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

Giulia Trauzzi

Published: Aug. 28, 2023

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

Language: Английский

Molecular signatures reveal intra-species divergence, undetectable by traditional morphology, in the deadly box jellyfish, Chironex yamaguchii (Cubozoa; Chirodropidae) of Western Pacific DOI Creative Commons
Sheldon Rey Boco,

Christine Gloria Grace Capidos,

Raffy Jay C. Fornillos

et al.

Regional Studies in Marine Science, Journal Year: 2025, Volume and Issue: unknown, P. 104033 - 104033

Published: Jan. 1, 2025

Language: Английский

Citations

1
Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics DOI Creative Commons
Karlijn Doorenspleet, Amalia A. Mailli,

Berry B. van der Hoorn

et al.

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19158 - e19158

Published: April 14, 2025

DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, their implementation as standardized monitoring is approaching. Evaluating the efficacy reliability these technological crucial for assessments. In this study, we compared three techniques assessing diversity bulk samples from Belgian North Sea. Specifically, amplicon using Illumina MiSeq portable real-time Oxford Nanopore versus shotgun NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served target region analysis. Our results indicate that had similar performances in terms alpha beta diversity, revealing highly location-specific community compositions. metagenomics method also resulted but slightly different compositions approach. Despite differences, were maintained across all platforms. Notably, read counts metagenomic analysis showed weakest correlation size corrected morphological abundance there mismatches between identification DNA based findings which likely caused by a combination factors such primer efficiency an incomplete reference database. underscore critical importance database completeness prior implementing method, especially metagenomics. Nevertheless, our emphasize proves be viable alternative conventional platform monitoring.

Language: Английский

Citations

0
Signs of local adaptation by genetic selection and isolation promoted by extreme temperature and salinity in the Mediterranean seagrass Posidonia oceanica DOI
Hung Manh Nguyen, Miriam Ruocco, Emanuela Dattolo

et al.

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(15), P. 4313 - 4328

Published: June 4, 2023

Adaptation to local conditions is known occur in seagrasses; however, knowledge of the genetic basis underlying this phenomenon remains scarce. Here, we analysed Posidonia oceanica from six sites within and around Stagnone di Marsala, a semi-enclosed coastal lagoon where salinity temperature exceed generally described tolerance thresholds species. Sea surface temperatures (SSTs) were measured plant samples collected for assessment morphology, flowering rate screening genome-wide polymorphisms using double digest restriction-site-associated DNA sequencing. Results demonstrated more extreme SSTs levels inside than outer regions. Morphological results showed significantly fewer shorter leaves reduced rhizome growth P. inner past events recorded only meadow farthest away lagoon. Using an array 51,329 single nucleotide polymorphisms, revealed clear structure among study confirmed isolation high clonality innermost site. In all, 14 outlier loci identified annotated with several proteins including those relate stress response, protein transport regulators plant-specific developmental events. Especially, five maximum allele frequency at site, likely reflecting adaptation regimes, possibly due selection resistant genotypes progressive restriction gene flow. Overall, helps us disentangle seagrass environmental may support future works on assisted evolution seagrasses.

Language: Английский

Citations

10
Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crabCarcinus maenas DOI Creative Commons
Marlene Jahnke,

Per‐Olav Moknes,

Alan Le Moan

et al.

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(7), P. 1980 - 1994

Published: Jan. 26, 2022

Most marine invertebrates disperse during a planktonic larval stage that may drift for weeks with ocean currents. A challenge larvae of coastal species is to return nursery habitats. Shore crab (Carcinus maenas L.) are known show tidal rhythmicity in vertical migration areas and circadian microtidal areas, which seems increase successful settlement. We studied genome-wide differentiation based on 24,000 single nucleotide polymorphisms 12 native populations shore sampled from large amplitude gradient macrotidal (~8 m) (~0.2 m). Dispersal recruitment success was assessed Lagrangian biophysical model, showed strong effect behaviour long-term connectivity, dispersal barriers partly coincided different environments. The genetic population structure subdivision the samples into three clusters, represent micro-, meso- areas. mostly driven by 0.5% outlier loci, allelic clines located at limits between Demographic modelling suggested two have origins. Differential gene expression clock genes (cyc pdp1) further highlighted phenotypic differences among clusters potentially linked behaviour. Taken together, our seascape genomic study suggests regime acts as selection force structure, consistent affecting success.

Language: Английский

Citations

10
2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation DOI Creative Commons
Miriam Ruocco, Marlene Jahnke, João Silva

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: May 16, 2022

Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences photoperiod temperature cues across latitudes influence major phenological events, such as timing flowering or seed dormancy. Here, we used an array 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation levels genetic genotypic diversity three the seagrass Cymodocea nodosa a gradient extending Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, Ebro Delta—Spain). Our main goal was search for potential outlier loci that could underlie adaptive distribution species. We hypothesized polymorphisms be related photoperiod-temperature regime occurring latitudes. The were clearly differentiated exhibited diverse clonality diversity. Mediterranean displayed highest richness, while Portuguese had values. Canaria lowest (as observed heterozygosity). Nine reliably identified outliers sites by two different methods BayeScan pcadapt), associated specific protein-coding genes screening available C. transcriptomes. Two SNPs-carrying contigs encoded transcription factors, other one enzyme specifically involved regulation time, namely Lysine-specific histone demethylase 1 homolog 2 . When analyzing biological processes enriched within whole dataset at least method, “regulation transcription” “signalling” among most represented. results highlight fundamental importance signal integration gene-regulatory networks, well epigenetic via DNA (de)methylation, have enabling adaptation environmental gradients.

Language: Английский

Citations

8
Connectivity and population structure in a marginal sea – a review DOI Creative Commons
Simon Henriksson, Per Erik Jorde, Charlotte Berkström

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

Abstract The current biodiversity crisis calls for conservation measures that limit the negative human impact on important habitats and sensitive wild populations. To effectively protect at all levels, including intraspecific diversity, should be aligned with connectivity genetic structure of In this review, we synthesise scientific literature population marine species in Skagerrak – a marginal sea northeast Atlantic Ocean. We discuss results relation to management practices region, as well general transferability our findings. is one most intensively studied regions within research field, findings show overall adjacent seas high, but asymmetric, species. Simultaneously, have populations distinct from both each other, those seas. Most associated convoluted coastline common among coastal between offshore many mobile species, multiple are temporally sympatric certain areas, retain their divergence through natal homing or other barriers gene flow. presence despite high challenge area-based protection measures, flexible also monitors diversity timescales.

Language: Английский

Citations

1
Temperature Extremes and Sex-Related Physiology, Not Environmental Variability, Are Key in Explaining Thermal Sensitivity of Bimodal-Breathing Intertidal Crabs DOI Creative Commons

Pedro J. Jiménez,

Lyle Dennis Vorsatz, Tânia Márcia Costa

et al.

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: March 25, 2022

Global temperature increases are predicted to have pronounced negative effects on the metabolic performance of both terrestrial and aquatic organisms. These may be even more in intertidal organisms that subject multiple, abruptly changing abiotic stressors land-sea transition zone. Of available studies targeting environment, emphasis has largely been water-breathing model this selective focus resulted limited reliable forecasts impact global warming primarily air-breathing species. We investigated thermal sensitivity six phylogenetically related fiddler crab species occupy different microhabitats shores from south America east Asia test how bimodal-breathing ectotherms cope with stress. examined physiology limits crabs by measuring their cardiac function oxygen consumption along a gradient. Their specific microhabitat was also appraised. found subtropical inhabiting vegetated lower upper lethal temperatures therefore greater comparison tropical counterparts. Additionally, females exhibited higher males. Our results contradict previous predictions latitudes experience variability broader latitudinal distributions, phenotypic plasticity sensitivity. Furthermore, demonstrated female respect males strongly suggests role gametogenesis physiological dimorphism observations ultimately, advocates for further sex-biased development-biased before drawing any generalizations based single sex or life stage.

Language: Английский

Citations

5
Sensory biology and behaviour DOI

Steven H. Jury,

Christopher C. Chabot, Jason S. Goldstein

et al.

Elsevier eBooks, Journal Year: 2023, Volume and Issue: unknown, P. 123 - 157

Published: Aug. 25, 2023

Language: Английский

Citations

2
Genetic–environment associations explain genetic differentiation and variation between western and eastern North Pacific rhinoceros auklet (Cerorhinca monocerata) breeding colonies DOI Creative Commons
Brendan A. Graham, J. Mark Hipfner, Kyle Wellband

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

Abstract Animals are strongly connected to the environments they live in and may become adapted local environments. Examining genetic–environment associations of key indicator species, like seabirds, provides greater insights into forces that drive evolution marine systems. Here we examined a RADseq dataset 19,213 SNPs for 99 rhinoceros auklets ( Cerorhinca monocerata ) from five western Pacific 10 eastern breeding colonies. We used partial redundancy analyses identify candidate adaptive loci quantify effects environmental variation on population genetic structure. identified 262 loci, which accounted 3.0% observed among Genetic was more associated with pH maximum current velocity, than sea surface temperature. Genetic–environment explain differences between populations; however, within Ocean populations appears follow pattern isolation‐by‐distance. This study represents first relationship this widely distributed species evolutionary act species.

Language: Английский

Citations

0
Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context DOI Open Access

Giulia Trauzzi

Published: Aug. 28, 2023

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

Language: Английский

Citations

0