scholarly journals Demonstration of the potential of environmental DNA as a tool for the detection of avian species

2017 ◽  
Author(s):  
Masayuki Ushio ◽  
Koichi Murata ◽  
Tetsuya Sado ◽  
Isao Nishiumi ◽  
Masamichi Takeshita ◽  
...  
Keyword(s):  
Water Samples ◽  
Bird Species ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Bird Communities ◽  
Avian Species ◽  
Universal Primers ◽  
Functional Roles ◽  
Detection And Identification ◽  
Miseq Platform

AbstractBirds play unique functional roles in the maintenance of ecosystems, such as pollina-tion and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthro-pogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with the Il-lumina MiSeq platform could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual detection and identification of bird species is difficult.

scholarly journals Environmental DNA enables detection of terrestrial mammals from forest pond water

2016 ◽  
Author(s):  
Masayuki Ushio ◽  
Hisato Fukuda ◽  
Toshiki Inoue ◽  
Kobayashi Makoto ◽  
Osamu Kishida ◽  
...  
Keyword(s):  
Water Samples ◽  
Cervus Nippon ◽  
Environmental Dna ◽  
Terrestrial Ecosystems ◽  
Illumina Miseq ◽  
Pcr Primers ◽  
Pond Water ◽  
Universal Primers ◽  
Taxonomic Assignment ◽  
Terrestrial Mammals

Terrestrial animals must have frequent contact with water to maintain their lives, implying that environmental DNA (eDNA) originating from terrestrial animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. After verifying the primers’ usefulness in silico and using water samples from zoo cages of animals with known species compositions, we collected five 500-ml water samples from ponds in two cool-temperate forests in Hokkaido, northern Japan. Using eDNA extracted from the water samples, we constructed amplicon libraries using MiMammal primers for Illumina MiSeq sequencing. MiMammal metabarcoding yielded a total of 75,214 reads, which we then subjected to data pre-processing and taxonomic assignment. We thereby detected species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Previous applications of the eDNA metabarcoding approach have mostly been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even in forest mammal biodiversity surveys.

scholarly journals eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

2020 ◽  
Author(s):  
Rebecca R Gehri ◽  
Wesley A. Larson ◽  
Kristen Gruenthal ◽  
Nicholas Sard ◽  
Yue Shi
Keyword(s):  
Community Composition ◽  
Lake Water ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Aquatic Systems ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Great Promise ◽  
Fish Diversity

AbstractUnderstanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (137 ha) in Michigan, USA from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Functional evenness of bird communities varies along the elevational gradient in Europe: Conservation implications

2019 ◽  
Author(s):  
Federico Morelli ◽  
Yanina
Keyword(s):  
Species Richness ◽  
Elevation Gradient ◽  
Bird Species ◽  
Elevational Gradient ◽  
Negative Association ◽  
Bird Communities ◽  
Breeding Bird ◽  
Bird Species Richness ◽  
Large Spatial Scale ◽  
Functional Evenness

ContextThe negative association between elevation and species richness is a well-recognized pattern in macro-ecology. ObjectivesThe aim of this study was to investigate changes in functional evenness of breeding bird communities along an elevation gradient in Europe. MethodsUsing the bird data from the EBCC Atlas of European Breeding Birds we estimated an index of functional evenness which can be assumed as a measure of the potential resilience of communities.ResultsOur findings confirm the existence of a negative association between elevation and bird species richness in all European eco regions. However, we also explored a novel aspect of this relationship, important for conservation: Our findings provide evidence at large spatial scale of a negative association between the functional evenness (potential community resilience) and elevation, independent of the eco region. We also found that the Natura2000 protected areas covers the territory most in need of protection, those characterized by bird communities with low potential resilience, in hilly and mountainous areas.ConclusionsThese results draw attention to European areas occupied by bird communities characterized by a potential lower capacity to respond to strong ecological changes, and, therefore, potentially more exposed to risks for conservation.

scholarly journals Prevalence and genetic diversity of avian haemosporidian parasites in wild bird species of the order Columbiformes

2021 ◽  
Author(s):  
Yvonne R. Schumm ◽  
Dimitris Bakaloudis ◽  
Christos Barboutis ◽  
Jacopo G. Cecere ◽  
Cyril Eraud ◽  
...  
Keyword(s):  
Host Species ◽  
Large Scale ◽  
Phylogenetic Reconstruction ◽  
Bird Species ◽  
Avian Species ◽  
Blood Parasites ◽  
Migration Strategy ◽  
Haemosporidian Parasites ◽  
Multiplex Pcr Assay ◽  
And Migration

AbstractDiseases can play a role in species decline. Among them, haemosporidian parasites, vector-transmitted protozoan parasites, are known to constitute a risk for different avian species. However, the magnitude of haemosporidian infection in wild columbiform birds, including strongly decreasing European turtle doves, is largely unknown. We examined the prevalence and diversity of haemosporidian parasites Plasmodium, Leucocytozoon and subgenera Haemoproteus and Parahaemoproteus in six species of the order Columbiformes during breeding season and migration by applying nested PCR, one-step multiplex PCR assay and microscopy. We detected infections in 109 of the 259 screened individuals (42%), including 15 distinct haemosporidian mitochondrial cytochrome b lineages, representing five H. (Haemoproteus), two H. (Parahaemoproteus), five Leucocytozoon and three Plasmodium lineages. Five of these lineages have never been described before. We discriminated between single and mixed infections and determined host species-specific prevalence for each parasite genus. Observed differences among sampled host species are discussed with reference to behavioural characteristics, including nesting and migration strategy. Our results support previous suggestions that migratory birds have a higher prevalence and diversity of blood parasites than resident or short-distance migratory species. A phylogenetic reconstruction provided evidence for H. (Haemoproteus) as well as H. (Parahaemoproteus) infections in columbiform birds. Based on microscopic examination, we quantified parasitemia, indicating the probability of negative effects on the host. This study provides a large-scale baseline description of haemosporidian infections of wild birds belonging to the order Columbiformes sampled in the northern hemisphere. The results enable the monitoring of future changes in parasite transmission areas, distribution and diversity associated with global change, posing a potential risk for declining avian species as the European turtle dove.

scholarly journals Bird communities in a degraded forest biodiversity hotspot of East Africa

2021 ◽  
Author(s):  
Moses Mulwa ◽  
Mike Teucher ◽  
Werner Ulrich ◽  
Jan Christian Habel
Keyword(s):  
Tropical Forests ◽  
Agricultural Land ◽  
Bird Species ◽  
Bird Communities ◽  
Natural Forest ◽  
Tree Plantations ◽  
Agricultural Fields ◽  
Degraded Forest ◽  
Forest Patches ◽  
Small Forest

AbstractTropical forests suffer severe habitat destruction. Thus, tropical forests frequently consist today of only a few small remnants that are often embedded within a matrix of agricultural fields and tree plantations. Forest specialist species have experienced severe population declines under these circumstances. We studied bird communities based on census plots set up in a near-natural forest block, as well as degraded forest patches, tree plantations, and agricultural fields, across the Taita Hills in southern Kenya. We classified each bird species according its ecology and behavior. We quantified the land cover and landscape configuration around each census plot. Typical forest species were mainly observed in the near-natural forest block, and to a lower extent in degraded forest patches. Plantations were almost devoid of birds. Bird communities of small forest fragments were more similar to that of agricultural land than the near-natural forest block. Most frugivorous, insectivorous and nectarivorous birds occurred in forest habitats, while granivorous bird species dominated the bird communities of agricultural land. The surrounding landscape had a marginal impact on bird species composition at local sites. Our study showed that the preservation of near-natural cloud forest, including small forest patches, is essential for the conservation of forest-dependent species, and that plantations do not serve as surrogate habitats.

scholarly journals Can clearcuts increase bird species richness in managed forests?

2008 ◽  
Vol 54 (No. 4) ◽  
pp. 189-193
Author(s):  
M. Żmihorski
Keyword(s):  
Species Richness ◽  
Bird Species ◽  
Bird Communities ◽  
Cumulative Number ◽  
Managed Forests ◽  
Managed Forest ◽  
Bird Species Richness ◽  
Forest Interior ◽  
Transect Counts ◽  
The Difference

Clearcuts are one of the results of forest management. The aim of this study was to assess the effect of clearcuts on bird communities in a managed forest in Western Poland. I applied the method of point transect counts. 20 points were located near clearcuts (less than 100 m from the nearest clearcut) and 25 points in the forest interior. In total, 36 bird species were recorded. On average, I found 9.20 bird species at points located near clearcuts and 6.72 species at points situated in the forest interior, and the difference was significant. The cumulative number of bird species for a given number of sampling points in the vicinity of clearcuts was higher than in the forest interior. The obtained results indicate that in managed, even-aged forests the generation of clearcuts can lead to an increase in local bird species richness.

A Multiplex PCR Assay Mediated by Universal Primers for the Detection of Adulterated Meat in Mutton

2019 ◽  
Vol 82 (2) ◽  
pp. 325-330 ◽  
Author(s):  
WANWAN LIU ◽  
XIAONAN WANG ◽  
JING TAO ◽  
BANGSHENG XI ◽  
MAN XUE ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Detection System ◽  
Meat Products ◽  
Pcr Primers ◽  
Rapid Identification ◽  
Food Samples ◽  
Detection Sensitivity ◽  
Universal Primers ◽  
Multiplex Pcr Assay ◽  
Multiple Pcr

ABSTRACT This study aimed to establish a multiplex PCR detection system mediated by “universal primers,” which would be able to determine whether mutton meat contained nonmutton ingredients from rats, foxes, and ducks. Based on the sequence variation of specific mitochondrial genes, nine different multiplex PCR primers were designed, and four kinds of meat products were rapidly identified by electrophoresis using an optimized multiplex PCR system based on the molecular weight differences of the amplified products. Multiplex PCR applications optimized for meat food source from food samples for testing was used to verify the accuracy of the identification method. The results showed that the primers in multiple PCR system mediated by universal primers could be used for the rapid identification of rat, fox, duck, and sheep meat in mutton products, and the detection sensitivity could reach 0.05 ng/μL. The identification of food samples validated the practical value of this method. Therefore, a multiplex PCR system mediated by universal primers was established, which can be used to quickly identify the origin of animal ingredients from rats, foxes, and ducks in mutton products.

Spring Bird Community Structure in Response to Habitat Heterogeneity in a Subtropical Hilly Landscape

2014 ◽  
Vol 1010-1012 ◽  
pp. 121-125
Author(s):  
Wen Bin Li ◽  
Zhi Ming Mo ◽  
Xing Ting Chen ◽  
Chun Huang ◽  
Ming Feng Xu
Keyword(s):  
Indicator Species ◽  
Habitat Heterogeneity ◽  
Southern China ◽  
Bird Species ◽  
Bird Communities ◽  
Bird Diversity ◽  
Indicator Species Analysis ◽  
Heterogeneous Habitats ◽  
Species Analysis ◽  
The Impact

To examine the impact of habitat heterogeneity on the bird communities, we investigated the structural differences of various bird communities occurring in heterogeneous habitats in the subtropical hilly areas of southern China. We used indicator Species Analysis (ISA) to test the association of specific bird species to particular habitats. We performed Two-way Cluster Analysis to find species patterning in response to habitat fragmentation. Our results demonstrated that heterogeneous habitats promoted bird diversity and human activities affected bird behavior. Indicator Species Analysis demonstrated that similar habitats had similar bird communities, while different habitats supported various bird indicator species. Although habitat diversity increased bird diversity of a region, it was unfavorable for the maintenance of specialized birds in the forests of the subtropical hilly area.

scholarly journals Bird communities in three forest types in the Pernambuco Centre of Endemism, Alagoas, Brazil

2013 ◽  
Vol 103 (2) ◽  
pp. 85-96 ◽  
Author(s):  
Lahert W. Lobo-Araújo ◽  
Mário T. F. Toledo ◽  
Márcio A. Efe ◽  
Ana C. M. Malhado ◽  
Marcos V. C. Vital ◽  
...  
Keyword(s):  
Species Richness ◽  
Bird Species ◽  
Bird Communities ◽  
Northeastern Brazil ◽  
Forest Fragments ◽  
Forest Types ◽  
Risk Of Extinction ◽  
Bird Fauna ◽  
Richness Patterns ◽  
Ombrophilous Forest

The Pernambuco Center of Endemism (PCE) in northeastern Brazil is highly fragmented and degraded. Despite its potential conservation importance the bird fauna in this area is still relatively unknown and there are many remnant fragments that have not been systematically surveyed. Here, we report the results of bird surveys in five forest fragments (one pioneer, two ombrophilous and two seasonal). In total, 162 taxa were recorded, 12 of which are endemic to the PCE. The frequency of endangered species was lower than what has been reported in studies from the same area and most of the taxa considered to be at risk of extinction were sub-species of uncertain taxonomic validity. The comparatively low number of endemic/threatened species may be due to the small size of the fragments in the present study - a consequence of the high levels of habitat loss in this region. Analysis of species richness patterns indicates that ombrophilous forest fragments are acting as refuges for those bird species that are most sensitive to environmental degradation.

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