Biodiversity in Paradise: A Natural History of Raja Ampat

By Federico Prado

Raja Ampat, which literally means 'Four Kings' in Bahasa Indonesia, is a group of islands located at the heart of the Coral Triangle. The archipelago boasts 69% of the world's stony coral species, 27% of the planet's coral reef fishes, and 10% of the Earth's known mantis shrimp species. Furthermore, t

• Language: English
• Publisher: Federico Prado
• Release date: Apr 12, 2022
• ISBN: 9798985748116

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BIODIVERSITY IN PARADISE

A Natural History of Raja Ampat

Federico Prado

Copyright © 2022 by Federico Prado

All rights reserved

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the author.

First Edition

ISBN: 979-8-9857481-0-9

Ebook ISBN: 979-8-9857481-1-6

Contents

Preface

Introduction

1. Climate, geography, and geology of the archipelago

2. A natural ‘species-making’ laboratory

3. The flow of energy and matter through the Four Kings

4. The West ‘discovers’ Raja Ampat

5. Marine ecosystems in the Four Kings

6. Terrestrial ecosystems and dominant plants

7. A cornucopia of marine invertebrates

8. A myriad of terrestrial and freshwater invertebrates

9. The most diverse and colorful fishes in the world

10. Amphibians and Reptiles in the archipelago

11. Raja Ampat birds and Paradisaeidae

12. Mammals in paradise

13. The Human Element

14. Paradise in peril

15. How to protect paradise

Illustrations

Photo and Illustration Credits

Literature cited

Acknowledgements

About the author

Preface

Raja Ampat, which literally means ‘Four Kings’ in Bahasa Indonesia, is a group of islands located off the western tip of New Guinea. Biodiversity in Paradise is mainly about three recurring themes: Raja Ampat’s biological richness, outstanding beauty, and its plethora of endemic organisms. First and foremost, as the title hints, the mind-blowing number of plant and animal species found in this Denmark-sized archipelago is truly amazing, particularly its marine life. Second, the breathtaking scenery and colorful creatures that a visitor encounters, both above and below sea level, make exploring and studying this little corner of the world a true joy. Finally, for such a tiny area, the number of endemic or near endemic species found in the Four Kings is quite remarkable. These include unique soft and hard corals, marine crustaceans, freshwater fishes, frogs, reptiles, birds, an echidna, cuscuses, and bats. The number of endemic terrestrial and freshwater invertebrates also appears to be very high.

However, the number of taxa that have been thoroughly surveyed remains sorely inadequate. There are countless things we do not know about Raja Ampat, many species to be discovered, ecological and evolutionary processes to be deciphered and understood, and animal behavior to be observed and reported. Further, more effective ways to manage forests and fisheries, to the benefit of local communities, need to be explored and implemented. More amazingly, Raja Ampat’s coral reefs have displayed a superb resilience to human pressure, perhaps holding the key (or keys) to the restoration of coral reefs elsewhere across the Indo-Pacific while setting the standard for how pristine reefs should look like in the future. Thus, there is an urgent need to explore, study, and understand the Four Kings better.

Located at, or very near, the center of marine biodiversity in the world, this beautiful archipelago boasts 553 stony corals (69% of the world’s known species), 42 mantis shrimps (10% of the world’s total), and 1,637 coral sea fishes (27% of the world’s). The islands are also home to lush rainforests and 315 terrestrial and freshwater birds (40% of New Guinea’s), 6 of which are endemic and 8 belong to the stunning ‘Bird of Paradise’ family. Biodiversity tries to capture the physical beauty and astounding diversity of the Four Kings through detailed descriptions of its climate, geography, complex geology, marine and terrestrial ecosystems, flora, fauna, and inhabitants. Further, the author discusses negative impacts to wildlife from human activities and ideas for ameliorating their harm. The book closes with a list of potential research questions for future investigators.

To gain a better understanding of the complexity of the archipelago, many fundamental principles of biology and biogeography are weaved in: What is a species? How do species arise? How are they classified and grouped? Why are there more species in the tropics than in polar zones? The author also explains other subjects of scientific interest: the theory of island biogeography, plate tectonics, the geological past of Raja Ampat, and basic concepts of physical ecology such as the flow of energy and matter through the Four Kings, trophic levels, food webs, and ecosystem services. Symbiosis, mimicry, sexual selection, invasive species, convergent evolution, extinction, and other concepts of evolutionary ecology, as they pertain to Raja Ampat, are also expanded upon. Many fascinating aspects of behavioral ecology are introduced: the superb adaptations of some colorful flatworms, nudibranchs and insects; the poorly understood associations between corals or echinoderms with all sorts of marine invertebrates; the mimic octopus, master of camouflage; parrotfishes and their night cocoons; sea anemones and their symbiotic clownfishes; fish cleaning stations; the ability of some reef fishes to change sex; the almost unbelievably powerful pincers of mantis shrimps and their equally remarkable eyes; mating systems, leks and courting behavior in birds of paradise; brood parasitism and many other intriguing behaviors.

This manuscript is the first of its kind to describe the Four Kings in a thorough and scholastic manner, providing an up to date reference list of research and surveys that have taken place in the archipelago. In a single volume, this work represents a unique compendium of all that is Raja Ampat while highlighting our large gaps in knowledge. Biodiversity in Paradise aims to entertain readers and inspire them to visit, explore, study, understand, and do everything in their hands to help protect this most beautiful and superbly pristine part of the world. Ultimately, however, the book argues for the need to establish a modern field research station at the heart of the archipelago. With new and fresh discoveries, and a deeper understanding of what makes the Four Kings tick, not only can we try to save this little jewel in the middle of the Coral Triangle, but also use this newfound knowledge to restore coral reefs across the Indo-Pacific to their former glory.

To my mother Ida Maria

In memory of my father Federico

and uncles Moises and Gerardo Brand

Introduction

In the early summer of 1992 I began a trip around the world that would last 10 months. This wonderful experience transformed my life in many ways, most notoriously, by compelling me to switch careers from electrical engineering to biology. While hiking in Nepal, I met a British couple also travelling around the planet, but in the opposite direction. They had recently learned to scuba dive at the Great Barrier Reef in Australia. I was headed that way, but had not really thought through my itinerary, let alone what I would do once there. The couple raved about the beauty of the shallow underwater world, and somehow convinced me to give it a try. From our conversations, they gathered that I would enjoy it. Not having even snorkeled once before in my life, I was vaguely familiar with corals and reef fishes, but it was not in my plans to learn to scuba dive. They recommended Queensland, the huge province in northeastern Australia with a long coast facing the South Pacific and the Great Barrier Reef. Eventually I made it to Cairns and obtained an open-water PADI scuba diving certificate. My friends were absolutely right: I fell madly in love with the tropical shallow underwater world. The reasons, of course, were the amazing colors, sizes, shapes, and forms of the many corals and fishes one encounters in a healthy reef. A coral garden full of sea anemones, sponges, sea stars, crustaceans, nudibranchs, and colorful fish is simply breathtaking. The views, combined with the ability to easily move in three dimensions and approach, within reason, any organism that grabs your attention, is almost better than bird watching or being on an African safari. In my experience, scuba diving is the closest thing to flying solo, without the aid of an engine or a glider. My introduction to the world of scuba was followed by later trips to more diving in several areas across the world. To a large degree, the joy of scuba diving has been a major engine behind the inspiration for this book.

In May 2014 I finally visited a place I had wanted to see for more than a decade. I was captivated by the geology, butterflies, and birds of paradise described in Alfred Wallace’s book ‘The Malay Archipelago’ during his only trip to Raja Ampat in 1860. I had also heard that scuba diving around New Guinea (the world’s second largest island after Greenland, and the largest tropical island on Earth) was among the best on the planet. Being by now both a passionate birdwatcher and a seasoned scuba diver, I became obsessed with visiting this remote part of Indonesia. As time passed, I found many stunning aerial views and underwater photographs from the region, and watched videos of two of the most beautiful birds in the world found only there. Then I came across two reports sponsored by Conservation International asserting that Raja Ampat exhibits some of the highest marine diversity on Earth in Scleractinian (hard or stone) corals, mollusks, and reef fishes. Other sources indicated that the warm waters surrounding the archipelago act as nurseries for many marine invertebrates and young fish and concluded that marine species living in this sea may be able to withstand some level of climate change. The waters surrounding Raja Ampat may also serve as reservoirs of marine life capable of reclaiming depleted parts of the ocean in the future, devastated by both global warming and ocean acidification.

Though I only visited a small section of the archipelago on this first trip, I was blown-away as the place exceeded all my expectations. On Waigeo Island, I was able to observe and photograph (albeit poorly) Wilson’s and Red Bird of Paradise, two endemic birds found nowhere else in the world, among many other colorful species of parrots and the fascinating Blyth’s Hornbill. From Warimpurem Homestay, one lazy afternoon after lunch, I observed for a long while several dolphin pods: close to 100 individuals swam along the shore, playing and fishing. Once I started scuba diving around Waigeo and Kri Islands, I realized that I had never seen so much abundance, diversity, beauty, and so many colors under the calm turquoise waters. From a high point on Kri Island, I witnessed a gorgeous landscape: an aquamarine ocean dotted by dozens of limestone islands, islets, cays and shoals, many of them fully covered by lush green vegetation. On a boat ride around Gam Island, I witnessed the loveliest and most peaceful coves I had ever seen; snorkeling in these tranquil waters afforded views of large seahorses and young colorful fish swimming among the aerial roots of mangrove trees. Raja Ampat offered so many magnificent sights and exciting moments that visiting the islands changed my life.

Since my return home, I only dreamt of going back. Fortunately, I was able to do so again and spend some time at a small island southeast of Misool a few years later. This time I swam in a marine lake full of stingless jellyfish, saw a myriad of soft and hard corals, got a brief glimpse of a sea porpoise, witnessed some lovely and apparently old rock paintings on the limestone walls of a small island, and took photos of a coral snake rolled under the paintings.

Raja Ampat is not only a hotspot of marine diversity and island endemics, it is also a vital source of food and other natural resources for local communities, and it has become a highly sought-after destination for professional divers and birdwatchers. Slowly, the world is learning about and becoming familiar with this natural paradise. With so much beauty in such a small area, I wished for a guidebook that would introduce me to the plants, animals, and ecosystems of the archipelago, similar to ‘A Neotropical Companion,’ an engaging book that does the same for the New World Tropics. However, that book did not exist; thus was born the idea for this manuscript. Here I attempt to provide a general introduction to the Natural History of this beautiful archipelago, acknowledging that the book is not complete, exhaustive, or up to date by the time it is published. It is an essay written for scuba divers, birdwatchers, explorers and adventurers, undergraduate students, conservation biology practitioners, marine protected area and nature reserve managers, and the general public, with a solid scientific foundation. It is my hope that this work will educate and entertain readers, and inspire them to visit, explore, study, and understand this most beautiful corner of the planet. Ultimately, this book is intended to further enhance ongoing research and conservation efforts in Raja Ampat.

1

Climate, geography, and geology of the archipelago

a. Location, weather, climate, tides, currents, winds

Raja Ampat, which literally means ‘Four Kings’ in Bahasa Indonesia, is a group of tropical islands located between 0°20’ Ν – 2°15’ S, and 129°35’ Ε – 131°20’ E. The archipelago is north of the Seram (Ceram) Sea and just off the northwestern tip of New Guinea, a region known as the Bird’s Head. New Guinea’s peculiar silhouette, long known for its bird-like shape, has been divided into four major segments, each with a fanciful name that has become biogeographically significant: (a) The Bird’s Head, just mentioned above, is known as ‘Kepala Burung’ in Indonesian or ‘Vogelkop’ in Dutch. This section consists of the Doberai Peninsula with its two compact but high mountain ranges, the Tamrau and Arfak. (b) The Bird’s Neck, the rugged isthmus that links the Bird’s Head with the main body of New Guinea. (c) The Bird’s Body refers to most of mainland New Guinea and includes the huge central cordillera known as the Central Ranges, the Northwestern lowlands, the Sepik-Ramu lowlands, the Southern lowlands, the dry savannah country known as the Trans-fly, and the Huon mountain system. (d) The Bird’s Tail refers to the extreme southeastern peninsula of New Guinea (Fig. 1).

Raja Ampat, also known biogeographically as the North-West (NW) Islands of New Guinea, encompasses over 4 million hectares (Erdmann and Pet 2002), approximately 45,000 km² of land and sea. Proximity to New Guinea (the largest tropical island in the world, second only to Greenland in size, as well as the island with the highest peaks on the planet and permanent glaciers), has endowed the Four Kings with a very peculiar and intriguing wildlife. This is because ‘New Guinea boasts the World’s largest and smallest parrots, the largest doves, the longest lizard, some of the smallest frogs, the largest butterflies and moths, some of the longest stick insects and widest-headed (staked-eyed) flies, the tallest tropical trees, the richest mangrove and seagrass flora, and many other forms and habitats unique and fascinating, if not extreme’ (Gressitt 1982). The NW islands share many of these wondrous plants and animals with their large neighbor to the east.

An elevational map of Raja Ampat is shown on the front cover endpaper. The red rectangle in the bottom-right inset shows the location of the ‘Four Kings’ in relation to New Guinea, Australia, and the rest of Indonesia. Raja Ampat’s area is roughly twice as large as the state of New Jersey or equivalent to the size of Denmark. The ‘Four Kings’ refer to the largest islands in the group: Waigeo, Misool, Salawati, and Batanta, but also includes between 600 and 1,500 small islands, islets, cays, and atolls, scattered amongst them (map 1). The peripheral islands of Sayang, Wayag, Quoy, Bag, Uranie, Balabalak, and Kawe to the northwest and Gag, Fam, Penemu, Kofiau, Eftorobi (Raja and Torobi), the Boo Islands, and Walo to the west, are also part of the archipelago. However, the Ayu (Ayau) and Asia Islands to the north, and Gebe to the west are not generally considered part of Raja Ampat (Erdmann and Pet 2002). Nevertheless, due to their close proximity and biogeographic affinities, some terrestrial vertebrates from Gebe are mentioned and listed in this book.

There are various spellings for some islands, and many, especially the smaller ones, appear nameless on most maps. The variety of names, not only for islands but also for villages, mountains, rivers, and many other geographic features, is a result of the ongoing use of colonial era Dutch names and spellings on current maps. This can cause a lot of confusion when trying to get around the archipelago. In this book, I made my best effort to use only the most current Bahasa names and spellings.

The wide range of unspoiled coral reefs and the lovely above-water scenery combine to make Raja Ampat a tropical paradise. The variety of islands in this natural wonderland ranges from coral cays that barely rise above the water studded with palm trees, to large islands with steep rain-forested slopes reaching elevations above 1100 m. Probably, the most attractive aspect of the above-water scenery is the so-called ‘drowned karst topography’, typified by limestone islets that form a maze of ‘forested beehives and mushrooms’ (McKenna et al 2002). Many promotional photos and videos from Kabui Bay (Waigeo), the Wayag Islands, and Dapunlol Island (southeast of Misool), show precisely this unique and picturesque landscape (Fig. 2).

Climate statistics for Raja Ampat are based on long-term observations taken at Sorong, on the West Papuan mainland (Fig. 3). Temperature and rainfall averages measured in Sorong do not necessarily reflect weather across the archipelago as a whole, as many, especially the big ‘Four Kings’, have microclimates that vary noticeably from that of the former provincial capital. Still, other islands such as Misool, Kofiau, Kawe and Sayang are far enough from Sorong to experience different local weather patterns. For instance, it is not unusual to spend a beautiful sunny day on Kri island, all the while watching storm clouds pour rain onto Waigeo’s highlands, just a few kilometers away. Nevertheless, data from the weather station in Sorong provide a general idea of typical conditions. Being on the equator guarantees Raja Ampat a year-round day length of about twelve hours, from 6:30 AM to 6:30 PM, and a reliable solar energy input throughout the year, resulting in nearly constant air temperatures: daytime average maximum of 31°C and a nightly minimum of 24°C, although it can often feel hotter due to the region’s average relative humidity of 83%. The ocean is warm year-round as well, having a mean surface temperature of 29°C. Sea temperatures generally hover between 19°C and 36°C and severe thermoclines or areas of upwelling are uncommon (McKenna et al 2002, Agostini et al 2012).

Raja Ampat experiences a typical monsoon regime of winds and rain. The dry season occurs during the northwest (NW) monsoon, when low humidity winds come predominantly from that direction between November and March. The wet season takes place during the southeast (SE) monsoon months from April-May to October when Raja Ampat receives the bulk of its annual rainfall. Winds are light and variable during the transitional periods of November, April and May. Though May, June and July are historically the wettest months, it does not rain 24 hours, 7 days a week during these months; rainfall is often short-lived, localized, and it can be intense or light. It is not unusual to find yourself afloat on a calm, sunny ocean while rainstorms pass by on the horizon. Average rainfall during the dry season is 170 mm per month but can reach 270 mm per month in the wet season.

The natural position and shape of the Raja Ampat Islands mostly determines the predominant surrounding oceanographic conditions. Located at the confluence of the western Pacific Ocean and the eastern Indian Ocean, the archipelago is exposed to the ‘Indonesian Throughflow’ (IT), a strong current system that runs from the Pacific Ocean at its northeast to the Indian Ocean at its southwest (Gordon and Fine 1996, Donnelly et al 2003). Salinity, temperature and chemical tracer data suggest that the flow of water that passes through Raja Ampat into the Halmahera and Seram seas represents only a minor component of the IT (Gordon and Fine 1996). Although the IT drives most large-scale current patterns, a strong clockwise eddy to the west (the Halmahera Eddy) also impacts Raja Ampat (Agostini et al 2012). While the current patterns in the area are certainly complex, there is a strong likelihood that Raja Ampat reefs retain an important function as sources for larval propagules to reefs of northern and central Maluku (Erdmann and Pet 2002), though this assumption will require population genetic studies to be substantiated. Erdmann and Pet (2002) believe that the issue of genetic and ecological connectivity of Raja Ampat reefs to nearby marine ecosystems in the region is a priority research topic for the sound development of conservation and management strategies for the area.

The passage of strong currents through the hundreds of small islands and reefs creates many local eddies and turbulence which can vary seasonally (Agostini et al 2012). Seasonal changes can also weaken or reverse the general current movement, particularly impacting northern islands during the northwest monsoon season (Gordon and Fine 1996, Erdmann and Pet 2002). In general, these currents can be influenced by the monsoons, moving eastward in the west monsoon and westward in the east monsoon. Average current speeds have been recorded at 2.32 km/h, with top speeds of 4.63 km/h (Palomares and Heymans 2006). Periodic strong currents are common throughout the area, especially in channels between islands. This is particularly noticeable by divers who explore the Kabui Channel, the narrow passage separating Waigeo from Gam Island.

An adrenaline-rush through the Kabui Strait

Exploring the underwater marine life in this channel was idyllic at first. A group of six scuba divers and our guide were diving at about 10 m in depth bordering the north side of Gam while enjoying close and intimate views of soft corals tinted in orange and purple. Fish life was abundant and colorful; the rather stationary waters were pleasant to navigate as it was easy to move from one creature to the next. We had been instructed that as soon as we entered the center of the strait, we would experience a strong eastward current, but I had no idea how fast it would be. We also were supposed to stay close to each other right before the signal to enter. I was perhaps a few seconds too slow because as soon as I got in, I could no longer see any of my diving buddies; they had all been carried away. More alarmingly, the current pushed me rapidly downstream, way too fast for comfort. It was a wild ride ‘flying’ underwater and seeing massive rocks and stony corals, right and left, pass by quickly. I was out of control and desperately trying to find a way to slow down my speed. My life seemed to be coming to an end, as quickly as the passing corals. Eventually, though, I was able to pull myself to a side of the channel and slow down my speed. After unsuccessfully looking around for a minute, hoping to find other divers nearby, I gave up and went to the surface. The diving boat picked me up, and it was another half hour before the rest of the team surfaced. Apparently I missed seeing many spectacular creatures.

In Raja Ampat, maximum daily tide fluctuation is approximately 1.8 m, with an average daily variation ranging from 0.9 to 1.3 m (McKenna et al 2002). For most of the year, the sea around the islands appears calm. However, during the middle of the wet season (June to September) there may be days with strong winds making sea conditions less pleasant. Most live-aboard diving boats abandon Raja Ampat during July and August because the likelihood of experiencing both wind and rain makes sailing less enjoyable and swells complicate entering and leaving the water. Choppy seas at this time of year also reduce underwater visibility, making diving less pleasant, and further limit small boat travel among the islands.

Year-round warmth and humidity provided by an equatorial location are ideal for life. Free from human disturbance, plants and animals thrive on land and sea in tropical settings. In Raja Ampat, lush rainforests cover the larger islands, coconut trees precariously hang from the edges of karst formations on rocky shores, flocks of birds from many species travel from one island to another, stingless jellyfish swim unconcerned in quiet and isolated marine lakes, fishes and corals of astonishing colors mingle in the commotion underwater. Biologists have argued for decades about the reasons tropical regions display much higher levels of biological diversity than temperate or polar regions (see Chapter II). Raja Ampat likely enjoys a higher diversity of plants and terrestrial animals compared to islands of similar size at higher latitudes. But what makes the archipelago unique is its marine megadiversity. Located at the heart of the Coral Triangle, the archipelago enjoys some of the highest counts of hard and soft coral, mollusk, mantis shrimp, and reef fish species in the world. Other tropical seas at similar latitudes do not enjoy anywhere near the dizzying array of marine life. This is why the Four Kings have become a highly sought-after Mecca for marine biologists, recreational divers, snorkelers and conservation biologists. Even more incredibly, many marine groups have been poorly surveyed, so Raja Ampat still holds many surprises. This applies to marine as well as terrestrial ecosystems. New species to science, or the discovery of new distributions for known species, await the intrepid scholar and explorer. The luxuriant marine life combined with some of the most beautiful birds on Earth (including my very favorite Wilson’s Bird of Paradise) and the stunning above-water scenery make Raja Ampat one of the most spectacular places on our blue planet.

Above, I briefly mentioned the Coral Triangle (CT), an area of 5.7 million km² of ocean waters that biologists delineate on a map to highlight the region of highest marine diversity in the world. The CT encompasses tropical seas of Indonesia, Malaysia, Papua New Guinea, the Philippines, Solomon Islands and Timor-Leste. As shown in figure 4, the vertices of the triangle are roughly the northern tip of the Philippines, the southeastern tip of the Solomon Islands in New Guinea, and a point somewhere between Java and Bali in Indonesia. The lines have been drawn primarily to emphasize areas of coral species distribution and richness with at least 500 species being present within each of 16 identified eco-regions (Veron et al 2011). Covering only 1.6% of the world oceans’ surface, the CT is home to at least 627 species of scleractinian (hard or stony) corals, representing 74% of all coral species worldwide (Veron et al 2015). This figure is astonishing; for comparison, the number of described hard coral species for the Caribbean Sea is just around 62. Higher stone coral diversity brings with it more types of food for coral feeders and a more complex reef structure that provides unique places for other animals to live, hide, and mate. This results in myriads of ecological niches unknown in Caribbean reefs. The CT is home to at least 2,228 coral reef fish species, equivalent to 52% of those found in the tropical west Indian and central Pacific oceans, or roughly 37% of the world’s reef fishes (Allen 2007a). In addition, it provides habitat for 6 out of the 7 known marine turtle species. The CT is thus called the ‘Amazon of the seas’ and is recognized as the epicenter of marine biodiversity, making it a global priority for conservation. Further, its marine resources sustain the lives of over 120 million people. According to the Coral Triangle Knowledge Network, about $3 billion in fisheries exports and another $3 billion in coastal tourism revenues are derived as annual foreign exchange income in the region. Raja Ampat is located at, or very near the heart of the CT, its bullseye so to speak, and thus enjoys some of the highest marine biodiversity within the triangle, and in the world.

b. Geography

Compared with other protected areas, Raja Ampat’s total land and sea surface area is only slightly larger than the Niassa Reserve in northern Mozambique (42,000 km²) and more than twice as large as Kruger, the famous National Park in northeast South Africa (19,485 km²). The bulk of land is shared amongst the largest six islands. Table 1 shows some physical features of the Four Kings in addition to Gam and Kofiau.

Waigeo, by far the largest island, is over 55% bigger than Misool and roughly 22 times the size of Kofiau. Its walnut-like contour is 692 km long and is characterized by a large depression in the middle, the shallow Mayalibit Bay, which itself connects to the Dampier Strait through the Rabia Channel at its southern end, but is separated from the Bougainville Strait to the north by a thin strip of land known as the Goh-Puah Isthmus. Slightly more than half of Waigeo’s area is found east of Mayalibit Bay. The Kabui Strait separates Waigeo from Gam Island on its southwestern corner. The irregularly shaped Alyui Bay dominates the island’s northwest. Waigeo’s relatively large size, complex geology, and rugged terrain have endowed it with 11 distinct vegetational communities (Chapter VI), the most on any island in the archipelago.

Waigeo’s many peaks are scattered across the island, but their names and recorded elevations vary, depending on source. The highest peak on East-Waigeo, at 1026 m above sea level (a.s.l.), is Mt Sau Lal. Waigeo’s most notable feature is probably the cone of Gunung Lok, Gunung Nok, or Buffalo Horn, known during Dutch colonial times as the Buffelhoorn. Situated near the northwest corner of East–Waigeo, this mountain reaches a height of 958 m (Mauro 2007, although Charlton et al 1991 estimated its height at only 670 m) and forms an impressive pinnacle. There are extensive areas at high elevation surrounding the summit of Mt Danai (918 m) in central East–Waigeo that have been poorly explored. Other high altitude areas in East–Waigeo include the Mnier–Werar Hills (reaching a maximum height of 912 m) on the east side and Rabia Hills (744 m) on the southwest. Mount Abaipap reaches 724 m and is located in north-central West–Waigeo. The current confusing altitudes and nomenclature for Waigeo’s peaks needs to be sorted out and catalogued more precisely, although here I follow Mauro (2007) and recent online maps.

Many creeks gather waters from higher ground and converge into rivers that meander across the island. Waigeo’s most prominent rivers include the Dusun, which flows south on West–Waigeo and drains into Kabui Bay; the Kabilol, Kamtabae, Warambiae, and Orobiae, all flowing into Mayalibit Bay; the Waribari and Yensner rivers which drain into the Dampier Strait; and the Bayon river in northern East–Waigeo. Other rivers that appear nameless on maps drain at multiple locations around the island.

Waigeo is very sparsely inhabited, with an approximate population of 20,620 as of 2017 (BPS 2020). Most people live in Waisai, the island’s capital and only real town, and in coastal villages such as Salio, Go, Lam Lam (located at the base of Fofak Bay), Missigit, Kabare, Warkori, Poeper, Yenbekaki, Urbinasopen, Wakre, Mumos, Wagailom, Wairemah, Rabia, Warsamdin, Tapokreng, Saporkren, Wauyai, Waisilip and Sarpeli. The interior of Waigeo is thickly covered by rain forest with only limited geological exposure, but uncovered sections, often excellent for geologists, are found around the coastline, particularly on the north coast (Charlton et al 1991).

Misool, with its arrowhead shape and west-pointing tip, is the southernmost island among the Four Kings. Although its peaks do not reach the heights of those from Batanta or Waigeo, its topography is nonetheless quite rugged. The highest point only reaches 440 m and has no apparent name. The Kasim River collects waters from several creeks along the central hills (including Waitama creek) and drains into the Seram Sea on the northwest of Misool. The Gam River originates near the headwaters of the Kasim but runs east and drains on the opposite side of the island. Lacking high elevation areas, Misool is home to only 8 plant communities. Like Waigeo, Misool is sparsely inhabited, with an estimated population of 10,723 in 2017 (BPS 2020). Most people also live in coastal villages such as Folley, Tamoelol, Fafanlap, Lelintah, Kapocol, Igom, Erwang, Waigama, Solal, Atkri, and Len Malaas. Other villages include Aduwey, Jangfubo, Gepo, Malolo, and Biga. Misool is traversed by two secondary roads, one from Waigama to Erwang, and the other from Atkri to Malolo.

Salawati is separated from mainland New Guinea by the Sele Strait, less than 1 km wide in some sections, and from Batanta to the north by the Pitt Strait, also known as the Sagawin (Sagewin) Strait. Salawati consists mostly of low elevation flat plains but its northern end is complex and dominated by the Wagon Mountains with its highest peak reaching 820 m. Multiple rivers drain the flat plains, including the south-flowing Maralol, the southeasterly-flowing Waisebi, and the east-flowing Waijan, the later two draining into the Sele Strait. Other rivers that run east, west (e.g. Doktor creek), and north drain the rugged northern hills but appear nameless on maps. Salawati is home to 9 distinctive plant communities, with forests on alluvium and flat plains dominating the landscape. With the exception of Sapraan, Waiboe, Flaur, and Mara, four interior villages, most of Salawati’s 17,200 inhabitants (ibid.) live on coastal communities such as Waiwo, Samate, Kampung Samodir, Sailolof, Kuluai, Warangke, and Waijaar. Salawati’s main road connects Sailolof to Flaur. Approximately 30% of Salawati’s area, on its south, along with a large portion of the Sele Strait to the east and offshore chunks to the south belong to what RH Petrogas Limited, an oil and gas company headquartered in Singapore, calls its Island Production Sharing Contract (PSC). This block, which covers an area of 1,097 km², is apparently one of the most prolific petroleum basins in Indonesia (http://www.rhpetrogas.com/oil_indonesia.html).

Batanta, only 7% the size of Waigeo, has the most rugged topography among the Four Kings and is home to the highest peak in Raja Ampat. The summit of this apparently nameless mountain reaches 1153 m. Batanta is separated from Waigeo by the Dampier Strait to the north. As with the other islands in the archipelago, the relatively short rivers that drain the highlands often appear nameless on maps, the main exception being the Wei Bin stream in the north. In spite of its size, Batanta is home to 7 terrestrial ecosystems, almost as many as Salawati, which is four times larger. Similar to the rest of Raja Ampat, most of Batanta’s 2,500 inhabitants (ibid.) live in coastal villages such as Marandanweser, Wensawai, Yenanas, and Wailebet.

Although Gam is Raja Ampat’s 5th largest island, the Kabui Strait that separates it from Waigeo is so narrow that in some sections it rather resembles a river. As a result, biogeographers and conservation biologists usually lump Gam with Waigeo together, a practice followed in this book. Gam possesses 3 plant communities and is dominated by lowland rainforest on limestone, with some patches of savannah. Gam’s main village is Besir (Bessir, Besin), located at its eastern coastline, and its highest peak reaches 370m.

Kofiau, a rather flat island on the Seram Sea, has an 88 km long coastline and its highest peak is only 284 m. Kofiau is home to 4 unique plant communities and, as Gam, is dominated by lowland rainforest on limestone. Kofiau’s main villages include Deer and Hebera, and the island’s population was estimated at 2,786 as of 2017 (ibid.).

Other noteworthy islands, either because of their size or attraction as tourist destinations, include Gag, Sayang, Kawe, Wayag, Quoy, Bag, Uranie, Eftorobi (Raja and Torobi islands, with Tolobi as the main village), Boo Besar, Manswar, Kri, Weeim (Babi), Yfpolee (Pelee or Pele), Wagmab, Fam, Batangpele (Runsuar), and Ayau. Hundreds of islets scattered across the archipelago lack names on maps.

c. Geology

Plate tectonics

The discovery that continents move around the surface of the Earth completely revolutionized the way we view our planet. When Alfred Wegener, a German polar researcher and meteorologist, described what he called continental drift in 1912, the idea of wandering continents was initially ignored and ridiculed, and later vehemently opposed. However, further observations, the development of more sophisticated instruments, and new measurements eventually convinced the scientific community that the theory is correct. Before this, geologists believed that continents were fixed on the surface of the Earth, and therefore unmovable. A few individuals thought it was odd that the eastern coast of South America could almost perfectly fit on the western coast of Africa, but this observation was no more than a curiosity. Similar fossil records and rock formations on both sides of the Atlantic were an oddity too. Later, magnetic and biogeographic information provided further evidence that perhaps those two great land masses had been connected in the past. In spite of the accumulating evidence, mechanisms that could explain how these two continents had broken apart and moved so far to their present positions were lacking. For one thing, if continents moved, where were the forces and materials necessary to push them apart coming from? Today, the theory of continental drift and plate tectonics is well understood and accepted; it makes powerful predictions and accurately explains many of the phenomena observed on Earth.

The outer shell of our planet, the lithosphere, is broken up into nine major plates: African, Antarctic, Eurasian, Indian, Indo-Australian, North American, Pacific, South American, and the newest named Zealandia (Mortimer et al 2017). Eleven minor plates (Somali, Philippine, Juan de Fuca, Cocos, Nazca, Caroline, Scotia, Caribbean, Burma, New Hebrides and Arabian), and several dozen microplates or terranes, each of the latter with an area smaller than 1 million km² and often grouped with an adjacent major plate on world maps, complete the picture. Terranes are fragments of crust bounded by faults with a distinctive stratigraphy and history. All plates, big and small, float on the fluid-like asthenosphere which allows the tectonic plates to undergo motion in different directions.

Depending on how plates move relative to one another, geologists define three types of boundaries:

(i) Divergent boundaries are characterized by plates moving away from one another while creating enormous ridges. An example is the mid-Atlantic Ridge. In the North Atlantic, it separates the Eurasian from the North American plate while in the South Atlantic it separates the African from the South American plate. As the continental plates split, a ridge formed at the spreading center, expanding the ocean basin and increasing the plate area, creating many small volcanoes and/or shallow earthquakes. Although the ridge is mostly underwater, portions of it have enough elevation to extend above sea level, an instance of which is the nation of Iceland.

(ii) Transform boundaries occur when one plate slides past another as in the San Andreas fault in California where the Pacific plate is sliding past the North American plate.

(iii) Convergent boundaries occur when two plates slide toward each other and form either a subduction zone (one plate moves underneath the other) or a continental collision.

A germane example of a convergent boundary zone is the collision of the very large, northward-moving Indo-Australian tectonic plate with the even larger, westward-moving Pacific plate, resulting in the formation of New Guinea (Polhemus 2007). The island of New Guinea can be thought of, in simplest geological terms, as the mountainous, tectonically deformed northern margin of Australia. Although we typically view New Guinea as a separate geographical entity, it is in fact only separated from northern Australia by the Torres Strait/Arafura Sea, a very shallow epicontinental sea less than 15 m deep, which did not even exist during most of the Pleistocene ice ages that spanned the last 20,000 years. The existence of New Guinea as a discrete island is thus a recent and transient product of the current warm interglacial period (ibid.).

Figure 5 shows Raja Ampat’s location at the convergence of three major plates (Pacific, Australian, and Eurasian), and two minor ones (Philippine and Caroline). Such position makes reconstruction of its geologic past complicated as the plates and microplates have moved (and continue to move) in different directions in relation to one another. In any case, the vast majority of the archipelago rests on either of two continental shelf areas separated by the Sagawin Strait. Waigeo, Gam, their surrounding islands, and Batanta sit on the Tosen microplate of Pacific origin (Webb 2005). These islands comprise one of only two oceanic terranes in this region of New Guinea and are collectively known as Greater Waitanta. Salawati, Misool, Kofiau, and most of the islands amongst them rest on the Australian shelf. They sit on the Kemun block of the Bird’s Head or Vogelkop microplate (ibid.) and are flatter than Waigeo and Batanta.

Biogeography and Tectonic reconstruction of New Guinea and Raja Ampat

In an attempt to put geological events in context, I include a geologic time chart with major Earth events, including some relevant to Raja Ampat (Fig. 6). Throughout this section I also mention in chronological order the estimated appearance, split, or radiation of prominent animal or plant groups in the New Guinea region when known.

The Vogelkop micro-continent had already separated from the Gondwana landmass during the early Mesozoic, subsequently drifting into its present position independently of the Australian craton (Pigram and Panggabean 1984, Pigram and Davies 1987, Hall 1998). At the beginning of the Paleocene, 65 Million years ago (Mya), the area where Raja Ampat is located today was deep under the sea (Lohman et al 2011, Hall 2013). For much of the Cenozoic, the New Guinea region is thought to have been composed of many low-lying islands of varying geological origin. This archipelago-like structure played an important role in the local radiation of rainbow fishes, a family of small and colorful freshwater fishes that today inhabit rivers, lakes and swamps of the region (Unmack et al 2013), and in the global evolution of major taxa, including the largest group of songbirds, the passerines, sometime between 50 and 20 Mya (Barker et al 2004, Jønsson et al 2011, Toussaint et al 2014, Jønsson et al 2016). Also known as perching birds, passerines are distinguished from other orders of birds by the arrangement of their toes (three pointing forward and one back), which facilitates perching, and by superior control of their syrinx muscles, which allows them to produce a wide range of songs and other vocalizations. Speciation events resulting from island arc collisions and orogenies (mechanisms by which mountains are built on continents) have been identified as key factors explaining the high biodiversity in Melanesia in general, and New Guinea in particular, of taxa such as birds, freshwater turtles, and insects from the orders Odonata, Hemiptera, and Heteroptera (Toussaint et al 2014).

In reconstructions by Hall (2002), the Tosen block originates as a mid-oceanic archipelago, being far from any mainland 50 Mya, and approaches its current position first from the East-North-East, and later from the East, as the main Papuan blocks of the Australian plate approached from the South (Pigram and Panggabean 1984, Pigram and Davies 1987, Hall 1998). The Pacific plate continued sliding past the Papuan blocks causing deep underwater troughs. Major changes began to take place in the Eocene as Australia had already separated from Antarctica and by 45 Mya was already moving rapidly northward. Between 40 and 30 Mya, during the upper Eocene to mid Oligocene, the Kemun block had emerged to a shallow sea composed of carbonate platforms (Hall 2013), e.g., sedimentary bodies that possess topographic relief and are composed of autochthonous calcareous deposits such as limestone. By the mid Oligocene (30 Mya), Vogelkop was still a detached microcontinent west of New Guinea proper and islands that would later become parts of Halmahera and Waigeo lay directly north of New Guinea at the southwest corner of the Caroline Plate (Fig. 7).

Recent analyses that use DNA sequences suggest that shortly after, around 28 Mya, Monarchs (Monarchidae) and birds-of-paradise (Paradisaeidae) split from the Corvidae or crow family (Irestedt et al 2009). Approximately two million years later, the Monarchs split from this combined group, giving rise to the birds of paradise (ibid.). Geologists propose that around this time, some 25 Mya, a major episode of contact between the terrestrial biotas of New Guinea and Australia also took place, ending during the early Miocene (Flannery 1995a). It seems reasonable to infer that much of the monotreme and marsupial fauna of New Guinea would have entered the island at this time. However, this assumption does not correlate well with the fossil evidence from Australia. Biochemical evidence (Aplin et al 1993) suggests that monotremes and marsupials arrived in New Guinea in three waves beginning in the Miocene as discussed below.

In the early Miocene, 23 Mya, the Australian plate made contact with the submerged Sundaland margin, a southeast extension of the Eurasian plate (Lohman et al 2011). The Sunda region began to rotate counterclockwise, initially keeping pace with Australia’s northward movement (ibid.). The split between Manucodes (birds of paradise in the genus Manucodia, that are medium-sized with black-glossed purple and green plumages) and the core birds of paradise is estimated to have occurred around this time (Irestedt et al 2009). By 20 Mya, the island of New Guinea began to emerge from the sea, probably as a group of small islands on its present northern edge, while most of the land that is now mountainous was still shallow sea (ibid.). The land corresponding to Salawati and Misool was once again submerged under a shallow sea (ibid., Hall 2013). It is at this time that the first wave of monotremes and marsupials are thought to have entered New Guinea. It is possible that ancestors of New Guinean bandicoots (Peroryctidae), cuscuses (Phalangerinae), and the Feather-tailed Possum (Distoechurus) arrived at this time (Flannery 1995a).

In the Middle Miocene, 15 Mya, the Vogelkop micro-continent was in the process of being sutured onto the western side of New Guinea proper, creating the limestone anticlines of the Bird’s Neck region. Islands that would later become parts of Halmahera and Waigeo were in close proximity to the northwestern coast of New Guinea (Fig. 8) and an island arc that had formed along the southeastern margin of the Caroline Plate in the Oligocene was beginning to collide obliquely with central and northern New Guinea (Hall 2002, Polhemus 2007). During this period Parotia, a bird of paradise genus, is estimated to have split from the rest of the family (Irestedt et al 2009). Hylid frogs likely reached New Guinea also in the course of the Miocene and have radiated extensively since (Allison 2007). The second wave of marsupials entering New Guinea occurred 12 to 10 Mya, when the ancestors of many New Guinean Ringtails (Pseudocheiridae), Trioks (Dactylopsila), a few species of Dorcopsis, and dasyurids may have arrived (Flannery 1995a).

In late Miocene times, around 10 Mya, the northern part of the Bird’s Head was already above sea level. Salawati and Misool were again carbonate platforms (Lohman et al 2011, Hall 2013) connected by land bridges to the Vogelkop microcontinent (Pigram and Panggabean 1984, Pigram and Davies 1987, Hall 2002), while Waigeo was where Biak is today. Five million years later, in early Pliocene times, the Bird’s Head had become completely sutured to the main body of New Guinea (Fig. 9). Halmahera and Waigeo had attained some semblance of their present form and continued moving westward beyond New Guinea approaching their current positions (Hall 2002, Polhemus 2007). During this period, plants of the lowland forests of New Guinea arrived from further west (Webb 2005). Between 5 and 2 Mya, the Misool and Salawati carbonate platforms appear to have been separated by a land arc extending from mainland New Guinea in the southeast (Lohman et al 2011, Hall 2013). At this time, 4.7 to 2.7 Mya, the third wave of marsupials that included additional Ringtails, Tree-kangaroos, and species of Myoictis possibly colonized New Guinea (Flannery 1995a). Waigeo and Batanta only assumed their present-day location by 2 Mya, during the upper Pliocene (Pigram and Panggabean 1984, Pigram and Davies 1987, Hall 2002). This late arrival may explain the relatively high number of endemic species on these islands. Colonization of Greater Waitanta by closely related species from New Guinea during more conducive periods of time and subsequent isolation of these colonizers from the mainland may have resulted in endemics such Waigeo Brushturkey, Red bird of paradise, Wilson’s bird of paradise, Raja Ampat Pitohui, and Waigeo cuscus. It may also explain the absence of cassowaries in Waigeo and their possible presence in Batanta, which is interesting given Waigeo’s current proximity to New Guinea (Webb 2005).

Fluctuations in temperatures and rainfall are likely to have been more extreme at intervals during the last million years than in the preceding 30 million years. Therefore, the last period of geological history, perhaps one million years or even much less, may have had a far greater influence on biogeographic patterns in Southeast Asia in general, and New Guinea in particular, than the much longer period before (Hall 1998). By around 20,000 years ago, during a glacial maxima in the late Pleistocene, sea levels lowered by as much as 130 meters (Fairbanks 1989, Lambeck 2014), connecting Salawati and Misool to New Guinea through a land-bridge covered with open woodland and savannah that allowed free back and forth migration and movement of species adapted to these ecosystems (Flannery 1995b). Meanwhile, Waigeo, Gam, and Batanta were connected into the ancient landmass of Greater Waitanta (ibid.).

Raja Ampat’s Geology

The Raja Ampat Islands consist mainly of extensive karst, acid volcanic and ultrabasic rocks.

Karst formations are very conspicuous on the islands and are formed by the dissolution of soluble rocks such as limestone and dolomite. Limestone is sedimentary rock composed largely of the minerals calcite and aragonite, which are different crystal forms of calcium carbonate (CaCO3). Aragonite is essential for coral calcification and reef formation; it is also found in macroalgae and molluscs. Other marine organisms deposit CaCO3 as calcite, high magnesium calcite, or in other slightly different crystalline forms. Most limestone is thus composed of skeletal fragments from marine organisms such as hard and soft corals, calcareous red algae, molluscs, echinoderms, and crustaceans. As rain falls, it picks up carbon dioxide (CO2) from the atmosphere. Once this mixture reaches the ground, it may pass through soil that yields further CO2, creating a weak carbonic acid solution capable of dissolving calcium carbonate from the limestone. The result is a porous structure full of holes of different sizes that look like beehives or Swiss cheese. There are sharp surfaces on these rocks and it is best to protect your feet with good shoes if you walk on them. Through physical erosion and chemical processes, seawater may also dissolve limestone, forming underwater caves and mushroom islets. These unmistakable and beautiful structures are quite common in Raja Ampat and a pleasure to divers because they form underwater caves and tunnels full of unique marine life.

Acid volcanic rocks are igneous boulders that contain more than 63% of silica (Silicon dioxide or SiO2) by weight. Granites are typical acid igneous rocks dominated by quartz and feldspar. They can be coarse or fine-grained and are typically found in continental crust.

Ultrabasic (or ultramafic) rocks on the other hand, are those containing less than 45% SiO2 by weight and are usually composed of mafic minerals (dark colored with high magnesium and iron content). Ultrabasic boulders dominate the upper mantle. Soils derived from these rocks are also often high in nickel (Ni) and relatively nutrient poor. These soils tend to be associated with distinctive plant communities (Chapter VI).

Waigeo and Batanta are predominantly oceanic basaltic rocks from the Tertiary period overlaid by Tertiary limestone (Webb 2005). The long history of rapid movement by the Tosen microplate has resulted in the formation of a wide variety of surface rocks. The volcanics are ‘basic to intermediate tuffs, agglomerates, lavas and dykes of the Tertiary Dore Home and Batanta formations’, with trapped slivers of many other exotic rocks in the fault zones, all metamorphosed to a greater or lesser extent (ibid.). Ultrabasic rocks are also common, adding to the diversity of substrates. As the latter hold significant nickel deposits, there are plans to mine the Goh-Puah isthmus. Tailings from such an operation would devastate the ecology of the shallow Mayalibit bay (ibid.).

The Wagon Mountains of northern Salawati are volcanic in origin from the Tertiary period, with areas of uplifted Jurassic sandstone dating from 201 to 145 million years old (ibid.). The plains to the south are recently uplifted Quaternary sediments or mudstones (ibid.).

The hills of southern Misool are classified as acid silicaceous metamorphics and Jurassic acid sedimentary rocks. Layered, deformed sandstone formations can be seen on several sections of the island. In the north of Misool, the limestone uplands are Jurassic, while the low northern rim is composed of recently uplifted Quaternary reefs (ibid.).

As Misool, Kofiau is primarily composed of Quaternary reefs which surfaced less than 2.6 Mya, with a few hills of older Tertiary igneous rocks (from 65 to 2.6 million years old) reaching up to 284 m above sea level (ibid.). Kofiau’s late appearance may explain in part the presence of two endemic birds, Kofiau Paradise Kingfisher, and Kofiau Monarch, whose ancestors may have arrived in Kofiau after that time, becoming isolated from New Guinea’s main populations.

2

A natural ‘species-making’ laboratory

Given the mind-blowing diversity of animals and plants in Raja Ampat, it makes sense to dwell on what the term ‘species’ means to biologists before we embark on describing and counting them. Although the concept is