Integrating detection probabilities in species distribution models of amphibians breeding in Mediterranean temporary ponds

Aim  The imperfect detection of species may lead to erroneous conclusions about species-environment relationships. Accuracy in species detection usually requires temporal replication at sampling sites, a time-consuming and costly monitoring scheme. Here, we applied a lower-cost alternative based on a double-sampling approach to incorporate the reliability of species detection into regression-based species distribution modelling.Location  Doñana National Park (south-western Spain).Methods  Using species-specific monthly detection probabilities, we estimated the detection reliability as the probability of having detected the species given the species-specific survey time. Such reliability estimates were used to account explicitly for data uncertainty by weighting each absence. We illustrated how this novel framework can be used to evaluate four competing hypotheses as to what constitutes primary environmental control of amphibian distribution: breeding habitat, aestivating habitat, spatial distribution of surrounding habitats and/or major ecosystems zonation. The study was conducted on six pond-breeding amphibian species during a 4-year period.Results  Non-detections should not be considered equivalent to real absences, as their reliability varied considerably. The occurrence of Hyla meridionalis and Triturus pygmaeus was related to a particular major ecosystem of the study area, where suitable habitat for these species seemed to be widely available. Characteristics of the breeding habitat (area and hydroperiod) were of high importance for the occurrence of Pelobates cultripes and Pleurodeles waltl. Terrestrial characteristics were the most important predictors of the occurrence of Discoglossus galganoi and Lissotriton boscai, along with spatial distribution of breeding habitats for the last species.Main conclusions  We did not find a single best supported hypothesis valid for all species, which stresses the importance of multiscale and multifactor approaches. More importantly, this study shows that estimating the reliability of non-detection records, an exercise that had been previously seen as a naïve goal in species distribution modelling, is feasible and could be promoted in future studies, at least in comparable systems.

Presence-absence versus abundance data for monitoring threatened species

Effective detection of population trend is crucial for managing threatened species. Little theory exists, however, to assist managers in choosing the most cost-effective monitoring techniques for diagnosing trend. We present a framework for determining the optimal monitoring strategy by simulating a manager collecting data on a declining species, the Chestnut-rumped Hylacola (Hylacola pyrrhopygia parkeri), to determine whether the species should be listed under the IUCN (World Conservation Union) Red List. We compared the efficiencies of two strategies for detecting trend, abundance, and presence-absence surveys, underfinancial constraints. One might expect the abundance surveys to be superior under all circumstances because more information is collected at each site. Nevertheless, the presence-absence data can be collected at more sites because the surveyor is not obliged to spend a fixed amount of time at each site. The optimal strategy for monitoring was very dependent on the budget available. Under some circumstances, presence-absence surveys outperformed abundance surveys for diagnosing the IUCN Red List categories cost-effectively. Abundance surveys were best if the species was expected to be recorded more than 16 times/year; otherwise, presence-absence surveys were best. The relationship between the strategies we investigated is likely to be relevant for many comparisons of presence-absence or abundance data. Managers of any cryptic or low-density species who hope to maximize their success of estimating trend should find an application for our results.

Decisions on Temporal Sampling Protocol Influence the Detection of Ecological Patterns

Within-site variability in species detectability is a problem common to many biodiversity assessments and can strongly bias the results. Such variability can be caused by many factors, including simple counting inaccuracies, which can be solved by increasing sample size, or by temporal changes in species behavior, meaning that the way the temporal sampling protocol is designed is also very important. Here we use the example of mist-netted tropical birds to determine how design decisions in the temporal sampling protocol can alter the data collected and how these changes might affect the detection of ecological patterns, such as the species-area relationship (SAR). Using data from almost 3400 birds captured from 21,000 net-hours at 31 sites in the Brazilian Atlantic Forest, we found that the magnitude of ecological trends remained fairly stable, but the probability of detecting statistically significant ecological patterns varied depending on sampling effort, time of day and season in which sampling was conducted. For example, more species were detected in the wet season, but the SAR was strongest in the dry season. We found that the temporal distribution of sampling effort was more important than its total amount, discovering that similar ecological results could have been obtained with one-third of the total effort, as long as each site had been equally sampled over 2 yr. We discuss that projects with the same sampling effort and spatial design, but with different temporal sampling protocol are likely to report different ecological patterns, which may ultimately lead to inappropriate conservation strategies.

The influence of environmental variables on capybara (Hydrochoerus hydrochaeris: Rodentia, Hydrochoeridae) detectability in anthropogenic environments of southeastern Brazil

Capybaras were monitored weekly from 1998 to 2006 by counting individuals in three anthropogenic environments (mixed agricultural fields, forest and open areas) of southeastern Brazil in order to examine the possible influence of environmental variables (temperature, humidity, wind speed, precipitation and global radiation) on the detectability of this species. There was consistent seasonality in the number of capybaras in the study area, with a specific seasonal pattern in each area. Log-linear models were fitted to the sample counts of adult capybaras separately for each sampled area, with an allowance for monthly effects, time trends and the effects of environmental variables. Log-linear models containing effects for the months of the year and a quartic time trend were highly significant. The effects of environmental variables on sample counts were different in each type of environment. As environmental variables affect capybara detectability, they should be considered in future species survey/monitoring programs.

Nestling detectability affects parental feeding preferences in a cavity-nesting bird

In many avian species, nestlings have evolved striking plumage, behaviours and mouth colours to obtain a greater share of parental investment. Studies revealing parental feeding preferences for nestlings with red gapes have proposed that red mouth colour in songbirds can act as a signal of nestling need or condition. Alternative hypotheses suggest that bright nestling mouths in cavity-nesting birds evolved to increase nestling detectability by the parents. We tested whether nestling mouth colour affects parental feeding preferences in great tits, Pants major L. In broods of six young, we experimentally painted mouth gapes and flanges either red or yellow and tested the effect of mouth colour on nestlings' mass gain under two lighting conditions. In nests with high luminosity, there was no significant effect of mouth colour on mass gain. In nests with low luminosity, nestlings with red gapes and flanges gained less mass than nestlings with red gapes and yellow flanges or both yellow gapes and flanges. Our results suggest that, in nests with low luminosity, red mouths decreased nestling detectability to the feeding parents and support the hypothesis that poor luminosity in nesting cavities can select for pale mouths. Overall, our results do not support the hypothesis that red mouth colour signals nestling need or condition to parent great tits.

Effects of detectability on estimates of geographic range size in bignonieae

Extinction risk has not been evaluated for 96% of all described plant species. Given that the Global Strategy for Plant Conservation proposes preliminary conservation assessments of all described plant species by 2010, herbarium specimens (i.e., primary occurrence data) are increasingly being used to infer threat components from estimates of geographic range size. Nevertheless, estimates of range size based on herbarium data may be inaccurate due to collection bias associated with interspecific variation in detectability. We used data on 377 species of Bignonieae to test the hypothesis that there is a positive relationship between detectability and estimates of geographic range size derived from herbarium specimens. This relationship is expected if the proportion of the true geographic range size of a species that is documented by herbarium specimens is given by the product of the true geographic range size and the detectability of the species, assuming no relationship between true geographic range size and detectability. We developed 4 measures of detectability that can be estimated from herbarium data and examined the relationship between detectability and 2 types of estimates of geographic range size: area of occupancy and extent of occurrence. Our results from regressing estimates of extent of occurrence and area of occupancy on detectability across genera provided no support for this hypothesis. The same was true for regressions of estimated extent of occurrence on detectability across species within genera. Nevertheless, regressions of estimated area of occupancy on detectability across species within genera provided partial support for our hypothesis. We considered 3 possible explanations for this mixed outcome: violation of the assumption of no relationship between true geographic range size and detectability; the relationships between estimated geographic range size and detectability may be an artifact of a negative relationship between estimated area of occupancy and the sampling variance of detectability; detectability may have had 2 opposite effects on estimated species range sizes: one determines the proportion of the true range of a species documented by herbarium specimens and the other determines the distribution of true range size for the species actually observed with herbarium data. Our findings should help improve understanding of the potential biases incurred with the use of herbarium data.

Assessment of detectability of neutral interstellar deuterium by IBEX observations

Context. The abundance of deuterium in the interstellar gas in front of the Sun gives insight into the processes of filtration of neutral interstellar species through the heliospheric interface and potentially into the chemical evolution of the Galactic gas. Aims: We investigate the possibility of detection of neutral interstellar deuterium at 1 AU from the Sun by direct sampling by the Interstellar Boundary Explorer (IBEX). Methods: Using both previous and the most recent determinations of the flow parameters of neutral gas in the local interstellar cloud (LIC) and an observation-based model of solar radiation pressure and ionization in the heliosphere, we simulated the flux of neutral interstellar D at IBEX for the actual measurement conditions. We assessed the number of interstellar D atom counts expected during the first three years of IBEX operation. We also simulated the observations expected during an epoch of high solar activity. In addition, we calculated the expected counts of D atoms from the thin terrestrial water layer covering the IBEX-Lo conversion surface, sputtered by neutral interstellar He atoms. Results: Most D counts registered by IBEX-Lo are expected to come from the water layer, exceeding the interstellar signal by 2 orders of magnitude. However, the sputtering should stop once the Earth leaves the portion of orbit traversed by interstellar He atoms. We identify seasons during the year when mostly the genuine interstellar D atoms are expected in the signal. During the first 3 years of IBEX operations about 2 detectable interstellar D atoms are expected. This number is comparable to the expected number of sputtered D atoms registered during the same time intervals. Conclusions: The most favorable conditions for the detection occur during low solar activity, in an interval including March and April each year. The detection chances could be improved by extending the instrument duty cycle, say, by making observations in the special deuterium mode of IBEX-Lo.

Hide-and-seek in vegetation: time-to-detection is an efficient design for estimating detectability and occurrence

Ecology and conservation require reliable data on the occurrence of animals and plants. A major source of bias is imperfect detection, which, however, can be corrected for by estimation of detectability. In traditional occupancy models, this requires repeat or multi-observer surveys. Recently, time-to-detection models have been developed as a cost-effective alternative, which requires no repeat surveys and hence costs could be halved. We compared the efficiency and reliability of time-to-detection and traditional occupancy models under varying survey effort. Two observers independently searched for 17 plant species in 44100m(2) Swiss grassland quadrats and recorded the time-to-detection for each species, enabling detectability to be estimated with both time-to-detection and traditional occupancy models. In addition, we gauged the relative influence on detectability of species, observer, plant height and two measures of abundance (cover and frequency). Estimates of detectability and occupancy under both models were very similar. Rare species were more likely to be overlooked; detectability was strongly affected by abundance. As a measure of abundance, frequency outperformed cover in its predictive power. The two observers differed significantly in their detection ability. Time-to-detection models were as accurate as traditional occupancy models, but their data easier to obtain; thus they provide a cost-effective alternative to traditional occupancy models for detection-corrected estimation of occurrence.

Detection histories for eight species of Amazona parrots in Venezuela during the NeoMaps bird surveys in 2010

Documenting changes in distribution is necessary for understanding species' response to environmental changes, but data on species distributions are heterogeneous in accuracy and resolution. Combining different data sources and methodological approaches can fill gaps in knowledge about the dynamic processes driving changes in species-rich, but data-poor regions. We combined recent bird survey data from the Neotropical Biodiversity Mapping Initiative (NeoMaps) with historical distribution records to estimate potential changes in the distribution of eight species of Amazon parrots in Venezuela. Using environmental covariates and presence-only data from museum collections and the literature, we first used maximum likelihood to fit a species distribution model (SDM) estimating a historical maximum probability of occurrence for each species. We then used recent, NeoMaps survey data to build single-season occupancy models (OM) with the same environmental covariates, as well as with time- and effort-dependent detectability, resulting in estimates of the current probability of occurrence. We finally calculated the disagreement between predictions as a matrix of probability of change in the state of occurrence. Our results suggested negative changes for the only restricted, threatened species, Amazona barbadensis, which has been independently confirmed with field studies. Two of the three remaining widespread species that were detected, Amazona amazonica, Amazona ochrocephala, also had a high probability of negative changes in northern Venezuela, but results were not conclusive for Amazona farinosa. The four remaining species were undetected in recent field surveys; three of these were most probably absent from the survey locations (Amazona autumnalis, Amazona mercenaria and Amazona festiva), while a fourth (Amazona dufresniana) requires more intensive targeted sampling to estimate its current status. Our approach is unique in taking full advantage of available, but limited data, and in detecting a high probability of change even for rare and patchily-distributed species. However, it is presently limited to species meeting the strong assumptions required for maximum-likelihood estimation with presence-only data, including very high detectability and representative sampling of its historical distribution.

Improving the efficiency of wildlife monitoring by estimating detectability: a case study of foxes (Vulpes vulpes) on the Eyre Peninsula, South Australia

Demonstrating the existence of trends in monitoring data is of increasing practical importance to conservation managers wishing to preserve threatened species or reduce the impact of pest species. However, the ability to do so can be compromised if the species in question has low detectability and the true occupancy level or abundance of the species is thus obscured. Zero-inflated models that explicitly model detectability improve the ability to make sound ecological inference in such situations. In this paper we apply an occupancy model including detectability to data from the initial stages of a fox-monitoring program on the Eyre Peninsula, South Australia. We find that detectability is extremely low (< 18%) and varies according to season and the presence or absence of roadside vegetation. We show that simple methods of using monitoring data to inform management, such as plotting the raw data or performing logistic regression, fail to accurately diagnose either the status of the fox population or its trajectory over time. We use the results of the detectability model to consider how future monitoring could be redesigned to achieve efficiency gains. A wide range of monitoring programs could benefit from similar analyses, as part of an active adaptive approach to improving monitoring and management.

Detectability of migrating raptors and its effect on bias and precision of trend estimates

Annual counts of migrating raptors at fixed observation points are a widespread practice, and changes in numbers counted over time, adjusted for survey effort, are commonly used as indices of trends in population size. Unmodeled year-to-year variation in detectability may introduce bias, reduce precision of trend estimates, and reduce power to detect trends. We conducted dependent double-observer surveys at the annual fall raptor migration count at Lucky Peak, Idaho, in 2009 and 2010 and applied Huggins closed-capture removal models and information-theoretic model selection to determine the relative importance of factors affecting detectability. The most parsimonious model included effects of observer team identity, distance, species, and day of the season. We then simulated 30 years of counts with heterogeneous individual detectability, a population decline (λ = 0.964), and unexplained random variation in the number of available birds. Imperfect detectability did not bias trend estimation, and increased the time required to achieve 80% power by less than 11%. Results suggested that availability is a greater source of variance in annual counts than detectability; thus, efforts to account for availability would improve the monitoring value of migration counts. According to our models, long-term trends in observer efficiency or migratory flight distance may introduce substantial bias to trend estimates. Estimating detectability with a novel count protocol like our double-observer method is just one potential means of controlling such effects. The traditional approach of modeling the effects of covariates and adjusting the index may also be effective if ancillary data is collected consistently.

Characterization Of Microsatellite Markers Developed From Prosopis Rubriflora And Prosopis Ruscifolia (leguminosae - Mimosoideae), Legume Species That Are Used As Models For Genetic Diversity Studies In Chaquenian Areas Under Anthropization In South America.

Prosopis rubriflora and Prosopis ruscifolia are important species in the Chaquenian regions of Brazil. Because of the restriction and frequency of their physiognomy, they are excellent models for conservation genetics studies. The use of microsatellite markers (Simple Sequence Repeats, SSRs) has become increasingly important in recent years and has proven to be a powerful tool for both ecological and molecular studies. In this study, we present the development and characterization of 10 new markers for P. rubriflora and 13 new markers for P. ruscifolia. The genotyping was performed using 40 P. rubriflora samples and 48 P. ruscifolia samples from the Chaquenian remnants in Brazil. The polymorphism information content (PIC) of the P. rubriflora markers ranged from 0.073 to 0.791, and no null alleles or deviation from Hardy-Weinberg equilibrium (HW) were detected. The PIC values for the P. ruscifolia markers ranged from 0.289 to 0.883, but a departure from HW and null alleles were detected for certain loci; however, this departure may have resulted from anthropic activities, such as the presence of livestock, which is very common in the remnant areas. In this study, we describe novel SSR polymorphic markers that may be helpful in future genetic studies of P. rubriflora and P. ruscifolia.

Development And Characterization Of Microsatellite Loci For Ocotea Species (lauraceae) Threatened With Extinction.

The Atlantic rainforest species Ocotea catharinensis, Ocotea odorifera, and Ocotea porosa have been extensively harvested in the past for timber and oil extraction and are currently listed as threatened due to overexploitation. To investigate the genetic diversity and population structure of these species, we developed 8 polymorphic microsatellite markers for O. odorifera from an enriched microsatellite library by using 2 dinucleotide repeats. The microsatellite markers were tested for cross-amplification in O. catharinensis and O. porosa. The average number of alleles per locus was 10.2, considering all loci over 2 populations of O. odorifera. Observed and expected heterozygosities for O. odorifera ranged from 0.39 to 0.93 and 0.41 to 0.92 across populations, respectively. Cross-amplification of all loci was successfully observed in O. catharinensis and O. porosa except 1 locus that was found to lack polymorphism in O. porosa. Combined probabilities of identity in the studied Ocotea species were very low ranging from 1.0 x 10-24 to 7.7 x 10-24. The probability of exclusion over all loci estimated for O. odorifera indicated a 99.9% chance of correctly excluding a random nonparent individual. The microsatellite markers described in this study have high information content and will be useful for further investigations on genetic diversity within these species and for subsequent conservation purposes.

Developmental Rate Of Immatures Of Two Fly Species Of Forensic Importance: Sarcophaga (liopygia) Ruficornis And Microcerella Halli (diptera: Sarcophagidae).

Since insect species are poikilothermic organisms, they generally exhibit different growth patterns depending on the temperature at which they develop. This factor is important in forensic entomology, especially for estimating postmortem interval (PMI) when it is based on the developmental time of the insects reared in decomposing bodies. This study aimed to estimate the rates of development, viability, and survival of immatures of Sarcophaga (Liopygia) ruficornis (Fabricius 1794) and Microcerella halli (Engel 1931) (Diptera: Sarcophagidae) reared in different temperatures: 10, 15, 20, 25, 30, and 35 ± 1 °C. Bovine raw ground meat was offered as food for all experimental groups, each consisting of four replicates, in the proportion of 2 g/larva. To measure the evolution of growth, ten specimens of each group were randomly chosen and weighed every 12 h, from initial feeding larva to pupae, and then discarded. Considering the records of weight gain, survival rates, and stability of growth rates, the range of optimum temperature for the development of S. (L.) ruficornis is between 20 and 35 °C, and that of M. halli is between 20 and 25 °C. For both species, the longest times of development were in the lowest temperatures. The survival rate at extreme temperatures (10 and 35 °C) was lower in both species. Biological data such as the ones obtained in this study are of great importance to achieve a more accurate estimate of the PMI.

Molecular And Morphological Evidence Reveals A New Species In The Phyllomedusa Hypochondrialis Group (hylidae, Phyllomedusinae) From The Atlantic Forest Of The Highlands Of Southern Brazil.

The taxonomic status of a disjunctive population of Phyllomedusa from southern Brazil was diagnosed using molecular, chromosomal, and morphological approaches, which resulted in the recognition of a new species of the P. hypochondrialis group. Here, we describe P. rustica sp. n. from the Atlantic Forest biome, found in natural highland grassland formations on a plateau in the south of Brazil. Phylogenetic inferences placed P. rustica sp. n. in a subclade that includes P. rhodei + all the highland species of the clade. Chromosomal morphology is conservative, supporting the inference of homologies among the karyotypes of the species of this genus. Phyllomedusa rustica is apparently restricted to its type-locality, and we discuss the potential impact on the strategies applied to the conservation of the natural grassland formations found within the Brazilian Atlantic Forest biome in southern Brazil. We suggest that conservation strategies should be modified to guarantee the preservation of this species.