Phylogeography of the Sponge Suberites diversicolor in Indonesia: Insights into the Evolution of Marine Lake Populations

Abstract

The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.

Pervasive genetic structure at different geographic scales in the coral-excavating sponge Cliona vermifera (Hancock, 1867) in the Mexican Pacific

“…Very low levels of nucleotide diversity (\1 %) reflected the small divergence among DNA sequences. Relative to other sponges, the nucleotide diversity (i.e., mean per nucleotide divergence) of COI in location II was higher than the one reported in other species such as C. crambe (Duran et al 2004c), Suberites diversicolor (Becking et al 2013), and A. willeyana (Wörheide 2006): p = 0.0006, 0.0006, and 0.00049, respectively. Of the three loci, ITS showed the highest gene diversity; however, it was somewhat smaller than in S. diversicolor (h = 0.82; Becking et al 2013).…”

“…Relative to other sponges, the nucleotide diversity (i.e., mean per nucleotide divergence) of COI in location II was higher than the one reported in other species such as C. crambe (Duran et al 2004c), Suberites diversicolor (Becking et al 2013), and A. willeyana (Wörheide 2006): p = 0.0006, 0.0006, and 0.00049, respectively. Of the three loci, ITS showed the highest gene diversity; however, it was somewhat smaller than in S. diversicolor (h = 0.82; Becking et al 2013). The mean divergence of ITS sequences found in C. vermifera was within the range reported in other Porifera from the Indian and Pacific oceans and from the Caribbean (ITS1, p = 0.0044, ITS2, p = 0.00369; Wörheide et al 2004), and in Indonesia (p = 0.0008-0.0056; Becking et al 2013).…”

“…Of the three loci, ITS showed the highest gene diversity; however, it was somewhat smaller than in S. diversicolor (h = 0.82; Becking et al 2013). The mean divergence of ITS sequences found in C. vermifera was within the range reported in other Porifera from the Indian and Pacific oceans and from the Caribbean (ITS1, p = 0.0044, ITS2, p = 0.00369; Wörheide et al 2004), and in Indonesia (p = 0.0008-0.0056; Becking et al 2013).…”

Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor

“…The connection between the marine lakes and the outer marine environment strongly influences the communities inhabiting these lakes (Saitoh et al 2011). Lakes with a limited connection tend to house a smaller number of species including numerous endemics (Becking et al 2013a(Becking et al , 2013b(Becking et al , 2016Strelkov et al 2014), whereas more connected lakes tend to house more species, but with a greater compositional similarity to open sea habitat. Lake size also influences the number of species, with larger lakes housing a higher number of species than smaller ones (Becking et al 2013b).…”

“…Lakes with a limited connection tend to house a smaller number of species including numerous endemics (Becking et al 2013a(Becking et al , 2013b(Becking et al , 2016Strelkov et al 2014), whereas more connected lakes tend to house more species, but with a greater compositional similarity to open sea habitat. Lake size also influences the number of species, with larger lakes housing a higher number of species than smaller ones (Becking et al 2013b). In addition to differences in species number, connectivity also influences the lake environment with less connected lakes usually characterised by lower pH, lower salinity and higher water temperature than more connected lakes (Becking et al 2011).…”