scholarly journals Environmental DNA in a Global Biodiversity Hotspot: Lessons from Coral Reef Fish Diversity Across the Indonesian Archipelago

2021 ◽  
Author(s):  
Onny N. Marwayana ◽  
Zachary Gold ◽  
Paul H. Barber
Keyword(s):  
Survey Methods ◽  
Marine Ecosystem ◽  
Sampling Site ◽  
Environmental Dna ◽  
Marine Biodiversity ◽  
Fish Diversity ◽  
Sampling Effort ◽  
Coral Triangle ◽  
Regional Patterns ◽  
Biodiversity Survey

AbstractIndonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring, yet our understanding of marine biodiversity in this region remains limited. This study uses environmental DNA (eDNA) to survey fish communities across a pronounced biodiversity gradient in Indonesia. A total of 12,939,690 sequence reads of MiFish12SrRNA from 39 sites spanning 7 regions of Indonesia revealed 4,146 Amplified Sequence Variants (ASVs). Regional patterns of fish diversity based on eDNA broadly conformed to expectations based on traditional biodiversity survey methods, with the highest fish biodiversity in Raja Ampat and generally lower diversity in Western Indonesia. However, eDNA performed relatively poorly compared to visual survey methods in site-by-site comparisons, both in terms of total number of taxa recovered and ability to assign species names to ASVs. This result stands in a stark contrast to eDNA studies of temperate and tropical ecosystems with lower diversity. Analyses show that while sequencing depth was sufficient to capture all fish diversity within individual seawater samples, variation among samples from individual localities was high, and sampling effort was insufficient to capture all fish diversity at a given sampling site. Interestingly, mean ASVs recovered per one-liter seawater was surprisingly similar across sites, despite substantial differences in total diversity, suggesting a limit to total ASVs (~200) per one-liter eDNA sample. Combined, results highlight two major challenges of eDNA in highly diverse ecosystems such as the Coral Triangle. First, reference databases are incomplete and insufficient for effective ASV taxonomic assignment. Second, eDNA sampling design developed from lower diversity temperate marine ecosystems are inadequate to fully capture diversity of biodiversity hotspots like the Coral Triangle.

scholarly journals Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle

2020 ◽  
Vol 287 (1930) ◽  
pp. 20200248 ◽  
Author(s):  
Jean-Baptiste Juhel ◽  
Rizkie S. Utama ◽  
Virginie Marques ◽  
Indra B. Vimono ◽  
Hagi Yulia Sugeha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Reference Database ◽  
Fish Diversity ◽  
Sampling Effort ◽  
Coral Triangle ◽  
Model Framework ◽  
Operational Taxonomic Units ◽  
Accumulation Curves ◽  
Seawater Samples

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

scholarly journals Species richness accelerates marine ecosystem restoration in the Coral Triangle

2017 ◽  
Vol 114 (45) ◽  
pp. 11986-11991 ◽  
Author(s):  
Susan L. Williams ◽  
Rohani Ambo-Rappe ◽  
Christine Sur ◽  
Jessica M. Abbott ◽  
Steven R. Limbong
Keyword(s):  
Marine Ecosystem ◽  
Ecosystem Restoration ◽  
Well Being ◽  
Coastal Ecosystems ◽  
Coastal Development ◽  
Marine Biodiversity ◽  
Coral Triangle ◽  
Mangrove Forests ◽  
Positive Role ◽  
Seagrass Meadows

Ecosystem restoration aims to restore biodiversity and valuable functions that have been degraded or lost. The Coral Triangle is a hotspot for marine biodiversity held in its coral reefs, seagrass meadows, and mangrove forests, all of which are in global decline. These coastal ecosystems support valuable fisheries and endangered species, protect shorelines, and are significant carbon stores, functions that have been degraded by coastal development, destructive fishing practices, and climate change. Ecosystem restoration is required to mitigate these damages and losses, but its practice is in its infancy in the region. Here we demonstrate that species diversity can set the trajectory of restoration. In a seagrass restoration experiment in the heart of the Coral Triangle (Sulawesi, Indonesia), plant survival and coverage increased with the number of species transplanted. Our results highlight the positive role biodiversity can play in ecosystem restoration and call for revision of the common restoration practice of establishing a single target species, particularly in regions having high biodiversity. Coastal ecosystems affect human well-being in many important ways, and restoration will become ever more important as conservation efforts cannot keep up with their loss.

scholarly journals An interactive atlas for marine biodiversity conservation in the Coral Triangle

2019 ◽  
Vol 11 (1) ◽  
pp. 163-174 ◽  
Author(s):  
Irawan Asaad ◽  
Carolyn J. Lundquist ◽  
Mark V. Erdmann ◽  
Mark J. Costello
Keyword(s):  
Biodiversity Conservation ◽  
Marine Protected Areas ◽  
Spatial Information ◽  
Marine Protected Area ◽  
Marine Ecosystem ◽  
Marine Biodiversity ◽  
Coral Triangle ◽  
Biodiversity Informatics ◽  
Conservation Values ◽  
Mpa Network

Abstract. An online atlas of the Coral Triangle region of the Indo-Pacific biogeographic realm was developed. This online atlas consists of the three interlinked parts: (1) Biodiversity Features; (2) Areas of Importance for Biodiversity Conservation; (3) recommended priorities for Marine Protected Area (MPA) Network Expansion (http://www.marine.auckland.ac.nz/CTMAPS). The first map, Biodiversity Features, provides comprehensive data on the region's marine protected areas and biodiversity features, threats, and environmental characteristics. The second provides spatial information on areas of high biodiversity conservation values, while the third map shows priority areas for expanding the current Coral Triangle MPA network. This atlas provides the most comprehensive biodiversity datasets that have been assembled for the region. The datasets were retrieved and generated systematically from various open-access sources. To engage a wider audience and to raise participation in biodiversity conservation, the maps were designed as an interactive and online atlas. This atlas presents representative information to promote a better understanding of the key marine and coastal biodiversity characteristics of the region and enables the application of marine biodiversity informatics to support marine ecosystem-based management in the Coral Triangle region.

scholarly journals Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

Authorea ◽  
2020 ◽  
Author(s):  
Jean Baptiste Juhel ◽  
Rizkie Utama ◽  
Virginie Marques ◽  
Indra Vimono ◽  
Hagi Sugeha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Fish Diversity ◽  
Coral Triangle ◽  
Coastal Fish ◽  
Accumulation Curves

scholarly journals Integrating Biodiversity and Environmental Observations in Support of National Marine Sanctuary and Large Marine Ecosystem Assessments

Oceanography ◽  
2021 ◽  
Vol 34 (2) ◽  
Author(s):  
Henry Ruhl ◽  
◽  
Jennifer Brown ◽  
Alexandra Harper ◽  
Elliot Hazen ◽  
...  
Keyword(s):  
Marine Ecosystem ◽  
Deep Ocean ◽  
Environmental Dna ◽  
Noise Pollution ◽  
Marine Biodiversity ◽  
Underwater Imaging ◽  
Science Data ◽  
Metadata Standards ◽  
Large Marine Ecosystem ◽  
Ocean Observing

Species and habitats are the subjects of legislation that mandates reporting of information on ecosystem conditions. Improvements in sensors, sampling platforms, information systems, and collaborations among experts and information users now enables more effective and up-to-date information to meet regional and national needs. Specifically, advances in environmental DNA (eDNA)-based assessments of biodiversity, community science data, various underwater imaging devices, and environmental, behavioral, and physiology observations from animal telemetry provide new opportunities to address multiple requirements for reporting status and trends, including insights into life in the deep ocean. Passive and active acoustic sensors help monitor marine life, boat traffic, and noise pollution. Satellites provide repeated, frequent, and long-term records of many relevant variables from global to local scales and, when combined with numerical computer simulations, allow planning for future scenarios. Metadata standards facilitate the transfer of data from machine to machine, thus streamlining assessments and forecasting and providing knowledge directly to the public. The Marine Biodiversity Observation Network (MBON) facilitates this exchange of information on life in the sea. The collaborative efforts of the Central and Northern California Ocean Observing System (CeNCOOS) of the US Integrated Ocean Observing System and its partners provide an example of a regional MBON process for information delivery. This includes linking policy and management needs, prioritizing observing data from various platforms and methods, streamlining data handling practices, and delivery of information for management such as for the Monterey Bay National Marine Sanctuary and the California Current Large Marine Ecosystem, with iterative process adaptation.

scholarly journals Optimizing Large-Scale Biodiversity Sampling Effort: Toward an Unbalanced Survey Design

Oceanography ◽  
2021 ◽  
Vol 34 (2) ◽  
Author(s):  
Enrique Montes ◽  
◽  
Jonathan Lefcheck ◽  
Edlin Guerra Castro ◽  
Eduardo Klein ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Composition ◽  
Statistical Power ◽  
Large Scale ◽  
Survey Design ◽  
Quality Data ◽  
Taxonomic Resolution ◽  
Marine Biodiversity ◽  
Sampling Effort ◽  
Biodiversity Survey

Acquiring marine biodiversity data is difficult, costly, and time-consuming, making it challenging to understand the distribution and abundance of life in the ocean. Historically, approaches to biodiversity sampling over large geographic scales have advocated for equivalent effort across multiple sites to minimize comparative bias. When effort cannot be equalized, techniques such as rarefaction have been applied to minimize biases by reverting diversity estimates to equivalent numbers of samples or individuals. This often results in oversampling and wasted resources or inaccurately characterized communities due to undersampling. How, then, can we better determine an optimal survey design for characterizing species richness and community composition across a range of conditions and capacities without compromising taxonomic resolution and statistical power? Researchers in the Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) are surveying rocky shore macroinvertebrates and algal communities spanning ~107° of latitude and 10 biogeographic ecoregions to address this question. Here, we apply existing techniques in the form of fixed-coverage subsampling and a complementary multivariate analysis to determine the optimal effort necessary for characterizing species richness and community composition across the network sampling sites. We show that oversampling for species richness varied between ~20% and 400% at over half of studied areas, while some locations were undersampled by up to 50%. Multivariate error analysis also revealed that most of the localities were oversampled by several-fold for benthic community composition. From this analysis, we advocate for an unbalanced sampling approach to support field programs in the collection of high-quality data, where preliminary information is used to set the minimum required effort to generate robust values of diversity and composition on a site-to-site basis. As part of this recommendation, we provide statistical tools in the open-source R statistical software to aid researchers in implementing optimization strategies and expanding the geographic footprint or sampling frequency of regional biodiversity survey programs.

scholarly journals POTENSI BAHARI PULAU DERAWAN MENUJU DESTINASI WISATA KOMPETITIF

2019 ◽  
Vol 3 (02) ◽  
pp. 55-87 ◽  
Author(s):  
Dadang Ilham Kurniawan Mujiono
Keyword(s):  
Cold War ◽  
Marine Ecosystem ◽  
Field Research ◽  
Scientific Paper ◽  
Marine Biodiversity ◽  
Coral Triangle ◽  
Marine Turtles ◽  
Tourist Destinations ◽  
East Kalimantan ◽  
The World

As a nation Indonesia famous throughout the world as archipelago state, and those islands provide plenty of tourist destinations. Nowadays, the power of nations unlike in cold war era, where traditional security is measured as the main source of power, however in today�s society non-traditional security become the main power, and one of them is tourism. As a country located in the coral triangle, Indonesia is surrounded by the shallow tropical marine ecosystem, where corals, fishes and other marine creatures are abundant. Indonesia in addition is the biggest contributor for the coral triangle area and Raja Ampat hosting the highest diversity of Marine world followed Derawan Island in East Kalimantan as the second place. This scientific paper will explain the potency of Derawan Island toward the competitive destination. In order to analyse the topic, the concept of hospitality will implement and the type of data research is primary, since the author conducting field research in Derawan Island and visiting number of official government agencies which related with the topic of research. The type of the research is descriptive explanative where the author will describe the data and explain about the potency of Derawan Island. The research shows that Derawan Island is located in the epicentre of marine biodiversity of the coral triangle. In addition Derawan Island also hosting two of six marine turtles in the world such as hawksbill and green turtle, in terms of dive spot, there are plenty of locations as the dive spot followed with extraordinary view and diversity of underwater world. Moreover related with accommodation, there are plenty of guesthouses, hotels and cottages and tourist can choose based on their budget.

scholarly journals Digital map of the Coral Triangle: An online atlas for marine biodiversity conservation

2018 ◽  
Author(s):  
Irawan Asaad ◽  
Carolyn J. Lundquist ◽  
Mark V. Erdmann ◽  
Mark J. Costello
Keyword(s):  
Biodiversity Conservation ◽  
Spatial Information ◽  
Marine Protected Area ◽  
Marine Ecosystem ◽  
Marine Biodiversity ◽  
Coral Triangle ◽  
Digital Map ◽  
Digital Maps ◽  
Conservation Values ◽  
Mpa Network

Abstract. An online atlas of the Coral Triangle region of the Indo Pacific biogeographic realm was developed. This online atlas consists of the three interlinked digital maps: (1) Biodiversity Features; (2) Areas of Importance for Biodiversity Conservation; (3) Recommended Priorities for Marine Protected Area (MPA) Network Expansion (www.marine.auckland.ac.nz/CTMAPS). The first map, Biodiversity Features, provides comprehensive data on the region's marine protected areas and biodiversity features, threats and environmental characteristics. The second provides spatial information on areas of high biodiversity conservation values, while the third map shows priority areas for expanding the current Coral Triangle MPA network. This digital map provides the most comprehensive biodiversity datasets yet assembled for the region. The datasets were retrieved and generated systematically from various open-access sources. To engage a wider audience and to raise participation in biodiversity conservation, the maps were designed as an interactive and online atlas. This digital map presents representative information to promote a better understanding of the key marine and coastal biodiversity characteristics of the region and enables the application of marine biodiversity informatics to support marine ecosystem-based management in the Coral Triangle region.

Predicting occurrences of geographically restricted rare floral elements with qualitative habitat data

2002 ◽  
Vol 10 (3) ◽  
pp. 167-190 ◽  
Author(s):  
A S MacDougall ◽  
J A Loo
Keyword(s):  
New Brunswick ◽  
Rare Species ◽  
Gap Analysis ◽  
Predictive Accuracy ◽  
Survey Methods ◽  
Land Resource ◽  
Ancillary Data ◽  
Biodiversity Survey ◽  
Reserve Network ◽  
Heterogeneous Habitats

Habitat-directed survey methods are often used for locating narrowly distributed rare species and communities across landscapes, though their predictive accuracy varies, depending on the element targeted and the type of data employed. We discuss habitat-directed surveys for rare floral elements in the context of landscape-level management planning, focusing in particular upon a case study from southern New Brunswick. Databases of rare species and community occurrences are important requisites for such planning, but existing information is usually deficient and expensive to develop. A habitat-based approach directs surveys to sites with a higher-than-random probability of hosting rare elements and avoids areas deemed unlikely to be of interest due to environment or disturbance factors. We describe a four-part survey procedure that uses readily available qualitative habitat descriptions and geographic information systems (GIS) based land resource data to identify sites potentially hosting rare biota. The procedure includes remote-sensed and on-site screening to confirm significance and collect ancillary data needed for conservation planning. The use of existing data is cost and time efficient, a necessity given often narrow planning windows and restricted budgets. The method described here is well suited to geographically restricted plant biota associated with distinct habitats, especially in unsurveyed or highly fragmented landscapes. However, the approach does not apply to species of wide-ranging and environmentally heterogeneous habitats. As well, by targeting only highly specific locations assumed to be "optimal" habitat, the occurrence of rare biota in other areas cannot be definitively determined and some sites will almost certainly be missed. The limitations of the procedure highlight the need for multifaceted biodiversity assessment over large areas.Key words: ecosystem management, rare species, gap analysis, habitat-directed biodiversity survey, reserve network, New Brunswick.

FISH DIVERSITY IN THE DOWNSTREAM REGION OF CIPANAS RIVER INDRAMAYU, WEST JAVA INDONESIA

Zoo Indonesia ◽  
2020 ◽  
Vol 29 (1) ◽  
Author(s):  
Titin Herawati ◽  
Gema Wahyudewantoro ◽  
Yuli Andriani ◽  
Heti Herawati ◽  
Naomi Masnida Yunisia Siregar
Keyword(s):  
Water Quality ◽  
Census Data ◽  
Fish Assemblages ◽  
Survey Methods ◽  
Upstream Region ◽  
Fish Diversity ◽  
West Java ◽  
Fish Collection ◽  
Java Sea ◽  
Downstream Area

Cipanas River is one river in West Java where its upstream region in Tampomas Mountain, Sumedang and it is emptied into the Java Sea, Indramayu. The study was aimed to investigate fish diversity in the downstream area of Cipanas River. The study was conducted by survey methods with census data collection techniques, taken place at 3 stations of Santing, Tempalong, and Cemara of Indramayu Regency. The parameters measured consisted water quality and fish assemblages. Water quality was measured referring to standard laboratory protocol, and fish collection was made by case net with different mesh sizes. The results showed that water quality conditions of the Cipanas River downstream was suitable for inhabiting fishes. There were as many as 548 individual fishes caught belonging to 21 species, 16 genera, and 14 families. Fish diversity was categorized as medium with 1.6 ≤ H ’≤ 2.2 indicating fairly good community structure, and the Evenness index was 0.81 ≤ E ≤ 0.86 to show highly evenly distributed.

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