Marine lakes of Indonesia

The objective of this thesis was to obtain insight into the processes that play a role in biodiversity patterns of tropical marine species by using marine lakes as a model. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea. Two regions in Indonesia were studied: Berau (East Kalimantan) and Raja Ampat (West Papua). The following questions were addressed: 1. What are the different types of marine lakes in Indonesia? 2. Are the species assemblages in marine lakes distinct from those in the adjacent coastal environments? 3. To what extent are the populations in the lakes isolated? 4. Can marine lakes in Indonesia be considered natural laboratories of evolution? There is a large diversity in types of marine lakes and many more remain to be documented in Indonesia. The spatial variation in sponge species composition in marine lakes, coastal mangroves and coral reefs show that marine lakes contain three groups of sponge species: (a) widespread species known from various locations in Indo-Pacific reefs, (b) lake species that only occur in lake systems, (c) endemic species restricted to a single lake. The patterns of genetic variation found in the marine lake populations are generally consistent with populations in isolated environments. The lakes appear to be both cradles and refuges of diversityLEI Universiteit LeidenDe Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO-ALW # 817.01.008) Naturalis Biodiversity Center National Geographic/Waitt Grant De Beukelaar – van der Hucht Stichting Koninklijke Nederlandse Akademie Wetenschappen INNO/Wereld Natuur Fonds subsidie Conservation International & David and Lucile Packard Foundation Alida M. Buidendijk Fonds Jan Joost Ter Pelkwijk Fonds Leids Universiteits FondsEvolutiebiologi

Bonaire Deep Reef Expedition I

From 30 May – 1 June 2013 the deep reef of Bonaire, Caribbean Netherlands, was explored with the aid of the “Curasub” submarine of Substation Curaçao. The shallow reefs of the Caribbean are considered a biodiversity-hotspot, an area with exceptional diversity of plants, animals and ecosystems yet surprisingly little is known about the flora and fauna of the deeper reefs. Particularly the deep reefs of Bonaire, St. Eustatius and Saba have hardly been explored. This represents a critical knowledge gap for developing future reef policies and management practices. In order to adequately protect the ecosystem and construct sustainable management plans it is essential to document the biodiversity and to gain an understanding of what processes keep it in place

Generic ecological assessment framework for coastal ecosystems in the Caribbean Netherlands

This report provides practical guidance and considerations on how to establish appropriate reference situations in a changing environment. The reference situations must be chosen using best available information about the physical and biological characteristics of the environment to ensure that they represent suitable reference conditions. Important factors to consider are summed up in this report

Marine assessment guideline for BOPEC and Nustar operations

As part of the permit, Rijkswaterstaat requested an ecological monitoring and evaluation framework guideline to accompany the permit-application for the activities of BOPEC (Bonaire) and Nustar (St. Eustatius), related to the activities of the loading and unloading of oil and oil-related-products. IMARES has been asked to develop a tailored guideline to assist in the design of a monitoring plan by BOPEC and Nustar. The current document is the requested guideline. A complete monitoring proposal by the license holder must subsequently be developed on the basis of this guideline. The generic framework developed by Becking and Slijkerman (2012) was applied and made more specific for this guideline. The basic steps undertaken were: 1. Establishing the context in which the project will take place. 2. Scoping of the project activities, their pressures and the environmental descriptors relevant to the potential impact area. 3. Assessment and evaluation of the anticipated pressures on the selected biological and environmental descriptors. The guidance thus contains an overview of relevant activities and their pressures. In addition, biological descriptors were selected based on the most important relationships to the planned activities and anticipated pressures. The scope of monitoring is based on the major linkages between activities, -pressures and -ecosystem descriptors. A distinction is made between baseline and accident monitoring. Baseline monitoring is necessary to guarantee that background levels and patterns of change over time are known. This should be done also at control sites to make sure that a natural pattern (e.g. bleaching) is not confused as an effect of pollution on the impact sites. Both control sites and impact sites to perform baseline monitoring are recommended in this report. Accident monitoring is the assessment of the environmental status following accidents. Polluted sites should be identified and monitored. In parallel, all baseline monitoring should be continued. Due to wind and currents, there is a high likelihood that oil spilled at Nustar will float to the coast of Saba. Therefor it is necessary to check the coast of Saba as well after an oil spill. The baseline monitoring should be a continuous process with and regular effort, while accident related monitoring is incidental, only but directly after a spill or accident. Each type of monitoring requires different frequencies (Chapter 6)

A review of coral reef restoration techniques

In this review the following three reef restoration techniques are discussed: 1. Coral gardening, 2. Larval seeding, and 3. Reef balls. In this report we provide a description of each method and review the pro/cons using the following criteria: 1. Survival of fragments and larvae before transplantation to the reef; 2. Survival of transplants at the restoration site; 3. Introduction of exonogous material; 4. Indirect effects of coral restoration on the reef; 5. Genetic diversity; 6. Feasibility and effectiveness. We also suggest further research to answer current gaps in our knowledge in the Dutch Caribbean

Phylogeography of the Sponge Suberites diversicolor in Indonesia: Insights into the Evolution of Marine Lake Populations

The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic specie

Proximate response of fish, conch, and sea turtles to the presence of the invasive seagrass Halophila stipulacea in Bonaire

In this report we examined the proximate response of fish assemblages, queen conch, and sea turtles on H. stipulacea meadows in Lac Bay, Bonaire, Caribbean Netherlands. Here we primarily focused on the differences between the invasive species H. stipulacea and the principal species of native sea grass in Lac Bay, namely turtle grass Thalassia testudinum