First extraction of eDNA from tree hole water to detect tree frogs: a simple field method piloted in Madagascar

Environmental DNA (eDNA) is becoming an increasingly used tool for monitoring cryptic species within terrestrial and aquatic systems. We present the first method for extracting water from tree holes for eDNA studies of tree-dwelling frogs, and the first use of eDNA for amphibian monitoring in Madagascar. This pilot study expands on a previously developed method and aims to provide a simple field protocol for DNA extraction from very small water samples, using a relatively inexpensive kit compared to other collection methods. We collected 20 ml of water from tree holes in Ambohitantely Special Reserve in Madagascar, with the aim to survey for the Critically Endangered tree frog Anodonthyla vallani, and we developed species specific cytochrome c oxidase 1 primers for this species. While our two samples did not detect A. vallani, we successfully extracted up to 16.6 ng/µl of eDNA from the samples and using 16S rRNA primers barcoded the tree frog Plethodontohyla mihanika in one of the samples. Despite just two samples being collected, we highlight the future potential of eDNA from tree holes for investigating cryptic habitat specialist amphibians given we extracted frog eDNA from just 20 ml of water. The method provides a rapid, simple, and cost-effective method which can assist cryptic species monitoring in challenging and time-consuming field conditions and should be developed further for frog surveying in Madagascar and beyond. The newly developed primers can be used for further work using this eDNA method to survey threatened Anodonthyla frog species

Comparison of eDNA and visual surveys for rare and cryptic bromeliad-dwelling frogs

Surveys of rare or cryptic species may miss individuals or populations that are actually present. Despite the increasing use of environmental DNA (eDNA) analysis to survey species in ponds, rivers, and lakes, very few studies have attempted to use eDNA for the detection of species using very small water bodies such as those accumulated within plants. Our aim was to investigate the feasibility of an eDNA sampling method for detecting Crossodactylodes itambe, an endemic bromeliad-dwelling frog from a remote location in Brazil. We collected water samples from 19 bromeliads for which we had observational data from direct visual surveys. We compared occupancy estimated from direct observations with the results from quantitative real-time PCR based eDNA assays. For observational surveys, we used a single season occupancy model. We applied a novel Bayesian occupancy model to estimate occupancy from eDNA samples, as well as false positives and false negatives at different stages of the workflow. eDNA from bromeliad tanks provided reliable estimates, with very low error levels and improved detection when compared to detectability from direct observation. Estimated occupancies using eDNA and visual survey methods were similar. The method is feasible for species restricted to small water bodies and exposed to direct UV radiation, and particularly useful to survey remote locations and confirm species presence. eDNA analysis provides a viable alternative to destructive sampling of bromeliads or direct observation methods that require logistically challenging repeated observations. Therefore, eDNA methods may be widely applicable to sampling programmes of other amphibians that live in plant

Conducting robust ecological analyses with climate data

Although the number of studies discerning the impact of climate change on ecological systems continues to increase, there has been relatively little sharing of the lessons learnt when accumulating this evidence. At a recent workshop entitled ‘Using climate data in ecological research’ held at the UK Met Office, ecologists and climate scientists came together to discuss the robust analysis of climate data in ecology. The discussions identified three common pitfalls encountered by ecologists: 1) selection of inappropriate spatial resolutions for analysis; 2) improper use of publically available data or code; and 3) insufficient representation of the uncertainties behind the adopted approach. Here, we discuss how these pitfalls can be avoided, before suggesting ways that both ecology and climate science can move forward. Our main recommendation is that ecologists and climate scientists collaborate more closely, on grant proposals and scientific publications, and informally through online media and workshops. More sharing of data and code (e.g. via online repositories), lessons and guidance would help to reconcile differing approaches to the robust handling of data. We call on ecologists to think critically about which aspects of the climate are relevant to their study system, and to acknowledge and actively explore uncertainty in all types of climate data. And we call on climate scientists to make simple estimates of uncertainty available to the wider research community. Through steps such as these, we will improve our ability to robustly attribute observed ecological changes to climate or other factors, while providing the sort of influential, comprehensive analyses that efforts to mitigate and adapt to climate change so urgently require

Predictors of abundance of a rare bromeliad-dwelling frog (Crossodactylodes itambe) in the Espinhaço Mountain Range of Brazil

Although tank bromeliads are used by many anuran species, bromeligenous frogs (species strictly dependent on bromeliads for reproduction) occur less frequently and are poorly understood. Crossodactylodes are small frogs confined to bromeliads where they lay their eggs and complete their life cycle without leaving the plant. The genus comprises five species and there is little information on their natural history. We focused on Crossodactylodes itambe – a species confined to a single summit of <0.5 km2 at 1700 m above sea level in the Espinhaço Mountain Range of Brazil. We surveyed frogs in 75 individual bromeliads during two consecutive years and we used a Generalized Linear Model to investigate the drivers of species abundance related to habitat structure and local climate. We recorded 446 adults, 267 tadpoles and 40 juveniles over the two years. Most bromeliads contained one adult frog and the mean number of tadpoles was 2-3. The structure of bromeliads influenced species abundance more than local climate. We found that bromeliad size, volume of central tank, and presence/absence of invertebrates and water influenced abundance of frogs. Abundance increased in larger bromeliads at higher elevation. Changes in the structure and size of bromeliads might therefore affect abundance. We provide the first species assessment and evaluation of threat categories for this poorly known species

Overcoming the lack of distribution data for range‐restricted habitat specialist frogs

With over 40% of species threatened with extinction, the distributional range of most amphibians is still unknown, generating uncertainty whether species are naturally rare, under‐sampled, or difficult to detect. We implemented a modelling approach that uses bromeliads as surrogates to predict the distribution of habitat specialist frogs that lack distributional data. We aimed to predict and survey potential new sites for the occurrence of a rare and microendemic bromeliad‐dwelling frog from the Atlantic Rainforest of Brazil. We used Maxent to predict suitable areas based on climate and topographic profiles, combined with 21 occurrence records of bromeliads within which our target frog species (Crossodactylodes itambe) is strictly restricted. The bromeliad‐based models identified four areas potentially suitable, and subsequent surveys revealed an entirely new species of a rare bromeliad‐dwelling frog in one of the areas. We demonstrate that using easy‐to‐survey surrogate species that have a strong relationship with species that are hard to detect has enormous potential to reveal crucial information on the potential ranges and distribution of cryptic taxa. Such a surrogate modelling approach could be extended to other habitat specialist species that lack distribution data, such as amphibians restricted to specific refugia and/or reproduction sites. This could improve the targeting of surveys and increase understanding of the patterns of rarity and the drivers of species distribution, especially for areas with high endemicity and range‐restricted frogs

A new species of Crossodactylodes (Anura: Leptodactylidae) from Minas Gerais, Brazil: first record of genus within the Espinhaço Mountain Range

Barata, Izabela M., Santos, Marcus T. T., Leite, Felipe S. F., Garcia, Paulo C. A. (2013): A new species of Crossodactylodes (Anura: Leptodactylidae) from Minas Gerais, Brazil: first record of genus within the Espinhaço Mountain Range. Zootaxa 3731 (4): 552-560, DOI: 10.11646/zootaxa.3731.4.

A new species of Crossodactylodes from the Espinhaço mountain range, Southeastern Brazil (Anura: Leptodactylidae: Paratelmatobiinae)

The bromeligenous genus Crossodactylodes, endemic to the Atlantic Forest domain and the “campo rupestre” ecosystem in Brazil, currently comprises five named species. Three additional putatively new species have already been proposed in a recent study based on mitochondrial and nuclear markers. Here we employ phenotypic data to corroborate the distinctiveness of one of these lineages, and describe it as a new species, from the Espinhaço Mountain Range in the municipality of Itamarandiba, state of Minas Gerais, southeastern Brazil. We also provide information on its natural history and conservation status. The new species is diagnosable from its congeners by a combination of characters, including the presence of vocal slits in adult males, the orange coloration of discs on fingers and toes, and the presence of vomerine odontophores. The new species is the second Crossodactylodes to be reported for the campo rupestre and it was only recorded in a small forest patch composed of low trees, shrubs, mosses, lichens, and a high density of bromeliads

First amphibian inventory of one of Madagascar’s smallest protected areas, Ankafobe, extends the range of the Critically Endangered Anilany helenae (Vallan, 2000) and the Endangered Boophis andrangoloaka (Ahl, 1928)

Using DNA barcoding, we present the first inventory of amphibians present in one of Madagascar’s smallest protected areas, Ankafobe. This small area represents some of the last remaining central high plateau forests in Madagascar. However, with just 27.89 ha of forest split into two fragments, Ankafobe is highly threatened by yearly grassland fires. We recorded a total of 382 individuals and identified 14 species of frogs. This list includes the Critically Endangered Anilany helenae which was previously thought to be micro-endemic and restricted to Ambohitantely Special Reserve, therefore increasing this tiny species’ range to a second protected area. Our results also imply an extension of the known range of the Endangered Boophis andrangoloaka. While our inventory likely underestimates the diversity of frog species present in Ankafobe, it provides a baseline for future conservation efforts at this site

largemammalrecords_VPSP_Ferreira et al 2017_Biotropica

Camera trap records of large mammals in Veredas do Peruaçu State Park, Minas Gerais, Brazil. Each sheet refers to one large mammal species recorded in VPSP. Species codes composed of first letter of the genus and first three letters of the specific name (refer to Table S1 of the paper for species names). Within sheet, each row is a camera trap site and each column is a 7-day survey occasion