Abstract
AB Aquatic Biology Contact the journal Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections AB 24:25-34 (2015) - DOI: https://doi.org/10.3354/ab00630 Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations Janina González-Ramos, Gemma Agell, Maria J. Uriz* Centre d’Estudis Avançats de Blanes (CEAB-CSIC), C/ Accés a la Cala St. Francesc, 14, 17300 Blanes (Girona), Spain *Corresponding author: iosune@ceab.csic.es ABSTRACT: 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. KEY WORDS: SSRs · Pyrosequencing · Population genetics · Genetic differentiation · Porifera · Hemimycale columella · Conservation genetics Full text in pdf format Supplementary material PreviousNextCite this article as: González-Ramos J, Agell G, Uriz MJ (2015) Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations. Aquat Biol 24:25-34. https://doi.org/10.3354/ab00630 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AB Vol. 24, No. 1. Online publication date: June 09, 2015 Print ISSN: 1864-7782; Online ISSN: 1864-7790 Copyright © 2015 Inter-Research.
Highlights
Sponges are one of the foremost groups in terms of diversity and abundance in marine benthic ecosystems (Gili & Coma 1998), where they play poorly studied but critical structural and trophic roles (Bell 2008)
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
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
Summary
Sponges are one of the foremost groups in terms of diversity and abundance in marine benthic ecosystems (Gili & Coma 1998), where they play poorly studied but critical structural and trophic roles (Bell 2008). Koskinen et al 2004) This might not be always the case, and we consider it worthwhile to optimize further studies on the population genetics of H. columella by ascertaining the minimal number and type of polymorphic microsatellite loci that would be required to detect significant genetic differentiation in sponge populations without losing accuracy. For this purpose, we investigated the number of loci/alleles needed to capture the genetic diversity of a population, and whether the use of imperfect or compound microsatellites (which have been considered undesirable for these studies because of a higher probability of presenting unnoticed size homoplasy; Angers et al 2000) produced biased results. By selecting the type and number of microsatellites that optimize costs and accuracy, this study provides guidelines for microsatellite-based approaches for studying population genetics of other genetically non-model marine invertebrates targeted for ecological or biotechnological reasons
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