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

2018 ◽  
Author(s):  
Lynsey R. Harper ◽  
Lori Lawson Handley ◽  
Christoph Hahn ◽  
Neil Boonham ◽  
Helen C. Rees ◽  
...  
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Gasterosteus Aculeatus ◽  
Abiotic Factors ◽  
Environmental Dna ◽  
Hypothesis Generation ◽  
Vertebrate Species ◽  
Mammal Species ◽  
Negatively Associated ◽  
Fulica Atra

AbstractEnvironmental DNA (eDNA) metabarcoding is revolutionising biodiversity monitoring, but has unrealised potential for ecological hypothesis generation and testing. Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T. cristatus detection at the pondscape. Furthermore, we test the status of T. cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T. cristatus and higher T. cristatus Habitat Suitability Index (HSI) scores. T. cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T. cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). T. cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus) and ninespine stickleback (Pungitius pungitius) were identified. T. cristatus detection was negatively correlated with mammal species richness, and T. cristatus was negatively associated with grey squirrel (Sciurus carolinensis). T. cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T. cristatus survey. Vertebrate species richness was significantly higher in T. cristatus ponds and broadly increased as T. cristatus HSI scores increased. We reaffirm reported associations (e.g. T. cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T. cristatus. Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring and research.

scholarly journals Testing biodiversity theory using species richness of reef-building corals across a depth gradient

2019 ◽  
Vol 15 (10) ◽  
pp. 20190493 ◽  
Author(s):  
T. Edward Roberts ◽  
Sally A. Keith ◽  
Carsten Rahbek ◽  
Tom C. L. Bridge ◽  
M. Julian Caley ◽  
...  
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Coral Species ◽  
Environmental Gradients ◽  
Abiotic Factors ◽  
Empirical Support ◽  
Null Model ◽  
Local Scale ◽  
Small Scale ◽  
Energy Availability

Natural environmental gradients encompass systematic variation in abiotic factors that can be exploited to test competing explanations of biodiversity patterns. The species–energy (SE) hypothesis attempts to explain species richness gradients as a function of energy availability. However, limited empirical support for SE is often attributed to idiosyncratic, local-scale processes distorting the underlying SE relationship. Meanwhile, studies are also often confounded by factors such as sampling biases, dispersal boundaries and unclear definitions of energy availability. Here, we used spatially structured observations of 8460 colonies of photo-symbiotic reef-building corals and a null-model to test whether energy can explain observed coral species richness over depth. Species richness was left-skewed, hump-shaped and unrelated to energy availability. While local-scale processes were evident, their influence on species richness was insufficient to reconcile observations with model predictions. Therefore, energy availability, either in isolation or in combination with local deterministic processes, was unable to explain coral species richness across depth. Our results demonstrate that local-scale processes do not necessarily explain deviations in species richness from theoretical models, and that the use of idiosyncratic small-scale factors to explain large-scale ecological patterns requires the utmost caution.

scholarly journals Environmental DNA for tracking waterhole visitation in savanna ecosystems

2020 ◽  
Author(s):  
Maxwell J. Farrell ◽  
Danny Govender ◽  
Mehrdad Hajibabaei ◽  
Michelle van der Bank ◽  
T. Jonathan Davies
Keyword(s):  
Large Scale ◽  
Environmental Dna ◽  
Camera Traps ◽  
Specific Reference ◽  
Arid Environments ◽  
Reference Library ◽  
Mammal Species ◽  
Biodiversity Indicator ◽  
Detection Rates

AbstractThe analysis of waterborne environmental DNA (eDNA) is effective for detecting invasive species and conducting large-scale biodiversity assessments, making it a potentially powerful tool for documenting diversity at sites where large numbers of species aggregate. We explore the utility of eDNA from waterholes for describing local mammal communities, quantifying patterns of species co-occurrences, and monitoring of rare or threatened species. In savanna ecosystems water can be a scarce resource during dry seasons and in periods of drought, promoting the aggregation of medium to large mammals. To explore the reliability of eDNA as a biodiversity indicator in these arid and semi-arid environments, we compare eDNA metabarcoding and camera traps for documenting waterhole use by mammals in the Kruger National Park, South Africa. We find that eDNA metabarcoding can recover the majority of mammal species detected in camera traps, but the DNA signatures of mammal visitation are temporally limited. Detection rates varied across sites, sampling time, species, and choice of reference library, with the best performance for water-dependent large bodied mammals visiting within two days of sampling, and matched to a curated system-specific reference library. Our results demonstrate that eDNA-based approaches can be used to track mammals of conservation concern, and reflect patterns of recent waterhole use and co-occurrence across water-dependent species, but also highlight limitations including the lack of long-term eDNA persistence in small and highly utilized waterholes and variability in detection rates among species. Sequencing of eDNA is a valuable tool for next-generation biodiversity sampling and has many exciting applications, but it is not sufficient to capture long-term waterhole visitation patterns or reliably detect rare and small-bodied species.

scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

2021 ◽  
Vol 5 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schütz ◽  
Jens Arle ◽  
Arne J. Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Environmental Dna ◽  
Federal State ◽  
Vertebrate Species ◽  
Biodiversity Monitoring ◽  
Species Detection ◽  
Terrestrial Species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

scholarly journals Large-scale assessment of commensalistic–mutualistic associations between African birds and herbivorous mammals using internet photos

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4520 ◽  
Author(s):  
Peter Mikula ◽  
Jiří Hadrava ◽  
Tomáš Albrecht ◽  
Piotr Tryjanowski
Keyword(s):  
Species Richness ◽  
Body Mass ◽  
Information Technologies ◽  
Large Scale ◽  
Bird Species ◽  
Null Model ◽  
Herd Size ◽  
Mammal Species ◽  
African Mammals ◽  
Herbivorous Mammals

Birds sitting or feeding on live large African herbivorous mammals are a visible, yet quite neglected, type of commensalistic–mutualistic association. Here, we investigate general patterns in such relationships at large spatial and taxonomic scales. To obtain large-scale data, an extensive internet-based search for photos was carried out on Google Images. To characterize patterns of the structural organization of commensalistic–mutualistic associations between African birds and herbivorous mammals, we used a network analysis approach. We then employed phylogenetically-informed comparative analysis to explore whether features of bird visitation of mammals, i.e., their mean number, mass and species richness per mammal species, are shaped by a combination of host mammal (body mass and herd size) and environmental (habitat openness) characteristics. We found that the association web structure was only weakly nested for commensalistic as well as for mutualistic birds (oxpeckers Buphagus spp.) and African mammals. Moreover, except for oxpeckers, nestedness did not differ significantly from a null model indicating that birds do not prefer mammal species which are visited by a large number of bird species. In oxpeckers, however, a nested structure suggests a non-random assignment of birds to their mammal hosts. We also identified some new or rare associations between birds and mammals, but we failed to find several previously described associations. Furthermore, we found that mammal body mass positively influenced the number and mass of birds observed sitting on them in the full set of species (i.e., taking oxpeckers together with other bird species). We also found a positive correlation between mammal body mass and mass of non-oxpecker species as well as oxpeckers. Mammal herd size was associated with a higher mass of birds in the full set of species as well as in non-oxpecker species, and mammal species living in larger herds also attracted more bird species in the full set of species. Habitat openness influenced the mass of birds sitting on mammals as well as the number of species recorded sitting on mammals in the full set of species. In non-oxpecker species habitat openness was correlated with the bird number, mass and species richness. Our results provide evidence that patterns of bird–mammal associations can be linked to mammal and environmental characteristics and highlight the potential role of information technologies and new media in further studies of ecology and evolution. However, further study is needed to get a proper insight into the biological and methodological processes underlying the observed patterns.

scholarly journals Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

2021 ◽  
Author(s):  
Holly A. Broadhurst ◽  
Luke M. Gregory ◽  
Emma K. Bleakley ◽  
Joseph C. Perkins ◽  
Jenna V. Lavin ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Environmental Dna ◽  
Community Diversity ◽  
Individual Species ◽  
Sampling Effort ◽  
Mammal Species ◽  
Terrestrial Mammals ◽  
Β Diversity

AbstractAimFinding more efficient ways to monitor, and estimate the diversity of, mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Yet, most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. In this study, we focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding rivers.LocationSoutheastern EnglandMethodsWe used eDNA metabarcoding on water samples collected along two rivers and a beaver enclosure over two days, targeting terrestrial and semi-aquatic mammals. Mammalian community diversity and composition was assessed based on species richness and β-diversity. Differences between river communities were calculated and partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling.ResultseDNA metabarcoding efficiently detected 25 wild mammal species from five orders in two days of sampling, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorph species) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers.Main conclusionseDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

scholarly journals Influence of the environmental factors on species diversity and quantitative development of zoobenthos in the Neva Bay

2018 ◽  
Vol 322 (1) ◽  
pp. 50-65
Author(s):  
E.V. Balushkina ◽  
M.S. Golubkov
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Primary Production ◽  
Large Scale ◽  
Structural Characteristics ◽  
Abiotic Factors ◽  
Chlorophyll Concentration ◽  
Benthic Fauna ◽  
Anthropogenic Stress ◽  
Neva Bay

Hydrochemical characteristics, primary production of plankton, taxonomic composition, species richness, species diversity and quantitative characteristics of the benthic fauna of the Neva Bay had been collected and analyzed at the end of July and the very beginning of August 2003–2012 by the method stepwise regression, calculated equations with a free constant. Effects of biotic and abiotic factors on the structural and functional characteristics of benthic communities in the Neva Bay were evaluated using multiregression analysis. Research period had been accompanied by revival of industry of Saint-Petersburg, construction of ports, active navigation, development of Sea facade and completion of the construction of the St. Petersburg Flood Prevention Facility Complex and a large-scale hydrotechnical works: building of a Marine Multifunctional Reloading Complex (MMRC) “Bronka” and approach fairway to it. Results of statistical analysis showed that the number of species and species diversity of bottom animals in the Neva Bay declined with increased primary production and chlorophyll a concentration. Analysis of the factors influencing the values of biomass of benthic animal communities shows that these characteristics increased with growing chlorophyll concentration. During the anthropogenic stress of 2006–2007, the existing links between the structural characteristics of the zoobenthos and the functional biotic characteristics of the Neva Bay were completely destroyed. Restoration period 2008–2012 was accompanied by an increase in the species richness and species diversity of zoobenthos to the level observed before anthropogenic stress.

scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

2021 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schuetz ◽  
Jens Arle ◽  
Arne J. Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Environmental Dna ◽  
Federal State ◽  
Vertebrate Species ◽  
Biodiversity Monitoring ◽  
Species Detection ◽  
Terrestrial Species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can often collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24%, and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 69% and 84%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called 'bycatch'. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

Large-scale mapping of the catenas vegetation in Subarctic tundra

1995 ◽  
pp. 3-21
Author(s):  
S. S. Kholod
Keyword(s):  
Spatial Distribution ◽  
Vegetation Cover ◽  
Large Scale ◽  
Block Diagram ◽  
Abiotic Factors ◽  
Ecological Factors ◽  
Spatial Arrangement ◽  
Geological Time ◽  
Ecological Barriers ◽  
Functional Zones

One of the most difficult tasks in large-scale vegetation mapping is the clarification of mechanisms of the internal integration of vegetation cover territorial units. Traditional way of searching such mechanisms is the study of ecological factors controlling the space heterogeneity of vegetation cover. In essence, this is autecological analysis of vegetation. We propose another way of searching the mechanisms of territorial integration of vegetation. It is connected with intracoenotic interrelation, in particular, with the changing role of edificator synusium in a community along the altitudinal gradient. This way of searching is illustrated in the model-plot in subarctic tundra of Central Chukotka. Our further suggestion concerns the way of depicting these mechanisms on large-scale vegetation map. As a model object we chose the catena, that is the landscape formation including all geomorphjc positions of a slope, joint by the process of moving the material down the slope. The process of peneplanation of a mountain system for a long geological time favours to the levelling the lower (accumulative) parts of slopes. The colonization of these parts of the slope by the vegetation variants, corresponding to the lowest part of catena is the result of peneplanation. Vegetation of this part of catena makes a certain biogeocoenotic work which is the levelling of the small infralandscape limits and of the boundaries in vegetation cover. This process we name as the continualization on catena. In this process the variants of vegetation in the lower part of catena are being broken into separate synusiums. This is the process of decumbation of layers described by V. B. Sochava. Up to the slope the edificator power of the shrub synusiums sharply decreases. Moss and herb synusium have "to seek" the habitats similar to those under the shrub canopy. The competition between the synusium arises resulting in arrangement of a certain spatial assemblage of vegetation cover elements. In such assemblage the position of each element is determined by both biotic (interrelation with other coenotic elements) and abiotic (presence of appropriate habitats) factors. Taking into account the biogeocoenotic character of the process of continualization on catena we name such spatial assemblage an exolutionary-biogeocoenotic series. The space within each evolutionary-biogeocoenotic series is divided by ecological barriers into some functional zones. In each of the such zones the struggle between synusiums has its individual expression and direction. In the start zone of catena (extensive pediment) the interrelations of synusiums and layers control the mutual spatial arrangement of these elements at the largest extent. Here, as a rule, there predominate edificator synusiums of low and dwarfshrubs. In the first order limit zone (the bend of pediment to the above part of the slope) one-species herb and moss synusiums, oftenly substituting each other in similar habitats, get prevalence. In the zone of active colonization of slope (denudation slope) the coenotic factor has the least role in the spatial distribution of the vegetation cover elements. In particular, phytocoenotic interactions take place only within separate microcoenoses of herbs, mosses and lichens. In the zone of the attenuation of continualization process (the upper most parts of slope, crests) phytocoenotic interactions are almost absent and the spatial distribution of vegetation cover elements depends exclusively on the abiotic factors. The principal scheme of the distribution of vegetation cover elements and the disposition of functional zones on catena are shown on block-diagram (fig. 1).

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