Stephen Sarre | University of Canberra (original) (raw)

Papers by Stephen Sarre

Biological Conservation, 2015

ABSTRACT Reptiles are in global decline with nearly 20% of species currently threatened with exti... more ABSTRACT Reptiles are in global decline with nearly 20% of species currently threatened with extinction. Despite these alarming trends, data documenting detailed changes in reptile populations remain sparse and the methods for detecting those changes are largely unevaluated. Rock turning is one commonly used method for detecting the presence or absence of reptiles. Here, we use data from four years of rock turning surveys for the endangered Tympanocryptis pinguicolla to estimate the probability of species occurrence while accounting for detectability. Our data set was zero-inflated with only 36 detections despite some 69,146 detection attempts (rocks turned) across 60 sites. Our analysis revealed the species probability of detection per detection attempt is extremely low (0.00098 (95% CI: 0.00064–0.00142)) and suggested that the species remained undetected at some sampling sites where it was present. Indeed, our estimate of actual site occupancy was nearly double the naïve estimate obtained when not accounting for detectability, suggesting the species is more widespread than previously thought. Our results highlight some important considerations for landscape conservation planning for T. pinguicolla and rupicoline (rock inhabiting) reptiles more generally. In particular, the application of rock turning as a sampling technique must be questioned given the low confidence of detecting a presence in the study reported here and the likely destructive nature of the approach. We recommend that the effectiveness of detection surveys by rock turning be fully evaluated for any species before it is applied widely as a detection technique and suggest that other approaches such as camera traps may prove equally or more effective while being less destructive.

1. Polymerase chain reaction (PCR) diagnostic tests are increasingly applied to the identificatio... more 1. Polymerase chain reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identifiedtest sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. 2. Here, we use an experimental case-control approach to estimate the sensitivity and specificity of a sequential PCR-based wildlife detection test used to identify incursions of red foxes into Tasmania from predator faeces (scats). 3. Our results show that the sensitivity of the fox test is high ( $ 94%) for the PCR-based test on its own, but this decreases to $ 84% when combined with the DNA sequencing step. In contrast, the specificity increases from $ 96% in the PCR-only test to~99Á6% after inclusion of the DNA sequencing step. 4. The intense public scrutiny of the fox eradication programme in Tasmania has undoubtedly influenced the application of a sequential PCR test that maximizes specificity at the expense of sensitivity and so increases the risk that scats containing fox DNA would not be detected. This could lead to the establishment of foxes in Tasmania as a consequence. 5. Synthesis and applications. Importantly, the estimation of the sensitivity and specificity of sequential tests enables decisions about the risk associated with mistaken identification (i.e. false negatives vs. false positives) to be quantified for decision-makers. The cost of false-negative errors should be balanced against the costs of false-positive errors, which could include the expenditure incurred in the application of unnecessary management actions were foxes not in fact present. Understanding the risks and costs associated with both false-negative and false-positive errors is therefore a key component to the decision-making process for the management of the Tasmanian fox incursion.

Identifving the characteristics that make a species vulnerable to extinction jtillowing habitat f... more Identifving the characteristics that make a species vulnerable to extinction jtillowing habitat fragmentation is one of the most pressing problems in conservation biology. One suggestion is that habitat specialists are less able to cope with rapid changes to their habitat or to move through the modljied landscape than habitat generalists and so will be more vulnerable to extinction. We examine this hypothesis by comparing the distributior of two species of gecko, Gehyra variegata and Oedura reticulata, in patches of remnant woodland. The former species is a habitat generalist relative to the latter and shows a markedly higher level of persistence (97% remnant occupancy vs 72%). Logistic regression modelling of the presence or absence of 0. reticulata revealed a sig-@cant correlation between the number of smoothbarked eucalypts (both species preferred by 0. reticulata) in the remnant and the presence of 0. reticulata. This suggests that the probability of extinction for a given population is related to the amount of suitable habitat in the remnant and is a function of processes operating at the population level rather than on a regional basis. Pit-falI trapping in this study and evidence from another long-term study suggest that the movement of 0. reticulata between remnants is negligible. As a consequence, this species has been unable to form a metapopulation at equilibrium. In contrast, it is likely that G. variegata is maintaining its widespread distribution through a metapopulation structure. These results demonstrate the importance of the ability to form a metapopulation for a species to maintain persistence in recently and highly fragmented ecosystems.

Forensic science international. Genetics, 2014

Biology Letters, 2014

Cite this article: Janes DE et al. 2014 Molecular evolution of Dmrt1 accompanies change of sex-de... more Cite this article: Janes DE et al. 2014 Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia. Biol. Lett. 10: 20140809. http://dx.

Conservation Genetics, 2003

Brushtail possums (Trichosurus vulpecula) were live-trapped for two years prior to and following ... more Brushtail possums (Trichosurus vulpecula) were live-trapped for two years prior to and following depopulation in two ~6-ha areas of native forest in New Zealand. The populations had recovered to 55% of the original density at one site and 40% of the original density at the other site, two years after the depopulation. The post-removal populations responded to reduced density with a higher proportion of females breeding, higher survival rate of young, and less seasonal fluctuation in body condition. The initial recolonisation was probably mainly due to surrounding animals shifting their ranges into the depopulated area, rather than long-range dispersal, which resulted in an even sex ratio in the recovering populations. The greater proportion of adult males in the postremoval populations is likely to increase sexual contact rates for females. This would enhance the dissemination of a viral-vectored biological control agent through the population, when used as part of an integrated control program.

Ten tetranucleotide microsatellite loci were isolated from an enriched library for the gecko Oedu... more Ten tetranucleotide microsatellite loci were isolated from an enriched library for the gecko Oedura reticulata . The species is endemic to the southwest of Western Australia, known to be a habitat specialist, and exposed to severe habitat fragmentation in the Western Australian wheatbelt. These highly polymorphic markers (two to 25 alleles) will facilitate the population genetic analyses of this species. In particular, they will enable estimates of gene flow between remnant populations -a critical element in assessing extinction dynamics in fragmented populations.

DNA-based identification of organisms is an important tool in biosecurity, ecological monitoring ... more DNA-based identification of organisms is an important tool in biosecurity, ecological monitoring and wildlife forensics. Current methods usually involve post-polymerase chain reaction (PCR) manipulations (e.g. restriction digest, gel electrophoresis), which add to the expense and time required for processing samples, and may introduce error. We developed a method of species identification that uses species-specific primers and melt-curve analysis, and avoids post-PCR manipulation of samples. The method was highly accurate when trialled on DNA from six large carnivore species from Tasmania, Australia. Because of its flexibility and cost-effectiveness, this method should find wide use in many areas of applied biological science.

Forensic Science International: Genetics Supplement Series, 2011

Forensic Science International: Genetics Supplement Series, 2011

Allele frequency data and knowledge of the population genetic features of relevant populations ar... more Allele frequency data and knowledge of the population genetic features of relevant populations are required to substantiate the strength of forensic DNA evidence. It is conceivable that population substructure exists within Indonesia given that it is an archipelago with over 17,000 islands and encompasses numerous distinct ethnic and linguistic groups. However, the population genetic features of forensic short tandem repeat

Molecular Ecology Notes, 2007

Microsatellites were identified from fully sequenced bacterial artificial chromosome clones from ... more Microsatellites were identified from fully sequenced bacterial artificial chromosome clones from the X chromosome and chromosome 2 of the tammar wallaby, Macropus eugenii . A total of 20 microsatellites were genotyped. Seven X chromosome loci and eight loci from chromosome 2 were polymorphic, with between two and 11 alleles per locus. These markers will facilitate genetic mapping in the tammar wallaby and will have wider applications in macropod population genetics. In particular, X chromosome microsatellites will provide a novel evolutionary perspective from which to view macropod mating systems and gene flow.

Biological Conservation, 2015

ABSTRACT Reptiles are in global decline with nearly 20% of species currently threatened with exti... more ABSTRACT Reptiles are in global decline with nearly 20% of species currently threatened with extinction. Despite these alarming trends, data documenting detailed changes in reptile populations remain sparse and the methods for detecting those changes are largely unevaluated. Rock turning is one commonly used method for detecting the presence or absence of reptiles. Here, we use data from four years of rock turning surveys for the endangered Tympanocryptis pinguicolla to estimate the probability of species occurrence while accounting for detectability. Our data set was zero-inflated with only 36 detections despite some 69,146 detection attempts (rocks turned) across 60 sites. Our analysis revealed the species probability of detection per detection attempt is extremely low (0.00098 (95% CI: 0.00064–0.00142)) and suggested that the species remained undetected at some sampling sites where it was present. Indeed, our estimate of actual site occupancy was nearly double the naïve estimate obtained when not accounting for detectability, suggesting the species is more widespread than previously thought. Our results highlight some important considerations for landscape conservation planning for T. pinguicolla and rupicoline (rock inhabiting) reptiles more generally. In particular, the application of rock turning as a sampling technique must be questioned given the low confidence of detecting a presence in the study reported here and the likely destructive nature of the approach. We recommend that the effectiveness of detection surveys by rock turning be fully evaluated for any species before it is applied widely as a detection technique and suggest that other approaches such as camera traps may prove equally or more effective while being less destructive.

1. Polymerase chain reaction (PCR) diagnostic tests are increasingly applied to the identificatio... more 1. Polymerase chain reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identifiedtest sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. 2. Here, we use an experimental case-control approach to estimate the sensitivity and specificity of a sequential PCR-based wildlife detection test used to identify incursions of red foxes into Tasmania from predator faeces (scats). 3. Our results show that the sensitivity of the fox test is high ( $ 94%) for the PCR-based test on its own, but this decreases to $ 84% when combined with the DNA sequencing step. In contrast, the specificity increases from $ 96% in the PCR-only test to~99Á6% after inclusion of the DNA sequencing step. 4. The intense public scrutiny of the fox eradication programme in Tasmania has undoubtedly influenced the application of a sequential PCR test that maximizes specificity at the expense of sensitivity and so increases the risk that scats containing fox DNA would not be detected. This could lead to the establishment of foxes in Tasmania as a consequence. 5. Synthesis and applications. Importantly, the estimation of the sensitivity and specificity of sequential tests enables decisions about the risk associated with mistaken identification (i.e. false negatives vs. false positives) to be quantified for decision-makers. The cost of false-negative errors should be balanced against the costs of false-positive errors, which could include the expenditure incurred in the application of unnecessary management actions were foxes not in fact present. Understanding the risks and costs associated with both false-negative and false-positive errors is therefore a key component to the decision-making process for the management of the Tasmanian fox incursion.

Identifving the characteristics that make a species vulnerable to extinction jtillowing habitat f... more Identifving the characteristics that make a species vulnerable to extinction jtillowing habitat fragmentation is one of the most pressing problems in conservation biology. One suggestion is that habitat specialists are less able to cope with rapid changes to their habitat or to move through the modljied landscape than habitat generalists and so will be more vulnerable to extinction. We examine this hypothesis by comparing the distributior of two species of gecko, Gehyra variegata and Oedura reticulata, in patches of remnant woodland. The former species is a habitat generalist relative to the latter and shows a markedly higher level of persistence (97% remnant occupancy vs 72%). Logistic regression modelling of the presence or absence of 0. reticulata revealed a sig-@cant correlation between the number of smoothbarked eucalypts (both species preferred by 0. reticulata) in the remnant and the presence of 0. reticulata. This suggests that the probability of extinction for a given population is related to the amount of suitable habitat in the remnant and is a function of processes operating at the population level rather than on a regional basis. Pit-falI trapping in this study and evidence from another long-term study suggest that the movement of 0. reticulata between remnants is negligible. As a consequence, this species has been unable to form a metapopulation at equilibrium. In contrast, it is likely that G. variegata is maintaining its widespread distribution through a metapopulation structure. These results demonstrate the importance of the ability to form a metapopulation for a species to maintain persistence in recently and highly fragmented ecosystems.

Forensic science international. Genetics, 2014

Biology Letters, 2014

Cite this article: Janes DE et al. 2014 Molecular evolution of Dmrt1 accompanies change of sex-de... more Cite this article: Janes DE et al. 2014 Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia. Biol. Lett. 10: 20140809. http://dx.

Conservation Genetics, 2003

Brushtail possums (Trichosurus vulpecula) were live-trapped for two years prior to and following ... more Brushtail possums (Trichosurus vulpecula) were live-trapped for two years prior to and following depopulation in two ~6-ha areas of native forest in New Zealand. The populations had recovered to 55% of the original density at one site and 40% of the original density at the other site, two years after the depopulation. The post-removal populations responded to reduced density with a higher proportion of females breeding, higher survival rate of young, and less seasonal fluctuation in body condition. The initial recolonisation was probably mainly due to surrounding animals shifting their ranges into the depopulated area, rather than long-range dispersal, which resulted in an even sex ratio in the recovering populations. The greater proportion of adult males in the postremoval populations is likely to increase sexual contact rates for females. This would enhance the dissemination of a viral-vectored biological control agent through the population, when used as part of an integrated control program.

Ten tetranucleotide microsatellite loci were isolated from an enriched library for the gecko Oedu... more Ten tetranucleotide microsatellite loci were isolated from an enriched library for the gecko Oedura reticulata . The species is endemic to the southwest of Western Australia, known to be a habitat specialist, and exposed to severe habitat fragmentation in the Western Australian wheatbelt. These highly polymorphic markers (two to 25 alleles) will facilitate the population genetic analyses of this species. In particular, they will enable estimates of gene flow between remnant populations -a critical element in assessing extinction dynamics in fragmented populations.

DNA-based identification of organisms is an important tool in biosecurity, ecological monitoring ... more DNA-based identification of organisms is an important tool in biosecurity, ecological monitoring and wildlife forensics. Current methods usually involve post-polymerase chain reaction (PCR) manipulations (e.g. restriction digest, gel electrophoresis), which add to the expense and time required for processing samples, and may introduce error. We developed a method of species identification that uses species-specific primers and melt-curve analysis, and avoids post-PCR manipulation of samples. The method was highly accurate when trialled on DNA from six large carnivore species from Tasmania, Australia. Because of its flexibility and cost-effectiveness, this method should find wide use in many areas of applied biological science.

Forensic Science International: Genetics Supplement Series, 2011

Forensic Science International: Genetics Supplement Series, 2011

Allele frequency data and knowledge of the population genetic features of relevant populations ar... more Allele frequency data and knowledge of the population genetic features of relevant populations are required to substantiate the strength of forensic DNA evidence. It is conceivable that population substructure exists within Indonesia given that it is an archipelago with over 17,000 islands and encompasses numerous distinct ethnic and linguistic groups. However, the population genetic features of forensic short tandem repeat

Molecular Ecology Notes, 2007

Microsatellites were identified from fully sequenced bacterial artificial chromosome clones from ... more Microsatellites were identified from fully sequenced bacterial artificial chromosome clones from the X chromosome and chromosome 2 of the tammar wallaby, Macropus eugenii . A total of 20 microsatellites were genotyped. Seven X chromosome loci and eight loci from chromosome 2 were polymorphic, with between two and 11 alleles per locus. These markers will facilitate genetic mapping in the tammar wallaby and will have wider applications in macropod population genetics. In particular, X chromosome microsatellites will provide a novel evolutionary perspective from which to view macropod mating systems and gene flow.