Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations

Using next-generation sequencing technology, we designed a pool of microsatellite primers and amplified them in 2 physically isolated populations of the Atlanto-Mediterranean sponge Hemimycale columella, which exhibits particular evolutionary, biological, and ecological features. The species has con...

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Autores principales:	J González-Ramos, G Agell, MJ Uriz
Formato:	article
Lenguaje:	EN
Publicado:	Inter-Research 2015
Materias:	Biology (General) QH301-705.5 Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/79114885039e45c4a7e7599c9962e4e7
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spelling	oai:doaj.org-article:79114885039e45c4a7e7599c9962e4e72021-11-18T09:17:04ZMicrosatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations1864-77821864-779010.3354/ab00630https://doaj.org/article/79114885039e45c4a7e7599c9962e4e72015-06-01T00:00:00Zhttps://www.int-res.com/abstracts/ab/v24/n1/p25-34/https://doaj.org/toc/1864-7782https://doaj.org/toc/1864-7790Using next-generation sequencing technology, we designed a pool of microsatellite primers and amplified them in 2 physically isolated populations of the Atlanto-Mediterranean sponge Hemimycale columella, which exhibits particular evolutionary, biological, and ecological features. The species has contrasting life cycles in shallow and relatively deep waters, and releases small, predictably low-dispersal larvae. This study experimentally evaluated how many polymorphic microsatellites would be necessary to detect genetic structure in H. columella populations, and whether or not the use of compound loci is advisable. By sequencing 1/2 454 GS-FLX run, we obtained a total of 4208 sequences enclosing microsatellite motifs. We selected 20 microsatellites, 15 of which proved adequate for the genetic study of the sponge populations. The 2 analyzed populations were genetically structured with all microsatellite combinations assayed, and the values of the Dest and FST statistics did not increase with increasing number of loci. A weak signal of genetic structure, however, was shown in bar plots representing membership coefficients for each individual to each sampling location even with all loci. We conclude that a few polymorphic loci can detect structure in H. columella populations, but using 12 or more loci notably enhances the power of the analyses. The study also describes a low-cost protocol for obtaining microsatellites by the hundreds from non-model, ecologically relevant species, which can be used to provide information about population isolation, adaptation, and vulnerability.J González-RamosG AgellMJ UrizInter-ResearcharticleBiology (General)QH301-705.5MicrobiologyQR1-502ENAquatic Biology, Vol 24, Iss 1, Pp 25-34 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5 Microbiology QR1-502
spellingShingle	Biology (General) QH301-705.5 Microbiology QR1-502 J González-Ramos G Agell MJ Uriz Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations
description	Using next-generation sequencing technology, we designed a pool of microsatellite primers and amplified them in 2 physically isolated populations of the Atlanto-Mediterranean sponge Hemimycale columella, which exhibits particular evolutionary, biological, and ecological features. The species has contrasting life cycles in shallow and relatively deep waters, and releases small, predictably low-dispersal larvae. This study experimentally evaluated how many polymorphic microsatellites would be necessary to detect genetic structure in H. columella populations, and whether or not the use of compound loci is advisable. By sequencing 1/2 454 GS-FLX run, we obtained a total of 4208 sequences enclosing microsatellite motifs. We selected 20 microsatellites, 15 of which proved adequate for the genetic study of the sponge populations. The 2 analyzed populations were genetically structured with all microsatellite combinations assayed, and the values of the Dest and FST statistics did not increase with increasing number of loci. A weak signal of genetic structure, however, was shown in bar plots representing membership coefficients for each individual to each sampling location even with all loci. We conclude that a few polymorphic loci can detect structure in H. columella populations, but using 12 or more loci notably enhances the power of the analyses. The study also describes a low-cost protocol for obtaining microsatellites by the hundreds from non-model, ecologically relevant species, which can be used to provide information about population isolation, adaptation, and vulnerability.
format	article
author	J González-Ramos G Agell MJ Uriz
author_facet	J González-Ramos G Agell MJ Uriz
author_sort	J González-Ramos
title	Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations
title_short	Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations
title_full	Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations
title_fullStr	Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations
title_full_unstemmed	Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations
title_sort	microsatellites from sponge genomes: the number necessary for detecting genetic structure in hemimycale columella populations
publisher	Inter-Research
publishDate	2015
url	https://doaj.org/article/79114885039e45c4a7e7599c9962e4e7
work_keys_str_mv	AT jgonzalezramos microsatellitesfromspongegenomesthenumbernecessaryfordetectinggeneticstructureinhemimycalecolumellapopulations AT gagell microsatellitesfromspongegenomesthenumbernecessaryfordetectinggeneticstructureinhemimycalecolumellapopulations AT mjuriz microsatellitesfromspongegenomesthenumbernecessaryfordetectinggeneticstructureinhemimycalecolumellapopulations
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Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations

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