leave-one-out cross-validation test and through 100% fishery simulations of 50 individuals and 1000 simulations. These methods provide less biased predictions of accuracy than conventional parametric bootstrapping procedures (Anderson et al 2008) and probably give more realistic estimates of the power of assignments. …”

mentioning

confidence: 99%

Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA

Kovach¹,

Breton²,

Berlinsky³

et al. 2010

Mar. Ecol. Prog. Ser.

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Atlantic cod Gadus morhua in US waters are currently managed as 2 stocks: (1) a Gulf of Maine stock and (2) a Georges Bank and south stock. This designation is decades old and warrants re-evaluation in light of concerns that fisheries management units may not reflect biologically meaningful population units. In this study, we used 10 microsatellite loci, the PanI locus, and 5 single nucleotide polymorphism markers to characterize the population genetic structure of cod in US waters. We found significant differentiation among temporally and spatially divergent populations of cod (global F ST = 0.0044), primarily stemming from 2 potentially non-neutral loci, and evidence for a population structure that strongly contradicts the current 2-stock management model. This genetic structure was stable over a 5 yr period. Our results indicate that cod in US waters are broadly structured into 3 groups: (1) a northern spring-spawning coastal complex in the Gulf of Maine (GOM), (2) a southern complex consisting of winter-spawning inshore GOM, offshore GOM and sites south of Cape Cod, Massachusetts, and (3) a Georges Bank population. The strongest differentiation occurs between populations in the northern and southern complex (mean F ST = 0.0085), some of which spawn in the same bays in different seasons. By means of mixture analysis, young-of-the-year fish sampled on juvenile nurseries were assigned to the spawning complex of their origin. Our findings contribute to a growing body of knowledge that Atlantic cod and other marine fish populations are structured on a finer scale than previously thought and that this structure supports biocomplexity and locally adapted populations. As such, it may be warranted to re-evaluate current management units and tailor management plans toward this finer scale.KEY WORDS: Atlantic cod · Microsatellite DNA · Single nucleotide polymorphism · Population genetic structure · Stock identification · Gadus morhua Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 410: [177][178][179][180][181][182][183][184][185][186][187][188][189][190][191][192][193][194][195] 2010 the importance of processes that limit dispersal and promote self-replenishment of local populations, such as sedentary adult life history strategies (Robichaud & Rose 2004, Howell et al. 2008, spawning site fidelity (Taggart 1997), natal homing (Thorrold et al. 2001, Svedäng et al. 2007), egg and larval retention (Jones et al. 1999, 2005, Bradbury et al. 2008) and local adaptation (McIntyre & Hutchings 2003, Conover et al. 2006, Hutchings et al. 2007). The implications of such fine-scale population structure are important for effective management (Palumbi 2003, Bradbury et al. 2008, Reiss et al. 2009).One marine fish species known to exhibit fine-scale population structure in parts of its distribution is Atlantic cod Gadus morhua L. (see reviews in Waldman 2005 andCarvalho 2008). Atlantic cod is one of the most commercially important marine fishes in the world and comprises a p...

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“…This deficiency limits the number of alleles represented in the simulated offspring and may even underestimate homoplasy, a common problem encountered with genetic stock identification of monitored fisheries (e.g. Anderson et al, 2008).…”

Section: Genetic Characterization Of Hybridsmentioning

confidence: 99%

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

DiBattista

Whitney

Craig

et al. 2016

Molecular Phylogenetics and Evolution

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Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes, Molecular Phylogenetics and Evolution (2016), doi: http:// dx.doi.org/10. 1016/j.ympev.2016.04.036 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. . japonicus and A. nigricans) are distinguishable only at a population or subspecies level (Φ ST = 0.6533, P < 0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had 3 concordance between mtDNA lineage and species identification based on external morphology, indicating that species integrity may not be eroding. The A. nigricans complex demonstrates a range of outcomes from incomplete speciation to secondary contact to decreasing hybridization with increasing evolutionary depth.

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An improved method for predicting the accuracy of genetic stock identification

Cited by 221 publications

References 27 publications

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

Science Advancements Key to Increasing Management Value of Life Stage Monitoring Networks for Endangered Sacramento River Winter-Run Chinook Salmon in California

Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA

Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

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