ArticlePDF Available
Fisheries
Research
164
(2015)
130–134
Contents
lists
available
at
ScienceDirect
Fisheries
Research
j
ourna
l
ho
me
pa
ge:
www.elsevier.com/locate/fishres
Short
Communication
DNA
barcoding
reveals
targeted
fisheries
for
endangered
sharks
in
Indonesia
Andrianus
Sembiringa,g,
Ni
Putu
Dian
Pertiwia,
Angka
Mahardinia,
Rizki
Wulandaria,
Eka
Maya
Kurniasihb,
Andri
Wahyu
Kuncoroc,
N.K.
Dita
Cahyania,
Aji
Wahyu
Anggoroa,
Maria
Ulfad,
Hawis
Madduppab,
Kent
E.
Carpentere,
Paul
H.
Barberf,
Gusti
Ngurah
Mahardikaa,
aThe
Indonesian
Biodiversity
Research
Centre,
The
Animal
Biomedical
and
Molecular
Biology
Laboratory
of
Udayana
University,
Jl
Sesetan-Markisa
6,
Denpasar,
Bali,
Indonesia
bFaculty
of
Fishery
and
Marine
Science,
Bogor
Agricultural
Institute,
Jl
Rasamala,
Bogor,
West
Java,
Indonesia
cMarine
Science
Department,
Faculty
of
Husbandry,
Fisheries,
and
Marine
Science,
University
State
of
Papua,
Jalan
Gunung
Salju
Amban,
Manokwari,
Papua,
Indonesia
dFlora
and
Fauna
International,
Jl
Cumi-Cumi
15,
Banda
Aceh,
Sumatra,
Indonesia
eDepartment
of
Biological
Sciences,
Old
Dominion
University,
Norfolk,
VA
23529,
USA
fDepartment
of
Ecology
and
Evolutionary
Biology,
University
of
California
Los
Angeles,
Los
Angeles,
CA
90095-7239,
USA
gMaster
program
in
Environmental
Sciences,
Udayana
University,
Jl
P.B.
Sudirman,
Denpasar,
Bali,
Indonesia
a
r
t
i
c
l
e
i
n
f
o
Article
history:
Received
9
October
2014
Received
in
revised
form
4
November
2014
Accepted
9
November
2014
Handling
Editor
Prof.
George
A.
Rose
Keywords:
Shark
DNA
barcoding
Indonesia
a
b
s
t
r
a
c
t
Sharks
are
apex
predators
and
keystone
species
that
have
a
profound
influence
on
the
ecology
and
food-web
dynamics
of
coral
reefs
and
epipelagic
marine
ecosystems.
However,
sharks
are
being
heavily
overfished
compromising
the
health
of
the
world’s
reefs
and
pelagic
environments.
Although
Indonesia
is
the
world’s
largest
and
most
diverse
coral
reef
ecosystem,
information
on
the
exploitation
of
sharks
in
this
region
is
scarce.
Results
of
DNA
barcoding
of
shark
fin
revealed
two
alarming
findings:
(1)
a
rar-
ity
of
reef
sharks
that
should
dominate
Indonesia’s
coastal
ecosystems,
and
(2)
a
fishery
that
targets
endangered
sharks.
The
diversity
and
number
of
threatened
species
recovered
in
this
study
highlights
the
urgent
need
for
improved
regulation
and
control
of
Indonesia’s
shark
fishery.
©
2014
Elsevier
B.V.
All
rights
reserved.
1.
Introduction
As
apex
predators,
many
sharks
are
keystone
species
that
have
a
significant
influence
on
the
ecology
and
food-web
dynamics
of
coral
reef
and
epipelagic
ocean
ecosystems
(Ferretti
et
al.,
2010;
Myers
et
al.,
2007).
However,
shark
populations
have
declined
globally
by
up
to
90%
(Myers
et
al.,
2007),
largely
as
a
result
of
a
multi-
billion
dollar
industry
that
harvests
hundreds
of
millions
of
sharks
annually
(Chapman
et
al.,
2013)
and
life
history
traits
such
as
low
fecundity,
late
maturity,
and
a
long
gestation
period
that
make
shark
populations
particularly
sensitive
to
overfishing
and
habitat
degradation
(Baum
et
al.,
2003).
Global
shark
fisheries
are
largely
Corresponding
author
at:
The
Indonesian
Biodiversity
Research
Centre,
The
Animal
Biomedical
and
Molecular
Biology
Laboratory
of
Udayana
University,
Jl
Sesetan-Markisa
6,
Denpasar,
Bali
80226,
Indonesia.
Tel.:
+62
361
8423061;
fax:
+62
361
223791.
E-mail
address:
gnmahardika@indosat.net.id
(G.N.
Mahardika).
driven
by
the
demand
for
shark
fins,
a
key
ingredient
in
the
Asian
delicacy,
shark
fin
soup.
The
Convention
on
International
Trade
in
Endangered
Species
of
Wild
Fauna
and
Flora
(CITES)
currently
lists
many
sharks
as
Appendix
I
(species
threatened
with
extinction)
or
Appendix
II
(species
where
trade
must
be
regulated
to
prevent
over-
utilization).
A
further
60
sharks
and
rays
are
listed
as
“vulnerable”
or
“near
threatened”
(Camhi
et
al.,
2009).
While
CITES
designation
should
promote
regulation
of
international
trade
in
shark
prod-
ucts,
the
primary
commodity
resulting
from
shark
fisheries
are
fins.
Whole
sharks
are
rarely
landed
at
commercial
ports
(Clarke
et
al.,
2006;
Liu
et
al.,
2013)
throughout
much
of
the
world;
instead
sharks
are
“finned”
at
sea,
a
process
by
which
fins
are
removed
and
bod-
ies
discarded,
and
then
fins
dried
for
sale
to
wholesalers
(Fig.
1).
This
process
is
common
whether
sharks
are
the
targeted
fisheries
species
or
the
result
of
by-catch
(Afonso
et
al.,
2012).
Dried
fins
typ-
ically
lack
key
diagnostic
features,
making
identification
of
fins
to
species,
and
therefore
regulation
of
trade
in
fins,
extremely
chal-
lenging.
While
DNA
barcoding
based
on
a
short
fragment
of
the
mitochondrial
cytochrome
oxidase
I
(COI)
gene
has
been
used
to
http://dx.doi.org/10.1016/j.fishres.2014.11.003
0165-7836/©
2014
Elsevier
B.V.
All
rights
reserved.
A.
Sembiring
et
al.
/
Fisheries
Research
164
(2015)
130–134
131
Fig.
1.
Photographs
of
shark
and
shark-fin
sample
collection.
Sun-dried
fins
(left)
in
Bali,
November
1,
2011;
whole
shark
and
elasmobranch
auction
at
the
harbour
in
Lombok
(right),
July
12,
2012.
Source:
Indonesian
Biodiversity
Research
Centre.
identify
fins
to
species
(Holmes
et
al.,
2009;
Moftah
et
al.,
2011;
Pinhal
et
al.,
2012;
Wong
et
al.,
2009),
this
technique
is
not
widely
used
to
promote
regulation
of
shark
fisheries.
Comprised
of
more
than
17,000
islands,
Indonesia
is
the
largest
geographic
area
and
heart
of
the
“Coral
Triangle”,
a
six-nation
region
of
South
East
Asia
that
is
home
to
the
world’s
most
diverse
seas
(Carpenter
et
al.,
2011;
Dubinsky
and
Stambler,
2011;
Roberts
et
al.,
2002).
Approximately
30%
of
the
world’s
shark
and
ray
species
are
present
in
this
region
(Last
and
Stevens,
1994)
including
regional
endemics
unique
to
the
Coral
Triangle
and
other
broadly
distributed
Indian
and
Pacific
Ocean
species
(Barnett
et
al.,
2012;
Bond
et
al.,
2012;
Campana
et
al.,
2011;
Nadon
et
al.,
2012;
Oliver
et
al.,
2011).
The
high
value
of
shark
fins
on
global
markets
has
sparked
rapid
growth
in
shark-fishing
in
Indonesia
focused
on
supplying
fins
to
growing
markets
in
Asia.
Comprised
of
a
mix-
ture
of
commercial
and
opportunistic
artisanal
fisheries,
the
total
elasmobranch
catch
in
Indonesia
was
estimated
at
more
than
110,000
tonnes
in
2007
(Camhi
et
al.,
2009),
representing
the
largest
recorded
harvest
in
the
world
(Tull,
2009).
Despite
the
size
and
value
of
Indonesian
shark
fisheries,
the
expansive
nature
of
Indonesia
combined
with
the
diffuse
nature
of
the
shark
fin
fishery
means
that
basic
fisheries
data
needed
for
effective
management
and
regulation
in
Indonesia
(e.g.
species
composition,
harvest
lev-
els,
etc.)
is
severely
lacking.
2.
Materials
and
methods
We
collected
582
shark
fins
from
traditional
fish
markets
and
shark-fin
exporters
across
Indonesia
from
mid-2012
to
mid-2014,
including
Aceh,
Jakarta,
West
Java,
Central
Java,
East
Java,
Bali,
West
Kalimantan,
South
Sulawesi,
North
Sulawesi,
Maluku,
and
West
Papua.
Additional
samples
were
collected
from
shark
fin
export
warehouses
in
Cilacap
(Central
Java)
and
Tanjung
Luar
(West
Nusa
Tenggara)
(Fig.
2).
We
sampled
a
thin
slice
of
tissue
from
dried
fins
in
fish
markets.
In
export
warehouses,
we
randomly
sampled
a
minimum
of
five
caudal
fins
from
boxes
of
fresh
fins.
The
total
num-
bers
of
dried
and
fresh
fins
were
164
and
418,
respectively.
Samples
were
preserved
in
96%
alcohol
for
subsequent
DNA
analysis.
Whole
DNA
was
extracted
using
a
simple
Chelex
protocol
(Walsh
et
al.,
1991).
A
fragment
of
the
mitochondrial
cytochrome
oxidase
C
subunit-1
(COI)
was
amplified
using
AmplyTaq
RedTM
(Applied
Biosystems)
and
the
standard
fish
DNA-barcoding
primers
Fish-BCL
and
Fish-BCH
(Baldwin
et
al.,
2009).
The
amplification
parameters
were
an
initial
denaturation
of
94 C
for
15
min,
38
cycles
of
94 C
for
30
s,
50 C
for
30
s,
and
72 C
for
45
s,
with
a
final
extension
of
72 C
for
5
min.
PCR
products
were
visualized
via
electrophoresis
on
agarose
gels
and
ethidium
bromide
staining.
The
COI
fragment
could
be
amplified
and
sequenced
from
all
samples.
The
sequencing
was
conducted
using
both
forward
and
reverse
directions
at
the
University
of
California
Berkeley
Sequencing
Facility.
The
result
was
aligned
using
MEGA5
(Tamura
et
al.,
2007).
We
then
determined
species
identity
by
compar-
ing
sequences
to
GenBank
and
Barcode
of
Life
Data
Systems
(http://www.boldsystems.org)
databases
enforcing
a
sequence
homology
threshold
of
>99%
as
previously
applied
(Liu
et
al.,
2013).
3.
Results
DNA
barcoding
of
a
600–654
bp
of
mitochondrial
COI
gene
suc-
cessfully
determined
the
species
identity
of
582
fins
collected
from
markets
across
the
Indonesian
archipelago
based
on
a
99%
sequence
similarity
criterion
in
GenBank
and
Barcode
of
Life
Data
Systems
(BOLD)
databases.
In
total,
analyses
determined
40
different
shark
species
(Table
1).
Five
species
(silky,
scalloped
hammerhead,
blue,
big
eye
thresher,
and
thresher
sharks)
represented
more
than
50%
of
the
total
fins
sampled.
Silky
(19.10%),
scalloped
hammerhead
(10.50%)
and
blue
sharks
(8.20%)
were
the
most
common
species
recovered,
followed
by
bigeye
thresher
(7.60%)
and
thresher
sharks
(7.20%).
In
contrast,
29
species
were
observed
at
less
than
2%
of
the
total
samples,
including
7
species
that
were
represented
by
only
one
or
two
samples.
The
vast
majority
of
the
samples
(92%)
were
listed
as
“endan-
gered”
(1)
“vulnerable”
(12)
or
“near
threatened”
(19)
while
only
4
species
were
listed
as
species
of
least
concern.
The
remaining
3
species
are
classified
as
data
deficient.
Similarly,
83%
of
species
identified
were
pelagic
species
of
shark
while
only
17%
were
reef
sharks.
4.
Discussion
Identification
of
unknown
shark
fins
from
Indonesian
fish
mar-
kets
revealed
a
fishery
that
is
heavily
exploiting
threatened
and
near
threatened
species.
In
total,
80%
of
the
species
identified
are
either
considered
“endangered”
(1
sample)
“vulnerable”
(12
sam-
ples)
or
“near
threatened”
(19
samples).
In
total,
38.5%
of
all
fins
came
from
sharks
classified
as
endangered
or
vulnerable
and
54.1%
of
fins
came
from
sharks
listed
as
near
threatened.
In
contrast,
only
7.2%
of
fins
harvested
came
from
three
species
categorized
132
A.
Sembiring
et
al.
/
Fisheries
Research
164
(2015)
130–134
Fig.
2.
Sampling
sites
of
shark-fin
collection
in
Indonesia
during
2012–2014.
The
sites
were
Lampulo,
Banda
Aceh
(1),
Lhokseumawe,
Banda
Aceh
(2),
Meulaboh,
West
Aceh
(3),
Langsa,
Banda
Aceh
(4),
Simeulue
Island,
Aceh
(5),
Muara
Baru,
Jakarta
(6),
Pelabuhan
Ratu,
West
Java
(7),
Pelabuhan
Perikanan
Samudra
Cilacap,
Central
Java
(8),
Pelabuhan
Perikanan
Muncar,
East
Java
(9),
Bali
(10),
Tanjung
Luar,
Lombok
(11),
Paotere,
Makassar,
South
Sulawesi
(12),
Pelabuhan
Perikanan
Bitung,
North
Sulawesi
(13),
Pasar
Remu
Sorong,
West
Papua
(14),
Pasar
Jimbatan
Puri
Sorong,
West
Papua
(15),
Pasar
Sanggeng
Manokwari,
West
Papua
(16),
Pelabuhan
Samudra
Ambon,
Maluku
(17),
Singkawang
West
Kalimantan
(18).
as
species
of
“least
concern”.
Given
that
sharks
are
characterized
by
low
fecundity,
late
maturity,
and
a
long
gestation
period
(Baum
et
al.,
2003),
the
finding
that
nearly
93%
of
all
fins
sampled
came
from
species
viewed
by
IUCN
as
threatened
with
extinction
or
vulnerable
to
over-exploitation
strongly
suggests
that
Indonesian
shark
fisheries
are
unsustainable.
Fishing
effort
for
sharks
was
strong
biased
with
more
than
50%
of
the
total
samples
coming
from
five
species:
silky,
scal-
loped
hammerhead,
blue,
big
eye
thresher,
and
thresher
sharks.
The
endangered
scalloped
hammerhead
(CITES
Appendix
1)
represented
more
than
10%
of
the
total
fins
sampled.
Most
dis-
turbing,
this
high
frequency
of
scalloped
hammerheads
was
seen
across
sampling
locations,
including
Aceh,
Java,
Lombok,
Sulawesi,
Kalimantan
and
Papua,
indicating
that
fisherman
are
likely
specif-
ically
targeting
these
endangered
sharks
across
the
Indonesian
archipelago.
Similarly,
the
vulnerable
thresher
and
big
eye
thresher
sharks
comprised
nearly
15%
of
the
total
catch,
while
the
nearly
threatened
silky
and
blue
sharks
represented
19.10%
and
8.20%
respectively.
The
high
frequency
of
these
species
across
Indonesia
strongly
suggests
that
they
are
not
the
result
of
by-catch
or
small-
scale
artisanal
fisheries,
but
instead
result
from
large-scale
targeted
shark
fisheries.
Another
disturbing
finding
of
our
study
was
that
the
vast
major-
ity
(83%)
of
the
species
recovered
were
pelagic
sharks,
while
common
Carcharhiniformes
such
as
Galapagos
(0.52%),
grey
reef
(01.20%),
black-tip
reef
(3.61%),
and
white-tip
reef
shark
(0.86%)
that
typically
dominate
coral
reef
ecosystems
were
extremely
rare
as
were
common
reef
Orectolobiformes,
such
as
tawny
nurse
(1.37%)
and
brown-banded
bamboo
(0.86%)
sharks.
On
pristine
coral
reefs,
reef
sharks
make
up
a
nearly
63%
of
total
fish
biomass
(Sandin
et
al.,
2008).
Because
the
greatest
fishing
pressure
in
Indonesian
waters
is
in
shallow
coastal
areas
where
reef
sharks
typically
thrive,
the
alarmingly
low
number
of
reef
sharks
recovered
in
our
sam-
pling
strongly
indicates
that
reef-shark
populations
in
Indonesia
have
collapsed,
most
like
due
to
overfishing
(Allen
and
Erdmann,
2012)
as
happened
in
the
Great
Barrier
Reef
(Robbins
et
al.,
2006),
and/or
reef
degradation
(Burke
et
al.,
2011).
Low
incidence
of
reef
sharks
is
consistent
with
the
rarity
of
shark
sightings
during
scuba
activities
across
most
of
Indonesia,
with
the
exception
of
regions
of
Eastern
Indonesia
such
as
Raja
Ampat
(M.
Erdmann,
pers.
com-
mun.).
Indeed
results
show
that
18
reef
shark
fins
were
identified
from
samples
in
Western
Indonesia
and
19
in
Java,
whereas
32
and
36
were
identified
from
Eastern
Indonesia
and
Central
Indonesia.
Even
the
most
common
reef
shark
in
our
sampling,
the
blacktip,
was
not
observed
in
75%
of
sampling
locations
and
59%
of
black-
tip
fins
came
from
one
locality
in
Papua.
These
data
suggest
that
many
reef
sharks
may
be
ecologically
extinct
in
parts
of
Indonesian
waters.
While
sampling
revealed
that
a
diversity
of
sharks
entering
the
Indonesian
shark
fin
trade,
three
species
represented
new
records
for
Indonesia,
including
the
western
spotted
gummy,
galapagos,
and
whitecreek
sharks.
It
is
not
clear
whether
these
sharks
were
caught
while
migrating
through
Indonesian
waters
or
whether
there
are
resident
populations.
If
the
former
is
true,
fishing
pressures
within
Indonesian
waters
could
have
a
negative
impact
on
resident
populations
outside
Indonesia.
If
the
latter
is
true,
the
rarity
of
these
species
in
our
sample
may
indicate
that
their
popu-
lations
are
heavily
depressed,
requiring
special
conservation
status
within
Indonesia.
Although
this
study
only
provides
a
snapshot
of
the
Indone-
sian
shark
fishery,
our
study
does
provide
some
critical
insight
into
changes
in
fishing
effort.
Previous
research
published
in
2009
indicated
that
the
most
common
commercially
harvested
sharks
in
this
region
were,
in
order,
dusky,
spot-tail,
blue,
and
scalloped
hammerhead
sharks
(Ovenden
et
al.,
2009).
However,
while
blue
and
scalloped
hammerhead
sharks
were
common
in
our
sample,
spot-tail
sharks
were
less
common
and
no
dusky
sharks
were
recovered
despite
extensive
sampling
across
the
entire
Indone-
sian
archipelago.
This
sharp
discrepancy
between
studies
four
years
apart
may
signal
that
even
some
pelagic
shark
species
may
be
heavily
overfished,
resulting
in
a
precipitous
drop
in
species
abun-
dance
across
the
archipelago.
A.
Sembiring
et
al.
/
Fisheries
Research
164
(2015)
130–134
133
Table
1
Distribution,
catch
frequency,
IUCN/CITES
status
of
various
shark
species
harvested
in
different
geographical
areas
in
Indonesia.
No
Species
Total
Frequency
IUCN
status
1
Carcharhinus
falciformis
111
19.07%
Near
threatened
Silky
shark
2
Sphyrna
lewini
61
10.48%
Near
threatened
Scalloped
hammerhead
3
Prionace
glauca 48
8.25%
Endangered
Blue
shark
4
Alopias
superciliosus
44
7.56%
Vulnerable
Thresher
shark
5
Alopias
pelagicus
42
7.22%
Vulnerable
Bigeye
thresher
shark
6
Carcharhinus
sorrah
39
6.70%
Near
threatened
Spottail
shark
7
Carcharhinus
limbatus
21
3.61%
Near
threatened
Blacktip
shark
8
Isurus
oxyrinchus
21
3.61%
Vulnerable
Shortfin
mako
9
Rhizoprionodon
acutus
18
3.09% Least
concern
White-eyed
shark
10
Squalus
hemipinnis
17
2.92%
Near
threatened
Indonesian
shortsnout
spurdog
11
Galeocerdo
cuvier
12
2.06%
Near
threatened
Tiger
shark
12
Isurus
paucus
11
1.89%
Vulnerable
Long
fin
mako
13
Carcharhinus
longimanus
10
1.72%
Vulnerable
Whitetip
oceanic
shark
14
Centrophorus
niaukang
10
1.72%
Near
threatened
Taiwan
gulper
shark
15
Carcharhinus
melanopterus
9
1.55
Near
threatened
Blacktip
reef
shark
16
Carcharhinus
sealei
9
1.55%
Near
threatened
Blackspot
shark
17
Carcharhinus
brevipinna
9
1.55%
Near
threatened
Spinner
shark
18
Hemipristis
elongata
8
1.37%
Least
concern
Snaggletooth
shark
19
Nebrius
ferrugineus
8
1.37%
Vulnerable
Tawny
nurse
shark
20
Carcharhinus
amblyrhynchos
7
1.20%
Near
threatened
Grey
reef
shark
21
Hemitriakis
falcata
7
1.20%
Least
concern
Sicklefin
hound
shark
22
Mustelus
lenticulatus
7
1.20%
Least
concern
Spotted
smoothhound
23
Hemigaleus
microstoma
6
1.03%
Vulnerable
Sickle
fin
weasel
shark
24
Loxodon
macrorhinus
6
1.03%
Least
concern
Jordan’s
blue
dogshark
25
Sphyrna
zygaena
6
1.03%
Vulnerable
Smooth
hammerhead
Table
1
(Continued)
No
Species
Total
Frequency
IUCN
status
26
Chiloscyllium
punctatum
5
0.86%
Near
threatened
Brownbanded
bamboo
shark
27
Triaenodon
obesus
5
0.86%
Near
threatened
Whitetip
reef
shark
28
Hemitriakis
indroyonoi
4
0.69%
Data
deficient
Indonesian
houndshark
29
Carcharhinus
albimarginatus
4
0.69%
Near
threatened
Silvertip
shark
30
Carcharhinus
galapagensis
3
0.52%
Vulnerable
Galapagos
shark
31
Carcharhinus
plumbeus
3
0.52%
Vulnerable
Sandbar
shark
32
Squalus
montalbani
2
0.34%
Vulnerable
Philippines
spurdog
33
Squatina
legnota
2
0.34%
Data
deficient
Data
deficient
34
Carcharhinus
leucas
1
0.17%
Near
threatened
Bull
shark
35
Carcharhinus
amboinensis
1
0.17%
Data
deficient
Pigeye
shark
36
Carcharhinus
coatesi
1
0.17%
Data
deficient
Whitecreek
shark
37
Heptranchias
perlo
1
0.17%
Near
threatened
Sharpnose
sevengill
shark
38
Pseudocarcharias
kamoharai
1
0.17%
Near
threatened
Crocodile
shark
39
Atelomycterus
marmoratus
1
0.17%
Near
threatened
Coral
catshark
40
Carcharhinus
obscurus
1
0.17%
Vulnerable
Dusky
shark
Indonesia’s
marine
ecosystems
are
an
extremely
valuable
nat-
ural
resource
that
contributes
significantly
to
its
GDP
and
food
needs
of
its
people
(Barber
et
al.,
2014).
Because
of
the
importance
of
sharks
in
maintaining
healthy
marine
ecosystems,
achieving
the
biodiversity
preservation
and
food
security
goals
of
the
Coral
Triangle
Initiative
(www.coraltriangleinitiative.org)
will
require
enforcement
of
existing
fisheries
regulations
and
expanding
the
management
of
shark
fisheries
to
protect
ecologically
impor-
tant,
but
highly
threatened
shark
species.
Recently,
the
West
Papua
Province
enacted
regulations
prohibiting
the
capture
of
sharks,
rays
and
certain
other
fish
species
in
Raja
Ampat
waters
(www.rajaampatkab.go.id/index.php).
This
initiative
serves
as
a
model
that
could
be
adopted
and
enforced
by
other
districts
in
Indonesia
to
prevent
a
further
decline
in
Indonesia’s
vulnera-
ble
shark
population,
further
jeopardizing
its
already
imperilled
marine
ecosystems
(Burke
et
al.,
2011).
5.
Conclusion
The
high
frequency
of
“endangered”,
“vulnerable”,
and
“near
threatened”
taxa,
the
predominance
of
pelagic
sharks
entering
the
Indonesian
shark
markets,
and
absence
of
a
once
abundant
shark
species
should
be
a
wakeup
call
to
the
Indonesian
Government.
134
A.
Sembiring
et
al.
/
Fisheries
Research
164
(2015)
130–134
Acknowledgements
This
study
was
funded
by
the
Partnerships
for
Enhanced
Engagement
in
Research
(PEER)
Science
Programme
(AID-OAA-A-
11-00012)
funded
by
the
United
States
Agency
for
International
Development
(USAID)
and
the
National
Science
Foundation
(NSF)
in
partnership
with
NSF
PIRE
Programme
(OISE-0730256).
Facil-
ities
and
training
for
this
study
were
provided
by
UCLA
and
the
Smithsonian
Institution
under
USAID
(grant
number
497-A-00-
10-00008-00).
We
thank
B.
Subhan,
A.A.
Wibowo,
I.A.
Putra,
S.
Bahri,
Rahmad,
N.
Akbar,
P.
Akna,
WWF
Indonesia,
D.
Suprapti,
Agri,
Masriana,
Reef
Check
Indonesia,
P.
Borsa,
N.
Putra,
A.
Yusma-
linda,
Ambariyanto,
S.
Indriawan,
A.A.
Tarekat,
Stevanus,
A.
Arimbi,
C.A.K.
Hardani,
Ma’rufah,
A.
Kusuma
for
their
assistance
with
sam-
ple
and/or
data
collection.
References
Afonso,
A.S.,
Santiago,
R.,
Hazin,
H.,
Hazin,
F.H.V.,
2012.
Shark
bycatch
and
mortality
and
hook
bite-offs
in
pelagic
longlines:
interactions
between
hook
types
and
leader
materials.
Fish.
Res.
131–133,
9–14.
Allen,
G.R.,
Erdmann,
M.V.,
2012.
Reef
Fishes
of
the
East
Indies.
Tropical
Reef
Research,
vol.
I.
University
of
Hawaii
Press,
Perth,
Australia.
Baldwin,
C.C.,
Mounts,
J.H.,
Smith,
D.G.,
Weigt,
L.A.,
2009.
Genetic
identification
and
color
descriptions
of
early
life-history
stages
of
Belizean
Phaeoptyx
and
Astrapogon
(Teleostei:
Apogonidae)
with
comments
on
identification
of
adult
Phaeoptyx.
Zootaxa
2008,
1–22.
Barber,
P.H.,
Ablan-lagman,
M.C.A.,
Ambariyanto
Berlinck,
R.G.S.,
Cahyani,
D.,
Cran-
dall,
E.D.,
Ravago-gotanco,
R.,
Juinio-me˜
nez,
M.A.,
Mahardika,
I.G.N.,
Shanker,
K.,
Starger,
C.J.,
Toha,
A.H.A.,
Anggoro,
A.W.,
Willette,
D.A.,
2014.
Advancing
biodi-
versity
research
in
developing
countries:
the
need
for
changing
paradigms.
Bull.
Mar.
Sci.
90,
187–210.
Barnett,
A.,
Abrantes,
K.G.,
Seymour,
J.,
Fitzpatrick,
R.,
2012.
Residency
and
spatial
use
by
reef
sharks
of
an
isolated
seamount
and
its
implications
for
conservation.
PLoS
One
7,
e36574.
Baum,
J.K.,
Myers,
R.A.,
Kehler,
D.G.,
Worm,
B.,
Harley,
S.J.,
Doherty,
P.A.,
2003.
Col-
lapse
and
conservation
of
shark
populations
in
the
Northwest
Atlantic.
Science
299,
389–392.
Bond,
M.E.,
Babcock,
E.A.,
Pikitch,
E.K.,
Abercrombie,
D.L.,
Lamb,
N.F.,
Chapman,
D.D.,
2012.
Reef
sharks
exhibit
site-fidelity
and
higher
relative
abundance
in
marine
reserves
on
the
Mesoamerican
Barrier
reef.
PLoS
One
7,
e32983.
Burke,
L.,
Reytar,
K.,
Spalding,
M.D.,
Perry,
A.,
2011.
Reefs
at
Risk
Revisited.
World
Resource
Institute,
Washington,
DC.
Camhi,
M.D.,
Valenti,
S.V.,
Fordham,
S.V.,
Fowler,
S.L.,
Gibson,
C.,
2009.
The
Conser-
vation
Status
of
Pelagic
Sharks
and
Rays:
Report
of
the
IUCN
Shark
Specialist
Group
Pelagic
Shark
Red
List
Workshop.
IUCN
Species
Survival
Commission
Shark
Specialist
Group,
Newbury,
UK,
x
+
78
p.
Campana,
S.E.,
Dorey,
A.,
Fowler,
M.,
Joyce,
W.,
Wang,
Z.,
Wright,
D.,
Yashayaev,
I.,
2011.
Migration
pathways,
behavioural
thermoregulation
and
overwintering
grounds
of
blue
sharks
in
the
Northwest
Atlantic.
PLoS
One
6,
e16854.
Carpenter,
K.E.,
Barber,
P.H.,
Crandall,
E.D.,
Ablan-Lagman,
M.C.A.,
Ambariyanto
Mahardika,
G.N.,
Manjaji-Matsumoto,
B.M.,
Juinio-Me˜
nez,
M.A.,
Santos,
M.D.,
Starger,
C.J.,
Toha,
A.H.A.,
2011.
Comparative
phylogeography
of
the
coral
trian-
gle
and
implications
for
marine
management.
J.
Mar.
Biol.
2011,
1–14.
Chapman,
D.D.,
Frisk,
M.G.,
Abercrombie,
D.L.,
Safina,
C.,
Gruber,
S.H.,
Babcock,
E.A.,
Feldheim,
K.A.,
Pikitch,
E.K.,
Ward-Paige,
C.,
Davis,
B.,
Kessel,
S.,
Hei-
thaus,
M.,
Worm,
B.,
2013.
Give
shark
sanctuaries
a
chance.
Science
339,
757.
Clarke,
S.C.,
Magnussen,
J.E.,
Abercrombie,
D.L.,
McAllister,
M.K.,
Shivji,
M.S.,
2006.
Identification
of
shark
species
composition
and
proportion
in
the
Hong
Kong
shark
fin
market
based
on
molecular
genetics
and
trade
records.
Conserv.
Biol.
20,
201–211.
Dubinsky,
Z.,
Stambler,
N.,
2011.
Coral
Reefs:
An
Ecosystem
in
Transition.
Springer
Science
+
Business
Media
B.V.
Ferretti,
F.,
Worm,
B.,
Britten,
G.L.,
Heithaus,
M.R.,
Lotze,
H.K.,
2010.
Patterns
and
ecosystem
consequences
of
shark
declines
in
the
ocean.
Ecol.
Lett.
13,
1055–1071.
Holmes,
B.H.,
Steinke,
D.,
Ward,
R.D.,
2009.
Identification
of
shark
and
ray
fins
using
DNA
barcoding.
Fish.
Res.
95,
280–288.
Last,
P.R.,
Stevens,
J.D.,
1994.
Sharks
and
Rays
of
Australia.
CSIRO
Publishing,
Victoria,
Australia.
Liu,
S.Y.V.,
Chan,
C.L.C.,
Lin,
O.,
Hu,
C.S.,
Chen,
C.A.,
2013.
DNA
barcoding
of
shark
meats
identify
species
composition
and
CITES-listed
species
from
the
markets
in
Taiwan.
PLoS
One
8,
e79373.
Moftah,
M.,
Aziz,
S.H.A.,
El
Ramah,
S.,
Favereaux,
A.,
2011.
Classification
of
sharks
in
the
Egyptian
Mediterranean
waters
using
morphological
and
DNA
barcoding
approaches.
PLoS
One
6,
e27001.
Myers,
R.A.,
Baum,
J.K.,
Shepherd,
T.D.,
Powers,
S.P.,
Peterson,
C.H.,
2007.
Cascading
effects
of
the
loss
of
apex
predatory
sharks
from
a
coastal
ocean.
Science
315,
1846–1850.
Nadon,
M.O.,
Baum,
J.K.,
Williams,
I.D.,
Mcpherson,
J.M.,
Zgliczynski,
B.J.,
Richards,
B.L.,
Schroeder,
R.E.,
Brainard,
R.E.,
2012.
Re-creating
missing
population
base-
lines
for
pacific
reef
sharks.
Conserv.
Biol.
26,
493–503.
Oliver,
S.P.,
Hussey,
N.E.,
Turner,
J.R.,
Beckett,
A.J.,
2011.
Oceanic
sharks
clean
at
coastal
seamount.
PLoS
One
6,
e14755.
Ovenden,
J.R.,
Kashiwagi,
T.,
Broderick,
D.,
Giles,
J.,
Salini,
J.,
2009.
The
extent
of
population
genetic
subdivision
differs
among
four
co-distributed
shark
species
in
the
Indo-Australian
archipelago.
BMC
Evol.
Biol.
9,
40.
Pinhal,
D.,
Shivji,
M.S.,
Nachtigall,
P.G.,
Chapman,
D.D.,
Martins,
C.,
2012.
A
stream-
lined
DNA
tool
for
global
identification
of
heavily
exploited
coastal
shark
species
(genus
rhizoprionodon).
PLoS
One
7,
e34797.
Robbins,
W.D.,
Hisano,
M.,
Connolly,
S.R.,
Choat,
J.H.,
2006.
Ongoing
collapse
of
coral-
reef
shark
populations.
Curr.
Biol.
16,
2314–2319.
Roberts,
C.M.,
McClean,
C.J.,
Veron,
J.E.N.,
Hawkins,
J.P.,
Allen,
G.R.,
McAllister,
D.E.,
Mittermeier,
C.G.,
Schueler,
F.W.,
Spalding,
M.,
Wells,
F.,
Vynne,
C.,
Werner,
T.B.,
2002.
Marine
biodiversity
hotspots
and
conservation
priorities
for
tropical
reefs.
Science
295,
1280–1284.
Sandin,
S.A.,
Smith,
J.E.,
Demartini,
E.E.,
Dinsdale,
E.A.,
Donner,
S.D.,
Friedlander,
A.M.,
Konotchick,
T.,
Malay,
M.,
Maragos,
J.E.,
Obura,
D.,
Pantos,
O.,
Paulay,
G.,
Richie,
M.,
Rohwer,
F.,
Schroeder,
R.E.,
Walsh,
S.,
Jackson,
J.B.C.,
Knowlton,
N.,
Sala,
E.,
2008.
Baselines
and
degradation
of
coral
reefs
in
the
Northern
Line
Islands.
PLoS
One
3,
e1548.
Tamura,
K.,
Dudley,
J.,
Nei,
M.,
Kumar,
S.,
2007.
MEGA4:
molecular
evolution-
ary
genetics
analysis
(MEGA)
software
version
4.0.
Mol.
Biol.
Evol.
24,
1596–
1599.
Tull,
M.,
2009.
The
History
of
Shark
Fishing
in
Indonesia.
Asia
Research
Centre,
Murdoch
University,
Perth,
Australia,
pp.
1–24.
Walsh,
P.S.,
Metzger,
D.A.,
Higuchi,
R.,
1991.
Chelex
100
as
a
medium
for
simple
extraction
of
DNA
for
PCR-based
typing
from
forensic
material.
Biotechniques
10,
506–513.
Wong,
E.H.K.,
Shivji,
M.S.,
Hanner,
R.H.,
2009.
Identifying
sharks
with
DNA
barcodes:
assessing
the
utility
of
a
nucleotide
diagnostic
approach.
Mol.
Ecol.
Resour.
9,
243–256.
... Furthermore, an increasing demand for shark meat and liver oil supplies a near USD 1 Billion industry (Dulvy et al. 2014;O'Bryhim et al. 2017). Even though many countries are obligated by international treaty, applied under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), to monitor the species of shark that are traded within, and through their Rev Fish Biol Fisheries boarders (Dulvy et al. 2017;Cardeñosa et al. 2020;Prasetyo et al. 2020), products from endangered species of shark are readily available to members of the public (Sembiring et al. 2015;Wainwright et al. 2018;Cardeñosa 2019;Liu et al. 2021). ...
... DNA barcoding techniques have long been used to overcome these challenges, they allow positive identifications to be made from small samples of dried and processed fins that would otherwise be impossible to identify. These methods have already been applied throughout the world to identify the species of shark that a fin or meat came from (Shivji et al. 2002;Ward et al. 2008;Sembiring et al. 2015;O'Bryhim et al. 2017;Fields et al. 2018;Appleyard et al. 2018;Hobbs et al. 2019;Abdullah et al. 2020;Liu et al. 2021;French and Wainwright 2022;Neo et al. 2022). ...
... Work examining the shark fin trade in East and Southeast Asia has tended to concentrate on Hong Kong (Fields et al., 2018), mainland China (Cardeñosa et al. 2020, Indonesia (Sembiring et al. 2015;Prasetyo et al. 2020) and Singapore (Wainwright et al. 2018), while each of these represents a major trade hub for shark products, there are other trade hubs in the region. It is important that conclusions and management decisions are based on representative data from all major shark markets and distribution centers. ...
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Southeast Asia is a major shark product trade hub, and many of the world’s largest shark product selling markets are located in the region. Malaysia is the second largest importer of shark fins in the world, approximately 2500 metric tonnes of fins were imported between 2000 and 2016. The country is also a major shark fisher—the eighth largest in the world in terms of yearly catch. Yet the composition of the species of shark involved in the Malaysian trade remains largely unknown. Not knowing the composition of the sharks involved in the fin trade in a major trade hub presents challenges when it comes to determining conservation goals, setting appropriate catch quotas and establishing new, or revisiting previous conservation listings. Using a fragment of the mtDNA COI gene we attempted to DNA barcode 147 dried shark fins. We identified a number of fins that belonged to species listed on either CITES appendix I, or II, and the composition of the sharks identified in samples collected from Peninsular Malaysia appears to be different from that of other trade hubs within the region. Given these differences, we suggest that further DNA barcoding studies be performed throughout the region at regularly repeated intervals to build a more comprehensive picture of the sharks involved in the trade within the region and globally, this information will be useful to policy makers and conservation planners.
... Reporting fisheries catches at a high taxonomic resolution for both mandatory target and non-targeted species is vital, as detailed fisheries catch data are needed for the effective assessment of the impacts of fishing on populations and ecosystems and thus the management of fisheries resources (Abella, 2011;Clarke et al., 2006;Pauly et al., 2013). Yet, our analysis supports previous findings that accurate reporting of landed and discarded catches is still lacking for formerly non-targeted species groups such as sharks or for species with relatively low-economic value such as neritic tunas, which support important fisheries in all tuna RFMOs and are now increasingly targeted and incidentally caught as bycatch (Clarke et al., 2006;Clarke et al., 2007;Sembiring et al., 2015). ...
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Tuna Regional Fisheries Management Organizations (RFMOs) are responsible for conservation and sustainable management of transboundary tuna resources in Exclusive Economic Zones and Areas Beyond National Jurisdiction (ABNJ). The data collected and analyses performed by tuna RFMOs are one of the main sources of scientific information supporting the management, sustainable use and conservation of biodiversity in the ABNJ. An understanding of the scope and availability of data provided by tuna RFMOs is timely, given the expected establishment of a new legally binding high seas agreement to protect marine biodiversity in the ABNJ. We examined official catch statistics and stock assessments that are accessible in the public domain for the five tuna RFMOs, and evaluated their taxonomic, spatial and temporal resolution. We found that the Atlantic and Indian Ocean tuna RFMOs report catches for a greater number of taxa compared to Pacific RFMOs. There are substantial gaps in the taxonomic resolution of sharks and rays and ‘other teleosts’, and only about half of the reported global catches are georeferenced, despite existing mandatory requirements. Additionally, the estimation and reporting of discards in all tuna RFMOs remains incomplete. Tuna RFMOs have made progress in implementing stock assessments for a wide range of taxa including targeted species with high economic value but also functionally important non‐target species with lower economic value. However, assessments should be expanded to cover other bycatch species. We emphasize the importance of accessible and accurate statistics, for supporting the research and societal oversight needed under any future ABNJ biodiversity treaty.
... Moreover, Indonesia is one of the countries in Asia comprising predominantly vulnerable and endangered fish species (Dharmadi et al. 2015). Some fish species with vulnerable (VU), endangered (EN), and critically endangered (CR) conservation status are still traded in Indonesia, especially sharks and rays, for instance, Alopias pelagicus, A. superciliosus, Isurus paucus, Prionace glauca, Maculabatis gerrardi and Rhina ancylostoma (Dharmadi et al. 2015;Sembiring et al. 2015;Prasetyo et al. 2021). In addition to this, previous reports have shown that some coral reef fish that play an important role in the reef ecosystem, such as families Acanthuridae, Siganidae, Pomacentridae, and Scaridae, are still sold in huge numbers with improper or negligent management (Campbell et al. 2014;Ferse et al. 2014;Madduppa et al. 2014). ...
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In this study, we first report a systematic checklist of commercial marine fish species from Weh Island, Indonesia, including notes on their distribution pattern, conservation status, and commercial value. Fish sampling was conducted at three major fish markets in Weh Island, and these specifically were Cangkoan Fish Market, Kuta Timu Fish Market, and Balohan Fish Market. A total of 50 fish species belonging to 8 orders and 24 families were documented. Carangidae (12%, 6 species) was the predominant family, followed by the Scaridae (10%, 5 species) and other families (78%, 22 families, 39 species). Based on the IUCN red list, commercial marine fish species in Weh Island were dominated by the "Least Concern" category (78%, 39 species), followed by the "Not Evaluated" (14%, 7 species), the "Near Threatened" (4%, 2 species), and the "Data Deficient" (4%, 2 species). The market price of the fish ranged from 0.34 USD/kg to 6.19 USD/kg, with three fish families included in the high commercial value, namely the Clupeidae, Carcharhinidae, and Serranidae.
... Accurate identification of a species is an essential condition for the sustainable utilization of biological resources. It could help relevant management departments to formulate corresponding protection and management measures for a certain group (Parveen et al., 2012;Sembiring et al., 2015;Liu et al., 2018). Traditional taxonomy is generally performed based on morphological characteristics, which depend upon taxonomists possessing rich knowledge on taxonomy and conducting careful analysis of specimens (Godfray, 2002;Li et al., 2011). ...
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The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH - psbA , and rbcL ) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa , which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions ( ycf1 , matK - trnG-GCC , rpoC1 , and matK ) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely “ F. omeiensis ” and “ F. hupehensis ” in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria , as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.
... Indonesia merupakan salah satu negara yang mengeksploitasi sumber daya tuna di Samudera Hindia dengan tingginya probabilitas tertangkapnya hiu mako sirip pendek sebagai tangkapan sampingan, baik dalam perikanan skala artisanal (Dharmadi et al., 2013;Sembiring et al., 2015;White et al., 2006) dan industri (Setyadji & Nugraha, 2012). Hingga saat ini penyusunan dokumen rencana aksi pengelolaan jenis hiu ini masih mengacu pada hasil penelitian yang dilakukan di perairan lainnya seperti Samudra Pasifik, Samudra Atlantik, dan Laut Mediterania (Rigby et al., 2019). ...
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Teregistrasi I tanggal: 11 Mei 2021; Diterima setelah perbaikan tanggal: 10 Agustus 2021; Disetujui terbit tanggal: 12 Agustus 2021 ABSTRAK Hiu mako sirip pendek (Isurus oxyrinchus) termasuk kedalam Famili Lamnidae dan banyak dieksploitasi sehingga telah dimasukkan ke dalam daftar merah IUCN serta Apendiks II CITES sejak 2019. Penangkapan dan perdagangannya perlu dipantau secara global untuk menghindari kepunahan. Penelitian ini bertujuan untuk mengkaji laju tangkap, kelimpahan, dan estimasi ukuran hiu mako yang tertangkap perikanan rawai tuna. Pengumpulan data dilakukan dengan menempatkan tenaga observer ilmiah diatas kapal penangkap ikan yang berbasis di empat pelabuhan utama rawai tuna pada rentang waktu tahun 2015 hingga 2019. Bobot tubuh ikan diestimasi dari ukuran panjang cagaknya berdasarkan persamaan hubungan panjang dan bobot dari penelitian-penelitian sebelumnya. Hasil penelitian mengungkap bahwa terjadi peningkatan upaya rawai tuna seiring dengan peningkatan cakupan sampling. Laju tangkap mencapai puncaknya pada tahun 2017 (0,2 ekor/1000 pancing), kemudian mengalami penurunan seiring dengan peningkatan upaya penangkapan. Secara spasial, hiu mako tersebar di wilayah perairan tropis dan subtropis, khususnya kurang dari 10 o Lintang Selatan. Pertumbuhan hiu mako bersifat isometrik dengan ukuran panjang cagak berkisar antara 50-211 cm. Rata-rata ukuran hiu yang tertangkap cenderung semakin besar dari tahun ke tahun sehingga dimungkinkan memiliki implikasi pada upaya pengelolaan dan konservasinya jenis yang terancam punah ini. ABSTRACT Shortfin mako shark (Isurus oxyrinchus) belongs to the Family Lamnidae and is widely exploited so it has been included in the IUCN red list as well as Appendix II CITES since 2019. Hence, its capture and trade need to be monitored globally to avoid extinction. This study aimed to investigate the catch rate, abundance, and size estimation of the shortfin mako shark caught by tuna longline. Data collection was conducted through the on-board scientific observer program on the fishing vessel at four main tuna longline ports during the period of 2015 to 2019. The whole-body weight was estimated by its length and weight relationship revealed from previous studies. The results showed that there was an increase in fishing efforts along with an increased sampling coverage. The catch rates peaked in 2017 (0.2 fish/1000 hooks), then, it decreased due to increased fishing efforts. Shortfin mako sharks were distributed spatially in both tropic and subtropic waters, mostly caught in area below than 10-degree South. An isometric growth was identified with the length size ranged between 50-211 cm. The average size of harvested fish tends to rise every year that may have implications to the establishment of management and conservation strategies for the endangered species.
... Major threats include habitat degradation, marine pollution, increasing global demand for marine products, coastal deforestation, and unsustainable fishing (Hoegh-Guldberg et al., 2009). Not only are reefs degrading, but even in healthier reef systems like Raja Ampat, Indonesia, larger species of fish such as grouper and Napoleon wrasse have experienced large reductions in population size (Allen, 2003) as have reef sharks, more broadly, across the Indonesian archipelago (Sembiring et al., 2015). These losses do not just impact biodiversity but they also impact ecosystem function and the human communities that depend on them (Burke et al., 2012). ...
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Indonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. This study uses environmental DNA (eDNA) to survey fish communities across a well-documented biodiversity gradient in Indonesia. A total of 6,608,693 sequence reads of MiFish 12S rRNA from 39 sites spanning seven regions of Indonesia revealed 1099 fish amplified sequence variants (ASVs), 80.4% of which could be identified to species. Regional fish diversity broadly conformed to expectations, with the highest fish biodiversity in Raja Ampat and lowest in Western Indonesia. Similarly, zeta diversity analysis showed greater community turnover in higher diversity reefs of Eastern Indonesia and greater community similarity in low diversity regions of Western Indonesia. However, despite a twofold difference in fish diversity between Eastern and Western Indonesia, mean ASVs recovered per 1-L seawater was relatively similar across all regions. Moreover, although ASV recovery from individual seawater samples saturated, ASV recovery did not saturate at the site or region level, indicating that sampling/sequencing efforts employed in lower diversity ecosystems are insufficient for biodiversity hotspots like the Coral Triangle. Despite these limitations, eDNA substantially increased (36.3%–84.1%; mean 57.1%) the number of fish species recorded during intensive visual surveys, adding pelagic (tuna, jacks, scads, mackerels), nocturnal (soldierfish, lanternfish), and crevice-dwelling species (eels, blennies, gobies) that are difficult to document in visual surveys. Results demonstrate the added value of eDNA in biodiversity hotspots like the Coral Triangle and highlight the need for research to understand how best to sample eDNA in high diversity regions to deliver on the promise of eDNA as a tool to monitor marine biodiversity effectively and efficiently.
... The differentiation of species at the molecular level was initially proposed by Hebert et al. (2003) using the mitochondrial gene Cytochrome c oxidase subunit 1 (COI) as an effective 'barcode' capable of identifying the species, and subsequently was critically reviewed by Krishna & Francis (2012). DNA barcoding has already been applied to provide forensic evidence of the various species (Jabado et al., 2015), Indonesia (Sembiring et al., 2015), and in some regions of Brazil (Rodrigues-Filho et al., 2009;Ramos et al., 2017;Staffen et al., 2017;Almer on-Souza et al., 2018;Bunholi et al., 2018;Feitosa et al., 2018;Calegari, Reis & Alho, 2019;Bernardo et al., 2020). ...
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• Elasmobranchs are apex predators that play a crucial role in marine ecosystems by regulating the dynamics of food webs, as well as connecting different trophic levels across habitats. • The large-scale removal of elasmobranchs impacts the energy transfer in trophic interactions. The pressure of unsustainable fisheries is considerable, as most elasmobranchs have reproductive strategies that render them unable to recover their demographic status after depletion. • In Brazil, elasmobranchs are broadly commercialized under the generalist common name of ‘cação’ (namely, shark meat). This allows threatened species to be commercialized and makes the tracking of different species difficult. • DNA barcoding of the Cytochrome c oxidase subunit 1 (COI) gene was applied to identify the different species sold as ‘cação’ along the coastline of Brazil. Fifty-seven samples from 33 cities in 15 coastal states of Brazil were purchased and analysed. • Bioinformatic analyses revealed the presence of 17 species that were sold as ‘cação’. Among them, Prionace glauca (blue shark) was the most abundant. Other species, listed as Endangered under the IUCN Red List of Threatened Species, were also uncovered as being in the shark meat trade, such as Sphyrna lewini (scalloped hammerhead), Isurus paucus (longfin mako shark), and Squatina guggenheim (angular angel shark). • These findings have reinforced the necessity to correctly label the commercialized species. Public actions towards species-specific management plans must be applied, as well as monitoring the supervised allied educational programmes.
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Mobula alfredi is a critically endangered species of the Mobulidae family that can be found in the subtropics, including Indonesia. However, population connectedness, which is critical for managing and conserving populations, was previously unknown. Based on 614-bp of cytochrome oxidase 1 (COI) mtDNA, this study looked into the genetic structure and genetic diversity of M. alfredi between three major populations in Indonesia (Raja Ampat, Komodo Island, and Nusa Penida). Between April and December 2016, 72 tissue samples were collected using the biopsy during expedition. Komodo Island has the largest haplotype diversity and nucleotide diversity, while Raja Ampat and Nusa Penida had the lowest. Low and non-significant genetic differences were discovered between groups. The genetic variation values from the entire population revealed a greater variety within the population. Individuals of M. alfredi from three populations were mixed over Indonesian seas, as shown by the phylogenetic reconstruction and haplotype network, which was divided into two groups. M. alfredi is vulnerable to environmental change because of its low genetic diversity.
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Bali, Indonesia sits within the coral triangle and is internationally recognised for its high coral reef diversity. The health of Bali’s marine ecosystems has declined in recent decades, and this is thought to be due to threats from climate change, destructive fishing practices, pollution, outbreaks coral eating invertebrates, coral disease and unsustainable tourism. As a response, multiple conservation strategies have been introduced by the island’s communities, non-government organisations and governments, with the aim of preventing further decline, as well as restoring already degraded coral reefs. This literature review provides an in-depth analysis of the tools used to conserve Bali’s coral reefs, and compares them to those used in other countries. In light of international ‘best practice’ in coral reef conservation, this review makes suggestions on how Bali could better conserve its coral reef ecosystems. These include (1) increasing its designation of official Marine Protected Areas (MPAS) and strengthening management of existing ones, (2) creating an MPA network, (3) substantially reducing marine plastic pollution, (4) continuing artificial reef construction in degraded habitats, (5) continuing to develop Bali as an ecotourism destination, (6) increasing engagement in global science to inform marine conservation decision-making, and (7) developing more marine monitoring programmes.
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To date, 19 species of spiny lobsters from the genus Panulirus have been discovered, of which only P. japonicus , P. penicilatus , P. stimpsoni , and P. versicolor have been documented in South Korean waters. In this study, we aimed to identify and update the current list of spiny lobster species that inhabit South Korean waters based on the morphological features and the phylogenetic profile of cytochrome oxidase I (COI) of mitochondrial DNA (mtDNA). Spiny lobsters were collected from the southern and eastern coasts of Jeju Island, South Korea. Phylogenetic analyses were performed using neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference (BI) methods. The ML tree was used to determine the spiny lobster lineages, thereby clustering the 17 specimens collected in this study into clades A, B, C, and D, which were reciprocally monophyletic with P. japonicus , P. homarus homarus , P. longipes , and P. stimpsoni , respectively. These clades were also supported by morphological examinations. Interestingly, morphological variations, including the connected pleural and transverse groove at the third abdominal somite, were observed in four specimens that were genetically confirmed as P. japonicus . This finding is novel within the P. japonicus taxonomical reports. Additionally, this study updates the documentation of spiny lobsters inhabiting South Korean waters as P. longipes and P. homarus homarus were recorded for the first time in this region.
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Phaeoptyx and Astrapogon are represented in the Caribbean by six species (P. conklini, P. pigmentaria, P. xenus, A. alutus, A. stellatus, and A. puncticulatus). Species identification of larvae and juveniles is problematic because characters used to distinguish adults (e.g., patterns of pigmentation and numbers of gill rakers) are absent, incomplete, or difficult to discern in the young stages. Neighbor-joining trees derived from mitochondrial cytochrome oxidase 1 sequences (DNA Barcoding) were used to match early life stages and adults. Subsequent comparative analysis of preserved voucher specimens from which the DNA was extracted or digital color photographs of those specimens taken prior to preservation yielded sufficient information to separate all early life-history stages of Belizean Phaeoptyx and Astrapogon and provided additional information for field identification of adult Phaeoptyx. Patterns of chromatophores in fresh material, combined with patterns of melanophores, provide the easiest means of separating the life-history stages of Phaeoptyx. Larvae of Astrapogon species are morphologically very similar, and some differences in pigmentation detected among them may reflect different stages of development. Continued implementation of the DNA Barcoding methods and field protocol outlined herein should prove valuable in accurately identifying much more of the ichthyoplankton fauna of the Caribbean.
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The world is in the midst of a biodiversity crisis, threatening essential goods and services on which humanity depends. While there is an urgent need globally for biodiversity research, growing obstacles are severely limiting biodiversity research throughout the developing world, particularly in Southeast Asia. Facilities, funding, and expertise are often limited throughout this region, reducing the capacity for local biodiversity research. Although western scientists generally have more expertise and capacity, international research has sometimes been exploitative “parachute science,” creating a culture of suspicion and mistrust. These issues, combined with misplaced fears of biopiracy, have resulted in severe roadblocks to biodiversity research in the very countries that need it the most. Here, we present an overview of challenges to biodiversity research and case studies that provide productive models for advancing biodiversity research in developing countries. Key to success is integration of research and education, a model that fosters sustained collaboration by focusing on the process of conducting biodiversity research as well as research results. This model simultaneously expands biodiversity research capacity while building trust across national borders. It is critical that developing countries enact policies that protect their biodiversity capital without shutting down international and local biodiversity research that is essential to achieve the long-term sustainability of biodiversity, promoting food security and economic development.
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An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan's fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits. In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan. Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias. DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.
Technical Report
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This report describes the results of a thematic Red List Workshop held at the University of Oxford's Wildlife Conservation Research Unit, UK, in 2007, and incorporates seven years (2000-2007) of effort by a large group of Shark Specialist Group members and other experts to evaluate the conservation status of the world's pelagic sharks and rays. It is a contribution towards the IUCN Species Survival Commission's Shark Specialist Group's "Global Shark Red List Assessment." The Red List assessments of 64 pelagic elasmobranch species are presented, along with an overview of the fisheries, use, trade, and management affecting their conservation. Pelagic sharks and rays are a relatively small group, representing only about 6% (64 species) of the world's total chondrichthyan fish species. These include both oceanic and semipelagic species of sharks and rays in all major oceans of the world. No chimaeras are known to be pelagic. Experts at the workshop used established criteria and all available information to update and complete global and regional species-specific Red List assessments following IUCN protocols. These assessments were agreed upon by consensus throughout the SSG network prior to submission to the IUCN Red List of Threatened Species TM . Overall, 32% of the world's pelagic sharks and rays (20 species) are threatened, which includes 6% that are Endangered and 26% that are Vulnerable. A further 24% are Near Threatened, 19% are assessed as Least Concern, and 25% are Data Deficient. As a group, pelagic elasmobranchs suffer significantly greater threats than do chondrichthyans as a whole. In addition, oceanic shark and ray species taken regularly in high-seas fisheries are more likely to be threatened (52%) than are pelagic elasmobranchs in general. Brief summaries of the Red List assessments, including the global and/or regional IUCN Red List Category, are presented for all known pelagic sharks and rays. Fishing, often driven by the demand for shark fins and meat, is the single most important threat to these species wherever they occur. Sharks are increasingly targeted by fisheries that once discarded them. National management, where it exists, is undermined because there are no catch limits on the high seas. Where regional management is in place, it is generic (not species specific), indirect (operating through controls on finning, rather than controls on catch or mortality), generally poorly enforced and inadequate to reverse population declines or rebuild stocks. Such illegal, unreported and unregulated (IUU) fishing contributes significantly to unsustainable catches of these inherently vulnerable species. The report's recommendations are intended to complement and enhance existing scientific advice regarding the conservation and management of pelagic sharks and rays. The information contained within this report can facilitate the further development and implementation of research, conservation, and management priorities for this group of vulnerable species. The IUCN Species Survival Commission's Shark Specialist Group (SSG) was established in 1991 to promote the sustainable use, wise management, and conservation of the world's chondrichthyan fishes. There are 180 SSG members from 90 countries distributed among 12 ocean-region subgroups, all of whom are actively involved in chondrichthyan research and fisheries management, marine conservation, or policy development and implementation. The SSG has recently concluded its 10-year Global Shark Red List Assessment programme by completing Red List assessments for every chondrichthyan species described in the scientific literature before the end of 2007. This is the first complete assessment of all members of a major marine taxonomic group, and will provide an important baseline for monitoring the global health of marine species and ecosystems.
Book
This book covers in one volume materials scattered in hundreds of research articles, in most cases focusing on specialized aspects of coral biology. In addition to the latest developments in coral evolution and physiology, it presents chapters devoted to novel frontiers in coral reef research. These include the molecular biology of corals and their symbiotic algae, remote sensing of reef systems, ecology of coral disease spread, effects of various scenarios of global climate change, ocean acidification effects of increasing CO2 levels on coral calcification, and damaged coral reef remediation. Beyond extensive coverage of the above aspects, key issues regarding the coral organism and the reef ecosystem such as calcification, reproduction, modeling, algae, reef invertebrates, competition and fish are re-evaluated in the light of new research and emerging insights. In all chapters novel theories as well as challenges to established paradigms are introduced, evaluated and discussed. This volume is indispensible for all those involved in coral reef management and conservation.
Chapter
Abstract Indonesia’s catches of elasmobranchs (sharks, skates and rays) grew rapidly from the 1970s, driven mainly by the demand for shark fins, and by the beginning of the twenty-first century Indonesia was the world’s leading elasmobranch producer. The Indonesian fishery is effectively an open access one and overfishing has led to declining yields in Indonesian waters. Fishers have pushed the geographical catch frontier outwards and this has led to illegal fishing, especially in the Australian Fisheries Zone. Traditionally small scale fishers utilised most of the sharks for food and value-processes including the production of leather, but a large amount of shark is caught as by-catch in industrial fisheries for high value species such as tuna and this has increased the frequency of ‘finning’, a wasteful and cruel practice. The competition from industrial fishing has adversely impacted small scale fishers and their families; the main beneficiaries of the lucrative shark fin trade have been boat owners and traders rather than fishers and their families. A National Plan of Action is needed but complicated by fiscal constraints and the division of powers between the national, Kabupaten (district/regency) and provincial governments. Governance failures in fisheries are unfortunately a widespread problem in the Indo-Pacific Region. Keywords Historical knowledge · Indonesia · Elasmobranch fisheries · Shark fins · Artisanal fisheries