Molecular Phylogenetics and Evolution 82 (2015) 200–210Contents lists available at ScienceDirect
Molecular Phylogenetics and Evolution
journal homepage: www.elsevier .com/locate /ympevSupport for a ‘Center of Origin’ in the Coral Triangle: Cryptic diversity,
recent speciation, and local endemism in a diverse lineage of reef fishes
(Gobiidae: Eviota)http://dx.doi.org/10.1016/j.ympev.2014.09.012
1055-7903/ 2014 Elsevier Inc. All rights reserved.
⇑ Corresponding author.
E-mail address: Luke.Tornabene@tamucc.edu (L. Tornabene).Luke Tornabene a,⇑, Samantha Valdez a, Mark Erdmann b,c, Frank Pezold a
aCollege of Science and Engineering, Texas A & M University – Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
bConservation International Indonesia Marine Program, Jl. Muwardi No. 17 Renon Denpasar, Bali 80235, Indonesia
cCalifornia Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USAa r t i c l e i n f o
Article history:
Received 2 July 2014
Revised 10 September 2014
Accepted 13 September 2014
Available online 6 October 2014
Keywords:
Phylogeny
Indo-Malay Archipelago
Phylogeography
Evolution
mtDNA
Sympatric speciationa b s t r a c t
The Coral Triangle is widely regarded as the richest marine biodiversity hot-spot in the world. One factor
that has been proposed to explain elevated species-richness within the Coral Triangle is a high rate of in
situ speciation within the region itself. Dwarfgobies (Gobiidae: Eviota) are a diverse genus of diminutive
cryptobenthic reef fishes with limited dispersal ability, and life histories and ecologies that increase
potential for speciation. We use molecular phylogenetic and biogeographic data from two clades of Eviota
species to examine patterns, processes and timing associated with species origination within the Coral
Triangle. Sequence data from mitochondrial and nuclear DNA were used to generate molecular phylog-
enies and median-joining haplotype networks for the genus Eviota, with emphasis on the E. nigriventris
and E. bifasciata complexes – two species groups with distributions centered in the Coral Triangle. The
E. nigriventris and E. bifasciata complexes both contain multiple genetically distinct, geographically
restricted color morphs indicative of recently-diverged species originating within the Coral Triangle.
Relaxed molecular-clock dating estimates indicate that most speciation events occurred within the Pleis-
tocene, and the geographic pattern of genetic breaks between species corresponds well with similar
breaks in other marine fishes and sessile invertebrates. Regional isolation due to sea-level fluctuations
may explain some speciation events in these species groups, yet other species formed with no evidence
of physical isolation. The timing of diversification events and present day distributions of Eviota species
within the Coral Triangle suggest that both allopatric speciation (driven by ephemeral and/or ‘soft’ phys-
ical barriers to gene flow) and sympatric speciation (driven by niche partitioning and assortative mating)
may be driving diversification at local scales within the Coral Triangle. The presence of multiple young,
highly-endemic cryptic species of Eviota within the Coral Triangle suggests that (i) the Coral Triangle is
indeed a ‘‘cradle’’ of reef fish biodiversity and that (ii) our current approximations of reef fish diversity
in the region may be significantly underestimated.
 2014 Elsevier Inc. All rights reserved.1. Introduction
1.1. Biodiversity within the Coral Triangle: origin, accumulation or
overlap?
The world’s richest marine biodiversity hot-spot is located in a
region known as the Coral Triangle (Allen andWerner, 2002; Veron
et al., 2009; Carpenter et al., 2011). The Coral Triangle (CT), also
known as the Indo-Malay Archipelago or the Indo-Australian
Archipelago, is a region of islands in the Western Pacific thatincludes the Philippines, Indonesia, Malaysian Borneo, Timor-
Leste, Papua New Guinea and the Solomon Islands (Veron et al.,
2009). The area is home to over 600 species of corals and over
2600 species of reef fishes (Veron et al., 2009; Allen and
Erdmann, 2012). Species richness across a wide array of marine
organisms declines with distance (both in latitude and longitude)
from the CT (Stehli and Wells, 1971; Veron, 1995; Briggs, 1999a;
Mora et al., 2003). Many hypotheses have been proposed to explain
the exceptional species-richness within this region, including: (1)
the center of origin hypothesis (Ekman, 1953; Briggs, 1999a,
1999b), which proposes that most species originate within the
CT, likely due to elevated rates of speciation within the region,
and that the abundance of new species originating within the CT
L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210 201provides a source of biodiversity for surrounding areas; (2) the
center of accumulation hypothesis, which states that speciation
occurs primarily in multiple peripheral regions, and fauna accumu-
late in the CT via dispersal of individual species (Ladd, 1960) or of
entire assemblages following tectonic events (Remington, 1968;
McKenna, 1973; Santini andWinterbottom, 2002); and (3) the cen-
ter of overlap hypothesis (Woodland, 1983), which proposes that
high biodiversity in the CT is due to its position straddling the
boundary between the Indian Ocean and the Pacific Ocean, with
each ocean having its own distinct fauna forming via vicariance
as the two basins were separated, and fauna subsequently overlap
in the CT as species expanded their ranges.
Empirical evidence in support of each of these hypotheses has
begun to emerge over the last two decades, most recently in the
form of molecular phylogeography studies (see Carpenter et al.,
2011; Briggs and Bowen, 2013; Gaither and Rocha, 2013 for
reviews). However, no single hypothesis has stood out as a front-
runner in explaining most of the biodiversity in the CT. Instead,
the processes proposed above are not mutually exclusive and may
act in concert to produce exceptional biodiversity (Mironov, 2006;
Halas and Winterbottom, 2009; Barber, 2009; Bowen et al., 2013).
Species richness in the CT can also be explained in part by the avail-
ability of stable coral reef habitat in this region, especially during
periods of quaternary glacial cycles, thus serving as an evolutionary
refuge for species (Bellwood and Hughes, 2001; Pellissier et al.,
2014). Pellissier et al. (2014) demonstrated a strong correlation
between present day reef fish diversity and historical proximity to
coral reef refugia during glacial cycles. Thus, in periods of dramatic
climate change and habitat loss, the CT may still function as both a
cradle of speciation as well as a repository for peripheral species.
The thousands of species of fishes that contribute to the diver-
sity within the CT exhibit a variety of mating systems, locomotive
behaviors, larval morphologies and dispersal capabilities, habitat
requirements, life spans, reproductive output, and parental care
regimes (Sale, 1993, 2002; Deloach, 1999; Leis and Carson-Ewart,
2000; Hixon, 2011 ). Each of these factors directly effects the
potential of a lineage to diversify in a given place and time. Thus,
one should not reasonably expect a single model to fit well when
comparing a broad range of reef fish families and genera that differ
dramatically in their ability to respond to a particular driver of spe-
ciation. On the other hand, one may expect that species that share
similar ecological and life history characteristics would show sim-
ilar patterns of evolution and biogeography, even if they belong to
vastly different phylogenetic lineages. Thus, rather than searching
for a single hypothesis explaining diversity across all organisms in
the CT, it may be more informative to ask whether a given hypoth-
esis is more likely to explain biogeographic patterns for a particular
suite of organisms that possess certain ecological and life history
characteristics. Conversely, by studying organisms exhibiting life
history traits conducive to a particular mode or pattern of specia-
tion we can examine evolutionary dynamics associated with the
speciation of clades and ultimately the factors contributing to spe-
cies richness within a region. Here we offer a model group of coral
reef fishes for studying the processes and events associated with
the origination of species within the CT.
1.2. Gobies and speciation within a center of origin
Empirical evidence suggests that sympatric, parapatric, and
allopatric speciation are all responsible for the diversity within
the CT (Briggs, 1999c, 2005; Bowen et al., 2013). If the CT indeed
produces species at elevated rates relative to peripheral regions,
these processes must be operating within very small geographic
scales and within rapid timeframes. Thus, evidence for the center
of origin hypothesis is likely to come from species with character-
istics that facilitate allopatric speciation even within a localizedregion where barriers to gene flow are ephemeral or ‘soft’ (e.g.
periodic sea-level fluctuations due to glaciations; major oceano-
graphic surface currents). Characteristics of such species would
include extremely limited adult mobility, limited larval dispersal
ability, fragmented populations and short life cycles with high
turnover, enabling them to form distinct species after only short
periods of physical reproductive isolation. On the other hand, spe-
ciation in sympatry is thought to occur very rapidly, perhaps even
faster than what is required for allopatric populations (Landry
et al., 2003; Coyne and Orr, 2004). Species that have increased
potential for rapid, ecologically-driven sympatric speciation within
the CT would have characteristics that facilitate the co-existence of
closely related species via the exploitation of underutilized niches
in a complex, heterogeneous reef environment, often in the face of
intense competition from other distantly related reef-associated
species. These characteristics facilitating both allopatric and/or
sympatric speciation are present in the family Gobiidae (gobies),
making them an excellent model group for elucidating processes
contributing to speciation within the CT.
Gobies are one of the most diverse families of vertebrates in the
world. With more than 1700 species spread across more than 200
genera, gobies make up a dominant fraction of the total fish diver-
sity in a broad range of ecosystems including coral reefs (Murdy,
2011a, 2011b; Keith and Lord, 2011; Patzner et al., 2011; Pezold,
2011; Thacker, 2011; Eschmeyer, 2014; Thacker and Roje, 2011;
Herler et al., 2011; Ahmadia et al., 2012).
One of the most diverse clades of coral-associated gobies is the
genus Eviota. Commonly referred to as dwarfgobies, species of Evi-
ota are miniscule in size (frequently less than 20 mm total length)
and occur on a broad range of microhabitats including a variety of
hard corals, coral rock, rubble, and sand ( Herler and Hilgers, 2005;
Herler, 2007; Herler et al., 2011; Ahmadia et al., 2012; Tornabene
et al., 2013a). With over 90 valid species of Eviota described to date,
dwarfgobies represent one of the most evolutionarily successful
lineages of coral reef fishes. Their remarkable diversity may be
explained by repeated habitat shifts from a strict obligate coral-
dwelling lifestyle into sand or rubble habitats, promoting subse-
quent speciation in novel and underutilized niches (Tornabene
et al., 2013a).
Evolutionary time scales may also be accelerated in dwarfgo-
bies relative to other reef fish. The maximum life span of Eviota
sigillata is 59 days and is the shortest known life cycle of any ver-
tebrate (Depczynski and Bellwood, 2005, 2006). Short generation
times (47–74 days) and high mortality result in rapid turnover of
populations (Depczynski and Bellwood, 2005, 2006). Reproduction
in dwarfgobies also likely plays a role in their evolutionary poten-
tial. Mating in Eviota occurs in pairs and is characterized by a series
of well-choreographed, species-specific spawning interactions
prior to deposition and fertilization of eggs (Sunobe, 1998;
Sunobe and Nakazono, 1999). Females often chose males with
stronger secondary sexual traits (e.g. dorsal fin length), and males
spend significant effort guarding nests after fertilization (Sunobe
and Nakazono, 1999; Sekiya and Karino, 2004; Karino and Arai,
2006). As a result, home ranges for mating pairs are very small,
and thus their small adult size, localized spawning, and short pela-
gic larval duration of 24–26 days produce populations that may be
genetically and demographically isolated. The combination of iso-
lation and high turnover may increase the rates at which dwarf-
goby populations respond to natural selection and are subjected
to genetic drift.
1.3. Tips of the Eviota tree: the E. nigriventris and E. bifasciata species
complexes
The Eviota nigriventris species complex is an ideal group for
studying recent speciation within the CT. For 78 years E. nigriventris
202 L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210was considered to be a single species until recent studies indicated
the presence of a complex containing at least three species with dis-
tinct coloration (Greenfield and Randall, 2011; Greenfield and
Tornabene, 2014). Similarly, E. bifasciata was considered a single
species until studies suggested the presence of a species complex
that includes at least two other taxa from the CT (Allen, 2001;
Allen et al., 2013). The distributions of both of these species com-
plex are centered in the CT and do not extend considerably into
the Indian Ocean or Central Pacific Ocean. Additional un-named
color morphs in both complexes exist in the CT and peripheral
regions. Therefore, these species complexes represent two indepen-
dent instances where recent speciation events may have occurred
within the CT, thus making them excellent groups to examine the
factors generating biodiversity within the region. Furthermore, a
comprehensive genetic survey of dwarfgobies in this region may
reveal additional cryptic species in other clades of Eviota, ultimately
resulting in a better understanding of the breadth of the diversity in
one of the world’s most diverse lineages of marine fishes.
The present study uses a molecular phylogenetic approach to
study diversification at the tips of the dwarfgoby phylogeny. Here
we present a time-calibrated molecular phylogeny for 133 speci-
mens of Eviota from within the Coral Triangle, as well as external
localities in Fiji, Pohnpei, Moorea, the Red Sea, Saipan, and Sey-
chelles. By focusing our taxon sampling efforts on the E. nigriventris
and E. bifasciata species complexes, we test several hypotheses
regarding speciation in Eviota and diversification in the CT, includ-
ing: (i) regional color morphs within the E. nigriventris and E. bifas-
ciata complexes reflect genetic differences associated with distinct
species; (ii) the timing of speciation events and the present day
biogeography of the E. nigriventris and E. bifasciata complexes
within the CT are consistent with the center of origin hypothesis;
and (iii) contemporary species boundaries in Eviota correspond to
well-documented genetic breaks found in other species within
the CT.2. Methods
We collected specimens of Eviota from throughout the Indo-
Pacific region and additional samples were utilized from museum
collections (Fig. 1; Supplementary Tables S1). Most specimens
were photographed underwater or immediately following collec-
tion to help confirm identification and record color patterns. Fish
were collected with hand-nets and a solution of clove oil anes-
thetic or ichthyocide. Specimens were stored whole in 95% ethanol
prior to DNA extraction with a Qiagen DNAeasy Blood and Tissue
Kit (Qiagen, Valencia, California). Mitochondrial cytochrome c oxi-
dase I (COI), and the nuclear gene protease III (Ptr) were amplified
via PCR using primers from Thacker (2003; GOBYL6468,Fig. 1. Localities of samples used in this study. The range of the E. nigriventris complex is
The Coral Triangle, as delineated by Veron et al. (2009), is outlined by a dotted line.GOBYH7696), Ward et al. (2005; FishF1-5, FishR1-5), and Yamada
et al. (2009; PtrF2, PtrR2), with GoTaq Hotstart Master Mix (Pro-
mega, Madison, Wisconsin). The thermal profile consisted of 2 min
at 95 C, followed by 35 cycles of 40 s at 95 C, 40 s at 52–55 C,
and 90 s at 72 C. Purification of PCR products and sequencing
was performed by Beckman Coulter Genomics (Danvers, Massa-
chusetts). The nuclear gene Ptr was included to help resolve rela-
tionships towards the root of the phylogeny, and very few
phylogenetically informative sites were found between closely-
related species at this locus. Sequences were assembled and
aligned in Geneious R6 (Biomatters Ltd., available at http://
www.geneious.com), and alignments were double checked by
eye. Several specimens used in this study were sequenced in previ-
ous studies using similar protocols (Tornabene et al., 2013a, 2013b;
Greenfield and Tornabene, 2014). Nexus files for sequence align-
ments are provided as Supplementary material.
Phylogeny of Eviotawas inferred using Bayesian methods on the
concatenated dataset partitioned by gene. Prior to concatenation,
COI and Ptr alignments were analyzed in jModeltest ver.0.1.1
(Posada, 2008) to determine the best fitting substitution models
based on Akaike Information Criterion (AIC) scores. The COI and
Ptr alignments were then concatenated and phylogeny was then
inferred using MrBayes ver.3.2, with each gene receiving its own
partition and substitution model. For each MrBayes analysis, two
parallel Metropolis-coupled Markov Chain Monte Carlo runs were
generated for 10,000,000 iterations with a sampling frequency of
1000 iterations. Stationarity and adequate mixing of each MCMC
run was determined using the program Tracer ver.1.5 (Rambaut
and Drummond, 2007). Branch length priors for MrBayes runs
were set to an unconstrained-exponential prior with a mean of
0.01 (default mean in MrBayes is 0.1) to remedy the common prob-
lem of MCMC chains converging on local optima with unrealisti-
cally long branch lengths (Brown et al., 2010; Marshall, 2010).
Outgroups included the two Coral Goby genera Gobiodon and Bry-
aninops, and the more distantly related Asterropteryx. Within the E.
nigriventris and E. bifasciata complexes, Network ver. 4.6.1.2 (avail-
able at http://www.fluxus-engineering.com/sharenet.htm) was
used to construct median-joining haplotype networks from the
COI datasets (Bandelt et al., 1999). Alignments for median-joining
analysis were truncated both in sequence length and in numbers
of samples (individuals with large amounts of missing data were
excluded) resulting in 1094 bp for the E. nigriventris group and
577 bp for the E. bifasciata group. Genetic distance matrices for
these datasets are listed in Supplementary Tables S2 and S3.
Divergence times were estimated from the COI dataset using
Bayesian methods in the program BEAST ver.1.7 (Drummond
et al., 2012). The fossil record for gobiids is depauperate and accu-
rately identified fossils that would be appropriate for dating our
tree do not exist. Therefore, our phylogeny was calibrated usingoutlined in a solid line, and the range of the E. bifasciata species complex is shaded.
L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210 203COI mutation rate estimates calculated from the divergence
between Evorthodus lyricus and Evorthodus minutus (approximately
0.048 mutations/site per 106 years), a geminate-pair of gobies sep-
arated by the Isthmus of Panama approximately 2.8 ma. Evorthodus
sequences used for estimating mutation rate were public data at
the Barcode of Life Data System (Ratnasingham and Hebert,
2013; http://www.boldsystems.org/, accessed 10 April 2014). An
uncorrelated lognormal relaxed molecular-clock prior was used
for the analysis, as our data deviated significantly from a strict glo-
bal molecular clock model (p < 0.05; likelihood ratio test). Muta-
tion rates were drawn from a prior with a normal distribution
centered on a mean of 0.05 with a standard deviation of 0.01.
The topology of the MrBayes multi-locus tree was used as starting
tree for the BEAST analysis.3. Results
The monophyly of the Eviota nigriventris complex and the E.
bifasciata complex were both well-supported, with the former
being sister to the E. lachdeberei complex, and the latter being sis-
ter to a clade containing an undescribed species from Saipan and
Pohnpei (Figs. 2 and 3). The precision of age estimations
decreased towards the root of the phylogeny, where the median
age estimate of the genus Eviota was 10.63 Ma with a wide 95%
credible interval of 6.5–16.8 Ma. Ranges for age estimates were
considerably narrower towards the tips of the phylogeny. The E.
nigriventris complex and E. bifasciata complex are both less than
2.5 million years old, and most species on our tree have origins
from the late Miocene through the late Pliocene (Fig. 3). However,
in groups where taxon sampling was more robust, divergence
times between recently-evolved lineages are of Pleistocene originFig. 2. Bayesian phylogeny of Eviota based on concatenated COI and Ptr datasets. Node
collapsed into polytomies. Eviota nigriventris and E. bifasciata complexes are collapsed a(<0.5 Ma in the E. nigriventris complex, <1.5 Ma in the E. bifasciata
complex).
The Eviota nigriventris complex includes six reciprocally mono-
phyletic lineages (Fig. 4); E. nigriventris, from the Banda Sea, Sulaw-
esi, Halmahera, Cendrawasih Bay, and Raja Ampat; E. dorsogilva,
from the type locality in Fiji; E. brahmi, from the type locality in
New Hanover, Papua New Guinea; E. dorsopurpurea, from the type
locality in Milne Bay, Papua New Guinea; and two lineages that are
similar to E. dorsogilva in morphology but are genetically distinct
and have unique coloration, from Ferguson Island and New Hano-
ver Island, respectively. The first split within this complex occurs
around 1.25 Ma (0.71–2.08 Ma 95% HPD interval) with the diver-
gence of a clade that includes E. dorsopurpurea and E. brahmi, the
two of which then separate within 60,000–230,000 years ago. Sub-
sequent splits within the E. nigriventris group occurred around
830 Ka (460 Ka–1.37 Ma), 330 Ka (170–560 Ka) and 210 Ka (90–
380 Ka).
The Eviota bifasciata complex also contains six lineages (Fig. 5);
E. pamae, from the type locality in the Kei Islands; E. raja, from the
type locality in Raja Ampat; three lineages that are identified as E.
bifasciata, with one from Cendrawasih Bay, a second from Bali and
Anambas, and a third from Milne Bay, Papua New Guinea; and a
unique eastern Indonesian color morph from the Banda Sea, Sulaw-
esi, Halmahera and Raja Ampat. The five major speciation events
within this complex occurred in rapid succession within a very
narrow time frame (approximately 1 million years). The rooted
phylogeny depicts the eastern Indonesia/Palau clade as the first
lineage to diverge from the common ancestor. However, the med-
ian-joining haplotype network depicts six missing haplotypes at
the center of the network that differ by less than 10 mutations. It
is from these central haplotypes that each of the six major lineages
diverge dramatically (12–37 mutations).values are Bayesian posterior probabilities. Nodes with values less than 0.50 are
s black triangles.
Fig. 3. Time-calibrated phylogeny of Eviota based on COI dataset. Units for the x-axis are 106 years. Node values represent the minimum and maximum values of the 95%
highest-posterior-density intervals (credible intervals) of age estimates. Tips of the E. bifasciata and E. nigriventris complexes are collapsed (black triangles). Asterisks indicate
relationships that are not supported in concatenated dataset.
204 L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–2104. Discussion
Renema et al. (2008) demonstrated the CT as a marine hotspot
formed approximately 23 Ma with the collision of Australia with
the Pacific arc and Southeast Asian margin. They summarize data
from the fossil record and from dated molecular phylogenies to
suggest that many groups that exist in the CT today have origins
that predate the origin of the current CT hotspot, and that most
of the recent diversification within the region pre-dates Pleisto-
cene sea-level fluctuations (occurring mainly in the Pliocene or
earlier). Our analysis of Eviota reveals that the genus as a whole
is young, forming in the mid- to late Miocene after the CT hotspot
was established. Most of the branching events on the phylogeny
are in the late Miocene to early Pliocene, which is in agreement
with the synopsis of Renema et al. (2008). However, species groups
that have been sampled from multiple localities (e.g. E. nigriventris
complex, E. bifasciata complex, E. guttata complex, E. lachdeberei, E.
atriventris) reveal multiple isolated genetic lineages (species) cor-
responding to regional color morphs that diverged more recently
in late Pliocene through the Pleistocene. This pattern suggests that
the lineages originating in the Miocene to Pliocene may have stemages that are old, but likely represent cryptic species complexes
comprised of recently-diverged lineages that have yet to be
sequenced throughout their range, thus inflating the estimated
ages of individual species. This would mirror the pattern found
in the gobiid genus Trimma where nearly all morphologically
defined ‘species’, when sequenced from multiple locations, repre-
sent complexes of cryptic lineages (Winterbottom et al., 2014). If
this pattern of widespread cryptic diversity holds true in Eviota,
the number of species in the genus may be well over 120–130 spe-
cies, considering there are currently 91 described species (most
based on morphology or color alone) and perhaps a dozen others
that await description (authors’ unpublished data; David Green-
field, pers. comm.).
The present-day distributions of the E. bifasciata and E. nigriven-
tris complexes are centered in the CT (Fig. 1). Both species groups
extend slightly beyond the CT in the north to the Ryukyu Islands
and Palau, as well as to the east off Australia, Vanuatu, New Cale-
donia and Fiji (E. nigriventris complex only). Thus, the ranges of the
groups themselves suggest an origin within the CT, as neither
group occurs well into the Indian Ocean or the Central Pacific
Ocean. Within each species group, there is strong agreement
Fig. 4. Time-calibrated phylogeny and median-joining haplotype network of the Eviota nigriventris complex based on COI dataset. Blue bars at nodes are 95% highest-
posterior-density intervals (credible intervals) for age estimates. Closed circles on the map are localities where samples from each lineage were collected. Open circles
represent localities where a particular lineage/color morph was observed but not collected. Size of circles on haplotype network represents the number of individuals with
that haplotype. Black circles represent missing haplotypes. Lines connecting haplotypes are one mutational step unless otherwise denoted by tick marks or numbers. (For
interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210 205between genetic divergence, coloration and geography. Each group
comprises at least six genetic lineages, with most lineages possess-
ing unique geographic distributions and color morphs. These data
indicate the presence of recent speciation occurring both within
the CT, and between the CT and bordering localities.
4.1. Eviota nigriventris complex
The most recent speciation even in the Eviota nigriventris com-
plex is between E. brahmi and E. dorsopurpurea. Eviota brahmi
occurs in the Bismarck Archipelago, the Solomon Islands, and Mil-
ne Bay (Papua New Guinea), although tissues were only available
from the Bismarck Archipelago. Eviota brahmi co-occurs with its
sister species E. dorsopurpurea in Milne Bay, where the latter spe-
cies is endemic. The sea-level fluctuations during the Pleistocene
are unlikely to have caused the split between this species pair, as
the waterways surrounding Papua New Guinea, the Bismarck
Archipelago, and the Solomon Islands remained open during that
period. The relatively widespread occurrence of E. brahmi suggests
that ocean currents such as the South Equatorial Current/NewGuinean Coastal Current (SEC/NGCC), which passes between
Milne Bay and the Bismarck Archipelago, may not be a barrier of
dispersal between these localities. Thus, the recent divergence of
E. dorsopurpurea represents a potential case of sympatric specia-
tion within Milne Bay. In Milne Bay, both species have been
observed in close proximity, but in distinct groups segregating
between different species of coral (Greenfield and Randall, 2011).
Thus, a combination of microhabitat partitioning and assortative
mating between E. brahmi and E. dorsopurpureamay be responsible
for creating and or maintaining species boundaries. Habitat
partitioning has also been observed between other closely related
sympatric species of Eviota (e.g. E. rubra and E. susanae in Hawaii:
Greenfield and Randall, 1999), as well as in sympatric pairs of
Caribbean neon gobies that possess identical coloration (Colin,
1975), and in sympatric sister-species of coral-dwelling Gobiodon
(Munday et al., 2004), with the latter example representing one
of the strongest cases for sympatric speciation in the sea. The shal-
low genetic divergence between the E. brahmi and E. dorsopurpurea
is striking given the dramatic color differences between the two,
and is even less than the intraspecific variation seen in other Eviota
Fig. 5. Time-calibrated phylogeny and median-joining haplotype network of the Eviota bifasciata complex based on COI dataset. Blue bars at nodes are 95% highest-posterior-
density intervals (credible intervals) for age estimates. Closed circles on the map are localities where samples from each lineage were collected. Open circles represent
localities where a particular lineage/color morph was observed but not collected. Size of circles on haplotype network represents the number of individuals with that
haplotype. Black circles represent missing haplotypes. Lines connecting haplotypes are one mutational step unless otherwise denoted by tick marks or numbers. (For
interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
206 L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210lineages. Nonetheless, the rooted phylogeny recovers the species as
reciprocally monophyletic, and this appears to be a situation where
divergence in color pattern evolved faster than mutations could
accumulate in the mitochondrial genome – a pattern also observed
in Centropyge (Gaither et al., 2014).
The divergence between Eviota nigriventris and a genetically-
distinct undescribed color morph from southeast Papua New Gui-
nea (Eviota cf. dorsogilva, Ferguson Island) corresponds with similar
genetic breaks between Papua New Guinea and eastern Indonesia
populations of nautilus, giant clams, stomatopods, and anemone-
fish (Wray et al., 1995; Benzie and Williams, 1997; Barber et al.,
2002, 2006; Timm et al., 2008; Huelsken et al., 2013). Concordant
genetic breaks in this region may be maintained by the eastward
reflection of the SEC/NGCC in the region north of the Bird’s Head,
West Papua that forms the Halmahera Eddy, an oceanographic fea-
ture that may present a barrier for dispersal of pelagic larvae. The
last split within this group separates E. dorsogilva (Fiji) from a
genetically distinct color morph in New Hanover, Papua New Gui-
nea. This split has also been observed in five species of reef fish,
Pomacentrus moluccensis, Amphiprion melanopus, Chrysiptera talboti,
Cirrhilabrus punctatus and Labroides dimidiatus (Drew et al., 2008).Four of those species also possess distinct multiple color morphs
that correspond with a Fiji/Indo-West Pacific genetic break.
Several lineages in the Eviota nigriventris complex have small
distributions and appear to be endemic to small regions within
the Coral Triangle or in the periphery. The notable exception is Evi-
ota nigriventris, which occurs throughout eastern Indonesia. This
species may also be more widespread than what is shown here,
as the genetic identity of Eviota nigriventris in the NW portion of
its range (Java, Sumatra, Philippines, Ryukyu Islands) is unknown.
This species complex fits well with the ‘peripheral budding’ model
proposed by Hodge et al. (2012, Fig 4c). Under this model, a large
widespread parent species repeatedly produces a series of ‘buds’,
or smaller isolated species via series of peripatric, parapatric or
sympatric speciation events. These budded species can be local
endemic species within the range of the larger species, or may be
located on the periphery of the parent species. The phylogeograph-
ic pattern left by this process shows the widespread species as
being very young on the phylogeny, despite it being the ancestral
‘parent’ species, as its sister species on the tree will always be
the most recently formed ‘bud’. In the case of the E. nigriventris
complex, the eastern Indonesian E. nigriventris may have been
L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210 207the parent population repeatedly ‘budding’ species to the east (and
perhaps to the NW as well), the first of which led to the E. brahmi/E.
dorsopurpurea lineage, the second led to the E. dorsogilva (Fiji)/E. cf.
dorsogilva (New Hanover) lineage, and the last to the E. cf. dors-
ogilva (Ferguson Island) lineage.
4.2. Eviota bifasciata complex
The Eviota bifasciata complex contains six reciprocally mono-
phyletic genetic lineages in the Coral Triangle (Fig. 5). Two of the
six lineages in this complex have been described as distinct spe-
cies; E. pamae from the Kei Islands, and E. raja from Raja Ampat.
Another lineage occurs in western Indonesia (Bali, Anambas). This
species has also been observed in Malaysia (Sabah), and near the E.
bifasciata type locality in the Philippines, thus we tentatively con-
sider this the ‘true’ Eviota bifasciata. However, this lineage pos-
sesses similar coloration to two other genetically distinct
lineages labeled ‘Eviota cf. bifasciata’, one occurring in Cendrawasih
Bay and a second in Milne Bay, the latter represented by a single
specimen. The last lineage, also labeled ‘Eviota cf. bifasciata’, occurs
in eastern Indonesia (Sulawesi, Halmahera, Banda Sea, Raja
Ampat). This lineage has unique coloration and has also been
observed in Palau. The five major speciation events within this
complex occurred in rapid succession within a very narrow time
frame (approximately 1 million years). The rooted phylogeny
depicts the eastern Indonesia/Palau clade as the first lineage to
diverge from the common ancestor. However, the median-joining
haplotype network depicts six missing haplotypes at the center
of the network that differ by less than 10 mutations. It is from
these central haplotypes that each of the six major lineages diverge
dramatically (12–37 mutations).
The biogeography of the Eviota bifasciata complex agrees well
with the paleoceanographic history of the region during Plio-
cene–Pleistocene sea level fluctuations. During glacial periods
beginning in the Pliocene, sea level in the CT dropped as polar
ice caps formed. Drops in sea level reached as low as 120 m below
current levels in the Pleistocene (Fig. 6; Voris, 2000). A sea level
drop of 30–50 m effectively isolates the South China Sea from the
Java Sea to the south via the exposure of the Sunda Shelf, and a
drop of 120 m results in near-complete isolation of the South China
Sea from the Celebes Sea to the east via the exposure and expan-
sion of the Palawan Islands and Sulu Archipelago. This initial sep-
aration likely restricted gene flow and initiated speciation between
the western Indonesian clade of E. bifasciata and populations to the
east. Sea level rise in subsequent interglacial periods would allow
for this species to expand its range south into the Java Sea, and east
into the Celebes Sea. Interestingly, the Bali sample of E. bifasciata
shows strong genetic divergence from the Anambas population,
despite having similar coloration. It is likely that, after an initial
southward range expansion, this Java Sea population was tempo-
rarily re-isolated from the South China Sea during subsequent gla-
cial cycles with the re-emersion of the Sunda Shelf. More samples
and photographs of the Java Sea population could help test this
hypothesis and clarify the status of the Bali E. bifasciata sample.
Present day gene flow between western Indonesian E. bifasciata
and species to the east may be impeded by the Indonesian
Throughflow, which passes 1–20 million m3 s1 of water through
the Makassar Strait between Borneo and Sulawesi and exits the
CT to the south via the Lombok Strait or to the east around the
tip of Timor-Leste (Fig. 6; Godfrey, 1996; Schiller et al., 2008). This
apparent genetic break between the South China Sea/western
Indonesia and eastern Indonesia has been observed in the scad
Decapterus russelli, the damselfish Chrysiptera rex, two species of
anemonefish in the genus Amphiprion, and seahorses of the genus
Hippocampus (Perrin and Borsa, 2001; Lourie et al., 2005; Timm
et al., 2008; Drew et al., 2010).A sea level drop of 40–120 m also further constricts the mouth
of Cendrawasih Bay to an opening less than 100 km wide via the
expansion of Yapen and Miosnum Islands (Fig. 6). This isolation
may have been sufficient to restrict gene flow and result in the
emergence of a unique Cendrawasih Bay haplotype. The presence
of a distinct haplotype in Cendrawasih Bay is emerging as a
repeated pattern in several groups of marine organisms including
the sea star Protoreaster nodosus, anemonefishes, boring giant
clams, and the stomatopod Haptosquilla pulchella (Barber et al.,
2006; Timm et al., 2008; DeBoer et al., 2008; Crandall et al.,
2008). Allen and Erdmann (2006) described an endemic wrasse
from Cendrawasih Bay, moreover noting that other anomalous
color morphs of reef fishes occur only within the bay. More
recently, Allen and Erdmann (2012) and Greenfield and Erdmann
(2014) list a total of 14 coral reef fish species (and mention a num-
ber of hard coral and mantis shrimp species) that are considered
restricted range endemics of Cendrawasih Bay, including the
dwarfgoby E. tetha. It has been hypothesized that the Tosem Block
of the South Caroline Arc moved across the opening of the bay in
the late Pliocene, resulting in an early period of isolation (Allen
and Erdmann, 2006, 2012; Hill and Hall, 2003). The north coast
of Papua receives a constant supply of surface water from eastern
Papua New Guinea via the SEC/NGCC; however, flow into Cen-
drawasih Bay is minimal as most of the water passes north of
the entrance and reflects eastward via the Halmahera Eddy
(Schiller et al., 2008). Thus, it is likely that the complex history of
tectonic movements, sea level fluctuations, and oceanographic cur-
rents (NGCC/Halmahera Eddy) all contribute to the isolation and
observed endemism within Cendrawasih Bay. The Cendrawasih
Bay haplotype is sister to a single specimen from Milne Bay, Papua
New Guinea, differing by 27 mutations (Fig. 5). The Milne Bay pop-
ulation may show the same color pattern as the Cendrawasih Bay
clade, however our only observation of Milne Bay E. bifasciata
comes from a single photograph, and additional genetic samples
and photos from Papua New Guinea are needed to help determine
whether these haplotypes represent multiple species.
Eviota pamae has the most restricted range within the E.
bifasciata complex, occurring only in the Kei Islands. The Kei
Islands lie on the west side of ‘Lydekker’s Line’, which is recog-
nized as the biogeographic divide between the Indo-Malay
region and the Australia–New Guinea region (Simpson, 1977).
No other member of the E. bifasciata complex has been
observed in the Kei Islands, however the eastern Indonesian E.
cf. bifasciata color morph was observed north of the Kei Islands
at Kaimana, West Papua. One possibility is that E. pamae is a
relic of a more widespread Sahul Shelf lineage that is now
restricted to the Kei Islands after sea level rise, due to the lack
of suitable coral habitat along most of the south coast of Papua.
This seems unlikely as the species does not occur in the Aru
Islands, which are home to reef-fish fauna typically associated
with the Australia–New Guinea province (Simpson, 1977; M.V.
Erdmann, pers. obs.). The mechanisms explaining the divergence
of E. pamae and subsequent maintenance of genetic isolation
remain obscure. Nevertheless, this species represents a clear
example of recent speciation occurring at small geographic dis-
tances within the CT.
The other highly endemic species within the E. bifasciata com-
plex is E. raja, which occurs in the Raja Ampat Islands. This species
co-occurs with the eastern Indonesian lineage of Eviota. cf. bifasci-
ata throughout the Raja Ampat Islands, and both species have been
observed cohabitating the same coral head (M.V. Erdmann, pers.
obs.). Thus, niche partitioning via habitat preference does not
appear to be occurring between these two lineages, and there are
no known occurrences of intermediate color morphs that would
suggest hybridization occurs in this contact zone. As with E. pamae,
the mechanism promoting speciation of the highly endemic E. raja
Fig. 6. Coral Triangle during glacial-maxima with sea-levels 120 m below current levels. Abbreviations: IT – Indonesian Throughflow; HE – Halmahera Eddy; SEC – South
Equatorial Current; SEC/NGCC – South Equatorial Current/New Guinea Coastal Current. Sea-level map modified from Voris (2000). Currents based on Godfrey (1996) and
Schiller et al. (2008).
208 L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210remains elusive, but nonetheless represents an intriguing example
of recent speciation and endemism within the CT.
4.3. Conclusions
In summary, concordance between color morphs, geography,
and genetics indicate the presence of multiple highly-restricted
endemic species these two species complexes from Milne Bay,
New Hanover, Ferguson, Kei Islands, Raja Ampat, and Cendraw-
asih Bay. Major branching events occurred within the Pleistocene,
and the patterns suggest speciation occurred in allopatry, parap-
atry and sympatry within the CT. On one hand, the timing of spe-
ciation events and present-day species distributions suggest that
sea level fluctuations and subsequent isolation of water bodies
likely played a part in the speciation process of some groups,
yet other lineages appear to have diverged in the absence of hard
physical barriers to gene flow. This suggests that a combination of
both physical and biological factors is responsible for driving
dwarfgoby speciation within the CT. The pelagic larval duration
(PLD) for Eviota species is 24–26 days, which is not exceptionally
short when compared to other fishes such as damselfishes and
blennioids (Depczynski and Bellwood, 2006; Wellington and
Victor, 1989; Riginos and Victor, 2001). Biophysical modeling sug-
gests that regional self-recruitment may be high within the CT
and may explain regional genetic structuring in individuals that
are capable of settling after 15–30 days in the water column
(Kool et al., 2011). Several studies have demonstrated that PLD
is not a strong predictor of true dispersal capability, range size
or levels of genetic structure (Victor and Wellington, 2000;
Imron et al., 2007; Weersing and Toonen, 2009; Mora et al.,
2012; Sotka, 2012; Luiz et al., 2013; but see Riginos and Victor,
2001). Instead, larval behavior, adult characteristics, or environ-
mental traits may be more important (Woodson and McManus,
2007; Sotka, 2012; Luiz et al., 2013). Larvae that actively forage
may disperse hundreds of km less than previous dispersal esti-
mates, as species may actively avoid high-flow offshore with less
primary productivity (Woodson and McManus, 2007). This may
be the case for Eviota larvae, who exhaust yolk-sac resources inthe first two days after hatching and must immediately begin for-
aging or risk starvation by days three or four (Sunobe and
Nakazono, 1987).
In the event of possible secondary contact between Eviota lin-
eages, interspecific competition for habitat could be a strong driver
of ecological partitioning (Hobbs and Munday, 2004; Munday,
2004a, 2004b; Munday et al., 2001). We see some evidence of this
in the sympatric contact zone of E. brahmi and E. dorsopurpurea in
Milne Bay, where closely related species show strong niche parti-
tioning and segregate into distinct groups of conspecifics, but not
in Eviota raja and the eastern Indonesian E. cf. bifasciata which fre-
quently co-occur over a single coral head. Mating between color
morphs of Eviota may also be prevented by their species-specific
pre-mating behaviors and females that are highly selective for
males with the strongest secondary sex characteristics (Sunobe,
1998; Sunobe and Nakazono, 1999; Sekiya and Karino, 2004;
Karino and Arai, 2006).
Lastly, the age of speciation events in our study contradict
Bellwood and Meyer’s (2009) observation that CT endemics have
origins dating back 4–25 Ma and likely represent the ‘last stand’
for previously wide-spread species that have seen their ranges
shrink over time. The discrepancy between our dates and those
of Bellwood and Meyer (2009) are likely due to differences in the
completeness of taxon sampling, and previous studies relying
mostly on taxonomically recognized species (ignoring cryptic spe-
cies), potentially inflating node ages (Rocha and Bowen, 2008).
Nonetheless, our findings highlight the importance of the CT for
generating new biodiversity, especially in groups with limited dis-
persal potential, that display evidence of local niche partitioning,
and that have potential for assortative mating. The presence of
numerous cryptic lineages across the Eviota phylogeny suggests
that previous estimates or species richness in Eviota, and of crypto-
benthic reef fishes in the CT in general, may be significantly under-
estimated. This places increased responsibility on taxonomists to
integrate this phylogeographic information into their naming and
circumscribing evolutionarily distinct lineages; named species
are far more likely to benefit from international conservation leg-
islation and planning tools (Mace, 2004).
L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210 209Acknowledgments
We thank David Greenfield of the California Academy of Sci-
ences for many valuable discussions on Eviota taxonomy. Gerry
Allen kindly contributed several specimens from Papua New Gui-
nea and information on species distributions and habitat. We
thank Gabby Ahmadia, Jocelyn Curtis Quick and the staff of Conser-
vation International’s Indonesia marine program for helping
acquire many specimens used in this study. Dave Catania at Cali-
fornia Academy of Sciences, Sue Morrison at the Western Austra-
lian Museum, and Leo Smith and Andy Bentley at University of
Kansas, Biodiversity Institute provided curatorial assistance. Fund-
ing for this project was provided by the American Museum of Nat-
ural History Lerner Gray Award (LT), the Louis Stokes Alliances for
Minority Participation program (SV), the Paine Family Trust (ME),
the Walton Family Foundation (ME), the Henry Foundation (ME)
and NSF OISE-0553910 (FP).Appendix A. Supplementary material
Supplementary data associated with this article can be found,
in the online version, at http://dx.doi.org/10.1016/j.ympev.2014.
09.012.References
Ahmadia, G.N., Pezold, F., Smith, D.J., 2012. Cryptobenthic fish biodiversity and
microhabitat use in healthy and degraded coral reefs in SE Sulawesi, Indonesia.
Mar. Biodivers. 42, 433–442.
Allen, G.R., Erdmann, M.V., 2006. Cirrhilabrus cenderawasih, a new wrasse (Pisces:
Labridae) from Papua, Indonesia. Aqua. Int. J. Ichthyol. 11, 125–131.
Allen, G.R., Erdmann, M.V., 2012. Reef Fishes of the East Indies. Tropical Reef
Research, Perth.
Allen, G.R., 2001. Description of two new gobies (Eviota, Gobiidae) from Indonesian
seas. Aqua, Int. J. Ichthyol. 4, 125–130.
Allen, G.R., Werner, T.B., 2002. Coral reef fish assessment in the ‘‘coral triangle’’ of
southeastern Asia. Environ. Biol. Fishes 65, 209–214.
Allen, G.R., Brooks, W.M., Erdmann, M.V., 2013. Eviota pamae, a new species of coral
reef goby (Gobiidae) from Indonesian seas. Aqua, Int. J. Ichthyol. 19, 79–84.
Bandelt, H.J., Forster, P., Rohl, A., 1999. Median-joining networks for inferring
intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48.
Barber, P.H., 2009. The challenge of understanding the Coral Triangle biodiversity
hotspot. J. Biogeogr. 36, 1845–1846.
Barber, P.H., Erdmann, M.V., Palumbi, S.R., 2006. Comparative phylogeography of
three codistributed stomatopods: origins and timing of regional lineage
diversification in the coral triangle. Evolution 60, 1825–1839.
Barber, P.H., Palumbi, S.R., Erdmann, M.V., Moosa, M.K., 2002. Sharp genetic breaks
among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to
larval transport: patterns, causes, and consequences. Mol. Ecol. 11, 659–674.
http://dx.doi.org/10.1046/j.1365-294X.2002.01468.x.
Bellwood, D.R., Hughes, T.P., 2001. The state of coral reef science – response. Science
293 (80), 1997.
Bellwood, D.R., Meyer, C.P., 2009. Searching for heat in a marine biodiversity
hotspot. J. Biogeogr. 36, 569–576.
Benzie, J.A.H., Williams, S.T., 1997. Genetic structure of giant clam (Tridacna
maxima) populations in the west Pacific is not consistent with dispersal by
present-day ocean currents. Evolution 51, 768–783. http://dx.doi.org/10.2307/
2411153.
Bowen, B.W., Rocha, L.A., Toonen, R.J., Karl, S.A., 2013. The origins of tropical marine
biodiversity. Trends Ecol. Evol. 28, 359–366.
Briggs, J.C., 1999a. Extinction and replacement in the Indo-West Pacific Ocean. J.
Biogeogr. 26, 777–783.
Briggs, J.C., 1999b. Coincident biogeographic patterns: Indo-West Pacific Ocean.
Evolution 53, 326–335.
Briggs, J.C., 1999c. Modes of speciation: Marine Indo-West Pacific. Bull. Mar. Sci. 65,
645–656.
Briggs, J.C., 2005. The marine East Indies: diversity and speciation. J. Biogeogr. 32,
1517–1522.
Briggs, J.C., Bowen, B.W., 2013. Marine shelf habitat: biogeography and evolution. J.
Biogeogr. 40, 1023–1035.
Brown, J.M., Hedtke, S.M., Lemmon, A.R., Lemmon, E.M., 2010. When trees grow too
long: investigating the causes of highly inaccurate Bayesian branch-length
estimates. Syst. Biol. 59, 145–161. http://dx.doi.org/10.1093/sysbio/syp081.
Carpenter, K.E., Barber, P.H., Crandall, E.D., Ablan-Lagman, M.C.A., Ambariyanto,
Mahardika, G.N., Manjaji-Matsumoto, B.M., Juinio-Menez, M.A., Santos, M.D.,
Starger, C.J., Toha, A.M.A., 2011. Comparative phylogeography of the Coral
Triangle and implications for marine management. J. Mar. Biol. 201, 1–14.Colin, P.L., 1975. The Neon Gobies: Comparative Biology of the Gobies of the genus
Gobiosoma, subgenus Elacatinus (Pisces: Gobiidae) in the Tropical Western
Atlantic. T.F.H. Publications, Neptune City.
Coyne, J.A., Orr, H.A., 2004. Speciation. Sinauer Associates, Sunderland.
Crandall, E.D., Jones, M.E., Munoz, M.M., Akinronbi, B., Erdmann, M.V., Barber, P.H.,
2008. Comparative phylogeography of two seastars and their ectosymbionts
within the Coral Triangle. Mol. Ecol. 17, 5276–5290.
DeBoer, T.S., Subia, M.D., Ambariyanto, Erdmann, M.V., Kovitvongsa, K., Barber, P.H.,
2008. Phylogeography and limited genetic connectivity in the endangered
boring giant clam across the Coral Triangle. Conserv. Biol. 22, 1255–1266.
http://dx.doi.org/10.1111/j.1523-1739.2008.00983.
Deloach, N., 1999. Reef Fish Behavior: Florida, Caribbean. New World Publications
Inc, Jacksonville, FL, Bahamas.
Depczynski, M., Bellwood, D.R., 2005. Shortest recorded vertebrate lifespan found in
a coral reef fish. Curr. Biol. 15, R288–R289.
Depczynski, M., Bellwood, D.R., 2006. Extremes, plasticity, and invariance in
vertebrate life history traits: insights from coral reef fishes. Ecology 87,
3119–3127.
Drew, J., Allen, G.R., Kaufman, L., Barber, P.H., 2008. Endemism and regional color
and genetic differences in five putatively cosmopolitan reef fishes. Conserv. Biol.
22, 965–975. http://dx.doi.org/10.1111/j.1523-1739.2008.01011.x.
Drew, J.A., Allen, G.R., Erdmann, M.V., 2010. Congruence between mitochondrial
genes and color morphs in a coral reef fish: population variability in the Indo-
Pacific damselfish Chrysiptera rex (Snyder, 1909). Coral Reefs 29, 439–444.
http://dx.doi.org/10.1007/s00338-010-0586-5.
Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A., 2012. Bayesian phylogenetics
with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973. http://
dx.doi.org/10.1093/molbev/mss075.
Ekman, S., 1953. Zoogeography of the Sea. Sidgwick and Jackson, London.
Eschmeyer, W.N., 2014. Catalog of Fishes: Genera, Species, References. <http://
research.calacademy.org/research/ichthyology/catalog/fishcatmain.asp> (accessed
10.03.14).
Gaither, M.R., Rocha, L.A., 2013. Origins of species richness in the Indo-Malay-
Philippine biodiversity hotspot: evidence for the centre of overlap hypothesis. J.
Biogeogr. 40, 1638–1648.
Gaither, M.R., Schultz, J.K., Bellwood, D.R., Pyle, R.L., DiBattista, J.D., Rocha, L.A.,
Bowen, B.W., 2014. Evolution of pygmy angelfishes: recent divergences,
introgression, and the usefulness of color in taxonomy. Mol. Phylogenet. Evol.
74, 38–47.
Godfrey, J.S., 1996. The effect of the Indonesian Throughflow on ocean circulation
and heat exchange with the atmosphere: a review. J. Geophys. Res. 101, 12217–
12237. http://dx.doi.org/10.1029/95jc03860.
Greenfield, D.W., Erdmann, M.V., 2014. Eviota tetha, a new species of dwarfgoby
from Cenderawasih Bay, West Papua, Indonesia (Teleostei: Gobiidae). J. Ocean
Sci. Found. 11, 23–31.
Greenfield, D.W., Randall, J.E., 1999. Two new Eviota species from the Hawaiian
Islands (Teleostei: Gobiidae). Copeia, 439–446.
Greenfield, D.W., Randall, J.E., 2011. Two new Indo-Pacific species in the Eviota
nigriventris complex (Teleostei: Gobiidae). Zootaxa, 54–66.
Greenfield, D.W., Tornabene, L., 2014. Eviota brahmi n.sp. from Papua New Guinea,
with a redescription of Eviota nigriventris (Teleostei: Gobiidae). Zootaxa 3793,
133–146.
Halas, D., Winterbottom, R., 2009. A phylogenetic test of multiple proposals for the
origins of the East Indies coral reef biota. J. Biogeogr. 36, 1847–1860.
Herler, J., Hilgers, H., 2005. A synopsis of coral and coral-rock associated gobies
(Pisces: Gobiidae) from the Gulf of Aqaba, northern Red Sea. Aqua. Int. J.
Ichthyol. 10, 103–132.
Herler, J., 2007. Microhabitats and ecomorphology of coral- and coral rock-
associated gobiid fish (Teleostei: Gobiidae) in the northern Red Sea. Mar. Ecol.
Evol. Perspect. 28, 82–94.
Herler, J., Munday, P.L., Hernaman, V., 2011. Gobies on coral reefs. In: Patzner, R.A.,
Van Tassel, J.L., Kovacic, M., Kapoor, B.G. (Eds.), The Biology of Gobies. Science
Publishers, Enfield, NH.
Hill, K.C., Hall, R., 2003. Mesozoic-Cenozoic evolution of Australia’s New Guinea
margin in a west Pacific context. In: Hillis, R.R., Müler, R.D. (Eds.), Evolution and
Dynamics of the Australian Plate. Geological Society of Australia Special
Publication 22 and Geological Society of America Special Paper 372, pp. 265–
290.
Hixon, M.A., 2011. 60 Years of coral reef fish ecology: past, present, future. Bull. Mar.
Sci. 87, 727–765. http://dx.doi.org/10.5343/bms.2010.1055.
Hobbs, J.P.A., Munday, P.L., 2004. Intraspecific competition controls spatial
distribution and social organisation of the coral-dwelling goby Gobiodon
histrio. Mar. Ecol. Prog. Ser. 278, 253–259. http://dx.doi.org/10.3354/
Meps278253.
Hodge, J.R., Read, C.I., van Herwerden, L., Bellwood, D.R., 2012. The role of peripheral
endemism in species diversification: Evidence from the coral reef fish genus
Anampses (Family: Labridae). Mol. Phylogenet. Evol. 62, 653–663. http://
dx.doi.org/10.1016/j.ympev.2011.11.007.
Huelsken, T., Keyse, J., Liggins, L., Penny, S., Treml, E.A., Riginos, C., 2013. A novel
widespread cryptic species and phylogeographic patterns within several giant
clam species (Cardiidae: Tridacna) from the Indo-Pacific Ocean. PLoS ONE 8.
http://dx.doi.org/10.1371/journal.pone.0080858. ARTNe80858.
Imron, Jeffrey, B., Hale, P., Degnan, B.M., Degnan, S.M., 2007. Pleistocene isolation
and recent gene flow in Haliotis asinina, an Indo-Pacific vetigastropod with
limited dispersal capacity. Mol. Ecol. 16, 289–304, doi:10.1111/j.1365-
294X.2006.03141.
210 L. Tornabene et al. /Molecular Phylogenetics and Evolution 82 (2015) 200–210Karino, K., Arai, R., 2006. Effect of clutch size on male egg-fanning behavior and
hatching success in the goby, Eviota prasina (Klunzinger). J. Exp. Mar. Bio. Ecol.
334, 43–50.
Keith, P., Lord, C., 2011. Systematics of Sicydiinae. In: Patzner, R.A., Van Tassel, J.L.,
Kovacic, M., Kapoor, B.G. (Eds.), The Biology of Gobies. Science Publishers,
Enfield, NH, pp. 119–128.
Kool, J.T., Paris, C.B., Barber, P.H., Cowen, R.K., 2011. Connectivity and the
development of population genetic structure in Indo-West Pacific coral reef
communities. Glob. Ecol. Biogeogr. 20, 695–706. http://dx.doi.org/10.1111/
j.1466-8238.2010.00637.x.
Ladd, H.S., 1960. Origin of the Pacific island molluscan fauna. Am. J. Sci. 258, 137–
150.
Landry, C., Geyer, L.B., Arakaki, Y., Uehara, T., Palumbi, S.R., 2003. Recent speciation
in the Indo-West Pacific: Rapid evolution of gamete recognition and sperm
morphology in cryptic species of sea urchin. Proc. R. Soc. Biol. Sci. Ser. B 270,
1839–1847.
Leis, J., Carson-Ewart, B. (Eds.), 2000. The larvae of Indo-Pacific coastal fishes: an
identification guide to marine fishes. Brill, Leiden, The Netherlands.
Lourie, S.A., Green, D.M., Vincent, A.C.J., 2005. Dispersal, habitat differences, and
comparative phylogeography of Southeast Asian seahorses (Syngnathidae:
Hippocampus). Mol. Ecol. 14, 1073–1094. http://dx.doi.org/10.1111/j.1365-
294X.2005.02464.x.
Luiz, O.J., Allen, A.P., Robertson, D.R., Floeter, S.R., Kulbicki, M., Vigliola, L., Becheler,
R., Madin, J.S., 2013. Adult and larval traits as determinants of geographic range
size among tropical reef fishes. Proc. Natl. Acad. Sci. U. S. A. 110, 16498–16502.
http://dx.doi.org/10.1073/pnas.1304074110.
Mace, G.M., 2004. The role of taxonomy in species conservation. Philos. Trans. R.
Soc. London B Biol. Sci. 359, 711–719.
Marshall, D.C., 2010. Cryptic failure of partitioned bayesian phylogenetic analyses:
lost in the land of long trees. Syst. Biol. 59, 108–117. http://dx.doi.org/10.1093/
sysbio/syp080.
McKenna, M.C., 1973. Sweepstakes, filters, corridors, Noah’s Arks, and beached
Viking funeral ships in palaeogeography. In: Tarling, D.H., Runcorn, S.K. (Eds.),
Implications of Continental Drift to the Earth Sciences. Academic Press, New
York, pp. 295–308.
Mironov, 2006. Centers of marine fauna redistribution. Entomol. Rev. 86, S32–S44.
Mora, C., Chittaro, P.M., Sale, P.F., Kritzer, J.P., Ludsin, S.A., 2003. Patterns and
processes in reef fish diversity. Nature 421, 933–936. http://dx.doi.org/10.1038/
Nature01393.
Mora, C., Treml, E.A., Roberts, J., Crosby, K., Roy, D., Tittensor, D.P., 2012. High
connectivity among habitats precludes the relationship between dispersal and
range size in tropical reef fishes. Ecography (Cop.) 35, 89–96. http://dx.doi.org/
10.1111/j.1600-0587.2011.06874.x.
Munday, P.L., 2004a. Habitat loss, resource specialization, and extinction on coral
reefs. Glob. Chang. Biol. 10, 1642–1647. http://dx.doi.org/10.1111/j.1365-
2486.2004.00839.x.
Munday, P.L., 2004b. Competitive coexistence of coral-dwelling fishes; the lottery
hypothesis revisited. Ecology 85, 623–628.
Munday, P.L., Jones, G.P., Caley, M.J., 2001. Interspecific competition and coexistence
in a guild of coral-dwelling fishes. Ecology 82, 2177–2189, doi:10.1890/0012-
9658(2001)082[2177:Icacia]2.0.Co;2.
Munday, P.L., van Herwerden, L., Dudgeon, C.L., 2004. Evidence for sympatric
speciation by host shift in the sea. Curr. Biol. 14, 1498–1504. http://dx.doi.org/
10.1016/j.cub.2004.08.029.
Murdy, E.O., 2011a. Systematics of Amblyopinae. In: Patzner, R.A., Van Tassel, J.L.,
Kovacic, M., Kapoor, B.G. (Eds.), The Biology of Gobies. Science Publishes,
Enfield, NH, pp. 107–118.
Murdy, E.O., 2011b. Systematics of Oxudercinae. In: Patzner, R.A., Van Tassel, J.L.,
Kovacic, M., Kapoor, B.G. (Eds.), The Biology of Gobies. Science Publishers,
Enfield, NH, pp. 99–106.
Patzner, R.A., Van Tassell, J.L., Kovacˇic´, M., Kapoor, B.G. (Eds.), 2011. The Biology of
Gobies, first ed. Science Publishers; Distributed by CRC Press, Enfield, NH Boca
Raton, FL.
Pellissier, L., Leprieur, F., Parravicini, V., Cowman, P.F., Kulbicki, M., Litsios, G., Olsen,
S.M., Wisz, M.S., Bellwood, D.R., Mouillot, D., 2014. Quaternary coral reef refugia
preserved fish diversity. Science 344 (80), 1016–1019.
Perrin, C., Borsa, P., 2001. Mitochondrial DNA analysis of the geographic structure of
Indian scad mackerel in the Indo-Malay archipelago. J. Fish Biol. 59, 1421–1426.
Pezold, F., 2011. Systematics of the family Gobionellidae. In: Patzner, R.A., Van
Tassell, J.L., Kovacic, M., Kapoor, B.G. (Eds.), The Biology of Gobies. CRC Press,
Oxfod and IBH Publishing Co., New Delhi.
Posada, D., 2008. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25,
1253–1256. http://dx.doi.org/10.1093/molbev/msn083, msn083 [pii].
Rambaut, A., Drummond, A.J., 2007. Tracer Version 1.5. <http://tree.bio.ed.ac.uk/
software/tracer/>.
Ratnasingham, S., Hebert, P.D.N., 2013. A DNA-based registry for all animal apecies:
the Barcode Index Number (BIN) System. PLoS ONE 8 (3), e66213. http://
dx.doi.org/10.1371/journal.pone.0066213.
Riginos, C., Victor, B.C., 2001. Larval spatial distributions and other early life-history
characteristics predict genetic differentiation in eastern Pacific blennioid fishes.
Proc. R. Soc. London Ser. B-Biological Sci. 268, 1931–1936.
Remington, C.L., 1968. Suture-zones of hybrid interaction between recently joined
biotas. Evol. Biol. 2, 321–428.Renema, W., Bellwood, D.R., Braga, J.C., Bromfield, K., Hall, R., Johnson, K.G., Lunt, P.,
Meyer, C.P., McMonagle, L.B., Morley, R.J., O’Dea, A., Todd, J.A., Wesselingh, F.P.,
Wilson, M.E.J., Pandolfi, J.M., 2008. Hopping hotspots: global shifts in marine
biodiversity. Science 321 (80), 654–657. http://dx.doi.org/10.1126/
science.1155674.
Rocha, L.A., Bowen, B.W., 2008. Speciation in coral-reef fishes. J. Fish Biol. 72, 1101–
1121.
Sale, P.F., 1993. The Ecology of Fishes on Coral Reefs. Academic Press, San Diego, CA.
Sale, P.F., 2002. Coral Reef Fishes: Dynamics and Diversity in a Complex Ecosystem.
Santini, F., Winterbottom, R., 2002. Historical biogeography of Indo-western Pacific
coral reef biota: is the Indonesian region a centre of origin? J. Biogeogr. 29, 189–
205.
Schiller, A., Oke, P.R., Brassington, G., Entel, M., Fiedler, R., Griffin, D.A., Mansbridge,
J.V., 2008. Eddy-resolving ocean circulation in the Asian-Australian region
inferred from an ocean reanalysis effort. Prog. Oceanogr. 76, 334–365. http://
dx.doi.org/10.1016/j.pocean.2008.01.003.
Sekiya, Y., Karino, K., 2004. Female mate preference in goby Eviota prasina: do
secondary sexual traits influence female choice? Zool. Sci. 21, 859–863.
Simpson, G.G., 1977. Too many lines; the limits of the Oriental and Australian
Zoogeographic regions. Proc. Am. Philos. Soc. 121, 107–120.
Sotka, E.E., 2012. Natural selection, larval dispersal, and the geography of phenotype
in the sea. Integr. Comp. Biol. 52, 538–545.
Stehli, F.G., Wells, J.W., 1971. Diversity and age patterns in hermatypic corals. Syst.
Biol. 20, 115–126.
Sunobe, T., 1998. Reproductive behavior in six species of Eviota (Gobiidae) in
aquaria. Ichthyol. Res. 45, 409–412.
Sunobe, T., Nakazono, 1999. Alternative mating tacitics in the gobiid fish, Eviota
prasina. Ichthyol. Res. 46, 212–215.
Sunobe, T., Nakazono, A., 1987. Embryonic development and larvae of genus Eviota
(Pisces: Gobiidae) I. Evota abax and E. storthynx. J. Fac. Agric. Kyushu Univ. 31,
287–295.
Thacker, C.E., 2003. Molecular phylogeny of the gobioid fishes (Teleostei:
Perciformes: Gobioidei). Mol. Phylogenet. Evol. 26, 354–368.
Thacker, C.E., 2011. Systematics of Gobiidae. In: Patzner, R.A., Van Tassel, J.L.,
Kovacic, M., Kapoor, B.G. (Eds.), The Biology of Gobies. Science Publishers,
Enfield, NH, pp. 129–138.
Thacker, C.E., Roje, D.M., 2011. Phylogeny of Gobiidae and identification of gobiid
lineages. Syst. Biodivers. 9, 329–347, doi:10(1080/14772000).2011.629011.
Timm, J., Figiel, M., Kochzius, M., 2008. Contrasting patterns in species boundaries
and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre
of marine biodiversity. Mol. Phylogenet. Evol. 49, 268–276. http://dx.doi.org/
10.1016/j.ympev.2008.04.024.
Tornabene, L., Ahmadia, G.N., Berumen, M.L., Smith, D.J., Jompa, J., Pezold, F., 2013a.
Evolution of microhabitat association and morphology in a diverse group of
cryptobenthic coral reef fishes (Teleostei: Gobiidae: Eviota). Mol. Phylogenet.
Evol. 66, 391–400.
Tornabene, L., Ahmadia, G.N., Williams, J.T., 2013b. Four new species of dwarfgobies
(Teleostei: Gobiidae: Eviota) from the Austral, Gambier, Marquesas and Society
Archipelagos, French Polynesia. Syst. Biodivers. 11, 363–380, doi:10(1080/
14772000).2013.819822.
Veron, J.E.N., 1995. Corals in Space and Time. Cornell University Press, Ithaca.
Veron, J.E.N., Devantier, L.M., Turak, E., Green, A., Kininmonth, S., Stafford-Smith, M.,
Peterson, N., 2009. Delineating the coral triangle. Galaxea, J. Coral Reef Stud. 11,
91–100.
Victor, B.C., Wellington, G.M., 2000. Endemism and the pelagic larval duration of
reef fishes in the eastern Pacific Ocean. Mar. Ecol. Prog. Ser. 205, 241–248.
http://dx.doi.org/10.3354/Meps205241.
Voris, H.K., 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river
systems and time durations. J. Biogeogr. 27, 1153–1167.
Ward, R.D., Zemlak, T.S., Innes, B.H., Last, P.R., Hebert, P.D.N., 2005. DNA
barcoding Australia’s fish species. Philos. Trans. R. Soc. London B Biol. Sci.
360, 1847–1857.
Weersing, K., Toonen, R.J., 2009. Population genetics, larval dispersal, and
connectivity in marine systems. Mar. Ecol. Prog. Ser. 393, 1–12. http://
dx.doi.org/10.3354/Meps08287.
Wellington, G.M., Victor, B.C., 1989. Planktonic larval duration of one hundred
species of Pacfiic and Atlantic damselfishes (Pomacentridae). Mar. Biol. 101,
557–567.
Winterbottom, R., Hanner, R.H., Burridge, M., Zur, M., 2014. A cornucopia of
cryptic species - a DNA barcode analysis of the gobiid fish genus Trimma
(Percomorpha, Gobiiformes). Zookeys 79–111. http://dx.doi.org/10.3897/
zookeys.381.6445.
Woodland, D.J., 1983. Zoogeography of the Siganidae (Pisces): an interpreation of
distribution and richness patterns. Bull. Mar. Sci. 33.
Woodson, C.B., McManus, M.A., 2007. Foraging behavior can influence dispersal of
marine organisms. Limnol. Oceanogr. 52, 2701–2709. http://dx.doi.org/
10.4319/lo.2007.52.6.2701.
Wray, C.G., Landman, N.H., Bonacum, J., 1995. Genetic-divergence and geographic
diversification in Nautilus. Paleobiology 21, 220–228.
Yamada, T., Sugiyama, T., Tamaki, N., Kawakita, A., Kato, M., 2009. Adaptive
radiation of gobies in the interstitial habitats of gravel beaches accompanied by
body elongation and excessive vertebral segmentation. BMC Evol. Biol. 9. http://
dx.doi.org/10.1186/1471-2148-9-145. Artn 145.