Hotspots of high species diversity are a prominent feature of modern global biodiversity patterns. Fossil and molecular evidence is starting to reveal the history of these hotspots. There have been at least three marine biodiversity hotspots during the past 50 million years. They have moved across almost half the globe, with their timing and locations coinciding with major tectonic events. The birth and death of successive hotspots highlights the link between environmental change and biodiversity patterns. The antiquity of the taxa in the modern Indo-Australian Archipelago hotspot emphasizes the role of pre-Pleistocene events in shaping modern diversity patterns.

Data from a comprehensive literature survey for the first time provide stage-level resolution of Early Cretaceous through Pleistocene species diversity for nongeniculate coralline algae. Distributions of a total of 655 species in 23 genera were compiled from 222 publications. These represent three family-subfamily groupings each with distinctive present-day distributions: (1) Sporolithaceae, low latitude, mainly deep water; (2) Melobesioid corallinaceans, high latitude, shallow water, to low latitude, deep water; (3) Lithophylloid/mastophoroid corallinaceans, mid- to low latitude, shallow water. Raw data show overall Early Cretaceous-early Miocene increase to 245 species in the Aquitanian, followed by collapse to only 43 species in the late Pliocene. Rarefaction analysis confirms the pattern of increase but suggests that scarcity of publications exaggerates Neogene decline, which was actually relatively slight. Throughout the history of coralline species, species richness broadly correlates with published global paleotemperatures based on benthic foraminifer δ ¹⁸ O values. The warm-water Sporolithaceae were most species-abundant during the Cretaceous, but they declined and were rapidly overtaken by the Corallinaceae as Cenozoic temperatures declined. Trends within the Corallinaceae during the Cenozoic appear to reflect environmental change and disturbance. Cool- and deep-water melobesioids rapidly expanded during the latest Cretaceous and Paleocene. Warmer-water lithophylloid/mastophoroid species increased slowly during the same period but more quickly in the early Oligocene, possibly reflecting habitat partitioning as climatic belts differentiated and scleractinian reef development expanded near the Eocene/Oligocene boundary. Melobesioids abruptly declined in the late Pliocene-Pleistocene, while lithophylloid/mastophoroids increased again. Possibly, onset of glaciation in the Northern Hemisphere (~2.4 Ma) sustained or accentuated latitudinal differentiation and global climatic deterioration, disrupting high-latitude melobesioid habitats. Simultaneously, this could have caused moderate environmental disturbance in mid- to low-latitude ecosystems, promoting diversification of lithophylloids/mastophoroids through the “fission effect.” Extinction events that eliminated >20% of coralline species were most severe (58–67% of species) during the Late Cretaceous and late Miocene-Pliocene. Each extinction was followed by substantial episodes of origination, particularly in the Danian and Pleistocene.