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Timor‐Leste
Marine Science
Training Handbook Last updated March 2016
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Contents 1 THE NATURAL HISTORY OF TIMOR‐LESTE ....................................................................................... 2
1.1 Timor‐Leste ............................................................................................................................. 2
1.2 The importance of the Coral Triangle ..................................................................................... 3
1.3 Climate of Timor‐Leste ............................................................................................................ 4
1.4 Conservation in Timor‐Leste ................................................................................................... 4
2 BLUE VENTURES CONSERVATION IN TIMOR‐LESTE ........................................................................ 5
2.1 Blue Ventures’ aims and objectives ........................................................................................ 5
3 INTRODUCTION TO TROPICAL MARINE ECOSYSTEMS .................................................................... 6
3.1 Coral Reefs .............................................................................................................................. 6
3.2 Seagrass beds ........................................................................................................................ 10
3.3 Mangroves ............................................................................................................................ 12
4 THREATS TO TROPICAL MARINE ECOSYSTEMS ............................................................................. 14
5 TROPICAL MARINE INVERTEBRATES ............................................................................................. 16
5.1 Sponges ................................................................................................................................. 16
5.2 Cnidarians ............................................................................................................................. 16
5.3 Molluscs ................................................................................................................................ 17
5.4 Echinoderms ......................................................................................................................... 17
5.5 Tunicates ............................................................................................................................... 18
6 INTRODUCTION TO FISH ............................................................................................................... 19
6.1 Introduction to common fish families .................................................................................. 19
7 KEY MARINE GROUPS .................................................................................................................... 25
7.1 Turtles ................................................................................................................................... 25
7.2 Marine mammals .................................................................................................................. 25
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1 THE NATURAL HISTORY OF TIMOR‐LESTE
1.1 Timor‐Leste
Timor is the largest of the Lesser Sunda Islands at the Eastern tip of the Indonesian archipelago in
Southeast Asia. The island is split between Timor‐Leste in the east and the Indonesian province of
East Nusa Tenggara in the west. Timor‐Leste has a landmass of just over 15,000km2, including
offshore islands Ataúro and Jaco as well as Oecusse, an exclave situated in Indonesian portion of
Timor. The population is estimated at about 1.3 million with a growth rate of approximately 2.5% a
year.
Located in the Coral Triangle, Timor‐Leste boasts high levels of species diversity among reef fish and
corals, and its reefs are relatively unexplored compared to those of neighbouring areas such as
Australia and Bali. Terrestrial biodiversity, similar to other island nations that have been separated
from nearby continents for a significant period of time is also interesting with Timor possessing a
number of endemic bird and reptile species, including the Timor python.
Map of Timor‐Leste showing districts and nearby islands (Source: UN)
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1.2 The importance of the Coral Triangle
Nowhere else on the planet can you find the levels of marine biodiversity present in the 6 million
km2 of the Coral Triangle, which is spread across six countries. Due to the combined factors of
tropical light, warm waters, and strong oceanic currents and upwellings in an area with great
topographical variation, the range is considered the epicentre of global coral reef biodiversity.
More than three quarters of all known coral species occur here, and although endemic marine
species are rarer than terrestrial ones, due to the indiscriminate spawning methods used by most
fish, coral and invertebrate species, there are relatively high numbers found in the Coral Triangle; 15
species of coral and at least 235 species of fish that are considered endemic or “locally restricted”.
Six out of the world’s seven turtle species are present, as well as mammals; whales, dolphins and
endangered dugongs, and elasmobranchs; sharks and rays.
Despite the wealth of marine life found here, more than 250 species are classified by IUCN as
“threatened with extinction”, little surprise given the combined pressures of pollution, destructive
fishing methods, rising sea temperatures and ocean acidification.
Tourism plays an important role in the coral triangle, with opportunities for alternative livelihoods to
relieve fishing pressures being one of the key strategies of conservation groups the world over. 120
million people depend on the resources of the Coral Triangle for their food and livelihoods, and
while the area is renowned for its productivity the pressures of such a large and continuously
growing population are huge.
Map showing the area known as the Coral Triangle (Source: WWF)
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1.3 Climate of Timor‐Leste
Located 953km from the Equator and 650km from the coast of Australia, Timor‐Leste has a tropical
climate, hot and humid year round with wet and dry seasons rather than summer and winter. The
temperature hovers around 30°C throughout the year, with moist winds coming from the northwest
from November to May, and dry winds coming from the southeast the rest of the year. Fluctuations
in temperature are more likely to come at higher altitudes or directly next to the sea. Ataúro, the
current Blue Ventures site in Timor‐Leste, is located 25km north of Dili. The site is rugged and
topographically diverse, and can feel very hot when becalmed and cool when the winds blow.
In‐water temperatures vary between 24°C and 28°C throughout the year depending on where the
currents are flowing from and the levels of rainfall. Visibility is usually good year‐round off Ataúro,
but can vary in off the mainland due to rainfall carrying sediment from the mountainous interior into
coastal waters via the country’s many rivers.
1.4 Conservation in Timor‐Leste
As a young nation, Timor‐Leste’s management of its natural resources is in a nascent and critical
stage. The country relies on a sovereign petroleum fund for much of its national spending but
revenues are decreasing annually and there is widespread acceptance that much greater levels of
economic diversification are required in order to tackle any future shortfalls.
Timor‐Leste has a total of 50 protected areas, the majority of which are currently at the proposal
stage. The largest and best supported protected area, and the only one with a marine component, is
Nino Konis Santana National Park in the east of Timor‐Leste. A further 120,000 hectares of seascape
are earmarked for protection, including much of the area surrounding Ataúro, but governmental
resources for conservation are limited, and there are few civil society organisations focused on
conservation with permanent activities in Timor‐Leste.
Despite the presence of these obstacles, Timor‐Leste has enshrined the conservation and protection
of natural resources in its constitution, and recognises that sound management of coastal and
marine resources are essential to guide sustainable livelihoods, development and poverty
alleviation.
With a wealth of comparatively untouched terrestrial and marine natural resources, Timor‐Leste has
an excellent opportunity to establish itself as a destination that showcases the splendour of the
Coral Triangle along with a ruggedly beautiful landscape with a rich colonial and cultural history.
Tourism in the Coral Triangle is worth US$16 billion annually, and although it can be an economic
boon to such countries, bringing money into local communities via a multitude of vectors, it can also
increase pressures on the environment if not managed carefully. Blue Ventures’ goal in Timor‐Leste
is to design a financially sustainable ecotourism project that generates economic benefits for local
communities, incentivising those communities to manage their local marine resources in an effective
and sustainable matter. By building capacity at community level, efforts for long term marine
management at a national level are supported, further safeguarding them for future generations.
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2 BLUE VENTURES CONSERVATION IN TIMOR‐LESTE
2.1 Blue Ventures’ aims and objectives
The Blue Ventures model is adapted for best use wherever we work, but loosely follows this pattern:
Working from Dili and Ataúro, BV will strive to implement an ecotourism programme that will
highlight the need for education, research and conservation to volunteers, while at the same time
immersing them in our efforts to implement our model.
Education
Education in marine conservation and
research for volunteers from all around the
world
Education for local communities in marine
conservation and ecotourism through open
days and workshops
Education in schools and universities in the
UK promoting marine conservation and
sustainable development
Research
Trained staff and volunteers conduct
monitoring and baseline survey work of key
areas in the country
Data gathered used by Blue Ventures
alongside local people and the scientific
community to develop a management
strategy for the coastal region
Conservation
Marine habitats are better understood and
consequently better protected through
increased awareness
Local villages and fishing communities
benefit from increased protection of coastal
zone, effective marine management, and
alternative livelihoods being generated
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3 INTRODUCTION TO TROPICAL MARINE ECOSYSTEMS
Coral reefs are one of the most well‐known and recognisable ecosystems world‐wide and a huge
focal point for global biodiversity protection efforts. However, their success in many areas is
dependent on interactions with two other equally valuable yet lesser known ecosystems, areas that
are also constantly under increasing climatic and anthropogenic pressures. Seagrass and Mangrove
ecosystems are tropical marine ecosystems that, together with coral reefs, form a tripod with each
‘leg’ interacting with the others, providing support and being supported. All are shallow water
ecosystems and their presence or absence is dependent on prevailing local conditions; coral reefs
are most prevalent in seaward areas, seagrass in more protected waters and mangroves in intertidal
areas. Blue Ventures expeditions will focus on documenting and assessing each of these habitats,
and their associated fauna. In conjunction with social, economic and fisheries knowledge this
information will form an important part of advising community based management in the future.
3.1 Coral Reefs
Overview Coral reefs comprise less than 0.25% of the ocean floor, an area of only 284,300km2, yet it is
estimated that more than 80% of marine species are in some way dependent on them. Home to a
quarter of all known marine species, reefs include more than 5,000 fish species and up to 2 million
species overall. Coral reefs are the most productive ecosystems in the marine environment and are
able to fix large amounts of carbon dioxide, making them vital to the future health of the planet.
Structure of coral reefs Most of the structure of a coral reef consists of the cumulative calcium carbonate deposits of reef‐
building (hermatypic) corals. The living creatures are restricted to a thin surface layer and are known
as polyps and each individual coral polyp usually forms part of a colony. Corals feed on plankton but
this only makes up about 10% of their diet; the rest comes from a symbiotic partnership with a type
of photosynthetic algae known as zooxanthellae. The algae, housed safely in the epidermal layer of
the polyp, uses light and waste products from the polyp to provide the rest of the coral’s needed
energy in the form of an excess of photosynthesised material. Each species of coral grows in a
different way and as the differences in polyp structure can be almost indecipherable between them,
and it is these growth forms that we teach and monitor.
Other organisms which contribute to the makeup of the reef include non‐reef‐building corals,
numerous sessile and mobile invertebrates and a variety of different types of algae. Coral reefs are
ever‐changing, constantly evolving ecosystems, delicately balanced and vulnerable to outside
Growth forms: fast‐growing branching coral, and slower, hardier encrusting coral
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factors. The structure of a fish population on a reef is a determining factor in the health and
structure of a coral reef with herbivores playing an important grazing role with their removal often
cited as the first stage in the degradation of a coral reef.
Factors controlling coral reef distribution Coral reef distribution is restricted by the factors that limit coral productivity and survival. The most
important factors that control coral reef distribution are light, temperature, salinity, nutrient levels
and sediment. Reefs grow in patterns across the world that seem strange unless all these factors are
taken into account.
Light
Light on a reef is an essential resource with fierce competition for space among corals and the
faster‐growing algae with both reliant on sunlight for growth. The deeper the reef, the less intense
the light, and coral species grow in different forms at different depths to reflect this.
Temperature
Most tropical reef‐building corals cannot tolerate prolonged periods of temperatures outside a very
narrow range, generally accepted to be between 23 and 29°C, although some corals can endure
higher temperatures for short times before damage occurs (see: Coral Bleaching).
Salinity
Reefs are only found in seawater, and are so intolerant of fresh water that they will not even form
near large river mouths (see also: Sediment).
Nutrients
Coral reefs thrive in clear rather than nutrient‐rich waters. Human influence, in the form of nutrient‐
heavy river run‐off from some agricultural and aquacultural practices boosts the growth of algal
species. Outcompeting slower growing corals, algal growth reduces the amount of light available to
them and eventually smothers them.
Sediment
Reefs do not form in areas with high levels of suspended sediment; light levels decrease in such
areas, and sediment can abrade or smother a reef if it is not washed away into deeper waters.
Where suspended particles settle onto the substrate it can also prevent coral recruits from settling,
thus inhibiting the reef’s further growth.
Reef development Coral produces planktonic larvae, called planulae, in order to propagate over large distances through
ocean currents reaching distant reefs to settle on and grow. Upon landing upon a suitable substrate,
the planulae attach themselves to the reef and form new polyps; a process called recruitment. Some
sites are more advantageous than others, depending on the substrate; a patch of reef that appears
to have been painted pink indicates the presence of crustose coralline algae (CCA), which acts as the
cement of the reef. Coral recruits which are situated on CCA are hardier and more likely to survive
and reproduce, growing into a large colony that can support life. Depending on where they settle
relative to land, one of three reef types forms. Charles Darwin postulated that these three
formations are just three stages of reef development as reefs form and land subsides, as shown
below:
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Fringing
Coral forming on or near the coast creates
what is known as a fringing reef. Shallow
waters and a substrate which slopes gently
out to deeper waters create conditions which
allow large, continuous reefs which follow the
coastline and are typically only separated
from it by a narrow stretch of water.
Barrier
Barrier reefs are also continuous, and tend to
run parallel to the closest land, but are
removed from it by a large, often quite deep
lagoon. The land here has subsided to the
point where there is no connection between
land and reef but their positions relative to
each other.
Atoll
An atoll is what is left when all land has
subsided and the coral reef has continuously
built on itself to maintain its position. Usually
round or oval having formed around a land
mass, they have a central lagoon and
sometimes islands at different tidal levels.
Regardless of how they formed and where, most reefs share a basic zonation and structural pattern;
the area between land and the reef crest is known as the reef flat, and the reef seawards from the
reef crest known as the fore reef, before walls (steeper in some areas than others) drop off into
much deeper waters.
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Back reef
The back reef, behind the reef crest, is protected from ocean swell but experiences limited water
movement making this section of the reef highly variable in temperature and salinity, so whilst many
invertebrates flourish in these protected waters, coral growth is limited.
Reef crest
This area takes the brunt of the wave action on the reef, and protects the back reef and any seagrass
lagoons present from the constant churn of water and sediment of the fore reef and beyond. Often
exposed for long periods at a time the crest can be home to fast‐growing branching corals where
wave action is limited, or virtually none where it is constant and severe.
Fore reef
Also known as the buttress zone for its distinctive structure, fore‐reefs often grow in a formation
known as “spur and groove”, with channels of sand separated by spires and ridges of coral, giving it
an instantly recognisable pattern from the surface. Designed to dissipate wave energy and drain
away excess sediment, the fore‐reef is a highly diverse area, with abundant resources in terms of
oxygen and sunlight, but occasional bouts of turbulence from storms or worse. Here thrive the
massive and encrusting corals, slow‐growing but sturdy, and any fish whose idea of perfection is to
live in shallow water, hide in a hole when predators come by, and eat algae all day long – and the
predators.
Deeper reef
As the reef slopes down to greater depths the available light decreases, as does wave action. If the
conditions on the patch where coral recruits have landed are conducive to that coral’s needs, it will
grow, and possibly flourish, particularly if it can grow in a formation which makes the most of its
current conditions. As depths exceed 40m, reef‐building corals give way to sponges, gorgonians (sea
whips and sea fans) and the non‐reef‐building (ahermatypic) corals, and the eye of the recreational
diver looks down wistfully, before ascending to safer and brighter depths.
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3.2 Seagrass beds
Despite first appearances, seagrasses are
actually flowering plants rather than a
type of seaweed. There are more than 70
extant species of seagrass; whilst their
meadows may not appear to be
particularly diverse to the casual eye and
tend to be overshadowed by more
exciting and charismatic biomes, they are
in reality one of the most productive types
of marine ecosystem worldwide, and thus
are extremely valuable.
An estimate from the Smithsonian Institute recently claimed that one acre of healthy seagrass can
support 40,000 fish and 50 million invertebrates. In one year, one acre of seagrass fixes the same
amount of carbon a typical car emits over a trip of 3,860 miles (6,212 km), while at the same time
producing nearly 15 million litres of oxygen through photosynthesis. If you need charisma to care,
consider that they are also the primary habitat of dugongs (vulnerable), manatees (vulnerable) and
green turtles (endangered), and are also the first stage nursery for many species of reef fish.
Seagrass diversity Seagrass beds can be found in all of
the world’s oceans and grow along
the shores of all continents except
Antarctica.
Seagrass meadows in temperate
waters however, tend to be less
diverse than those of the tropics
where it is not uncommon to find
upwards of ten species in a small
area, particularly in the Indopacific.
The adjacent key describes some
common Indopacific seagrass
species with species from genera
Thallassia, Enhalus and
Syringodinium being the most
common constituents of
Indopacific seagrass beds.
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Blue carbon The carbon locked up in the world’s oceans and coastal ecosystems is collectively known as blue
carbon. Stored in a variety of organic forms from living biomass to coastal sediments, blue carbon is
a sizeable and critical component of the global carbon cycle. Seagrass meadows store an estimated
10‐18% of all oceanic carbon despite only accounting for 0.1% of the world’s seafloor. Whilst some
of this carbon is held in the living biomass of the seagrass, the vast majority (more than 90%) is
sequestered in the organic sediments beneath. If a seagrass meadow is lost, the carbon within the
sediments below is no longer stored in an inert form and the meadow becomes a potential emitter
of carbon dioxide instead.
The surveys of Timor‐Leste’s seagrass meadows completed each expedition mark the beginning of a
project aimed at assessing the state of seagrass resources and working with communities to
conserve them and their most threatened inhabitant, the dugong (Dugong dugon), (see: Marine
mammals). Seagrass beds are continually threatened through development, dredging and
destructive fishing methods, and a global lack of awareness of their importance is a key factor in this.
There are very few shallow coastal regions in the world that do not play host to at least one type
of blue carbon ecosystem. The above map outlines the estimated global extent of mangroves,
seagrass meadows and salt marshes (a third, equally important coastal carbon store) The Coral
Triangle has an abundance of all of them along with exemplary coral reef coverage.
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3.3 Mangroves
Mangrove adaptations Mangroves are among the most fascinating organisms in the botanical world, living in harsh saline
environments that would quickly kill other plants and trees. As salt‐loving organisms (facultative
halophytes), each species has developed various adaptations to the conditions of the coastal zone.
Mangrove ecosystems are restricted to inter‐tidal and estuarine areas with a clear progression of
species, each with differing
survival strategies
progressing from low to high
tide and beyond.
Prop roots
Species of mangrove found
at low water are often those
exposed to the greatest level
of water movement and thus
have significant adaptation
to ensure they remain rooted
in place. Prop roots are roots
that suspend mangrove trees
above the water line,
stabilising and protecting the main body of the plant.
Salt intake
Whilst described as 'salt loving', all species of mangrove have a number of adaptations to exclude
and excrete the salt in the water they uptake. All mangrove roots are impregnated with suberin, a
compound that acts as a selective barrier, excluding up to 97% of salt at the point of intake. The salt
intake still in excess of what is required by the plant is excreted as salt crystals on the underside of
the leaves by many species of
mangrove.
Pneumatophores
One of the most striking features of
mangroves stands are the swathes of
upward facing pneumatophores found
in dense aggregations around the base
of trees exposed at low tide. Also
known as ‘finger roots’, they act as
breathing tubes for a tree. Growing
roots that emerge from the soil into
the atmosphere enable a tree to
breathe because mangroves sediments are extremely oxygen poor.
Vivipary
Mangroves produce live young; buoyant seedlings known as propagules germinate on their branches
and, when mature, drop into the water to drift on currents and create new stands of trees once a
suitable environment has been reached.
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Mangroves support a phenomenal
number of organisms both above
and below the waterline. Birds and
insects, numerous reptiles and
invertebrates in droves inhabit
their thick leaves above land, and
such habitats are decreasing in
their abundance on a global scale.
Beneath the surface though, lies an
equally diverse and little seen
underwater wonderland.
Mangrove roots play host to a
wealth of anemones, tunicates and
sponges which thrive on in waters
rich with plankton and suspended organic matter.
Mangrove roots act as a secondary nursery for many species of reef fish during the transition
between juvenile and adult life stages. The small spaces between roots provide shelter from
predators, and the richness of planktonic and invertebrate life provides an ample source of
sustenance.
Mangroves grow in formations known as mangals, and new mangals can form from settled
propagules tangling together in shallow, sediment‐heavy waters; once established they begin to
accrete sediment and new islands can spring up relatively fast. Conversely, when mangroves are
removed from a coastline their protection from erosion is also lost; in the last decade alone 35% of
the world’s mangroves has been destroyed, either for wood to build or burn, for land clearance or
even just to improve the view for tourism.
Blue carbon Mangroves, along with seagrass meadows and salt marshes, are part of the blue carbon ecosystem
and are responsible for approximately 15% of marine carbon storage worldwide. Mangroves are
resilient to climatic disturbances such as floods and cyclones but are arguably under the greatest
threat of any tropical marine ecosystem; coastal development, shellfish fisheries, and many
mangrove species’ utility as a building material and firewood are all significant causes of mangrove
habitat loss in the last 50 years.
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4 THREATS TO TROPICAL MARINE ECOSYSTEMS
Coastal marine ecosystems across the world face a host of threats. Some are climatic and naturally
occurring, others are climatic but amplified by human activity; an ever increasing proportion are a
direct result of human activity. Timor‐Leste is at as great a risk as any other coastal state from
climatic threats, amplified or otherwise, but as an emerging nation still forming a consensus on
sustainable development, there is hope that preventative action can be taken against some direct
human impacts.
Coastal development Coastal zones around the world are being developed at a phenomenal rate in an attempt to exploit
their economic potential, sometimes with very little thought spared for sustainability or damage to
the environment. Mangroves are cleared to make room for new developments and seagrass beds
are dredged to create channels deep enough to allow ships close to shore. Carbon rich sediments,
released by the removal of these habitats, often impact local coral reefs by reducing water clarity,
with long term climatic ramifications resulting from the re‐entry of the previously sequestered
carbon back into the local carbon cycle.
Fishing The gross value of Timor‐Leste’s fisheries output was last published in 2004 at nearly US$6 million,
only 1.25% of the country’s GDP, although reliable data are rare and records kept during the
Indonesian occupation may not be accurate or well‐maintained. Most people are subsistence fishers,
only taking what they need to feed themselves and make a small living. This type of fishing occurs
mostly on shallow reefs, as currents make fishing in deep waters in a small boat dangerous. In some
areas, local fishers use small‐meshed nets and/or poisons on the reefs, both of which are damaging,
and boat anchors are used at different locations daily, spreading impact damage across wide areas.
Many of the fish available for sale locally are reef fish, including important herbivores such as
parrotfish, whose removal can have serious consequences for reef health.
Tourism Tourism can be a blessing and a curse to developing nations, with the potential for quick profits
overshadowing the prospective damage caused by unsustainable or unscrupulous practices. From
boats anchoring on reefs to guides feeding marine life to attract the charismatic species sought by
tourists, without robust and widely agreed upon guidelines, tourism can, in a very short time, have a
negative impact on marine ecosystems. Cruise ships are frequent contributors to plastic waste
problems in the marine environment, and even the sunscreen that visitors are encouraged to put on
several times a day contains chemicals that are harmful to coral. Snorkelers standing on reefs or
molesting sea life and divers taking home souvenirs or sitting on corals to have their photo taken are
all scenarios we have witnessed first‐hand, and these are typically done by people with no idea that
they are damaging the reef.
Climate change As we have observed over recent years, global weather patterns are greatly affected by climate
change and the impacts humans are having on the environment. El Niño and La Niña events over the
last two decades have become more severe, with El Niño events in 1982, 1998, 2005 and 2010
causing mass devastation to coral reefs across the tropics (see: Bleaching). Tropical storms are
deleterious to any type of coastal ecosystem, with the storm surges generated by even small
hurricanes capable of pulverising reefs, gouging up vast tracts of seagrass and uprooting stands of
mangroves. In addition to the clearing of these coastal ecosystems by storms, events in the
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aftermath can often prevent them from regaining a foothold if faster plants or algae move into the
breach instead (emphasising the importance of herbivorous fish). The timescales for the
proliferation of tropical marine ecosystems are often measured in decades rather than years, and
increasingly frequent large storms or periods of several storms in quick succession can often
seriously inhibit ecosystem recovery.
Temperature When temperatures in the water exceed
a coral polyp’s optimum level for a
sustained period of time the colony
undergoes a process known as
bleaching; symbiotic zooxanthellae,
coral’s main source of energy as well as
what gives them their distinct colours,
are expelled from the coral, leaving the
polyp translucent and malnourished,
characterised by a distinctive white
appearance. The theory behind this
process is that it is an adaptation that
clears space for other, more heat‐tolerant species of zooxanthellae to propagate within the colony,
and thus be more successful in the higher temperatures. If the temperature returns to previous
levels in time, then the original algae may return to the coral. If not, the coral generally dies, leaving
only its skeleton. With global ocean temperatures on the rise, and coral reefs restricted to the
surface layers of water that are most affected, the projected ramifications are not good.
Ocean acidification Ocean acidification is the ongoing decrease in the pH of the world’s oceans, and poses a very real
threat to any and all organisms that build a shell or skeleton out of calcium carbonate. Increased
levels of carbon dioxide absorbed by the oceans globally have led to a 30% decrease in the pH of
seawater since the 1800s. Reef building corals are affected particularly harshly, as greater acidity
dissolves the coral's calcium carbonate skeleton and at the same time reduces the amount of
carbonate available to the coral to draw out of seawater to use in growth and rebuilding. Ocean
acidification is almost certain to result in a reduction in diversity of all calcifying organisms
worldwide; some models cite ocean acidification as a major cause of future coral reef die‐off events,
easily as serious as coral bleaching.
A massive coral showing signs of bleaching
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5 TROPICAL MARINE INVERTEBRATES
A spineless majority consisting of 95% of the 1.4 million recorded species are classed as
invertebrates. Of this number, 1.2 million of these species are Arthropods; the crustaceans, insects,
spiders and other creatures possessing an exoskeleton and jointed legs. In the marine environment,
invertebrates occupy a huge diversity of size, form and function; from the microscopic polyps of
numerous reef building corals to the giant squid. Invertebrates that can be found in tropical waters
include representatives of the oldest still‐extant group of multi‐cellular organisms on Earth, and
some of the most prolific architects on the planet. Whilst some tropical marine invertebrates are
small, cryptic or concealed and need a large amount of time and energy to find in the first place, we
focus our survey efforts on the conspicuous species which provide an indicator of the health and
status of a reef.
5.1 Sponges Sponges are the oldest known living group of multi‐cellular organisms, and their longevity can likely
be attributed to their exceedingly simple physiology and life strategy. They have a simple body plan,
drawing water through tiny inhalant pores called ostia and filtering it of bacteria and food particles
before pumping it out through larger exhalant holes. A large sponge can cycle through up to 20,000
times its volume in a single 24 hour period.
5.2 Cnidarians Cnidarians are a large and diverse group consisting of sessile and motile invertebrates, united by the
fact that all members of the group are armed with stinging cells called nematocysts. The class of
cnidarians we are most concerned with are the anthozoans, which includes all species of coral.
Hard corals are covered in greater detail elsewhere in this guide but we will be paying attention to
soft corals, sea anemones and hydroids.
Soft corals Soft corals unsurprisingly take their name from their lack of a skeletal structure. Most are filter
feeders, and only a few species also host symbiotic zooxanthellae; the relationship between host
and tenant in these instances is not as beneficial as it is to hard corals. Some close relatives of the
soft corals, such as the gorgonians, do possess some skeletal structure but these sea fans and sea
whips are nowhere near as rigid as the reef building species, using a more pliable endoskeleton to
remain erect whilst facing the prevailing current and filter feeding from the passing water.
Sea anemones Close relatives of hard corals, sea anemones take the form of distinctive and often large solitary
polyps that are notable for the wide variety of animal symbionts that take advantage of the
protection afforded by their stinging tentacles. Whilst anemonefish are the best known type of
tenant (thanks Pixar!), shrimps, crabs and some species of pipefish also reside in large anemones.
Close relatives of the anemones, the corallimorphs, possess a starkly different feeding strategy; they
are known to engulf small fish like a Venus Fly Trap, rather than act as a shelter!
Hydroids This is a diverse group of colonial organisms with forms ranging from small, feather‐like, branched
colonies to large calcareous colonies such as those of the family Milleporidae or ‘fire corals’. All
hydroids are capable of providing a painful sting to unwary divers, with one particular type of
floating colony being world renowned: the "Portuguese man‐o'war". Often confused with jellyfish,
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they are actually highly specialised colonial hydroids, with individual polyps responsible for a single
purpose such as feeding or reproduction.
5.3 Molluscs The molluscs are a gloriously diverse group of over 160,000 species, of which about half are marine.
Gastropods, bivalves and cephalopods are the three major marine classes and all are well
represented in tropical waters.
Gastropods Comprising 80% of all living molluscs, gastropods are the most successful and most commonly seen
class of the phylum. They have a single shell, within which the body is protected from predators. All
gastropods feed using their feet, rasping food from rocky surfaces, and range in size from numerous
species no larger than a grain of sand to the queen triton trumpet, large enough to be one of the few
predators of the notorious Crown‐of‐thorns starfish.
Not all gastropods have visible shells; some, such as sea slugs and nudibranchs instead rely on a
combination of bright colours to signify their likely lethal toxicity to potential predators.
Bivalves Bivalves have a pair of hinged shells, opened and closed by large abductor muscles, a mechanism
that doubles as a mode of propulsion in some free living species. Bivalves include clams, oysters,
mussels and scallops, of which the giant clams can reach up to 250kg and 100 years old. Many
species burrow in soft sediment, but conspicuous reef dwellers such as the giant clam are mostly
found wedged and cemented into reef crevices.
Cephalopods With large, complex eyes and a nervous system considered to be the most advanced in the
invertebrate kingdom, cephalopods are known as some of the most intelligent of all marine life, and
are certainly among the most charismatic. Despite being molluscs, shells within most cephalopods
are best described as vestigial with two notable exceptions; evolution has led to cuttlefish shells
being adapted to serve as an internal buoyancy control device, and the elusive nautilus retains a
striking, chambered shell used for camouflage and propulsion.
Cephalopods are rarely noticed on dives due to their excellent camouflage, created by colour
changing cells called chromatophores which are also used in communication. Often the only
indication that you are passing close to an octopus or squid is a plume of ink as the animal darts off,
though some spcecies tend to be less skittish and may face and observe divers, only retreating if
approached quickly.
5.4 Echinoderms The name echinoderm literally means ‘spiny‐skinned’ and refers to the tough, calcareous
exoskeleton that characterises this phylum. Whilst echinoderms are chiefly known for their ability to
regenerate lost body parts, they are also notable for using an internal structure akin to a hydraulic
system for everything from locomotion to feeding on prey.
Sea stars Usually sea stars have five arms radiating from a central disc‐shaped body, but in some species the
number can be over twenty and in others the arms are not distinct, with the animal appearing
almost circular. The most notorious member of this class is Acanthaster planci, the Crown‐of‐thorns
starfish, which, when present in large numbers, will feed on and decimate a coral reef.
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Sea cucumbers Sea cucumbers are elongate animals with a mouth surrounded by short tentacles at the front end of
the body. Normally seen lying on the sandy bottom where they ingest large amounts of sand and
digest any organic material, sea cucumbers often leave a trail of sand as they feed. Despite this, they
are considered a delicacy in a number of regions.
5.5 Tunicates Tunicates are the invertebrates most closely related to humans, possessing a notochord (which
develops into a backbone in the vertebrates) in their free‐living larval stage. When the larvae lands
upon a suitable substrate, the tunicate irreversibly attaches itself to the surface, widens its mouth
and absorbs the notochord. This is known as retrogressive metamorphosis, and is a rare transition in
which the resulting adult form is less advanced than the larvae.
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6 INTRODUCTION TO FISH
Fish as we know them are divided into cartilaginous fish (sharks and rays) and bony fish (everything
else). The main bulk of fish that you will see and learn about in Timor‐Leste will be Osteichthyes,
bony fish, although we hope you will get to see your fair share of sharks and rays as well. “Fish” is
actually a tricky term to define, and as a group there is so much variation in form and function that a
true scientific classification is surprisingly difficult; if you’re not being too pedantic though, a fish can
be classed as something that lives underwater, breathes through a gill mechanism and has various
types of fins and scales. Worldwide there are more than 20,000 known fish species, and coral reefs
are home to more than their fair share with about 25% of these. In the Coral Triangle the number
currently stands at 2,228, but new species are being classified or discovered all the time, particularly
as diving techniques become safer at greater depths and submarine technology grows more
sophisticated.
Fish species are grouped into families and subfamilies, though taxonomy can get complicated.
Though over 75 reef fish families exist, we tend to look at no more than 25 when surveying in a
single habitat, as well as their associated sub‐families. An ecosystem is a finely balanced food web,
with huge numbers of interactions relating to predation or its lack.
Typically there are certain families whose presence in significant numbers is indicative of the health
of a reef, or seagrass meadow and the addition or removal of certain groups can be damaging to the
whole ecosystem. Lionfish, exciting and exotic sightings in the Indo‐Pacific, are an invasive species in
the Caribbean; the presence of large bodied carnivores such as groupers and sharks often indicates a
healthy ecosystem, and large numbers of butterflyfish, which are corallivores, can point to healthy
amounts of hard coral on a reef; abundant damselfish can indicate too much algal growth on the
reef surface, particularly in areas where herbivorous grazers such as surgeonfish and parrotfish are
heavily fished, and that is barely scratching the surface. Putting these observations together with
data collected over a long term we can measure the health of a reef system and assist local
stakeholders in reacting accordingly.
Behaviour on a reef is a whole study of its own, and can be fascinating to the casual observer with
just a little background knowledge; many recreational divers, upon learning a little, remark on how
much it has enriched their underwater experiences. From mimicry to symbiosis, nuclear hunting to
cleaning stations, beneath the veneer of beauty a wealth of drama ensues.
6.1 Introduction to common fish families
This guide is designed as a brief overview, and you are by no means expected to know everything
about reef fish by the time you arrive! We look at a number of characteristics when identifying fish:
size, colour, accompanied by, location, eating, swimming (SCALES), and the more of these factors
you can note down the better. When we state a preferred food for a family, remember that all fish
are opportunistic feeders, and even herbivores are known to temporarily switch to carnivory if the
opportunity arises! Another key point is that all fish can, to some degree, change their colouration,
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from the appearance of blotches when hiding in seagrass to complete colour changes when
courting. Each change depends very much on the fish and on circumstances.
We will be studying more than just these families, as well as some species which comprise a family
all by themselves, but an introduction has to start somewhere… (All drawings from Reef Fish
Identification, Tropical Pacific; Gerald Allen, Roger Steene, Paul Humann and Ned Deloach.)
Angels ‐ Pomacanthidae Among the most classic reef fish and the ones that many
people think of when envisioning a coral reef. Angels are
colourful, with ventrally compressed bodies and distinctive
fins. They are clearly identifiable to family level, and
although the juvenile of a species often has a very different
appearance from the adult, there is no sexual dimorphism
in adults. There are two forms in the family; one is large,
robust, has flamboyant fins and can be quite unafraid of divers; the other is smaller and more
cryptic, and can be confused with damselfish. Most species primarily eat sponges, for which they
have very little competition due to the low nutrient count and stony texture. Angelfish are
protogynous hermaphrodites, capable of changing from female to male if the need arises.
Butterflies ‐ Chaetodontidae These small reef fish are monogamous, with pairs mating for
the duration of their lives, which can be an identifying
characteristic in itself. Round, laterally compressed bodies
with protruding snouts for eating coral (their main food
source) make them nice and easy to pick out, and there are no
differences between adult and juvenile stages of life or
between sexes. Until fairly recently they were classed as one
family with the angelfish, until enough taxonomical differences
were confirmed. The largest species grows to 30cm, and is
considered a bit of an outlier.
Cardinalfish ‐ Apogonidae Cardinals are among the lesser spotted reef fish as they are
neither large nor flamboyant, usually between 5cm and
15cm. Preferring dark crevices and overhangs to open reef
by day, they have large eyes to aid nocturnal vision, and are
usually some shade of dark red or orange. Identifying characteristics tend to be located on the eye or
the tail.
Damsels ‐ Pomacentridae Damselfish are one of the most numerous families on any reef
worldwide, and have been categorized into several sub‐families
to deal with the huge number of adaptations they have evolved.
As a family they all tend to be small (under 15cm) and most are
territorial. Juveniles can differ in colouration from adults, depending on the species.
Anemonefish – for those of you who haven’t seen Finding Nemo, an anemonefish is classed as any
damselfish that lives in symbiosis with any species of anemone. The fish has a protective coating of
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mucous to prevent it being stung by the anemone’s tentacles, but predators wary of such stings tend
to leave the small fish alone.
Chromis – these members of the damsel family are more likely to be found in the crowd of plankton
feeders above the reef than hiding in it, in loose aggregations that can number into the thousands in
the right area. Tails that are more forked than their cousins’ give them a slightly more streamlined
look.
Damsels – these are classic reef dwellers who make their homes in holes with associated small
patches of algae which they farm for food, eating both the algae and the various small crustaceans
that come with it. The males defend their eggs with ferocity and will even nip a diver whose hand
gets too close.
Dascyllus – the shyest of the bunch, dascyllus hover mere centimetres above their chosen coral
head, diving into the branches for cover when threatened.
Sergeants – bulkier than the other family members and striped vertically, sergeants spend most of
their time patrolling in the same area of water as the chromis, but when nesting they become very
defensive of their nests and stick very close to
their territory on the reef substrate.
Emperors ‐ Lethrinidae Well known as excellent food fish, emperors are
less colourful than traditional reef fish and have a
tendency to make their skin take on a mottled
colouration when at a standstill, before returning
to their usual silvery hues when moving. With slanted heads and flat‐bottomed bodies, these fish
tend to be found off the sides of the reef, eating crustaceans and whatever else they can find on the
sand. They can grow up to 1m, but are likely to be 30‐50cm.
Fusiliers ‐ Caesionidae Above the reef and off to the side in the blue water we
find our slender, schooling fusiliers. Schooling fish avoid
collisions using the feel of water movement over their
lateral line, and in fusiliers this line is often marked in
some way. With its slim, fusiform body, between 15
and 35cm, and forked tail with a very narrow base,
fusiliers are reef fish adapted for a pelagic, open water
lifestyle.
Goatfish ‐ Mullidae Taking their name from their terrestrial counterparts,
goatfish have two chemosensory appendages, known
as barbels, for tracking down food under loose sand;
if you see a small cloud of sand being created,
chances are there’s a goatfish at its centre. When not in use a goatfish’s barbels are tucked up under
its chin, but these fish are still identifiable through their shape and behaviour; a very flat underside is
required when bottom‐feeding, and a nicely forked tail gives a clear ID; goatfish tend to be around
30‐40cm.
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Groupers ‐ Serranidae Many people often assume that a grouper
must be enormous, and forget the numerous
small species among the aptly named
Goliath Grouper which can reach 300cm.
Many of the species we monitor are small,
30‐70cm, but large bodied compared to their
other reef denizens. No matter what their
size, they are expert ambush predators, with
enormous mouths used to engulf prey whole
and wide, flared fins to hold them in position until they are ready to pounce, and powerful tails for
short bursts of speed when required. This is another family of fish which practises hermaphroditism,
both sequential and protogynous, and removal of too many in one size bracket may leave an
imbalance of one sex or the other. Groupers are often found at cleaning stations, as the folds of skin
around their mouths and gills are often colonised by a range of parasitic organisms.
Anthias (Anthiinae) – scattered above the reef close to
open water in loose, colourful aggregations are the anthias,
confusing to identify as the tend to mix their schools, but
spectacular to look at, and barely seeming related to the
heavy groupers at all at a maximum size of 20cm. Males
and females tend to have different colourations and this
can make them tricky to identify to species level as there
are lots of similarities between species. Luckily they’re not
that spooked by divers, so you can take a good long look at them.
Jacks and Trevallies – Carangidae Instantly recognisable with their silvery skin and powerful forked tails, these are the real ocean‐going
pelagic swimmers, and make excellent food
fish due to their almost constant muscle use
and large size, up to 120cm. Coming in to
the reef to feed on fish and crustaceans,
jacks are sometimes solitary but usually
aggregate in loose schools, and the
differences between them and the reef fish
in shape and colour makes identifying them
very easy.
Parrotfish – Scaridae Descended from wrasses, parrotfish are one of the
more specialised groups of fish on a reef. Their teeth,
fused into powerful beaks, are modified for scraping
algae off rocks and coral, often taking in a large
amount of inorganic content at the same time; much
of the sand on glorious white beaches around the world has actually passed through a parrotfish in
this process. Parrotfish swim primarily with their pectoral fins, flapping over the reef with the
occasional peck at some algae (an image which further solidifies the bird comparison), and their
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thick bodies and large, clearly defined scales make identification easy to family level. Their familial
structure is key to identification further, with three life phases in each species showing three distinct
appearances, and colour changing with sex; size can also be a key factor with large amounts of
variation across the species, from 18‐150cm!
Snapper – Lutjanidae The importance of snapper as a food fish cannot
be overstated, and neither can its importance on
a reef. Like emperors, they operate at the edges
of reefs, primarily eating fish but supplementing
their diet with any invertebrates they can hunt
along the way. Most hunt nocturnally, but they
are good all‐rounders, with balanced bodies,
negligible colouration and large mouth with
protruding canines. Some species can grow quite large, up to 1m, with most growing to 40‐50cm.
Soldierfish and Squirrelfish – Holocentridae Like cardinalfish, soldiers and squirrels are nocturnal,
and can generally be found in holes and crevices on
reefs, or under overhangs. They both have large eyes
and reddish colouration, with clearly defined scales
and spiny dorsal fins, but differ from each other in the
shape of their face; soldierfish have blunt, rounded
snouts while squirrelfish faces are much more pointed.
Squirrels also have a spine in front of their gill‐cover which can be venomous. They tend to be small
to medium sized, rarely exceeding 30cm.
Surgeonfish – Acanthuridae Surgeonfish, common in mixed groups on reefs, are named for the bony blade that protrudes from
the tail base, the scalpel, which can either be a tiny nub or a well‐developed blade; in the subfamily
unicornfish each member has a pair of blades on each side. These are often marked out and are one
of the key identification traits for this family. Surgeons and unicorns both swim primarily with their
pectoral fins, as do parrotfish and wrasses, and can be found cruising above the reef or feeding
among the corals. They are typically small fish, around 30cm, but can reach 60cm.
Surgeons – for another Finding Nemo reference, look
no further than Dory the ditzy palette surgeon.
Accurately represented in the film with a classic oval
body that is ventrally compressed and swimming with
the pectoral fins, these fish are grazers that often move
over the reef in large aggregations which swarm down
on algal growth; small protruding mouths with a pouty
look are the perfect adaptation for this feeding style.
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Unicorns – as mentioned previously these fish have a
pair of scalpels either side of their tail base rather than
just one, and they are generally less flamboyantly
coloured than their cousins. The oval body shape is
there, but slightly elongated as if stretched from the
tail, and some species show the key trait of the mythical
unicorn, a protruding horn above their mouth; in some
species it is no more than a bump, in others a full
narwhal‐like horn.
Triggerfish – Balistidae Triggerfish are among the most charismatic reef
dwellers, with flamboyant colours and an instantly
recognisable swimming method. Their bodies are
diamond‐shaped and they have a primary dorsal fin
which, when locked into its distinctive trigger shape in
a threat display, gives the family its name, and they
swim with their secondary dorsal fine and their anal fin
in a sideways oscillation. Species rang e from very small
to quite large, with the Titan Trigger reaching 75cm, and can be fiercely protective when nesting; if
challenged they may bite, so swim clear of the cone‐shaped area of water they may be defending.
Filefish – closely related to triggers in body shape and
swimming mechanism, filefish are more cryptic and far
less showy. Their bodies are more compressed than their
cousins, and they are far more likely to hide in a hole than
bite; they also have a long trigger fin, but it is flipped up
when threatened, rather than locked in place.
Wrasses – Labridae Wrasses are one of the most numerous and
varied families of fish you will encounter on a
reef, with adult sizes that range from 6cm‐
230cm; in the Indo‐Pacific they are
outnumbered only by gobies in sheer species
numbers. All share certain characteristics
though, such as swimming with their pectoral fins as parrotfish and surgeonfish do. Wrasses tend to
be among the more opportunistic feeders on a reef, first to appear when another fish has found a
meal, among the dust clouds kicked up by goatfish, and developing symbiotic relationships whereby
their role as a cleaner protects them from predation. Large canines make light work of most
crustaceans or small invertebrates, and wrasses of any size can be seen using their teeth to great
effect. In a life cycle similar to their close relatives, the parrotfish, each species has noticeably
different appearances during each of its three life phases.
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7 KEY MARINE GROUPS
7.1 Turtles
The Coral Triangle is home to six of the world’s seven extant species of marine turtles. Turtles are
reptiles that have evolved for life underwater, with a more streamlined carapace than their
terrestrial cousins, and fins rather than legs. They are capable of remaining underwater for up to
forty minutes, and are mostly omnivorous, though most show a preference for some things over
others; hawksbills tend towards sponges, leatherbacks eat mainly jellyfish, and green turtle adults
tend to favour seagrass as their sole source of food. This is particularly important, because few
animals subsist solely on seagrass, and their constant grazing keeps the seagrass meadows healthy in
the same way that a lawn needs cutting regularly; it leads to healthier grass that spreads across a
wider area, which is essential as global seagrass depletion rates are approaching 7% per year.
Despite conservation and awareness raising over decades, all marine turtle species are still at risk;
hawksbill and Kemp’s ridley turtles are listed by the IUCN as Critically Endangered, the green turtle
as Endangered and the loggerhead, Olive’s ridley and leatherback turtles are all Vulnerable (the
flatback turtle, not found in Timor‐Leste, is listed as “data deficient”). In some areas of the world
conservation efforts and changed laws are having an effect, with success in the Caribbean in terms
of increased nesting sites and larger numbers of hatchlings, but no improvement in the Philippines
where there is still demand for turtle eggs, and laws making the catching of turtles and taking of
eggs illegal have had little effect.
Little is known about turtle habits in Timor‐Leste, but various NGOs are working towards gathering
data and implementing conservation actions; no‐take zones are critical to allow fish and turtles
space to breed undisturbed, and large campaigns are running against the disturbing of turtle nests.
7.2 Marine mammals
Cetaceans The Wetar and Ombai Straits are migratory channels for many species of whale and dolphin, and the
area has been described as a cetacean hotspot. Short‐finned pilot, melon‐headed, humpback, blue,
beaked and sperm whales are all regular visitors, as well as spotted, spinner, bottle‐nosed, striped,
Risso’s, Fraser’s and rough‐toothed dolphins – quite a list for a small country with huge ecotourism
potential. These waters reach depths of 3,000m, providing more than enough space, and food, for
such vast numbers of mammals. Blue whales are listed as Endangered and sperm whales as
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Vulnerable, and to see either with regularity is exciting; to know that these are migratory channels is
particularly valuable for monitoring efforts.
Dugongs These charismatic marine mammals are the last extant members of the family Dugongidae, related
to the three manatee species, all four members of the order Sirenia, but not crossing ranges with
them anywhere worldwide. Their smooth bodies and fluked tails can be confused with dolphins at
first sight, but they lack a dorsal fin and have a highly mobile face, with an upper lip that has adapted
for foraging for seagrass.
With a limited range and a long life‐cycle they are at risk from boat collisions, hunting and habitat
loss, dugongs being another species in addition to the green turtle which lives only on seagrass.
Known populations are fragmented, and in several places they are at risk of becoming locally extinct;
they are listed as Vulnerable by IUCN, but population estimates are inexact due to their elusive
nature and the turbidity and remoteness of their chosen habitat.
Blue Ventures’ work in Timor‐Leste includes designing a replicable model for ecotourism through
marine conservation which incentivises dugong and seagrass conservation for the local population.
Through education and awareness raising, the presence of dugongs will be highlighted as valuable
natural resource and source of civic pride for coastal communities throughout Timor‐Leste.
Dugong photo ©Peter Berquist
