Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)

Domingues, Rodrigo Rodrigues; Mastrochirico-Filho, Vito A.; Mendes, Natália J.; Hashimoto, Diogo Teruo; Coelho, Rui; Antunes, Agostinho; Foresti, Fausto; Mendonça, Fernando Fernandes

doi:10.1007/s00227-022-04094-z

Cited by 3 publications

(2 citation statements)

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“…However, high throughput sequencing approaches such as restriction-site associated DNA sequencing (RAD-seq) now enable such assessments to be conducted at a much higher genomic resolution (Narum et al, 2013;Andrews et al, 2016;Catchen et al, 2017). Notably, research has increasingly focused on investigating genome-wide variation and population genetic structure in various species sampled across wide natural biogeographical contexts, including elasmobranchs such as the grey reef shark Carcharhinus amblyrhynchos (Lesturgie et al, 2023), the blue shark Prionace glauca (Nikolic et al, 2023), the shortfin mako Isurus oxyrinchus (Domingues et al, 2022), the silky shark Carcharhinus falciformis (Kraft et al, 2020), the smallspotted catsharkScyliorhinus canicula (Manuzzi et al, 2019), and the bonnethead shark Sphyrna tiburo (Díaz-Jaimes et al, 2021). Additionally, the field of landscape genomics, and by extension, seascape genomics, has expanded (Bragg et al, 2015;Li et al, 2017;Liggins et al, 2020), aiming to correlate specific genomic regions and bioclimatic variables through genotype-environment association (GEA) approaches (Riginos and Liggins, 2013;Lasky et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Regional population and seascape genomics of the smooth hammerhead shark Sphyrna zygaena reveals adaptive clinal variation despite high gene flow

Grobler,

Klein,

Dicken

et al. 2024

Preprint

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Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains comparatively understudied compared to other members of the family Sphyrnidae, and despite its Vulnerable status, a comprehensive understanding of its genetic landscape remains lacking. The present study aimed to conduct a fine-scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa’s coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (3RAD). A combination of differentiation-based outlier detection methods (OUTFlank and pcadapt) and Genotype-Environment Association (GEA) (Redundancy Analysis) analysis in Sphyrna zygaena were employed. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Amongst these, notable correlations between adaptive variation and sea-surface dissolved oxygen and salinity, in addition to spatial factors were evident. Conversely, analysis of 110, 965 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches, including an assessment of isolation-by-distance (IBD) and isolation-by-environment (IBE), genetic clustering analyses (LEA, fastSTRUCTURE, and find.clusters), and a discriminant analysis of principal components (DAPC). These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena.

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Section: Introductionmentioning

confidence: 99%

Regional population and seascape genomics of the smooth hammerhead shark Sphyrna zygaena reveals adaptive clinal variation despite high gene flow

Grobler,

Klein,

Dicken

et al. 2024

Preprint

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“…Second-generation sequencing (i.e., that provided by the Illumina platform), on the other hand, focusses on low coverage sequencing producing millions of reads up to 500 bp in length (Slatko et al, 2018) and represents a much more cost-effective reduced representation of the variability of the entire genome (Etter, 2011;He et al, 2014). The further development of Restriction Associated DNA sequencing (RAD-seq) combined with the mass parallel sequencing of short Illumina reads allowed the discovery of markers such as single nucleotide polymorphisms (SNPs) that putatively represent the variation of the whole genome and that have been successfully employed in population genetics and seascape genetics studies (Etter, 2011;Asaduzzaman et al, 2020;Cheng et al, 2021;Maroso et al, 2021;van der Zee et al, 2021;Selmoni et al, 2021;Delaval et al, 2022;Domingues et al, 2022).…”

Section: Advancements In Methodologies For Population Geneticsmentioning

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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Genome analysis reveals three distinct lineages of the cosmopolitan white shark

Wagner,

Smolina,

Koop

et al. 2024

Current Biology

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Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)

Cited by 3 publications

References 58 publications

Regional population and seascape genomics of the smooth hammerhead shark Sphyrna zygaena reveals adaptive clinal variation despite high gene flow

Regional population and seascape genomics of the smooth hammerhead shark Sphyrna zygaena reveals adaptive clinal variation despite high gene flow

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

Genome analysis reveals three distinct lineages of the cosmopolitan white shark

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