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Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island


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Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ ST = 0.49, P < 0.0001; 16S: Φ ST = 0.34, P < 0.0001; H3: Φ ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.
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1 23
Conservation Genetics
ISSN 1566-0621
Volume 17
Number 4
Conserv Genet (2016) 17:811-821
DOI 10.1007/s10592-016-0823-8
Genetic population structure and low
genetic diversity in the over-exploited
sea cucumber Holothuria edulis Lesson,
1830 (Echinodermata: Holothuroidea) in
Okinawa Island
Taha Soliman, Iria Fernandez-Silva &
James Davis Reimer
1 23
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Genetic population structure and low genetic diversity in the
over-exploited sea cucumber Holothuria edulis Lesson, 1830
(Echinodermata: Holothuroidea) in Okinawa Island
Taha Soliman
Iria Fernandez-Silva
James Davis Reimer
Received: 24 July 2015 / Accepted: 10 February 2016 / Published online: 19 February 2016
ÓSpringer Science+Business Media Dordrecht 2016
Abstract Understanding genetic connectivity is funda-
mental for ecosystem-based management of marine resour-
ces. Here we investigate the metapopulation structure of the
edible sea cucumber Holothuria edulis Lesson, 1830 across
Okinawa Island, Japan. This species is of economic and
ecological importance and is distributed from the Red Sea to
Hawai‘i. We examined sequence variation in fragments of
mitochondrial cytochrome oxidase subunit I (COI) and 16S
ribosomal RNA (16S), and nuclear histone (H3) at six
locations across Okinawa Island. We found higher haplotype
diversity for mtDNA (COI: Hd =0.69 and 16S: Hd =0.67)
and higher heterozygosity of nDNA (H3: H
=0.39) in
populations from the west coast of Okinawa compared to
individuals from populations on the east coast (COI:
Hd =0.40; 16S: Hd =0.21; H3: H
=0.14). Overall
population structure was significant (AMOVA results
for COI: U
=0.49, P\0.0001; 16S: U
P\0.0001; H3: U
=0.12, P\0.0001). One population
in the east, Uruma, showed elevated pairwise U
values in
comparisons with all other sites and a marked reduction of
genetic diversity (COI: Hd =0.25 and 16S: Hd =0.24),
possibly as a consequence of a shift to a more dominant
asexual reproduction mode. Recent reports have indicated
that coastal development in this area influences many marine
organisms, and ecosystem degradation in this location could
cause the observed decrease of genetic diversity and isola-
tion of H. edulis in Uruma. Our study should provide valu-
able data to help with the urgently needed management of sea
cucumber populations in Okinawa, and indicates particular
attention needs to be paid to vulnerable locations.
Keywords Genetic diversity Coastal development
Genetic structure mtDNA Okinawa Sea cucumber
Okinawa Main Island is located in the central Ryukyu
Archipelago, a chain of islands along the eastern boundary
of the East China Sea and the western boundary of the
Philippine Sea. Located at 26°N, Okinawa Main Island
harbors some of the northernmost coral reefs in the world,
owing to the warm northward-flowing Kuroshio Current,
that through larval dispersal and nutrient transport main-
tains the populations of many coral reef organisms in this
unique region (Kamidaira et al. 2014).
Sea cucumbers play an important role in many marine
ecosystemsbecause of their influence on benthic communities
Electronic supplementary material The online version of this
article (doi:10.1007/s10592-016-0823-8) contains supplementary
material, which is available to authorized users.
&Taha Soliman
Molecular Invertebrate Systematics and Ecology Laboratory,
Graduate School of Engineering and Science, University of
the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213,
Aquaculture Department, National Institute of Oceanography
and Fisheries, Kayet-Bay, El-Anfoushy, Alexandria 21556,
Okinawa Institute of Science and Technology Graduate
University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
Section of Ichthyology, California Academy of Sciences, 55
Music Concourse Dr., Golden Gate Park, San Francisco,
CA 94118, USA
Department of Biochemistry, Genetics and Immunology,
University of Vigo, Vigo 36310, Spain
Tropical Biosphere Research Center, University of the
Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
Conserv Genet (2016) 17:811–821
DOI 10.1007/s10592-016-0823-8
Author's personal copy
(Power et al. 1996; Lessios et al. 2001; Uthicke et al. 2009).
These deposit feeders process carbonate sand and rubble
through their digestive tract and dissolve CaCO
as part of
their digestive process (Schneider et al. 2011). However, sea
cucumbers have recently come under increasingly strong
fishing pressure in many parts of the world (Toral-Granda
2008) due to rapidly rising consumer demand in East Asia
(Purcell et al. 2014a,b), and many populations have become
threatened or even locally extirpated (Friedman et al. 2011),
with extinction risks rising for more valuable species (Purcell
et al. 2014a,b). In Okinawa and the Ryukyu Archipelago sea
cucumber harvesting is a common practice (Fig. 1), but the
fishery has only recently (since 2013) become regulated.
Given the increase in demand and the ecological importance
of these ecosystem engineers, gaining a deeper understanding
of the population dynamics is needed to help inform man-
agement decisions. The study of genetic diversity and gene
flow is relevant to understanding the mechanisms by which
demographic exchange can overcome local extirpation. The
degree of interpopulation connectivity and the location of
genetic breaks shared among species in the community define
the spatial scale at which management is most effective in
ensuring population persistence (Toonen et al. 2011).
The edible sea cucumber, Holothuria edulis Lesson,
1830, is widely distributed in the Indo-Pacific region,
including the Ryukyu Archipelago, where it is known as
‘akamishikiri’. It inhabits a wide range of depths from 1 to
20 m and a broad variety of habitats, including coral reefs,
rocky reefs, and mudflats (Conand 2008; Purcell et al.
2009). As seen in many sea cucumbers, it reproduces both
sexually by pelagic spawning and asexually by fission, yet
the conditions that trigger each mode of reproduction are
not yet fully understood (Uthicke 1997). Holothuria edulis
is an edible species that is experiencing an increase in
demand following overexploitation of other, higher-value
sea cucumber species (Conand and Muthiga 2007; Choo
2008; Dissanayake and Stefansson 2010), as seen in Viet-
nam after the decline of Holothuria scabra (Choo 2008).
We have recently observed the harvesting of large quan-
tities of H. edulis (Fig. 1) around Okinawa Main Island,
where it is prepared and dried for food, medicine, or export
overseas. In the present study we have undertaken popu-
lation genetic analyses of the sea cucumber species H.
edulis to (i) investigate patterns of genetic diversity and
connectivity around Okinawa Main Island; and (ii) to infer
the demographic history of these populations. This is the
first investigation of population genetic structure of H.
edulis in Okinawa Main Island, and this study will con-
tribute useful information for the management of this
fishery in this region.
Specimens of the sea cucumber H. edulis were collected by
snorkeling or SCUBA diving between April to October
Fig. 1 Observations of large quantities of dried sea cucumbers around Okinawa Main Island, (a,b) near Awase fishing port (taken by Taha
Soliman, 23 November 2014)
812 Conserv Genet (2016) 17:811–821
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2014 at six locations around Okinawa Main Island, Japan
(Table 1; Fig. 2), including four localities along the west
coast in the East China Sea [Motobu (HDM), Oyama
(HDO), Ryugu (HDR), and Sunabe (HDS)], and two on the
east coast facing the Philippine Sea [Uruma (HDU) and
Awase (HDW)]. We covered a large area for sampling at
each site (five people sampled H. edulis), and covered an
area of approximately 2000 m
to avoid any replicate
sampling. Samples of H. edulis were obtained non-lethally
through body wall-tissue biopsy and preserved in 99 %
ethanol in the field, and live animals were released back to
the location from where they were collected.
DNA extraction and PCR
Total genomic DNA was extracted from a small piece of
body wall tissue using a DNeasy Blood and Tissue
extraction kit (Qiagen, Tokyo, Japan) following the man-
ufacturer’s protocol. Polymerase chain reactions (PCR)
were used to amplify fragments of two mitochondrial DNA
markers; cytochrome oxidase subunit I (COI) and 16S
ribosomal RNA (16S), and one fragment of the nuclear
histone H3 (H3) gene, using the following primers: COIe-F
GCT CGT GTR TCT ACR TCC AT-30(Arndt et al. 1996),
(Palumbi et al. 1991), and H3a: 50-ATG GCT CGT ACC
ATR ATR GTG AC-30(Colgan et al. 1998), respectively.
PCR reactions were carried out in a 15 ll volume con-
taining 5–20 ng of template DNA, 0.5 lM of each primer,
and 10 ll of HotStarTaq
Master Mix (Qiagen, Tokyo,
Japan), in deionized water. PCR reactions were performed
on Astec Thermocyclers (Astec Co., Ltd, Japan) with an
initial denaturation step at 95 °C during 15 min, 35 cycles
of denaturation at 94 °C for 1 min, annealing at 45 °C for
1 min, and extension at 72 °C for 1 min, and a final
extension step at 72 °C for 10 min. The amplification
products were purified with Exonuclease I and Alkaline
Phosphatase Shrimp (Takara) and incubated at 37 °C for
20 min, followed by deactivation at 83 °C for 30 min.
Purified PCR products were sequenced using an ABI Prism
automated sequencer at Fasmac Co., Kanagawa, Japan
(, in both in forward
and reverse directions.
Table 1 Molecular diversity of populations of Holothuria edulis sampled across locations of the west and east coasts of Okinawa Main Island,
inferred from mtDNA and nDNA sequences
Location Populations (Code) Latitude and longitude N H Hd S pFu’s F
Fu’s F
West coast Motobu (HDM) 26°40045.800 N 127°52055.400 E 19 5 0.65 6 0.0029 0.48 0.37
Oyama (HDO) 26°17001.200N 127°44020.500 E 30 6 0.77 8 0.0033 0.47 0.41
Ryugu (HDR) 26°31048.600N 127°55034.800 E 15 3 0.59 2 0.0015 0.11 0.39
Sunabe (HDS) 26°20026.200N 127°44039.000 E 24 5 0.74 7 0.0039 0.64 0.65
East coast Uruma (HDU) 26°19040.800N 127°56019.400 E 36 2 0.25 4 0.0022 3.50 0.93
Awase (HDW) 26°18027.100N 127°50010.300E 25 3 0.54 4 0.0034 2.72 0.92
16S rRNA
West coast Motobu (HDM) 26°40045.800 N 127°52055.400 E 21 6 0.65 5 0.0037 0.79 0.31
Oyama (HDO) 26°17001.200N 127°44020.500 E 22 6 0.68 5 0.0027 1.66 0.11
Ryugu (HDR) 26°31048.600N 127°55034.800 E 14 4 0.69 4 0.0041 0.85 0.73
Sunabe (HDS) 26°20026.200N 127°44039.000 E 20 4 0.66 2 0.0017 0.78 0.23
East coast Uruma (HDU) 26°19040.800N 127°56019.400 E 37 2 0.24 1 0.0006 0.48 0.37
Awase (HDW) 26°18027.100N 127°50010.300E 29 3 0.59 3 0.0029 2.24 0.88
H3 Na H
West coast Motobu (HDM) 26°40045.800 N 127°52055.400 E 24 7 0.12 0.35 0.0991 -1.75 0.18
Oyama (HDO) 26°17001.200N 127°44020.500 E 22 9 0.04 0.41 0.0004 0.32 0.68
Ryugu (HDR) 26°31048.600N 127°55034.800 E 14 9 0.02 0.29 0.0223 0.36 0.66
Sunabe (HDS) 26°20026.200N 127°44039.000 E 23 9 0.00 0.51 0.0000 5.71 1.00
East coast Uruma (HDU) 26°19040.800N 127°56019.400 E 40 10 0.02 0.16 0.1002 1.78 0.19
Awase (HDW) 26°18027.100N 127°50010.300E 23 10 0.03 0.41 0.1001 0.41 0.76
Nsample size, Hnumber of haplotypes, Hd haplotype diversity, Snumber of polymorphic sites, pnucleotide diversity, Na allele number, H
observed heterozygosity and H
Expected heterozygosity, HWE Hardy–Weinberg equilibrium
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Data analysis
Consensus sequences of COI, 16S, and H3 were aligned
and edited using Geneious v.8.1.3 (http://www.geneious.
com, Kearse et al. 2012), and MEGA v.6.0 (Tamura
et al. 2013). Numbers of haplotypes, haplotype diversity,
number of polymorphic sites and nucleotide diversity
were estimated with DNASP v.5.10.01 (Librado and
Rozas 2009). To investigate the demographic history of
H. edulis we conducted a neutrality test based on Fu’s
(Fu 1997) using Arlequin (Excoffier and
Lischer 2010).
Fig. 2 a Map showing sampling sites of the sea cucumber Holothuria
edulis across Okinawa Island, Japan. Diagrams represent the distri-
bution of haplotypes (concatenated sequence of COI and 16S, as
defined by Fig. 4and Table 1), Chlorophyll a (b) and CDOM
(c) levels across Okinawa Island, Japan; averages from July 2002 to
January 2015. Chlorophyll a and CDOM data for 2002–2014, derived
from satellites, were downloaded from the National Aeronautic and
Space Administration Giovanni website (Acker and Leptoukh 2007),
developed and maintained by the NASA Goddard Earth Sciences
Data and Information Services Center. Yearly average chlorophyll a
and CDOM data and maps used in this study were derived from 9 and
4 km resolution data, respectively
814 Conserv Genet (2016) 17:811–821
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Allelic states of nuclear DNA (H3) sequences were
calculated using Phase 2.1 (Stephens and Donnelly 2003)
as implemented in DNASP v.5.10.01 (Librado and Rozas
2009). Three replicate phase runs were conducted using
100 burn-in steps and 1000 iterations. Phase results were
used to estimate observed heterozygosity (Ho), expected
heterozygosity (H
) and an exact test of Hardy–Weinberg
equilibrium (HWE) using 100,000 steps of Markov chain
in Arlequin (Excoffier and Lischer 2010).
The best-fit model of DNA sequence evolution was
estimated using MEGA v.6.0 (Tamura et al. 2013). The
AIC (Akaike Information Criterion) indicated that Jukes-
Cantor (JC) for COI and 16S, and Tamura 3-parame-
ter ?Gamma (T92 ?G), with gamma value (G =0.05)
for H3 were the best-fit models. We computed pairwise U
for all pairs of populations that incorporates a model of
sequence evolution (Weir and Cockerham 1984; Excoffier
et al. 1992). The significance of the genetic distances was
tested by permuting the haplotypes or individuals between
the populations (10,000 iterations) in Arlequin, and
simultaneous tests correction adjusted using the modified
false discovery rate (FDR) method (Narum 2006).
To test genetic partitioning among different populations
and population groups (shown in Table 3)ofH. edulis,we
tested the significance of the covariance components
associated with the different possible levels of genetic
structure (within individuals, within populations, within
groups of populations, among groups) using non-paramet-
ric permutation procedures as part of the AMOVA
framework implemented in Arlequin (Excoffier et al.
1992). In order to visualize the genetic relationships
between populations, GENALEX 6.5 (Peakall and Smouse
2012) was used to construct a principle coordinate analysis
(PCoA) of the pairwise U
matrix. PopArt software
( was used for inferring and
visualizing genealogical relationships among populations
using median joining network approach (Bandelt et al.
1999). In order to estimate the isolation by distance, we
performed a Mantel test for each marker (COI, 16S and
H3). The significance of correlation between genetic dis-
tance (U
, log) and geographic distance (log) were cal-
culated using IBDWS 3.23 (Jensen et al. 2005). The
geographic distances among sampling locations were
measured along Okinawa Main Island coast using Google
Maps (
We sequenced a 545 bp fragment of the COI gene for 149
individuals and a 431 bp fragment of 16S for 143 indi-
viduals of H. edulis sampled across six locations of Oki-
nawa Main Island (Fig. 2; Table 1). Individual numbers
per population (N), number of haplotypes (H), haplotype
diversity (Hd), number of polymorphic sites (S), and
nucleotide diversity (p) for COI and 16S are listed in
Table 1. Overall, the numbers of haplotypes in COI and
16S were 8 and 9 respectively, and the corresponding
haplotype diversity was relatively similar in both COI
(Hd =0.84) and 16S (Hd =0.82). The average haplotype
diversity on the west coast (COI: Hd =0.69 and 16S:
Hd =0.67) was higher than that on the east coast (COI:
Hd =0.40 and 16S:Hd =0.21). We also sequenced a
327 bp of nDNA H3 for 146 specimens. Average values of
observed and expected heterozygosity in west coast pop-
ulations (Ho =0.05 and H
=0.39) were higher than that
in east coast population (Ho =0.03 and H
(Table 1). Non-significant Fu’s Fs tests provide no statis-
tical support for recent demographic changes in Okinawan
populations of H. edulis (Table 1).
The median-joining parsimony networks (Fig. 3a, b)
based on mtDNA haplotypes sampled across all Okinawan
populations of H. edulis revealed the presence of a mod-
erate number of mid-frequency haplotypes. Consistently,
the networks were not characterized by a starburst shape
(i.e. a few very common haplotypes and many singletons),
which is the most commonly observed pattern in popula-
tions of shallow coral reef organisms that has been attrib-
uted to population expansion following Pleistocene post-
glacial range expansion (Conroy and Cook 2000).
The networks also allow inferring trends of genetic
partitioning (Fig. 3). Seven COI haplotypes were sampled
in the east coast sites and four were detected in the west
(eight and four 16S haplotypes respectively). Although
most haplotypes were shared across sites, shifts in haplo-
type frequencies indicate a certain degree of genetic iso-
lation among sites (Fig. 2). The haplotype networks and
maps illustrate a decrease of genetic diversity and high
degree of isolation of the Uruma population (HDU) indi-
cated by the low number of shared haplotypes with other
sites. The parsimony networks constructed with H3 indi-
cated a majority of shared haplotypes with frequency shifts
among populations (Fig. 3c).
Pairwise comparisons among populations revealed a
high degree of genetic structuring of H. edulis across
Okinawa Island. Twelve of fifteen pairwise comparisons
had high and significant values of F
(Appendix S1) and
inferred from mitochondrial COI after correcting for
multiple comparisons (thirteen significant comparisons
inferred from 16S). Most comparisons between east and
west sites were significant (Table 2) and the degree of
genetic connectivity among sites at either side of the island
was also different. Whereas in the west, genetic cohesion
was indicated by lower pairwise U
values and less sig-
nificant comparisons (Table 2), populations in the east
showed high and significant pairwise U
values between
Conserv Genet (2016) 17:811–821 815
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Uruma and Awase (COI: U
=0.75, P\0.0001; 16S:
=0.49, P\0.0001; Table 2). Thus far, only these
sites on the eastern coast of the Island have been confirmed
to harbor H. edulis; during the course of this study we
searched many other locations and we did not find any
other H. edulis populations (T. Soliman, unpublished data).
The AMOVA indicated that overall population structure
was significant (COI: U
=0.490, P\0.0001; 16S:
=0.341, P\0.0001; H3: U
=0.121, P\0.0001).
Although grouping populations into east and west coast sites
had no statistical support (COI: U
=0.077, P\0.40;
16S: U
=0.003, P=0.47; H3: U
=–0.046, P=0.92;
Table 3), this was possibly driven by further genetic struc-
turing among sites within each coast as indicated by high and
significant U
=0.450, P\0.0001; 16S:
=0.340, P\0.0001; H3: U
P\0.0001). However, additional subdivision into four
groups [(1) HDS ?HDO, (2) HDR ?HDM, (3) HDW, (4)
HDU] resulted in a marginally significant among groups
variance component (COI: U
=0.517, P=0.02; 16S:
Fig. 3 Haplotype networks inferred from aCOI, b16S rRNA, and
cH3 sequences from Holothuria edulis across Okinawa Island, Japan.
Each circle represents a different haplotype, with size proportional to
its frequency. The colors represent the proportion of individuals from
each sampling site carrying a particular haplotype. Black circles are
unsampled haplotypes. HDM Motobu, HDO Oyama, HDR Ryugu,
HDS Sunabe, HDU Uruma, and HDW Awase
816 Conserv Genet (2016) 17:811–821
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=0.241, P=0.11; H3: U
=0.169, P=0.06;
Table 3). The Mantel test indicated significant correlations
between genetic distance and geographic distance among
populations for both COI (r=0.63, P=0.008) and 16S
(r=0.62, P=0.007), but this was not significant for H3
(r=–0.1688, P=0.67) (Fig. 4). Overall, the results of
mtDNA and nuclear DNA haplotype analyses of the sea
cucumber H. edulis showed a relatively clear geographical
pattern between east and west coast populations (Fig. 3).
The PCoA confirmed the genetic isolation of the Uruma
(HDU) based on mtDNA (COI and 16S), while H3 showed
the isolation of Uruma (HDU) and Sunabe (HDS) from the
other populations (Fig. 5). However, PCoA showed that
Motobou (HDM) and Oyama (HDO) were isolated from
other populations in the western coast of the Island.
Our examination of mtDNA (COI and 16S) sequences
showed high levels of haplotype diversity and low levels of
nucleotide diversity among five populations of H. edulis
(HDM, HDO, HDS, HDR, HDW). Similar patterns have
previously been reported in other sea cucumber species
such as Holothuria mammata (Borrero-Pe
´rez et al. 2011);
H. polii (Vergara-Chen et al. 2010), H. arguinensis (Ro-
drigues et al. 2015), and H. atra and H. whitmaei (Skillings
et al. 2014). However, our study showed low haplotype
diversity and low nucleotide diversity in the Uruma (HDU)
population, and for nuclear DNA (H3) the HDU population
also had a low level of expected heterozygosity compared
to the other populations.
Our results indicate the genetic variation of H. edulis is
highly structured across Okinawa Main Island, and also
that there is a correlation between geographic distance and
genetic distance. Previously, Skillings et al. (2014)
observed a high degree of genetic structure over relatively
short geographic distances in H. atra in the Central Pacific,
and Vergara-Chen et al. (2010) observed genetic isolation
between sites inside and outside of a lagoon in Spain for H.
polii (but see Valente et al. 2014). Reduced gene flow in
sea cucumbers is counter-intuitive given the potential for
dispersal of the larval stages and the extended distribu-
tional ranges of some species (Skillings et al. 2014).
Although details of the larval biology of sea cucumbers are
largely unknown, the pelagic larval duration (PLD) has
been documented to be at least 20 days for some species
(Laxminarayana 2005), and sufficient for maintaining
species cohesion over the large geographic areas that H.
edulis,H. atra, and, to a lesser extent, H. polli are dis-
tributed in. In H. edulis, we observed a strong reduction of
gene flow over an unprecedentedly small geographic scale.
One possibility is that the biogeographic characteristics or
physical barriers of Okinawa Main Island promote such a
reduction of gene flow. White et al. (2015) recently
demonstrated that the amphipod species Leucothoe vul-
garis, which has limited larval dispersal, has different east
and west coast genotypes on Okinawa Main Island, and
speculated this was caused by Pleistocene sea level chan-
ges (Ni et al. 2014) and/or geographic discontinuity (Cas-
telin et al. 2012).
Another possibility to explain our observed results is
that the life history traits or reproduction patterns of H.
edulis favor low dispersal capability. Uthicke (1997)
revealed that *24 % of H. edulis undertake fission each
year and it has the same asexual reproduction pattern with
two other species of sea cucumber, H. atra and Stichopus
chloronotus. Uthicke’s estimate of annual fission rates
emphasizes that asexual reproduction is an important
method of population size maintenance for all holothurian
species on all reefs studied.
The most striking result of the present study was the
genetic break between the H. edulis population in Uruma
(HDU) and all other populations, which was supported by
genetic data from all three DNA markers examined.
Haplotype diversity was lower in the Uruma population
than in all the other populations, with low numbers of
haplotypes for the COI, 16S, and H3 markers, and with no
exclusive haplotypes located in this area. Strikingly, we
observed a high degree of genetic isolation between Uruma
and Awase (HDU and HDW), despite these sites being
very close to each other (*10 km apart).
Table 2 U
pairwise values for Holothuria edulis across Okinawa
Main Island inferred from mtDNA and nDNA
COI (above diagonal) and 16S (below diagonal)
HDM 0.14* -0.01 0.18* 0.64* 0.40*
HDO 0.37* 0.04 0.02 0.59* 0.35*
HDR 0.13 0.16 0.09 0.69* 0.38*
HDS 0.39* 0.01 0.07 0.61* 0.26*
HDU 0.27* 0.71* 0.47* 0.72* 0.75*
HDW 0.24* 0.11* 0.01 0.19* 0.49*
HDO 0.17
HDR 0.41* 0.14
HDS 0.16* -0.23 0.23
HDU 0.50* 0.18* -0.11 -0.26
HDW -0.25 -0.68 0.56* 0.27 0.06
Sample sites are indicated in Table 1and Fig. 1.HDM Motobu, HDO
Oyama, HDR Ryugu, HDS Sunabe, HDU Uruma, and HDW Awase
* Significant values after correcting for multiple comparisons
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Table 3 Analysis of molecular variance (AMOVA) of Holothuria edulis for tests of different geographical groupings: A, B, C and D
Variation A B C D
Var. (%) Fixation indices Pvalue Var. (%) Fixation indices P value Var. (%) Fixation indices Pvalue Var. (%) Fixation indices Pvalue
Among groups 7.73 U
=0.077 0.40 53.37 U
=0.533 0.06 53.04 U
=0.530 0.17 51.67 U
=0.517 0.02*
A. pop. within groups 41.48 U
=0.449 \0.0001* 4.53 U
=0.093 \0.0001* 11.12 U
=0.237 \0.0001* 0.50 U
=0.010 0.27
Within populations 50.78 U
=0.492 \0.0001* 42.28 U
=0.577 \0.0001* 35.84 U
=0.642 \0.0001* 47.83 U
=0.522 \0.0001*
16S rRNA
Among groups 0.27 U
=0.003 0.47 8.75 U
=0.088 0.33 21.25 U
=0.213 0.15 24.09 U
=0.241 0.11
A. pop. within groups 34.18 U
=0.343 \0.0001* 27.25 U
=0.299 \0.0001* 20.63 U
=0.262 \0.0001* 11.78 U
=0.155 0.03*
Within populations 65.55 U
=0.344 \0.0001* 64.00 U
=0.360 \0.0001* 58.12 U
=0.419 \0.0001* 64.13 U
=0.241 \0.0001*
Among groups -4.58 U
=-0.046 0.92 16.68 U
=0.167 0.13 7.37 U
=0.074 0.33 16.99 U
=0.170 0.07
A. pop. within groups 16.42 U
=-0.157 \0.0001* 7.02 U
=0.084 \0.0001* 15.42 U
=0.167 \0.0001* 4.21 U
=0.051 0.04*
Within populations 88.16 U
=0.118 \0.0001* 76.30 U
=0.237 \0.0001* 77.21 U
=0.228 \0.0001* 78.80 U
=0.212 \0.0001*
region variance component relative to total variance; U
between population within region variance component divided by the sum of itself and within population variance; U
sum of the
variance due to region and population within region divided by the total variance
AEast (g1) and West (g2), BWest (g1), BAwase (g2) and Uruma (g3), CWest & Awase (g1) and Uruma (g2) and D-g1(HDS&HDO), g2 (HDR&HDM), g3 HDW and g4 HDU
* Significant values (P\0.05)
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The observed reduction in genetic diversity and genetic
isolation at Uruma may be a consequence of a shift to
asexual reproduction. Previously, high rates of asexual
reproduction have been observed in Holothuria atra at
eutrified sites compared to pristine reefs (Conand 1996).
The Uruma population is located near the Kaichu-Doro
Causeway, the construction of which was recently shown
to have impacted much of the marine biota in the area,
although echinoderms were not examined in detail (Reimer
et al. 2015). As well, Kin Bay’s environment has much
higher chlorophyll a and CDOM levels than the sur-
rounding oligotrophic waters of Okinawa (Fig. 1), and
historical records indicate environmental degradation (red
tides, oil spills) occurring within Kin Bay from the 1970s
(Reimer et al. 2015). Such environmental differences and/
or degradation could at least partially explain the observed
differences in the Uruma population. However, much more
data are needed before such theories can be confirmed or
denied, and this is an area of research that should be
examined in more detail in future studies.
Fig. 4 MANTEL test for matrix correlation between log (genetic distance: U
) and log (geographic distance) of COI, 16S and H3 among 6
populations of sea cucumber Holothuria edulis across Okinawa Island, Japan
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Friedman et al. (2011) noted that many of the Pacific’s
sea cucumber fisheries are under-performing due to over-
exploitation and ecological stress causing relatively large-
scale depletions of stock. Therefore, countries with rela-
tively less fisheries management have not been able to
preserve sea cucumber stocks to appropriate levels. Bio-
logical conservation of exploited species such as sea
cucumbers depends on local-level regulatory measures and
international organizations that regulate trade (Purcell et al.
2014a,b). Regardless of the causes of our observed results,
these results have important implications for the manage-
ment of H. edulis in Okinawa. The results highlight the
need to empirically investigate genetic connectivity, and
demonstrate the difficulty of making predictions for marine
resources without fine-scale data. The reduced gene flow
observed here at a reduced geographic scale (*10 km)
highlights the importance of local management of resour-
ces. Given the degree of genetic isolation, the Uruma
population may be demographically closed, implying the
risk of local extirpation is high. Therefore, studies on other
sea cucumber species in the Kaichu-Doro area and Oki-
nawa are needed to aid in the management this important
marine resource in Okinawa.
Acknowledgments The authors thank Dr. Franc¸ois Michonneau for
providing technical advice during the DNA extraction and T. Ohara,
O. Takama, K. Hamamoto, Dr. J. Montenegro, M. Mizuyama, and R.
Diaz for help with sample collection. T.S. was supported by Ministry
of Higher Education of the Egyptian Government during this study in
Japan. J.D.R. was funded by a Japan Society for the Promotion of
Science (JSPS) ‘Zuno-Junkan’ grant entitled ‘Studies on origin and
maintenance of marine biodiversity and systematic conservation
planning’. I.F.-S. was funded by a JSPS postdoctoral fellowship for
overseas researchers. We thank two anonymous reviewers for their
constructive comments, which improved the manuscript.
Acker JG, Leptoukh G (2007) Online analysis enhances use of NASA
earth science data. EOS Trans Am Geophys Union 88(2):14–17
Arndt A, Marquez C, Lambert P, Smith MJ (1996) Molecular
phylogeny of eastern Pacific sea cucumbers (Echinodermata:
Holothuroidea) based on mitochondrial DNA sequence. Mol
Phylogenet Evol 6:425–437
Bandelt H, Forster P, Ro
¨hl A (1999) Median-joining networks for
inferring intraspecific phylogenies. Mol Biol Evol 16(1):37–48
´rez G, Gonza
¨emert M, Pe
´rez-Ruzafa A, Marcos
C (2011) Phylogeography of the Atlanto-Mediterranean sea
cucumber Holothuria (Holothuria) mammata: the combined
effects of historical processes and current oceanographical
pattern. Mol Ecol 20:1964–1975
Castelin M, Lorion J, Brisset J, Cruaud C, Maestrati P, Utge J, Samadi
S (2012) Speciation patterns in gastropods with long-lived larvae
from deep-sea seamounts. Mol Ecol 21:4828–4853
Choo PS (2008) Population status, fisheries and trade of sea
cucumbers in Asia. In: M.V. Toral-Granda, A. Lovatelli, M.
Vasconcellos. (ed.), Sea cucumbers. A global review on fisheries
and trade. FAO, Rome
Colgan DJ, McLauchlan A, Wilson GDF, Livingston S, Macaranas J,
Edgecombe GD, Cassis G, Gray MR (1998) Molecular
Coord. 2 (9.77%)
Coord. 1 (87.32%)
Coord. 2 (12.50%)
Coord. 1 (84.79%)
Coord. 2 (30.57%)
Coord. 1 (61.76%)
Fig. 5 Principal coordinate analysis (PCoA) based on pairwise U
values of COI, 16S and H3 for Holothuria edulis from the east (blue)
and west (red) coasts of Okinawa Island, Japan. HDM Motobu, HDO
Oyama, HDR Ryugu, HDS Sunabe, HDU Uruma, and HDW Awase.
(Color figure online)
820 Conserv Genet (2016) 17:811–821
Author's personal copy
phylogenetics of the Arthropoda: relationships based on histone
H3 and U2 snRNA DNA sequences. Aust J Zool 46:419–437
Conand C (1996) Asexual reproduction by fission in Holothuria atra:
variability of some parameters in populations from the tropical
Indo-Pacific. Oceanol Acta 19(3–4):209–216
Conand C (2008) Population status, fisheries and trade of sea
cucumbers in Africa and Indian Ocean, In Toral-Granda V.,
Lovatelli A. and Vasconcellos M. (eds). Sea cucumbers. A
global review on fishery and trade. FAO Fisheries Technical
Paper No. 516. FAO, Rome, pp 153–205
Conand C, Muthiga N. (eds) (2007) Commercial sea cucumbers: a
review for the Western Indian Ocean. WIOMSA Book Series
No. 5
Conroy CJ, Cook JA (2000) Phylogeography of a post-glacial
colonizer: Microtus longicaudus (Rodentia: Muridae). Mol Ecol
Dissanayake DCT, Stefansson G (2010) Abundance and distribution
of commercial sea cucumbers in the coastal waters of Sri Lanka.
Aquat Living Resour 23(3):303–313
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series
of programs to perform population genetics analyses under
Linux and Windows. Mol Ecol Resour 10:564–567
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular
variance inferred from metric distances among DNA haplotypes:
application to human mitochondrial DNA restriction data.
Genetics 131:479–491
Friedman K, Eriksson H, Tardy E, Pakoa K (2011) Management of
sea cucumber stocks: patterns of vulnerability and recovery of
sea cucumber stocks impacted by fishing. Fish Fish 12:75–93
Fu YX (1997) Statistical tests of neutrality of mutations against
population growth, hitchhiking and background selection.
Genetics 147:915–925
Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web
service. BMC Genetics 6:13. v.3.23
Kamidaira Y, Uchiyama Y, Mitarai S, Sakagami T (2014) Effects of
the submesoscale anticyclonic eddies induced by Kuroshio in
East China Sea. Proceedings of the Twenty-fourth International
Ocean and Polar Engineering Conference Busan, Korea, June
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S,
Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton
B, Mentjies P, Drummond A (2012) Geneious Basic: an
integrated and extendable desktop software platform for the
organization and analysis of sequence data. Bioinformatics
Laxminarayana A (2005) Induced spawning and larval rearing of the
sea cucumbers, Bohadschia marmorata and Holothuria atra in
Mauritius. SPC Beche-de-mer Inf Bull 22:48–52
Lessios HA, Kessing BD, Pearse JS (2001) Population structure and
speciation in tropical seas: global phylogeography of the sea
urchin Diadema. Evolution 55:955–975
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive
analysisof DNA polymorphism data.Bioinformatics25:1451–1452
Narum SR (2006) Beyond Bonferroni: less conservative analyses for
conservation genetics. Conserv Genet 7:783–787
Ni G, Li Q, Kong L, Yu H (2014) Comparative phylogeography in
marginal seas of the northwestern Pacific. Mol Ecol 23:534–548
Palumbi SR, Martin AP, Romano S, Mcmilla WO, Stice L,
Grabowski G (1991) The simple fool’s guide to PCR. Depart-
ment of Zoology, University of Hawai‘i, Honolulu
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel.
Population genetic software for teaching and research-an update.
Bioinformatics 28:2537–2539
Power ME, Tilman D, Estes JA, Menge BA, Bond WJ, Mills LS,
Gretchen D, Castilla JC, Lubchenco J, Paine RT (1996)
Challenges in the quest for keystones. Bioscience 46:609–620
Purcell SW, Gossuin H, Agudo NS (2009) Status and management of
the sea cucumber fishery of La Grande Terre, New Caledonia.
WorldFish Center Studies and Reviews. Penang, Malaysia: The
WorldFish Center
Purcell SW, Lovatelli A, Pakoa K (2014a) Constraints and solutions
for managing Pacific Island sea cucumber fisheries with an
ecosystem approach. Mar Policy 45:240–250
Purcell SW, Polidoro BA, Hamel J-F, Gamboa RU, Mercier A
(2014b) The cost of being valuable: predictors of extinction risk
in marine invertebrates exploited as luxury seafood. Proc R Soc
Reimer JD, Yang S-Y, White KN, Asami R, Fujita K, Hongo C, Ito S,
Kawamura I, Maeda B, Mizuyama M, Obuchi M, Sakamaki T,
Tachihara K, Tamura K, Tanahara A, Yamaguchi A, Jenke-
Kodama H (2015) Effects of causeway construction on envi-
ronment and biota of subtropical tidal flats in Okinawa, Japan.
Mar Pollut Bull 94(1–2):153–167
Rodrigues F, Valente S, Gonza
¨emert M (2015) Genetic
diversity across geographical scales in marine coastal ecosys-
tems: Holothuria arguinensis a model species. J Exp Mar Biol
Ecol 463:158–167
Schneider K, Silverman J, Woolsey E, Eriksson H, Byrne M, Caldeira
K (2011) Potential influence of sea cucumbers on coral reef
CaCO3 budget: a case study at One Tree Reef. J Geophys Res
Skillings DJ, Bird CE, Toonen RJ (2014) Comparative population
structure of two edible Indo-Pacific coral reef sea cucumbers
(Echinodermata: Holothuroidea). Bull Mar Sci 90(1):359–378
Stephens M, Donnelly P (2003) A comparison of Bayesian methods
for haplotype reconstruction from population genotype data. Am
J Hum Genet 73:1162–1169
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013)
MEGA6: molecular Evolutionary Genetics Analysis version 6.0.
Mol Biol Evol 30:2725–2729
Toonen RJ, Andrews KR, Baums IB, Bird CE, Concepcion CT, Daly-
Engel TS, Eble JA, Faucci A, Gaither MR, Iacchei M, Puritz JB,
Schultz JK, Skillings DJ, Timmers MA Bowen BW (2011)
Defining boundaries for applying ecosystem-based management:
a multispecies case study of marine connectivity across the
Hawaiian Archipelago. J Mar Biol #460173
Toral-Granda V (2008) Galapagos Islands: a hotspot of sea cucumber
fisheries in Central and South America. In V. Toral-Granda, A.
Lovatelli and M. Vasconcellos (eds). Sea cucumbers. A global
review of fisheries and trade. FAO Fisheries and Aquaculture
Technical Paper. No. 516. Rome, FAO, pp 231–253
Uthicke S (1997) The seasonality of asexual reproduction in
Holothuria (Halodeima) atra,Holothuria (Halodeima) edulis
and Stichopus chloronotus (Holothuroidea: Aspidochirotida) on
the Great Barrier Reef. Mar Biol 129:435–441
Uthicke S, Schaffelke B, Byrne M (2009) A boom–bust phylum?
Ecological and evolutionary consequences of density variations
in echinoderms. Ecol Monogr 79:3–24
Valente S, Serra
¨emert M (2014) West ver-
sus East MediterraneanSea: origin and geneticdifferentiationof the
sea cucumber Holothuria polii. Mar Ecol. doi:10.1111/maec.12156
Vergara-Chen C, Gonza
¨emert M, Marcos C, Perez-Ruzafa
A (2010) Genetic diversity and connectivity remain high
in Holothuria polii (Delle Chiaje 1823) across a coastal
lagoon-open sea environmental gradient. Genetica 138:895–906
Weir BS, Cockerham CC (1984) Estimating F–statistics for the
analysis of population structure. Evolution 38:1358–1370
White KN, Lorion J, Reimer JD (2015) Preliminary analyses reveal
strong genetic structure in populations of Leucothoe vulgaris
(Crustacea: Amphipoda: Leucothoidae) from Okinawa Japan.
Syst Biodivers. doi:10.1080/14772000.2015.1078856
Conserv Genet (2016) 17:811–821 821
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Supplementary resource (1)

... The Kuroshio Current, which is a warm tropical current that runs north along the Ryukyu Islands in southern Japan, is known as one of the most important oceanographic features across this region (Barkley, 1970), and is thought to be important in structuring the population of coral reef species in this region (Yasuda et al., 2014: Zayasu et al., 2016. In the central Ryukyus around Okinawajima Island, population genetic research has been conducted on local scale on the sea cucumber species Holothuria (Halodeima) edulis Lesson, 1830(Soliman et al., 2016a and Stichopus chloronotus Brandt, 1835(Soliman et al., 2016b. These studies have indicated that even within small geographic areas around Okinawajima Island, genetically different populations can be distinguished in these species. ...
... Potential reported causes of genetic diversity decline have included over-harvesting , coastal development (Soliman et al., 2016a), and coastal alteration (Nehemia and Kochzius, 2017). Our study partially supports these previous observations as Chatan and Uruma, which have comparatively well-developed urban coastlines (Masucci and Reimer, 2019), had the smallest number of COI haplotypes. ...
... Likewise, Kin and Uruma, separated by 13 km on Okinawajima Island's east coast, were significantly different. Similar results were previously observed for H. edulis in Okinawa (Soliman et al., 2016a), H. atra in Hawai'i (Skillings et al., 2011), H. scabra in Australia, (Uthicke and Benzie, 2001), and also for H. mammata (Grube, 1840) and H. polii (Borrero-Pérez et al., 2011;Valente et al., 2015) in the Mediterranean Sea. These results indicate that even geographically close sea cucumber populations may retain unique genetic diversity, and therefore each population may be needed to be protected separately. ...
Full-text available
Recently, sea cucumbers (Echinodermata: Holothuroidea) have been over-exploited in many areas of the world, including in the Ryukyu Islands, southern Japan, due to increases in their economic importance. Nevertheless, management and protection of sea cucumbers are insufficient worldwide. The black sea cucumber Holothuria (Halodeima) atra Jaeger, 1833, inhabits a large range across the Indo-West Pacific Ocean and is a widely harvested species. Here we conducted population genetic analyses on H. atra using partial mitochondrial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) to examine 11 different populations around three island groups in the middle Ryukyus; Okinawajima Island, the Kerama Islands, and the Sakishima Islands, all within Okinawa Prefecture. We found 27 haplotypes for COI and 16 haplotypes for 16S. Locations within national and quasi-national parks (Zamami Island, Keramas, and Manza, Okinawajima; managed by the national Ministry of Environment and Okinawa Prefecture, respectively) had the highest number of haplotypes, whereas locations with less management and more anthropogenic pressure had lower numbers The mean of all samples' genetic diversity indices was moderate with regards to both haplotype and nucleotide diversity. According to our results, Zamami Ama was the most genetically diverse location based on both markers used, likely because it is located within Kerama-Shoto National Park with comparatively stricter regulations than most other locations. Based on our COI sequences, three-quarters of the locations with the highest haplotype diversity were found to be distant from Okinawajima Island, indicating that the genetic diversity of H. atra was reduced around Okinawajima Island. Our results possibly reflect negative impacts from anthropogenic pressures such as over-harvesting and coastal development, although future comprehensive research including sequences of nuclear loci is needed to confirm this hypothesis.
... Both sexual reproduction and asexual reproduction of H. edulis were observed in nature (Uthicke 1997). So far, there are only a few DNA sequences such as COX1 and 16S rRNA of H. edulis were reported (Soliman et al. 2016). Lack of genetic resources has hindered conservation and utilization of H. edulis. ...
Full-text available
The complete mitochondrial genome of Holothuria edulis was obtained and described in this study. This complete mitochondrial genome is 15,743 bp in length and consists of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Except ND6 and 5 tRNAs, the others were encoded by the heavy strand. The overall base composition of the heavy-strand was 32.29% A, 15.25% G, 25.88% C, and 26.57% T, with a high A + T content of 58.86%. The phylogenetic analysis suggested that H. edulis was closest to H. pervicax. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Holothuroidea.
... Therefore, several efforts have been made to study and catalogue sea cucumber exploitation hotspots all over the world. Over-exploitation caused genetic flow loss among populations and in some places their complete extinction (Friedman et al., 2011;Soliman et al., 2016). One of the main reasons of this excessive harvest is the rising demand of the Asian luxury food and traditional medicine markets (Purcell et al., 2014). ...
Sea cucumbers (Holothuroidea) are ecologically important organisms for their bioturbation and alkalinization activities of the seabed. These species are extensively fished as they are considered luxury food. Sea cucumbers are also relevant for biomedical studies and the production of bioactive compounds. A few initiatives are recently evaluating sea cucumbers as novel aquaculture species. The aim of this study was to provide morphological and genetic information useful for the identification of Holothuria polii, the white spot sea cucumber (a common species of the Mediterranean Sea). We generated the complete sequence of the mitochondrial DNA (mtDNA) genome of this species and combined it with a detailed ossicle characterization of the sequenced specimen by scanning electron microscopic analysis. Ossicles (known also as sclerites) are anatomical features that can discriminate Holothuroidea species, including the closely related ones of the genus Holothuria. The complete mitochondrial genome was assembled, functionally annotated and then used to evaluate the phylogenetic relationship of H. polii against the other few Holothuroidea species for which the whole mtDNA was available. The 15,907 bp H. polii mtDNA sequence has the same gene order already reported for H. scabra, H. forskali and other species of the same class. Cox1 and 16S gene sequences were informative for species identification across the genus and could be used for the authentication of commercialized Holothuria spp. The mitochondrial genome sequence presented here provides the basis to a future analysis of the variability of H. polii populations in the Mediterranean region.
... Current circulation as influenced by coastal topography may further interact with the genetic effects of large variance in individual reproductive success to generate genetic structure over fine spatial scales (Banks et al., 2007;Nicastro et al., 2008). Similar patterns of genetic structure over small spatial scales has been observed for H. scabra in the Solomon Islands (Uthicke and Benzie, 2001b), and other Holothuria species such as H. edulis (Soliman et al., 2016), H. atra (Skillings et al., 2014), and H. polii (Vergara-Chen et al., 2010). Excluding the ELN and COR samples from the IBD analysis results in a significant correlation between geographic and genetic distance (Fig. 4B). ...
Sea cucumber (bêche-de-mer, Echinodermata: Holothuroidea) is one of the top internationally traded seafood varieties. Besides its direct nutritional benefits, it is continuously used in the traditional medicine in different areas and cultures in the world. This world-wide interest triggered various issues related to stocks´ declining and risks of species extinction. For these reasons, the current study was designed to provide molecular tools for accurate discrimination between two sea cucumber species that prevail the Mediterranean and Red Sea catches of these echinoderms in Egypt, that are Holothuria polii and H. sanctori. The power of three gene markers, i.e., 16S rDNA, 28S rDNA, and Histone H3 in achieving accurate DNA-based identification, as well as elucidating clear phylogenetic and genetic diversity differences between those two species was assessed. Among the three genes, 16S rDNA showed the highest potentials as genetic and phylogenetic species discrimination marker. Both 28s rDNA and H3 exhibited the least number of holothuroid reference sequences in the GenBank database. For genetic diversity within each species population, 16s rDNA exhibited the best potentials, followed by H3. 28s rDNA showed no genetic polymorphism at all. Moreover, the collective data of both H3 and 16s rDNA suggested a possible role of asexual reproduction behavior in H. sanctori in the reduction of genetic diversity, as a possible response to overfishing. Hence, the current research can recommend the simultaneous application of both 16s rDNA and H3 as accurate markers for genetic discrimination among H. polii, H. sanctori and other different holothuroid species.
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Crown-of-thorns starfish, Acanthasterplanci (COTS), are common in coral reefs of Indo-Pacific Ocean. Since they are highly fecund predators of corals, periodic outbreaks of COTS cause substantial loss of healthy coral reefs. Using complete mitochondrial DNA sequences, we here examined how COTS outbreaks in the Ryukyu Archipelago, Japan are reflected by the profile of their population genetics. Population genetics of the blue starfish, Linckia laevigata , which lives in the Ryukyu Archipelago, but not break out and the northern Pacific sea star, Asterias amurensis , which lives in colder seawater around the main Islands of Japan, were also examined as controls. Our results showed that As. amurensis has at least two local populations that diverged approximately 4.7 million years ago (MYA), and no genetic exchanges have occurred between the populations since then. Linckialaevigata shows two major populations in the Ryukyu Archipelago that likely diverged ∼6.8 MYA. The two populations, each comprised of individuals collected from coast of the Okinawa Island and those from the Ishigaki Island, suggest the presence of two cryptic species in the Ryukyu Archipelago. On the other hand, population genetics of COTS showed a profile quite different from those of Asterias and Linckia. At least five lineages of COTS have arisen since their divergence ∼0.7 MYA, and each of the lineages is present at the Okinawa Island, Miyako Island, and Ishigaki Island. These results suggest that COTS have experienced repeated genetic bottlenecks that may be associated with or caused by repeated outbreaks.
Population genetics of sandfish Holothuria scabra originated from four different locations (Phangnga, Satun, Trang and Krabi) in the Andaman Sea (west of peninsular Thailand) was examined by polymorphism of 12S rDNA sequences and microsatellites. In total, 30 haplotypes of 12S rDNA were observed (N=23, 14, 25 and 27 for respective samples). Limited sequence divergence (π=0.820%) but high haplotype diversity (0.873) were found. θST (0.0853) indicated that the female gene pool between Phangnga and Krabi samples was genetically differentiated (P < 0.05). In addition, significant genetic heterogeneity in haplotype distribution frequencies was observed between Phangnga and other samples and between Satun and Trang (P < 0.05). Microsatellite analysis revealed a moderate level of genetic diversity of these samples (N=31, 16, 30 and 42 for respective samples). The average number of alleles per locus and observed heterozygosity within geographic samples ranged from 6.667–10.667 and 0.604–0.699. Significant genetic differentiation was found for overall samples (FST=0.081, P < 0.05) and between Phangnga and each of the other samples (P < 0.01). An analysis of molecular variance (AMOVA) indicated that the gene pool of H. scabra in the Andaman Sea was genetically differentiated into 2 genetic stocks: Phangnga (A) and the remaining samples; Krabi, Satun and Trang (B) (P < 0.05). Phylogenetic and structure analyses revealed a distinct separation between these stocks. Our results provide valuable genetic information for management of natural stocks of H. scabra in Thailand.
Full-text available
Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world’s coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995–2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on ‘marine protected areas’ and ‘herbivory’ was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAR, RES, and GBR (4.6–8.4 times). Coral reefs in the RYS feature high levels of both endemism and anthropogenic threats, and subsequently they contain a concentration of some of the world’s most critically endangered marine species. To protect these threatened species and coral reef ecosystems, more data are needed to fill the research gaps identified in this study.
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In Japan, the subtropical Ryukyu Archipelago (RYS; also known as the Nansei Islands) with its coral reefs has been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of scientific literature in the Web of Science (WoS; 1995-2017) on six selected representative taxa spanning from protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate the clear need to study ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), and to study ‘understudied areas’ of some sub-regions away from marine research stations. Second, we compared the numbers of scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAB), Great Barrier Reef (GBR), and the Red Sea (RES). Not unexpectedly, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, research in the RYS on ‘marine protected areas’ and ‘herbivory’ was an order of magnitude lower than numbers in other regions. Additionally, while manuscript numbers on the RYS have increased from 1995 to 2016, the rate of increase (4.0 times) was seen to be lower than those in the CAB, RES, and GBR (4.6 to 8.4 times). As the RYS are considered to contain among the most critically endangered coral reef biodiversity in the world due to high levels of both endemism and anthropogenic threats, much work is urgently needed to address the areas of relative research weakness identified in this study.
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Given predicted increases in urbanization in tropical and subtropical regions, understanding the processes shaping urban coral reefs may be essential for anticipating future conservation challenges. We used a case study approach to identify unifying patterns of urban coral reefs and clarify the effects of urbanization on hard coral assemblages. Data were compiled from 11 cities throughout East and Southeast Asia, with particular focus on Singapore, Jakarta, Hong Kong, and Naha (Okinawa). Our review highlights several key characteristics of urban coral reefs, including “reef compression” (a decline in bathymetric range with increasing turbidity and decreasing water clarity over time and relative to shore), dominance by domed coral growth forms and low reef complexity, variable city-specific inshore-offshore gradients, early declines in coral cover with recent fluctuating periods of acute impacts and rapid recovery, and colonization of urban infrastructure by hard corals. We present hypotheses for urban reef community dynamics and discuss potential of ecological engineering for corals in urban areas.
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Sea cucumbers (Holothurians) are a group of marine invertebrates that are harvested worldwide in tropical and subtropical countries. Over the past decades, a signifi cant increase in the demand for sea cucumber has led to an explosion in exploitation often resulting in population declines in many producing nations. Because of the importance of sea cucumbers as a source of livelihood for many artisanal fi shers from developing countries and as a globally traded product, much interest has been generated for information on their biology, ecology and fi sheries management. Although management agencies and fi shing communities have recognized that sea cucumber fi sheries are in trouble worldwide, attempts at management have been largely unsuccessful due to several factors including: 1) the vulnerability of sea cucumbers to harvesting, 2) the artisanal nature of the fi shery that prevents fi sher communities from using alternative coping mechanisms and 3) the institutional and socio-economic barriers to management. Sea cucumber production has been declining in nations of the Western Indian Ocean in the last ten years. The reasons for the decline include: 1) a lack of ecological information for understanding species life histories, 2) a lack of understanding of the socio-economic realities of the fi shery and 3) inadequate monitoring and enforcement of fi shery regulations. The Western Indian Ocean Marine Science Association (WIOMSA) as part of its aim to serve the information needs of resource managers and communities for the sustainable management of marine resources in the WIO, approved a ‘Regional Sea Cucumber Project’ in 2006. This review was prepared as the baseline study of the project and aims to provide a comprehensive synthesis of the current state of knowledge on sea cucumbers in the WIO. The information used in the review comes from many sources including journal articles, theses and dissertations, and reports on all aspects of sea cucumbers in the region. Although the report focuses on the fi ve countries (Kenya, La Reunion, Madagascar, Seychelles, Tanzania) that are involved in the project, a brief description of the status of sea cucumbers in other countries of the WIO is also included.
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Echinoderms are the targets of considerable global artisanal and commercial fisheries, but efforts to effectively manage them suffer from poor understanding of population demographics and connectivity. Here we report population genetic data (mitochondrial COI sequence) for two congeneric sea cucumbers, Holothuria atra (Jaeger, 1833) and Holothuria whitmaei (Bell, 1887), throughout the Hawaiian Archipelago and Johnston Atoll to inform resource management. These two species share a wide range across the Indo-Pacific region, and are the most ubiquitous species on Hawaiian coral reefs. Both species have roughly similar haplotype diversity (h = 0.88 for H. atra, 0.83 for H. whitmaei), but the nucleotide diversity (π = 0.0087 and 0.0067, respectively) and effective number of alleles (AE = 8.3 and 5.9, respectively) were both lower for H. whitmaei. Regardless of the metric of population differentiation used, H. atra shows evidence for restricted gene flow relative to the congeneric H. whitmaei; global φST was 0.165 with 12.65% of variation in analysis of molecular variance is distributed among groups for H. atra, whereas global φST was –0.006 and 100% of the variation is within the three groups (Main Hawaiian Islands, Northwestern Hawaiian Islands, Johnston Atoll) for H. whitmaei. These data contribute to the growing body of literature cautioning against the extrapolation of single-species exemplar studies to management and highlight that even for such broadly-distributed species, local-scale management is justified because migration between the Main and Northwestern Hawaiian islands does not occur within ecologically relevant time frames.
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The ecosystem approach to fisheries (EAF) is a holistic paradigm that considers stocks of exploitable species, marine ecosystems and stakeholders. Management agencies must strike a balance between their capacity constraints and the requisites of management measures. Most small-scale sea cucumber fisheries of Pacific Islands have been plundered while others are being opened to commercial exploitation. Data from fishery managers and a regional workshop were used to assess the current problems, institutional constraints and solutions to the management of sea cucumber fisheries in 13 Pacific Island countries (PICs). Technical capacity was often strong for some management actions such as developing marine reserves but weak for others, such as enforcement. Using multi-disciplinary indicators, half of the fisheries were diagnosed by their managers as being overfished or depleted, despite evidence of optimistic bias. Fishery governance varied greatly among the PICs, and co-management frameworks were not typical of any cultural region. Management objectives were prioritised differently among managers but most highly ranked was to protect ecological resilience. The fishery managers proposed different sets of regulatory measures and various management actions, such as surveys to collect socio-economic and fishery-dependent data, support for local governance and strong enforcement – all widely under-practised. Pacific sea cucumber fisheries exemplify how the transition to an EAF by management institutions must involve reorganisation of their technical and human-resource capacities among management tasks. Levies on exports need to be internalised to fund improved management. Management agencies should consider a shift in resources from developing marine reserves, conducting underwater surveys and aquaculture-based restocking to strengthening enforcement capacity, stakeholder involvement and communication with fishers. In concert with these actions, short fishing seasons, shortlists of allowable species and tighter enforcement at export points may serve to turn the tide on boom-and-bust exploitation and safeguard biodiversity.
For maintaining biological diversity in the coral coasts around Ryukyu Islands, Japan, a role played by the adjacent Kuroshio warm current is anticipated to be necessary for larval and nutrient transport. In order to understand dynamics and mixing between Kuroshio and the islands, we develop a detailed ocean downscaling model around Ryukyu Islands in a doubly nested configuration using ROMS at horizontal resolutions down to 1km, forced by the assimilative JCOPE2 and JMAGSM/ MSM. The model successfully reproduces anticyclonic eddies that are significantly retained on the western side of the islands to promote lateral mixing in the area. Copyright © 2014 by the International Society of Offshore and Polar Engineers (ISOPE).
Preliminary phylogenetic analyses of specimens of a leucothoid amphipod, Leucothoe vulgaris, collected from sponges, ascidians, and coral rubble from Okinawa, Japan, were completed using mitochondrial COI and nuclear 18S ribosomal DNA sequences. Analyses of sequences from 83 specimens demonstrate that populations of L. vulgaris likely entail at least two cryptic species, which are reciprocally monophyletic and reproductively isolated. These two potentially cryptic species live in sympatry but are apparently morphologically identical, suggesting a geographically driven divergence process and secondary contact. Within each clade, two major subclades corresponding to the east and west coast of Okinawa Island were present, with divergence times of approximately 1.61–1.83 mya. This last result suggests a role of Pleistocene sea level changes in the current patterns of intra-specific genetic structure and highlights the need for a more comprehensive sampling of L. vulgaris throughout the Indo-west Pacific. © The Trustees of the Natural History Museum, London 2015. All Rights Reserved.
Okinawa, Japan is known for its high marine biodiversity, yet little work has been performed on examining impacts of numerous large-scale coastal development projects on its marine ecosystems. Here, we examine apparent impacts of the construction of the Kaichu-Doro causeway, which was built over 40years ago. The causeway is a 4.75km long embankment that divides a large tidal flat and has only two points of water exchange along its entire length. We employed quadrats, transects, sampling, visual surveys, and microbial community analyses combined with environmental, water quality data, and 1m cores, at five stations of two paired sites each (one on each side of Kaichu-Doro) to investigate how the environment and biota have changed since the Kaichu-Doro was built. Results indicate reduction in water flow, and site S1 was particularly heavily impacted by poor water quality, with low diversity and disturbed biotic communities. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.