scholarly journals Environmental DNA diffusion of reef fishes along a distance gradient from four isolated islands of the Western Indian Ocean

2021 ◽  
Vol 4 ◽  
Author(s):  
Mélissa Jaquier ◽  
Camille Albouy ◽  
Wilhelmine Bach ◽  
Conor Waldock ◽  
Viriginie Marques ◽  
...  
Keyword(s):  
Distance Sampling ◽  
Environmental Dna ◽  
Western Indian Ocean ◽  
Reef Fishes ◽  
Species Distribution Modelling ◽  
Model Systems ◽  
Reference Database ◽  
Developmental Phase ◽  
Marine Environments ◽  
Habitat Types

Islands have traditionally served as model systems to study ecological and evolutionary processes (Warren et al. 2015) and could also represent a relevant system to study environmental DNA (eDNA). Isolated island reefs that are affected by climatic threats would particularly benefit from cost- and time-efficient biodiversity surveys to set priorities for their conservation. Among time efficiency methods, eDNA has emerged as a novel molecular metabarcoding technique to detect biodiversity from simple environmental samples even in remote marine environments. However, eDNA monitoring techniques for marine environments are at a developmental phase, with a few remaining unknowns related to DNA residence time and movement. In particular, the redistribution of eDNA, via ocean currents, could blur the composition signal and its association with local environmental conditions (Goldberg et al. 2016). Here, we investigated the detection variation of eDNA along a distance gradient across four islands in the French Scattered Islands. We collected 30 L of surface water per filter at an increasing distance from the islands reefs (0m, 250m, 500m, 750m). Using a metabarcoding protocol, we used the teleo primers to target a fraction of 12S mitochondrial DNA to detect Actinopterygii and Elasmobranchii. We then applied a sequence clustering approach to generate Molecular Taxonomic Units (MOTUs), which were assigned to a taxonomic group using a reference database. By assigning eDNA sequences to species using a public reference database, we classified species according to their preferred habitat types between benthic/demersal and pelagic. Our results show no significant relationship between distance and MOTUs richness for both habitat types. By using a Joint Species Distribution Modelling approach (JSDM, Hierarchical Modelling of Species Communities), we retained the multidimensional information captured by eDNA and detect species- and family-specific responses to distance (Fig. 1). We showed that benthic MOTUs were found in closer proximity to the reef, while typical pelagic MOTUs were found at greater distances from the reef. Hence, MOTU-level analyses coupled with JSDM were more informative that when aggregating it into coarser richness. Altogether, our eDNA distance sampling gradient detected an ecological signal of habitat selection by fish species, which suggest that eDNA could help understand the behavior of species and their distribution in marine environments at a fine spatial scale.

Linkage between fish functional groups and coral reef benthic habitat composition in the Western Indian Ocean

2016 ◽  
Vol 98 (2) ◽  
pp. 387-400 ◽  
Author(s):  
Kennedy Osuka ◽  
Marc Kochzius ◽  
Ann Vanreusel ◽  
David Obura ◽  
Melita Samoilys
Keyword(s):  
Coral Reef ◽  
Indian Ocean ◽  
Functional Groups ◽  
Habitat Type ◽  
Western Indian Ocean ◽  
Reef Fishes ◽  
Coralline Algae ◽  
Benthic Habitat ◽  
Habitat Types ◽  
Habitat Composition

Benthic habitat composition is a key factor that structures assemblages of coral reef fishes. However, natural and anthropogenic induced disturbances impact this relationship. This study investigates the link between benthic habitat composition and fish functional groups in four countries in the Western Indian Ocean (WIO). Benthic composition of 32 sites was quantified visually from percentage cover of hard and soft corals, rubble, turf, fleshy and crustose coralline algae. At each site, abundance of 12 coral-associated fish functional groups in 50 × 5 m transects was determined. Cluster analysis characterized reefs based on benthic cover and revealed five habitat types (A, B, C, D and E) typified by decreasing cover of hard corals, increasing cover of turf and/or fleshy algae and differences in benthic diversity. Habitat type A was present in all four countries. Other habitats types showed geographic affiliations: notably Comoros sites clustered in either habitats B or E, northern Madagascar had B, C and D type habitats, whereas sites in central Tanzania and northern Mozambique had habitats D and E. Fish functional groups showed significant linkages with some habitat types. The abundances of corallivores, invertivores, detritivores and grazers were higher in habitat B, whereas planktivores and small excavators showed lower abundances in the same habitat. These linkages between benthic habitat types and fish functional groups are important in informing priority reefs that require conservation and management planning.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals Environmental DNA (eDNA) metabarcoding surveys extend the range of invasion for non-indigenous freshwater species in Eastern Europe.

2021 ◽  
Author(s):  
Gert-Jan Jeunen ◽  
Tatsiana Lipinskaya ◽  
Helen Gajduchenko ◽  
Viktoriya Golovenchik ◽  
Michail Moroz ◽  
...  
Keyword(s):  
Surface Water ◽  
Water Samples ◽  
False Negative ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
Reference Database ◽  
Indigenous Species ◽  
Freshwater Species ◽  
Traditional Approaches ◽  
Surface Water Samples

Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e., an ichthyological, hydrobiological, and eDNA survey, whereby DNA was extracted from 500 mL surface water samples and amplified with two 16S rRNA primer assays targeting the fish and macro-invertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous sediment-living macro-invertebrates were detected by traditional surveys, while seven NIS eDNA signals were picked up, including four fish, one aquatic and two sediment-living macro-invertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey could be attributed to (i) preferential amplification of aquatic over sediment-living macro-invertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximize the probability of early detection of non-native organisms.

scholarly journals Disentangling drivers of the abundance of coral reef fishes in the Western Indian Ocean

2019 ◽  
Vol 9 (7) ◽  
pp. 4149-4167 ◽  
Author(s):  
Melita A. Samoilys ◽  
Andrew Halford ◽  
Kennedy Osuka
Keyword(s):  
Coral Reef ◽  
Indian Ocean ◽  
Western Indian Ocean ◽  
Reef Fishes ◽  
Coral Reef Fishes

scholarly journals Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

2021 ◽  
Author(s):  
Giulia Francesca Azzurra Donati ◽  
Niklaus Zemp ◽  
Stéphanie Manel ◽  
Maude Poirier ◽  
Thomas Claverie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Evolution ◽  
Neutral Theory ◽  
Species Abundance ◽  
Western Indian Ocean ◽  
Reef Fishes ◽  
Ecological Traits ◽  
Interspecific Differences ◽  
Tropical Reef ◽  
Species Ecology

ABSTRACTIntraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. In contrast to what is expected by the neutral theory of molecular evolution, we find that the α and γ components of genetic diversity are negatively associated with species abundance, which can be explained by larger variance in reproductive success in large populations and/or higher introgression in less frequent species. Pelagic larval duration, an important dispersal trait in marine fishes, is found to be negatively related to genetic β diversity, as expected by theory. We conclude that the neutral theory of molecular evolution may not be sufficient to explain genetic diversity in tropical reef fishes and that additional processes influence those relationships.

scholarly journals How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

2021 ◽  
Author(s):  
Salome Stauffer ◽  
Meret Jucker ◽  
Thomas Keggin ◽  
Virginie Marques ◽  
Marco Andrello ◽  
...  
Keyword(s):  
False Negative ◽  
Dynamic Environment ◽  
Environmental Dna ◽  
Water Volume ◽  
Marine Biodiversity ◽  
Marine Environments ◽  
Tropical Regions ◽  
Paired Samples ◽  
Promising Tool ◽  
Accumulation Curves

Quantifying the diversity of species in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, the reliability of biodiversity detection from eDNA samples can be low in marine environments because eDNA density is low and certainly patchy in this vast, heterogenous and dynamic environment. So, the number of sampling replicates and filtered volume necessary to obtain accurate estimates of biodiversity in rich tropical marine environments using eDNA metabarcoding is still unknown. Here, we used a paired sampling design of 30L per replicate on 68 reef transects from 8 sites in three tropical regions and identified fish Molecular Taxonomic Units (MOTUs) using a 12S marker. We quantified local biodiversity variation as MOTU richness, compositional turnover and compositional nestedness between replicated pairs of seawater samples. We report strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one-another. As a result, localised diversity accumulation curves showed that even 6 replicates (180L) in the same location underestimated local diversity (for an area <1km). However, sampling of regional diversity using ~25 replicates in variable locations (often covering 10s of km) achieved saturation of biodiversity accumulation curves. Our results demonstrate high variability of diversity estimates perhaps arising from heterogeneous and local distribution of eDNA distribution in seawater or highly skewed frequencies of eDNA traces. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes of local assemblages. Future biomonitoring efforts could be strongly undermined by a high level of false-negative detections under low replication protocols. We reveal the need to increase replicates or increase sampled water volume to better inform management of marine biodiversity using eDNA.

Composition and behavior of mixed-species foraging groups of reef fish in the Lakshadweep islands, India

2021 ◽  
Author(s):  
Anne Heloise Theo ◽  
Kartik Shanker
Keyword(s):  
Reef Fishes ◽  
Mixed Species ◽  
Habitat Types ◽  
Nuclear Species ◽  
Herbivorous Species ◽  
And Behavior ◽  
Large Groups ◽  
Lakshadweep Archipelago ◽  
Habitat Affinity ◽  
Lakshadweep Islands

Mixed-species foraging groups of reef fishes, although relatively common in occurrence, have historically received little attention. Most studies on this topic have been descriptive accounts of specific associations. In this study, we collected data on mixed-species foraging groups seen in the Lakshadweep islands, resulting in a dataset of 1289 groups. Data was collected from both reefs and lagoons of three islands (Kadmat, Kavaratti, and Agatti) within the Lakshadweep Archipelago over a period of three years. Cluster analysis revealed nine categories based on species composition in groups: parrotfish, juveniles, surgeonfish (small), surgeonfish (large), Anampses spp., wrasses, Parupeneus macronema, Parupeneus barberinus, and other goatfish groups. The clusters are named based on the nuclear species or most frequently seen species within the groups. These groups are distinct not only in terms of composition but also other parameters such as behavior (shoaling or attendant groups), habitat affinity, and group cohesion. Groups comprising herbivorous species such as parrotfish and surgeonfish were almost entirely shoaling in nature (large groups without nuclear individuals), whereas goatfish and wrasses tended to form smaller attendant associations. Groups also occupied different habitat types; for example, parrotfish and P. barberinus groups were seen mostly in lagoons while surgeonfish, wrasses, and P. macronema groups were more abundant on reefs. Our findings suggest that mixed-species foraging groups in fishes are comprised of distinct compositional categories that vary in behavior, cohesion, and habitat affinity.

scholarly journals Not equal in the face of habitat change: closely related fishes differ in their ability to use predation-related information in degraded coral

2017 ◽  
Vol 284 (1852) ◽  
pp. 20162758 ◽  
Author(s):  
Maud C. O. Ferrari ◽  
Mark I. McCormick ◽  
Bridie J. M. Allan ◽  
Douglas P. Chivers
Keyword(s):  
Reef Fishes ◽  
Community Change ◽  
Live Coral ◽  
Alarm Cues ◽  
Habitat Types ◽  
Coral Rubble ◽  
Related Information ◽  
Mixed Response ◽  
Risk Of Predation ◽  
The Face

Coral reefs are biodiversity hotpots that are under significant threat due to the degradation and death of hard corals. When obligate coral-dwelling species die, the remaining species must either move or adjust to the altered conditions. Our goal was to investigate the effect of coral degradation on the ability of coral reef fishes to assess their risk of predation using alarm cues from injured conspecifics. Here, we tested the ability of six closely related species of juvenile damselfish (Pomacentridae) to respond to risk cues in both live coral or dead-degraded coral environments. Of those six species, two are exclusively associated with live coral habitats, two are found mostly on dead-degraded coral rubble, while the last two are found in both habitat types. We found that the two live coral associates failed to respond appropriately to the cues in water from degraded habitats. In contrast, the cue response of the two rubble associates was unaffected in the same degraded habitat. Interestingly, we observed a mixed response from the species found in both habitat types, with one species displaying an appropriate cue response while the other did not. Our second experiment suggested that the lack of responses stemmed from deactivation of the alarm cues, rather than the inability of the species to smell. Habitat preference (live coral versus dead coral associates) and phylogeny are good candidates for future work aimed at predicting which species are affected by coral degradation. Our results point towards a surprising level of variation in the ability of congeneric species to fare in altered habitats and hence underscores the difficulty of predicting community change in degraded habitats.

scholarly journals Seascape Configuration Leads to Spatially Uneven Delivery of Parrotfish Herbivory across a Western Indian Ocean Seascape

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 434
Author(s):  
Linda Eggertsen ◽  
Whitney Goodell ◽  
César A. M. M. Cordeiro ◽  
Thiago C. Mendes ◽  
Guilherme O. Longo ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Life Histories ◽  
Spatial Configuration ◽  
Spatial Scales ◽  
Western Indian Ocean ◽  
Habitat Types ◽  
Opposite Pattern ◽  
Seagrass Meadows ◽  
Alternative Habitat ◽  
Mobile Links

Spatial configuration of habitat types in multihabitat seascapes influence ecological function through links of biotic and abiotic processes. These connections, for example export of organic matter or fishes as mobile links, define ecosystem functionality across broader spatial scales. Herbivory is an important ecological process linked to ecosystem resilience, but it is not clear how herbivory relates to seascape configuration. We studied how herbivory and bioerosion by 3 species of parrotfish were distributed in a multi-habitat tropical seascape in the Western Indian Ocean (WIO). We surveyed the abundance of three species with different life histories—Leptoscarus vaigiensis (seagrass species), Scarus ghobban (juvenile-seagrass/adults-reefs) and Scarus rubroviolaceus (reef species) —in seagrass meadows and on reefs and recorded their selectivity of feeding substrate in the two habitats. Herbivory rates for L. vaigiensis and S. ghobban and bioerosion for S. rubroviolaceus were then modelled using bite rates for different size classes and abundance and biomass data along seascape gradients (distance to alternative habitat types such as land, mangrove and seagrass). Bioerosion by S. rubroviolaceus was greatest on reefs far from seagrass meadows, while herbivory rates by S. ghobban on reefs displayed the opposite pattern. Herbivory in seagrass meadows was greatest in meadows close to shore, where L. vaigiensis targeted seagrass leaves and S. ghobban the epiphytes growing on them. Our study shows that ecological functions performed by fish are not equally distributed in the seascape and are influenced by fish life history and the spatial configuration of habitats in the seascape. This has implications for the resilience of the system, in terms of spatial heterogeneity of herbivory and bioerosion and should be considered in marine spatial planning and fisheries management.

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