scholarly journals Genetic signatures of ecological diversity along an urbanization gradient

2016 ◽  
Author(s):  
Ryan P. Kelly ◽  
James L O'Donnell ◽  
Natalie C. Lowell ◽  
Andrew O. Shelton ◽  
Jameal F. Samhouri ◽  
...  
Keyword(s):  
Life Histories ◽  
Environmental Science ◽  
Survey Methods ◽  
Environmental Dna ◽  
Biological Data ◽  
Ecological Communities ◽  
Human Land Use ◽  
Ecological Sampling ◽  
Genetic Signatures ◽  
Diversity Of Life

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

scholarly journals Genetic signatures of ecological diversity along an urbanization gradient

2016 ◽  
Author(s):  
Ryan P. Kelly ◽  
James L O'Donnell ◽  
Natalie C. Lowell ◽  
Andrew O. Shelton ◽  
Jameal F. Samhouri ◽  
...  
Keyword(s):  
Life Histories ◽  
Environmental Science ◽  
Survey Methods ◽  
Environmental Dna ◽  
Biological Data ◽  
Ecological Communities ◽  
Human Land Use ◽  
Ecological Sampling ◽  
Genetic Signatures ◽  
Diversity Of Life

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

scholarly journals Genetic signatures of ecological diversity along an urbanization gradient

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2444 ◽  
Author(s):  
Ryan P. Kelly ◽  
James L. O’Donnell ◽  
Natalie C. Lowell ◽  
Andrew O. Shelton ◽  
Jameal F. Samhouri ◽  
...  
Keyword(s):  
Life Histories ◽  
Environmental Science ◽  
Survey Methods ◽  
Environmental Dna ◽  
Biological Data ◽  
Ecological Communities ◽  
Human Land Use ◽  
Ecological Sampling ◽  
Genetic Signatures ◽  
Diversity Of Life

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.

Challenges for Diadromous Fishes in a Dynamic Global Environment

2009 ◽  
Keyword(s):  
Life Cycle ◽  
Life Histories ◽  
Life Cycles ◽  
Partial Migration ◽  
Environmental Stochasticity ◽  
Species Dynamics ◽  
Life Cycle Pattern ◽  
Aquatic Sciences ◽  
Diversity Of Life

<em>Abstract</em>.-In the study of species life histories and the structure of diadromous populations, an emerging trend is the prevalence of life cycle diversity-that is, individuals within populations that do not conform to a single life cycle pattern. A rapid rise in publications documenting within-population variability in life cycles has resulted in the use of numerous terms and phrases. We argue that myriad terms specific to taxa, ecosystem types, and applications are in fact describing the same phenomenon-life cycle diversity. This phenomenon has been obscured by the use of multiple terms across applications, but also by the overuse of typologies (i.e., anadromy, catadromy) that fail to convey the extent of life cycle variations that underlay population, metapopulation, and species dynamics. To illustrate this, we review migration and habitat-use terms that have been used to describe life cycles and life cycle variation. Using a citation index (Cambridge Scientific Abstracts © Aquatic Sciences and Fisheries Abstracts), terms were tallied across taxonomic family, ecosystem, type of application, analytical approach, and country of study. Studies on life cycle diversity have increased threefold during the past 15 years, with a total of 336 papers identified in this review. Most of the 40 terms we identified described either sedentary or migratory lifetime behaviors. The sedentary-migratory dichotomy fits well with the phenomenon of partial migration, which has been commonly reported for birds and Salmonidae and is postulated to be the result of early life thresholds (switch-points). On the other hand, the lexicon supports alternate modes of migration, beyond the simple sedentary-migratory dichotomy. Here more elaborate causal mechanisms such as the entrainment hypothesis may have application. Diversity of life cycles in fish populations, whether due to partial migration, entrainment, or other mechanisms, is increasingly recognized as having the effect of offsetting environmental stochasticity and contributing to long-term persistence.

scholarly journals Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics across a river catchment

2021 ◽  
Author(s):  
Rosetta C Blackman ◽  
Hsi-Cheng Ho ◽  
Jean-Claude Walser ◽  
Florian Altermatt
Keyword(s):  
Food Web ◽  
Environmental Dna ◽  
Ecological Communities ◽  
Food Web Structure ◽  
Spatial And Temporal Scales ◽  
Natural Systems ◽  
Α Diversity ◽  
Link Density ◽  
Spatio Temporal ◽  
Taxonomic Groups

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network through time using environmental DNA. We find contrasting biodiversity patterns, with richness (α-diversity) of fish increasing towards downstream positions within the catchment, while freshwater bacteria and invertebrates having an invariant and minimal decrease in richness, respectively, with downstream position. Food-web characteristics, such as link density and nestedness, however, were relatively conserved across space, but varied over season. Patterns of biodiversity across major taxonomic groups are thus not directly scalable to food-web structures at the same spatial and temporal scales, indicating that effective conservation measures must consider them jointly.

scholarly journals Environmental DNA sampling in a terrestrial environment: methods to detect a critically endangered frog and a global pathogen

2020 ◽  
Author(s):  
Thomas J. Burns ◽  
Nick Clemann ◽  
Anthony R. van Rooyen ◽  
Ben C. Scheele ◽  
Andrew R. Weeks ◽  
...  
Keyword(s):  
Field Experiments ◽  
Survey Methods ◽  
Environmental Dna ◽  
Wash Water ◽  
Critically Endangered ◽  
Chytrid Fungus ◽  
Amphibian Skin ◽  
Natural Habitats ◽  
Amphibian Species ◽  
Terrestrial Environment

AbstractEnvironmental DNA techniques have become established as a useful tool for biological monitoring and are used extensively to determine species presence in aquatic systems. However, their application in terrestrial systems has been more limited, likely in part due to difficulties in choosing where to sample and ensuring that collected DNA reflects current species presence. We developed methods to sample eDNA in the terrestrial environment and trialled them under controlled and field conditions. We targeted three species, an elusive critically endangered frog, an abundant non-threatened frog, and the globally distributed amphibian skin pathogen chytrid fungus, which has been implicated in the decline of over 500 amphibian species. We used a sandpaper-sampling surface to ‘trap’ DNA. After sampling, we washed the surface and filtered the wash water to gather material for DNA extraction and subsequent qPCR. Our controlled condition experiments demonstrated that frog and chytrid fungus DNA was detectable after as few as five contacts between a frog and the sampling surface. Furthermore, this DNA remained detectable after two weeks in cool, shaded, outdoor conditions. Our field experiments demonstrated that these techniques were transferable to natural habitats, where we detected both the common and rare amphibian target species, as well as chytrid fungus. Field sampling eDNA results were broadly consistent with those derived from conventional survey methods. Our methods have potential application in non-invasive sampling of amphibians and other species in terrestrial systems, broadening the applicability of eDNA techniques for species detection and monitoring.

scholarly journals Environmental DNA for the enumeration and management of Pacific salmon

2018 ◽  
Author(s):  
Taal Levi ◽  
Jennifer M. Allen ◽  
Donovan Bell ◽  
John Joyce ◽  
Joshua R. Russell ◽  
...  
Keyword(s):  
Stream Flow ◽  
Life Histories ◽  
Pacific Salmon ◽  
Environmental Dna ◽  
Flow Data ◽  
Counting Method ◽  
Daily Sampling ◽  
Fish Abundances ◽  
Management Challenge ◽  
Keystone Resource

AbstractPacific salmon are a keystone resource in Alaska, generating annual revenues of well over ∼US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.

Stable isotope analysis of eye lenses from invasive lionfish yields record of resource use

2020 ◽  
Vol 637 ◽  
pp. 181-194 ◽  
Author(s):  
JS Curtis ◽  
MA Albins ◽  
EB Peebles ◽  
CD Stallings
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Analysis ◽  
Resource Use ◽  
Life Histories ◽  
Trophic Position ◽  
Isotope Analysis ◽  
Eye Lens ◽  
Ecological Communities ◽  
Individual Fish ◽  
Analytical Approaches

Patterns of stable isotopes recorded in metabolically stable, serially synthesized, structures such as eye lenses can yield robust descriptions of resource use across the life histories of individual fish. We performed stable isotope analysis of eye lenses sampled from invasive lionfishes Pterois spp. and a potentially competitive native mesopredator, the graysby Cephalopholis cruentata, to compare lifelong patterns of trophic resource use on a coral reef ledge in Biscayne National Park, Florida, USA. In both lionfishes and graysby, stable isotope values increased logarithmically with eye-lens radius, likely reflecting increases in trophic position with growth. Tissue samples toward the interior of the lens were the most isotopically similar between lionfish and graysby, suggesting interspecific resource use overlap may be strongest in smaller fish. We observed substantial variation in isotopic chronologies around the underlying logarithmic trend within individual fish, potentially driven by patterns of movement across measured environmental isotopic gradients, intraspecific variation in resource use specificity, or other ecological variables of interest. These results are the first to describe patterns of size-structured resource use across the life of individual lionfish, an important objective for researchers studying the interactions of this highly invasive species with the surrounding ecological communities. Additionally, through this example, we illustrate analytical approaches and considerations for the application of eye-lens stable isotope analysis to the study of vertebrate ecology.

Monitoring post-release survival of the northern corroboree frog, Pseudophryne pengilleyi, using environmental DNA

2018 ◽  
Vol 45 (7) ◽  
pp. 620 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne Gleeson ◽  
Elise M. Furlan
Keyword(s):  
Water Samples ◽  
Survey Methods ◽  
Quantitative Polymerase Chain Reaction ◽  
Environmental Dna ◽  
Life Stages ◽  
Breeding Programs ◽  
Non Invasive ◽  
Naturally Occurring ◽  
Cause Of Failure

Context Translocations are becoming an increasingly important conservation tool to combat rising levels of species extinction. Unfortunately, many translocation efforts fail; yet, the timing and cause of failure often remain unknown. Monitoring individuals in the days and weeks following release can provide valuable information on their capacity to survive this initial hurdle. In Australia, breeding programs have been established for the endangered northern corroboree frog, Pseudophryne pengilleyi, to enable reintroduction to the wild via captive-reared individuals, typically, early life stages such as eggs or juvenile frogs that cannot be monitored via traditional survey methods that target adult frogs (e.g. shout–response). Environmental DNA (eDNA) detects trace amounts of DNA that organisms release into their environment and could provide a means to infer population persistence for wildlife releases and translocations. Aims In the present study, we aim to develop an eDNA assay capable of detecting both sexes of P. pengilleyi across multiple life stages, and use it to monitor their survival. Methods An eDNA assay was developed to target the two corroboree frog species (P. pengilleyi and P. corroboree, the southern corroboree frog) and was tested for its sensitivity and specificity in silico and in vitro. Pseudophryne pengilleyi eggs were released into three naturally occurring ponds and water samples were, subsequently, collected from each pond on several occasions over a period of 78 days. Quantitative polymerase chain reaction was used to detect P. pengilleyi eDNA from water samples. Key Results The developed assay was shown to be sensitive and specific to corroboree frogs. eDNA monitoring of reintroduced P. pengilleyi detected the species’ DNA at three of three release ponds and DNA remained detectable until at least 78 days post-release at two of three ponds. Conclusions We show how the development of a corroboree frog-specific assay allowed us to monitor the post-release survival of P. pengilleyi in naturally occurring pools. Implications eDNA surveys may provide a useful tool to monitor post-release survival of translocated populations in a non-invasive manner, with the potential to identify the timing and causes of failure. Such knowledge can be used to inform the management of translocated populations and future release strategies.

scholarly journals Noninvasive Method for a Statewide Survey of Eastern HellbendersCryptobranchus alleganiensisUsing Environmental DNA

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Amy J. Santas ◽  
Tyler Persaud ◽  
Barbara A. Wolfe ◽  
Jenise M. Bauman
Keyword(s):  
Population Density ◽  
Survey Methods ◽  
Aquatic Organisms ◽  
Environmental Dna ◽  
Specific Primers ◽  
Filtration Time ◽  
Sampling Protocols ◽  
Welfare Implications ◽  
Historical Accounts ◽  
Eastern Hellbender

Traditional survey methods of aquatic organisms may be difficult, lengthy, and destructive to the habitat. Some methods are invasive and can be harmful to the target species. The use of environmental DNA (eDNA) has proven to be effective at detecting low population density aquatic macroorganisms. This study refined the technique to support statewide surveys. Hellbender presence was identified by using hellbender specific primers (cytochrome b gene) to detect eDNA in water samples collected at rivers, streams and creeks in Ohio and Kentucky with historical accounts of the imperiled eastern hellbender (Cryptobranchus a. alleganiensis). Two sampling protocols are described; both significantly reduced the amount of water required for collection from the previously described 6 L collection. Two-liter samples were adequate to detect hellbender presence in natural waterways where hellbenders have been previously surveyed in both Ohio and Kentucky—1 L samples were not reliable. DNA extracted from 3 L of water collected onto multiple filters (1 L/filter) could be combined and concentrated through ethanol precipitation, supporting amplification of hellbender DNA and dramatically reducing the filtration time. This method improves the efficiency and welfare implications of sampling methods for reclusive aquatic species of low population density for statewide surveys that involve collecting from multiple watersheds.

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