In many organisms, particularly terrestrials, molecular markers have been used to answer questions about the structure and connectivity of populations, the potential of dispersal or the history of species, and these data were of crucial help in conservation and management of species. Most of these studies used allozymes and, more recently, mitochondrial or nuclear sequences with success. Also, microsatellite markers are being developed and applied with terrific success in many species. Unfortunately, application of molecular markers in marine environments lags much behind, especially for invertebrate organisms, where population genetic studies are still scarce and most of them involve only allozymes. Thus, this study attempts to contribute to the development and application of molecular markers for ecological and population genetic studies in marine invertebrates. Most marine invertebrate organisms are benthic, and many of them sessile, with larvae as the main form of dispersal. Because of the intrinsic difficulty on following larval movements in natural environments, molecular markers appear as the perfect tool to track and characterize populations, and even individuals. Hence, in this thesis several molecular markers have been applied in a sponge species, and with the complementary help of previous ecological and biological knowledge of the species, the present-day population structure of this sponge has been studied, trying to uncover which factors are affecting and might have affected in the past the structure found, while comparing the resolution and the “snapshot” information recovered with each of the markers used.

The first chapter corresponds to the introduction to the “molecular ecology philosophy” with especial emphasis on the history and facts of the markers used, a quick look at the works published in this field for marine invertebrate organisms as well as to what we do know about the biology and ecology of the sponge studied.

The second chapter includes the use of mtDNA sequences of the gene Cytochrome Oxidase subunit I to characterize 7 populations from the western Mediterranean and one population from the Canaries Islands, 86 individuals in total. This study represents the first survey of sequence variation of mtDNA genes among populations of any sponge species. (Mar Biol 2004,144:31-35)

In the third chapter the ribosomal Internal Transcribed Spacer-1 (ITS-1), 5.8S rRNA, and the Internal Transcribed Spacer-2 (ITS-2) have been analyzed for the same populations and individuals used in the mtDNA study plus a few other populations, reaching a total of 11 populations and 121 individuals. (Mol Ecol 2003, 13:109-122)

The fourth chapter describes the development and characterization of polymorphic microsatellite loci from a partial genomic DNA enriched library; allelic variation of the loci described is assessed and compared for two distant populations in order to weigh up the utility of microsatellites as high-resolution genetic markers for this species. These are the first microsatellite loci reported from any species in the phylum. (Molecular Ecology Notes 2002, 2:478-480).

In the fifth chapter, the formerly developed microsatellite loci are genotyped for the same 11 populations as in chapter 3, the number of individuals analyzed has been increased to 286. This is the first study to use microsatellites in ascertaining population structure of a sponge. (Mol Ecol 2004, 13: in press).