Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Bayona‐Vásquez, Natalia J.; Glenn, Travis C.; Pierson, Todd W.; Hoffberg, Sandra L.; Scott, Peter; Bentley, Kerin E.; Finger, John W.; Louha, Swarnali; Troendle, Nicholas J.; Díaz‐Jaimes, Píndaro; Mauricio, Rodney; Faircloth, Brant C.

doi:10.1101/205799

Cited by 38 publications

(57 citation statements)

References 42 publications

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“…Our results also suggest that hybrid females are not selective of parental species in their mate choice. The reduced-representation genomic data obtained with a 3RAD approach 42 confirmed the introgression level of some backcrossed hatchlings using 2,405 3RAD loci. This is the first time that backcrosses with loggerhead turtles are confirmed by genome-wide sequencing analysis.…”

Section: Discussionsupporting

confidence: 55%

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Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output

Arantes

Ferreira

Driller

et al. 2020

Sci Rep

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Hybridization between sea turtle species occurs with particularly high frequency at two adjacent nesting areas in northeastern Brazil. To understand the outcomes of hybridization and their consequences for sea turtle conservation, we need to evaluate the extent of hybridization occurrence and possible deleterious effects in the hybrid progeny. Thus, we investigated the hypothesis of the existence of a new hybrid spot offshore of Brazil’s northeastern coast. The Abrolhos Archipelago is surrounded by the largest and richest coral reefs in the South Atlantic and is known to be a nesting site for loggerhead turtles (Carettacaretta). In this study, we performed a multidisciplinary investigation into levels of hybridization in sea turtles and their reproductive output in the Abrolhos beaches. Genetic data from mitochondrial DNA (mtDNA) and six autosomal markers showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelysimbricata) and loggerhead females, and backcrossed hatchlings from both parental species. The type and extent of hybridization were characterized using genomic data obtained with the 3RAD method, which confirmed backcrossing between F1 hybrids and loggerhead turtles. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.

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Section: Discussionsupporting

confidence: 55%

“…We used the 3RAD protocol as described by Bayona-Vásquez et al 42 to analyze hatchlings from six different nests collected at Abrolhos. Briefly, we digested 100 ng of genomic DNA with the enzymes MseI, EcoRI and CviQI (New England Biolabs) at 10 U/μL and the specific combination of adapters for each sample for 1 h at 37 °C.…”

Section: Methodsmentioning

confidence: 99%

Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output

Arantes

Ferreira

Driller

et al. 2020

Sci Rep

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“…Libraries were prepared using the 3RADseq methodology proposed by Bayona‐Vásquez et al . (2019). The technique modifies typical double‐digest restriction site‐associated DNA sequencing (Peterson et al ., 2012) by including a third restriction enzyme that recognizes and cleaves adapter dimer.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and structure of circumtropical almaco jack, Seriola rivoliana: tool for conservation and management

Mendoza‐Portillo¹,

Galván‐Tirado

Portnoy

et al. 2020

Journal of Fish Biology

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The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific‐1 in central Pacific, Pacific‐2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific‐3), whereas that of mtDNA did not. This mito‐nuclear discordance is likely explained by a recently diverged Pacific‐3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with rm < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (rm > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.

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“…Reduced‐representation genotyping approaches constitute a powerful tool for conducting in‐depth population genetics studies for any species of interest. Following the introduction of restriction‐site‐associated DNA sequencing (Baird et al., 2008), a wide range of related methodologies utilizing restriction enzymes have been introduced like genotyping by sequencing (Elshire et al., 2011), ddRAD‐seq (Peterson, Weber, Kay, Fisher, & Hoekstra, 2012), 2b‐RAD (Wang, Meyer, McKay, & Matz, 2012), ezRAD (Toonen et al., 2013), quaddRAD (Franchini, Monné Parera, Kautt, & Meyer, 2017), and 2RAD/3RAD (Bayona‐Vásquez et al., 2019). The aforementioned platforms have been used extensively in studies on aquatic organisms focusing both in population genetic aspects (Andrews, Good, Miller, Luikart, & Hohenlohe, 2016) and in studying traits of interest for farming purposes (Houston et al., 2020; You, Shan, & Shi, 2020).…”

Section: Introductionmentioning

confidence: 99%

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Nyinondi

Mtolera

Mmochi

et al. 2020

Ecology and Evolution

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Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all‐male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double‐digest restriction‐site‐associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (Fst) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (Fst = 0.34). Isolation‐by‐distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p‐value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross‐validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.

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Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Cited by 38 publications

References 42 publications

Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output

Genomic evidence of recent hybridization between sea turtles at Abrolhos Archipelago and its association to low reproductive output

Genetic diversity and structure of circumtropical almaco jack, Seriola rivoliana: tool for conservation and management

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

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