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DNA Barcoding reveals targeted fisheries for endangered sharks in Indonesia

Authors:
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.
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... This thorough and long identification process is unfortunately not a priority for ecologists who can often achieve the same outcomes by utilising morphospecies names for statistical analysis purposes; potentially new species consequently remain undiscovered. Although today the use of DNA barcoding based on the mitochondrial cytochrome oxidase 1 (CO1) gene to rapidly identify Indonesian marine species (especially fish) is becoming more popular (e.g., Sembiring et al., 2015;Nuryanto et al., 2017;Wibowo et al., 2018;Fadli et al., 2020), this method alone should not replace the morphological approach to officially describe a new species-although a recent study controversially did do just that (Sharkey et al., 2021). ...
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Even though it is a global marine biodiversity hotspot, the contribution of Indonesia to marine species discovery has been disproportionately small, and despite the amount of biodiversity research conducted by local scientists, many species in this country remain undescribed. In this article, we used the discovery rate of Indonesian polychaete species as a case example to investigate the contributory factors leading to the slow rate of marine species discovery in the country. In addition, we evaluated ecological studies on Indonesian polychaetes and enumerated the number of local marine taxonomists along with the number of Indonesian species that they described. We found that throughout Indonesia's history, the country only had a few marine taxonomists and that past marine species discoveries have been largely dependent on overseas scientists. This has been the primary factor causing the slow rate of marine species discovery in the country and has led to limited taxonomic literature on local species, resulting in many species either remaining unidentified or incorrectly identified, as local researchers typically used identification keys written for other geographic regions. We further found that limited access to natural history collections, uneven distribution of research facilities, a lack of collaborative research and funding, and strict requirements for research permits for foreign researchers have also hampered discoveries of marine species new to science in Indonesia. Long term recruitment of local marine taxonomists through the job vacancies regularly offered (annually) by the Indonesian government along with taxonomic training by relevant governmental research institutions are the first immediate actions to address these problems. Moreover, collaborative work and the establishment of Indonesian marine reference collections, databases, and identification keys are other strategies to end taxonomic impediments in the nation. For polychaetes, provided that such actions are made, our model forecasts that between 120 and 270 more Indonesian species will be discovered by the end of this century. Any taxonomic investigations conducted in the Coral Triangle are likely to uncover greater numbers of undescribed marine species compared to any other location in Indonesia or the world.
... The pelagic thresher shark is estimated to have a high post-release mortality rate related to capture fisheries or recreational fishing, as modeled for the A. vulpinus, with a mortality rate of 78% and 0% if hooked on the tail and mouth, respectively (Sepulveda et al. 2015). Studies on pelagic thresher sharks in Indonesia are mostly about its fisheries and biology, while their ecological aspects are still rarely studied despite their importance in providing better information for species management (Dharmadi et al. 2015a;Sembiring et al. 2015;Arostegui et al. 2020). The catch of this species in the Indian Ocean has declined since 2002-2021, especially from commercial tuna fisheries. ...
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Alghozali FA, Salsabila R, Gustianto MWD, Putri HMIH, Himawan MR, Yuneni RR, Hatmoro CK, Rezkiani M. 2023. Diet analyses of the pelagic thresher shark, Alopias pelagicus (Lamniformes: Alopiidae), from the Lombok Strait waters, Indonesia. Biodiversitas 24: 3708-3714. The pelagic thresher shark, Alopias pelagicus, is an endangered shark species estimated to be declining in the Pacific and Indian Oceans because of overexploitation, including from target fisheries and bycatch. Despite its importance in providing better information for species management, the ecological aspects of this species are still rarely studied. This study aims to provide information on the feeding ecology of the pelagic thresher sharks from the Lombok Strait. Stomach samples from 178 specimens were sampled from 2020-2021, and 149 stomachs that contained food contents were analyzed for species diet characterization. Prey Species Accumulation Curve slope values are <0.1 and the percentage of prey coverage for all sharks combined is 92.1%, suggesting reliable inventory in the number of prey represented. The resulting diet indexes suggest that A. pelagicus in Lombok Strait waters is a specialist predator (Ba=0.3) with few prey variations (H=2.21) and no competition between sexes and maturity stages of the species (C=0.64 and 0.81, respectively). The top three prey species found for A. pelagicus in the study area are the Auxis thazard (85.8 %IRI), Sthenoteuthis oualaniensis (8.5 %IRI), and Dasyscopelus spinosus (1.11 %IRI). A better understanding of the overlap of A. pelagicus and its diet, which includes economic fish commodities, will inform authorities to develop better fisheries and conservation management for the species in Indonesia.
... Globally, Indonesia is the main exporter of sharks and shark fins, of around 100,000 tonnes a year since the year 2000 [6]. There is uncertainty about how much of the shark catch in Indonesian waters is taken as bycatch of fisheries (using longlines, driftnets, handlines, and purse seines), how much of the fisheries is targeted specifically at sharks, and to what extent shark fisheries contribute to the livelihood for many artisanal fishers [7,8]. International policy responses to the negative effects of shark fishing have resulted in the implementation of shark finning bans in some areas, whereas others focused on promoting the full use of dead sharks such as discouraging carcass discards after defining [3]. ...
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Illegal, unreported, and unregulated fishing, including that of sharks, poses a significant threat to marine ecosystems and individual species. I use data from the media, tourists, and artisan fishermen to gain insight into the trade in the world’s largest fish, the whale shark (Rhincodon typus). I focus on the Indonesian island of Java where, along its south coast, whale sharks are landed and butchered on the beach in view of hundreds of people and local media. Whale sharks are typically caught in fishing nets and dragged alongside boats to the shallows, where they are butchered. The meat and oil (valued at ~USD 2000 per shark) are sold and distributed within the community. I document 58 landings of mainly immature whale sharks (2002–2022). Artisanal fishermen see the landing of whale sharks as a fortuitous event, but the species is protected, and Indonesia is a signatory to various international agreements that preclude the fishing of whale sharks. It is imperative for the conservation of whale sharks that the various parties in Indonesia adhere better to their own rules and regulations protecting this species.
... In Western Sumatera (Lampulo and Sibolga), 12 specimens were recorded between October 2013 to June 2014 [9]. A study on DNA barcoding of shark fins between 2012-2014 identified eight N. ferrugineus from 582 market samples across the country [10]. ...
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Nebrius ferrugineus , or tawny nurse shark, is a species of carpet shark distributed across the tropical Indo-Pacific region. This species has little species-specific information on biology and fisheries. The tawny nurse shark is listed as “Vulnerable” on IUCN Redlist and is rarely seen, recorded, and studied in Indonesia. We recorded this species during SCUBA diving in Morotai waters in April 2022. Recorded live encounters by SCUBA diving activities in Indonesia are even more scarce. In Morotai, North Maluku, this species anecdotally exists by reports from SCUBA divers, however, have not been documented very well. Scientific record of this species is highly important for conservation and habitat management. The government of Indonesia also recognised the significance of biodiversity and potential marine tourism in Morotai by declaring 65,520.75 hectares of Marine Protected Area (MPA) named Taman Wisata Perairan (TWP) Pulau Rao - Tanjung Dehegila. This MPA focuses on protecting marine biodiversity, historical object preservation (World War II underwater relics) and sustainable small-scale fisheries. However, species-specific protection for tawny nurse sharks does not exist in Indonesia. In Morotai, where this species is recorded, marine protected areas are only effective in conserving shark if it is sufficiently large, well-enforced, and monitored.
... PCR was conducted using Red Taq Mix (BIOLINE) following a cycle: 94°C initial denaturation for 5 minutes; 35 cycles of denaturation at 94°C 1 minute, primer annealing at 58°C for 30 seconds and extension at 72°C for 1 minute; and post extension 72°C for 7 minutes. PCR products were then visualized for DNA band using electrophoresis on a 1% agarose gel and EtBr (Ethidium Bromide) staining (Sembiring et al. 2015). PCR products were sequenced by PT. ...
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Kanedi MM, Wijayanti DP, Widowati I, Malik MDA, Yusmalinda NLA, Sembiring A. 2023. Genetic diversity of bigeye thresher shark (Alopias superciliosus Lowe, 1841) landed in Palabuhanratu Fishing Port, Sukabumi, West Java, Indonesia. Biodiversitas 24: 3488-3494. The bigeye thresher shark Alopias superciliosus (Lowe, 1841) is a highly migratory marine shark, widely distributed globally in tropical and temperate seas. The bigeye thresher shark is listed as a Vulnerable/VU species on the red list of the International Union for Conservation of Nature (IUCN) and listed on Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Genetics is a substantial essential approach to conservation, management, and sustainability. This study investigates the bigeye thresher shark's genetic diversity and structure populations A. superciliosus that landed in Palabuhanratu Fishing Port, Sukabumi, West Java, Indonesia. Samples were collected in Palabuhanratu (n=16) and secondary data from the Atlantic Ocean (n=212) and Indian Ocean (n=16) sequences were obtained from GenBank. A total of 16 sequences of A. superciliosus have been amplified using mitochondrial DNA control region (dloop) with 857 bp in size sequenced. The Genetic diversity result showed haplotype diversity value in Palabuhanratu (Hd=0.86667; π=0.01048) considered a high value. Overall, AMOVA and FST results showed significant differences in population structure between Palabuhanratu, Atlantic, and Indian Ocean with an FST value of 0.04420 (p-value <0.05). Based on the result, an effective strategy is needed to manage A. superciliosus sharks, both with the government and the private sector.
... Difficulties in the identification of batoids have been reported in previous studies, mostly due to the presence of few diagnostic morphological characteristics, juvenile specimens, or the inability to distinguish the pectoral fins of butchered specimens through morphological characteristics (Cerutti-Pereyra et al. 2012;Smith et al. 2009;John et al. 2018). To overcome these limitations, DNA barcode sequencing using a specific region of the mitochondrial DNA has been shown to be a fast and efficient tool to support taxonomic assignments of elasmobranch species (Bunholi et al. 2018;Hobbs et al. 2019;Sembiring et al. 2015;Zeng et al. 2016;Bineesh et al. 2017;Ferrette et al., 2019;Velez-Zuazo et al. 2015;Biffi et al. 2020;Marín et al. 2018;Velez-Zuazo et al. 2021). Considering the current taxonomic identification challenges with mobulids in Peru, and their high catch rates by small-scale fisheries (IMARPE 2021), we (1) investigated which species of mobulids are being captured by small-scale driftnet fisheries in northern Peru, and (2) applied a taxonomy-based cross-validation species identification through the application of morphological and molecular approaches (DNA barcoding). ...
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Peru has globally important elasmobranch fisheries, and mobulids are no exception. However, little is known about Peru’s small-scale mobulid fisheries. Mismatches between fishing reports and studies regarding species occurrence suggest a problem in identification methodologies of mobulids at the species level. This is supported by evidence of external resemblance between species, landings of incomplete bodies, and the use of a single name for the five species known to occur in Peruvian waters (“Manta” for Mobula birostris, Mobula munkiana, Mobula mobular, Mobula tarapacana and Mobula thurstoni). Given the need for improved conservation and management measures of mobulids in Peru, we tested the applicability of DNA barcoding combined with morphological identification to better understand mobulid catches by small-scale fisheries in north Peru. A total of 137 samples of muscle tissue from mobulids captured during fishing activities were collected of which 99 amplified and analysed for Cytochrome C Oxidase Subunit I (COI). Samples of the five species known to occur in Peru were obtained, confirming captures of all of them by local fisheries. Morphological identification allowed us to correctly identify more than 94% of specimens to the species level even though most of them arrived butchered (e.g., only pectoral fins). Increased capacity building and training for morphological identification of mobulid species by field observers, authorities, and fishermen, combined with molecular tools, is highly recommended to avoid mistakes in landings reports and to correctly enforce conservation measures for these species.
... DNA barcoding-more specifically, CO1 analysis-has been used widely to aid in the species identification of elasmobranchs from various regions, such as Australia [36,42,43], China [44], the Philippines [50], Indonesia [51], Singapore [45,47], India [19,52,53], Bangladesh [54], Southern Africa [46,55], the United Kingdom [56], the Mediterranean Sea [57], the North Atlantic Ocean [58], the United States [49], and Brazil [59][60][61]. To date, limited published DNA barcoding studies in Malaysia have focused on rays but not on sharks [9,34]. ...
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Simple Summary One-third of shark and ray species are threatened due to overfishing, but a lack of information on each species makes conservation decisions difficult. To address this issue, we conducted a study to identify the different species of sharks and rays in Malaysian waters using DNA barcoding of the CO1 gene, which is akin to DNA fingerprinting for species. We collected 175 individuals between June 2015 and June 2022, randomly selecting up to six specimens from each species. We successfully generated DNA barcodes for 67 species, belonging to 44 genera, 20 families, and 11 orders. Accurate species identification will improve species-specific catch landing data and accelerate the identification of use and illegal trade in Malaysia. Abstract The data provided in this article are partial fragments of the Cytochrome c oxidase subunit 1 mitochondrial gene (CO1) sequences of 175 tissues sampled from sharks and batoids collected from Malaysian waters, from June 2015 to June 2022. The barcoding was done randomly for six specimens from each species, so as to authenticate the code. We generated barcodes for 67 different species in 20 families and 11 orders. DNA was extracted from the tissue samples following the Chelex protocols and amplified by polymerase chain reaction (PCR) using the barcoding universal primers FishF2 and FishR2. A total of 654 base pairs (bp) of barcode CO1 gene from 175 samples were sequenced and analysed. The genetic sequences were blasted into the NCBI GenBank and Barcode of Life Data System (BOLD). A review of the blast search confirmed that there were 68 valid species of sharks and batoids that occurred in Malaysian waters. We provided the data of the COI gene mid-point rooting phylogenetic relation trees and analysed the genetic distances among infra-class and order, intra-species, inter-specific, inter-genus, inter-familiar, and inter-order. We confirmed the addition of Squalus edmundsi, Carcharhinus amboinensis, Alopias superciliosus, and Myliobatis hamlyni as new records for Malaysia. The establishment of a comprehensive CO1 database for sharks and batoids will help facilitate the rapid monitoring and assessment of elasmobranch fisheries using environmental DNA methods.
... falciformis), scalloped hammerhead (S. lewini), and pelagic thresher (A. pelagicus) sharks should be prioritized in tropical and subtropical regions (e.g., Eastern Tropical Pacific) since they represent some of the most common species in industrial and artisanal fisheries around the world (Diop & Dossa, 2011;Clarke et al., 2014;Mart ınez-Ortiz et al., 2015;Sembiring et al., 2015;Humber et al., 2017). In addition, these species are among the most traded species to large shark fin trade hubs in Southeast Asia (Cardeñosa et al., 2018a(Cardeñosa et al., , 2020a. ...
Article
Illegal trade in shark fins can be a driver of overexploitation and is a global law enforcement issue given that some frequently traded species are listed on CITES Appendix II. Shark fins are usually traded dried or frozen and are not processed until they reach supply chain end points in southeast Asia, which allows for visual species identification in many of the commonly traded species. All external tissue is removed during processing, eliminating characters that are crucial for visual species identification. If processing occurs early in the supply chain, law enforcement personnel face the challenge of identifying fins to the species level and detecting illegal trade without the ability to do so visually. Here, we apply mini‐barcoding and real‐time PCR methods to a case study in Colombia where seized processed shark fins were sampled and analyzed using these methods. Five species of shark were identified, all of which are listed under CITES Appendix II, and four of which have been assessed to be in threatened categories by the IUCN Red List of Threatened Species. Threatened and CITES‐listed species comprised 96.3% and 100% of the analyzed samples, respectively. The case study presented here raises concerns about the changes occurring when processing takes place in the supply chain, impeding any kind of identification of illegally traded shark fins without genetic tools. If early‐supply chain processing becomes the norm, it will introduce significant identification challenges for law enforcement throughout the rest of the supply chain. This underscores the need for in‐port genetic testing capacity building in nations and regions where shark products are highly traded to detect CITES‐listed and prohibited/regulated species at any point of the supply chain and regardless of the nature of the product. El comercio ilegal de aletas de tiburón puede ser un factor de sobreexplotación y es un problema para la aplicación de la ley a nivel mundial dado que algunas especies que se comercializan con frecuencia están incluidas en el Apéndice II de CITES. Las aletas de tiburón generalmente se comercializan secas o congeladas y no se procesan hasta que llegan a los puntos finales de la cadena de suministro en el sudeste asiático, lo que permite la identificación visual de muchas de las especies comúnmente comercializadas. Todo el tejido externo se elimina durante el procesamiento, eliminando caracteres que son cruciales para la identificación visual. Si el procesamiento ocurre temprano en la cadena de suministro, el personal encargado de hacer cumplir la ley enfrenta el desafío de identificar las aletas a nivel de especie y detectar el comercio ilegal sin la capacidad de hacerlo visualmente. Aquí, aplicamos métodos de código de barras y PCR en tiempo real a un caso en Colombia donde se tomaron muestras de aletas de tiburón procesadas incautadas y se analizaron utilizando estos métodos. Se identificaron cinco especies de tiburones, las cuales están incluidas en el Apéndice II de CITES, y cuatro de las cuales han sido evaluadas como amenazadas por la Lista Roja de Especies Amenazadas de la UICN. Las especies amenazadas e incluidas en CITES comprendieron el 96,3 % y el 100 % de las muestras analizadas respectivamente. El caso presentado aquí plantea preocupaciones sobre los cambios en el momento en que se realiza el procesamiento en la cadena de suministro, lo que impide cualquier tipo de identificación de aletas de tiburón comercializadas ilegalmente sin herramientas genéticas. Si el procesamiento temprano en la cadena de suministro se convierte en la norma, se presentarán importantes desafíos de identificación para las fuerzas del orden en el resto de la cadena. Esto subraya la necesidad de desarrollar capacidades de pruebas genéticas en puerto en países y regiones donde los productos de tiburón son altamente comercializados para detectar especies incluidas en CITES, o prohibidas/reglamentadas, en cualquier punto de la cadena de suministro y sin importer la naturaleza del producto/muestra. When shark fins are processed and as a consequence visual characteristics are removed, law enforcement officers are only left with DNA for identification of regulated/prohibited species. Here we used a case study from El Dorado International export in Colombia, to show the application of two different molecular protocols to detect CITES‐listed species in cases where processed shark fins are being illegally traded at any point of the supply chain.
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Western Indian Ocean countries have banned elasmobranch finning and enacted legislation to protect endangered elasmobranchs, however finned and morphologically deformed specimens are still landed and traded on Tanzanian fish markets. Such specimens are difficult to identify morphologically, and it is possible that protected elasmobranchs are among these. This study used DNA barcoding to uncover protected elasmobranchs in 102 specimens traded on Tan-zanian fish markets. The sampled specimens revealed 23 elasmobranch species, 12 of which (52.1 %) were classified as endangered (EN) or critically endangered (CR) on the IUCN Red List. Three of the identified species (great hammerhead Sphyrna mokarran, oceanic whitetip shark Carcharhinus longimanus, and pelagic thresher Alopias pelagicus) are protected by Tanzanian laws. Hence, it is advised that steps be taken to strengthen law enforcement at landing sites and fish markets in the country. Furthermore, the Third Schedule of Fisheries (Amendment) Regulations of 2009 should be updated to include 11 EN and CR elasmobranchs that are not on the list. Additionally, national and regional elasmobranch conservation plans should be developed to prevent the exploitation of endangered elasmobranchs.
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The Indonesian greeneye spurdog (or a dogfish shark), Squalus montalbani Whitley, 1931, is widely distributed in the warm temperate to tropical waters of Indonesia, Philippines, the island of Taiwan, and Australia. Previous studies suggested that the distribution of dogfish shark species in the South China Sea is composed of two species, Squalus mitsukurii Jordan et Snyder, 1903 and Squalus brevirostris Tanaka, 1917. In March 2020 a dogfish shark specimen was collected from the Nansha (Spratly) Islands, South China Sea. We identified it as S. montalbani based on morphology and mitochondrial DNA barcoding. Our results confirmed the presence of S. montalbani in the South China Sea, leading us to conclude that it represents a new species record of the genus Squalus in the region. Furthermore, our findings demonstrate that the combined approach is highly effective in identifying Squalus species that share similar morphological characteristics.
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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.
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Background. 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. Methods. 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. Results. 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. Conclusion. 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.
Article
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.
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