Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an... more Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.
1. Species population dynamics are driven by spatial and temporal changes in the environment, ant... more 1. Species population dynamics are driven by spatial and temporal changes in the environment, anthropogenic activities, and conservation management actions. Understanding how populations will change in response to these drivers is fundamental to a wide range of ecological applications, but there are few open-source software options accessible to researchers and managers that allow them to predict these changes in a flexible and transparent way. 2. We introduce an open-source, multi-platform R package, steps, that models spatial changes in species populations as a function of drivers of distribution and abundance, such as climate, disturbance, landscape dynamics, and species ecological and physiological requirements.
Lizards and snakes (squamate reptiles) are the most diverse vertebrate group in Australia, with a... more Lizards and snakes (squamate reptiles) are the most diverse vertebrate group in Australia, with approximately 1000 described species, representing about 10% of the global squamate diversity. Squamates are a vital part of the Australian ecosystem, but their conservation has been hindered by a lack of knowledge of their diversity, distribution, biology and key threats. The Action Plan for Australian Lizards and Snakes 2017 provides the first comprehensive assessment of the conservation status of Australian squamates in 25 years. Conservation assessments are provided for 986 species of Australian lizards and snakes (including sea snakes). Over the past 25 years there has been a substantial increase in the number of species and families recognised within Australia. There has also been an increase in the range and magnitude of threatening processes with the potential to impact squamates. This has resulted in an increase in the proportion of the Australian squamate fauna that is considere...
A critical step towards reducing the incidence of extinction is to identify and rank the species ... more A critical step towards reducing the incidence of extinction is to identify and rank the species at highest risk, while implementing protective measures to reduce the risk of extinction to such species. Existing global processes provide a graded categorisation of extinction risk. Here we seek to extend and complement those processes to focus more narrowly on the likelihood of extinction of the most imperilled Australian birds and mammals. We considered an extension of existing IUCN and NatureServe criteria, and used expert elicitation to rank the extinction risk to the most imperilled species, assuming current management. On the basis of these assessments, and using two additional approaches, we estimated the number of extinctions likely to occur in the next 20 years. The estimates of extinction risk derived from our tighter IUCN categorisations, NatureServe assessments and expert elicitation were poorly correlated, with little agreement among methods for which species were most in ...
information, and considered more realistic scenarios and constraints. Active engagement with prac... more information, and considered more realistic scenarios and constraints. Active engagement with practitioners led to productive revisions of a model that estimates the effectiveness of a landscape barrier to contain spread of the invasive cane toad Rhinella marina. Benefits also include greater confidence in model predictions, improving our assessment of the cost and feasibility of containing the spread of toads.
Effective management of alien species requires detecting populations in the early stages of invas... more Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental variables (water depth, rainfall, ambient temperature) were not clearly correlated with detection probabilities estimated via trapping, whereas eDNA detection probabilities were negatively correlated with water depth, possibly reflecting higher eDNA concentrations at lower water levels. Our findings demonstrate that eDNA sampling can be an order of magnitude more sensitive than traditional methods, and illustrate that traditional-and eDNA-based surveys can provide independent information on species distributions when occupancy surveys are conducted over short timescales.
Darwin's naturalization hypothesis predicts that the success of alien invaders will decrease with... more Darwin's naturalization hypothesis predicts that the success of alien invaders will decrease with increasing taxonomic similarity to the native community. Alternatively, shared traits between aliens and the native assemblage may preadapt aliens to their novel surroundings, thereby facilitating establishment (the preadaptation hypothesis). Here we examine successful and failed introductions of amphibian species across the globe and find that the probability of successful establishment is higher when congeneric species are present at introduction locations and increases with increasing congener species richness. After accounting for positive effects of congeners, residence time, and propagule pressure, we also find that invader establishment success is higher on islands than on mainland areas and is higher in areas with abiotic conditions similar to the native range. These findings represent the first example in which the preadaptation hypothesis is supported in organisms other than plants and suggest that preadaptation has played a critical role in enabling introduced species to succeed in novel environments.
Proceedings. Biological sciences / The Royal Society, Jan 24, 2016
The impact of an invasive species depends upon the extent of area across which it ultimately spre... more The impact of an invasive species depends upon the extent of area across which it ultimately spreads. A powerful strategy for limiting impact, then, is to limit spread, and this can most easily be achieved by managing or reinforcing natural barriers to spread. Using a simulation model, we show that rapid evolutionary increases in dispersal can render permeable an otherwise effective barrier. On the other hand, we also show that, once the barrier is reached, and if it holds, resultant evolutionary decreases in dispersal rapidly make the barrier more effective. Finally, we sketch a strategy-the genetic backburn-in which low-dispersal individuals from the range core are translocated to the nearside of the barrier ahead of the oncoming invasion. We find that the genetic backburn-by preventing invasion front genotypes reaching the barrier, and hastening the evolutionary decrease in dispersal-can make barriers substantially more effective. In our simulations, the genetic backburn never re...
Herpetological Conservation and Biology, Apr 1, 2009
Recent studies have highlighted negative effects of agricultural activity on populations of the W... more Recent studies have highlighted negative effects of agricultural activity on populations of the Wood Turtle (Glyptemys insculpta). Mitigating effects of agriculture on this imperiled species will require a thorough understanding of sexual and spatio-temporal differences in the use of fields by turtles. We investigated these factors using radio-telemetry data collected at the northeastern limit of the species' range in Nova Scotia, Canada. Males used hayfields more frequently and for a greater proportion of the active season than did females, exposing them to greater risk of machineryrelated mortality. Maintaining 43 m riparian buffer zones would protect males 95% of the time, although such buffers would encompass less than 65% of female movements. The only two mortalities recorded in our study were males. Perhaps more importantly, these males were killed during the second harvest, illustrating that the recommendations of a previous study, which suggested that disc mower blades be raised only during the first harvest, might not apply throughout the species' range. Possible strategies for conserving Wood Turtles within agricultural landscapes are discussed.
ABSTRACT A series of 1,4-di-[2-aryl-1-diazenyl]-2-methylpiperazines (4a–n) have been synthesized ... more ABSTRACT A series of 1,4-di-[2-aryl-1-diazenyl]-2-methylpiperazines (4a–n) have been synthesized by the reaction of 2-methylpiperazine with 2 equiv. of the appropriate diazonium salt. The products have been characterized by IR and NMR spectroscopy, and the molecular composition has been verified by HR-EIMS, with accurate mass measurement of the molecular ion. The presence of a chiral centre at C2 of the piperazine ring in the bistriazene 4 creates a multitude of diastereotopic protons in the methylene groups of the piperazine ring, as evidenced by the complexity of the NMR spectra, which nevertheless can be fully assigned in some cases, such as the tolyl- (4h) and phenyl- (4j) derivatives. These two compounds also show a discrimination between the two N-arydiazenyl groups, as evidenced by the doubling of several aromatic-carbon signals in the 13C NMR spectra. The assignment of the proton and carbon signals in 4h and 4j has been aided by the use of 2D NMR spectroscopy. A DEPT spectrum of 4j clearly discriminates the methylene carbons and also indicates the methine carbons of the piperazine ring. COSY spectra provide clear information about the interactions between diastereotopic protons; when these results are combined with the results of HSQC spectroscopy, the proton and carbon signals can be fully correlated, leading to an unequivocal assignment of the proton and carbon atoms of the piperazine ring. The HSQC spectrum of 4j also gives a complete correlation of the aromatic-proton and -carbon signals. These results compare favorably with the previously reported assignments of proton and carbon signals for triazenes of type 1 and bistriazenes of type 3.Key words: triazene, bistriazene, piperazine, 2-methylpiperazine, diastereotopic protons, diazonium coupling, 2D NMR, COSY, DEPT, HSQC.
Environmental DNA (eDNA) sampling is prone to both false positive and false negative errors. We r... more Environmental DNA (eDNA) sampling is prone to both false positive and false negative errors. We review statistical methods to account for such errors in the analysis of eDNA data, and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad-hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability, and false positive rates. We advocate alternative approaches to account for false positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false positive errors. We illustrate the advantages of these approaches over ad-hoc classifications of detec...
Ecological applications : a publication of the Ecological Society of America, 2015
Effective management of alien species requires detecting populations in the early stages of invas... more Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental var...
Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an... more Environmental DNA, or eDNA—DNA shed from organisms and extracted from environmental samples—is an emerging survey technique that has the potential to transform biodiversity monitoring in freshwater ecosystems. We provide a brief overview of the primary methodological aspects of eDNA sampling that ecologists should consider before taking environmental samples in the field. We outline five key methodological considerations: (i) targeting single species vs multiple species; (ii) where and when to sample; (iii) how much water to collect; (iv) how many samples to take; and (v) recognising potential sources of false positives. The need to account for false negatives and false positives in eDNA surveys, and the power of species occupancy detection models in accounting for imperfect detection, is also discussed.
1. Species population dynamics are driven by spatial and temporal changes in the environment, ant... more 1. Species population dynamics are driven by spatial and temporal changes in the environment, anthropogenic activities, and conservation management actions. Understanding how populations will change in response to these drivers is fundamental to a wide range of ecological applications, but there are few open-source software options accessible to researchers and managers that allow them to predict these changes in a flexible and transparent way. 2. We introduce an open-source, multi-platform R package, steps, that models spatial changes in species populations as a function of drivers of distribution and abundance, such as climate, disturbance, landscape dynamics, and species ecological and physiological requirements.
Lizards and snakes (squamate reptiles) are the most diverse vertebrate group in Australia, with a... more Lizards and snakes (squamate reptiles) are the most diverse vertebrate group in Australia, with approximately 1000 described species, representing about 10% of the global squamate diversity. Squamates are a vital part of the Australian ecosystem, but their conservation has been hindered by a lack of knowledge of their diversity, distribution, biology and key threats. The Action Plan for Australian Lizards and Snakes 2017 provides the first comprehensive assessment of the conservation status of Australian squamates in 25 years. Conservation assessments are provided for 986 species of Australian lizards and snakes (including sea snakes). Over the past 25 years there has been a substantial increase in the number of species and families recognised within Australia. There has also been an increase in the range and magnitude of threatening processes with the potential to impact squamates. This has resulted in an increase in the proportion of the Australian squamate fauna that is considere...
A critical step towards reducing the incidence of extinction is to identify and rank the species ... more A critical step towards reducing the incidence of extinction is to identify and rank the species at highest risk, while implementing protective measures to reduce the risk of extinction to such species. Existing global processes provide a graded categorisation of extinction risk. Here we seek to extend and complement those processes to focus more narrowly on the likelihood of extinction of the most imperilled Australian birds and mammals. We considered an extension of existing IUCN and NatureServe criteria, and used expert elicitation to rank the extinction risk to the most imperilled species, assuming current management. On the basis of these assessments, and using two additional approaches, we estimated the number of extinctions likely to occur in the next 20 years. The estimates of extinction risk derived from our tighter IUCN categorisations, NatureServe assessments and expert elicitation were poorly correlated, with little agreement among methods for which species were most in ...
information, and considered more realistic scenarios and constraints. Active engagement with prac... more information, and considered more realistic scenarios and constraints. Active engagement with practitioners led to productive revisions of a model that estimates the effectiveness of a landscape barrier to contain spread of the invasive cane toad Rhinella marina. Benefits also include greater confidence in model predictions, improving our assessment of the cost and feasibility of containing the spread of toads.
Effective management of alien species requires detecting populations in the early stages of invas... more Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental variables (water depth, rainfall, ambient temperature) were not clearly correlated with detection probabilities estimated via trapping, whereas eDNA detection probabilities were negatively correlated with water depth, possibly reflecting higher eDNA concentrations at lower water levels. Our findings demonstrate that eDNA sampling can be an order of magnitude more sensitive than traditional methods, and illustrate that traditional-and eDNA-based surveys can provide independent information on species distributions when occupancy surveys are conducted over short timescales.
Darwin's naturalization hypothesis predicts that the success of alien invaders will decrease with... more Darwin's naturalization hypothesis predicts that the success of alien invaders will decrease with increasing taxonomic similarity to the native community. Alternatively, shared traits between aliens and the native assemblage may preadapt aliens to their novel surroundings, thereby facilitating establishment (the preadaptation hypothesis). Here we examine successful and failed introductions of amphibian species across the globe and find that the probability of successful establishment is higher when congeneric species are present at introduction locations and increases with increasing congener species richness. After accounting for positive effects of congeners, residence time, and propagule pressure, we also find that invader establishment success is higher on islands than on mainland areas and is higher in areas with abiotic conditions similar to the native range. These findings represent the first example in which the preadaptation hypothesis is supported in organisms other than plants and suggest that preadaptation has played a critical role in enabling introduced species to succeed in novel environments.
Proceedings. Biological sciences / The Royal Society, Jan 24, 2016
The impact of an invasive species depends upon the extent of area across which it ultimately spre... more The impact of an invasive species depends upon the extent of area across which it ultimately spreads. A powerful strategy for limiting impact, then, is to limit spread, and this can most easily be achieved by managing or reinforcing natural barriers to spread. Using a simulation model, we show that rapid evolutionary increases in dispersal can render permeable an otherwise effective barrier. On the other hand, we also show that, once the barrier is reached, and if it holds, resultant evolutionary decreases in dispersal rapidly make the barrier more effective. Finally, we sketch a strategy-the genetic backburn-in which low-dispersal individuals from the range core are translocated to the nearside of the barrier ahead of the oncoming invasion. We find that the genetic backburn-by preventing invasion front genotypes reaching the barrier, and hastening the evolutionary decrease in dispersal-can make barriers substantially more effective. In our simulations, the genetic backburn never re...
Herpetological Conservation and Biology, Apr 1, 2009
Recent studies have highlighted negative effects of agricultural activity on populations of the W... more Recent studies have highlighted negative effects of agricultural activity on populations of the Wood Turtle (Glyptemys insculpta). Mitigating effects of agriculture on this imperiled species will require a thorough understanding of sexual and spatio-temporal differences in the use of fields by turtles. We investigated these factors using radio-telemetry data collected at the northeastern limit of the species' range in Nova Scotia, Canada. Males used hayfields more frequently and for a greater proportion of the active season than did females, exposing them to greater risk of machineryrelated mortality. Maintaining 43 m riparian buffer zones would protect males 95% of the time, although such buffers would encompass less than 65% of female movements. The only two mortalities recorded in our study were males. Perhaps more importantly, these males were killed during the second harvest, illustrating that the recommendations of a previous study, which suggested that disc mower blades be raised only during the first harvest, might not apply throughout the species' range. Possible strategies for conserving Wood Turtles within agricultural landscapes are discussed.
ABSTRACT A series of 1,4-di-[2-aryl-1-diazenyl]-2-methylpiperazines (4a–n) have been synthesized ... more ABSTRACT A series of 1,4-di-[2-aryl-1-diazenyl]-2-methylpiperazines (4a–n) have been synthesized by the reaction of 2-methylpiperazine with 2 equiv. of the appropriate diazonium salt. The products have been characterized by IR and NMR spectroscopy, and the molecular composition has been verified by HR-EIMS, with accurate mass measurement of the molecular ion. The presence of a chiral centre at C2 of the piperazine ring in the bistriazene 4 creates a multitude of diastereotopic protons in the methylene groups of the piperazine ring, as evidenced by the complexity of the NMR spectra, which nevertheless can be fully assigned in some cases, such as the tolyl- (4h) and phenyl- (4j) derivatives. These two compounds also show a discrimination between the two N-arydiazenyl groups, as evidenced by the doubling of several aromatic-carbon signals in the 13C NMR spectra. The assignment of the proton and carbon signals in 4h and 4j has been aided by the use of 2D NMR spectroscopy. A DEPT spectrum of 4j clearly discriminates the methylene carbons and also indicates the methine carbons of the piperazine ring. COSY spectra provide clear information about the interactions between diastereotopic protons; when these results are combined with the results of HSQC spectroscopy, the proton and carbon signals can be fully correlated, leading to an unequivocal assignment of the proton and carbon atoms of the piperazine ring. The HSQC spectrum of 4j also gives a complete correlation of the aromatic-proton and -carbon signals. These results compare favorably with the previously reported assignments of proton and carbon signals for triazenes of type 1 and bistriazenes of type 3.Key words: triazene, bistriazene, piperazine, 2-methylpiperazine, diastereotopic protons, diazonium coupling, 2D NMR, COSY, DEPT, HSQC.
Environmental DNA (eDNA) sampling is prone to both false positive and false negative errors. We r... more Environmental DNA (eDNA) sampling is prone to both false positive and false negative errors. We review statistical methods to account for such errors in the analysis of eDNA data, and use simulations to compare the performance of different modelling approaches. Our simulations illustrate that even low false positive rates can produce biased estimates of occupancy and detectability. We further show that removing or classifying single PCR detections in an ad-hoc manner under the suspicion that such records represent false positives, as sometimes advocated in the eDNA literature, also results in biased estimation of occupancy, detectability, and false positive rates. We advocate alternative approaches to account for false positive errors that rely on prior information, or the collection of ancillary detection data at a subset of sites using a sampling method that is not prone to false positive errors. We illustrate the advantages of these approaches over ad-hoc classifications of detec...
Ecological applications : a publication of the Ecological Society of America, 2015
Effective management of alien species requires detecting populations in the early stages of invas... more Effective management of alien species requires detecting populations in the early stages of invasion. Environmental DNA (eDNA) sampling can detect aquatic species at relatively low densities, but few studies have directly compared detection probabilities of eDNA sampling with those of traditional sampling methods. We compare the ability of a traditional sampling technique (bottle trapping) and eDNA to detect a recently established invader, the smooth newt Lissotriton vulgaris vulgaris, at seven field sites in Melbourne, Australia. Over a four-month period, per-trap detection probabilities ranged from 0.01 to 0.26 among sites where L. v. vulgaris was detected, whereas per-sample eDNA estimates were much higher (0.29-1.0). Detection probabilities of both methods varied temporally (across days and months), but temporal variation appeared to be uncorrelated between methods. Only estimates of spatial variation were strongly correlated across the two sampling techniques. Environmental var...
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