Spatial and temporal variation in population dynamics of Andean frogs: Effects of forest disturbance and evidence for declines

Araújo M, Kaefer IL, Lima AP. Hierarchical effects of historical and environmental factors on lizard assemblages in the upper Madeira River, Brazilian Amazonia

Investigating the role of historical and ecological factors structuring assemblages is relevant to understand mechanisms and processes affecting biodiversity across heterogeneous habitats. Considering that community assembly often involves scale-dependent processes, different spatial scales may reveal distinct factors structuring assemblages. In this study we use arboreal and leaf-litter lizard abundance data from 83 plots to investigate assemblage spatial structure at two distinct scales in southwestern Brazilian Amazonia. At a regional scale, we test the general hypothesis that the Madeira River acts as a barrier to dispersal of some lizard species, which results in distinct assemblages between river banks. At a local scale, we test the hypothesis that assemblages are not evenly distributed across heterogeneous habitats but respond to a continuum of inadequate-to-optimal portions of environmental predictors. Our results show that regional lizard assemblages are structured by the upper Madeira River acting as a regional barrier to 29.62% of the species sampled. This finding suggests species have been historically isolated at one of the river banks, or that distinct geomorphological features influence species occurrence at each river bank. At a local scale, different sets of environmental predictors affected assemblage composition between river banks or even along a river bank. These findings indicate that environmental filtering is a major cause of lizard assemblage spatial structure in the upper Madeira River, but predictor variables cannot be generalized over the extensive (nearly 500 km) study area. Based on a single study system we demonstrate that lizard assemblages along the forests near the banks of the upper Madeira River are not randomly structured but respond to multiple factors acting at different and hierarchical spatial scales.

DCG++: A data-driven metric for geometric pattern recognition

Clustering large and complex data sets whose partitions may adopt arbitrary shapes remains a difficult challenge. Part of this challenge comes from the difficulty in defining a similarity measure between the data points that captures the underlying geometry of those data points. In this paper, we propose an algorithm, DCG++ that generates such a similarity measure that is data-driven and ultrametric. DCG++ uses Markov Chain Random Walks to capture the intrinsic geometry of data, scans possible scales, and combines all this information using a simple procedure that is shown to generate an ultrametric. We validate the effectiveness of this similarity measure within the context of clustering on synthetic data with complex geometry, on a real-world data set containing segmented audio records of frog calls described by mel-frequency cepstral coefficients, as well as on an image segmentation problem. The experimental results show a significant improvement on performance with the DCG-based ultrametric compared to using an empirical distance measure.

Dynamic and diverse amphibian assemblages: Can we differentiate natural processes from human induced changes?

Amphibians are sensitive to anthropogenic habitat alterations but also respond to natural drivers of assemblage composition at many levels. Additionally, they are usually hard to detect in field inventories. We used a multiscale approach, from microhabitat to the landscape levels, to try to understand the effects of natural changes, and try to distinguish them from the effects of landscape level anthropogenic changes, on dynamic and diverse anuran assemblages, taking imperfect detection into account. We conducted thorough field inventories in 16 streams at Serra do Cipó, in the southern portion of Espinhaço Mountain Range, southeastern Brazil, during two time periods separated by 16 years. We compared species richness and diversity between periods, sampling both tadpoles and adult frogs. We quantified tadpole microhabitat availability, alterations in immediate riparian vegetation, and changes in classes of land cover within buffers around streams (adult habitats) to test for their effects on species composition. We also tested for effects of human occupancy around streams on nestedness and turnover components of species diversity. Microhabitats and riparian vegetation explained some of the changes in species composition (or detection) between time periods. Nestedness seemed to be influenced by the stability of the landscape. Detectabilities were too low to support robust occupancy estimates for most species. Natural changes in local habitats occupied by anurans in montane meadows are likely to influence species distribution. Some species with robust estimates experienced change in their occupancy over the studied 16-year interval, although no anthropogenic causes could be directly associated with such changes. The low detectability of most species, even with thorough sampling effort, makes it very hard to detect amphibian declines and possibly tell them apart from natural population fluctuations. New techniques are needed that improve species detectability in such diverse tropical habitats.

Diversidade local e influência da sazonalidade sobre taxocenoses de anfíbios e répteis na Reserva Extrativista Chico Mendes, Acre, Brasil

RESUMO Apesar da elevada riqueza de anfíbios e répteis conhecida para a porção Sul-Ocidental da Amazônia brasileira, o conhecimento sobre estes é pontual e poucos estudos avaliaram as variações temporais na ocorrência e abundância das espécies. Os objetivos deste estudo foram descrever as taxocenoses de anfíbios e répteis em uma localidade da Reserva Extrativista Chico Mendes, verificar quais variáveis climáticas influenciam as flutuações temporais na riqueza e abundância e identificar as principais espécies de anfíbios e répteis influenciadas por elas. A área de estudo está localizada na região do Seringal Etelvi, porção sudoeste da Reserva, município de Brasiléia, estado do Acre. A coleta de dados ocorreu entre outubro de 2011 e setembro de 2012, num total de 48 dias de amostragem, com os métodos de procura limitada por tempo e armadilhas de interceptação e queda. Foram registrados 978 espécimes de 31 espécies de anfíbios e 54 de répteis. Maior riqueza e abundância de anfíbios ocorreram durante o período chuvoso, sendo a abundância associada positivamente com a temperatura média. Apenas a abundância de répteis foi maior durante o período chuvoso. Porém, tanto riqueza quanto abundância mensais foram associadas positivamente com a temperatura média. Quatro anfíbios, Allobates gr. marchesianus, Hamptophryne boliviana (Parker, 1927), Hypsiboas geographicus (Spix, 1824) e Rhinella marina (Linnaeus, 1758), e dois répteis, Kentropyx pelviceps Cope, 1868 e Norops fuscoauratus (D’Orbigny, 1837), tiveram suas abundâncias mensais associadas positivamente com a temperatura média. O lagarto Dactyloa punctata (Daudin, 1802) teve a abundância mensal associada com a precipitação. Foi possível verificar o aumento da riqueza e abundância de anfíbios e répteis durante períodos em que a disponibilidade de recursos é favorável para muitas espécies. As espécies podem reagir de formas diferentes às variações climáticas, enquanto algumas são sensíveis às flutuações, outras parecem não responder facilmente ou não reduzir suas abundâncias em períodos potencialmente desfavoráveis.

Extrapolating demography with climate, proximity and phylogeny: approach with caution

Plant population responses are key to understanding the effects of threats such as climate change and invasions. However, we lack demographic data for most species, and the data we have are often geographically aggregated. We determined to what extent existing data can be extrapolated to predict population performance across larger sets of species and spatial areas. We used 550 matrix models, across 210 species, sourced from the COMPADRE Plant Matrix Database, to model how climate, geographic proximity and phylogeny predicted population performance. Models including only geographic proximity and phylogeny explained 5-40% of the variation in four key metrics of population performance. However, there was poor extrapolation between species and extrapolation was limited to geographic scales smaller than those at which landscape scale threats typically occur. Thus, demographic information should only be extrapolated with caution. Capturing demography at scales relevant to landscape level threats will require more geographically extensive sampling.

Locally dispersing populations in heterogeneous dynamic landscapes with spatiotemporal correlations. I. Block disturbance

Locally dispersing populations are generally favorably affected by increasing the scale of habitat heterogeneity because they can exploit contiguous patches of suitable habitat. Increasing the spatial scale of landscape disturbances (such as by applying a pesticide to control an unwanted species) drives down population density because of reasons including dispersal-limited recolonization and the resulting increase in temporal variability. Here, we examine how population density changes as the spatial scale of landscape disturbance increases: does it increase due to increases in spatial correlations in landscape habitat type, or does it decrease due to the various spatial and temporal effects of larger-scale disturbances? We use simulations, mean field approximations, pair approximations, landscape-improved pair approximations (LIPA), and block probabilities to investigate a model of a locally dispersing species on a dynamic landscape with spatiotemporally structured heterogeneous habitat. Pesticide is applied at a given spatial scale, leaving habitat unsuitable for some time before dissipating and allowing the habitat to revert to a suitable state. We found that increasing the spatial scale of disturbances (while keeping the overall disturbance rate fixed) can increase population density, but generally only when landscape turnover is slow relative to population dynamics and when the population is somewhat close to its extinction threshold. Applying control measures at larger spatial scales may allow them to be more effective with the same overall treatment rate. The optimal spatial strategy for applying disturbances depends on both habitat availability as well as the turnover rate of the control measure being used. For the large-scale habitat dynamics in our model, it is possible to analytically calculate spatial correlations in habitat types over arbitrary scales. However, including exact habitat correlations at the triplet scale but approximating population correlations at that scale still neglects information needed to accurately predict simulation results, showing that larger-scale correlations in the population distribution have an important effect on dynamics.

A new species of Noblella (Amphibia, Anura, Craugastoridae) from the humid montane forests of Cusco, Peru

A new species of Noblella is described from the humid montane forest of the Región Cusco in Peru. Specimens were collected at 2330–2370 m elevation in Madre Selva, near Santa Ana, in the province of La Convención. The new species is readily distinguished from all other species of Noblella by having a broad, irregularly shaped, white mark on black background on chest and belly. The new species further differs from known Peruvian species of Noblella by the combination of the following characters: tympanic membrane absent, small tubercles on the upper eyelid and on dorsum, tarsal tubercles or folds absent, tips of digits not expanded, no circumferential grooves on digits, dark brown facial mask and lateral band extending from the tip of the snout to the inguinal region. The new species has a snout-to-vent length of 15.6 mm in one adult male and 17.6 mm in one adult female. Like other recently described species in the genus, this new Noblella inhabits high-elevation forests in the Andes and likely has a restricted geographic distribution.

Variation in the Presence of Anti-Batrachochytrium dendrobatidis Bacteria of Amphibians Across Life Stages and Elevations in Ecuador

Amphibian populations are decreasing worldwide due to a variety of factors. In South America, the chytrid fungus Batrachochytrium dendrobatidis (Bd) is linked to many population declines. The pathogenic effect of Bd on amphibians can be inhibited by specific bacteria present on host skin. This symbiotic association allows some amphibians to resist the development of the disease chytridiomycosis. Here, we aimed (1) to determine for the first time if specific anti-Bd bacteria are present on amphibians in the Andes of Ecuador, (2) to monitor anti-Bd bacteria across developmental stages in a focal amphibian, the Andean marsupial tree frog, Gastrotheca riobambae, that deposits larvae in aquatic habitats, and (3) to compare the Bd presence associated with host assemblages including 10 species at sites ranging in biogeography from Amazonian rainforest (450 masl) to Andes montane rainforest (3200 masl). We sampled and identified skin-associated bacteria of frogs in the field using swabs and a novel methodology of aerobic counting plates, and a combination of morphological, biochemical, and molecular identification techniques. The following anti-Bd bacteria were identified and found to be shared among several hosts at high-elevation sites where Bd was present at a prevalence of 32.5%: Janthinobacterium lividum, Pseudomonas fluorescens, and Serratia sp. Bd were detected in Gastrotheca spp. and not detected in the lowlands (sites below 1000 masl). In G. riobambae, recognized Bd-resistant bacteria start to be present at the metamorphic stage. Overall bacterial abundance was significantly higher post-metamorphosis and on species sampled at lower elevations. Further metagenomic studies are needed to evaluate the roles of host identity, life-history stage, and biogeography of the microbiota and their function in disease resistance.