A population genomics insight by 2b‐RAD reveals populations' uniqueness along the Italian coastline in <i>Leptopsammia pruvoti</i> (Scleractinia, Dendrophylliidae)

Boscari, Elisa; Abbiati, Marco; Badalamenti, Fabio; Bavestrello, Giorgio; Benedetti‐Cecchi, Lisandro; Cannas, Rita; Cau, Alessandro; Cerrano, Carlo; Chimienti, Giovanni; Costantini, Federica; Fraschetti, Simonetta; Ingrosso, Gianmarco; Marino, Ilaria A. M.; Papetti, Chiara; Paterno, Marta; Ponti, Massimo; Zane, Lorenzo; Congiu, Leonardo

doi:10.1111/ddi.12918

Cited by 15 publications

(15 citation statements)

References 95 publications

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“…Restriction-site associated DNA sequencing libraries were constructed with the 2bRAD genotyping approach (Wang et al 2012) using protocols outlined in Boscari et al (2019) to obtain genome-wide SNPs. (More information can be found in ESM2.docx file of the Supplementary Material).…”

Section: Brad Library Preparationmentioning

confidence: 99%

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Population genomic structure of the black coral Antipathella subpinnata in Mediterranean Vulnerable Marine Ecosystems

et al. 2021

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Antipathella subpinnata (Ellis and Solander 1786) is one of the most frequently observed black corals at mesophotic depths (60–200 m) of the Mediterranean Sea, particularly in the northwestern part of the basin, where its populations can reach high densities and create forest-like aggregations, both along the coast and in offshore locations such as seamounts. Similar to other marine underwater forests, black coral gardens host a rich associated fauna and attract numerous species of commercial interest. As such, these corals are targeted by recreational and artisanal fisheries and are vulnerable to human impact due to their arborescent morphology and low growth rates. Genetic connectivity can provide valuable insight into the processes of population maintenance and replenishment following environmental disturbance and is often used as a proxy for population resilience. In our study, a restriction-site associated DNA analysis (2bRAD) was used to evaluate fine-scale population structure of the Mediterranean black coral A. subpinnata, and to understand which populations could serve as a potential source of genetic diversity for adjacent populations. Colonies from two offshore localities (a Ligurian seamount and a Tyrrhenian canyon) and four coastal populations from Liguria and Sicily were sampled and genotyped. Significant genetic differentiation was recorded between coastal and offshore localities. Moreover, offshore localities were genetically distinct from one another, while all coastal populations were characterized by panmixia. This indicates that offshore A. subpinnata gardens are potentially less resilient to human impact (i.e., demersal fishing activities) due to a limited influx of larvae from adjacent habitats. In addition, they are unlikely to supply coral propagules to coastal populations. Overall, this study highlights the vulnerability of Mediterranean A. subpinnata forests, and the importance of enforcing conservation and management measures to achieve Good Environmental Status (GES, EU Marine Strategy Framework Directive) of these valuable marine ecosystems.

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Section: Brad Library Preparationmentioning

confidence: 99%

“…Ligation adapters, CspCI restriction enzyme recognition sites, Coral Reefs and low-quality basecalls (Phred score \ 20) were trimmed to obtain high-quality 2bRAD fragments of uniform length (32 bp), using the Eli Meyer pipeline (https://github. com/Eli-Meyer/2bRAD_utilities) and as done in Boscari et al (2019).…”

Section: Bioinformatics Pipeline and Data Analysismentioning

confidence: 99%

Population genomic structure of the black coral Antipathella subpinnata in Mediterranean Vulnerable Marine Ecosystems

et al. 2021

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“…RAD-seq) sensitive to missing data and genotyping error, thus necessitating appropriate filtering strategy (e.g. Shafer et al, 2017;Andrews et al, 2018;Boscari et al, 2019). How then can we find an adequate distance threshold for collapsing slightly distinct genotypes into clonal lineages?…”

Section: Rad-seq As a Powerful Tool For Detection Of Clonal Lineagesmentioning

confidence: 99%

Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

et al. 2021

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Partial clonality, mode of reproduction, heterozygote excess, population genomics, kelp The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal reproduction). We analysed genome-wide variation with dd-RAD sequencing using 4077 SNPs in L. rodriguezii and 7364 SNPs in L. digitata. As predicted for partially clonal populations, we show that the distribution of FIS within populations of L. rodriguezii is shifted toward negative values, with a high number of loci showing heterozygote excess. This finding is the opposite of what we observed within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, we observed distinct distributions of FIS among populations of L. rodriguezii, which is congruent with the predictions of theoretical models for different levels of clonality and genetic drift. These findings highlight that the empirical distribution of FIS is a promising feature for the genomic study of asexuality in natural populations. Our results also show that the populations of L. rodriguezii analysed here are genetically differentiated and probably isolated. Our study provides a conceptual framework to investigate partial clonality on the basis of RAD-sequencing SNPs. These results could be obtained without any reference genome, and are therefore of interest for various non-model species.

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“…Many studies focusing on population structure in non‐model organisms have implemented different RAD technologies, such as RADseq (Lim et al, 2017; Xu et al, 2014), ddRAD (Lavretsky, DaCosta, Sorenson, McCracken, & Peters, 2019; Portnoy et al, 2015), GBS (Carreras et al, 2017; Hess et al, 2015), and 2b‐RAD (Boscari et al, 2019; Galaska, Sands, Santos, Mahon, & Halanych, 2017). By shifting the realms of genomics from laboratory‐based studies of model species towards studies of natural populations of ecologically well‐characterized organisms, researchers can now start to address important ecological and evolutionary questions on a scale and precision that, only a few years ago, was unrealistic (Ekblom & Galindo, 2011).…”

Section: Introductionmentioning

confidence: 99%

Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species

Barbanti

Torrado

Macpherson

et al. 2020

Molecular Ecology Resources

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High-throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b-RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b-RAD protocols on non-model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b-RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade-off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective-base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b-RAD protocols on non-model organisms with different genome sizes, helping decision-making for a reliable and cost-effective genotyping.

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A population genomics insight by 2b‐RAD reveals populations' uniqueness along the Italian coastline in Leptopsammia pruvoti (Scleractinia, Dendrophylliidae)

Cited by 15 publications

References 95 publications

Population genomic structure of the black coral Antipathella subpinnata in Mediterranean Vulnerable Marine Ecosystems

Population genomic structure of the black coral Antipathella subpinnata in Mediterranean Vulnerable Marine Ecosystems

Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species

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