Genome-wide SNPs reveal complex fine scale population structure in the California market squid fishery (Doryteuthis opalescens)

Cheng, Samantha H.; Gold, Mark; Rodriguez, Nichole; Barber, Paul H.

doi:10.1007/s10592-020-01321-2

Cited by 17 publications

(14 citation statements)

References 86 publications

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“…Previously in the SCB, yearround spawning had only been inferred from statolith-based age estimation (Jackson & Domeier 2003, Reiss et al 2004. A recent genetic study provided molecular evidence supporting year-round spawning throughout regions of California and indicated that squid self-recruit to their natal regions ;66% of the time (Cheng 2015). Although self-recruitment was not tested, it is the most parsimonious explanation for the timing of squid spawning observed during the study.…”

Section: Discussionmentioning

confidence: 92%

Essential Market Squid (Doryteuthis opalescens) Embryo Habitat: A Baseline for Anticipated Ocean Climate Change

Navarro

Parnell

Levin

2018

Journal of Shellfish Research

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The market squid Doryteuthis opalescens deposits embryo capsules onto the continental shelf from Baja California to southern Alaska, yet little is known about the environment of embryo habitat. This study provides a baseline of environmental data and insights on factors underlying site selection for embryo deposition off southern California, and defines current essential embryo habitat using (1) remotely operated vehicle-supported surveys of benthos and environmental variables, (2) SCUBA surveys, and (3) bottom measurements of T, S, pH, and O 2 . Here, embryo habitat is defined using embryo capsule density, capsule bed area, consistent bed footprint, and association with [O 2 ] and pH (pCO 2 ) on the shelf. Spatial variation in embryo capsule density and location appears dependent on environmental conditions, whereas the temporal pattern of year-round spawning is not. Embryos require [O 2 ] greater than 160 mmol and pH T greater than 7.8. Temperature does not appear to be limiting (range: 9.9°C-15.5°C). Dense embryo beds were observed infrequently, whereas low-density cryptic aggregations were common. Observations of dense embryo aggregation in response to shoaling of low [O 2 ] and pH indicate habitat compression. Essential embryo habitat likely expands and contracts in space and time directly with regional occurrence of appropriate O 2 and pH exposure. Embryo habitat will likely be at future risk of compression given secular trends of deoxygenation and acidification within the Southern California Bight. Increasingly localized and dense spawning may become more common, resulting in potentially important changes in market squid ecology and management.

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Section: Discussionmentioning

confidence: 92%

Essential Market Squid (Doryteuthis opalescens) Embryo Habitat: A Baseline for Anticipated Ocean Climate Change

Navarro

Parnell

Levin

2018

Journal of Shellfish Research

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“…Moreover, in the case of highly migratory squid species, genomic data could enable monitoring of migrations and correct identification of stocks independent of their geographical or temporal presence, or could facilitate locating spawning grounds. High resolution insights into connectivity of explored stocks can provide fishery assessment and management with information on stocks recruitment patterns, source-sink dynamics and demographic (in)dependence, and thus indirectly also on the long-term stock resilience due to replenishment upon local environmental perturbations (Waples and Naish 2009;Cisneros-Mata et al 2019;Silva et al 2019b;Cheng et al 2020;Lee and O'Malley 2020;Mejía-Ruíz et al 2020;Timm et al 2020). In addition, obtained fine scale patterns of stock connectivity can be very useful in designing spatial management tools (Katsanevakis et al 2011;Domínguez-Contreras et al 2018).…”

Section: Shared Major Life History Traits With Many Cephalopodsmentioning

confidence: 99%

Incorporating evolutionary based tools in cephalopod fisheries management

Sabolić

Baltazar‐Soares²,

Štambuk

2021

Rev Fish Biol Fisheries

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“…Kardos, Taylor, Ellegren, Luikart, & Allendorf, 2016), the discovery of subtle, previously undetectable population structure (e.g. Cheng, Gold, Rodriguez, & Barber, 2021; Gaither et al, 2018), reconstruction of demographic histories (Prada et al, 2016), the precise identification of distant pedigree relationships (e.g. Baetscher et al, 2019), uncovering cryptic species (e.g.…”

Section: Introductionmentioning

confidence: 99%

Metadata preservation and stewardship for genomic data is possible, but must happen now

Crandall

Toczydlowski

Liggins

et al. 2022

Preprint

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Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a “distributed datathon” to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 492 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 82% of these 492 datasets (N = 401 BioProjects comprising 42,104 individuals or BioSamples). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

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Genome-wide SNPs reveal complex fine scale population structure in the California market squid fishery (Doryteuthis opalescens)

Cited by 17 publications

References 86 publications

Essential Market Squid (Doryteuthis opalescens) Embryo Habitat: A Baseline for Anticipated Ocean Climate Change

Essential Market Squid (Doryteuthis opalescens) Embryo Habitat: A Baseline for Anticipated Ocean Climate Change

Incorporating evolutionary based tools in cephalopod fisheries management

Metadata preservation and stewardship for genomic data is possible, but must happen now

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