Population genomics and phylogeography of a benthic coastal shark (<i>Scyliorhinus canicula</i>) using 2b-RAD single nucleotide polymorphisms

Manuzzi, Alice; Zane, Lorenzo; Muñoz‐Mérida, Antonio; Griffiths, Andrew M.; Veríssimo, Ana

doi:10.1093/biolinnean/bly185

Cited by 24 publications

(27 citation statements)

References 74 publications

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“…These samples came from Sauce Lagoon (N=10) and Uruguay River Basin (N= 11) belonging to two divergent lineages [29]. Finally, two nearby populations without genetic differentiation of small-spotted catshark (S. canicula) from North Sea (N= 13) and Irish Sea (N= 15) were analysed [30]. All information from samples analysed is summarized in supplementary material (Table S6).…”

Section: Samples Studiedmentioning

confidence: 99%

“…DNA extraction and 2b-RAD libraries preparation using AlfI IIB RE followed the same protocol except for small-spotted catshark [30] where CspCI IIB RE was used instead. The libraries were sequenced using Illumina sequencing platforms (i.e.…”

Section: Library Preparationmentioning

confidence: 99%

“…HiSeq 1500 for small-spotted catshark, NextSeq500 for the remaining species) following a 50 bp single-end chemistry. For details see [29,30].…”

Section: Library Preparationmentioning

confidence: 99%

“…A range of population parameters were compared in the ve species applying similar parameter settings for each pipeline (description of pipelines in Methods). The two marine bivalve species from the Order Veneroida show high polymorphism and low population structure [25,26]; the brown trout belongs to the order Salmoniformes, which suffered a speci c genome duplication event [27], and shows one of the highest population structuring among vertebrates [28]; isolated populations from different ecosystems were analysed in the silver cat sh, a freshwater species from the order Siluriformes living in uvial and costal lagoon environments [29]; nally, the small-spotted catshark (order Carcharhiniformes) is a benthic species which populations here used show low genetic differentiation [30]. To date, two of the species used in this study have a reference genome available: Manila clam (genome size: 1.123 Gb; 19 chromosomes [31]) and brown trout (2.370 Gb; 40 chromosomes [32]).…”

Section: Introductionmentioning

confidence: 99%

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Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Casanova

Maroso

Blanco

et al. 2020

Preprint

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Background The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. Results Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. Conclusions Building-loci pipelines seem not to have a substantial influence on population genetics inference. Anyway, we recommend being careful with certain building-loci pipeline parameters and SNP filtering steps, especially when a de novo approach is used. Preliminary trials with subsets of data should be performed for comparison of genetic diversity and differentiation, but always considering the specific goals of the study.

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Section: Samples Studiedmentioning

confidence: 99%

Section: Library Preparationmentioning

confidence: 99%

“…HiSeq 1500 for small-spotted catshark, NextSeq500 for the remaining species) following a 50 bp single-end chemistry. For details see [29,30].…”

Section: Library Preparationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Casanova

Maroso

Blanco

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…A range of population parameters were compared in the ve species applying similar parameter settings for each pipeline (description of pipelines in Methods). The two marine bivalve species from the Order Veneroida show high polymorphism and low population structure [26,27]; the brown trout belongs to the order Salmoniformes, which suffered a speci c genome duplication event [28], and shows one of the highest population structuring among vertebrates [29]; isolated populations from different ecosystems were analysed in the silver cat sh, a freshwater species from the order Siluriformes living in uvial and costal lagoon environments [30]; nally, the small-spotted catshark (order Carcharhiniformes) is a benthic species which populations here used show low genetic differentiation [31]. Despite these species represent different population genetics and evolutionary scenarios, this does not mean that they necessarily comprehend all the models for the manifold scenarios used to check the performance of building-loci pipelines.…”

Section: Introductionmentioning

confidence: 99%

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Casanova

Maroso

Blanco

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Background: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. without reference genomes. Here, the performances of two building-loci pipelines, STACKS 2 and Meyer’s 2b-RAD v2.1 pipeline, were compared using a diverse set of aquatic species representing different genomic and/or population structure scenarios. Two bivalve species (Manila clam and common edible cockle) and three fish species (brown trout, silver catfish and small-spotted catshark) were studied. Four SNP panels were evaluated in each species to test both different building-loci pipelines and criteria for SNP selection. Furthermore, for Manila clam and brown trout, a reference genome approach was used as control. Results: Despite different outcomes were observed between pipelines and species with the diverse SNP calling and filtering steps tested, no remarkable differences were found on genetic diversity and differentiation within species with the SNP panels obtained with a de novo approach. The main differences were found in brown trout between the de novo and reference genome approaches. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons. Conclusions: Tested building-loci pipelines seem not to have a substantial influence on population genetics inference. Preliminary trials with bioinformatic pipelines are suggested to evaluate their influence in population parameters related to the specific goals of the study.

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Population genetic divergence of bonnethead sharks Sphyrna tiburo in the western North Atlantic: Implications for conservation

Díaz‐Jaimes¹,

Bayona‐Vásquez

Escatel‐Luna

et al. 2020

Aquatic Conservation

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Sharks are a priority for conservation because numerous species, including small‐sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and preventing population declines. Limited dispersal is an important factor promoting population divergence for several coastal shark species. The genetic variation in 14 microsatellite loci and 21,006 single nucleotide polymorphisms genotyped using restriction‐site‐associated DNA sequencing was analysed to assess the genetic structure of the bonnethead shark, Sphyrna tiburo, in the western North Atlantic. Genetic differences were identified among three well‐defined regions: the western Florida coast, the south‐eastern US Atlantic coast, and the southern Gulf of Mexico. Results support previous studies based on mitochondrial DNA sequences in defining differences among these regions and suggest limitations of bonnethead sharks in routinely performing long‐distance migrations. The limited connectivity among regions explains the pattern of genetic divergence but also reported divergence at the species/subspecies level. These genetically discrete bonnethead populations have independent evolutionary histories that may include local adaptations to specific areas. Bonnethead sharks are currently managed as two stocks in the USA owing to recent genetic, tagging, and life history studies; however, no stock assessments or management plans exist for Mexico. These results not only serve to reinforce US management strategies and provide critical data about the extent of gene flow and sex dispersal among populations, but also begin the process of effective management in the waters of Mexico to ensure the long‐term productivity and resilience of this species. With an absence of gene flow between populations from US waters and the southern Gulf of Mexico, there is a need for management plans based upon independent biological and population dynamics data since limited or no opportunities for populations to interchange individuals may occur to re‐establish population viability.

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Population genomics and phylogeography of a benthic coastal shark (Scyliorhinus canicula) using 2b-RAD single nucleotide polymorphisms

Cited by 24 publications

References 74 publications

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Genomic outcomes from diverse SNP panels obtained with different de novo building-loci pipelines in a varied species context: Can pipelines be influencing biological interpretations?

Population genetic divergence of bonnethead sharks Sphyrna tiburo in the western North Atlantic: Implications for conservation

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