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The 15N content of tissue from the coral Porites lobata was enriched, relative to corals from reference sites, at 5 of 7 Indo-Pacific sewage-affected reefs. Enrichment was as high as 3.7. The 13C of sewage-affected corals suggests they maintained a highdegree of autotrophic nutrition. 15N-enriched wastewater dissolved inorganic nitrogen (DIN), derived from untreated sewage, isthe most likely cause for enrichment in coral tissue 15N,though changes in coral nutrition, metabolism and zooxanthellae population dynamics are possible additional factors. Isotopic measurements of coral tissue can provide a simple means of detecting wastewater uptake by corals. [ABSTRACT FROM AUTHOR]

The degree of bioerosion of live massive corals and rubble from branching corals were measured on nine reefs from two regions of Indonesia: the Java Sea and Ambon. Bioerosion in massive corals was measured by collecting live corals, cutting and X-raying slabs, and measuring the cross-sectional area removed from each slab by the various bioeroding organisms. A technique analyzing branching coral rubble was developed and similarly used to evaluate the degree of bioerosion on the reefs. This rubble technique has potential advantages over the massive coral technique since it does not require the expense and technicalexpertise of making and analyzing X-rays, nor does it require the destruction of living coral heads. The effectiveness of this rubble technique is evaluated here. Levels of bioerosion in massive coral headsand rubble from branching corals are each compared with environmental variables and health parameters of the nine reefs. Overall, both techniques showed that bioerosion levels were positively correlated with environmental variables indicative of eutrophication. Bioerosion oflive massive corals and of branching coral rubble were positively correlated. At the Ambon sites, where the eutrophication levels differ only slightly compared to the Java sites, bioerosion in coral rubble was a more sensitive indicator of eutrophication stress than bioerosion measured from massive coral heads. The rubble technique we outlineis a useful rapid reef assessment technique that could be a valuablecontribution to the reef survey toolbox. [ABSTRACT FROM AUTHOR]

Massive coral growth rates may be poor indicators of coral reef health where coral reefs are subject to combined eutrophication and sedimentation. Massive coral growth (vertical extension) rates on pollutedreefs were not different from extension rates on unpolluted reefs, while live coral cover was low and bioerosion intensity high, leading to net reef erosion and death of the polluted reefs. These combined patterns of coral growth rates, coral cover and bioerosion were documented on reefs affected by land-based pollution in the Java Sea, SouthSulawesi and Ambon, Indonesia. Acid-insoluble content in coral skeletons reflected land-based pollution stress on reefs more reliably than did coral extension rates. Coral skeletal density was lower on polluted Java Sea reefs than on unpolluted reefs used as reference sites,but coral calcification rates were not significantly different. The most eutrophied Java Sea reefs had net carbonate loss, indicating netreef erosion, while a fringing reef adjacent to mangroves and two unpolluted coral cays both had positive net carbonate production. Coralgrowth and reef growth were decoupled, in that coral growth rates did not reliably predict rates of reef accretion. The apparently paradoxical combination of normal to rapid coral growth and net reef erosion on polluted reefs illustrates the need for a whole-reef perspectiveon coral reef health. [ABSTRACT FROM AUTHOR]

Insular biodiversity hotspots of Southeast Asia are remarkable for their biodiverse faunas. With a marine larval phase lasting up to several months, the freshwater fish subfamily Sicydiinae has colonized most islands of these hotspots. However, Sicydiinae diversity is still poorly understood in Southeast Asia. With the objective of estimating intraspecific genetic diversity and inferring past demography, we conducted the molecular inventory of Sicydiinae species in Sundaland and Wallacea using 652 bp of the mitochondrial cytochrome oxidase I gene, species delimitation methods, and Bayesian Skyline plot reconstructions. In total, 24 Molecular Operational Taxonomic Units are delimited among the 603 sequences belonging to 27 species and 5 genera. Two cases of discordance between morphology and mitochondrial sequence are observed, suggesting ongoing speciation and/or introgression in 2 genera. Multiple new occurrences are reported, either for a single biodiversity hotspot or both, some of which correspond to observations of a few individuals far from the range distribution of their conspecifics. Among the 10 species or species groups whose intraspecific diversity was examined, high levels of genetic diversity and past population expansion are revealed by Tajima's D tests and Bayesian Skyline Plot reconstructions. Together, these results indicate that long-distance dispersal is common and suggest that most endemic species originated through founder events followed by population expansion. Patterns of sexual dimorphism and males' coloration among diverging species pairs seem to point to sexual selection as an important mechanism contributing to speciation in the Sicydiinae of Sundaland and Wallacea., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Syngnathidae are a charismatic family of teleost fishes, represented by seahorses, seadragons, and pipefishes. Syngnathidae are mainly composed of marine species, but about 30 species of pipefishes inhabit freshwater insular environments of the Indo-Pacific realm. Recent research has shown that some freshwater pipefish species are amphidromous and exhibit high intraspecific divergences across their distribution range, like Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia and Microphis retzii (Bleeker, 1856) distributed from Taiwan to Indonesia. In this study, we used the mitochondrial cytochrome oxidase I (COI) partial gene of 91 specimens of M. brachyurus and 30 specimens of M. retzii from localities representative of their respective distribution area to improve knowledge on the population structure of these two widespread species. Genetic species delimitation and phylogeographic analyses were combined to explore spatial patterns of genetic diversity across the distribution ranges of the two species. We have highlighted deep genetic structuring within the two species and relate these results to various biotic and abiotic factors. For M. brachyurus, the population in Polynesia is distinct from those in the West Pacific, suggesting its distinctiveness and recognition as an evolutionary significant unit (ESU). For M. retzii, three lineages are delimited in its range distribution, suggesting the existence of two distinct species in Southeast Asia (Bali/Java/Lombok and China/Taiwan). Pipefish species are particularly vulnerable to anthropogenic pressures (inherent to Syngnathidae and insular environments). The present results, revising species delimitation and geographic distribution, will help implement effective conservation and management measures., (© 2024 The Author(s). Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

A new species of freshwater pipefish, Microphis arrakisae sp. nov., is described from the West Indonesian Islands (Java, Bali and Lombok). This species is morphologically very close to Microphis retzii (Bleeker, 1856), which is found in the eastern Indonesian Islands (Sulawesi, Ceram, Ambon and Papua). However, it can be distinguished by its in vivo coloration. Furthermore, genetic analysis of the partial COI gene (barcoding) indicates that it represents a distinct genetic lineage in the Indonesian region.

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning., Competing Interests: Competing interests statement:The authors declare no competing interest.

Wallacea-the meeting point between the Asian and Australian fauna-is one of the world's largest centers of endemism. Twenty-three million years of complex geological history have given rise to a living laboratory for the study of evolution and biodiversity, highly vulnerable to anthropogenic pressures. In the present article, we review the historic and contemporary processes shaping Wallacea's biodiversity and explore ways to conserve its unique ecosystems. Although remoteness has spared many Wallacean islands from the severe overexploitation that characterizes many tropical regions, industrial-scale expansion of agriculture, mining, aquaculture and fisheries is damaging terrestrial and aquatic ecosystems, denuding endemics from communities, and threatening a long-term legacy of impoverished human populations. An impending biodiversity catastrophe demands collaborative actions to improve community-based management, minimize environmental impacts, monitor threatened species, and reduce wildlife trade. Securing a positive future for Wallacea's imperiled ecosystems requires a fundamental shift away from managing marine and terrestrial realms independently., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)

The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so., Competing Interests: None declared., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Much controversy surrounds the identity and origin of human hepatic stem and progenitor cells in part because of a lack of small animal models in which the developmental potential of isolated candidate cell populations can be functionally evaluated. We show here that adoptive transfer of CD34(+) cells from human fetal liver into sublethally irradiated NOD-SCID Il2rg(-/-) (NSG) mice leads to an efficient development of not only human hematopoietic cells but also human hepatocyte-like cells in the liver of the recipient mice. Using this simple in vivo assay in combination with cell fractionation, we show that CD34(+) fetal liver cells can be separated into three distinct subpopulations: CD34(hi) CD133(hi), CD34(lo) CD133(lo), and CD34(hi) CD133(neg). The CD34(hi) CD133(hi) population contains hematopoietic stem/progenitor cells (HSPCs) as they give rise to T cells, B cells, NK cells, dendritic cells, and monocytes/macrophages in NSG mice and colony-forming unit (CFU)-GEMM cells in vitro. The CD34(lo) CD133(lo) population does not give rise to hematopoietic cells, but reproducibly generates hepatocyte-like cells in NSG mice and in vitro. The CD34(hi) CD133(neg) population only gives rise to CFU-GM and burst-forming unit-erythroid in vitro. Furthermore, we show that the CD34(lo) CD133(lo) cells express hematopoietic, hepatic, and mesenchymal markers, including CD34, CD133, CD117, epithelial cell adhesion molecule, CD73, albumin, α-fetal protein, and vimentin and transcriptionally are more closely related to HSPCs than to mature hepatocytes. These results show that CD34(lo) CD133(lo) fetal liver cells possess the hepatic progenitor cell properties and that human hepatic and hematopoietic progenitor cells are distinct, although they may originate from the same precursors in the fetal liver., (Copyright © 2013 AlphaMed Press.)

Aim: In this study, we investigate whether pH (low) insertion peptide (pHLIP) can target regions of lung injury associated with influenza infection., Materials & Methods: Fluorophore-conjugated pHLIP was injected intraperitoneally into mice infected with a sublethal dose of H1N1 influenza and visualized histologically., Results: pHLIP specifically targeted inflamed lung tissues of infected mice in the later stages of disease and at sites where alveolar type I and type II cells were depleted. Regions of pHLIP-targeted lung tissue were devoid of peroxiredoxin 6, the lung-abundant antioxidant enzyme, and were deficient in pneumocytes. Interestingly, a pHLIP variant possessing mutations that render it insensitive to pH changes was also able to target damaged lung tissue., Conclusion: pHLIP holds potential for delivering therapeutics for lung injury during influenza infection. Furthermore, there may be more than one mechanism that enables pHLIP variants to target inflamed lung tissue.