ArticlePDF Available

Allopatric divergence and speciation in coral reef fish: The three-spot dascyllus, Dascyllus trimaculatus, species complex


Abstract and Figures

Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex includes four recognized species and four main color morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a noncongruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.
Content may be subject to copyright.
Matthieu Leray,1,2Ricardo Beldade,1Sally J. Holbrook,3Russell J. Schmitt,3Serge Planes,2
and Giacomo Bernardi1,4
1Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California 95060
2UMR 5244, CNRS-EPHE-UPVD, Centre de Biologie et d’Ecologie Tropicale et M´
editerran ´
eenne, Universit ´
e de Perpignan,
66860 Perpignan Cedex, France
3Coastal Research Center, Marine Science Institute, and Department of Ecology, Evolution, and Marine Biology, University
of California Santa Barbara, Santa Barbara, California 93106
Received July 30, 2009
Accepted November 5, 2009
Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in
marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to
evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex includes four recognized species and four main color
morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a noncongruence between
color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three
clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear
microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of
seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent
lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative
mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that
primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.
KEY WORDS: Allopatry, coral reef fish diversity, microsatellites, phylogeny, speciation.
Species level phylogenies provide indirect records of the evo-
lutionary history of speciation. A link between phylogeny and
distribution range can then be used to infer the most parsimo-
nious geographical mode of speciation (Barraclough and Vogler
2000; Barraclough and Nee 2001) under two major assumptions:
(1) the current distribution range of species reflects their mode of
diversification and (2) the gene tree is congruent with the species
tree as substantiated by multiple independent molecular markers.
In addition, environmental characteristics, life-history traits, and
biological interactions gained from field observations and exper-
iments can inform the processes that drive diversification.
In the context of understanding speciation mechanisms,
as described above, marine systems challenge conventional al-
lopatric speciation. The paucity of physical barriers combined
with the potential for long-range dispersal of early life-history
stages makes the study of speciation in marine organisms a unique
2010 The Author(s).
challenge. This is particularly true for coral reef organisms, where
extreme diversity seems to coincide with highly connected envi-
ronments. Additional factors also play important roles: (1) Dis-
persal of planktotrophic larvae increase potential for connectivity.
Most coral reef fish have a bipartite life cycle (Leis 1991) with
sedentary adults and pelagic larvae that spend from a few days
to several months in the water column (Wellington and Victor
1989). Although biotic (Planes 1993; Riginos and Victor 2001;
Ovenden et al. 2004) and abiotic (Frith et al. 1986; Shulman and
Bermingham 1995; Lessios et al. 1999) processes drive exchanges
between patchily distributed reefs, evidence of current and histor-
ical long distance dispersion and colonization have already been
documented for coral reef fish (Lessios et al. 1998). A number
of taxa in various families have widespread ranges of distribution
coupled with genetic homogeneity (Randall 1998; McMillan et al.
1999; Planes and Fauvelot 2002; Horne et al. 2008). (2) Besides
the permanent hard continental barriers that have led to separa-
tion between ocean basins (e.g., the rise of the Isthmus of Panama
between the Atlantic and Pacific Oceans, Lessios 2008), only a
few barriers to coral reef fish dispersal such as oceanic currents
(Lessios et al. 1999; Barber et al. 2000), open-ocean distances
(Vermeij 1987; Lessios and Robertson 2006), and freshwater out-
flows (Rocha 2004; Floeter et al. 2008; Beldade et al. 2009) have
been identified as important factors in marine speciation (but see
Connolly et al. 2003 for critical assessment). (3) Barriers that
are currently recognized have changed over time. Environmental
variations such as sea level fluctuations related to climatic cycles
are also likely to have impacted the effectiveness of these barriers
(Fauvelot et al. 2003; Rocha et al. 2005a; Bowen et al. 2006;
Robertson et al. 2006; Renema et al. 2008).
Due to all the factors mentioned above, dispersal abilities
probably play only a modest role in allopatric speciation in the
marine realm (Mayr 1954; Hellberg 1998). As a result, the con-
cept of ecological speciation, already recognized in the terrestrial
environment, was suggested as a potential explanation for coral
reef fish diversity (Streelman et al. 2002; Rocha et al. 2005b;
Choat 2006).
Selective pressure on color polymorphisms, so striking in
coral reef fish, may result from ecological factors such as com-
munication, competition, camouflage, habitat differences, and
mating behavior (DeMartini and Donaldson 1996; Crook 1997;
Marshall et al. 2003; Munday et al. 2003; Moland and Jones 2004).
Although the role of color variation in speciation processes has
not yet been very well established, Planes and Doherty (1997) and
Puebla et al. (2007) demonstrated the potential for this phenotypic
trait to drive diversification via assortative mating (prezygotic iso-
lation). By contrast, Rocha et al. (2005b) found that ecological
speciation was mediated by differential temperature between ad-
jacent habitats and Munday et al. (2004) demonstrated the key
role of competition for limited resources in host shift for sym-
patric species of Gobiodon. Taken together, these studies suggest
a strong influence of ecological pressure in speciation processes
in coral reef fish.
In this study, we evaluated the geographic mechanisms of
speciation in a group of coral reef fish, the three-spot dascyl-
lus (Dascyllus trimaculatus) species complex where geographic
distance, allopatry, coloration patterns, and ecological special-
ization are all encountered in differing degrees of intensity. To
that end, we combined phylogenetic data (mitochondrial control
region sequences and nuclear microsatellite genetic partitioning
investigation), and range distributions to infer species boundaries
and modes of speciation, as well as life-history traits and environ-
mental characteristics to evaluate the role of ecological pressure
on speciation.
Our results underscore the high resolution of nuclear mi-
crosatellites for investigations of macroevolutionary phenomena
of speciation and reveal that in this complex, despite strong disper-
sal abilities, geographic isolation appears to be the key mechanism
underlying initial speciation.
Materials and Methods
The complex comprises four species, D. trimaculatus (R¨
1828–30), D. albisella (Gill 1862), D. strasburgi (Klausewitz
1960), and D. auripinnis (Randall and Randall 2001). Dascyllus
trimaculatus, a black fish with three small white spots, has the
widest range of distribution, from the East African Coast to the
Central Pacific, whereas the three remaining species have much
more restricted distributions. Dascyllus albisella, a black fish with
white flanks is endemic to Hawaii, D. strasburgi is a grayish fish
that is restricted to the Marquesas Islands and the recently de-
scribed D. auripinnis has yellow fins, a yellow lower body and is
only found in the Line and Phoenix Islands (Fig. 1). All species
have a nonoverlapping distribution with the exception of D. aurip-
innis that shows a parapatric distribution to D. trimaculatus with
a small sympatric area in the Northern Cook Islands (Randall and
Randall 2001; H. Debelius, pers. comm.). Some small local vari-
ation in morphology have been observed. For example, in Fiji,
fish that are described as D. trimaculatus have some yellow on
their body, potentially due to the presence of turbid waters (Allen
1991; Randall and Randall 2001). In Oman, D. trimaculatus tends
to be brownish (G. Bernardi, pers. obs.). In Johnston Atoll, a
few individuals, recorded as D. albisella, have yellow fin tips
(E. DeMartini, pers. comm.). Molecular studies revealed that the
four species of the D. trimaculatus complex, which display only
small morphometric and meristic differences, have only recently
diverged from the D. reticulatus complex (3.9 million years ago—
Pleistocene) (Bernardi and Crane 1999; McCafferty et al. 2002).
The four species present a mating system that involves conspecific
Figure 1. Distribution range of the four species in the Dascyllus trimaculatus species complex. Each species is labeled with a color code
and symbol, D.trimaculatus (circle), D. albisella (triangle), D. auripinnis (square), and D. strasburgi (star). Sampling localities are shown
with their acronyms as described in Table 1. NC denotes the location of the northern Cook Islands.
recognition using sound (Lobel and Mann 1995) followed by ex-
ternal fertilization of benthic eggs. After three or four days (Fricke
and Holzberg 1974; Thresher 1984), larvae hatch and disperse in
the water column for 22–26 days (Wellington and Victor 1989).
Settlement substrata vary according to species. Dascyllus trimacu-
latus,D. strasburgi,andD. auripinnis recruit mainly on anemones
where they remain protected for a few months whereas D. al-
bisella use branching corals (Fautin and Allen 1992; Holbrook and
Schmitt 1997; Ramon et al. 2008). On very rare occasions, how-
ever, D. trimaculatus have been observed to settle on corals, both
in the Indian Ocean (Oman) and the Pacific (Moorea) (pers. obs.).
Recent divergence, unbalanced distribution range, extensive
dispersal capabilities, small morphological differences, strong
habitat association, and specific biological interaction, that char-
acterize the members of the D. trimaculatus complex, make its
members excellent candidates for studying speciation processes in
coral reef fish. Several phylogenetic studies have already focused
on the D. trimaculatus complex describing relationships among
the species (Bernardi and Crane 1999; Bernardi et al. 2001, 2002,
2003; McCafferty et al. 2002). A study based on mitochondrial
control region sequences found, as expected, that individuals of
D. albisella and D. strasburgi were reciprocally monophyletic
(Bernardi et al. 2002). In contrast, despite their morphological
similarity throughout the Indo-Pacific, D. trimaculatus individu-
als clustered into three mitochondrial clades that were separated
geographically. The Indian Ocean clade was considered as the
ancestral population within the complex, the two other clades
corresponded to the Tuamotu/Society Islands of French Poly-
nesia and the “West-Central Pacific.” Mitochondrial control re-
gions also clustered D. auripinnis individuals together with D.
trimaculatus West-Central Pacific individuals, raising doubts re-
garding the validity of D. auripinnis as a species. In addition,
Bernardi et al. (2003) found that 4% of D. trimaculatus individu-
als from Polynesia (termed OC3 haplotypes) also clustered with
West-Central Pacific individuals (Fig. 2). Thus, although much
information has already been gathered on the three-spot dascyllus
Figure 2. Summarized phylogenetic relationship between 563 in-
dividuals sampled in the D. trimaculatus species complex based
on mitochondrial control regions using the Maximum Likelihood
method. Numbers indicate bootstrap support (100 replicates). Only
nodes and branches supported with bootstrap values superior to
50 are presented. Size of pie charts is proportional to the number
of individuals. A full tree with all samples is provided in Supporting
species complex, many questions regarding speciation processes
and species relationships remained unanswered.
To study the early speciation processes in the recently diverged D.
trimaculatus species complex, 563 specimens were collected over
the complete distribution range of the species (Table 1, Fig. 1).
Individuals were collected using hand spears while free or scuba
Tab l e 1 . Number of sampled individuals per location used for mi-
tochondrial control region (Dloop) and microsatellites (SSR) phy-
logenetic analysis. Numbers in parentheses are the new samples
that were sequenced. The sample grouping was based on (1)
the mitochondrial DNA genetic partitioning described in Bernardi
et al. (2002) and (2) the described morphological species. Localities’
acronyms are used on the map (Fig. 1).
Sample size
Species Group locality Acronym
Dloop SSR
D. trimaculatus Indian Ocean 42 44
Eilat EIL 7 0
Zanzibar ZAN 6 0
Mayotte MAY 11 0
Oman OMA 12 44
Seychelles SEY 3 0
Cocos Keeling CKE 3 0
French Polynesia 283 71
Moorea, Maiao, MOO 277 60
Rangiroa RM 6 11
West Central Pacific 76 48
Japan JAP 9 9
Vietnam NAM 11 9
Indonesia MAN 10 0
Palau PAL 4 3
Philippines CAM 13 0
Marshall Island MAR 5 0
Fiji FIJ 10 15
Wallis WAL 8 9
Great Barrier Reef GBR 3 3
D. auripinnis Line\Phoenix Is 24 49
Christmas Island XMA 20 18
Kingman reef KIN 2 11
Baker Island BAK 2 10
D. strasburgi Marquesas MRQ 33 44
D. albisella Hawai +Johnston 105 60
Hawai, Oahu HAW 21 0
Kure, PH, Midway KUR 49 23
French Frigate FFS 25 13
Johnston atoll JOH 10 24
Total 563 316
diving. Immediately after collection, fin clips were placed in 95%
ethanol and stored at ambient temperature in the field, and then
at 4C in the laboratory. Total genomic DNA was prepared from
20 mg of fin tissue by proteinase K digestion in lysis buffer
(10 mM Tris, 400 mM NaCl, 2 mM EDTA, 1% SDS) overnight at
55C. This was followed by purification using phenol/chloroform
extractions and alcohol precipitation (Sambrook et al. 1989).
Previously published sequences from the mitochondrial control
region (Dloop) were included in this study (Bernardi and Crane
1999; Bernardi et al. 2001, 2002, 2003; Ramon et al. 2008),
together with an additional 126 new samples (Table 1). These
samples represent the entire distribution of the species complex
except for the region comprised between western Australia and
Cocos-Keeling. Using microsatellites markers allowed to com-
pare nuclear genetic partitioning within the D.trimaculatus com-
plex with the genetic partitioning observed using mitochondrial
DNA sequences and reveal patterns and processes such as incom-
plete lineage sorting, hybridization, and introgression. Therefore,
the selection of samples used for microsatellite data analysis was
based on described morphological species and on the mitochon-
drial clades. At least 48 individuals per clade were randomly
selected for screening and all the D. auripinnis available (49 in-
dividuals) were also genotyped. Within the West-Central Pacific
and Hawaiian archipelago, where particular processes of interest
seem to take place based on previous mitochondrial DNA anal-
ysis, the selection of samples included a few individuals from
different locations chosen to integrate all the genetic variability.
Finally, all Polynesian samples that cluster with the West-Central
Pacific mitochondrial clade as previously described (OC3 samples
of Bernardi et al. 2003) were genotyped.
Sequence data of 366 bp for the mitochondrial control region
were amplified for 126 new samples using previously detailed
conditions (Bernardi et al. 2001) and primers (Lee et al. 1995).
Mitochondrial sequences were aligned using Bioedit (Hall 1999).
For microsatellite analyses, we tested 52 loci isolated from a
D. trimaculatus individual sampled in Moorea (French Polyne-
sia). Of these, 13 successfully amplified all samples and were
found to be highly polymorphic. Leray et al. (2009) provide a full
description of amplification procedures and microsatellite char-
acteristics. GENEMAPPER3.7 Applied Biosystems (Foster City,
CA) was used for scoring microsatellite genotypes.
To evaluate phylogenetic relationships based on mitochondrial
control regions, 10 independent maximum likelihood (ML)
replicates were computed using the program GARLI (Zwickl
2006) that uses a genetic algorithm approach to simultaneously
find the topology, branch lengths and model parameters that max-
imize the likelihood of the tree. Out of the 10 best trees, the one
with the highest likelihood overall was selected. Branch support
on the resulting best tree was assessed via 100 bootstraps imple-
mented by GARLI. In addition to using a ML approach, pairwise
genetic distances were estimated using Arlequin 3.0 (Excoffier
et al. 2005) to quantify the divergence between previously iden-
tified groups. To infer which model of nucleotide substitution
best fit the data, Modeltest (Posada and Crandall 1998) was used.
To account for differences between gene divergence and popula-
tion divergence due to the presence of ancestral polymorphisms
(Edwards and Beerli 2000), average pairwise distances between
populations were the mean number of pairwise differences be-
tween two populations minus the average distance between in-
dividual within those populations. Significance was tested with
10,000 replicates and a sequential Bonferroni correction for the
level of significance was used.
Samples were divided into groups previously identified based on
the ML phylogenetic tree. Haplotype diversity, nucleotide diver-
sity, and mean number of pairwise differences were calculated
with DNAsp (Rozas et al. 2003).
Based on predefined groups (mitochondrial clades and morpho-
logical species), the number of alleles, observed and expected
heterozygosities were computed per locus using Fstat (Goudet
1995). Linkage disequilibrium between loci and deviations from
Hardy–Weinberg equilibrium (HWE) were also tested for each
locus and group. Significance was tested with 10,000 replicates.
Levels of significance for multiple comparisons of loci across
samples were adjusted using a standard Bonferroni correction
(Rice 1989). Departures from HWE can be caused by inbreeding,
Wahlund effect, or technical causes such as null alleles, misscor-
ing due to stuttering, and allelic dropout. The proportion of null
alleles that could influence the genetic signal was evaluated using
the algorithm implemented in FREENA (Dempster et al. 1977;
Chapuis and Estoup 2007).
To explore and decompose the genetic variability into gene pools
without providing prior information on the geographical origin
of the samples, a Bayesian clustering approach implemented in
Structure 2.2 was used (Pritchard et al. 2000). The program si-
multaneously defines clusters and assigns individual multilocus
genotypes to the defined clusters. Allele frequencies were pre-
sumed uncorrelated and null alleles were coded as recessive to
take into account the presence of null alleles in the dataset (Falush
et al. 2007). The most likely number of clusters in the dataset was
identified based on posterior probabilities and 10 runs were im-
plemented in Structure 2.2 to test for robustness of the results
following Pritchard et al. (2000).
Historical demography parameters were examined for groups
based on genetic partitioning and morphology to evaluate pos-
sible events of population fluctuation based on a coalescent ap-
proach. Estimates of (=2Nμ,whereμis the mutation rate)
were made for each genetic group as well as the whole species
complex. The parameter was estimated under two conditions:
an unconstrained exponential growth parameter and an assump-
tion of constant N (g=0). We used FLUCTUATE (Kuhner et al.
1998) to estimate the ML of the parameters and g(the ex-
ponential growth parameter in units μ1). Seeds for all analyses
were generated randomly. Analyses were repeated 10 times per
region to ensure stability of parameters estimates. Final analyses
of each dataset employed 10 short Monte Carlo chains of 200 steps
each and five long chains of length 20,000, with a sample incre-
ment of 20. Exchanges and range expansions (immigration) be-
tween groups were investigated with MIGRATE 2.0 (Beerli and
Felsenstein 2001; Beerli 2003) to identify reproductively isolated
entities, quantify gene flow, and evaluate the direction of gene flow
between genetic partitions and morphological species. Multiple
runs were computed with progressively increasing constraints and
length of the analysis until reaching consistent results. The final
parameters used 10 short Monte Carlo chains with 5000 recorded
genealogies and six long chains with 50,000 recorded genealo-
gies. To explore more genealogies, a method that allows swapping
between chains running (in parallel) at different temperatures was
implemented, the “colder” chain exploring less genealogy space
than the “hotter” one. Again 10 replicates were realized to ensure
the reproducibility and stability of the estimation.
The time of coalescence was estimated by assuming that
coalescence was reached when the population size was reduced
to 1% of its present day value, following Wares and Cunningham
(2001). To estimate coalescence time, we used the mutation rate
(μ=substitutions per site per generation) that was determined
for the mitochondrial control region for other damselfish species,
the Panama Trans-Isthmian geminates Chromis atrilobata and C.
multilineata (Domingues et al. 2005).
Phylogenetic results
Samples partitioned into five well-supported major clades (Fig. 2).
Although the dataset used here was more extensive, results were
consistent with previously published data (Bernardi et al. 2002,
2003). The Indo-Pacific separated into five distinct geograph-
ical areas: the Indian Ocean (clade 1), the West-Central Pacific
(clade 2) which stretches from Japan to Fiji and Wallis to Vietnam,
Society and Tuamotu islands, southern French Polynesia (clade 3),
the Marquesas Islands, northern French Polynesia (clade 4), and
the Hawaiian archipelago (clade 5) including Johnston atoll.
Dascyllus strasburgi and D. albisella each segregated into
monophyletic clades, corresponding to Marquesas (clade 4) and
Hawaii (clade 5) samples, respectively. The West-Central Pacific
group (clade 2) included D.trimaculatus from West-Central Pa-
cific locales, a small number of D.trimaculatus from Society and
Tuamotu islands (OC3 samples), and all D.auripinnis individ-
uals. The genetic partitioning across the rest of the Indo-Pacific
did not match with taxonomically described species. Indeed, the
wide-ranging D. trimaculatus separated into three deeply diver-
gent groups (clade 1, 2, and 3, Fig. 2). Moreover, within the
West-Central Pacific, where the two species D. auripinnis and
D. trimaculatus occur, all sampled individuals grouped in a sin-
gle well-supported clade (clade 2). Within clade 2, two subclades
(weakly supported and not shown) were found, suggesting poten-
tial population structure within this clade. D.auripinnis individ-
uals were found in both subclades.
Genetic diversity and historical demography in the
D. trimaculatus complex
Genetic diversity reflected the historical demography of the dif-
ferent genetic entities of the D.trimaculatus species complex.
Tab l e 2. Genetic characteristics of Dascyllus trimaculatus clades based on the mitochondrial control region. Genetic diversity and
coalescence data are presented, with numbers in parentheses being standard deviations. Estimated coalescence times are given in
millions of years (My).
Clade 1 Clade 2 Clade 3 Clade 4 Clade 5
Indian Ocean Pacific Rim Tuam\Soc Marquesas Hawaii
Genetic diversity:
Number of sequences 40 142 267 37 105
Number of segregating sites 86 69 99 57 44
Haplotype diversity 0.997 0.972 0.986 0.974 0.933
(0.006) (0.007) (0.002) (0.018) (0.016)
Nucleotide diversity 0.031 0.013 0.020 0.019 0.020
(0.002) (0.001) (0.001) (0.003) (0.001)
Mean number of nucleotide 10.86 4.41 5.46 6.67 4.43
differences (4.9) (2.17) (2.60) (3.13) (2.18)
Theta (variable) 0.281 0.230 0.827 0.085 0.203
(0.012) (0.017) (0.035) (0.002) (0.008)
Theta (constant) 2.716 1.264 2.518 0.173 0.731
(0.468) (0.355) (0.452) (0.035) (0.140)
g(growth) 267.17 329.08 154.07 144.38 244.65
(26.41) (33.31) (10.36) (29.59) (41.64)
Coalescence time (My) 0.19–0.21 0.15–0.17 0.32–0.36 0.34–0.39 0.20–0.23
Genetic diversity was highest in the Indian Ocean (Table 2). For
example, the mean number of nucleotide differences between
Indian Ocean haplotypes was twice that in all the other clades
(Table 2). Conversely, the genetic diversity of the West-Central
Pacific was the lowest despite the broad geographic origin of
the individuals: all West-Central Pacific samples (two described
species D. trimaculatus and D. auripinnis) and 25 samples from
Society and Tuamotu islands (OC3 samples).
Overall coalescence for the D.trimaculatus complex oc-
curred approximately between 560,000 and 630,000 years ago
(ya). Coalescence estimates are more recent for the Indian Ocean
(190,000–210,000 ya) than for the Pacific Ocean (470,000–
530,000 ya). In addition, coalescence estimates for each clade,
which ranged from 150,000 to 400,000 ya, were lower for the
West-Central Pacific clade than for Society +Tuamotu, Marque-
sas, and even Hawaii clades (Table 2).
Genetic partitioning based on nuclear microsatellites
Specific characteristics of the microsatellite data used here are
provided in Table S1. A partition of our samples in seven clusters
was found to best fit the observed microsatellite variability using
the clustering method (Fig. 3, and Table S2). All individuals from
the Indian Ocean, Hawaii, and the Marquesas Islands showed very
high levels of reassignment to their own cluster (average: 0.995).
Similarly, individuals from Society and Tuamotu islands were also
assigned to their own cluster (reassignment =0.996), including
the OC3 samples that in the mitochondrial dataset clustered with
Figure 3. Bayesian population assignment test based on 13 microsatellites loci. The seven clusters that partition the data are displayed
with different colors and mapped on the lower panel. Each vertical line represent one individual and its assignment likelihood to belong
to one of the cluster (Y scale) is shown by the color. Black vertical lines represent the limit between predefined groups. These are the five
mitochondrial clades, Indian Ocean (dark blue), Western Central Pacific (blue), Tuamotu +Society Islands (pale blue), Hawaii (green), and
Marquesas Islands (red). Within the Hawaiian Archipelago, Johnston Atoll +some French Frigate shoals individuals (dark green) separate
from other Hawaiian individuals (green). Within the Western Central Pacific, we have separated D. trimaculatus (blue) and D. auripinnis
(yellow). The arrow represents the increasing physical distance to D. auripinnis distribution range for D. trimaculatus individuals sampled
in the West-Central Pacific.
the West-Central Pacific haplotypes (Fig. 3). Within the Hawaii
cluster, samples were divided in two different subclusters. One
subcluster comprised all 20 sampled individuals from Johnston
Atoll (JOHN) and five samples from the northwestern Hawai-
ian island of French Frigate Shoals (FFS), and one subcluster
comprised all other remaining Hawaiian samples (this cluster in-
cluded samples both from the main island group and from the
Northwestern Hawaiian island of Kure, Table 1). West-Central
Pacific individuals presented a mosaic picture. Unlike the mito-
chondrial results, genotype assignment divided D. auripinnis and
D. trimaculatus in two clusters (Fig. 3). All D. auripinnis were
assigned to a single cluster, except one individual (collected in
Palmyra) that clustered with D. trimaculatus.
We specifically chose a suite of D. trimaculatus individuals
from the West-Central Pacific that would span a region with
varying distances to the contact zone between D. trimaculatus
and D. auripinnis. Of these 48 samples, 19 clustered with D.
auripinnis,andthepresenceofD. auripinnis genotypes occurred
in a decreasing proportion with increasing distance from the Line
Islands. Indeed, five of eight fish in Wallis and nine Fijian indi-
viduals of 15 displayed a D. auripinnis genotype. Although no
coloration pattern was available for the Wallis samples, samples
from Fiji displayed yellow anal and pelvic fins with streaks of or-
ange in the caudal fin and the spinous part of the dorsal fin (Allen
1991, pers. obs.). This color variant, intermediate between the
bright yellow D. auripinnis and the pure black D. trimaculatus, is
consistent with a mixed D. auripinnisD. trimaculatus genotype.
Mitochondrial molecular markers have extensively been used to
infer phylogenetic relationships and species boundaries. In the
case of the D.trimaculatus complex, nuclear markers were mostly
consistent with previously published results solely based on mi-
tochondrial markers. However, the use of highly variable mi-
crosatellites allowed for additional information that could not be
obtained with mitochondrial markers alone.
Nuclear and mitochondrial molecular markers were consis-
tent in genetically identifying the two species D. strasburgi and
D. albisella endemic to the Marquesas and Hawaii, respectively.
Within D. albisella, mitochondrial sequences put Johnston Atoll
individuals in a single cluster within the remaining Hawaiian
samples (Ramon et al. 2008), whereas nuclear microsatellites,
with more segregating power, grouped Johnston Atoll individ-
uals, with five samples collected at FFS (Northwestern Hawai-
ian islands) and separated them from the remaining Hawaiian
individuals. Based on the mitochondrial control region, strong
population structure also exists (not presented) within the D.
albisella distribution range and warrants further investigation
(Ramon et al. 2008). Thus, overall, for both D. albisella and
D. strasburgi coloration patterns coincide with genetic partitions
even though a cryptic divergence appears to be occurring within
D. albisella.
In contrast, no simple relationship between color morphs and
genetic partitioning was found in D.trimaculatus (Bernardi et al.
2002). Although intraspecific morphological, behavioral, or eco-
logical variation have not been specifically investigated (Fishelson
1966; Fricke 1973), both mitochondrial and nuclear markers di-
vided the widespread D. trimaculatus into three deeply divergent
genetic partitions that separate the Indo-Pacific biogeographical
region in three distinct zones: Indian Ocean, West-Central Pacific,
and southern French Polynesia.
Although Indian Ocean and southern French Polynesian re-
gions seem well defined genetically, complex processes seem to
take place within the West-Central Pacific. Dascyllus auripinnis
had been considered a phenotypic variant of D. trimaculatus,and
only recently was described as a new species based on striking
different color patterns but “modest” morphometric differences
measured on a small number of samples (Randall and Randall
2001). These include a larger size, one fewer gill raker, and a
shorter average length of the paired fins. Although Bernardi et al.
(2002) could not determine whether D. auripinnis was a valid
species, an emerging species, or an isolated population of D. tri-
maculatus, based on mitochondrial DNA sequences, the combina-
tion of both nuclear and mitochondrial DNA in the present dataset
provided new insights in the geographic dynamic of introgression
in the West-Central Pacific, with a clinal zone between yellow and
black phenotypes. These results are consistent with “directional”
mating that, very likely, is driving introgression from D. aurip-
innis into D. trimaculatus through repeated backcrossing. In the
contact zone, where both species live in sympatry, at the north-
ern Cook Islands of Penhryn (Tongareva) and Suwarrow Islands
(Randall and Randall 2001), the yellow form is much more abun-
dant than the black form (H. Debelius, pers. comm.). Therefore,
if hybridization occurs at this location, rare chance events of in-
trogression of the yellow on the black fish are more likely than in
the opposite direction. Directional hybridization in species with
different abundances has also been observed in other coral reef
species (Yaakub et al. 2006). Although assortative mating based
on coloration pattern is likely to be present, as seen in other dam-
selfish (Planes et al. 2001; van Herwerden and Doherty 2006), a
direct examination of mating behavior in this area (sneak mating
was observed in Yaakub et al. 2006), coupled with paternity anal-
ysis, would allow a test of this hypothesis. An alternative to this
ecological explanation, that would require further testing, is that
a selective sweep may be responsible for the clinal distribution of
this haplotype (e.g., Galtier et al. 2000).
The use of multiple markers to infer the phylogeny of a very
recently diverged group such as the D.trimaculatus species com-
plex allows inferences about geographical modes of speciation
using comparison of present day distribution range between sister
species (Barraclough and Vogler 2000; McCafferty et al. 2002).
Recently allopatrically diverged taxa will likely have a nonover-
lapping distribution. Both D. albisella and D. strasburgi group
in monophyletic clades and cluster based on mitochondrial and
nuclear DNA. Bernardi et al. (2002) suggested that these species
emerged as the result of rare chance long-distance dispersal of
propagules, which once they settled in remote locations diverged
in allopatry as the result of low level of gene flow. The congru-
ent biogeographical and genetic patterns shared by several taxa
and independent genetic markers support the allopatric speciation
scenario in the Marquesas and Hawaiian archipelagos (Planes
and Fauvelot 2002). Although the Hawaii separation is mainly
explained by its geographical isolation, the separation between
the Marquesas and Society +Tuamotu islands is likely related
to the barrier of larval exchange created by the South Equatorial
(Marquesas) Countercurrent flowing from east to west in opposite
direction to the South Equatorial Current (Vermeij 1987; Planes
1993). Importantly, although such an oceanographic barrier may
potentially prevent any larval crossing, an interchange of a few
propagules may still be possible. In this case, however, the rela-
tive success of the recruits is probably the cause of the observed
At a smaller scale, emerging divergence was detected within
the D. albisella distribution range based on nuclear and mitochon-
drial DNA. Because all samples from the most remote location,
Johnston Atoll, group together, the phylogenetic structure is very
likely the outcome of reduced gene flow between islands within
the Hawaiian archipelago. Larval transport simulations described
in Ramon et al. (2008) also support this hypothesis. Indeed, sev-
eral dispersion corridors were identified between Johnston Atoll
and the Hawaiian archipelago but only for organisms with a
pelagic larval duration (PLD) longer than 40 days (Kobayashi
2006). However, although PLD is short in D. albisella (approxi-
mately 25 days), the presence of five samples from the Hawaiian
archipelago (FFS) in the Johnston Atoll microsatellite cluster sug-
gests long distance, but rare, larval exchange.
Allopatric speciation, as observed within D. trimaculatus,
match numerous previous genetic comparisons between West-
ern Pacific and Indian Ocean populations of marine invertebrates
and fish (e.g., Lacson and Clark 1995; McMillan and Palumbi
1995; Chenoweth et al. 1998; Duda and Palumbi 1999; Lessios
et al. 1999; Barber et al. 2000; Hobbs et al. 2009). The gener-
ally accepted explanation for this observed pattern in many taxa
is that sea level fluctuations culminating during the last Pleis-
tocene glaciation, exposed the Sunda shelf, between Malaysia
and northern Australia, thus limiting water exchange between the
two oceanic provinces. In the case of D. trimaculatus, the Pacific
and Indian Oceans cryptic species are genetically partitioned for
both mitochondrial DNA and nuclear markers, indicating a cur-
rent absence of gene flow, despite their adjacent distribution. The
contact zone, represented in our samples by the Cocos-Keeling
population, does not seem to indicate the presence of gene flow
in the region of secondary contact either. However, defining the
precise boundary between the Indian Ocean and West-Central
Pacific clades will require additional sampling in the Western
Australia–Cocos-Keeling area. Indeed, as for other genetic stud-
ies, it is likely that Western Australia samples may group with
West-Central Pacific samples rather than Indian Ocean ones,
and additional samples from Cocos-Keeling/Christmas Island
may reveal some level of gene exchange in the region (Hobbs
et al. 2009).
The second genetic boundary within the D. trimaculatus
species, between the Tuamotu\Society Islands and the West-
Central Pacific results from a different process. Mitochondrial
DNA indicates that few Polynesian (Society and Tuamotu Islands)
individuals (OC3) group with the West-Central Pacific clade,
whereas microsatellite analysis clustered those same individu-
als exclusively with the Polynesian group. Bernardi et al. (2002)
suggested that the presence of two distinct clades in Polynesia
was the result of larval transport from the West-Central Pacific
to South Polynesia. The present study, with new information pro-
vided by highly polymorphic microsatellites, is consistent with
such an ecological explanation combined with introgression. Al-
ternatively, it may also be indicative of incomplete lineage sorting
with a lack of resolution for the mitochondrial DNA. Using the
mitochondrial control region, genetic structure between South
Polynesia and West-Central Pacific has previously been observed
for the widespread Lutjanus kasmira (FST =0.12–0.25, S. Planes,
unpubl. data) and D.aruanus (FST =0.20–0.63, S. Planes, unpubl.
data), two species that have a comparable PLD to D. trimacula-
tus (Juncker et al. 2006). In comparison Acanthurus triostegus,
a species with a PLD twice as long, 60–70 days (Randall 1961;
Juncker et al. 2006), does not show significant genetic structure
(S. Planes, unpubl. data). Therefore, these patterns suggest that
highly restricted gene flow (which may be linked to the PLD or
to differential survival of the propagules) between the two geo-
graphical areas is consistent among different species, resulting in
a strong genetic break between South Polynesia and the West-
Central Pacific.
Within the West-Central Pacific, D. auripinnis and D. trimac-
ulatus have very different sizes of geographic range. The range
of D. auripinnis is less than 5% of the range of D. trimaculatus.
In itself, this may suggest peripatric speciation, as divergence of
a peripheral population in allopatry (Losos and Glor 2003). The
small overlapping range observed in the Northern Cook Islands
would also be an indication of a range shift. The hypothesis of
peripatric speciation assumes the temporary emergence of a bar-
rier that isolated a peripheral population in the Line and Phoenix
Islands. It is possible, however, that a parapatric ecological mode
of speciation (Wu and Ting 2004), or rapid sexual selection, may
have played a role in the divergence of this species.
Taken together, the geography of speciation in the D.trimac-
ulatus species complex points toward allopatric and parapatric
modes of speciation that led to the diversification of the com-
plex with no evidence for sympatric speciation given the overall
lack of overlap of the distribution range of the genetic partitions
(Fig. 4). Our data cannot distinguish whether the divergence was
due to natural selection, drift, or both. Besides simple geographic
partitioning, it is possible that additional ecological pressure on
speciation may also have played an important role in the diversi-
fication process (e.g., Hemmer-Hansen et al. 2007).
Rocha et al. (2005b) argued that the paradox of reef fish diversity
and their high dispersal capabilities may be solved by ecological
speciation. They demonstrated that differential selection would
operate in adjacent habitats with contrasting environments and
promote diversification. Habitat structure, climate, resource avail-
ability, predation, and competition are also thought to promote
divergent or disruptive selection leading to speciation via charac-
ter displacement (increasing morphological polymorphism), habi-
tat, or behavioral changes with or without geographic isolation
(Schluter 2000; Rundle and Nosil 2005). Munday et al. (2004)
presented a case of speciation via host shift in highly specialized
species of coral dwelling fish (genus Gobiodon), and proposed a
key role for competition in the divergence. In general, D. trimac-
ulatus remain protected from predators within anemones during
their juvenile phase (12 months). Yet, D. albisella, a species en-
demic to the Hawaiian Archipelago, where suitable anemones are
virtually absent, recruit on branching corals. Although species in
the D. trimaculatus complex most likely arose in allopatry, early
host shift may therefore have played an important role in their
divergence. Occasionally, D. trimaculatus settles on branching
corals or on Diadema urchins (G. Bernardi, pers. obs.), indicating
that ecological divergence in the D. trimaculatus species complex
is observed. An additional ecological signal may be uncovered
Figure 4. Schematic representation of potential modes of speciation in the Dascyllus trimaculatus species complex. The different sizes
of the arrow represent unbalanced levels of gene flow.
in the D. auripinnis–D. trimaculatus hybrid zone. Indeed, the
presence of sound production during mating, the variation in col-
oration patterns, and the imbalance between D. auripinnis versus
D. trimaculatus haplotypes and genotypes suggest that female
choice, assortative mating, and sexual selection may play an im-
portant, yet unexplored role in the genetic partitioning of individ-
The combined analysis of mitochondrial and nuclear markers
presented here provides interesting insights on early processes
of speciation in the D.trimaculatus species complex. Mitochon-
drial markers allowed us to broadly define five genetic clades that
served as the basis of understanding of the complex relationship
between established taxonomy, distribution, and coloration pat-
terns of the species. Highly variable nuclear markers refined this
view by settling alternative scenarios (the presence of unsorted
OC3 haplotypes in south Polynesian samples), and uncovering
subtle differences (Johnston Atoll individuals, D. trimaculatus
D. auripinnis hybrid zone). The study of speciation processes in
marine organisms is complex, yet a combination of extensive geo-
graphic sampling and use of different molecular markers provides
an opportunity to shed light on such intricate systems.
We would like to thank R. Galzin and C. Fauvelot for comments and
discussion, and Editor M. Hellberg and three anonymous reviewers for
comments. We would like to very much thank G. Lecaillon for providing
so many samples over the years from Mayotte, Philippines, and Vietnam.
We would also like to thank P. Nelson, D. R. Robertson, J. H. Choat,
and J. McIlwain for providing samples. NSF MCR LTER Award OCE
04-17412, and the Gordon and Betty Moore Foundation provided funding
for this research.
Allen, G. R. 1991. Damselfishes of the world. Mergus, Germany
Balloux, F., and N. Lugon-Moulin. 2002. The estimation of population differ-
entiation with microsatellite markers. Mol. Ecol. 11:155–165.
Balloux, F., H. Brunner, N. Lugon-Moulin, J. Hausser, and J. Goudet. 2000.
Microsatellites can be misleading: an empirical and simulation study.
Evolution 54:1414–1422.
Barber, P. H., S. R. Palumbi, M. V. Erdmann, and M. K. Moosa. 2000. Bio-
geography – A marine Wallace’s line? Nature 406:692–693.
Barraclough, T. G., and S. Nee. 2001. Phylogenetics and speciation. Trends
Ecol. Evol. 16:391–399.
Barraclough, T. G., and A. P. Vogler. 2000. Detecting the geographical pattern
of speciation from species-level phylogenies. Am. Nat. 155:419–434.
Beerli, P. 2003. Migrate—a maximum likelihood program to estimate
gene flow using the coalescent, Tallahassee/Seattle. http://evolution.
Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a
migration matrix and effective population sizes in n subpopulations by
using a coalescent approach. Proc. Natl. Acad. Sci. USA 98:4563–4568.
Beldade, R., J. B. Heiser, D. R. Robertson, J. L. Gasparini, S. Floeter, and
G. Bernardi. 2009. Historical biogeography and speciation in the Creole
wrasses (Labridae, Clepticus). Mar. Biol. 156:679–687.
Bernardi, G., and N. L. Crane. 1999. Molecular phylogeny of the humbug
damselfishes inferred from mtDNA sequences. J. Fish Biol. 54:1210–
Bernardi, G., S. J. Holbrook, and R. J. Schmitt. 2001. Gene flow at three
spatial scales in a coral reef fish, the three-spot dascyllus, Dascyllus
trimaculatus. Mar. Biol. 138:457–465.
Bernardi, G., S. J. Holbrook, R. J. Schmitt, N. L. Crane, and E. DeMartini.
2002. Species boundaries, populations and color morphs in the coral reef
three-spot damselfish (Dascyllus trimaculatus) species complex. Proc.
R. Soc. Lond. B 269:599–605.
Bernardi, G., S. J. Holbrook, R. J. Schmitt, and N. L. Crane. 2003. Genetic
evidence for two distinct clades in a French Polynesian population of
the coral reef three-spot damselfish Dascyllus trimaculatus. Mar. Biol.
Bowen, B. W., A. Muss, L. A. Rocha, and W. S. Grant. 2006. Shallow mtDNA
coalescence in atlantic pygmy angelfishes (Genus Centropyge) indicates
a recent invasion from the Indian Ocean. J. Hered. 97:1–12.
Chapuis, M. P., and A. Estoup. 2007. Microsatellite null alleles and estimation
of population differentiation. Mol. Biol. Evol. 24:621–631.
Chenoweth, S. F., J. M. Hughes, C. P. Keenan, and S. Lavery. 1998. When
oceans meet: a teleost shows secondary intergradation at an Indian-
Pacific interface. Proc. R. Soc. Lond. B 265:415–420.
Choat, J. H. 2006. Phylogeography and reef fishes: bringing ecology back into
the argument. J. Biogeogr. 33:967–968.
Connolly, S. R., D. R. Bellwood, and T. P. Hughes. 2003. Indo-Pacific bio-
diversity of coral reefs: deviations from a mid-domain model. Ecology
Crook, A. C. 1997. Colour patterns in a coral reef fish—Is background com-
plexity important? J. Exp. Mar. Biol. Ecol. 217:237–252.
DeMartini, E. E., and T. J. Donaldson. 1996. Color morph-habitat relations in
the arc-eye hawkfish Paracirrhites arcatus (Pisces: Cirrhitidae). Copeia
Dempster, A. P., N. M. Laird, and D. B. Rubin. 1977. Maximum likeli-
hood from incomplete data via the EM algorithm. J. R. Stat. Soc.
Domingues, V., G. Bucciarelli, V. C. Almada, and G. Bernardi. 2005. Historical
colonization and demography of the Mediterranean damselfish, Chromis
chromis. Mol. Ecol. 14:4051–4063.
Duda, T. F., and S. R. Palumbi. 1999. Population structure of the black tiger
prawn, Penaeus monodon, among western Indian Ocean and western
Pacific populations. Mar. Biol. 134:705–710.
Edwards, S. V., and P. Beerli. 2000. Perspective: gene divergence, population
divergence, and the variance in coalescence time in phylogeographic
studies. Evolution 54:1839–1854.
Excoffier, L. G. Laval, and S. Schneider.2005. Arlequin ver. 3.0: an integrated
software package for population genetics data analysis. Evolutionary
Bioinformatics Online 1:47–50.
Falush, D., M. Stephens, and J. K. Pritchard. 2007. Inference on population
structure using multilocus genotype date: dominant markers and null
alleles. Mol. Ecol. Notes 7:574–578.
Fautin, D. G., and G. R. Allen. 1992. Field guide to the anemone fishes and
their host anemones. Western Australian Museum, Perth.
Fauvelot, C., G. Bernardi, and S. Planes. 2003. Reductions in the mitochondrial
DNA diversity of coral reef fish provide evidence of population bottle-
necks resulting from Holocene sea-level change. Evolution 57:1571–
Fishelson, L. 1966. Observations on the biology and behaviour of Red Sea
coral fishes. Contribution to the knowledge of the Red Sea, No. 30.
Deep-Sea Res. 13:322.
Floeter, S. R., L. A. Rocha, D. R. Robertson, J. C. Joyeux, W. Smith-Vaniz, P.
Wirtz, A. J. Edwards, J. P. Barreiros, C. E. L. Ferreira, J. L. Gasparini,
et al. 2008. Atlantic reef fish biogeography and evolution. J. Biogeogr.
Fricke, H. W. 1973. Ecology and social behavior of the coral reef fish Dascyllus
trimaculatus Pisces Pomacentridae. Z. Tierpsychol. 32:225–256.
Fricke, H. W., and S. Holzberg. 1974. Social units and hermaphroditism in a
pomacentrid fish. Naturwissenschaften 61:367–368.
Frith, C. A., J. M. Leis, and B. Goldman. 1986. Current in the Lizard Island
region of the Great Barrier Reef Lagoon and their relevance to potential
movements of larvae. Coral Reefs 5:81–92.
Galtier, N., F. Depaulis, and N. H. Barton. 2000. Detecting bottlenecks and
selective sweeps from DNAsequence polymorphism. Genetics 155:981–
Gill, T. N. 1862. Catalogue of the fishes of Lower California in the Smith-
sonian Institution, collected by Mr. J. Xantus. Proc. Acad. Natl. Sci.
Philadelphia 14:140–151.
Goudet, J. 1995. Fstat version 1.2: a computer program to calculate F statistics.
J. Hered. 86:485–486.
Hall, T. 1999. BioEdit: a user-friendly biological sequence alignment editor
and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser.
Hellberg, M. E. 1998. Sympatric seashells along the sea’s shore: the geography
of speciation in the marine gastropod Tegula. Evolution 52:1311–1324.
Hemmer-Hansen, J., E. E. Nielsen, J. Frydenberg, and V. Loeschcke. 2007.
Adaptive divergence in a high gene flow environment: Hsc70 varia-
tion in the European flounder (Platichthys flesus L.). Heredity 99:592–
Hobbs, J.-P. A., A. J. Frisch, G. R. Allen, and L. Van Herwerden. 2009.
Marine hybrid hotspot at Indo-Pacific biogeographic border. Biol. Lett.
Holbrook, S. J., and R. J. Schmitt. 1997. In situ nocturnal observations of reef
fishes using infrared video. Pp. 805–812 in B. S. J. Y. Sire, ed. Proceed-
ings 5th Indo-Pacific Fish Conference, Noum´
ea, New Caledonia.
Horne, J. B., L. van Herwerden, J. H. Choat, and D. R. Robertson. 2008.
High population connectivity across the Indo-Pacific: congruent lack of
phylogeographic structure in three reef fish congeners. Mol. Phylogenet.
Evol. 49:629–638.
Juncker, M., L. Wantiez, and D. Ponton. 2006. Flexibility in size and age at
settlement of coral reef fish: spatial and temporal variations in Wallis
Islands (South Central Pacific). Aquat. Living Resour. 19:339–348.
Klausewitz, W. 1960. Dascyllus strasburgi, ein neuer Fisch aus dem Pazifik.
(Pisces, Perciformes, Pomacentridae). Bull. Aquat. Biol. 2:45–49.
Kobayashi, D. R. 2006. Colonization of the Hawaiian Archipelago via
Johnston Atoll: a characterization of oceanographic transport corri-
dors for pelagic larvae using computer simulation. Coral Reefs 25:407–
Kuhner, M. K., J. Yamato, and J. Felsenstein. 1998. Maximum likelihood
estimation of population growth rates based on the coalescent. Genetics
Lacson, J. M., and S. Clark. 1995. Genetic divergence of Maldivian and
Micronesian demes of the Damselfishes Stegastes nigricans, Chrysiptera
biocellata, C. glauca and C. leucopoma (Pomacentridae). Mar. Biol.
Lee, W. J., J. Conroy, W. H. Howell, and T. D. Kocher. 1995. Structure and
evolution of Teleost mitochondrial control regions. J. Mol. Evol. 41:54–
Leis, J. M. 1991. The pelagic stage of reef fishes: the larval biology of coral reef
fishes. In P. F. Sale, ed. The ecology of fishes on coral reefs. Academic
Press, San Diego, CA.
Leray, M., R. Beldade, S. J. Holbrook, R. J. Schmitt, S. Planes, and G.
Bernardi. 2009. Isolation and characterization of 13 polymorphic nu-
clear microsatellite primers for the widespread Indo-Pacific three-spot
damselfish, Dascyllus trimaculatus, and closely related D. auripinnis.
Mol. Ecol. Res. 9:213–215.
Lessios, H. A. 2008. The Great American Schism: divergence of marine
organisms after the rise of the Central American Isthmus. Annu. Rev.
Ecol. Evol. Syst. 39:63–91.
Lessios, H. A., and D. R. Robertson. 2006. Crossing the impassable: genetic
connections in 20 reef fishes across the eastern Pacific barrier. Proc.
Roy. S. Lond. B 273:2201–2208.
Lessios, H. A., B. D. Kessing, and D. R. Robertson. 1998. Massive gene flow
across the world’s most potent marine biogeographic barrier. Proc. R.
Soc. Lond. B 265:583–588.
Lessios, H. A., B. D. Kessing, D. R. Robertson, and G. Paulay. 1999. Phy-
logeography of the pantropical sea urchin Eucidaris in relation to land
barriers and ocean currents. Evolution 53:806–817.
Lobel, P. S., and D. A. Mann. 1995. Spawning sounds of the damselfish, Das-
cyllus albisella (Pomacentridae), and relationship to male size. Bioa-
coustics 6:187–198.
Losos, J. B., and R. E. Glor. 2003. Phylogenetic comparative methods and the
geography of speciation. Trends Ecol. Ecol. 18:220–227.
Marshall, N. J., K. Jennings, W. N. McFarland, E. R. Loew, and G. S. Losey.
2003. Visual biology of Hawaiian coral reef fishes. III. Environmental
light and an integrated approach to the ecology of reef fish vision. Copeia
Mayr, E. 1954. Geographic speciation in tropical echinoids. Evolution 8:1–18.
McCafferty, S., E. Bermingham, B. Quenouille, S. Planes, G. Hoelzer, and K.
Asoh. 2002. Historical biogeography and molecular systematics of the
Indo-Pacific genus Dascyllus (Teleostei : Pomacentridae). Mol. Ecol.
McMillan, W. O., and S. R. Palumbi. 1995. Concordant evolutionary pat-
terns among Indo-West Pacific Butterflyfishes. Proc. R. Soc. Lond. B
McMillan, W. O., L. A. Weigt, and S. R. Palumbi. 1999. Color pattern evolu-
tion, assortative mating, and genetic differentiation in brightly colored
Butterflyfishes (Chaetodontidae). Evolution 53:247–260.
Moland, E., and G. P. Jones. 2004. Experimental confirmation of aggressive
mimicry by a coral reef fish. Oecologia 140:676–683.
Munday, P. L., P. J. Eyre, and G. P. Jones. 2003. Ecological mechanisms for
coexistence of colour polymorphism in a coral-reef fish: an experimental
evaluation. Oecologia 137:519–526.
Munday, P. L., L. van Herwerden, and C. Dudgeon. 2004. Evidence for sym-
patric speciation by host shift in the sea. Curr. Biol. 14:1498–1504.
Ovenden, J. R., J. Salini, S. O’Connor, and R. Street. 2004. Pronounced genetic
population structure in a potentially vagile fish species (Pristipomoides
multidens, Teleostei: Perciformes : Lutjanidae) from the East Indies
triangle. Mol. Ecol. 13:1991–1999.
Planes, S. 1993. Genetic differentiation in relation to restricted larval dispersal
of the convict surgeonfish Acanthurus triostegus in French Polynesia.
Mar. Ecol. Prog. Ser. 98:237–246.
Planes, S., and P. J. Doherty. 1997. Genetic relationships of the colour morphs
of Acanthochromis polyacanthus (Pomacentridae) on the northern Great
Barrier Reef. Mar. Biol. 130:109–117.
Planes, S., and C. Fauvelot. 2002. Isolation by distance and vicariance drive
genetic structure of a coral reef fish in the Pacific Ocean. Evolution
Planes, S., P. J. Doherty, and G. Bernardi. 2001. Unusual case of extreme ge-
netic divergence in a marine fish, Acanthochromis polyacanthus, within
the Great Barrier Reef and the Coral Sea. Evolution 55:2263–2273.
Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of
DNA substitution. Bioinformatics 14:817–818.
Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population
structure using multilocus genotype data. Genetics 155:945–959.
Puebla, O., E. Bermingham, F. Guichard, and E. Whiteman. 2007. Colour
pattern as a single trait driving speciation in Hypoplectrus coral reef
fishes? Proc. R. Soc. Lond. B 274:1265–1271.
Ramon, M. L., P. A. Nelson, E. De Martini, W. J. Walsh,and G. Bernardi. 2008.
Phylogeography, historical demography, and the role of post-settlement
ecology in two Hawaiian damselfish species. Mar. Biol. 153:1207–1217.
Randall, J. E. 1961. A contribution to the biology of convict surgeonfish
of the Hawaiian islands, Acanthurus triostegus sandwicensis. Pac. Sci.
———. 1998. Zoogeography of shore fishes of the Indo-Pacific region. Zool.
Stud. 37:227–268.
Randall, J. E., and H. E. Randall. 2001. Dascyllus auripinnis, a new pomacen-
trid fish from atolls of the central Pacific Ocean. Zool. Stud. 40:61–67.
Renema, W., D. R. Bellwood, J. C. Braga, K. Bromfield, R. Hall, K. G.
Johnson, P. Lunt, C. P. Meyer, L. B. McMonagle, R. J. Morley, et al.
2008. Hopping hotspots: global shifts in marine biodiversity. Science
Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223–225.
Riginos, C., and B. C. Victor. 2001. Larval spatial distributions and other
early life-history characteristics predict genetic differentiation in eastern
Pacific blennioid fishes. Proc. R. Soc. Lond. B 268:1931–1936.
Robertson, D. R., F. Karg, R. L. de Moura, B. C. Victor, and G. Bernardi.
2006. Mechanisms of speciation and faunal enrichment in Atlantic par-
rotfishes. Mol. Phylogenet. Evol. 40:795–807.
Rocha, L. A. 2004. Mitochondrial DNA and color pattern variation in three
western Atlantic Halichoeres (labridae), with the revalidation of two
species. Copeia 2004:770–782.
Rocha, L. A., D. R. Robertson, C. R. Rocha, J. L. Van Tassell, M. T. Craig,
and B. W. Bowen. 2005a. Recent invasion of the tropical Atlantic by an
Indo-Pacific coral reef fish. Mol. Ecol. 14:3921–3928.
Rocha, L. A., D. R. Robertson, J. Roman, and B. W.Bowen. 2005b. Ecological
speciation in tropical reef fishes. Proc. R. Soc. Lond. B 272:573–579.
Rozas, J., J. C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP,
DNA polymorphism analyses by the coalescent and other methods.
Bioinformatics 19:2496–2497.
Rundle, H. D., and P. Nosil. 2005. Ecological speciation. Ecol. Lett. 8:336–
uppell, W. P. E. S. 1828–30. Atlas zu der Reise im n¨
ordlichen Africa. Fische
des Rothen Meeres. Fische Rothen Meeres 1:141–143.
Sambrook, J., E. F. Fritschi, and T. Maniatis. 1989. Molecular cloning: a
laboratory manual. Cold Spring Harbor Laboratory Press, New York.
Schluter, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press,
Oxford, U.K.
Shulman, M. J., and E. Bermingham. 1995. Early life histories, ocean currents,
and the population genetics of Caribbean reef fishes. Evolution 49:897–
Streelman, J. T., M. Alfaro, M. W. Westneat, D. R. Bellwood, and S. A. Karl.
2002. Evolutionary history of the parrotfishes: biogeography, ecomor-
phology, and comparative diversity. Evolution 56:961–971.
Thresher, R. E. 1984. Reproduction in reef fishes. TFH Publishing, NJ.
Van Herwerden, L., and P. J. Doherty. 2006. Contrasting genetic structures
across two hybrid zones of a tropical reef fish, Acanthochromis polya-
canthus (Bleeker 1855). J. Evol. Biol. 19:239–252.
Vermeij, G. J. 1987. The dispersal barrier in the tropical Pacific—Implications
for molluscan speciation and extinction. Evolution 41:1046–1058.
Wares, J. P., and C. W. Cunningham. 2001. Phylogeography and his-
torical ecology of the north Atlantic intertidal. Evolution 55:2455–
Wellington, G. M., and B. C. Victor. 1989. Planktonic larval duration of 100
species of Pacific and Atlantic Damselfishes (Pomacentridae). Mar. Biol.
Wu, C. I., and C. T. Ting. 2004. Genes and speciation. Nat. Rev. Genet.
Yaakub, S. M., D. R. Bellwood, L. van Herwerden, and F. A. Walsh. 2006.
Hybridization in coral reef fishes: introgression and bi-directional gene
exchange in Thalassoma (family Labridae). Mol. Phylogenet. Evol.
Zwickl, D. J. 2006. Genetic algorithm approaches for the phylogenetic analysis
of large biological sequence datasets under the maximum likelihood
criterion. Ph.D. dissertation, The Univ. of Texas at Austin, TX.
Associate Editor: M. Hellberg
Supporting Information
The following supporting information is available for this article:
Figure S1. Phylogenetic relationship between 563 individuals sampled in the D. trimaculatus species complex based on mitochon-
drial control regions using the Maximum Likelihood method. A simplified tree is provided in the inset with size of pie charts being
proportional to the number of individuals.
Table S 1 . Number of alleles (Na), expected heterozygosity (He), and observed heterozygosity (Ho) across 13 loci and six groups.
Table S 2 . Proportion of membership of each predefined population in each of the seven clusters which best partition the microsatellite
Supporting Information may be found in the online version of this article.
(This link will take you to the article abstract).
Please note: Wiley-Blackwell is not responsible for the content or functionality of any supporting information supplied by the
authors. Any queries (other than missing material) should be directed to the corresponding author for the article.
... The family Pomacentridae, commonly known as damselfishes, contains 29 genera and over 400 species (Allen 1991;Tang et al. 2021), with most of these species occurring in the Indowest and central Pacific region (Allen 1991;Tang et al. 2021). The three-spot damselfish, Dascyllus trimaculatus has a wide distribution that extends from the Red Sea to the Central Pacific and belongs to a species complex with three other recognized species (Bernardi et al. 2001;Leray et al. 2010). Here, we present, for the first time, the fully assembled mitochondrial genome of D. trimaculatus (R€ uppell, 1829) to aid in future studies of this species complex. ...
... In addition, a Neighbor-Joining phylogenetic tree based on 375 bp of the variable control region (D-loop) of our sample and an additional 636 different D. trimaculatus individuals (obtained from the literature, Leray et al. 2010) was established to locate the geographic origin of our sample (Supplementary Figure S2). Results suggests that the organism we sequenced is from the West Pacific Rim clade, with closest individuals from the Visayas (Philippines) and Manado (Indonesia). ...
Full-text available
Damselfishes (family Pomacentridae) comprise approximately 400 species that play an important ecological role in temperate and coral reefs. Here, for the first time, we assemble and annotate the mitochondrial genome of Dascyllus trimaculatus, the three-spot dascyllus, a planktivorous damselfish that primarily recruits in anemones. The circular genome of D. trimaculatus is 16,967 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Gene arrangement and codon usage is similar to reported mitochondrial genomes of other damselfish genera, and a phylogenetic analysis of a set of damselfish representatives is consistent with known evolutionary analyses.
... Toutefois, les résultats d'analyses moléculaires de Lord et al. (in press) suggèrent que les populations de S. lagocephalus de l'ouest de l'océan Indien sont principalement axées sur de l'autorecrutement à l'échelle des Mascareignes et des Comores, avec peu ou pas de recrutement allochtone en provenance de l'océan Pacifique. Dans le cas de flux géniques restreints, des adaptations locales peuvent émerger en réponse aux pressions environnementales locales , Leray et al. 2010). Ainsi, la DVL de S. lagocephalus est plus courte dans le Pacifique qu'à la Réunion , ce qui suggère la possibilité d'une sélection sur les traits d'histoire de vie larvaire. ...
... A genetic structure was highlighted between populations of West Indian Ocean and Pacific Ocean (Lord 2009, Lord et al. accepted). In the case of restricted gene flow populations, local adaptations may emerge , Leray et al. 2010) related to environmental conditions . ...
Full-text available
Les Sicydiinae amphidromes constituent une part importante des peuplements piscicoles insulaires de la région Indo-Pacifique et sont vulnérables à de nombreuses pressions anthropiques (i.e. pêcherie, dégradation et fragmentation des habitats). La reproduction a lieu en eau douce, puis les jeunes dévalent en mer où ils débutent leur croissance pendant quelques mois avant de coloniser les rivières. L’objectif est d’acquérir des connaissances sur les traits de vie de S. lagocephalus (cosmopolite) et de C. acutipinnis (endémique). Les travaux de terrain démontrent que le choix de l’habitat quotidien est fortement lié aux interactions sociales, alors que l’habitat de fraie montre une forte sélection pour des conditions morphodynamiques favorisant l’oxygénation des œufs. Les mâles sélectionnent des sites de ponte et gardent les œufs. L’étude expérimentale de la survie en eau douce confirme que tous les embryons libres possèdent la capacité à rejoindre la mer. L’analyse des traits de vie marins à partir des otolithes des post-larves révèle des variations saisonnières d’âge et de taille au recrutement, en lien avec la croissance et la température marine. L’examen histologique des ovaires permet de décrire les variations spatiales et temporelles de l’activité de reproduction chez les femelles en rivière et de déterminer la fécondité et la taille de première reproduction. Les variations inter et intra-spécifiques des traits de vie sont comparées en lien avec la répartition géographique des deux espèces. Ces travaux permettent d’identifier des perspectives concrètes dans le domaine de la gestion et de la conservation sur la base des caractéristiques de la stratégie amphidrome.
... This computational approach simulates the movement and dispersal of virtual particles and incorporates physical characteristics of the surrounding environment as well as complex biological components to make predictions of larval dispersal. Ideally these models are grounded with empirical data (Bowen, 2016;Galindo et al., 2010;Leray et al., 2010;White et al., 2010), particularly by matching genetic connectivity to oceanic circulation models . Despite some success, model predictions often fail to match what is observed in nature (Selkoe et al., 2016), possibly due to unknown behavioural and life-history traits, along with ever-changing environmental ...
Full-text available
The gap between spawning and settlement location of marine fishes, wherein the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches offer some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, we apply this methodology to the endemic Hawaiian Convict Tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of ~54–77 days. We collected 606 adults and 607 juveniles from 23 locations around the island of Oʻahu, Hawaiʻi. Based on 399 SNPs, we assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artifact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi‐enclosed Kāneʻohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāneʻohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self‐recruitment, when a juvenile returns to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for A. triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.
... Dascyllus is a genus of coral reef damselfishes comprising 11 species distributed in the Indian and Pacific Oceans, with two widespread species complexes (i.e. D. aruanus/abudafur (Borsa et al., 2014) and D. trimaculatus (Leray et al., 2010)) that share habitats with other local/endemic Dascyllus species. Our two studied species, D. marginatus and D. abudafur, commonly occur in branching corals throughout the Red Sea. ...
Several marine biogeographical provinces meet at the Arabian Peninsula. Where and how these junctions affect species is poorly understood. We herein aimed to identify the barriers to dispersal and how these shape fish populations, leading to differing biogeographies despite shared habitat and co‐ancestry. Dascyllus marginatus (endemic) and Dascyllus abudafur (widespread). Coral reefs from the Red Sea (RS), Djibouti, Yemen, Oman, and Madagascar. We tested potential barriers to gene flow using RADseq‐derived SNPs and identified whether population genetic differences on each side of these barriers were neutral or selective to relate this to the biogeography of the species. Seven locations (ranging over 5100 km) were sampled for the endemic and six (ranging over 7400 km) for the widespread species, taking 20 individuals per location, with two exceptions. Dascyllus marginatus populations (comprising 5648 SNPs) had an order of magnitude higher genetic differentiation compared to D. abudafur (comprising 10,667 SNPs), as well as several outlier loci that were absent in D. abudafur despite equal sampling locations. In both species, the RS and Djibouti specimens formed one genetic cluster separated from all other locations. Although ranging from the RS to Madagascar, D. abudafur was absent in Yemen and Oman. Stronger genetic structure at smaller geographical scales and outlier loci in the endemic species seem associated with faster adaptation to environmental differences and selective pressure. Genetic differentiation in the widespread species is neutral and only occurs at large geographical distances. Restrictive transitions (between the Gulf of Aqaba and the RS or the RS and the Gulf of Aden) do not hinder gene flow in either species, and the environmental shift within the RS (at 22°N/20°N) only affected the endemic species. The genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.
... Early work on speciation in marine fishes was thought to be a consequence of geographic isolating mechanisms. The formation of land barriers (Bermingham et al., 1997;Bernardi et al., 2004), islands (Leray et al., 2010), and physical boundaries generated from oceanographic processes (Gaither & Rocha, 2013;Hubert et al., 2012) were used from a biogeographical perspective to describe speciation patterns in marine fishes. However, the role of pelagic larval duration in contributing to gene flow among populations suggested that allopatric divergence may be rarer in marine fish (reviewed in Bindea et al., 2013). ...
Full-text available
Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes, and yet it is unclear how adaptation along these gradients' shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth‐segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here, we present exome data on two species pairs of rockfishes that are depth‐segregated and have different degrees of divergence: S. chlorostictus–S. rosenblatti and S. crocotulus–S. miniatus. We were able to reliably identify “islands of divergence” in the species pair with more recent divergence (S. chlorostictus–S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment. To determine the genomic responses and demographic history of speciation, we sequenced exome‐enriched sequences in species pairs of rockfish (genus Sebastes) that are depth‐segregated. We found shared islands of divergence between the two species pairs and found neurosensory genes enriched in these islands for one species pair. Demographic histories were similar for the two species pairs, suggesting similar modes of diversification.
... Marine waters, which are open ecosystems that allow genetic exchange between populations, also will enable a population to adapt and have different characteristics from their peers even though genetic mutations occur pretty long. The specialisation process on coral reef ecosystems is quite complex and exciting to continue to study biodiversity and various influential factors (Leray et al., 2010;Rocha and Bowen, 2008). ...
Full-text available
Highlight ResearchThe leopard coral grouper Plectropomus leopardus was identified and analysed based on molecular approach.Genetic diversity within two regions in Gorontalo, Sulawesi successfully performed using connectivity analysis.Three haplotypes of Plectropomus leopardus from two region in Gorontalo as one of economical important marine fish species. AbstractBar-cheek coral trout (P. leopardus) is the flagship of the grouper in the live fish market in Asia. Unfortunately, the potential of the grouper is still partly produced from natural catches. Even though hybridisation activities have also started to be carried out, there still have not been many studies on the genetic diversity of these fish. The application of molecular identification has been widely applied in marine aquatic animal species, which are very likely to occur due to errors in terms of shape and colour in the morphological character. DNA information has been beneficial in efforts to the breeding program and develop grouper aquaculture activities. DNA barcoding was used for the molecular identification and haplotype analysis of P. leopardus from two locations in Gorontalo, Sulawesi, Indonesia. A total of 14 fish samples were collected from two traditional fish markets around Kwandang and Sumalata Gulf in the northern part of Gorontalo Province, Sulawesi. This study identified and found three haplotypes from both regions. Molecular identification using Cytochrome c Oxidase subunit I (COI) gene region on mitochondrial DNA. Besides Mega7 for phylogenetic reconstruction, the data analysis using DnaSP6, Arlequin Ver., and Network The first Haplotype is a mixed population between the Kwandang Gulf and the Sumalata Gulf, then the Kwandang Gulf haplotype and the Sumalata Gulf haplotype. The genetic distance between Kwandang Gulf haplotype and Sumalata Gulf haplotype is 0.003984, classified as a shallow genetic distance and needs more samples from another region to figure out leopard coral grouper around Indonesia.
... the present study on A. perideraion is the first in the area and revealed the genetic differentiation between the regions, providing useful data to guide future studies and inform regional management. the genetic variation was also found in other Indo-Pacific coral reef species such as Chlorurus sordidus (Bay et al., 2004) and Tridacna crocea (DeBoer et al., 2008) or Dascyllus trimaculatus (Leray et al., 2010). These species have the same characteristics as the pink anemonefish in that they lay demersal eggs (Riginos et al., 2011), have a short larval development phase (PLD ~ 18 days), and adults, once settled, remain very to their resident sea anemone (Madduppa et al., 2014). ...
... Despite the distribution range of P. andamanensis, considering either Bangladesh or Indonesian specimens seems very limited, several phylogeographic studies have flagged strong and geographically sharp genetic discontinuity in Indonesia for Indo-Pacific species (for details see Carpenter et al. 2011, Hubert et al. 2012). The complex geological history of Sunda shelf during the glacial periods may have promoted allopatric speciation events such as in the pomacentrid fish Dascyllus trimaculatus (Leray et al. 2009). ...
Full-text available
We document a ~700 km northward range extension of the rare Andaman grunt, Pomadasys andamanensis McKay and Satapoomin 1994, to the Bangladesh coast of the north-eastern Bay of Bengal. Sixteen specimens (82–129 mm SL) were collected from fishermen catches in Ukhia, Teknaf and Zinjira Island, south-eastern Bangladesh, during 2014–2019 and their counts, measurements and descriptions are provided in detail. In addition, underwater videography (near Zinjira Island), shows an individual swimming over sand-gravel-rock bottom covered with a dense bed of brown algae, predominantly Padina and Dictyota. Using the Cytochrome Oxidase subunit I (COI) region sequence variation of mitochondrial DNA, four specimens were found genetically indistinguishable from the topotype (Andaman Sea coast of Thailand) specimens collected in this study. Long regarded as an endemic species to the Andaman Sea (type locality), the distribution range of P. andamanensis now extends from Phuket Island in the south to the Inani Coast in Cox’s Bazar, Bangladesh in the north, spanning roughly 1500 km in the Andaman Sea and eastern Bay of Bengal. Comparison between published COI barcode data of P. andamanensis and the barcodes generated in this study indicates the presence of a cryptic sibling species from southern Bali, Indonesia, in the south-western end of the Coral Triangle. A deeper phylogenetic and taxonomic investigation covering more Pomadasys spp. in the Bay of Bengal and neighboring region is suggested to resolve species level ambiguities.
... As with other marine fauna, more recent siganid diversification potentially occurred during periods of fluctuating sea levels during the Pliocene/Pleistocene epochs [67,68]. The emergence of the Sunda Shelf between the Indo-Malay region and northern Australia at this time could have facilitated the divergence of S. virgatus and S. doliatus ( Figure 7A) [69]. Closely related sister species, including S. guttatus-S. ...
Full-text available
rabbitfish; cytochrome oxidase I (COI); nuclear rhodopsin retrogene (RHO); nuclear DNA; morphology; phylogenetic; molecular clock
... As with other marine fauna, more recent siganid diversification potentially occurred during periods of fluctuating sea levels during the Pliocene/Pleistocene epochs [67,68]. The emergence of the Sunda Shelf between the Indo-Malay region and northern Australia at this time could have facilitated the divergence of S. virgatus and S. doliatus ( Figure 7A) [69]. Closely related sister species, including S. guttatus-S. ...
Full-text available
Rabbitfish (Siganidae) are coral reef fish that are distributed across diverse habitats that include estuaries, mangroves, reefs, and even seaweed mats. Given their ecological diversity and natural widespread distributions across the Indo-Pacific region, we were interested to investigate the evolutionary history of this group and patterns of divergence that have contributed to their present-day distributions. In the present study, samples were collected from the South China Sea to study taxonomic and phylogenetic relationships, and divergence times. We investigated the taxonomic relationships among modern rabbitfish species, reconstructed their molecular phylogeny, and estimated divergence times among selected lineages based on a fragment of the mtDNA cytochrome oxidase I (COI) and sequences of the nuclear rhodopsin retrogene (RHO). Our results indicate that modern rabbitfish likely originated in the Indo-West Pacific during the late Eocene [37.4 million years ago (mya)], following which they diverged into three major clades during the Pliocene/Pleistocene. Subsequent diversification and origins of the majority of siganids may likely be associated with episodes of paleo-oceanographic events, including greenhouse and glaciation events (Eocene–Miocene) as well as major plate tectonic events (Pliocene–Pleistocene). Some modern siganid species may naturally hybridize with congeneric species where their geographical ranges overlap. A comprehensive taxonomic analysis revealed that the phylogeny of Siganidae (cladogenesis of Clades I, II, and III) is characterized by divergence in several external morphological characters and morphometric parameters. Our study demonstrates that morphological characteristics, geographical heterogeneity, and environmental change have contributed to siganids’ historical diversification.
Full-text available
Stretches of deep ocean constitute barriers to the dispersal of many shallow-water marine species in the tropical Pacific. The purpose of this study was to assess the selectivity of these barriers with respect to the habitat characteristics, adult size, and predation-related shell architecture of gastropods, and to explore the implications of this selectivity for macroevolutionary patterns of extinction and speciation. The dispersal barrier between continental islands (represented in my collections by species from eastern Indonesia, the southern Philippines, and the north coast of New Guinea) and the nearby oceanic Palau Islands was studied by evaluating the percentage of each architectural and habitat category that is present on the continental islands but missing in Palau. The barrier is significantly more effective against sand-dwelling species than against rock-dwellers, and among rock-dwellers it is most effective against aperturally unarmored taxa. Barriers between Palau and Guam, Guam and the Hawaiian Islands, and the Line Islands and the tropical Eastern Pacific are generally unselective with respect to substratum type and architecture. The fact that narrow-apertured species are less affected by the barrier between the continental islands and Palau than are other rock-dwelling gastropods is consistent with the interpretation that this group has been unusually resistant to extinction and highly susceptible to founder speciation when oceanic circulation is altered. These patterns of susceptibility and geographical distribution may explain why armored gastropods have increased in numbers relative to unarmored ones in the tropical Pacific during the Cenozoic.
Tropical reef fishes, along with many benthic invertebrates, have a life cycle that includes a sedentary, bottom-dwelling reproductive phase and a planktonic stage that occurs early in development. The adult benthic populations occupy disjunct, patchy habitats; the extent of gene flow due to dispersal of the planktonic life stage is generally unknown.
In butterflyfishes (Chaetodontidae), color pattern evolves rapidly and is often the only morphological trait separating closely related species. Vivid coloration is frequently assumed to provide critical signals for mate recognition and mate choice, but few direct experimental tests are available. Here we analyze the relationship between color pattern change, mate choice, and genetic differentiation in a group of three very closely related allopatric butterflyfishes. We found that in only one member of this group, Chaetodon multicinctus, is color pattern evolution associated with mate preference and genetic divergence. For its two sister species, C. punctatofasciatus and C. pelewensis, color pattern change has not resulted in assortative mating (based on laboratory pairing experiments and field observations) or in significant mtDNA or allozyme differentiation. In a contact zone on reefs in the Solomon Islands and Papua New Guinea, hybridization between the two forms has nearly homogenized color pattern differences. Outside these areas, however, color pattern remains distinct. Genetic variation is homogeneous over a much larger geographic scale. Sequence variation in the tRNA-proline end of the mitochondrial control region and allozyme variation was distributed widely within C. punctatofasciatus and C. pelewensis, which suggests few constraints to mitochondrial or nuclear gene flow across the color pattern boundary. These contrasting patterns strongly suggest that selection is maintaining color pattern differences in allopatry in the face of potentially homogenizing levels of gene flow. The mating pattern data show that this selection is not operating on mate recognition in the strictest sense, but probably on some other aspect of the social system of these territorial fish. In this case, divergence in mating preference can follow color pattern evolution, but is not contemporaneous with it.
Uncertainty and controversy surround the geographical and ecological circumstances that create genetic differences between populations that eventually lead to reproductive isolation. Two aspects of marine organisms further complicate this situation: (1) many species possess planktonic larvae capable of great dispersal; and (2) obvious barriers to movement between populations are rare. Past studies of speciation in the sea have focussed on identifying the effects of past land barriers and on biogeographical breakpoints. However, assessing the role such undeniable barriers actually play in the initial divergence leading to reproductive isolation requires phylogenetic studies of recent radiations living in varying degrees of sympatry and allopatry to see which barriers (if any) tend to separate sister species. Here I infer phylogenetic relationship between 23 species of the marine snail Tegula using DNA sequences from two regions of the mitochondrial genome: cytochrome c oxidase I (COI) and the small ribosomal subunit (12S) These snails possess planktonic larvae with moderate dispersal capabilities and have speciated rapidly with over 40 extant species arising since the genus first appeared in the mid-Miocene (about 15 M.Y.B.P.). Trees constructed from the COI and 12S regions (which yielded 205 and 137 phylogenetically informative sites, respectively) were robust with respect to tree-building method, bootstrapping, and the relative weightings of transitions, transversions, and gaps Within clades where all extant species have been sampled, five of six identified sister species pairs broadly coexist on the same side of biogeographical boundaries. These data suggest strong geographical barriers to gene flow may not always be required for speciation in the sea; transient allopatry or even ecological barriers may suffice. A survey of the geographic distributions of marine radiations suggests that coastal distributions may favor the sympatry of sister taxa more than island distributions do.
The pantropical sea urchin genus Eucidaris contains four currently recognized species, all of them allopatric: E. metularia in the Indo-West Pacific, E. thouarsi in the eastern Pacific, E. tribuloides in both the western and eastern Atlantic, and E. clavata at the central Atlantic islands of Ascension and St. Helena. We sequenced a 640-bp region of the cytochrome oxidase I (COI) gene of mitochondrial DNA to determine whether this division of the genus into species was confirmed by molecular markers, to ascertain their phylogenetic relations, and to reconstruct the history of possible dispersal and vicariance events that led to present-day patterns of species distribution. We found that E. metularia split first from the rest of the extant species of the genus. If COI divergence is calibrated by the emergence of the Isthmus of Panama, the estimated date of the separation of the Indo-West Pacific species is 4.7-6.4 million years ago. This date suggests that the last available route of genetic contact between the Indo-Pacific and the rest of the tropics was from west to east through the Eastern Pacific Barrier, rather than through the Tethyan Sea or around the southern tip of Africa. The second cladogenic event was the separation of eastern Pacific and Atlantic populations by the Isthmus of Panama. Eucidaris at the outer eastern Pacific islands (Galapagos, Isla del Coco, Clipperton Atoll) belong to a separate clade, so distinct from mainland E. thouarsi as to suggest that this is a different species, for which the name E. galapagensis is revived from the older taxonomic literature. Complete lack of shared alleles in three allozyme loci between island and mainland populations support their separate specific status. Eucidaris galapagensis and E. thouarsi are estimated from their COI divergence to have split at about the same time that E. thouarsi and E. tribuloides were being separated by the Isthmus of Panama. Even though currents could easily convey larvae between the eastern Pacific islands and the American mainland, the two species do not appear to have invaded each other's ranges. Conversely, the central Atlantic E. clavata at St. Helena and Ascension is genetically similar to E. tribuloides from the American and African coasts. Populations on these islands are either genetically connected to the coasts of the Atlantic or have been colonized by extant mitochondrial DNA lineages of Eucidaris within the last 200,000 years. Although it is hard to explain how larvae can cross the entire width of the Atlantic within their competent lifetimes, COI sequences of Eucidaris from the west coast of Africa are very similar to those of E. tribuloides from the Caribbean. FST statistics indicate that gene flow between E. metularia from the Indian Ocean and from the western and central Pacific is restricted. Low gene flow is also evident between populations of E. clavata from Ascension and St. Helena. Rates of intraspecific exchange of genes in E. thouarsi, E. galapagensis, and E. tribuloides, on the other hand, are high. The phylogeny of Eucidaris confirms Ernst Mayr's conclusions that major barriers to the dispersal of tropical echinoids have been the wide stretch of deep water between central and eastern Pacific, the cold water off the southwest coast of Africa, and the Isthmus of Panama. It also suggests that a colonization event in the eastern Pacific has led to speciation between mainland and island populations.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from
The East Indian region (Indonesia, New Guinea, and the Philippines), with perhaps as many as 2800 species of shore fishes, has the richest marine fish fauna of the world. The numbers of species of fishes decline, in general, with distance to the east of the East Indies, ending with 566 species in Hawaii and 126 at Easier Island. The richness of the marine fauna of the East Indies is explained in terms of its relatively stable sea temperature during ice ages, its large size and high diversity of habitat, in having many families of shore fishes adapted to the nutrient-rich waters of continental and large island shelves that are lacking around oceanic islands, in having many species with larvae unable to survive in plankton-poor oceanic seas or having too short a life span in the pelagic realm for long transport in ocean currents, and in being the recipient of immigrating larvae of species that evolved peripherally. It is also a place where speciation may have occurred because of a barrier to east-west dispersal of marine fishes resulting from sea-level lowering during glacial periods (of which there have been at least 3 and perhaps as many as 6 during the last 700 000 years), combined with low salinity in the area from river discharge and cooling from upwelling. There could also have been speciation in embayments or small seas isolated in the East Indian region from sea-level lowering. Sixty-five examples are given of possible geminate pairs of fishes from such a barrier, judging from their similarity in color and morphology. Undoubtedly many more remain to be elucidated, some so similar that they remain undetected today. Fifteen examples are listed of possible geminate species of the western Indian Ocean and western Pacific that are not known to overlap in the East Indies, and 8 examples of color variants in the 2 oceans that are not currently regarded as different enough to be treated as species. Five examples of species pairs are cited for the Andaman Sea and western Indonesia that may be the result of near-isolation of the Andaman Sea during the Neogene. Explanation is given for distributions of fishes occurring only to the east and west of the East Indies in terms of extinction there during sea-level lows. The causes of antitropical distributions are discussed. The level of endemism of fishes for islands in the Pacific has been diminishing as a result of endemics being found extralimitally, as well as the discovery of new records of Indo-Pacific fishes for the areas. Hawaii still has the highest, with 23.1% endemism, and Easter Island is a close second with 22.2%. The use of subspecies is encouraged for geographically isolated populations that exhibit consistent differences but at a level notably less than that of similar sympatric species of the genus. In order to ensure continuing stability in our classification of fishes, a plea is given not to rank characters obtained from molecular and biochemical analyses higher than the basic morphological characters that are fundamental to systematics.