The origins and evolution of the indo- pacific reef coralline algae

Resum

The purpose of this PhD thesis is to study the evolutionary history of crustose coralline algae (CCA) associated to coral reefs, especially in the Indo-Pacific. This research has been conducted within the frame of the THROUGHFLOW Project which was aimed to investigate with a multidisciplinary approach the onset of the biodiversity hotspot in South East Asia and to find the biotic responses to the major environmental changes that took place in the region during the Miocene. Fossil coralline algal samples were collected in Miocene reefs in East Kalimantan (Borneo, Indonesia) in order to detect first occurrences of recent reef-related taxa, previously included in the subfamilies Mastophoroideae Setchell sensu Harvey et al., 2003 and Lithophylloideae Setchell. The fossil CCA found were used additionally as paleoenvironmental indicators, especially for paleodepth interpretation, in Miocene patch reefs and coral-reef related deposits in the Miocene proto-Mahakam delta. On the other hand, living coralline algae were sampled in Indo-Pacific reefs and in the western Mediterranean. The DNA of coralline algae belonging to Mastophoroideae sensu Harvey et al., 2003 and Lithophylloideae was extracted for the use of five genetic markers to build a molecular phylogeny and a time tree combining the molecular data and the paleontological information of first appearances of the studied and related taxa. The taxonomic implications of the obtained results led to the proposal of two new genera (Adeylithon and Harveylithon), one new subfamily (Spongitoideae) and the emendation of another subfamily (Porolithoideae Kato & Baba). Corallinaceae (Corallines possessing uniporate tetrasporangial conceptacles) separated from Hapalidiaceae in late Early Cretaceous. Mastophoroideae (Setchell) Kato & Baba, Spongitoideae subfam. nov. and Neogoniolithoideae Kato & Baba originated in the Cretaceous, having in common the formation of tetrasporangial conceptacle roofs by filaments surrounding the sporangial initials. Hydrolithoideae Kato &Baba emerged at the Cretaceous-Paleogene boundary and share with all the later diverging clades the formation of tetrasporangial conceptacle roofs by filaments surrounding to and interspersed between the sporangial initials. The later diverging clades include Porolithoideae Kato & Baba with an emended circumscription, Lithophylloideae Setchell and a monophyletic group consisting of taxa from the southern Hemisphere. These three clades originated in the Oligocene and diversified in the Miocene, the time of the onset of the SE Asian biodiversity hotspot.