Combining surface and soil environmental DNA with artificial cover objects to improve terrestrial reptile survey detection.

Reptiles are increasingly of conservation concern due to their susceptibility to habitat loss, emerging disease, and harvest in the wildlife trade. However, reptile populations are often difficult to monitor given the frequency of crypsis in their life history. This difficulty has left uncertain the conservation status of many species and the efficacy of conservation actions unknown. Environmental DNA (eDNA) surveys consistently elevate the detection rate of species they are designed to monitor, and while their use is promising for terrestrial reptile conservation, successes in developing such surveys have been sparse. We tested the degree to which inclusion of surface and soil eDNA sampling into conventional artificial-cover methods elevates the detection probability of a small, cryptic terrestrial lizard, Scincella lateralis. The eDNA sampling of cover object surfaces with paint rollers elevated per sample detection probabilities for this species 4-16 times compared with visual surveys alone. We readily detected S. lateralis eDNA under cover objects up to 2 weeks after the last visual detection, and at some cover objects where no S. lateralis were visually observed in prior months. With sufficient sampling intensity, eDNA testing of soil under cover objects produced comparable per sample detection probabilities as roller surface methods. Our results suggest that combining eDNA and cover object methods can considerably increase the detection power of reptile monitoring programs, allowing more accurate estimates of population size, detection of temporal and spatial changes in habitat use, and tracking success of restoration efforts. Further research into the deposition and decay rates of reptile eDNA under cover objects, as well as tailored protocols for different species and habitats, is needed to bring the technique into widespread use.

El interés por la conservación de los reptiles es cada vez mayor debido a su susceptibilidad ante la pérdida del hábitat, enfermedades emergentes y la captura para el mercado de fauna. Sin embargo, las poblaciones de reptiles son difíciles de monitorear por lo frecuente que es la cripsis en sus historias de vida. Esta dificultad deja incierto el estado de conservación de muchas especies y desconocida la eficacia de las acciones de conservación. Los censos de ADN ambiental (DNAa) elevan sistemáticamente la tasa de detección de las especies que monitorean, y aunque su uso es prometedor para la conservación de los reptiles terrestres, han sido escasos los éxitos en el desarrollo de dichos censos. Analizamos el grado al que la inclusión del muestreo de DNAa superficial y del suelo a los métodos convencionales de cobertura artificial eleva la probabilidad de detección de una pequeña lagartija terrestre críptica: Scincella lateralis. El muestreo de DNAa de las superficies con cobertura de objetos con rodillos de pintura elevó las probabilidades de detección por muestra para esta especie 4-16 veces más que los censos visuales. Detectamos fácilmente el DNAa de S. lateralis bajo los objetos de cubierta hasta dos semanas después de la última detección visual y en algunos objetos de cubierta en donde no se había observado en los meses previos a S. lateralis. Con suficiente intensidad de muestreo, el análisis de DNAa del suelo bajo objetos de cubierta produjo probabilidades de detección por muestra comparables como métodos de rodillo superficial. Nuestros resultados sugieren que la combinación del DNAa y los métodos de objetos de cobertura puede incrementar considerablemente el poder de detección de los programas de monitoreo de reptiles, lo que permite estimaciones más precisas del tamaño poblacional, detección de los cambios espaciales y temporales en el uso de hábitat y el éxito de rastreo de los esfuerzos de restauración. Además, se necesita la investigación sobre las tasas de depósito y descomposición del DNAa de reptiles bajo objetos de cubierta, así como los protocolos hechos para diferentes especies y hábitats, para que la técnica entre al uso difundido.

Quantifying the probability of detection of wild ungulates with the Judas technique.

The Judas technique is often used in control or eradication of particular vertebrate pests. The technique exploits the tendency of individuals to form social groups. A radio collar is affixed to an individual and its subsequent monitoring facilitates the detection of other conspecifics. Efficacy of this technique would be improved if managers could estimate the probability that a Judas individual would detect conspecifics. To calculate this probability, we estimated association rates of Judas individuals with other Judas individuals, given the length of time the Judas has been deployed. We developed a simple model of space-use for individual Judas animals and constrained detection probabilities to those specific areas. We then combined estimates for individual Judas animals to infer the probability that a wild individual could be detected in an area of interest via Judas surveillance. We illustrated the method by using data from a feral goat eradication program on Isla Santiago, Galápagos, and a feral pig eradication program on Santa Cruz Island, California. Association probabilities declined as the proximity between individual areas of use of a Judas pair decreased. Unconditional probabilities of detection within individual areas of use averaged 0.09 per month for feral pigs and 0.11 per month for feral goats. Probabilities that eradication had been achieved, given no detections of wild conspecifics, and an uninformative prior probability of eradication were 0.79 (90% CI 0.22-0.99) for feral goats and 0.87 (90% CI 0.44-1.0) for feral pigs. We envisage several additions to the analyses used that could improve estimates of Judas detection probability. Analyses such as these can help managers increase the efficacy of eradication efforts, leading to more effective effects to restore native biodiversity.

La técnica de Judas se usa con frecuencia en el control de ciertas plagas de vertebrados. La técnica se aprovecha de la tendencia a formar grupos sociales que tienen los individuos. Un radio-collar es colocado en uno de los individuos y el monitoreo subsecuente facilita la detección de otros miembros de la misma especie. La eficacia de esta técnica mejoraría si los gestores pudieran estimar la probabilidad que tiene un Judas de detectar a miembros de su especie. Para calcular esta probabilidad, estimamos las tasas de asociación de los Judas con otros Judas, dado el tiempo que el Judas ha sido enviado. Desarrollamos un modelo simple del uso del espacio para animales Judas individuales y limitamos las probabilidades de detección a esas áreas específicas. Después combinamos los estimados de un animal Judas individual para inferir la probabilidad de que un individuo silvestre pudiera ser detectado en un área de interés mediante la vigilancia Judas. Ilustramos el método con los datos de un programa de erradicación de cabras ferales en Isla Santiago, las Galápagos, y uno de cerdos ferales en la Isla de Santa Cruz, California. Las probabilidades de asociación declinaron conforme disminuyó la proximidad entre las áreas individuales de uso de un par de Judas. Las probabilidades incondicionales de detección dentro de las áreas individuales de uso promediaron 0.09 por mes para los cerdos ferales y 0.11 por mes para las cabras ferales. Las probabilidades de que se había logrado la erradicación, dada la ausencia de detecciones de miembros de la misma especie y una mal informada probabilidad previa de erradicación, fueron de 0.79 (90% CI 0.22 - 0.99) para las cabras ferales y 0.87 (90% CI 0.44 - 1.0) para los cerdos ferales. Contemplamos varias adiciones al análisis que usamos que podrían mejorar los estimados de la probabilidad de detección de Judas. Análisis como este pueden ayudar a los gestores a incrementar la efectividad de los esfuerzos de erradicación, lo que resulta en efectos más efectivos para restaurar la biodiversidad nativa.

Quantifying population declines based on presence-only records for red-list assessments.

Accurate trend estimates are necessary for understanding which species are declining and which are most in need of conservation action. Imperfect species detection may result in unreliable trend estimates because this may lead to the overestimation of declines. Because many management decisions are based on population trend estimates, such biases could have severe consequences for conservation policy. We used an occupancy-modeling framework to estimate detectability and calculate nationwide population trends for 14 Swiss amphibian species both accounting for and ignoring imperfect detection. Through the application of International Union for Conservation of Nature Red List criteria to the different trend estimates, we assessed whether ignoring imperfect detection could affect conservation policy. Imperfect detection occurred for all species and detection varied substantially among species, which led to the overestimation of population declines when detectability was ignored. Consequently, accounting for imperfect detection lowered the red-list risk category for 5 of the 14 species assessed. We demonstrate that failing to consider species detectability can have serious consequences for species management and that occupancy modeling provides a flexible framework to account for observation bias and improve assessments of conservation status. A problem inherent to most historical records is that they contain presence-only data from which only relative declines can be estimated. A move toward the routine recording of nonobservation and absence data is essential if conservation practitioners are to move beyond this toward accurate population trend estimation.

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments / Historia, aplicaciones, aspectos metodológicos y perspectivas para el uso del ADN ambiental (ADNa) en ecosistemas marinos y de agua dulce

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980’s and phytoplankton communities in the water column since the early-1990’s. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.

El material genético que liberan los organismos en los componentes no vivos del ecosistema (aire, suelo, agua y sedimentos) recibe el nombre de ADN ambiental (ADNa) (eDNA, por su nombre en inglés). Este ADN previamente definido como ADN particulado ha sido utilizado desde mediados de la década de los ochenta y principios de los noventas para describir la composición de las comunidades microbianas en sedimentos marinos y de comunidades microbianas y fitoplanctónicas en la columna de agua. Recientemente el ADNa es utilizado principalmente para la detección y monitoreo de especies invasoras y en peligro. No obstante, existen múltiples áreas en las que este método puede ser utilizado como por ejemplo en ciencias forenses, ecología de poblaciones y comunidades, y taxonomía. Esta revisión proporciona información sobre esta nueva herramienta molecular, sus actuales y futuras aplicaciones, historia, principales consideraciones metodológicas y áreas emergentes para su uso en ecología y conservación de ambientes marinos y de agua dulce.

Distribución y abundancia de murciélagos en bosques con diferente grado de intervención en el Parque Nacional Natural Gorgona (Colombia) / Distribution and abundance of bat assemblages among different forest covers in Gorgona National Natural Park, Colombia

Bats are important for maintenance of ecological processes in tropical forests since they are among the most abundant mammals and play a crucial role in tropical succession. Due to the importance of bats to forest dynamics and to the lack of ecological information, a study was conducted to quantify the variation in species richness, abundance and occurrence of bats in forest with different levels of perturbation in Gorgona National Natural Park; accounting for imperfect detectability. Bats were captured with mist-nets in three areas that differed in their perturbation levels (2 sites per area). A total of 670 bats representing 10 species and three families (Emballonuridae, Phyllostomidae y Vespertilionidae) were captured. The frugivorous species Dermanura rosenbergi (44.1%), Carollia brevicauda (20.9%) and Artibeus lituratus (30.1%) were the most captured species, and 6 out of 10 were insectivorous. Detection probability (p) increased with the increase in perturbation level (p perturbed>p secondary>p primary), and was highest for frugivorous bats. The best model for occurrence (Ψ) revealed that probabilities of occurrence increased with perturbation levels (Ψperturbed>Ψsecondary>Ψprimary) and differed among species. Substantial differences in abundance were due to an additive effect of perturbation level, body size, and guild. Abundance increased with perturbation level (Nperturbed>Nsecondary>Nprimary), decreased with body size, and was highest for frugivorous bats. Bats had higher occurrence and abundance values in most disturbed areas, but they also occurred in less disturbed areas. Consequently, bats can potentially eat fruits from different stages of succession, promoting seed movement among zones that are suitable for colonization. Bats should be considered a conservation target for Gorgona. Rev. Biol. Trop. 62 (Suppl. 1): 419-434. Epub 2014 February 01.

Se cuantificó la variación de la comunidad de murciélagos en bosques con diferente grado de intervención en el Parque Nacional Natural Gorgona. Para esto se realizaron capturas en tres zonas (dos sitios en cada zona) durante tres eventos de muestreo. El análisis de datos consideró la detección imperfecta, permitiendo realizar una inferencia confiable acerca de los cambios en presencia, abundancia y riqueza entre tipos de coberturas. Los resultados evidenciaron una considerable variación en detectabilidad relacionada con variaciones entre gremios tróficos y tipos de cobertura. Las tasas de presencia aumentaron al disminuir la cobertura boscosa (Ψb.intervenido>Ψb. secundario>Ψb. primario) y fueron diferentes entre especies. La abundancia incrementó al aumentar el nivel de intervención (Nb.intervenido>Nb.secundario>Nb primario), disminuyó con el tamaño corporal y fue mayor para frugívoros y nectarívoros que para insectívoros. Los resultados sugieren que las comunidades de murciélagos despliegan fuertes respuestas al grado de intervención. Aunque se presentó mayor presencia y abundancia en el área más intervenida, los murciélagos también utilizaron las menos intervenidas. Esto puede incrementar el movimiento de las semillas entre diferentes estadíos sucesionales. Por lo tanto, el estudio de la comunidad de murciélagos puede ser importante para monitorear el estado de recuperación de los bosques del PNN Gorgona y para entender los procesos ecológicos que generan la recuperación de estos.

Spatially explicit power analyses for occupancy-based monitoring of wolverine in the U.S. Rocky Mountains.

Conservation scientists and resource managers often have to design monitoring programs for species that are rare or patchily distributed across large landscapes. Such programs are frequently expensive and seldom can be conducted by one entity. It is essential that a prospective power analysis be undertaken to ensure stated monitoring goals are feasible. We developed a spatially based simulation program that accounts for natural history, habitat use, and sampling scheme to investigate the power of monitoring protocols to detect trends in population abundance over time with occupancy-based methods. We analyzed monitoring schemes with different sampling efforts for wolverine (Gulo gulo) populations in 2 areas of the U.S. Rocky Mountains. The relation between occupancy and abundance was nonlinear and depended on landscape, population size, and movement parameters. With current estimates for population size and detection probability in the northern U.S. Rockies, most sampling schemes were only able to detect large declines in abundance in the simulations (i.e., 50% decline over 10 years). For small populations reestablishing in the Southern Rockies, occupancy-based methods had enough power to detect population trends only when populations were increasing dramatically (e.g., doubling or tripling in 10 years), regardless of sampling effort. In general, increasing the number of cells sampled or the per-visit detection probability had a much greater effect on power than the number of visits conducted during a survey. Although our results are specific to wolverines, this approach could easily be adapted to other territorial species.