Abstract
The Indonesian archipelago hosts 1218 freshwater fish species disseminated across 14,000 islands. Encompassing three majors geographic assemblages (Sundaland, Wallacea, Sahul) separated by two majors faunistic transitions (Wallace and Lyddeker lines), Indonesian islands display heterogeneous levels of species richness resulting from diverse geological and paleoecological histories. Sundaland itself hosts 68% of the total number of freshwater fish species and constitutes one of the world’s most endangered fauna worldwide. By contrast with Wallacea that results from an early settlement through subduction around 40 Mya, Sundaland (Borneo, Sumatra and Java) has acquired its modern configuration during the last 5 Mya through a combination of continental fragmentation and subduction. The alarming state of Sundaland ichthyodiversity, combined with major taxonomy and distribution knowedge gaps, urges for a modern reapparaisal through standardized DNA-based methods. The ichtyodiversity of Java in particular, is the most threatened and the less known of Sundaland. This dissertation aims at addressing two main questions: (1) Is DNA barcoding a suitable approach to characterize the ichthyodiversity of Java? (2) Is the geological and paeloecological history of Java a good predictor of diversity patterns and population genetic structure? The main results evidence: (1) large discrepancies between the checklist of the Java freshwater fishes based on historical records and a modern re-appraisal through DNA barcodes. Reasons invoqued are the taxonomic bias related to the interrupted inventory of Java ichthyofauna during the last 3 centuries and the rarefaction of several species targeted by artisanal fisheries. (2) A DNA-based reappraisal of species boundaries and distribution for the genera Nemacheilus and Rasbora indicated two new taxa, several cases of cryptic diversity and several cases of wrong assignement of populations to the species levels. Species range distributions appear to be much more restricted than previously thoughts and question the persistence of these species in changing landscapes. (3) A DNA-based assessment through DNA barcodes of the population genetic structure of three widespread species in Java evidences high levels of cryptic diversity and deep genetic divergences among geographically restricted and non-overlapping mitochondrial lineages. Consistent with a fragmentation related to the rise of volcanic arches in Java that prompted a long-term declines of historical effective population size, this pattern argue for the sensitive conservation status of these mitochondrial lineages. The results presented here highlights the benefits of using a standardized DNA-based approach for the fast characterization of a poorly known fauna and open new perspectives in the conservation of the ichtyofauna of Java and Bali.