Journal of Biogeography (J. Biogeogr.

) (2013) 40, 1638–1648

SYNTHESIS Origins of species richness in the

Indo-Malay-Philippine biodiversity
hotspot: evidence for the centre
of overlap hypothesis
Michelle R. Gaither* and Luiz A. Rocha

California Academy of Sciences, Section of ABSTRACT

Ichthyology, San Francisco, CA, 94118, USA
*Correspondence: Michelle R. Gaither,
California Academy of Sciences, Section
of Ichthyology, 55 Music Concourse Drive,
San Francisco, CA 94118, USA.
E-mail: michellergaither@gmail.com
The Indo-Malay-Philippine (IMP) biodiversity hotspot, bounded by the Philip-
pines, the Malay Peninsula and New Guinea, is the epicentre of marine biodi-
versity. Hypotheses to explain the source of the incredible number of species
found there include the centre of overlap hypothesis, which proposes that in
this region the distinct faunas of the Pacific and Indian Oceans overlap. Here
we review the biogeographical evidence in support of this hypothesis. We
examined tropical reef fish distributions, paying particular attention to sister
species pairs that overlap in the IMP hotspot. We also review phylogeographi-
cal studies of wide-ranging species for evidence of lineage divergence and over-
lap in the IMP region. Our synthesis shows that a pattern of isolation between
the Pacific and the Indian Ocean faunas is evident across a wide range of taxa.
The occurrence of sister species, with one member in each ocean, indicates that
the mechanism(s) of isolation has been in effect since at least the Miocene,
while phylogeographical studies indicate more recent divergences in the Pleisto-
cene. Divergence in isolation followed by population expansion has led to an
overlap of closely related taxa or genetic lineages in the hotspot, contributing
to diversity and species richness in the region. These findings are consistent
with the centre of overlap hypothesis and highlight the importance of this pro-
cess in generating biodiversity within the IMP.
Keywords
Biogeography, centre of accumulation, centre of origin, coral reefs, Coral
Triangle, IMP hotspot, marine biodiversity, phylogenetics, phylogeography,
species distributions.

Malay-Philippine biodiversity hotspot (IMP hotspot; Fig. 1).

INTRODUCTION
The region bounded by the Philippines, the Malaysian penin-
sula, New Guinea and northern Australia has long been rec-
ognized as a biodiversity hotspot (Stehli & Wells, 1971;
Veron, 1993; Randall, 1998; Bellwood et al., 2012; Briggs &
Bowen, 2013). The geographical boundaries and shape of this
hotspot differ with the viewpoint of the biogeographer, and
there have been various names assigned to the region. The
Coral Triangle defined by Veron et al. (2009) extends from
the Philippines to the Solomon Islands but does not include
the Coral Sea, while the Indo-Australian Archipelago defined
by Bellwood & Hughes (2001) is inclusive of the Coral Tri-
angle but extends considerably north and south (Fig. 1; see
also Fig. 1C in Renema et al., 2008). Regardless of where the
exact boundaries are drawn there is wide agreement that this
region is the epicentre of marine biodiversity (Cowman &
Bellwood, 2013), and herein we refer to it as the Indo-
Over 2600 species of reef fishes and 600 species of corals are
found in the IMP region (Veron et al., 2009; Allen & Erd-
mann, 2012). Taxonomic diversity declines with distance
from the area, both latitudinally and longitudinally: a pattern
identified in corals by Stehli & Wells (1971) and since recog-
nized across a broad array of taxa (Paulay, 1990; Veron,
1995; Briggs, 1999). The generality of this pattern has led
many researchers to conclude that a common mechanism
may be responsible for the high biodiversity in the region.
Several hypotheses have been proposed to explain the species
richness in the IMP hotspot and these can be grouped into
four major categories: (1) centre of origin, (2) centre of
accumulation, (3) centre of survival, and (4) centre of over-
lap. Contemporary species distributions (and most recently
biogeographical modelling; Cowman & Bellwood, 2013) are
the most common line of evidence used to test these hypoth-
eses, and, amidst the jockeying of competing models, some

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doi:10.1111/jbi.12126

Indo-Polynesian
West Indian
Ocean
Figure 1 Map of the Indo-Pacific region showing Indo-
Polynesian (grey) and West Indian Ocean (blue) biogeographical
provinces (modified from Briggs & Bowen, 2012). Boundaries
are drawn to outline major regions of coral reef habitat (for
detailed distributions visit http://www.google.com/gadgets/
directory?synd=earth&id=696770371738/). Variations in the
boundaries of the west Indo-Pacific biodiversity hotspot are
shown: dashed line, the Coral Triangle (Veron et al., 2009);
solid black line, the Indo-Malay-Philippine (IMP) biodiversity
hotspot (Carpenter & Springer, 2005), which is nearly identical
to the East Indies Triangle (Briggs, 2003) and the Indo-Malayan
Triangle (Donaldson, 1986); solid red line, Indo-Australian
Archipelago (Bellwood & Hughes, 2001; Renema et al., 2008).
For the purpose of this study we define the hotspot using the
IMP boundary of Carpenter & Springer (2005). The arrow
indicates the Cocos-Keeling Islands in the eastern Indian Ocean.
have acquired vocal proponents while others receive compar-
atively little consideration.
First proposed by Ekman (1953), the hypothesis that has
received the most attention is that of the centre of origin.
Ekman (1953) and others who have followed (Briggs, 1999,
2003) suggest that the high number of species in the IMP
hotspot is a product of an unusually high rate of speciation
in the region, with new species radiating from this centre of
origin. Mechanisms invoked to explain the elevated specia-
tion rate include the fracturing of populations as a result of
the geological complexity of the region and eustatic sea-level
changes (McManus, 1985). Others have suggested that
increased rates of speciation in the hotspot are driven by
intense competition (Briggs, 2005; Bowen et al., 2013) and
differing selection pressures in a highly heterogeneous envi-
ronment (Rocha & Bowen, 2008). Several years after Ekman
proposed the centre of origin hypothesis, Ladd (1960) coun-
tered with the centre of accumulation hypothesis. This model
proposes speciation in peripheral locations with subsequent
dispersal of novel taxa into the IMP hotspot. The long his-
tory of the Pacific archipelagos, some of which date to the
Cretaceous, the possibility of isolation in these peripheral
habitats, and ocean current and wind patterns that favour
dispersal towards the IMP region have been suggested as
mechanisms in support of this hypothesis (Ladd, 1960; Jokiel
& Martinelli, 1992). Still others suggest that the habitat-rich
IMP region is a centre of survival that provides a refuge
from elevated extinction rates, which should be more com-
mon in peripheral locations (Paulay, 1990; Jackson et al.,
1993; Bellwood & Hughes, 2001).
First proposed by Woodland (1983), the centre of overlap
hypothesis maintains that the high species diversity in the
Journal of Biogeography 40, 1638–1648
ª 2013 Blackwell Publishing Ltd
Evidence for the centre of overlap hypothesis
IMP hotspot is due in part to the overlap of distinct faunas
from the Pacific and Indian Oceans (Briggs, 1974; Wood-
land, 1983). Under both the centre of accumulation and the
centre of overlap hypothesis, speciation occurs in locations
outside the hotspot, with subsequent dispersal into the IMP
region. The difference between these two hypotheses lies in
the mechanism driving divergence and the resulting distribu-
tion of sister taxa. The centre of overlap hypothesis is based
on the premise that the isolating mechanism is the shallow
Sunda and Sahul shelves of Indonesia, Malaysia and North-
ern Australia, known as the Indo-Pacific Barrier (IPB;
Fig. 2). Under this hypothesis, the faunas of the Pacific and
Indian Oceans gained distinction during historical low sea-
level stands when dispersal was restricted between ocean
basins. Following sea-level rise, the geographical ranges of
sister taxa formerly separated by the IPB expanded and even-
tually came to overlap in the IMP hotspot. Under the centre
of accumulation hypothesis, speciation is also thought to
occur in peripheral locations but no specific mechanism is
implicated; sister taxa can reside anywhere in the range, and
the overlap of closely related taxa at the IMP region is not
required.
The literature is replete with examples that support one
hypothesis over another. Efforts to compile the evidence have
largely sought to uncover the prevailing mechanism responsi-
ble for the species richness of the IMP hotspot but have not
elevated any single hypothesis (Connolly et al., 2003; Mora
et al., 2003; Halas & Winterbottom, 2009). Emerging from
decades of debate is a growing recognition that the compet-
ing hypotheses are not mutually exclusive but in fact are
likely to be working in conjunction to create the species rich-
ness of the region (Bellwood & Hughes, 2001; Rocha et al.,
2008; Bowen et al., 2013; Briggs & Bowen, 2013; Cowman &
Bellwood, 2013). In an effort to contribute to the growing
understanding of the complexity of this issue we present a
review of the evidence in support of the centre of overlap
(C-O) hypothesis. Here, we describe the mechanism of isola-
tion and provide evidence of the partial, and at times nearly
complete, isolation of the Pacific and Indian Ocean faunas
since at least the Miocene.
THE MECHANISM OF ISOLATION
Woodland (1983), in his work on rabbitfishes (family Sigani-
dae), noticed pairs of sister species within which one had a
distribution centred in the Pacific Ocean whilst the other’s
was centred in the Indian Ocean, with the tails of these
ranges overlapping in the IMP region. He surmised that at
least part of the species richness in the hotspot was due to
the overlapping of distinct faunas from these two ocean
basins. Since then, the list of sister species that share this dis-
tribution pattern has grown (Donaldson, 1986; Blum, 1989;
Randall, 1998). Originally, Woodland (1983) suggested that
Pleistocene low sea-level stands may have led to the isolation
of populations in the Pacific and Indian Oceans (Fig. 2).
However, subsequent phylogenetic work suggests an older
1639
M. R. Gaither and L. A. Rocha

Indonesian Throughway

Present-day land
Land extent at -130 m sea level

Figure 2 Map of the Indo-Malay-Philippine region. During the Oligocene and early Miocene, the Pacific and Indian Oceans were
connected via an extension of the Southern Equatorial Current known as the Indonesian Seaway (see Figure 2 in Carpenter & Springer,
2005). Today, however, flow between the ocean basins is relegated to a narrow and convoluted path through the Indonesian
Archipelago known as the Indonesian Throughway (current patterns modified from Gordon, 2005). Shaded areas show the effect of
lowered sea level on habitat in the region during Pleistocene glacial maxima. (Figure credit: Eric Franklin.)

date for most extant species (Renema et al., 2008), indicating
that tectonic rearrangements in the Miocene may have
restricted water flow between oceans even without dramatic
changes in sea level.
During the Oligocene and early Miocene, the Pacific and
Indian Oceans were connected via an extension of the South-
ern Equatorial Current known as the Indonesian Seaway
(Hall, 2002; see also Figure 2 in Carpenter & Springer,
2005). Through this seaway, water could flow between
oceans with little impediment. During the mid-Miocene (c.
16–8 Ma), however, the Australian and Eurasian plates col-
lided, resulting in shallow seas and land barriers in the
region that deflected equatorial currents and greatly reduced
flow between ocean basins (Kennett et al., 1985). Today,
after millennia of continued tectonic movement, water flow
between the Pacific and Indian Oceans is largely confined to
the Indonesian Throughflow (Fig. 2), which, while capable of
carrying large volumes of water (10 million m3 s 1), must
follow a narrow and restricted path through the Indonesian
Archipelago (Gordon, 2005).
Accentuating the isolation of the Pacific and Indian
Oceans were eustatic changes in sea level in the recent past.
The shallow continental shelves of the IPB have been sub-
jected to lower sea levels repeatedly since at least the Pliocene
(Naish et al., 2009). During the Pleistocene, there were three
to six glacial cycles that lowered sea level to as much as
130 m below present levels (Fig. 2; Chappell, 1981; Potts,
1983; Voris, 2000; Naish et al., 2009). During low sea-level
stands, species on the continental shelves were extirpated,
and presumably there was a major reduction in the already
restricted gene flow between Pacific and Indian Ocean
populations. Associated with the change in sea level were
concomitant changes in oceanographic current patterns and
altered freshwater and sediment discharge of local rivers,
with corresponding changes in temperature and salinity
(Tjia, 1966; van Andel et al., 1967). The narrow seaways that
remained were likely under the influence of cooler upwelling,
further limiting the availability of suitable habitat for tropical
marine organisms (Galloway & Kemp, 1981; Potts, 1983;
McManus, 1985; Fleminger, 1986; Voris, 2000). During these
exceptionally low sea-level stands, population sizes were
reduced (Bellwood & Wainwright, 2002) and isolation of the
Pacific and Indian Oceans was nearly complete.
The restriction of flow between the Pacific and Indian
Oceans since the mid-Miocene has played a role in isolating
the fauna in the Pacific and Indian Oceans. However, per-
haps of equal significance is the paucity of coral reef habitat
in the north and central Indian Ocean. Notably, there is little
coral development along the coasts of Bangladesh, India and
Pakistan, owing to diminished habitat and large freshwater
outflows. The Cocos-Keeling and Christmas Islands in the
eastern Indian Ocean are known regions of faunal overlap
and hybridization between Pacific and Indian Ocean reef fish
fauna (Hobbs et al., 2009). West of here, a 2800-km stretch
of open ocean separates Indonesia and Western Australia
from the central Indian Ocean (Fig. 1). This oceanic desert
is the western boundary of the Indo-Polynesia Province.
Another 1000 km of open ocean separates the Saya de Malha
banks in the Western Indian Ocean from the Indo-Polyne-
sian Province (Fig. 1; Briggs & Bowen, 2012), a region that
has an enormous influence on the biogeography of the
Indian Ocean (Sheppard et al., 2012). Of course, the Pacific

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and Indian Ocean basins are not fully isolated, as evidenced
by the large number of species whose distributions span both
oceans (Randall, 1998). However, the presence of distinct
faunas in the Western Indian Ocean and the Indo-Polynesian
Province indicates restricted dispersal perhaps across the IPB
and certainly across the central Indian Ocean, which is possi-
bly amplified by ecological differences between these regions.
SPECIES DISTRIBUTIONS
The C-O hypothesis predicts that isolation of intraspecific
populations persisted long enough for speciation to occur.
According to fossil and phylogenetic data, most extant reef
fauna have a Pliocene (1.6–5.3 Ma) or Miocene (5.3–
23.7 Ma) origin (Renema et al., 2008). Corresponding with
these ages is the restriction of water flow between the Pacific
and Indian Oceans that has been in place since the mid-Mio-
cene, when the Asian and Australian plates collided and land
barriers arose. While this may be sufficient to explain the
origin of many recognized species, this should not be inter-
preted as implying that speciation did not occur during the
Pleistocene. Instead, this finding may be, in part, a result of
our tendency to name species only with clear and definable
morphological characters (Rocha & Bowen, 2008; see ‘Intra-
specific Comparisons’, below). Moreover, several lines of evi-
dence indicate that isolation neither has to be absolute nor
of long duration for speciation to occur (Gavrilets et al.,
2007; Rocha & Bowen, 2008). Selection driven by ecological
factors could accelerate divergence despite gene flow or con-
tinue generating divergence that began in isolation. Alterna-
tively, sexual selection or assortative mating might reinforce
isolating mechanisms in parapatric populations. Regardless
of the mechanism of isolation, there is ample evidence of
divergence across the IPB dating back to at least the late
Miocene.
The strongest evidence comes from distributional patterns
of pairs of sister species (Table 1). Here we define sister spe-
cies as taxa that share a common ancestor and are each
other’s closest living relative. The C-O hypothesis predicts
that one member of each pair will have a distribution cen-
tred in the Pacific Ocean with the other centred in the
Indian Ocean. In some cases, species remain largely isolated
in either ocean basin or exhibit asymmetric expansion into
the IMP region (Fig. 3a). However, population expansion
following speciation can lead to a pattern where closely
related species overlap in the region (Fig. 3b). This pattern is
the most convincing evidence for the C-O hypothesis (see
Fig. 4); however, it might be considered an intermediate
stage of population expansion. Given enough time and ade-
quate dispersal ability the end result might be two closely
related species with widely overlapping distributions (Fig. 3c;
Lynch, 1989). It is important to note that these distributions
are not inconsistent with other hypotheses. For instance, the
pattern in Fig. 3(b) (and Fig. 4) could arise from the con-
traction of previously large widespread populations, or, con-
versely, the pattern in Fig. 3(c) could be the result of an
Journal of Biogeography 40, 1638–1648
ª 2013 Blackwell Publishing Ltd
Evidence for the centre of overlap hypothesis
expansion of populations historically restricted to the IMP
region. However, the finding of numerous examples of sister
taxa whose distributions overlap only in areas adjacent to the
IPB and the lack of such a pattern in other areas provide evi-
dence for the C-O hypothesis.
Most pairs of sister species have been defined based on
taxonomic work (reviewed in Randall, 1998). In fishes, sis-
ter species are often delineated based on subtle differences
in colour patterns, body measurements, or fin-ray counts.
As a consequence, species pairs that are morphologically
indistinguishable (cryptic species) and those that are mor-
phologically more divergent than expected are omitted from
consideration. Molecular phylogenies would be a useful tool
to confirm the sister status of these pairs; however, few
data are available for most groups, with few exceptions
(e.g. butterflyfishes). Phylogenies, even for well-studied
groups, are often incomplete, thus elevating the age of lin-
eages and obscuring relationships (Alfaro et al., 2007). Only
small groups, such as wrasses of the genus Anampses (fam-
ily Labridae), have complete phylogenies (Hodge et al.,
2012). Another complication is the lack of detailed species
checklists for much of Indonesia and Malaysia where over-
lap is expected. Only a few areas in the region have been
sampled adequately. Undoubtedly, the importance of the
IPB in species formation will become clearer as phyloge-
netic data accumulate and biodiversity surveys become
available.
INTRASPECIFIC COMPARISONS
Evolution is an ongoing process, with changes in allele fre-
quencies and genetic divergence being an indication of evo-
lutionary change at the population level. So while
intraspecific patterns of genetic variation are not often
directly employed to address questions concerning the gener-
ation of species, they provide a historical perspective that
may not be apparent with contemporary species distributions
(Palumbi, 1997; Avise, 2000). Pleistocene sea-level fluctua-
tions resulted in repeated widespread extirpations on the
continental shelves of the IMP region. The resulting inter-
ruptions in gene flow between Pacific and Indian Ocean
populations are recorded in intraspecific patterns of genetic
diversity in many taxa (Fig. 5). Since the end of the Last
Glacial Maximum about 18,000 years ago, the land bridge
that limited dispersal between the Pacific and Indian Oceans
submerged and the rising sea level not only widened dis-
persal pathways but also was accompanied by an approxi-
mately 10-fold increase in suitable shallow reef habitat
(Bellwood & Wainwright, 2002).
Each hypothesis concerning the origin of species richness
in the IMP hotspot results in specific predictions about the
geographical positioning of lineages within species (Palumbi,
1997; Drew & Barber, 2009). The centre of origin hypothesis
predicts that the oldest and most diverse populations will be
centred in the hotspot, with decreasing haplotype diversity
emanating from the centre that parallels the observed decline
1641
M. R. Gaither and L. A. Rocha

Table 1 Sister species pairs of fishes based on morphology and/or molecular data with distributions that overlap in the Indo-Malay-
Philippine (IMP) biodiversity hotspot. More examples are given by Randall (1998), but we have restricted our list to sister species pairs
within which one has a distribution centred in the Pacific Ocean and the other has one centred in the Indian Ocean, with the tails of
these ranges overlapping in the IMP hotspot. Divergence times, as reported in source articles, are listed in millions of years ago (Ma).
Divergence times in bold were calculated from mitochondrial cytochrome b sequences downloaded from GenBank, assuming a
molecular clock of 2% per million years between lineages (Bowen et al., 2001; Lessios, 2008; Reece et al., 2010).

Divergence
Species pairs time (Ma) Sources

Scorpaenidae (scorpionfishes)
Pterois miles (Bennett, 1828) – P. volitans (Linnaeus, 1758) Schultz (1986)
Inimicus sinensis (Valenciennes, 1833) – I. cuvieri (Gray, 1835) Eschmeyer & Rama-Rao (1979)
Epinephelidae (groupers)
Cephalopholis nigripinnis (Valenciennes, 1828) – C. urodeta (Forster, 1801) Randall & Heemstra (1991)
Apogonidae (cardinalfishes)
Ostorhinchus cyanosoma (Bleeker, 1853) – O. rubrimacula Randall & Kulbicki (1998)
(Randall & Kulbicki, 1998)
Zoramia fragilis (Smith, 1961) – Z. gilberti (Jordan & Seale, 1905) Fraser & Lachner (1985)
Chaetodontidae (butterflyfishes)
Chaetodon baronessa Cuvier, 1829 – C. triangulum Cuvier, 1831 Allen (1979)
C. falcula Bloch, 1795 – C. ulietensis Cuvier, 1831 0.3 Kuiter & Debelius (1994), Fessler & Westneat (2007)
C. melannotus Bloch & Schneider, 1801 – C. ocellicaudus Cuvier, 1831 Allen (1979)
C. guttatissimus Bennett, 1833 – C. punctatofasciatus Cuvier, 1831 1.0 Hsu et al. (2007)
C. trifasciatus Park, 1797 – C. lunulatus Quoy & Gaimard, 1825 2.4 Hsu et al. (2007), Bellwood et al. (2010)
C. meyeri Bloch & Schneider, 1801 – C. ornatisimus Cuvier, 1831 1.7 Fessler & Westneat (2007), Bellwood et al. (2010),
DiBattista et al. (2012b)
Hemitaurichthys zoster (Bennett, 1831) – H. polylepis (Bleeker, 1857) Fessler & Westneat (2007)
Heniochus pleurotaenia Ahl, 1923 – H. varius (Cuvier, 1829) Allen (1979)
Pomacanthidae (angelfishes)
Centropyge eibli Klausewitz, 1963 – C. vrolikii (Bleeker, 1853) 3.5 Pyle & Randall (1994), DiBattista et al. (2012a)
Pomacentridae (damselfishes)
Dascyllus carneus Fischer, 1885 – D. reticulatus (Richardson, 1846) 2.5 Randall & Allen (1977), McCafferty et al. (2002)
Amphiprion akallopisos Bleeker, 1853 – A. perideraion Bleeker, 1855 2.4 Quenouille et al. (2004)
A. sebae Bleeker, 1853 – A. polymnus (Linnaeus, 1758) Allen (1975)
Labridae (wrasses and parrotfishes)
Anampses lineatus Randall, 1972 – A. melanurus Bleeker, 1857 3.6 Kuiter & Debelius (1994), Hodge et al. (2012)
Bodianus diana (Lacep
ede, 1801) – B. dictynna Gomon, 2006 Kuiter & Debelius (1994)
Chlorurus sordidus (Forssk al, 1775) – C. spilurus (Valenciennes, 1840) 1.6 Choat et al. (2012)
Gomphosus caerulaeus Lacep
ede, 1801 – G. varius Lacep
ede, 1801 3.2 Bernardi et al. (2004)
Halichoeres scapularis (Bennett, 1832) – H. trimaculatus Barber & Bellwood (2005)
(Quoy & Gaimard, 1834)
H. leucoxanthus Randall & Smith, 1982 – H. chrysus Randall, 1981 Randall & Smith (1982)
H. hartzfeldii (Bleeker, 1852) – H. zeylonicus (Bennett, 1833) Randall & Smith (1982)
H. marginatus R€ uppell, 1835 (IO) – H. marginatus (PO) 1.7 Barber & Bellwood (2005)
H. nebulosus (Valenciennes, 1839) – H. margaritaceus (Valenciennes, 1839) 4.5 Kuiter & Randall (1981), Barber & Bellwood (2005)
H. vrolikii (Bleeker, 1852) – H. melanurus (Bleeker, 1851) Kuiter (1992)
Scarus spinus (Kner, 1868) – S. viridifucatus (Smith, 1956) 1.4 Satapoomin et al. (1994), Choat et al. (2012)
S. ghobban Forssk al, 1775 (IO) – S. ghobban (PO) 1.4 Choat et al. (2012)
Gobiidae (gobies)
Ctenogobiops feroculus Lubbock & Polunin, 1977 – C. pomastictus Myers (1989)
Lubbock & Polunin, 1977
Siganidae (rabbitfishes)
Siganus stellatus (Forsskal, 1775) – S. punctatus (Schneider & Forster, 1801) Woodland (1983)
Acanthuridae (surgeonfishes)
Acanthurus olivaceus Bloch & Schneider, 1801 – A. tennentii G€ unther, 1861 3.2 M.R. Gaither et al., unpublished data
Acanthurus pyroferus Kittlitz, 1834 – A. tristis Randall, 1993 Randall (1998)
N. elegans (R€uppell, 1829) – N. lituratus (Forster, 1801) 5.2 Klanten et al. (2004)
Naso tonganus (Valenciennes, 1835) – N. tuberosus Lacep
ede, 1801 6.6 Klanten et al. (2004)
Tetraodontidae (pufferfishes)
Arothron immaculatus (Bloch & Schneider, 1801) – A. manilensis Randall (1985)
(Marion de Proce, 1822)

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(a)
(b)
(c)
Figure 3 Species distribution patterns expected following
isolation across the Indo-Pacific Barrier during historical low
sea-level stands (a) with asymmetrical expansion into the Indo-
Malay-Philippine biodiversity hotspot (Chaetodon interruptus
Ahl, 1923 and C. unimaculatus Bloch, 1787); (b) following
geographical expansion with overlap in the hotspot
(Siganus stellatus and S. punctatus); and (c) with extensive
population expansion across the Indo-Pacific
[Echidna leucotaenia Schultz, 1943 and E. polyzona (Richardson,
1845)]. Regions shaded in purple (and indicated by arrows)
represent areas of overlap. (Photos: J.E. Randall and
J.T. Williams.)
in species richness (sensu Bowen et al., 1998). Similarly, the
centre of overlap hypothesis predicts that the most diverse
populations will be centred on the IMP hotspot. In this case,
however, the high diversity is the result of the overlap of
divergent lineages from peripheral regions (i.e. bimodal mis-
match distributions).
Distinct genetic lineages that date to Pleistocene sea-level
fluctuations and whose distributions are consistent with the
C-O hypothesis have been detected in many coral reef
organisms (reviewed in Gaither et al., 2010). In some taxa,
effective migration between ocean basins is absent, as
evidenced by a lack of shared haplotypes between oceans
(e.g. Penaeus monodon, Duda & Palumbi, 1999; Chloru-
rus sordidus, Bay et al., 2004). These cases possibly reflect lim-
ited population expansion since the Pleistocene and perhaps
the early stages of allopatric speciation. Other widespread taxa
demonstrate strong evidence of historical isolation but lack
contemporary spatial structure (e.g. Naso brevirostris, Horne
et al., 2008; the Centropyge flavissima complex, DiBattista
Journal of Biogeography 40, 1638–1648
ª 2013 Blackwell Publishing Ltd
Evidence for the centre of overlap hypothesis
(a)
(b)
(c)
Figure 4 Distribution patterns of sister species pairs (see
Table 1) that are thought to have diverged during periods of
isolation across the Indo-Pacific Barrier with subsequent
expansion into the Indo-Malay-Philippine biodiversity hotspot.
(a) Scarus viridifucatus and S. spinus; (b) Halichoeres scapularis
and H. trimaculatus; (c) Chaetodon trifasciatus and C. lunulatus.
Regions shaded in purple (and indicated by arrows) represent
areas of overlap. (Photos: J.E. Randall.)
et al., 2012a) indicating extensive dispersal and introgression
following sea-level rise. In other species we detect evidence of
isolation across the IPB with population expansion and over-
lap in the IMP hotspot. As predicted by the C-O hypothesis,
distinct lineages, one of which is widely distributed in the
Pacific Ocean and the other in the Indian Ocean, demonstrate
contemporary mixing in the IMP region (Fig. 5). Analyses of
these patterns are limited in many cases owing to gaps in
sampling, but the overall signal of isolation of Pacific and
Indian Ocean lineages with overlap in the hotspot is sup-
ported across a variety of taxa, including two teleosts, an elas-
mobranch, an echinoderm and a gastropod (Fig. 5).
Undoubtedly, more examples will emerge as studies across
the region accumulate.
CONCLUSIONS
The region bounded by the Philippines, the Malay Peninsula,
New Guinea and northern Australia is an epicentre of marine
biodiversity (Ekman, 1953; Stehli & Wells, 1971; Veron,
1993; Randall, 1998; Bellwood et al., 2012; Briggs & Bowen,
2013). The explanation for the high number of species in the
region has long been debated. There now seems to be an
1643
M. R. Gaither and L. A. Rocha

x20 x7

COI Cyt b
Linckia laevigata Myripristis berndti

Sphyrna lewini

Control
Cephalopholis argus Cyt b Sphyrna lewini Region

21 bp

18 bp

Nerita albicilla COI

Figure 5 Phylogeographical studies that demonstrate divergent genetic lineages across the Indo-Pacific Barrier with overlap in the Indo-
Malay-Philippine biodiversity hotspot. Haplotype networks for Linckia laevigata based on cytochrome c oxidase subunit I, COI
(Kochzius et al., 2009), Myripristis berndti based on cytochrome b, cyt b (Craig et al., 2007), Cephalopholis argus based on cyt b (Gaither
et al., 2011), Sphyrna lewini based on the control region (Duncan et al., 2006) and Nerita albicilla based on COI (Crandall et al., 2008)
were recreated from the original data sets or replicated from the published network. Networks for species in bold were simplified (i.e.
singletons omitted) for graphical representation. (Photos: J.B. Puritz and J.E. Randall.)

emerging consensus that no single mechanism is driving spe- Cowman & Bellwood, 2013). Species distributions and intra-
ciation, and instead the debate has shifted to the relative specific molecular studies highlight the role of the IPB in
importance of the various processes (Bowen et al., 2013; contributing to the distinction of the Pacific and Indian

1644 Journal of Biogeography 40, 1638–1648

ª 2013 Blackwell Publishing Ltd

Ocean faunas. Times of divergence across sister species pairs
indicate that diminished gene flow across this barrier has
been in effect since at least the Miocene and was accentuated
during Pleistocene sea-level fluctuations. Population expan-
sion following divergence has resulted in the sympatric dis-
tribution of sister species pairs and/or genetic lineages in the
IMP region, adding to the species/genetic richness there. An
understanding of the relative contribution of the IPB to bio-
diversity in the region is limited by gaps in our knowledge
of the evolutionary relationships among coral reef species, by
a lack of phylogeographical data from the Indian Ocean, as
well as by a lack of detailed species checklists for many
regions. However, as the data accumulate it is becoming
clear that Woodland (1983) was correct: the overlap of dis-
tinct faunas from the Pacific and Indian Oceans has contrib-
uted to the species richness of the IMP biodiversity hotspot.
ACKNOWLEDGEMENTS
We thank Brian Bowen for lively discussions and intellectual
input; Jean-Paul Hobbs and Shelley Jones for comments on
the manuscript; and Kanesa Duncan and Toby Daly-Engel
for sharing their data set. Jonathan B. Puritz, John E. Randall
and Jeffery Williams allowed us to use their photographs.
Suggestions by Michael Dawson, Cynthia Riginos and one
anonymous referee greatly improved the final version.
This work was supported by the California Academy of Sci-
ences.
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BIOSKETCHES
Michelle R. Gaither is a postdoctoral fellow in the Section
of Ichthyology at the California Academy of Sciences. Her
interests include introduced species, the biogeography of
marine fishes, and the genomics of speciation.
Luiz A. Rocha is the curator of Ichthyology at the Califor-
nia Academy of Sciences. His interests are centred around
the mechanisms that cause the diversification of coral reef
fishes. His current research includes a genome-wide analysis
of fishes that searches for signatures of different modes of
speciation, the phylogeography of Red Sea reef fishes and the
evolution of fishes from mesophotic coral reefs.
Editor: Michael Dawson
Journal of Biogeography 40, 1638–1648
ª 2013 Blackwell Publishing Ltd