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

被引:6
作者
Gonzalez-Ramos, Janina [1 ]
Agell, Gemma [1 ]
Uriz, Maria J. [1 ]
机构
[1] CSIC, CEAB, Blanes 17300, Girona, Spain
来源
AQUATIC BIOLOGY | 2015年 / 24卷 / 01期
关键词
SSRs; Pyrosequencing; Population genetics; Genetic differentiation; Porifera; Hemimycale columella; Conservation genetics; MULTILOCUS GENOTYPE DATA; SIZE HOMOPLASY; CHEMICAL ECOLOGY; PROGRAM; LOCI; DIFFERENTIATION; INFERENCE; SOFTWARE; POECILOSCLERIDA; PATTERNS;
D O I
10.3354/ab00630
中图分类号
Q17 [水生生物学];
学科分类号
071004 ;
摘要
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 D-est and F-ST 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.
引用
收藏
页码:25 / 34
页数:10
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