Marine Biodiversity Records, page 1 of 9.

# Marine Biological Association of the United Kingdom, 2014

doi:10.1017/S1755267214000207; Vol. 7; e18; 2014 Published online

Cetaceans in the global centre of marine

biodiversity
anna isabel ender1, muhajir2, sangeeta mangubhai2,3, joanne r. wilson2,4, purwanto2
and andreas muljadi2,5
1
James Cook University, 1 James Cook Drive, Douglas, QLD 4811, Australia, 2The Nature Conservancy, Indonesia Marine Program,
Jl. Moh. Yamin V No.7, Desa Sumerta Kelod, Denpasar Timur 80235, Indonesia, 3IUCN Oceania Regional Office, 5 Ma’afu Street,
Suva, Fiji, 4Sea Solutions, 1/2 Miller Place, Pottsville, NSW 2489, Australia, 5Coral Triangle Center, Jl. Tamblingan 78, Sanur 80228,
Bali, Indonesia

Indonesia has a diverse range of cetacean species, yet there are few records of their distribution, especially from remote regions.
Incidental sightings from aerial surveys were conducted in 2006 and boat-based surveys were conducted from 2006 –2011 in
Raja Ampat in the Bird’s Head Seascape, Indonesia. This paper is the first to provide a species list and an indication of the
spatial and temporal distribution of cetaceans in central and southern Raja Ampat. Seven dolphin and six whale species were
documented, including Indo-Pacific humpback dolphins Sousa chinensis, Bryde’s Balaenoptera edeni, sperm Physeter
macrocephalus, killer Orcinus orca and pygmy killer Feresa attenuata whales. Temporal differences in sightings suggest
Raja Ampat is an important area for migratory whale species and resident populations of Indo-Pacific humpback Sousa chi-
nensis, spinner Stenella longirostris and common bottlenose Tursiops truncatus dolphins. Cetacean diversity was highest in
the months of January –February, May and October –November, with most sightings recorded in Kofiau marine protected
area and Dampier and Sagewin Straits. Diversity and species distribution data are critical for managing cetaceans in
Indonesia. Emerging threats to cetaceans in Raja Ampat include seismic surveys for seabed oil and gas exploration, potential
strikes from increasing ship traffic, entanglement in fishing nets and increasing discharge of plastic pollution from urban
areas. In addition to regulations for marine protected areas, a wider conservation strategy is required to address or better
manage emerging threats to Raja Ampat, and to ensure the long-term protection of resident and migratory dolphin and
whale species.

Keywords: Raja Ampat, Bird’s Head Seascape, Coral Triangle, marine mammals, distribution, noise pollution, seismic surveys

Submitted 30 June 2013; accepted 8 December 2013

INTRODUCTION harvesting in Indonesian waters. Cetaceans however, face

The Indonesian archipelago encompasses 5.8 million square
kilometres of coastal and oceanic waters within the Coral
Triangle (Coral Triangle Initiative, 2009). While well known
for coral and reef fish diversity, Indonesia also hosts 31
species of cetaceans (Rudolf et al., 1997; Tomascik et al.,
1997). Within Indonesia, the Bird’s Head Seascape (BHS)
has the highest near-shore marine diversity (Veron et al.,
2009; Allen & Erdmann, 2012) and is a national priority for
conservation (Huffard et al., 2009). There are unpublished
studies and anecdotal evidence which indicate that the BHS
also provides critical habitat for a number of large, endangered
marine species such as whales, dolphins, sea turtles and
dugong, especially in the waters of Raja Ampat (see review
in Mangubhai et al., 2012).
Indonesia was a popular whaling ground for sperm whales
in the 19th Century (Rudolf et al., 1997). With the exception
of traditional hunting in two villages in Solor, East Nusa
Tenggara (Barnes, 1996), cetaceans are now protected from
Corresponding author:
S. Mangubhai
Email: smangubhai@gmail.com
increasing threats and stressors from ship strikes, entangle-
ment in fishing nets, and noise and plastic pollution
(Mangubhai et al., 2012). To date, marine conservation
efforts in Raja Ampat include the establishment of a
network of seven marine protected areas (MPAs) encompass-
ing over 1 million hectares of coastal and oceanic habitats,
designation of the region as a maritime Regency, and a ban
on the hunting and killing of all large marine fauna.
However, MPAs were designed predominantly for protection
of coastal habitats and to support sustainable local fisheries,
and therefore may not be the most effective management
tool for large, highly mobile cetaceans in their current config-
uration. Information on cetacean species, their behaviour and
their spatial and temporal distribution is urgently needed in
Raja Ampat to inform the future management of specific
threats to cetaceans.
In many parts of the world, information on the distribu-
tion, population size and behaviour of cetaceans is poorly
known (MacLeod et al., 2006), partly because cetacean
surveys can be costly, time consuming and logistically challen-
ging (Kiszka et al., 2007; Schick et al., 2011). This knowledge
gap is evident in Indonesia, where expertise and financial
resources are lacking and information is often from incidental
sightings (Borsa & Nugroho, 2010), strandings (e.g. Mustika

1
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
 2 isabel ender et al.
et al., 2009), from short surveys published in grey literature
(Kahn, 2007, 2009; Kreb, 2008), and from long-term studies
in Kalimantan (Kreb & Budiono, 2005a, b, 2012). While the
shorter term and stranding studies do not provide estimates
of population size or comprehensive temporal and spatial dis-
tribution, these data can be used to develop region specific
species lists and identify general areas of likely importance
for cetacean aggregation. Importantly, these can form the
basis for more comprehensive studies.
Incidental sightings or stranding observations are particu-
larly important in remote areas like Raja Ampat with a rapidly
developing economy and growing pressures on natural
resources (Mangubhai et al., 2012). Only one study has been
published to date from Raja Ampat which documented six
species of cetaceans during a short 3-week survey (Borsa &
Nugroho, 2010). While there have been other efforts to docu-
ment cetaceans (Kahn, 2007; Conservation International,
unpublished data), the goal of this paper is to document in
the international scientific literature incidental sightings data
collected over 6 years from Raja Ampat, to raise the profile
of this area as an important region for cetaceans. This is the
first published study which provides a species list and an indi-
cation of the spatial and temporal distribution of cetaceans in
the Raja Ampat Regency. Data are also presented on the pres-
ence and fine-scale distribution of cetaceans within the two
southern-most protected areas in the Raja Ampat MPA
network.
Fig. 1. Distribution of whales and dolphins in Raja Ampat recorded in aerial surveys in January (A) and September (B) in 2006. Marine protected areas shown:
1, Ayau-Asia; 2, Kawe; 3, Mayalibit Bay; 4, Panjang Islands; 5, Dampier Strait; 6, Kofiau; 7, Misool.
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
MATERIALS AND METHODS
Site description
The Raja Ampat archipelago in West Papua Province,
Indonesia encompasses 4 million hectares of land and sea,
including four large islands (Waigeo, Batanta, Salawati and
Misool), hundreds of smaller islands and two large straits
(Dampier and Sagewin) (Figure 1). A diversity of coastal
and marine habitats exist ranging over shallow coastal habitats
supporting diverse coral reefs and seagrass beds with small
areas of mangrove, deep channels, seamounts, pinnacles and
straits (see review in Mangubhai et al., 2012). Raja Ampat is
strongly influenced by the ‘Indonesian throughflow’, which
is the major oceanic exchange between Pacific and Indian
Oceans (Vranes & Gordon, 2005) and there are strong tides
which generate turbulence and local eddies between islands.
The two most southerly MPAs are Kofiau (129837′ E
1816′ S) and Misool (130833′ E 2802′ S), which encompass
170,000 ha and 366,000 ha of islands and coastal waters,
respectively (Figure 1). Kofiau MPA has 44 small islands in
two major island groups (Kofiau and Boo) with shallow frin-
ging reefs along the majority of the coastline. Deeper water
(.200 m) is found within a few hundred metres to 0.5 –
2 km of the coastline. In the passage between Boo and
Kofiau Islands water depth reaches .500 m. In contrast,
Misool MPA encompasses the south-east coastline and

dozens of offshore islands of the large island of Misool and is
characterized by a labyrinth of geologically unique karst struc-
tures on a shallow shelf (,100 m).
Incidental sightings—coastal resources aerial
surveys
Cetacean sightings were recorded during two aerial surveys in
2006 designed to document coastal resource use. Surveys were
conducted from a small fixed wing aircraft, a Pilatus PC-6
(‘Pilatus Porter’) at an approximate height of 700 feet and
speed of 100 km/h. The first survey was conducted from
9– 13 January 2006 and the second between 8 and 22
September 2006. The same method was adopted for both
the January and September surveys with each survey lasting
for 30 hours over 5 days and covering approximately
4000 km along a targeted flight path. This allowed for direct
comparison of the data. The survey team consisted of one
navigator, two fishery observers (port and starboard) and
two mappers (port and starboard) plus photographers.
Observers recorded observations in an area extending 1.5
nautical miles from either side of the plane and recorded the
GPS positions and took photographs of all whale and
dolphin sightings. The flight path and survey methods were
developed to allow maximum coverage of the near-shore
reef areas of Raja Ampat to obtain information on the distri-
bution and type of resource use activities in Raja Ampat, and
marine mammal sightings were recorded opportunistically.
Cetaceans could not be identified to species and were only
recorded collectively as ‘whales and dolphins’. The distribu-
tion and abundance of cetaceans were plotted in ArcGIS.
Incidental sightings—boat-based surveys
Incidental sightings of cetaceans were made during boat-based
surveys for reef health (annual) or resource use (4 –16 days/
year across different months), while traversing within Kofiau
and Misool MPAs, or while travelling between the city of
Sorong and the MPAs (Figure 1). Sightings were documented
over 6 years from June 2006 to December 2011, with the
exception of the months of June to August when all surveys
ceased due to rough seas associated with the south-east
monsoon season. Sightings were recorded in accordance
with the ‘Occasional Observation Protocol’ developed by
The Nature Conservancy (Muljadi & Nugrahaeni, 2006;
Pratomo et al., 2006) and using identification keys in
Carwardine (1995, 2002). Data were collected by trained
local scientists with over 5 years’ experience in the field iden-
tifying cetacean species. There were two experts per MPA
collecting data. Surveys were done with the naked eye at
150 –170 cm above sea-level, and binoculars used to confirm
identification. The number of survey trips taken per month
was comparable and survey times ranged from 3 –5 hours.
Uncommon species were confirmed by showing photographs
to other cetacean experts working in the region. If there was a
concern about the identification of the animal, it was listed as
dolphin or whale in the database. Observations were made
only during the day. When cetaceans were sighted, the boat
slowed or stopped and data were recorded including the
GPS location of each sighting, species (where possible) and
number of individuals, direction, distance of the observer
from the target mammal, and behaviour of these mammals.
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
cetaceans in raja ampat 3
Both MPAs are accessed across the same months, and at
approximately the same frequency. Sightings were entered
into a central database and analysed with ArcGIS and
Microsoft Excel.
RESULTS
Incidental sightings—aerial surveys
Cetaceans were sighted throughout Raja Ampat with concen-
trations around southern Waigeo Island, the straits between
Salawati and Batanta Islands, Kofiau MPA and small islands
north of Misool Island (Figure 1A, B). The total number of
whales and dolphins sighted in January (N ¼ 629) was
almost three times higher than in September (N ¼ 241).
This was particularly evident at Kofiau and the islands north
of Misool Island, which had high counts of whales and dol-
phins in January but no or few sightings in September 2006
(Figure 1B). In contrast, whales and dolphins were abundant
in the narrow Strait of Sagewin between southern Batanta
and the Salawati Islands and in the Dampier Strait during
both January and September (Figure 1A, B).
Although it was not possible to identify cetaceans to species
level during the aerial surveys, observers sometimes noted and
photographed species which are readily identified including
killer (Orcinus orca Linnaeus, 1758) and false killer whales
(Pseudorca crassidens Owen, 1846) (A. Muljadi, personal
observations).
Incidental sightings—boat-based surveys
Whales and dolphins were encountered during boat-based
surveys on 351 occasions between 2006 and 2011, over 417
days. The majority of sightings (300) were dolphins, compris-
ing 3391 individuals. A total of 514 individual whales were
encountered during 51 sightings. Because boat-based surveys
were opportunistic, any potential inter-annual variation is
more likely to result from the variation in survey effort and/
or the variation in species distribution and abundance.
dolphins
A total of seven species of dolphins were sighted in Raja
Ampat (Table 1). Six dolphin species were observed in the
Kofiau MPA, while only two species were sighted in Misool
MPA (Table 2). Indo-Pacific humpback dolphins were
recorded north of Misool Island (Table 2). This is the first
study to record the occurrence of Fraser’s dolphins
(Lagenodelphis hosei Fraser, 1956) in Raja Ampat. Overall,
the most common dolphins sighted in Raja Ampat were
common bottlenose (Tursiops truncatus Montagu, 1821)
(51.5% of all sightings) and spinner dolphins (Stenella longir-
ostris Gray, 1828) (37.0% of sightings) (Table 2). The other 5
species were rarely seen in Raja Ampat and account for ,1%
of overall sightings. More dolphins were recorded in Kofiau
MPA (1780 individuals) than in Misool MPA (516 indivi-
duals), over the 6 years of surveys. Common bottlenose and
spinner dolphins were sighted year-round with no apparent
temporal pattern (Table 3).
Dolphins were generally distributed throughout the entire
area of Kofiau MPA (Figure 2A). Spinner dolphins were
most frequently found in areas of deep water (.500 m) in
the strait between Kofiau and Boo Island, south of Boo
 4 isabel ender et al.

Table 1. Summary of species of dolphins and whales sighted in Raja Ampat. IUCN (2012) status: DD, Data Deficient; VU, Vulnerable; NT, Near
Threatened; LC, Least Concern. Bryde’s whale is synonymous with pygmy Bryde’s whale (IUCN, 2012).

Common name Scientific name IUCN status Source

Spinner dolphin Stenella longirostris DD This study, Kahn (2007), Borsa & Nugroho (2010)
Common bottlenose dolphin Tursiops truncatus LC This study, Kahn (2007), Borsa & Nugroho (2010)
Fraser’s dolphin Lagenodelphis hosei LC This study
Indo-Pacific bottlenose dolphin Tursiops aduncus DD This study, Kahn (2007), Borsa & Nugroho (2010)
Risso’s dolphin Grampus griseus LC This study, Kahn (2007), Borsa & Nugroho (2010)
Pantropical spotted dolphin Stenella attenuata LC This study, Kahn (2007)
Indo-Pacific humpback dolphin Sousa chinensis NT This study, Kahn (2007)
Short-finned pilot whale Globicephala macrorhynchus DD This study, Borsa & Nugroho (2010)
Orca/ killer whale Orcinus orca DD This study
False killer whale Pseudorca crassidens DD This study, Kahn (2007), Borsa & Nugroho (2010)
Pygmy killer whale Feresa attenuata DD This study
Bryde’s whale Balaenoptera edeni DD This study, Kahn (2007)
Sperm whale Physeter macrocephalus VU This study, Kahn (2007), Borsa & Nugroho (2010)
Dwarf sperm whale Kogia sima DD Kahn (2007)

Island and also south of Kofiau Island. The two dolphin
species sighted at Misool Island (spinner and common
bottlenose) were sighted throughout the MPA (Figure 2B).
Dolphins were commonly found in the waters between
Sagewin Strait and Kofiau MPA (Figure 2C).
whales
Six species of whales were recorded in Raja Ampat during boat-
based incidental sightings—short-finned pilot (Globicephala
macrorhynchus Gray, 1846), Bryde’s (Balaenoptera edeni
Anderson, 1879), sperm (Physeter macrocephalus Linnaeus,
1758), pygmy killer (Feresa attenuata Gray, 1875), false killer
and killer whales (Tables 1 & 2). While killer and pygmy
killer whales have been recorded in other parts of Indonesia,
this is the first study to document the occurrence of these
species in Raja Ampat.
Overall, short-finned pilot whales were the most common-
ly sighted whale species (39.1% of sightings) in Raja Ampat,
often seen in groups of around 20 individuals (Table 2).
Killer whales (17.4%) were documented in groups of 2–6
individuals. Bryde’s whales (19.6%) and sperm whales
(13.1%) were also frequently sighted individually or in pairs.
Of the 6 records of sperm whales in Raja Ampat, 2 individuals
were listed as stranded. These were the only stranded whales
documented in Raja Ampat between 2006 and 2011. False
killer and pygmy killer whales were sighted only three times
during the survey in groups of 30 and 50, respectively. Six
species of whales were sighted in the Kofiau MPA while
only three species were seen at Misool MPA (Table 2).
Most of the whales sighted in the Kofiau MPA were in deep
waters (.500 m) in the straits between Kofiau Island and Boo
Island, with short-finned pilot whales being the most domin-
ant species observed (Figure 2D). In Misool MPA, whales were
only sighted in 2009 and 2010 (Figure 2E). All three sightings
of short-finned pilot whales in Misool MPA were accompan-
ied by pods of common bottlenose dolphins (up to 30 indivi-
duals) in close proximity. Orcas (2 individuals) and Bryde’s
whales (1 individual) were only sighted once in Misool in
2010 in the months of September and May, respectively.
Although the area was less frequented by the speedboat,

Table 2. Percentage composition (%), number of sightings (No.) and pod size range of incidental sightings of dolphins and whales at Kofiau and Misool
marine protected areas (MPAs), and other locations in Raja Ampat (‘Other’) from boat-based surveys from 2006–2011. Hyphens indicate the species was
not sighted.

Common name Scientific name Kofiau Misool Other % of all

sightings
% No. Pod size % No. Pod size % No. Pod size

Spinner dolphin Stenella longirostris 44.4 56 1 –115 20.2 22 2–15 51.6 32 2 –250 37.0
Common bottlenose dolphin Tursiops truncatus 39.7 50 1–20 78.9 86 1–15 27.4 17 1–25 51.5
Fraser’s dolphin Lagenodelphis hosei 0.8 1 100 – – – 1.6 1 200 0.7
Indo-Pacific bottlenose dolphin Tursiops aduncus 1.6 2 15–20 – – – – – – 0.7
Indo-Pacific humpback dolphin Sousa chinensis – – – – – – 3.2 2 4–6 0.7
Risso’s dolphin Grampus griseus 0.8 1 25 – – – – – – 0.3
Pantropical spotted dolphin Stenella attennuata 0.8 1 20 – – – – – – 0.3
Unidentified dolphin 11.9 15 1–8 0.9 1 4 16.1 10 1–6 8.8
Short-finned pilot whale Globicephala macrorhynchus 31.8 7 6–50 66.7 4 2–29 38.9 7 8–50 39.1
Killer whale Orcinus orca 27.3 6 2–6 16.7 1 2 5.6 1 2 17.4
Bryde’s whale Balaenoptera edeni 18.2 4 1 16.7 1 1 22.2 4 1–3 19.6
Sperm whale Physeter macrocephalus 9.1 2 1 – – – 22.2 4 1–2 13.0
False killer whale Pseudorca crassidens 9.1 2 30 – – – – – – 4.3
Pygmy killer whale Feresa attenuata 4.5 1 50 – – – – – – 2.2
Unidentified whale – – – – – – 11.1 2 1 4.3

https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press

 cetaceans in raja ampat 5

whales were documented in Dampier and Sagewin Straits, and

December
the oceanic waters between Sagewin Strait and Kofiau MPA

(+)
(+)

(+)

(+)

4
2
2
(Figure 2F).
November
Table 3. Whale and dolphin species sighted in different months between 2006 and 2011 during boat-based surveys in Raja Ampat. (+), indicates species was sighted at least once during this month.

(+) DISCUSSION
(+)
(+)

(+)

(+)
(+)
(+)
(+)

8
4
4
Cetacean diversity
This and other studies have documented a total of 14 species
October

(+)
(+)

(+)
(+)
(+)

(+)
of cetacean to date in Raja Ampat from incidental sightings

6
2
4
from aerial and boat-based surveys (Kahn, 2007; Borsa &
Nugroho, 2010; this study), which represents almost half of
September

the 31 cetacean species recorded in Indonesia (Rudolf et al.,

1997; Tomascick et al., 1997). This is the first published list
(+)
(+)

(+)

3
2
1
of cetacean species from the region, and includes species
such as Fraser’s dolphins, killer and pygmy whales, which
have not been recorded previously in Raja Ampat. Within
August

the areas surveyed (central and southern Raja Ampat), the

(+)

(+)

2
1
1
highest cetacean diversity and abundances were recorded in
Dampier and Sagewin Straits and in Kofiau MPA. Incidental
sightings from Raja Ampat suggest this Regency is an import-
July

(+)
(+)

(+)
(+)
(+)

5
3
2

ant area for cetaceans in Indonesia, and it is likely that

additional systematic surveys by cetacean experts would docu-
June

(+)
(+)

(+)

(+)

ment even more species.

4
3
1

With the exception of Komodo National Park which

recorded 18 species of cetaceans over 71 fieldwork days
May

(+)
(+)

(+)
(+)
(+)
(+)

(Kahn & Pet, 2003), all other surveys in Indonesia have

6
2
4

recorded lower number of cetaceans. For example, incidental

sightings from similar boat-based surveys over multiple years
April

(+)
(+)

(+)
(+)

(+)

5
2
3

in Derawan and Wakatobi MPAs in central Indonesia docu-

mented only 6 and 9 species of cetaceans, respectively (The
Nature Conservancy, unpublished data). Kreb & Budiono
March

(+)
(+)

(+)

(2005) documented 10 species of cetaceans over 80 days of

3
3

survey in the Derawan Archipelago. Boat-based surveys in

the Solor-Alor Straits recorded 12 species of cetaceans
February

(Kahn, 2005), while Kaimana (south of Raja Ampat) recorded

(+)
(+)
(+)

(+)

(+)

(+)
(+)

7
4
3

6 species (Kahn, 2009).

Dampier and Sagewin Straits have been suggested to be
important cetacean migration corridors (Kahn, 2007; Wilson
January

et al., 2010), and this study provides further evidence to

(+)
(+)
(+)

(+)
(+)
(+)

(+)

7
2
5

support this. Raja Ampat is strongly influenced by the

Indonesian flowthrough, the major oceanic exchange
between the West Pacific and Indian Ocean (Vranes &
Globicephala macrorhynchus

Gordon, 2005) and large whales, such as blue and sperm

whale are known to migrate to Indonesia from both the
Physeter macrocephalus
Pseudorca crassidens

Indian and Pacific Oceans (Carwardine, 2002). Corridors

Lagenodelphis hosei

Stenella attennuata
Stenella longirostris

Balaenoptera edeni
Tursiops truncatus

Tursiops aduncus

can be highly important for the long-term viability of cetacean

Grampus griseus

Feresa attenuata
Scientific name

Sousa chinensis

populations (Reeves, 2000).

Orcinus orca

Short-finned pilot whales, a species known to associate

with other cetaceans (Jefferson et al., 1993) were the most
commonly sighted whale in Raja Ampat. The Bryde’s whale
are considered by some as the least known tropical marine
mammal in the Asia-Pacific (Kahn, 2007), yet they were com-
Indo-Pacific humpback dolphin
Indo-Pacific bottlenose dolphin

monly seen in Raja Ampat and other parts of the BHS (Kahn,
Common bottlenose dolphin

Total no. of species sighted

Pantropical spotted dolphin

No. dolphin species sighted

2009; Mangubhai et al., 2012). This suggests that Raja Ampat

No. whale species sighted
Short-finned pilot whale

and the wider BHS is a regional stronghold for Bryde’s whales.

Common bottlenose and spinner dolphins were observed
Pygmy killer whale
False killer whale
Spinner dolphin
Common name

Fraser’s dolphin

year-round, which suggests that there may be resident popu-

Risso’s dolphin

Bryde’s whale
Sperm whale

lations in the Regency.

Killer whale

The abundance of top predators, such as bottlenose dol-

phins is considered by some as an indicator of the health of
coastal habitats (Hart, 2011; Reif, 2011). Similar to Borsa &

https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press

 6 isabel ender et al.
Fig. 2. Distribution of dolphin species in Kofiau (A), Misool (B) and other areas of Raja Ampat (C); and the distribution of whale species in Kofiau (D), Misool (E)
and other areas in Raja Ampat (F). Data pooled from 2006 – 2011.
Nugroho (2010), our study found spinner dolphins were the
most common dolphin species in Raja Ampat. There may
be two potential sub-species of spinner dolphins in the
Regency—the pelagic and dwarf species (Borsa & Nugroho,
2010), that warrant further study. A resident population of
Indo-Pacific humpback dolphins has also been documented
in Mayalibit Bay MPA, north of Dampier Strait (Kahn,
2007; Conservation International, unpublished data).
The high cetacean diversity in Raja Ampat is likely due to
the complex bathymetry which includes deep sea (.500 m)
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
areas close to the coast, the presence of seamounts and pinna-
cles and ‘bottlenecks’ for cetacean movement through the
straits (Kahn, 2007). Nutrient rich waters and seasonal upwel-
lings (Mangubhai et al., 2012) likely support important
feeding grounds for migrating and resident cetaceans (Borsa
& Nugroho, 2010; Wilson et al., 2010). Cetacean distribution
is dependent on habitat characteristics, such as bathymetry
(Cañadas & Sagarminada, 2000; Kiszka et al., 2007) and dis-
tinct habitat partitioning may occur along depth gradients.
For example, bottlenose dolphins are thought to be

continental shelf species, while short-finned pilot whales and
Risso’s dolphins (Grampus griseus Cuvier, 1812) are upper
continental slope species, and sperm whales are lower contin-
ental slope species (Davis et al., 1998, 2002; Baumgartner
et al., 2001). During aerial surveys in January and
September 2006, cetaceans were sighted both in shallow
coastal areas and in water deeper than 500 m. The wider
depth range found at Kofiau possibly contributes to the
higher diversity and numbers of cetaceans sighted within
and around the MPA compared with Misool further south.
While this study recognizes the limitations of incidental
sightings for understanding spatial and temporal patterns in
cetacean distribution, the data are invaluable as a basis for
more detailed and comprehensive surveys in the region, and
can be used by managers to better manage threats to these
species (see below). The study adds new data to at least 7
species of cetaceans listed as ‘Data Deficient’ by IUCN
(2012), and highlights the importance of Raja Ampat not
only for coral and reef fish diversity, but also for resident
and migratory cetaceans. The data presented in this paper
can be used by policy and decision makers responsible for pro-
tecting and managing these species in Indonesia.
Emerging threats and challenges
Government policies are being revised to encourage the rapid
expansion of oil and gas exploration and production through-
out Indonesia, including Raja Ampat and other parts of the
BHS (Mangubhai et al., 2012). Seismic testing and other
forms of extreme underwater noise can disturb and displace
cetaceans (McCauley et al., 2000; Stone & Tasker, 2006;
Castellote et al., 2012) and their prey (McCauley et al., 2003;
MacKenzie, 2004), and even lead to strandings (Yang et al.,
2008). Several mining leases have already been issued for
areas identified as potential migratory pathways in Raja
Ampat, and at least four vessels were reported conducting
seismic surveys in the Regency in 2010 (Mangubhai et al.,
2012). Currently seismic vessels operating within Indonesia
are not legally required to comply with international stan-
dards to reduce impacts to cetaceans (Kahn, 2010).
Aerial surveys also documented high numbers of vessels in
January and September 2006 in Kofiau (.50 vessels) and
Dampier Strait MPAs (.40 vessels) (Wilson et al., 2010). In
addition, high numbers of vessels (150– 200) were recorded
in the area around Sorong city and Batanta and Waigeo
Islands, including freight and industrial vessels (5 – 15).
These areas of high vessel traffic overlapped with key areas
where cetaceans were sighted, and therefore these species
face increasing risk of strikes and noise pollution from
vessel traffic in and out of the port of Sorong. Vessel collisions
can injur or kill cetaceans (Ford et al., 2000) and high traffic
can lead to disturbance and displacement from habitats
(Bejder et al., 2006). Similar to seismic surveys, vessel noise
can mask echolocation signals and impair foraging (Erbe,
2002; Aguilar Soto et al., 2006). Bomb fishing continues in
Raja Ampat (including occassionally in MPAs) and may add
additional noise stress to cetaceans residing or frequenting
the Regency’s waters (Purwanto & Muhajir, personal
observations).
Entanglement in coastal fishing nets can drown or chron-
ically injure cetaceans (Moore & Van der Hoop, 2012), and
this can have population-wide effects even if a small percent-
age of the population is captured (Negri et al., 2012). Many of
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
cetaceans in raja ampat 7
the vessels documented by Wilson et al. (2010) were engaged
in fishing activities. Where the distribution of cetaceans over-
laps with MPAs, regulations to manage commercial fishing
may provide some protection. However, other areas such as
Sagewin Strait and some parts of Dampier Strait are outside
MPA boundaries (Figure 2) and do not have regulations in
place to manage potential threats to resident or migrating
cetaceans.
High levels of plastic pollution occur around urban areas in
Raja Ampat such as Sorong and Waisai, especially after high
rainfall (Mangubhai et al., 2012; Purwanto & Muhajir, person-
al observations). Plastic and marine debris is an increasing
‘cryptic’ threat to cetaceans worldwide and if ingested can
cause illness to or death of cetaceans (Jacobsen et al., 2010;
Simmonds, 2012) and could impact populations residing or
migrating to Raja Ampat.
The high diversity and large number of cetaceans relatively
close to shore in Raja Ampat creates a unique additional
opportunity for the burgeoning dive-based tourism industry.
As the Regency expands its tourism sector, there may be
opportunities to offer whale watching to visitors which may
bring additional revenue to the government and local commu-
nities. However, to ensure the maintenance of healthy and
diverse cetacean assemblages in Raja Ampat, a wider conser-
vation strategy will need to be put in place to address or
better manage emerging threats to Raja Ampat, and to
ensure the long-term protection of resident and migratory
dolphin and whale species.
ACKNOWLEDGEMENTS
We thank T. Nugrahaeni, R. Lantang, M. Syakir, D.A.
Wibowo and the supporting boat captains and crew for con-
tributing to this dataset. We are grateful to B. Kahn for
confirming photo-identification of cetacean species where
needed, and to S. Leahy for assisting with GIS maps. This
work was funded by the David and Lucille Packard
Foundation, Walton Family Foundation, USAID and private
donors, and conducted under a memorandum of under-
standing between The Nature Conservancy and the Nature
Conservation Agency of the Indonesian Ministry for Forestry.
REFERENCES
Aguilar Soto N.A., Johnson M., Madsen P.T., Tyack P.L., Bocconcelli
A. and Borsani J.F. (2006) Does intense ship noise disrupt foraging
in deep-diving Cuvier’s beaked whales (Ziphius cavirostris)? Marine
Mammal Science 22, 690–699.
Allen G.R. and Erdmann M.V. (2012) Reef fishes of the East Indies.
Volumes I–III. Perth, Western Australia: Tropical Reef Research.
Baumgartner M., Mullin K., May L. and Leming T. (2001) Cetacean
habitats in the northern Gulf of Mexico. Fisheries Bulletin 99, 219–239.
Barnes R.H. (1996) Lamakera, Solor. Ethnographic notes on a Muslim
whaling village of eastern Indonesia. Anthropos 91, 75–88.
Bejder L., Samuels A., Whitehead H. and Gales N. (2006) Decline in
relative abundance of bottlenose dolphins exposed to long-term dis-
turbance. Conservation Biology 20, 1791–1798.
Borsa P. and Nugroho D.A. (2010) Spinner dolphin (Stenella longirostris)
and other cetaceans in Raja Ampat waters, West Papua.
 8 isabel ender et al.
Marine Biodiversity Records e49. DOI: http://dx.doi.org/10.1017/
S175526721000045X.
Cañadas A. and Sagarminaga R. (2000) The northeastern Alboran Sea,
an important breeding and feeding ground for the long-finned pilot
whale (Globicephala melas) in the Mediterranean Sea. Marine
Mammal Science 16, 513–529.
Carwardine M. (1995) Eye witness handbook: whales, dolphins and por-
poises. The visual guide to all world’s cetaceans. New York: Dorling
Kindersley Ltd.
Carwardine M. (2002) Whales, dolphins and porpoises. London:
Smithsonian Handbooks and Dorling Kindersley Ltd.
Castellote M., Clark C.W. and Lammers M.O. (2012) Acoustic and
behavioural changes by fin whales (Balaenoptera physalus) in response
to shipping and airgun noise. Biological Conservation 147, 115 –122.
Coral Triangle Initiative (2009) Regional Plan of Action on Coral
Triangle Initiative on Coral Reefs, Fisheries and Food Security.
Indonesia: Interim Regional CTI Secretariat.
Davis R., Fargion G., May N., Leming T., Baumgartner M., Evans W.E.,
Hansen L.J. and Mullin K. (1998) Physical habitat of cetaceans along
the continental slope in the north-central and western Gulf of Mexico.
Marine Mammal Science 14, 490–507.
Davis R.W., Ortega-Ortiz J.G., Ribic C.A., Evans W.E., Biggs D.C.,
Ressler P.H., Cady R.B., Leben R.R., Mullin K.D. and Würsig B.
(2002) Cetacean habitat in the northern oceanic Gulf of Mexico.
Deep-Sea Research 49, 121–142.
Erbe C. (2002) Underwater noise of whale-watching boats and potential
effects on killer whales (Orcinus orca), based on an acoustic impact
model. Marine Mammal Science 18, 394–418.
Ford J.K.B., Ellis G.M. and Balcomb K.C. (2000) Killer whales: the
natural history and genealogy of Orcinus orca in British Columbia
and Washington. 2nd edition. Vancouver: University of British
Columbia Press.
Hart L.B. (2011) The use of longitudinal and cross-sectional photographic
data to study skin disease in wild bottlenose dolphins (Tursiops trunca-
tus). PhD thesis. Medical University of South Carolina.
Huffard C.L., Erdmann M.V. and Gunawan T. (2009) Defining geo-
graphic priorities for marine biodiversity conservation in Indonesia.
Indonesia: USAID Coral Triangle Support Partnership, 103 pp.
IUCN (2012) The IUCN Red List of Threatened Species. Version 2012.2.
Available at: http://www.iucnredlist.org (accessed 1 December 2013).
Jacobsen J.K., Massey L. and Gulland F. (2010) Fatal ingestion of floating
net debris by two sperm whales (Physeter macrocephalus). Marine
Pollution Bulletin 60, 765 –767.
Jefferson T.A., Leatherwood S. and Webber M.A. (1993) FAO species
identification guide: marine mammals of the world. Rome:
United Nations Environment Programme Food and Agriculture
Organization of the United Nations.
Kahn B. (2005) Indonesia Oceanic Cetacean Program Activity Report:
April–June 2005. Bali: Apex Environmental, 31 pp.
Kahn B. (2007) Marine Mammals of the Raja Ampat Islands: Visual
and Acoustic Cetacean Survey and Training Program. Bali: Apex
Environmental, 57 pp.
Kahn B. (2009) Marine Mammal Survey and Training in Triton Bay, West
Papua, Indonesia: Management Implications for Resident Bryde’s
Whales. Bali: Apex Environmental, 32 pp.
Kahn B. (2010) Seismic Surveys and Offshore Exploration in Highly
Sensitive Marine Areas: Regulatory Guidelines and Best Practices for
Contractors and Operators Working in the Indonesian Seas. Bali:
Apex Environmental, 30 pp.
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
Kahn B. and Pet J. (2003) Long-term visual and acoustic cetacean surveys
in Komodo National Park, Indonesia 1999–2001: management
implications for large marine migratory marine life. In Beumer J.P.,
Grant A. and Smith D.C. (eds) Proceedings of the World Congress on
Aquatic Protected Areas 2002. Murdoch, Western Australia:
Australian Society for Fish Biology, pp. 625–673.
Kiszka J., Macleod K., Van Canneyt O., Walker D. and Ridoux V.
(2007) Distribution, encounter rates, and habitat characteristics of
toothed cetaceans in the Bay of Biscay and adjacent waters from
platform-of-opportunity data. ICES Journal of Marine Science 64,
1033–1043.
Kreb D. (2008) Sulawesi Sea Cetacean Project 2007–2008. Final technical
report. Conservation and diversity of marine cetaceans in the Berau
Archipelago, East Kalimantan, Indonesia. Indonesia: RASI Conservation
Foundation, Kalimantan Timur, 22 pp.
Kreb D. and Budiono. (2005a) Conservation management of small core
areas: key to survival of a Critically Endangered population of
Irrawaddy river dolphins Orcaella brevirostris in Indonesia. Oryx 39,
1–11.
Kreb D. and Budiono. (2005b) Cetacean diversity and habitat preferences
in tropical waters of East Kalimantan, Indonesia. Raffles Bulletin of
Zoology 53, 149–155.
Kreb D. and Budiono. (2012) Final technical report. East Kalimantan
Cetacean Conservation Project 2009–2012. Conservation and diversity
of cetaceans within a new potential MPA in East Kalimantan,
Indonesia. RASI Conservation Foundation, Kalimantan Timur, 27 pp.
MacLeod K., Simmonds M.P. and Murray E. (2006) Abundance of fin
(Balaenoptera physalus) and sei whales (Balaenoptera borealis) amid
oil exploration and development off northwest Scotland. Journal of
Cetacean Research and Management 8, 247–254.
MacKenzie D. (2004) Seismic surveys may kill giant squid. New Scientist
184, 15.
Mangubhai S., Erdmann M.V., Wilson J.R., Huffard C.L., Ballamu F.,
Hidayat N.I., Hitipeuw C., Lazuardi M.E., Muhajir, Pada D., Purba
G., Rotinsulu C., Rumetna L., Sumolang K. and Wen W. (2012)
Papuan Bird’s Head Seascape: emerging threats and challenges in
the global center of marine biodiversity. Marine Pollution Bulletin
64, 2279–2295.
McCauley R.D., Fewtreli J., Duncan A.J., Jenner C., Jenner M.N.,
Penrose J.D., Prince R.I.T., Adhitya A., Murdoch J. and McCabe
K. (2000) Marine seismic surveys—a study of environmental implica-
tions. APPEA Journal 40, 692 –708.
McCauley R.D., Fewtrell J. and Popper A.N. (2003) High intensity
anthropogenic sound damages fish ears. Journal of the Acoustical
Society of America 113, 638–42.
Moore M.J. and Van der Hoop J.M. (2012) The painful side of trap and
fixed net fisheries: chronic entanglement of large whales. Journal of
Marine Biology. Article ID 230653. http://dx.doi.org/10.1155/2012/
230653.
Muljadi A.H. and Nugrahaeni T. (2006) Pengamatan Insidental di
Kofiau, Raja Ampat. Protokol monitoring versi 1.0. Kofiau, Raja
Ampat: The Nature Conservancy—Coral Triangle Center, 26 pp.
Mustika P.L.K., Hutasoit P., Madusari C.C., Purnomo F.S., Setiawan
A., Tjandra K. and Prabowo W.E. (2009) Whale strandings in
Indonesia, including the first record of a humpback whale
(Megaptera novaeangliae) in the archipelago. Raffles Bulletin of
Zoology 57, 199–206.
Negri M.F., Denuncio P., Panebianco M.V. and Cappozzo H.L. (2012)
Bycatch of franciscana dolphins Pontoporia blainvillei and the
dynamic of artisanal fisheries in the species’ southernmost area of dis-
tribution. Brazilian Journal of Oceanography 60, 149–158.

Pratomo A., Setiawan A., Wiadnya G., Barmawi M. and Mous P.J.
(2006) Pengamatan Insidental di sekitar Misool Timur Selatan.
Protokol monitoring versi 1.0. Bali: The Nature Conservancy—Coral
Triangle Center, 26 pp.
Reeves R.R. (2000) The Value of Sanctuaries, Parks, and Reserves
(Protected Areas) as Tools for Conserving Marine Mammals. Report
prepared for the Marine Mammal Commission, 4340 East-West
Highway, Bethesda, Maryland 20814, USA, 54 pp.
Reif J.S. (2011) Animal sentinels for environmental and public health.
Practice Articles, Public Health Reports, 2011 Supplements 126, 50–56.
Rudolf P., Smeenk C. and Leatherwood S. (1997) Preliminary checklist
of Cetacea in the Indonesian Archipelago and adjacent waters.
Zoologische Verhandilingen 312, 3 –48.
Schick R.S., Halpin P.N., Read A.J., Urban D.L., Best B.D., Good C.P.,
Roberts J.J., LaBrecque E.A., Dunn C., Garrison L.P., Hyrenbach
K.D., McLellan W.A., Pabst D.A., Palka D.L. and Stevick P.
(2011) Community structure in pelagic marine mammals at large
spatial scales. Marine Ecology Progress Series 434, 165–181.
Simmonds M.P. (2012) Cetaceans and marine debris: the great unknown.
Journal of Marine Biology. Article ID 684279. http://dx.doi.org/10.
1155/2012/684279.
Stone C.J. and Tasker M.L. (2006) The effects of seismic airguns on ceta-
ceans in UK waters. Journal of Cetacean Research and Management 8,
255–263.
Tomascik T., Mah A.J., Nontji A. and Moosa M.K. (1997) Seagrasses.
In Tomascik T., Mah A.J., Nontji A. and Moosa M.K. (eds) The
https://doi.org/10.1017/S1755267214000207 Published online by Cambridge University Press
cetaceans in raja ampat 9
ecology of the Indonesian Seas VIII, Part II. Oxford: Oxford
University Press, pp. 829 –906.
Veron J.E.N., DeVantier L.M., Turak E., Green A.L., Kininmonth S.,
Stafford-Smith M. and Peterson N. (2009) Delineating the Coral
Triangle. Galaxea 11, 91–100.
Vranes K. and Gordon A.L. (2005) Comparison of Indonesian through-
flow transport observations, Makassar Strait to eastern Indian Ocean.
Geophysical Research Letters 32, 1 –5.
Wilson J., Rotinsulu C., Muljadi A.M., Wen W., Barmawai M. and
Mandagi S. (2010) Spatial and temporal patterns in marine resource
use within Raja Ampat Region from aerial surveys 2006. Bali: The
Nature Conservancy, 44 pp.
and
Yang W.C., Chou L.S., Jepson P.D., Brownell R.L., Cowan D., Chang
P.H., Chiou H.I., Yao C.J., Yamada T.K., Chiu J.T., Wang P.J.
and Fernández A. (2008) Unusual cetacean mortality event in
Taiwan, possibly linked to naval activities. Veterinary Record 162,
184–186.
Correspondence should be addressed to:
S. Mangubhai
IUCN Oceania Regional Office
5 Ma’afu Street
Suva
Fiji
email: smangubhai@gmail.com