Obura-Journal_of_Biogeography

Journal of Biogeography (J. Biogeogr.) (2015) 

SYNTHESIS 

An Indian Ocean centre of origin 

revisited: Palaeogene and Neogene 

influences defining a biogeographic 

realm 

David O. Obura* 

CORDIO East Africa, Mombasa 80101, 

Kenya 

ABSTRACT 

Aim The biogeography and origins of the shallow marine fauna in the western 

and northern Indian Ocean are poorly known. Focusing on scleractinian corals, 

this study synthesizes evidence from extant biogeographical patterns, phylogenetics, 

plate tectonics and palaeoceanography to provide new support for a 

hypothesis on an Indian Ocean ‘centre of origin’ for shallow marine taxa. 

Location The western and northern Indian Ocean, from approximately 90°E 

westwards, including the Red Sea and Arabian Sea. 

Methods Synthesis of primary observations and published literature. 

Results Ten per cent of western and northern Indian Ocean coral species are 

endemic, with the genera Acropora, Anomastrea, Coscinaraea, Craterastrea, Ctenella, 

Gyrosmilia, Horastrea, Sclerophyllia, Siderastrea and Stylophora presenting 

evidence for deep and shallow evolutionary origins unique to the region. Evidence 

for origins in the Eocene Tethys Sea and Oligocene East Africa-Arabian 

Province, the global hotspots of shallow tropical marine biodiversity in their 

time, is derived from the fossil record, clade age, presence of relict species, 

intra- and inter-specific genetic diversity, Atlantic affinities and extant distributions. 

Evidence for Neogene origins in geologically active subregions of the 

Indian Ocean (Red Sea, Arabian Sea, Mascarene Islands) is derived from intraand 

inter-specific genetic diversity and endemism. The passive tectonic remnant 

margins of Gondwana (East Africa and Madagascar coasts), combined 

with prevailing ocean currents, are hypothesized to have provided a stable evolutionary 

refuge and region of species accumulation, perhaps since the Palaeogene. 

Main conclusions The evidence supports multiple ‘centres of origin’ for 

Indian Ocean corals, first in the Palaeogene Tethys Sea, then in the Neogene 

Red Sea, Arabian Sea and Mascarene Islands. The tectonically inactive East 

African and Madagascar coasts provide an evolutionary museum for old and 

new lineages, forming a second and phylogenetically distinct peak of global 

tropical scleractinian coral biodiversity in the Northern Mozambique Channel. 

*Correspondence: David Obura, CORDIO East 

Africa, Box 10135 Mombasa 80101, Kenya. 

E-mail: dobura@cordioea.net 

Keywords 

biodiversity hotspot, corals, East Africa-Arabian Province, Eocene, Indian 

Ocean, Miocene, Northern Mozambique Channel, Oligocene, Tethys Sea 

INTRODUCTION 

The tropical Indo-Pacific covers a vast swathe of the oceans 

across 240° of longitude from 40° E on the East African 

coast to 80° W on the west coast of the Americas. The faunal 

similarity in shallow tropical species, exemplified in coral 

reefs, across this largest part of the earth’s circumference is 

notable. Nevertheless, efforts to divide the continental shelves 

of the Indo-Pacific into biogeographical realms, starting with 

Longhurst (1998), have intensified in recent decades. Spalding 

et al. (2007), using a variety of environmental and biogeographical 

data, divided the Indo-Pacific into four realms. 

ª 2015 John Wiley & Sons Ltd http://wileyonlinelibrary.com/journal/jbi 1 

doi:10.1111/jbi.12656

D. O. Obura 

Work on individual taxonomic groups shows some variation 

from this structure, recently focusing on the two best-studied 

taxa on coral reefs – scleractinian corals (Bellwood & 

Hughes, 2001; Veron et al., 2009, 2015) and reef-associated 

fish (Briggs & Bowen, 2012; Bowen et al., 2013; Kulbicki 

et al., 2013). 

In general, species diversity across the Indo-Pacific declines 

in all directions from the high-diversity centre in the Indo- 

Australian Archipelago (IAA), with the evidence for corals 

and fish being held as proxies for tropical taxa in general 

(Bellwood & Hughes, 2001). Primary attention has remained 

squarely on the global diversity hotspot in the IAA and subregional 

centres of endemism (Briggs & Bowen, 2012). Comparatively 

little attention has been paid to the Indian Ocean 

(Wafar et al., 2011), in spite of Rosen (1971) and Pichon 

(1978) noting evidence for a ‘second centre origin’ for coral 

species in it. This gap is now being addressed; for example, 

in differentiating Indian versus Pacific Ocean species within 

what were previously thought to be Indo-Pacific-wide species 

of corals (Y. Chuang, unpublished data; Stefani et al., 2011) 

and fish (Gaither et al., 2011; Eble et al., 2011), as well as 

further splitting within the Indian Ocean of iconic taxa such 

as the coral Stylophora pistillata (Keshavmurthy et al., 2013), 

and the crown of thorns seastar Acanthaster planci (V€ogler 

et al., 2008). Further, a peak of species diversity has now 

been recognized in the western part of the Ocean, in particular 

in the northern Mozambique Channel, shown by scleractinian 

corals (Obura, 2012a; Veron et al., 2015) and 

stomatopods (Reaka et al., 2008), with some corroboration 

in phylogenetic analysis in ophiuroids (Hoareau et al., 2013) 

and fish (Muths et al., 2014). In addition, phylogenetic work 

on corals focused in the Red Sea and Arabian Sea is building 

increasing evidence for the evolutionary distinctiveness of 

Indian Ocean coral taxa (Stefani et al., 2011; Arrigoni et al., 

2012, 2014; Benzoni et al., 2012). 

This paper reviews major aspects of the tectonic and 

palaeoceanographic history of the Indian Ocean in order to 

propose mechanisms underlying phylogenetic and biogeographical 

relationships in ‘Indian Ocean corals’, in a region 

from Sri Lanka and India westwards that is referred to here 

as the western and northern Indian Ocean (W&NIO), and 

loosely described as ‘the Indian Ocean’. Analysis focuses on 

two major periods of earth history during the Cenozoic 

era: the Eocene-Oligocene (in the Palaeogene), when 

shallow marine diversity was in full recovery following the 

Pg-T (K-T) extinction that marked the beginning of the 

Cenozoic, and the Miocene-Pliocene (the Neogene), when 

the marine diversity peak in the IAA (Renema et al., 2008) 

came to dominate global marine biodiversity patterns. 

THE EVIDENCE 

The Palaeogene (Eocene – Oligocene) 

The Eocene (56–33.9 Ma) and Oligocene (33.9–23 Ma), the 

last two epochs of the Palaeogene, mark a time of tectonic 

2 

change in what is now the northern and central Indian 

Ocean (Table 1, Fig. 1a). At this time Africa was drifting 

northwards and colliding with the Eurasian land mass, 

resulting in narrowing of the Tethys Sea and bringing to a 

close its dominance of global oceanographic patterns and 

shallow marine biodiversity that started with its formation 

about 200 Ma (Stow, 2010). Coincident with the transition 

from the Eocene to the Oligocene (33.9 Ma), the Mascarene- 

Reunion hotspot was active, creating an island chain across 

the centre of the Indian Ocean that now comprises the submerged 

carbonate banks of Saya de Malha, Nazareth and 

Cargados Carajos, capping the volcanic Mascarene Ridge. In 

contrast, the passive plate margins of the East African coast, 

produced by the initial rift of Gondwana some 140–180 Ma 

(Parson & Evans, 2004; Yoder & Nowak, 2006), formed what 

is now the Mozambique Channel, and the east coast of 

Madagascar, produced by the rifting of Australia, Antarctica 

and India from Madagascar, formed between 120 and 

90 Ma. 

The palaeoceanography of the Indian Ocean has received 

little attention other than as a sidebar to other interests, such 

as general ocean circulation and climate interactions (Brass 

et al., 1982; Bickert et al., 2008), or exchanges between 

Madagascan, African and Asian terrestrial faunae during the 

Cenozoic (Masters et al., 2006; Ali & Huber, 2010). During 

the early Eocene it is likely that the west-flowing circumequatorial 

current of the Tethys Sea passed between India 

and the Asian landmass, and as this narrowed, the current 

was deflected southwards by the Indian land mass (Brass 

et al., 1982). Following collision of India with Asia, the remnants 

of the Tethys Sea closed during the Oligocene, slowly 

obliterating the once-abundant shallow habitats found there 

(R€ogl, 1998). It is also likely that the then emergent Mascarene 

Ridge islands (Fig. 1a) formed an intermittent north– 

south barrier that would have further isolated the western 

Indian Ocean (WIO). These have been considered in island 

stepping-stone models for both terrestrial (e.g. Masters et al., 

2006) and marine fauna (e.g. Postaire et al., 2014), but without 

consideration of their potential effect on currents (e.g. 

Ali & Huber, 2010). 

Modelling of global circulation during the Oligocene suggests 

a strong westward current akin to the present South 

Equatorial Current (SEC) but farther south, and a clockwise 

gyre in the northern Indian Ocean (von der Heydt and Dijkstra, 

2006), and during the Miocene, weak circulation 

between the Tethys Sea and WIO (Bickert et al., 2008). 

These currents would have provided a mechanism for transport 

from the Tethys Sea into the WIO and towards the 

incipient IAA. Overall, it appears that what is now the WIO 

may have been relatively isolated in a semi-enclosed sea during 

the Oligocene (Fig. 1b), with the greatest degree of connectivity, 

in terms of both currents and larval sources, with 

the Tethys Sea. 

The Tethys Sea between North Africa/the Arabian Peninsula 

and the Eurasian land mass became the hotspot of shallow 

marine diversity, initially in the West Tethys (WT; 

Journal of Biogeography 

ª 2015 John Wiley & Sons Ltd

Indian Ocean centre of origin 

Table 1 Major geological, oceanographic and climatic features affecting the coral reef and shallow marine biota of the Indian Ocean during the Cenozoic. Time units are in millions of 

years before present (Ma), following Cohen et al. (2013). Adapted from Obura, 2012b. 

Periods Epochs Time (Ma) Plate Tectonics Tethys Sea Mascarene Hotspot Currents and dispersal Diversity 

Quarternary Holocene Present Current configuration reached Dominance of I-P diversity 

patterns by IAA and West 

Pacific species 

Pleistocene 0.01–2.58 Reunion (2 Ma) Full establishment of E–W 

connectiveity and dispersal 

Mauritius (7–8 Ma) Diversity hotpot developing 

in IAA 

Tertiary 

Neogene Pliocene 2.58–5.33 

Miocene 5.33–23.0 Full development of IAA Closure of Tethys Sea, 

by 15 Ma 

Diversity hotspot in Arabian 

region (EAAP) 

Palaeogene Oligocene 23.0–33.9 Collision of Asian and 

Australian plates (25 Ma) 

Collision of India with Asia (35 Ma) Diversity hotspot in West 

Isolation of WIO by India & 

Mascarene plateau, likely 

flow from Tethys 

Narrowing of Tethys Sea Mascarene plateau/central 

IO banks formed 

(30–45 Ma) 

Tethys. 

Eocene 33.9–56.0 Rapid northward migration of India ‘Palaeogene gap’ in fossil 

record 

western Europe/north Africa) in the Eocene, and subsequently 

in the East Africa-Arabian Province (EAAP) in the 

Oligocene (Harzhauser et al., 2007; Renema et al., 2008). As 

the primary region of tectonic collision shifted from this 

region to the Indo-Australian region in the Miocene, due to 

collision of the Australian and Asian plates, this latter region 

became the new hotspot of shallow marine diversity (Wilson 

& Rosen, 1998). At the same time, further collision in the 

Tethyan region resulted in uplift of the active crusts and 

obliteration of the Tethys Sea (Renema et al., 2008). 

The Neogene (Miocene-Pliocene) 

The Neogene, comprising the Miocene (23–5.33 Ma) and 

Pliocene (5.33–2.58 Ma), is defined by collision of the Australian 

and Asian plates, forming a new biodiversity hotspot 

in the IAA (Wilson & Rosen, 1998; Renema et al., 2008; 

Fig. 1c), now dubbed the Coral Triangle (Roberts et al., 

2002; Hoeksma, 2007). While the gap between Australia and 

Asia has narrowed during this time, the configuration of the 

Indian Ocean has remained relatively stable. The Tethys Sea 

finally closed about 15 Ma, and the Mascarene-Reunion hotspot 

produced just the two relatively small islands of Mauritius 

(7–8 Ma) and Reunion (2 Ma). Westward flow of the 

SEC (Schott & McCreary, 2001) has likely remained consistent 

during the Neogene, the main differences with the 

Palaeogene being less obstruction across the Mascarene Ridge 

(Fig. 1c) and a growing source fauna of newly diversifying 

species in the IAA. 

Coral phylogenetics and biogeography 

Recent advances in coral phylogenetics and systematics using 

genetic techniques and microstructural characters are revealing 

the true phylogeny of corals (Fukami et al., 2008; Budd 

et al., 2010; Budd & Stolarski, 2011). The main macromorphological 

features historically used in coral taxonomy (e.g. 

Wells, 1956) experience considerable convergence, resulting 

in incorrect phylogenetic reconstructions. As a result, the 

accepted phylogeny of corals was strongly biased by the locations 

and primary material studied by taxonomists, focusing 

on the Atlantic and IAA, and Tethyan fossil sites. Poorly 

studied regions such as the Indian Ocean were therefore 

poorly treated in evolutionary interpretations. This section 

outlines emerging phylogenetic relationships of corals 

(Table 2) that show concordance with tectonic and oceanographic 

patterns (Table 1). 

The genus Acropora, known mostly for its extreme species 

radiation associated with the IAA in the Neogene and 

Quaternary (Wallace, 1999) shows its first fossil appearance 

in Somalia, in the Eocene East Africa/Arabian Province 

(Carbone et al., 1994). This was followed by radiation of 9 

of 20 currently recognized species groups in the WT 

(Wallace & Rosen, 2006). Subsequent eastward migration of 

the diversity hotspot during the late Oligocene and early 

Miocene is associated with the proliferation of Acropora in 


ª 2015 John Wiley & Sons Ltd 

3


(a) (b) (c) 

Figure 1 Tectonic configurations during (a) the Eocene (45 Ma) and (b) the Oligocene (30 Ma) where shallow marine diversity was 

highest in the West Tethys Sea (WT) and East Africa-Arabian Province (EAAP), respectively, and (c) in the Miocene (15 Ma), when 

diversity was highest in the Indo-Australian Archipelago (IAA). The Mascarene Banks (MB) are shown in grey as it is uncertain to what 

extent they were submerged or emergent islands. Figure adapted from Lawver et al. (2010). 

Table 2 Extant western and northern Indian Ocean (W&NIO) coral genera and species showing evidence of Palaeogene and Neogene 

origins. 

Taxa Palaeogene (Eocene/Oligocene) processes Neogene (Miocene-Pliocene) processes Sources 

Acropora A. rudis, A. roseni A. hemprichii, A. 

forskali and A. variolosa – Eocene 

fossils in Somalia and Europe; basal 

clade species endemic or most 

common in W&NIO 

Coscinaraeidae Newly described family uniting poorly 

known mono-specific genera restricted 

to the W&NIO: Anomastrea 

irregularis, Horastrea indica, 

Craterastrea levis. Regional endemics, 

long unbranched clades, characteristics 

of relict species 

Euphylliidae Gyrosmilia interrupta and Ctenella 

chagius – regional endemics, long 

unbranched clades, characteristics of 

relict species. 

Stylophora Genetic divergence dated to Eocene, 

ancestral species found in Red Sea. 

Siderastrea 

Sclerophyllia 

Regional and sub-regional endemic spp. 

– A. maryae, branchi 

One W&NIO regional endemic 

Coscinaraea sp.,one species - C. monile 

– that is more characteristic of the 

WIO than the West Pacific 

Regional and sub-regional endemic spp. 

– 3 species in W&NIO, 2 endemic 

species in the Red Sea; Greater genetic 

diversity 

W&NIO species a sister clade to Atlantic species, derived from Pacific species 

(S. savignyana) (divergence date not established) 

Revived genus with just two species, restricted to the Red Sea, Arabian Sea and 

Gulfs. The age of the genus currently unknown. 

Carbone et al. (1994), Wallace (1999) 

and Wallace & Rosen (2006) 

Veron (2000), Claereboudt (2006), 

Benzoni et al. (2012) and Obura 

(2012a) 

Obura, (2012a) 

Flot et al. (2011); Stefani et al. (2011) 

and Keshavmurthy et al. (2013) 

Chuang (2006), Obura et al. (2007) 

and Y. Chuang, unpublished data 

Arrigoni et al., (2014) 

the IAA and surrounding regions, and the massive radiation 

of species that occurs today. The oldest clades of extant Acropora 

species are characteristic of the W&NIO, in particular 

A. rudis, A. roseni and a group including A. hemprichii, 

A. forskali and A. variolosa (Fig. 2a–c). Contrary to the radiation 

of lineages in the IAA in the late Oligocene and early 

Miocene, these taxa show little radiation of species, and limited 

dispersal eastwards to the IAA (Wallace & Muir, 2005). 

The Coscinaraeidae (Benzoni et al., 2012) is a newly 

described family uniting two monospecific genera previously 

classified in the Siderastreidae (Anomastrea, Horastrea), with 

one sometimes classified in the Agariciidae (Craterastrea), 

and Coscinaraea (Fig. 2d–f). Coscinaraea is widely distributed 

4 

across the Indian Ocean and West Pacific, though one undescribed 

species (Fig. 2g) appears restricted to the Gulf of 

Aden and WIO (Obura, 2012a). This species, a congener predominantly 

distributed in the WIO (C. monile, Veron, 

2000), and the monospecific genera, tend to be uncommon 

and found in turbid, extreme or marginal reef habitats (e.g. 

Benzoni et al., 2012; Obura, 2012a; Smit, 2014). The family 

demonstrates the deep evolutionary history and low degree 

of radiation in W&NIO coral lineages comprising the ‘Indian 

Ocean fauna’ (Rosen, 1971; Pichon, 1978). 

Three other monospecific genera restricted to the Indian 

Ocean have variously been classified in the Caryophillidae and 

Meandrinidae, but are now reassigned to the Euphylliidae 




(a) (b) (c) 

(d) (e) (f) 

(g) (h) (i) 

(j) (k) (l) 

Figure 2 Selection of endemic coral species of the western and northern Indian Ocean for which a Palaeogene/Tethyan origin is 

proposed; (a) Acropora roseni, Chagos Archipelago; (b) A. hemprichii, St. Brandons Island, Cargados Carajos Shoals, Mauritius; (c) 

A. variolosa, Djibouti; (d) Anomastrea irregularis, NE Madagascar; (e) Horastrea indica, Nacala, N. Mozambique; (f) Craterastrea levis, 

NE Madagascar; (g) Coscinaraea sp., Inhambane, S. Mozambique; this species is identified as an undescribed Psammocora species in 

Claereboudt (2006); (h) Siderastrea savignyana, Kiunga, N. Kenya; (i) Stylophora pistillata (morph M in Stefani et al., 2011, clade 4 in 

Keshavmurthy et al., 2013), Farquhar Atoll, Seychelles; (j) Ctenella chagius, St. Brandons Island, Cargados Carajos Shoals, Mauritius; (k) 

Gyrosmilia interrupta, Nacala, N. Mozambique; (l) Stylophora madagascarensis (in Stefani et al., 2012, Stylophora pistillata clade 3 in 

Keshavmurthy et al., 2013), NE Madagascar. All photos: David Obura. 

(Budd et al., 2012) – Gyrosmilia and Ctenella in the W&NIO 

(Fig. 2j,k), and Montigyra in the Eastern Indian Ocean. Like 

the monospecific genera in the Coscinaraeidae, two of these 

are highly restricted within the W&NIO. Ctenella is recorded 

only from the Chagos Archipelago and St. Brandons Island by 

Obura (2012a), with additional locations from Madagascar 



and Mauritius reported by Veron et al. (2015; and see Moothien 

Pillay et al., 2002). Additionally, the species are found in 

marginal habitats; turbid reefs for Gyrosmilia, and the seagrass-dominated 

Mascarene Banks for Ctenella. 

A recent revision adding to the ‘Indian Ocean fauna’ is 

the revived genus Sclerophyllia, with just two species, and 

5


currently known only from the Red Sea and Gulf of Aden 

(Arrigoni et al., 2014). S. margaritifera had erroneously been 

classified in Symphyllia and Cynarina, and its congener 

S. maxima in Acanthastrea. As with the Coscinaraeids and 

Euphylliids mentioned above, genetic studies were necessary 

to overcome the problems associated with morphological 

classification. 

The genus Siderastrea is more species rich in the Atlantic 

than the Indo-Pacific, with until recently four nominal species 

in the Atlantic and a single species in the Indo-Pacific 

(Veron, 2000). The Indo-Pacific species (S. savignyana) is 

now differentiated into two allopatric species, one in the 

WIO (Oman and Kenya), the other in the West Pacific 

(Taiwan and Australia) (Chuang, 2006). Divergence between 

the Indo-Pacific species preceded divergence of the Atlantic 

and WIO species (Y. Chuang, unpublised data), indicating 

isolation first across the Eastern Indian Ocean, then by closure 

of the Tethys Sea. This is corroborated by morphology, 

where the Indian Ocean species shows characteristics that are 

more similar to certain Atlantic species than to the Pacific 

species (Obura et al., 2007). 

Finally, the genus Stylophora is undergoing heavy revision 

(Fig. 2i,l). Three branching morphs were distinguished phylogenetically 

by Stefani et al. (2011) and four by Keshavmurthy 

et al. (2013), who dated branch divergence to the 

Eocene (50 Ma) and late Oligocene (30–35 Ma). These studies 

and Flot et al. (2011) found the greatest species and 

genetic diversity in the W&NIO, and the ancestral taxa in 

the group are found in the Red Sea. Moreover two encrusting 

species, S. wellsi and S. mammilata, are endemic to the 

Red Sea (Veron, 2000). 

DISCUSSION 

An Indian Ocean coral fauna 

The most recent global biogeographical analysis of corals 

(Veron et al., 2015) shows a distinct fauna in the Indian 

Ocean west of 90° E, on the basis of 2–3% of Indo-Pacific 

corals being restricted to the Indian Ocean (inferring < 20 

species). In a more restricted analysis based on the IUCN 

Red List (2011), Obura (2012a) found a similar distinct 

Indian Ocean fauna: in a field data set from the W&NIO of 

369 species, he found 10% of species to be restricted to the 

region. Reef fish show a similar pattern of a dominant widespread 

Indo-Pacific fauna, though with higher levels of regional 

differentiation; approximately 25% of reef fish species in 

the Indian Ocean are endemic (Allen, 2008; Briggs & Bowen, 

2012). The most recent review of Indo-Pacific fish biogeography 

(Kulbicki et al., 2013) concurs with Obura’s (2012a) and 

Veron et al.’s (2015) division between the Indian Ocean and 

Indo-Pacific faunae, at the large gap in coral reef habitats in 

the Bay of Bengal, at about 90° E (Fig. 4). This division lies 

between those proposed in the Marine Ecoregions of the 

World (Spalding et al., 2007), in which the eastern Indian 

Ocean is grouped with the W&NIO, and Briggs & Bowen 

6 

(2012, 2013), in which South Asia and Chagos are grouped 

with the Central Indo-Pacific (Fig. 4). 

Focusing on ‘Indian Ocean’ species west of the 90 o E division, 

two sets of coral species are apparent – those with older 

origins in the Palaeogene, and those with younger origins in 

the Neogene (Table 2, Figs 2 & 3). 

Palaeogene origins 

The evidence for Palaeogene origins of a Tethyan fauna is 

provided by seven coral genera (Acropora, Anomastrea, Coscinaraea, 

Craterastrea, Ctenella, Gyrosmilia and Horastrea; 

Table 2, Fig. 2). It is based on tectonic, palaeoceanographic 

and phylogenetic grounds, and is consistent with the theory 

of tectonic drivers of major biodiversity hotspots in shallow 

seas (Renema et al., 2008). The mono-specific genera that 

are endemic to the W&NIO show characteristics that are 

consistent with expectations for relict species and late stages 

in the ‘taxon cycle’ (Ricklefs, 2011), where species persist in 

isolated pockets of once-larger distributions. These include 

species with highly restricted distributions (e.g. Ctenella chagius, 

Craterastrea levis) and species with distributions that are 

wide-ranging but rare (e.g. Gyrosmilia interrupta, Horastrea 

indica, Anomastrea irregularis). All of these species also have 

long clade branch lengths. This contrasts with expectations 

for new species, which should show a contiguous restricted 

range (Bellwood & Meyer, 2009), and short branch lengths 

between sister species. These genera also failed to disperse to 

or survive in the IAA in the late Oligocene/Miocene. Thus, 

they apparently ‘stalled’ in the EAAP in the Oligocene, failing 

to take advantage of new evolutionary opportunities available 

in the tectonically active IAA. Instead, these genera were preserved 

in the tectonically inactive W&NIO, supporting a 

hypothesis that they are remnants from the Tethys/EAAP 

with once broader distributions, having dispersed southwards 

into the W&NIO due to restricted circulation up to and 

including in the Oligocene (Table 1). 

The question arises whether supporting evidence for 

Palaeogene origins in Indian Ocean taxa is found in other 

taxonomic groups. The clam subfamily Tridacninae was represented 

by 5 genera and 15 species in the WT in the Eocene 

(Harzhauser et al., 2008). Progressive extinction of tridacnines 

first in the WT in the Eocene, and then in the EAAP in 

the Oligocene, was associated with closure of the Tethys Sea 

(R€ogl, 1998), followed by migration to the IAA in the Miocene 

and Quaternary (Harzhauser et al., 2008). However, tridacnines 

did not subsequently diversify in the IAA, 

remaining with two genera and nine species in the Indo- 

West Pacific (Newman & Gomez, 2000). 

Among soft corals (Octocorallia), three taxa show some 

support. The family Melitheidae shows a deep division 

between W&NIO versus Central Indo-Pacific taxa (Reijnen 

et al., 2014), and within the former, between western and 

northern Indian Ocean species (Fig. 4). The order Helioporaceaea 

has only five species in three genera (Heliopora, 

Epiphaxum, Nanipora), with origins dating back to the 




Cretaceaous, and little diversification. One species of Epiphaxum 

was first found in the WT in the Eocene, and the 

genus shows evidence of speciation prior to closure of the 

Tethys Sea, with two extant species in the Caribbean and 

two in the Indo-Pacific (Lozouet & Molodtsova, 2008). 

However, as with scleractinian corals, traditional taxonomy 

of soft corals based on macro-morphological characters does 

not match, and in fact did much to hide, phylogenetic and 

biogeographical pattern, and the gaps in phylogenetic and 

palaeo-geographical knowledge of soft corals (McFadden 

et al., 2010) are still too large for strong support (or rejection) 

of this hypothesis. Among reef fish, deeper evolutionary 

relationships from the Eocene and Oligocene are evident in 

some families (Cowman & Bellwood, 2011), though in contrast 

with corals, they do not show evidence of higher diversity 

in the Tethys Sea than in the Indo-Australian region of 

the time. 

The continental shorelines of the WIO have an unusually 

stable tectonic history of some 150 Myr, and though some 

latitudinal shift has occurred, the coastlines of what is now 

the Mozambique Channel have changed little over this time 

(Yoder & Nowak, 2006). The continental crust shorelines 

(including that of Madagascar) are steep, minimizing the 

effect of sea level fluctuations on habitat migration, connectivity 

and speciation/extinction processes (see Potts, 1985). 

There are no large carbonate platforms in the WIO from the 

Cenozoic, providing further evidence of the absence of extensive 

shallow seas and complex habitats associated with active 

tectonic margins (Wilson & Rosen, 1998; Renema et al., 

2008; Cowman & Bellwood, 2011). Finally, the Africa/Madagascar 

plate has migrated northwards some 15° during the 

Cenozoic, potentially tracking the narrowing tropical belt 

during Oligocene cooling (Brass et al., 1982). Consequently, 

the African and Madagascan coasts, and the Mozambique 

Channel in particular, may have had an unusually stable climate 

for much of the Cenozoic, presenting a refuge for species 

throughout the era. The WIO continental slopes may 

thus have acted as a museum preserving relict species of the 

once-dominant Tethyan fauna from the Palaeogene. 

Neogene origins 

The evidence for Neogene origins of Indian Ocean corals is 

shown by four coral genera (Acropora, Coscinaraea, Siderastrea 

and Stylophora; Table 2, Fig. 3), with Sclerophyllia a possible 

fifth. It is based on phylogenetic and biogeographical 

grounds, and is consistent with general drivers of speciation 

on coral reefs (Cowman & Bellwood, 2011; Bowen et al., 

2013). However, the evidence for Neogene origins in Indian 

Ocean corals is weaker than it is for Palaeogene origins, and 

will require considerably more systematic and phylogenetic 

work (e.g. Arrigoni et al., 2012). By contrast, reef fish illustrate 

these patterns more strongly, and research on reef fish 

has tended to focus on Neogene speciation, particularly in 

the Coral Triangle and in hotspots of endemism where these 

processes are strongest (e.g. Potts, 1985; Carpenter et al., 



2011; Briggs & Bowen, 2012; Bowen et al., 2013; Kulbicki 

et al., 2013). Within the Indian Ocean the Mascarene Islands 

and Red Sea have historically been the focus of reef fish biogeographical 

studies, due to having the highest levels of 

endemism (Allen, 2008; Briggs & Bowen, 2012), and have 

been identified as centres of diversity (DiBattista et al., 2013; 

Postaire et al., 2014), a situation also reflected among corals 

(Sheppard, 1987; Veron et al., 2015). Not coincidentally, 

these are the two main regions of geological activity in the 

Indian Ocean during the Neogene. 

The Northern Indian Ocean (NIO), and particularly its 

peripheral seas, the Red Sea, Gulf of Aden and Arabian Sea 

have been tectonically active during the Neogene (Bosworth 

et al., 2005). The Red Sea and Gulf of Aden formed by rifting 

processes beginning some 25–31 Ma, though marine 

habitats that support coral reefs likely did not appear in the 

Red Sea until much later, in the Pleistocene (DiBattista 

et al., 2013). Thus the fauna of the Red Sea and Arabian 

Sea is likely derived from the broader W&NIO species pool 

with more recent and smaller scale processes resulting in 

differentiation from this pool. The origination of species in 

this northern region is suggested by phylogenetic patterns 

for younger clades of Acropora (e.g. A. maryae), maximal 

genetic and species diversity in Stylophora, and in recent 

restoration of the coral genus Sclerophyllia (Arrigoni et al., 

2014; Table 2), and is abundantly supported in phylogeographical 

patterns of fish (DiBattista et al., 2013). Many 

species initially described as Red Sea endemics due to the 

focus of work there (e.g. the corals Pleasiastrea devantieri, 

Acropora maryae; Veron, 2000) have with further surveys 

been found to be more widespread in the W&NIO (Obura, 

2012a). Vectors for dispersal between the Red Sea/Arabian 

Sea and the broader Indian Ocean are the northern Indian 

Oean gyre and the reversing Somali Current, with ‘northern’ 

species being recorded in locations such as northern Kenya 

and the northern Seychelles islands (Obura, 2012a), and in 

the Chagos Archipelago (see Sheppard et al., 2012). 

The Mascarene Ridge is strung north–south across the 

middle of the WIO over 20° of latitude, creating a string of 

shallow banks and emergent islands of varying sizes and configurations 

over the last 40 Myr (Fig. 1). During the Eocene 

and Oligocene, with no source fauna in what is now the 

IAA, the main effect of the island chain may have been to 

isolate the WIO from open ocean currents from the east, 

thus enhancing connectivity with the Tethyan hotspots to 

the north. During the Miocene, however, with an increasingly 

‘leaky’ barrier resulting from production of smaller 

islands by the hotspot, island chain subsidence, northward 

crustal migration, intensification of westerly equatorial currents, 

and an actively diversifying source fauna in the IAA, 

transport of genetic material from east to west would have 

increased. This may have been enhanced through a steppingstone 

effect of the Mascarene islands (Postaire et al., 2014) 

mirroring their role for terrestrial fauna dispersing from Asia 

to Madagascar (e.g. Warren et al., 2010; Strijk et al., 2012). 

Nevertheless, this effect may be relatively minor due to the 

7


(a) (b) (c) 

(d) (e) (f) 

Figure 3 Selection of endemic coral species of the western and northern Indian Ocean for which a recent (Neogene) origin is possible; 

(a) Acropora appressa, Grande Comores; (b) A. branchi, NE Madagascar; (c) A. maryae, Farquhar Atoll, Seychelles; (d) Goniastrea peresi 

(though see Huang et al., 2014) Kisite, S. Kenya; (e) Favites spinosa, Nacala, NE Mozambique; (f) Plesiastrea devantieri, Mnazi Bay, S. 

Tanzania. All photos: David Obura. 

Figure 4 High level (realm) biogeographical divisions 

separating the Indian Ocean from the Central Indo-Pacific 

(letters, black lines) and finer divisions within the western and 

northern Indian Ocean (W&NIO) (i’s, grey lines) discussed in 

the text. (a) Obura (2012a)/this study and Veron et al. (2015), 

reef corals; (b) Briggs & Bowen (2012, 2013), primarily based on 

reef fish; (c) Kulbicki et al. (2013), reef fish; and (d) Spalding 

et al. (2007), based on multiple taxa and biophysical conditions. 

In each case, the fauna to the east of the line is described as 

‘Central Indo-Pacific’ while the fauna to the west is labelled 

‘Indian Ocean’, or W&NIO. Within the W&NIO, subregional 

divisions include: (i) between the tectonically inactive WIO and 

active northern Indian Ocean and seas (Briggs & Bowen, 2012; 

Reijnen et al., 2014), (ii) the Mascarene islands, banks and 

Seychelles islands (Allen, 2008; Borsa et al., 2015; Briggs & 

Bowen, 2012; Hoareau et al., 2013; Muths et al., 2014; Postaire 

et al., 2014), and (iii) a hotspot of diversity in the northern 

Mozambique Channel (Obura, 2012a; Reaka et al., 2008). 

8 

small number of island arcs in the Indian Ocean compared 

to the Central and West Pacific. The combination of these 

factors would result in lower diversification and survival 

rates and a less diverse fauna originating in the Indian Ocean 

island groups, concordant with overall lower diversity in the 

Indian Ocean than in the West Pacific coral fauna (Cowman 

& Bellwood, 2011). 

More recently in the Plio-Pleistocene, sea level and 

climatic fluctuations and their effect on dispersal–vicariance 

may have acted as a diversity pump, driving the evolution of 

new species. This effect is likely to be least on the steep continental 

margins of the East Africa and Madagascar coasts, 

and highest on the isolated island slopes and semi-isolated 

Red Sea and Arabian Gulfs. The Mascarene Ridge may thus 

have served as a diversity pump for speciation of neo-endemics 

and dispersal through stepping-stone processes during 

the Neogene (Borsa et al., 2015; Hoareau et al., 2013; Muths 

et al., 2014; Postaire et al., 2014). Similarly, fluctuating isolation 

and connectivity of the Red Sea and Arabian Gulf, due 

to their shallow and restricted openings to the northern 

Indian Ocean, have been implicated in speciation processes 

in both seas (Sheppard et al., 1992; DiBattista et al., 2013). 

This would contribute to differentiation of both subregions 

as centres of endemism (Allen, 2008; Briggs & Bowen, 2012; 

Bowen et al., 2013; Kulbicki et al., 2013), and at the same 

time contribute through dispersal to the broader species pool 

shared across the W&NIO and subsequently preserved in the 

tectonically inactive WIO and Mozambique Channel centre 

of diversity (Obura, 2012a; Bowen et al., 2013). Less importantly 

for the tropical fauna, climatic fluctuations have a 




diversity-generating influence around the temperate tip of 

South Africa. Here invasion and establishment of Atlantic 

species, and diversification of temporarily isolated Indian 

Ocean populations, may occur with climatic and sea level 

fluctuations affecting connectivity and dispersal around 

southern Africa (Teske et al., 2011). 

Synthesis 

Figure 5 Schematic of the evolutionary changes in scleractinian 

corals during the Cenozoic, focused on patterns described in this 

paper for the western and northern Indian Ocean (W&NIO). 

Tropical marine regions are aligned on the horizontal axis from 

west (left) to east (right). Time is on the vertical axis from 

about 65 Ma (bottom) to the present (top, not to scale), and 

the major geological periods and epochs (Table 1) are labelled. 

Major stages described in the text: A – the Tethyan period, 

including transition of the biodiversity hotspot from the West 

Tethys (WT) to the East African/Arabian Plate (EAAP) in the 

Palaeogene; B – closure of the Tethys Sea during the Miocene 

(25–15 Ma); C – migration of species from the Tethys/EAAP to 

the Indo-Australian Archipelago (IAA) prior to and during the 

Miocene (25–15 Ma); D – westward invasion of the W&NIO by 

IAA species as east-west connectivity across the equatorial 

Indian Ocean increases. E – diversification of Neogene endemics 

within tectonically active subregions of the W&NIO. The 

percentages at the top give the approximate composition of 

extant Indian Ocean Neogene (left/darker, 5%), Indian Ocean 

Palaeogene (centre, 5%) and Indo-Pacific (right, 90%) species 

(see text and Obura, 2012a). Broad evolutionary divergence is 

illustrated by colouration. Figure adapted from Obura (2012b). 



The following major steps in origins of W&NIO corals can 

be deduced from these results (Fig. 5): (A) The circumequatorial 

Tethys Sea promoted a relatively uniform tropical/equatorial 

coral fauna. During the Palaeogene the Tethys 

was progressively narrowing, with the hotspot for species 

diversity shifting from the WT in the Eocene to the EAAP 

in the Oligocene. At the same time, as a result of the migration 

of India northwards and the formation of the Mascarene 

Ridge, the W&NIO remained relatively isolated from 

the Eastern Indian Ocean/Central Indo-Pacific, which at this 

time was an open oceanic region with very little shallow 

habitat in tropical latitudes. (B) During the final stages of 

closure of the Tethys Sea in the late Oligocene/early Miocene, 

differentiation between Atlantic and Indo-Pacific faunae 

intensified. (C) During the late Oligocene, as shallow 

habitats in the IAA began to form, invasion of species from 

the Tethys/EAAP occurred, seeding later stages of speciation 

during the Miocene (Wilson & Rosen, 1998; Harzhauser 

et al., 2008). This fauna differentiated from the lineages that 

remained in the W&NIO, which can be attributed at least 

partially to different radiation pressures in the tectonically 

active IAA vs the tectonically inactive W&NIO. (D) During 

the Miocene the present configuration of ocean currents 

likely became established, conveying species from the IAA 

westwards. Younger species often have greater ‘vigour’ than 

older ones (Ricklefs, 2011), and certainly the IAA/West Pacific 

fauna has come to dominate coral reef communities in 

the W&NIO and throughout the Indo-Pacific (Bowen et al., 

2013; Veron et al., 2015). (E) Simultaneously, diversification 

within the tectonically active subregions of the W&NIO (the 

Red Sea, Arabian Seas and the Mascarene islands/banks), has 

led to diversity/endemism hotspots in these two sub-regions 

and a recent (Neogene) contribution to the W&NIO regional 

fauna. At present, the extant hard coral fauna comprises 

three groups: wide-ranging Indo-Pacific species, relict species 

with Tethyan (Palaeogene) origins (Fig. 2) and new species 

originating within the W&NIO during the Neogene (Fig. 3). 

These results suggest a more complex ‘Indian Ocean origins’ 

hypothesis (Rosen, 1971; Pichon, 1978) with multiple 

temporal and spatial dimensions. First, a Tethys Sea centre 

of origin during the Palaeogene (with two sequential centres 

in the WT then the EAAP), from which tectonic drivers of 

speciation (Renema et al., 2008) are recorded in deeper phylogenetic 

levels (genus and family, Table 2). Next, Neogene 

processes of dispersal, vicariance, accumulation and survival 

(e.g. Carpenter et al., 2011; Teske et al., 2011; Bowen et al., 

2013; Pellissier et al., 2014) acted in geologically dynamic 

subregions of the Indian Ocean, particularly in the Red and 

Arabian Seas, and in the Mascarene Islands, recorded in shallower 

phylogenetic levels (species and intra-species, Table 2). 

In terms of differentiating an Indian Ocean fauna from the 

Central Indo-Pacific, and in reconciling differences among 

biogeographical classification schemes (Fig. 4) (Spalding 

et al., 2007; Briggs & Bowen, 2012; Obura, 2012a; Kulbicki 

et al., 2013; Veron et al., 2015), this analysis suggests these 

W&NIO endemic groups (Tethyan relicts and Neogene species) 

should be the focus for further analysis, against the 

homogenizing background of the majority (90%) of Indo- 

Pacific species. 

The phylogenetic patterns described here are based on an 

incomplete revision of hard coral phylogenetics (Fukami 

et al., 2008; Budd et al., 2010) and on increasing research 

effort on Indian Ocean locations and their taxa. Further 

advances in both areas may provide additional evidence in 

support of this hypothesis. Once the ongoing revision of 

hard coral phylogenetics is complete the full membership of 

species in the two W&NIO groups – Tethyan relicts versus 

Neogene endemics – can be determined, and a more 

complete assessment of the hypothesis can be done. One 

9


glaring gap is the absence of Palaeogene and Neogene coral 

fossils from the WIO, to complement those found in the 

Asian coastlines of the Indian Ocean (see Wilson & Rosen, 

1998; McMonagle et al., 2011). It is possible this gap may 

never be filled, as it appears extensive carbonate deposits 

were not created in the WIO, whether due to tectonic inactivity 

(affecting shallow deposits) or due to other factors 

such as marine climate (see Peterson & Backman, 1990), 

deepening the ‘Palaeogene gap’ for Indian Ocean reef-coral 

biodiversity (Johnson et al., 2015). 

Patterns of coral and reef fish diversity are among the 

most extensively studied for tropical marine taxa, and are 

widely used as evidence for general patterns that may also be 

found in other taxonomic groups (Bellwood & Hughes, 

2001; Roberts et al., 2002; Reaka et al., 2008; Veron et al., 

2009; Tittensor et al., 2010; Briggs & Bowen, 2012, 2013; 

Bowen et al., 2013). This suggests that the hypotheses presented 

here, of deep and shallow evolutionary influences on 

coral biogeographical pattern, could be considered in refining 

biogeographical classifications for other taxa as well (e.g. 

Spalding et al., 2007; Briggs & Bowen, 2012). This is relevant 

to current interest in marine conservation, as evolutionary 

diversity is not uniformly spread among species, and attention 

to old, relict lineages with more unique genetic diversity 

can be an important criterion in biodiversity conservation 

and management (Jetz et al., 2014; Curnick et al., 2015). 

Analyses would be enriched by considering diverse taxa 

showing a range of evolutionary rates, from slow to fast (e.g. 

Brown et al., 1979; Shearer et al., 2002), to ensure different 

processes and periods of genetic differentiation are 

addressed. 

The tectonically inactive WIO appears to act as a stable 

‘museum’ for species, and Obura (2012a) suggests that currents 

in the Mozambique Channel, particularly in the north, 

accumulate and preserve species in a second hotspot for shallow 

marine biodiversity after the Coral Triangle. The present 

configuration of currents in the Channel, of energetic mesoscale 

eddies in both cyclonic and anticyclonic directions, 

result in profound ecosystem and productivity consequences 

within the channel, including high connectivity and larval 

recruitment (Ternon et al., 2014). The eddies are driven by 

vorticity induced in the South Equatorial Current when it is 

forced around the northern tip of Madagascar (Backeberg & 

Reason, 2010), a feature that has likely persisted throughout 

the Neogene and was perhaps also present even during the 

Eocene and Oligocene when Africa and Madagascar were further 

south, as was the main equatorial current from the east 

(Brass et al., 1982). The Mozambique Channel and stable 

African continental slopes to the north and south are also 

where the coelacanth Latimeria chalumnae has persisted, having 

disappeared from the fossil record across the globe at the 

Pg/T extinction, marking the start of the Cenozoic (Smith, 

1939). This provides additional corroboration for this 

hypothesis that the Mozambique Channel forms a tectonically 

and oceanographically stable region that preserves old 

lineages reliant on continental shelf habitats. Thus this centre 

10 

of diversity (Obura, 2012a) may act as a centre of accumulation, 

with complex feedbacks to the centres of origin hypothesized 

here being likely (see Bowen et al., 2013). 

Finally, two questions emerge on present and future 

dynamics. First, will the present condition of high connectivity 

across the Indian Ocean lead to greater homogenization 

of the Indo-Pacific fauna in the W&NIO above current 

levels? The fate of the W&NIO Tethyan relict species is likely 

to be eventual loss, though their competitive inferiority with 

younger species (Ricklefs, 2011) is belied by their persistence 

over tens of millions of years. The contribution of new species 

created through ongoing speciation in sub-regions of the 

W&NIO (Bowen et al., 2013) should, by contrast, persist. 

Second, given the inevitable obliteration of the IAA by continued 

continental collision, will the tectonically inactive 

WIO become a museum for IAA lineages and W&NIO endemics 

as the next biodiversity hotspot for shallow marine species 

establishes in a new region of tectonic collision? 

ACKNOWLEDGEMENTS 

The original work on this hypothesis was supported through 

a research grant (MASMA/OR/2008/05) and then a writing 

grant (MASMA/books/02/12) from the Marine Science for 

Management (MASMA) programme of the Western Indian 

Ocean Marine Science Association (WIOMSA). The ideas 

presented here have benefited from discussions and common 

regional interests with colleagues, in particular with Francesca 

Benzoni and Allen Chen, and the work of their collaborators 

and students establishing some of the lines of 

evidence supporting these hypotheses, and with Melita 

Samoilys. My thanks especially go to two anonymous referees 

and the editor, whose comments greatly improved the manuscript. 

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BIOSKETCH 

David O. Obura is a coral reef ecologist and Director of 

the non-profit research organization CORDIO East Africa. 

His research has focused on coral bleaching, coral reef resilience 

and regional biogeography of corals in the western 

Indian Ocean, as well as work in the Phoenix Islands, Kiribati. 

His work mixes primary research with trying to ensure 

sustainability for coral reefs and people in Africa and the 

western Indian Ocean. 

Editor: Luiz Rocha 

14

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