Development of novel microsatellite markers for the spider genus<i>Loxosceles</i>(Sicariidae) using next-generation sequencing

Planas, Enric; Bernaus, Laia; Ribera, Carles

doi:10.1636/b13-88.1

Cited by 5 publications

(2 citation statements)

References 15 publications

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“…Arachnida is one of many branches in the tree of life that continues to benefit from the advent of highthroughput sequencing technologies (Brewer et al 2014;Ellegren 2014). Transcriptomics and pyrosequencing approaches have been adapted to the study of venoms and silks (Clarke et al , 2015Haney et al 2014;Sanggaard et al 2014), phylogenomics (Hedin et al 2012a;Sharma et al 2014;Fern andez & Giribet 2015;Garrison et al 2015), population biology (Mattila et al 2012;Planas et al 2014) and parasite-vector interactions (Schwarz et al 2013). In spite of these unique applications and diverse systems, few complete chelicerate genomes are available (Grbi c et al 2011;Cao et al 2013;Ellegren 2014).…”

Section: Introductionmentioning

confidence: 99%

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Burns

Starrett

Derkarabetian

et al. 2016

Molecular Ecology Resources

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Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6-base pair cutter EcoRI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.

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Section: Introductionmentioning

confidence: 99%

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Burns

Starrett

Derkarabetian

et al. 2016

Molecular Ecology Resources

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“…We genotyped 148 individuals sampled from 19 localities across the Mediterranean Basin (Fig 1) for seven microsatellite loci developed specifically for L . rufescens [29]. We conducted PCR reactions in a final volume 10 μl using Biotools Pfu DNA Polymerase (Biotools).…”

Section: Methodsmentioning

confidence: 99%

The Mediterranean as a melting pot: Phylogeography of Loxosceles rufescens (Sicariidae) in the Mediterranean Basin

2018

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The species Loxosceles rufescens is native to the Mediterranean but considered cosmopolitan because it has been dispersed worldwide. A previous study revealed 11 evolutionary lineages across the Mediterranean, grouped into two main clades, without any clear phylogeographic pattern. The high genetic diversity within this species (p-distances of up to 7.8% in some Mediterranean lineages), together with the results obtained with different species delimitation methods (GMYC, TCS) could indicate the existence of cryptic species. Here we compare the mitochondrial and microsatellite diversity to elucidate if the lineages of L. rufescens in the Mediterranean should be considered different species (cryptic species) or populations of the same species. To do so, we analyzed the cox1 diversity of 196 individuals, of which, we genotyped 148, sampled from 19 localities across the Mediterranean. STRUCTURE analyses of microsatellite data identified two genetic clusters of L. rufescens. One cluster included individuals from Western Mediterranean localities (Iberian Peninsula, Morocco, Balearic Islands) and Israel, while the second one grouped individuals from Italian and Greek localities, including Sardinia, Sicily and Tunisia. These patterns suggest that geographic proximity is the more significant factor in the clustering with microsatellite data and shows the existence of gene flow between the nearest geographic areas, even if the individuals belong to different mitochondrial lineages or clades. The lack of correspondence between both genetic markers suggests that the evolutionary lineages found within L. rufescens should not be considered different species. We conclude that these phylogenetic linages and their distribution may be the result of the maternal evolutionary history of the species and human-mediated dispersion.

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Characterization of four hypervariable microsatellite loci in a nuptial gift-giving spider and its prospect for paternity analyses

et al. 2020

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Development of novel microsatellite markers for the spider genusLoxosceles(Sicariidae) using next-generation sequencing

Cited by 5 publications

References 15 publications

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

The Mediterranean as a melting pot: Phylogeography of Loxosceles rufescens (Sicariidae) in the Mediterranean Basin

Characterization of four hypervariable microsatellite loci in a nuptial gift-giving spider and its prospect for paternity analyses

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