Whole genome resequencing reveals signatures of rapid selection in a virus‐affected commercial fishery

Holland, Owen J.; Toomey, Madeline; Ahrens, Collin W.; Hoffmann, Ary A.; Croft, Larry; Sherman, Craig D. H.; Miller, Adam D.

doi:10.1111/mec.16499

Cited by 8 publications

(4 citation statements)

References 125 publications

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“…Previous studies have shown that adaptation to culture environments can occur in as little as a single generation in fishes, crustaceans and molluscs (Araki et al 2007;Araki and Schmid 2010;Christie et al 2012). Additionally, Holland et al (2022) recently demonstrated evidence of rapid selection in H. rubra following a single generation of exposure to disease. Considering the potential for rapid evolutionary responses, it might be expected that multiple generations of captive rearing would be sufficient for local adaptation.…”

Section: The Influence Of Provenance On Ct Maxmentioning

confidence: 99%

Size-dependent thermal limits in Australian hybrid abalone: implications for productivity shifts with ocean warming

Holland,

Smythe,

Clark

et al. 2023

Rev Fish Biol Fisheries

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Ocean warming and extreme heatwaves threaten marine species supporting commercial fisheries and aquaculture. Predicting the responses of these industries to chronic and acute warming depends on understanding which life stages are most vulnerable, the potential for stocks to adapt to changing thermal environments, and the availability of thermally adapted genotypes to help enhance stock resilience through strategic interventions. Here, we shed light on some of these knowledge gaps by quantifying the critical thermal maximum (CTmax) of ~ 10–210 g hybrid abalone (Haliotis rubra × H. laevigata) from two farms representing contrasting thermal environments from south-eastern Australia. CTmax was not dependent on body size or provenance (farm) when heating rates were rapid (1 °C per h), but a significant relationship between CTmax and body size was observed when heating rates were slower and more ecologically realistic (1 °C per 12 h). Histological analyses revealed a negative relationship between CTmax and the stage of gonadal development when abalone were exposed to chronic thermal stress conditions. These results suggest that marine heatwaves and ongoing ocean warming might favour smaller, less fecund animals in natural and farm settings. This could potentially impact future harvestable biomass, recruitment and population dynamics in wild-capture fisheries, and production of larger, high-value animals in farm settings. This study adds to a growing body of literature pointing to complex and often negative effects of climate change on commercial fisheries, and the potential need for interventions aimed at bolstering fisheries resilience against the effects of ocean warming.

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Section: The Influence Of Provenance On Ct Maxmentioning

confidence: 99%

Size-dependent thermal limits in Australian hybrid abalone: implications for productivity shifts with ocean warming

Holland,

Smythe,

Clark

et al. 2023

Rev Fish Biol Fisheries

Self Cite

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“…Although we know relatively little about the mechanisms underlying recovery (14,15), host evolution is one possibility (3,16). This process is known from a diversity of wildlife populations (17)(18)(19)(20), and often results in increased host resistance and/or tolerance (see 21, for definitions). However, linking these evolutionary responses to population recoveries is difficult and few clear examples exist.…”

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confidence: 99%

Reintroduction of resistant frogs facilitates landscape-scale recovery in the presence of a lethal fungal disease

Knapp¹,

Wilber

Byrne

et al. 2023

Preprint

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Vast alteration of the biosphere by humans is causing a sixth mass extinction. Adaptation to modified environments often is the only means for species to persist, but the extent to which such "evolutionary rescue" can prevent or reverse biodiversity loss is largely unknown. Using results from genomic analyses, a 15-year reintroduction effort, and population modeling, we provide a compelling example of evolution reversing the declines of an imperiled amphibian and allowing the reestablishment of extirpated populations. The once-common mountain yellow-legged (MYL) frog is threatened with extinction by the human-facilitated emergence of a lethal fungal pathogen (Batrachochytrium dendrobatidis; "Bd"). Although most MYL frog populations are extirpated following disease outbreaks, some persist and eventually begin to recover. Using an exome capture approach, we show that MYL frogs have undergone substantial evolutionary change following disease outbreaks. Moreover, in naturally recovering populations observed changes in immune function loci are associated with increased resistance/tolerance to Bd infection. Large-scale reintroduction of frogs from rescued populations resulted in the establishment of reproducing populations despite ongoing disease. In addition, results from viability modeling suggest that established populations have a low probability of extinction over 50 years. Collectively, these results provide a rare example of how evolutionary rescue and the reintroduction of resistant/tolerant individuals can allow the landscape-scale recovery of disease-impacted species. This example has potentially broad implications for the many taxa worldwide that are threatened with extinction by anthropogenic stressors.

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“…Science-based fishery management (SBFM) is a management framework where decision-making process is based on the best available science (BAS) (Ogawa & Reyes, 2021;Su et al, 2021) regardless of the strength and limitations of the methodologies implemented (reviewed by Breen, 1992): the pāua management system can be considered to be a sciencebased one. Nonetheless, given the increase in scientific literature on economically important species in New Zealand and especially genomics-based studies (Ashby, 2019;Koot et al, 2021;Holland et al, 2022;Papa et al, 2022, current thesis), the New Zealand fishery management system framework has potential to be reformed to integrate the use of this new type of data for pāua with the fishery data currently in use.…”

Section: Integrated Interpretation Of the Main Results And The Impact...mentioning

confidence: 99%

“…for what is now referred to as "fishery genomics" with the increasing number of molecular markers that can be employed and analysed at once (reviewed by Benestan, 2019). Despite the fact that finfish are still the most targeted taxonomic group for these studies (Reiss et al, 2009; reviewed by Benestan, 2019;Benestan et al, 2021;Bertram et al, 2022), the use of genomics has been successful in increasing information about biological units and suggesting reviews of stocks and management units for economically important molluscan species (e.g., Pecten novaezelandiae, Silva & Gardner, 2015;Pinctada margaritifera, Lal et al, 2016;Doryteuthis opalescens, Cheng et al, 2021;Buccinum undatum, Morrissey et al, 2022) and abalone species (Miller et al, 2014;Mejía-Ruíz et al, 2020;Mares-Mayagoitia et al, 2021, Holland et al, 2022.…”

Section: Fisheries Management Has Benefitted From Newly Developed Gen...mentioning

confidence: 99%

Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context

Trauzzi

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The blackfoot pāua, Haliotis iris Gmelin 1791 is one of three endemic species of abalone (Haliotis spp.) found in New Zealand. This marine gastropod is a taonga (highly prized or treasured) species and a traditional kai moana (seafood) in the Māori culture. The increase in commercial interest around the exploitation of pāua shells and meat in the early 1960s led to the development of fishing restrictions and in 1986/87 and to the pāua fishery management system based on quota management areas (QMAs). In 2016, the Kaikōura earthquake generated a coastal uplift along the Kaikōura region where one of the country’s most productive pāua fisheries is located. Pronounced mortality of seaweed and marine intertidal invertebrates was reported in the affected region. Subsequently, the pāua fishery along approximately 110 km of coastline and encompassing two QMAs (PAU3A and PAU7) was closed for 5 years with substantial losses in annual revenue. It was reopened for 3 months on the 1st December 2021. The fishery was closed again at the end of February 2022 and at the time of writing remains closed. The goals of this thesis are to: 1) identify patterns of global population genetic structure and genetic connectivity within the genus Haliotis by reviewing the published literature to provide context to the findings obtained for the blackfoot pāua from New Zealand; 2) describe the population genetic connectivity, genetic diversity and population genetic structure of pāua populations from the Kaikōura region before and after the 2016 earthquake for the first time through genotyping-by-sequencing (GBS)-derived molecular markers (single nucleotide polymorphisms - SNPs); 3) investigate potential genotypic-environmental associations (GEAs) between the variation at microsatellite markers and environmental variation for pāua populations at the national scale; and 4) identify significant GEAs between neutral genetic variation at SNP loci for pāua at Kaikōura and environmental (i.e., ecological and oceanographic data) data before and after the 2016 earthquake. Abalone are widely understudied and the literature is strongly biased towards certain species of economic relevance in developed countries where most biological stocks do not correspond to fishing management units. Abalone species worldwide are generally characterised by weak population genetic structure that can be explained by the geomorphology of the coasts (i.e., headlands, bays) and correlated physical oceanography (i.e., ocean currents and upwelling). For the blackfoot pāua from Kaikōura, weak genetic structure (differentiation from other sites) was found at Cape Campbell, a headland, the northernmost site in the region and a well-known biogeographic boundary in New Zealand. High levels of gene flow and the large effective population sizes (Ne) of all populations in the Kaikōura region may have counterbalanced the effects of the Kaikōura earthquake on this species. Based on the current dataset, no direct effect of the 2016 earthquake was evident for the pāua populations from Kaikōura. Differences in the genetic connectivity patterns between adults and juveniles in PAU3A were detected. This finding could be explained by different scenarios including but not limited to local recruitment, variability in ocean currents and/or cohort effect. Collection of long-term genomic data may further clarify the stability of this pattern and its possible causes. Seascape genetics revealed the association between the genetic differentiation of pāua at Cape Campbell with higher sedimentation levels and higher sea surface temperatures (SST) that may act as barriers to gene flow for pāua to other (regional) sites. Chlorophyll-a and SST were also associated with patterns of genetic connectivity in juveniles in PAU3A and loosely followed a geographic pattern. Multiple estimates of SST, proxies for ocean currents, oceanic fronts and productivity levels of the waters around New Zealand, were significantly associated with variation at microsatellite loci for pāua at the national scale. This research reports the successful development of high throughput genomic data and its applications to pāua management in New Zealand at regional scales and the use of novel genetic analyses to pāua at the national scale. The overlap between the genetic split detected for pāua at Cape Campbell and the original boundary between the two QMAs (based on the boundary between iwi tribes) denoted how the QMS in New Zealand took into consideration Māori stewardship over marine resources since its beginning. The detection of a genetic break at small spatial scales supports the ongoing shift towards a finer scale fishery management in New Zealand and suggests the implementation of advanced genomic tools to inform management decisions. Seascape genetics analyses carried out in this thesis highlighted a relationship between genetic and environmental variations for pāua at both small and large spatial scales that could inform restoration efforts as well as focus on stocks at potential risk. Increased levels of sedimentation and high SST were recorded in the Marlborough region where pāua stocks are declining. Attention to pāua stocks in areas where these two environmental factors are increasing is suggested especially considering climate global change. The integration of genomic tools into fishery management represents the next big advancement in the long-term sustainable exploitation of pāua stocks in New Zealand.

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Whole genome resequencing reveals signatures of rapid selection in a virus‐affected commercial fishery

Abstract: The spread of infectious diseases is recognized as one of the most pressing global threats to biodiversity and ecosystem function

Cited by 8 publications

References 125 publications

Size-dependent thermal limits in Australian hybrid abalone: implications for productivity shifts with ocean warming

Size-dependent thermal limits in Australian hybrid abalone: implications for productivity shifts with ocean warming

Reintroduction of resistant frogs facilitates landscape-scale recovery in the presence of a lethal fungal disease

Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context

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