scholarly journals Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

2019 ◽  
Author(s):  
Naiara Guimarães Sales ◽  
Mariane da Cruz Kaizer ◽  
Ilaria Coscia ◽  
Joseph C. Perkins ◽  
Andrew Highlands ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Mammalian Species ◽  
Environmental Dna ◽  
Camera Trapping ◽  
Critically Endangered ◽  
Neotropical Mammals ◽  
Dna Metabarcoding ◽  
Biomonitoring Tool

AbstractThe application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased in the last decade. However, most studies have focused on aquatic macro-organisms in temperate areas (e.g., fishes). We apply eDNA metabarcoding to detect the mammalian community in two high-biodiversity regions of Brazil, the Amazon and Atlantic Forest. We identified critically endangered and endangered mammalian species in the Atlantic Forest and Amazon respectively and found congruence with species identified via camera trapping in the Atlantic Forest. In light of our results, we highlight the potential and challenges of eDNA monitoring for mammals in these high biodiverse areas.

scholarly journals Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

Mammal Review ◽  
2020 ◽  
Vol 50 (3) ◽  
pp. 221-225 ◽  
Author(s):  
Naiara Guimarães Sales ◽  
Mariane da Cruz Kaizer ◽  
Ilaria Coscia ◽  
Joseph C. Perkins ◽  
Andrew Highlands ◽  
...  
Keyword(s):  
Atlantic Forest ◽  
Environmental Dna ◽  
Neotropical Mammals ◽  
Dna Metabarcoding

Is camera-trapping an efficient method for surveying mammals in Neotropical forests? A case study in south-eastern Brazil

2005 ◽  
Vol 21 (1) ◽  
pp. 121-125 ◽  
Author(s):  
Ana Carolina Srbek-Araujo ◽  
Adriano Garcia Chiarello
Keyword(s):  
Atlantic Forest ◽  
Indirect Evidence ◽  
Camera Traps ◽  
Camera Trapping ◽  
Neotropical Forests ◽  
South Eastern ◽  
Eastern Brazil ◽  
Line Transects

Although highly diverse (Fonseca et al. 1996), the Atlantic forest mammal fauna is still poorly known, with very few sites exhaustively inventoried or subjected to long-term studies (Passamani et al. 2000). Although the first surveys using camera traps were carried out in the 1920s (e.g. Chapman 1927), most studies are rather recent (Karanth & Nichols 1998). This is not different in Brazil, where few studies have been published (Marques & Ramos 2001, Santos-Filho & Silva 2002, Silveira et al. 2003, Trolle 2003, Trolle & Kéry 2003). Given this, the objective of this paper is to assess the efficiency of camera trapping as an inventory technique for Neotropical forests in general and Atlantic forest in particular. The study was conducted at the Santa Lúcia Biological Station (SLBS), a biologically rich Atlantic Forest preserve located in south-eastern Brazil (Mendes & Padovan 2000) where mammals have been intensively live-trapped, observed from line-transects or had indirect evidence of their presence (faeces, footprints, scratches, etc.) recorded in earlier years (Passamani et al. 2000).

scholarly journals Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika

2019 ◽  
Vol 2 (1) ◽  
pp. 24-41 ◽  
Author(s):  
Christopher J. Doble ◽  
Helen Hipperson ◽  
Walter Salzburger ◽  
Gavin J. Horsburgh ◽  
Chacha Mwita ◽  
...  
Keyword(s):  
Lake Tanganyika ◽  
Fish Communities ◽  
Environmental Dna ◽  
Tropical Fish ◽  
Dna Metabarcoding

scholarly journals Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian

2020 ◽  
Vol 2 (2) ◽  
pp. 184-199 ◽  
Author(s):  
Lynsey R. Harper ◽  
Lori Lawson Handley ◽  
Christoph Hahn ◽  
Neil Boonham ◽  
Helen C. Rees ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Dna Metabarcoding

scholarly journals Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

2020 ◽  
Author(s):  
Ryohei Nakao ◽  
Ryutei Inui ◽  
Yoshihisa Akamatsu ◽  
Masuji Goto ◽  
Hideyuki Doi ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Environmental Dna ◽  
Illumina Miseq ◽  
Common Species ◽  
Species Numbers ◽  
Amplicon Library ◽  
Dna Metabarcoding ◽  
Biomonitoring Tool ◽  
The Common ◽  
Conventional Methods

AbstractEnvironmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples, and it is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding, one of the eDNA analysis approaches. The Illumina iSeq 100 (hereafter, iSeq) is one of the numerous high-throughput sequencers (HTS). It has a relatively simple workflow and is potentially more affordable than other sequencers for deployment in HTS environments. However, to date, only a few studies have adopted iSeq, and its utility in eDNA metabarcoding has still not been investigated comprehensively. In the present study, we applied fish eDNA metabarcoding to river and lake environmental samples using iSeq and MiSeq approaches. We also assessed differences in fish species detectability among iSeq, MiSeq, and conventional approaches. Twenty-seven river and 13 lake samples were amplified using MiFish primers and sequenced with iSeq and MiSeq, respectively. The iSeq and MiSeq metabarcoding achieved high detectability for fish taxa in the ecosystems. Species numbers and compositions in each river detected using iSeq were almost consistent with those of MiSeq, indicating detectability of both techniques was comparable. The comparison of the species compositions of the two HTSs with those of conventional methods showed that the common species between each HTS and the conventional methods were exactly similar. According to the results, if the same amplicon library were used for sequencing, there would be negligible detectability differences between iSeq and MiSeq based on eDNA metabarcoding.

scholarly journals Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryohei Nakao ◽  
Ryutei Inui ◽  
Yoshihisa Akamatsu ◽  
Masuji Goto ◽  
Hideyuki Doi ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Illumina Miseq ◽  
Lake Ecosystems ◽  
Similar Performance ◽  
Amplicon Library ◽  
Significant Difference ◽  
Dna Metabarcoding ◽  
Biomonitoring Tool ◽  
The Difference ◽  
Sequence Quality

AbstractEnvironmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.

scholarly journals Snapshot of the Atlantic Forest canopy: surveying arboreal mammals in a biodiversity hotspot

2021 ◽  
Author(s):  
Mariane C. Kaizer ◽  
Thiago H.G. Alvim ◽  
Claudio L. Novaes ◽  
Allan D. Mcdevitt ◽  
Robert J. Young
Keyword(s):  
Atlantic Forest ◽  
Forest Canopy ◽  
Forest Cover ◽  
Mammalian Species ◽  
Ground Level ◽  
Camera Traps ◽  
Camera Trapping ◽  
Conservation Strategies ◽  
Arboreal Mammal ◽  
First Time

AbstractThe Atlantic Forest of South America supports some of the greatest terrestrial biodiversity on our planet but is now reduced to only a small extent of its original forest cover. It hosts a large number of endemic mammalian species but our knowledge on arboreal mammal ecology and conservation has been hindered by the challenges of observing arboreal species from ground level. Camera trapping has proven to be an effective tool in terrestrial mammal monitoring, but the technique has rarely been used for arboreal species. Here we generated data on the arboreal mammal community based on canopy camera trapping for the first time in the Atlantic Forest, focusing on Caparaó National Park, Brazil. We placed 24 infrared camera traps in the forest canopy distributed in seven areas within the Park, operating continuously from January 2017 to June 2019. In this time, they accumulated 4,736 camera-days and generated 2,256 sets of pictures and 30 second videos of vertebrates. Canopy camera traps were able to detect arboreal mammals spanning a wide variety of body sizes. The local mammal assemblage comprised of 15 identifiable species, including the critically endangered northern muriqui (Brachyteles hypoxanthus) and the buffy-headed marmoset (Callithrix flaviceps), and other rare, nocturnal and inconspicuous species. For the first time, we confirmed the occurrence of the thin-spined porcupine (Chaetomys subspinosus) in the Park. Species richness varied across sampling areas and forest types. Our findings demonstrate the potential of canopy camera trapping for future surveying efforts to better inform conservation strategies for mammals.

scholarly journals Mammals recorded in isolated remnants of Atlantic Forest in southern Goiás, Brazil

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Analice Calaça ◽  
Marluci Fachi ◽  
Diego Afonso Silva ◽  
Seixas Rezende Oliveira ◽  
Fabiano Rodrigues de Melo
Keyword(s):  
Species Richness ◽  
Habitat Fragmentation ◽  
Atlantic Forest ◽  
Mammalian Species ◽  
Camera Trapping ◽  
Line Transect ◽  
Brazilian Atlantic Forest ◽  
Mammal Species ◽  
Cerrado Savanna

Abstract: Habitat fragmentation is one of the principal causes of the decline of species worldwide, and the Brazilian Atlantic Forest and Cerrado savanna biomes are among the most severely affected by this process. While highly fragmented, remnants of Atlantic Forest can still be found within the Cerrado domain of southern Goiás, where previous studies have revealed high levels of biodiversity. To inventory the mammalian species that occur in the region, two fragments of semideciduous Atlantic Forest were sampled between 2011 and 2016, using line transect surveys and camera trapping. A total of 1016 records were obtained of 30 mammal species, of which eleven are under some threat of extinction. The species richness recorded on this study was similar to or higher than the values reported from other areas of Goiás, which reinforces the importance of the maintenance of these remnants, located in private properties, for the conservation of the region's mammals.

scholarly journals Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals:

2018 ◽  
Author(s):  
Allan D McDevitt ◽  
Naiara Guimaraes Sales ◽  
Samuel S Browett ◽  
Abbie Sparnenn ◽  
Stefano Mariani ◽  
...  
Keyword(s):  
Fish Assemblages ◽  
Fish Communities ◽  
Environmental Dna ◽  
Cost Effective ◽  
Aquatic Habitats ◽  
Dna Metabarcoding ◽  
Canal Systems ◽  
Rapid Tool ◽  
Fish Monitoring

Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring of aquatic habitats. Man-made canal systems are among the least-studied environments in terms of biodiversity in Britain. Here we focus on a case study along an English canal comparing eDNA metabarcoding with two types of electrofishing techniques (wade-and-reach and boom-boat). In addition to corroborating data obtained by electrofishing, eDNA provided a wider snapshot of fish assemblages. Given the semi-lotic nature of canals, we encourage the use of eDNA as a fast and cost-effective tool to detect and monitor whole fish communities.

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