A new, more complete, five-marker (SSU, LSU, psbA, COI, 23S) molecular phylogeny of the family Corallinaceae, order Corallinales, shows a paraphyletic grouping of seven well-supported monophyletic clades. The taxonomic implications included the amendment of two subfamilies, Neogoniolithoideae and Metagoniolithoideae, and the rejection of Porolithoideae as an independent subfamily. Metagoniolithoideae contained Harveylithon gen. nov., with H. rupestre comb. nov. as the generitype, and H. canariense stat. nov., H. munitum comb. nov., and H. samoënse comb. nov. Spongites and Pneophyllum belonged to separate clades. The subfamily Neogoniolithoideae included the generitype of Spongites, S. fruticulosus, for which an epitype was designated. Pneophyllum requires reassesment. The generitype of Hydrolithon, H. reinboldii, was a younger heterotypic synonym of H. boergesenii. The evolutionary novelty of the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae was the development of tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials.

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The Kutai Basin (East Kalimantan, Indonesia) contains a rich and well-preserved Miocene fossil record of small patch reefs that developed under the influence of high siliciclastic input associated with the progradation of the Mahakam Delta. In this study, we reconstruct the biodiversity and paleoenvironments on one of these delta-front, mixed carbonatesiliciclastic systems that developed at the Serravallian-Tortonian boundary near the city of Samarinda. In two newly exposed sections, we analyzed the sedimentology and distribution of the main fossil biota including corals, foraminifers, coralline algae, and bryozoans. Seven facies are herein defined, including two dominated by platy corals and two by larger benthic foraminifera. Facies distributions were driven by changes in depth and variations in terrigenous input within a range of delta-front habitats. Despite the turbid conditions, fossil assemblages are highly diverse, including 69 coral species and 28 bryozoan species that occur in coral-dominated facies. Crustose coralline algae were mainly associated with the coral-dominated facies. Larger benthic foraminifera showed broader ecological tolerance within the range represented in the studied sections and thus are common in most facies. These diverse patch reef ecosystems were able to cope with high siliciclastic input during the early development of the Miocene coral reef biota.

The temporal dimension of the most recent Corallinaceae (order Corallinales) phylogeny was presented here, based on first occurrence time estimates from the fossil record. Calibration of the molecular clock of the genetic marker SSU entailed a separation of Corallinales from Hapalidiales in the Albian (Early Cretaceous ~105 mya). Neither the calibration nor the fossil record resolved the succession of appearance of the first three emerging subfamilies: Mastophoroideae, Corallinoideae, and Neogoniolithoideae. The development of the tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials was an evolutionary novelty emerging at the Cretaceous-Paleogene boundary (~66 mya). This novelty was shared by the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae, which diverged in the early Paleogene. Subclades within the Metagoniolithoideae and Lithophylloideae diversified in the late Oligocene-middle Miocene (~28-12 mya). The most common reef corallinaceans (Hydrolithon, Porolithon, Harveylithon, "Pneophyllum" conicum, and subclades within Lithophylloideae) appeared in this interval in the Indo-Australian Archipelago.