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At least six main hypotheses have been put forward to explain the centre of biodiversity. The ‘Centre of Origin’ hypothesis considers the centre of biodiversity to be the centre of origin, with speciation occurring inside the centre with successive outward dispersal to adjacent areas (Briggs 1999). Successive periods of glaciations and low sea‐level stands caused the emergence of barriers and the isolation of populations in deep sea basins in between the island groups of Indonesia and the Philippines, although this idea does not explain the high biodiversity along northern New Guinea. As the hypothesis indicates, however, it is the species that are successful that have given rise to phyletic lines leading to new genera and families. It is relatively easy for species of probable origins within the Coral Triangle to penetrate other tropical regions. Indeed, many species have achieved circumtropical distributions. There is some support based on molecular phylogenetic and biogeographic data to support the centre of origin hypothesis. Molecular data for reef dwarf gobies (Gobiidae: Eviota) indicate that two species complexes contain multiple genetically distinct, geographically restricted, colour morphs indicative of recently diverged species originating in the Coral Triangle (Tornabene et al. 2015). These data also suggest that regional isolation due to sea‐level fluctuations may explain some speciation, but other species show no evidence of physical isolation, thus both allopatric and sympatric speciation may have taken place within the region.

TABLE 5.1 Key tectonic events of the Cenozoic and their effects on the oceans and paleocurrents.

Source: Briggs (1974, 2006) and Lomolino et al. (2016). © John Wiley & Sons.

Event	Effects
Isolation of Antarctica
Early Eocene (50 Ma)‐full deep‐water separation of South Tasman Rise	First indications of global cooling at 50–40 Ma and significant 2°C temperature drops in both the late–middle Eocene and middle–late Eocene boundary. Further isolation of Antarctic marine fauna.
Eocene–Oligocene boundary (37 Ma)	Major cooling of both surface and bottom waters by 5°C. Onset of widespread Antarctic glaciation.
Opening of Drake Passage (36–23 Ma)	Almost complete isolation of Antarctic marine fauna.
Mid‐Miocene (15 Ma)‐full establishment of Antarctic Circumpolar Current	Latitudinal temperature gradient like that of today. Development of Polar Frontal Zone.
Closure of Tethyan Seaway
End of Cretaceous period (75–65 Ma)‐vast circumpolar‐equatorial tropical ocean	Major westerly flowing equatorial current system. Some faunal differentiation but no clear high‐diversity loci.
Paleogene (65–23 Ma)‐continuity of the tropical Tethyan Ocean	Largely homogenous tropical fauna. Major pulse in coral reef development at the end of Oligocene (23 Ma); marked similarities between western Tethys (Mediterranean) and Caribbean/ Gulf of Mexico.
Early Miocene (20 Ma)‐closure of Tethyan Seaway by northward movement of Africa/Arabia landmass	Westerly flowing tropical current drastically curtailed. Mediterranean Sea excluded from reef belt. Caribbean and eastern Pacific regions become progressively isolated marking beginning of the distinction between IWP and Atlantic Caribbean–East Pacific (ACEP) foci. Further development through the Neogene (<20 Ma) sees relative impoverishment of ACEP and enrichment of IWP.
Collision of Australia/New Guinea with Southeast Asia
Beginning of Cenozoic era (65 Ma)‐Australia/New Guinea separated from SE Asia by deep‐water gateway	Single tropical Tethyan ocean. No differentiation between Indian and Pacific Oceans.
Paleogene (65–23 Ma)‐progressive closure of Indo‐Pacific gateway; northward subduction of Indian–Australian lithosphere beneath the Sunda–Java–Sulawesi arcs
Mid‐Oligocene (30 Ma)‐gap narrowed but still a clear deep‐water passage formed by oceanic crust
Latest Oligocene (25 Ma)‐New Guinea collides with leading edge of eastern Philippines–Halmahara–New Guinea arc system
Early Miocene (20 Ma)‐deep water passage between Indian and Pacific Oceans closes	Major reorganisation of tropical current systems; new shallow‐water habitats appear in Indonesian region.
Early‐late Miocene (20–10 Ma)‐continued northward movement of Australia/New Guinea. Rotation of several plate boundaries and formation of tectonic provinces that are recognizable today	Widespread growth of coral reefs in IWP region; huge rise in numbers of reef and reef‐associated taxa; many modern genera and species evolve.
Later Neogene (10 Ma–present)‐continued northern movement of Australia/New Guinea; in Early Pliocene (4 Ma)‐a critical point when close contact is made with the island of Halmahara	Warm Pacific waters deflected eastward at the Halmahera eddy to form Northern Equatorial Counter Current. Warm waters in ITF are replaced by relatively cold ones from the North Pacific. These changes affect heat balance between East and West Pacific and help promote onset of Northern Hemisphere glaciation.
Uplift of Central American Isthmus (CAI)
Mid Miocene (15–13 Ma)‐sedimentary evidence of earliest phases of shallowing	Still a deep‐water connection at CAI.
Latest Miocene–early Pliocene (6–4 Ma)‐continued shallowing to <100 m depth	Major effect on oceanic circulation. Gulf Stream begins to deflect warm shallow waters northward to eventually initiate the major “conveyor belt” of deep ocean circulation.
Mid‐Pliocene (3.6 Ma)‐further closure of CAI	North Atlantic thermohaline circulation system intensifies; Arctic Ocean isolated from warm Atlantic leading eventually to onset of Northern Hemisphere glaciation at 2.5 Ma.
Late Pliocene (3 Ma)‐complete closure of CAI	Final separation of shallow water Atlantic–Caribbean and Eastern Pacific Provinces. Reverse flow of water through the Bering Strait; this influences Pliocene–Pleistocene patterns of thermohaline circulation in Arctic and North Atlantic Oceans.

There are two basic versions of the centre of origin hypothesis. The first is what Bellwood et al. (2012) have called the ‘spreading dye model’ in which species originating within the Coral Triangle expanded their geographic range by chance. The second version states that new species with superior competitive abilities displaced older, inferior competitors towards the periphery of the region’s boundaries. Thus, in theory, newer species will be at the centre of the boundary and that there would be a “peripheral halo” of predominantly older species that will also have greater geographic range.

The second hypothesis is the ‘Centre of Overlap’ (or Vicariance) model. This idea states that the centre of biodiversity consists of overlapping distribution ranges that extend into either the Pacific or the Indian Ocean resulting from either larval dispersal or ancient plate tectonics. These biogeographic boundaries are well recognised, but any subsequent expansion or movement of ranges would lead to an overlap of geographic ranges and a localised increase in species richness in the overlap zone (Santini and Winterbottom 2002). The inherent complexity of the physical environment within the Coral Triangle makes it highly likely that this area exhibited many such divisions that were susceptible to frequent changes through time. It may thus be considered a ‘dynamic mosaic’ (Bellwood et al. 2012) of constantly changing distributions driven by continual climatic, geologic, and oceanographic processes. This hypothesis has found some support from reef fish (Woodland 1986), corals (Wallace 2002), crustaceans (Fransen 2007), and gastropods (Reid et al. 2006).

The third hypothesis is the ‘Centre of Accumulation’ model that is the opposite of the centre of origin hypothesis. It proposes that species arose in peripheral locations, around, or at some distance from the margin of the centre and that they subsequently moved into the centre. New species can be from anywhere outside the centre. It does not require overlap with related taxa. There are two distinct versions of this hypothesis. First, the centre of accumulation by individuals places the emphasis on isolation on peripheral oceanic islands in underpinning the speciation process. Second, the centre of accumulation by faunas reflects the accumulation of entire faunas on moving land masses. In this version, species richness may be enhanced by the merging of entire faunas via the merging of island arcs on the north coast of New Guinea with the numerous land fragments from Asia, Gondwana, and Australia.

The fourth hypothesis is the ‘Centre of Survival’ idea that is a composite hypothesis emphasising persistence and survival in an area rather than on origin of the species in question. The key aspect of this hypothesis is regional variation in the relative rates of extinction, and it makes no assumptions about the rates or location of origin of species. Speciation may thus have occurred anywhere. The centre of biodiversity is just an area of survival with species extinctions outside the centre’s boundaries. The maintenance of habitat diversity and the availability of sufficient abundance for each species is an important condition for this hypothesis.

The fifth hypothesis is the ‘Centre of Mid‐Domain Overlaps’ idea that is a variation on the second hypothesis. In this version, a maximum in species richness in the middle of a geographical area has formed by overlying randomised distributions of the locations of individual geographic ranges within species groups. The maximum is predicted to occur where the probability of maximum of species range overlaps is highest, that is, if the ranges are randomly placed within the Indo‐Pacific, the resultant pattern of species richness forms a peak in the middle. The hotspot is thus the result of random placement of species’ geographic ranges (Bellwood et al. 2012).

The sixth hypothesis is ‘Reticulate Evolution’ that is arguably the main mechanism of evolutionary change in most marine taxa (Veron et al. 2009). It recognises “(a) that currents are both genetic barriers (as in vicariance) and paths of genetic connectivity, (b) that species fuse as well as divide over time and space, (c) that species are generally not isolated units and (d) that evolution is driven by the physical environment (especially ocean currents) rather than biological mechanisms (e.g., competition). Furthermore, reticulate evolution does not deny the existence of Darwinian evolution which could become uppermost were genetic mixing to weaken sufficiently to create isolated gene pools. This would allow evolution to occur through biological selection. Conditions which promote reticulate evolution are at a maximum in the Coral Triangle (sometimes referred to as an ‘evolutionary cauldron’) because of habitat diversity and the ever‐changing complexity of ocean surface currents.”

Another hypothesis based on fossil and molecular evidence is the idea of ‘hopping hotspots’ (Renema et al. 2008). There is good evidence for the fact that during the past 50 Ma, there have been at least three marine biodiversity hotspots that have moved across half the globe, with their timing and locations coinciding with major movements of the earth’s plates. Based on generic diversity of large benthic foraminifera, three successive movements of biodiversity hotspots have been identified: (a) in the late Middle Eocene (42–39 Ma), (b) in the early Miocene (23–16 Ma), and (c) in the present day (Renema et al. 2008). These are known as the West Tethys, Arabian, and Indo‐Australian Archipelago biodiversity hotspots. During the Eocene, diversity peaked in SW Europe, NW Africa, and along the eastern shore of the Arabian Peninsula, Pakistan, and West India. The fossil record of mangroves and reef corals suggests maximal global diversity in the West Tethyan hotspot. By the late Eocene, the highest diversity was recorded in the Arabian hotspot that has an overlapping taxonomic composition with the earlier West Tethys and the later Indo‐Australian Archipelago hotspots. The Miocene is the most diverse period in Southeast Asia for both large benthic foraminifera and mangroves. Regional uplift during the Arabia–Eurasia collision resulted in the demise of the Arabian hotspot during the middle to late Miocene. The present hotspot appeared with the disappearance of the Arabian hotspot and has been extant at least since the early Miocene (20 Ma) as shown by fossil records of foraminifera, corals, mangroves, and gastropods (Renema et al. 2008).

It is unlikely that there is a single explanation to account for the Coral Triangle hotspot, although for corals and most major taxa equatorial temperatures and habitat diversity are highly explanatory. The relative importance of any one hypothesis will change with increases in data and methodology. Some faunal groups, such as the stomatopods and the bryopsidale algae, do not conform to any of the hypotheses. What is clear is that there is a biodiversity hotspot in the Coral Triangle in which species richness patterns differ little from random expectations. Also, there are strong correlations between total species richness and a limited range of key environmental factors; the consensus among taxa is that there is a shared evolutionary and geological history with most taxa in the Coral Triangle being primarily of Miocene origin with ancestors from the Cenozoic hotspots of West Tethys and Arabia (Bellwood et al. 2012).

With respect to the origins of tropical marine biodiversity, it is clear that (i) physical isolation (allopatric speciation) is not the sole mechanism for speciation, (ii) oceanic archipelagos that were thought to be peripheral habitats for speciation are in fact regions that can export biodiversity, and (iii) opportunities are fewer for allopatric speciation in the oceans leaving greater opportunity for speciation along ecological boundaries (Di Martino et al. 2018). Bowen et al. (2013) have emphasised that areas such as the Coral Triangle and the Caribbean produce and export species but can also accumulate biodiversity produced in marginal habitats. This benefit has been dubbed the “biodiversity feedback” (Bowen et al. 2013).