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Anchialine lakes are landlocked marine water bodies, which may contain swarms of scyphozoan jellyfish (Becking et al. 2011). Because most jellyfish are pelagic, published examples of their predation by sessile benthic organisms are rare and, in the case of anthozoan predators, only single prey species have been clearly documented (Fautin and Fitt 1991; Jarms and Tiemann 2004; Alamaru et al. 2009). Experiments have shown that E. medusivora is also able to ingest non-scyphozoan prey (Fautin and Fitt 1991), which suggests that the number of its prey species depends on supply rather than selection. Recently discovered landlocked basins in Indonesia reveal high habitat diversity in anchialine systems.

The Phyllidiidae (Gastropoda, Heterobranchia, Nudibranchia) is a family of colourful nudibranchs found on Indo-Pacific coral reefs. Despite the abundant and widespread occurrence of many species, their phylogenetic relationships are not well known. The present study is the first contribution to fill the gap in our knowledge on their phylogeny by combining morphological and molecular data. For that purpose 99 specimens belonging to 16 species were collected at two localities in Indonesia. They were photographed and used to make a phylogeny reconstruction based on newly obtained cytochrome oxidase subunit (COI) sequences as well as sequence data from GenBank. All mitochondrial 16S sequence data available from GenBank were used in a separate phylogeny reconstruction to obtain information for species we did not collect. COI data allowed the distinction of the genera and species, whereas the 16S data gave a mixed result with respect to the genera Phyllidia and Phyllidiella. Specimens which could be ascribed to species level based on their external morphology and colour patterns showed low variation in COI sequences, but there were two exceptions: three specimens identified as Phyllidia cf. babai represent two to three different species, while Phyllidiella pustulosa showed highly supported subclades. The barcoding marker COI also confirms that the species boundaries in morphologically highly variable species such as Phyllidia elegans, Phyllidia varicosa, and Phyllidiopsis krempfi, are correct as presently understood. In the COI as well as the 16S cladogram Phyllidiopsis cardinalis was located separately from all other Phyllidiidae, whereas Phyllidiopsis fissuratus was positioned alone from the Phyllidiella species by COI data only. Future studies on phyllidiid systematics should continue to combine morphological information with DNA sequences to obtain a clearer insight in their phylogeny.

Plakobranchus papua Meyers-Muñoz & van der Velde, sp. n. from West Papua (Papua Barat province, Indonesia), is described based on its external morphology, colour pattern, internal anatomy, radula and reproductive system. In a molecular phylogenetic study specimens of this new species were compared with those of ten candidate taxa under the name Plakobranchus ocellatus van Hasselt, 1824. DNA analyses of COI mtDNA showed a clear distinction between Plakobranchus papua sp. n. and \"Plakobranchus ocellatus\". Plakobranchus papua, sp. n. also differed from all taxa that have been synonymised with Plakobranchus ocellatus. The genus is in dire need of taxonomic revision, preferably based on an integrative analysis involving morphology and DNA of all known Plakobranchus varieties.

. In order to manage and conserve coral reefs it is essential to understand the factors that structure reef communities. In Indonesia’s Jakarta Bay – Pulau Seribu reef complex, pronounced on-to-offshore variation in a number of variables was observed. Live coral cover, and echinoderm and fish species richness were higher in midshore sites than either in- or offshore sites. Variation in habitat structure, the abiotic environment, distance between sample sites and covariation of these factors separately explained 9.6 to 15.1% of the spatial variation in the composition of corals, echinoderms and fishes. Together, all three components explained > 50% of the variation in composition. This indicates that spatial and environmental factors influence the distribution of species across the study area and have important implications for the large-scale management of this reef ecosystem. Large scalemanagement and protection of these reefs will probably be important because the majority or reefs were in poor to very poor condition as exemplified by low (<25%) coral cover. The coral cover of some inshore reefs was particularly low (< 1%). Inshore coral assemblages tended to be composed of stress-tolerant or specialised pioneers of highly perturbed environments. There were also locally high densities of potentially destructive species such as the sea urchin Diadema setosum . Midshore sites had relatively high coral cover comprising Acropora and Montipora spp. that were rare or absent elsewhere, presumably due to their sensitivity to pollution and mechanical damage. Most of the offshore sites had relatively low live coral cover and were dominated by rapidly growing pioneers or by stress- or –sediment-tolerant species. Spatial variation in the composition of taxa is discussed in the context of past-and-ongoing disturbances, including land-based pollution, coral mining, sedimentation and destructive fishing practices.

Coral reefs are diverse, ecologically important and globally threatened ecosystems. Numerous studies have reported on the threats to coral reefs, which include both local perturba- tions, such as pollution and overfishing, and widespread phenomena, such as bleaching. Here, we report on the history of the Jakarta Bay−Thousand Islands reef system from 1985 to 2011. Over this period, we recorded significant shifts in coral generic composition and an overall decline in coral cover with widely different trajectories between in-, mid- and offshore zones. In 1985, coral cover exhibited a clear on-to-offshore gradient with low coral cover inshore (10%), moderate cover mid- shore (49%) and high cover offshore (74%). The low coral cover inshore contrasts strongly with reports of high coral cover for inshore reefs in 1929. Inshore, coral cover declined from 10% in 1985 to <5% in 1995. The greatest change in coral cover and composition, however, occurred in offshore reefs, where mean cover declined from 74 to <20% between 1985 and 1995. Acropora species were particularly affected and declined from 36 to just 5% cover offshore. Recovery of coral cover occurred offshore between 1995 and 2005. From 2005 to 2011, however, a less severe loss in coral cover was observed. With the exception of inshore reefs, which appear to be on an ongoing trajectory of decline that started before the 1985 surveys, the reefs of the Jakarta Bay−Thousand Islands system have shown a propensity to recover.

In this article, the variability of physical settings of anchialine systems in Indonesia is discussed together with the consequences these settings have for the environment and biota within the systems. Exploration in two karstic areas (Berau, East Kalimantan and Raja Ampat, West Papua) has resulted in the discovery of 20 previously unknown anchialine systems in Indonesia. Based on parameters such as bathymetry, size, coastline, salinity, water temperature, pH, degree of connection to the sea, and the presence-absence of selected key taxa we distinguish three types of (non-cave) anchialine systems in the Indo-Pacific: (1) Marine lakes with large and deep basins containing brackish to almost fully marine waters. Marine lakes show a range in the degree of connection to the sea with the result that the higher the connection the more the lake resembles a lagoon in both water chemistry and biota, while the more isolated lakes have brackish water and contain unique species that are rarely found in the adjacent sea. (2) Anchialine pools with small and shallow basins containing brackish water and low diversity of macrofauna. (3) Blue pools in chasms that contain water with a clear halocline and are possibly connected to anchialine caves. Study of the many unique features of anchialine systems will enhance our understanding of the physical and ecological processes responsible for diversification in tropical shallow marine environments.

Coral reefs are diverse, ecologically important and globally threatened ecosystems. Numerous studies have reported on the threats to coral reefs, which include both local perturbations, such as pollution and overfishing, and widespread phenomena, such as bleaching. Here, we report on the history of the Jakarta Bay-Thousand Islands reef system from 1985 to 2011. Over this period, we recorded significant shifts in coral generic composition and an overall decline in coral cover with widely different trajectories between in-, mid- and offshore zones. In 1985, coral cover exhibited a clear on-to-offshore gradient with low coral cover inshore (10%), moderate cover midshore (49%) and high cover offshore (74%). The low coral cover inshore contrasts strongly with reports of high coral cover for inshore reefs in 1929. Inshore, coral cover declined from 10% in 1985 to <5% in 1995. The greatest change in coral cover and composition, however, occurred in offshore reefs, where mean cover declined from 74 to <20% between 1985 and 1995. Acropora species were particularly affected and declined from 36 to just 5% cover offshore. Recovery of coral cover occurred offshore between 1995 and 2005. From 2005 to 2011, however, a less severe loss in coral cover was observed. With the exception of inshore reefs, which appear to be on an ongoing trajectory of decline that started before the 1985 surveys, the reefs of the Jakarta Bay-Thousand Islands system have shown a propensity to recover.