A dataset for benchmarking Neotropical anuran calls identification in passive acoustic monitoring.

Global change is predicted to induce shifts in anuran acoustic behavior, which can be studied through passive acoustic monitoring (PAM). Understanding changes in calling behavior requires automatic identification of anuran species, which is challenging due to the particular characteristics of neotropical soundscapes. In this paper, we introduce a large-scale multi-species dataset of anuran amphibians calls recorded by PAM, that comprises 27 hours of expert annotations for 42 different species from two Brazilian biomes. We provide open access to the dataset, including the raw recordings, experimental setup code, and a benchmark with a baseline model of the fine-grained categorization problem. Additionally, we highlight the challenges of the dataset to encourage machine learning researchers to solve the problem of anuran call identification towards conservation policy. All our experiments and resources have been made available at https://soundclim.github.io/anuraweb/ .

Long-term Ecological Research: Chasing fashions or being prepared for fashion changes?

Long-term-ecological-research (LTER) faces many challenges, including the difficulty of obtaining long-term funding, changes in research questions and sampling designs, keeping researchers collecting standardized data for many years, impediments to interactions with local people, and the difficulty of integrating the needs of local decision makers with "big science". These issues result in a lack of universally accepted guidelines as to how research should be done and integrated among LTER sites. Here we discuss how the RAPELD (standardized field infrastructure system), can help deal with these issues as a complementary technique in LTER studies, allowing comparisons across landscapes and ecosystems and reducing sampling costs. RAPELD uses local surveys to understand broad spatial and temporal patterns while enhancing decision-making and training of researchers, local indigenous groups and traditional communities. Sampling of ecological data can be carried out by different researchers through standardized protocols, resulting in spatial data that can be used to answer temporal questions, and allow new questions to be investigated. Results can also be integrated into existing biodiversity networks. Integrated systems are the most efficient way to save resources, maximize results, and accumulate information that can be used in the face of the unknown unknowns upon which our future depends.

Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest.

Background: The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex. Methods: We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations. Results: Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.

The Program for Biodiversity Research in Brazil: The role of regional networks for biodiversity knowledge, dissemination, and conservation.

The Program for Biodiversity Research (PPBio) is an innovative program designed to integrate all biodiversity research stakeholders. Operating since 2004, it has installed long-term ecological research sites throughout Brazil and its logic has been applied in some other southern-hemisphere countries. The program supports all aspects of research necessary to understand biodiversity and the processes that affect it. There are presently 161 sampling sites (see some of them at Supplementary Appendix), most of which use a standardized methodology that allows comparisons across biomes and through time. To date, there are about 1200 publications associated with PPBio that cover topics ranging from natural history to genetics and species distributions. Most of the field data and metadata are available through PPBio web sites or DataONE. Metadata is available for researchers that intend to explore the different faces of Brazilian biodiversity spatio-temporal variation, as well as for managers intending to improve conservation strategies. The Program also fostered, directly and indirectly, local technical capacity building, and supported the training of hundreds of undergraduate and graduate students. The main challenge is maintaining the long-term funding necessary to understand biodiversity patterns and processes under pressure from global environmental changes.

FragSAD: A database of diversity and species abundance distributions from habitat fragments.

Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species' assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

Concerted evolution in the mitochondrial control region of the Amazon small-bodied frog Pseudopaludicola canga (Anura, Leiuperidae).

This study presents evidence of concerted evolution in the mitochondrial control region of the frog Pseudopaludicola canga. Four repeat units of 88 bp (as well as a fifth, incomplete unit) were observed in the 5' domain, with the duplicated segments of the same specimen being more related to one another than to the equivalent regions in other specimens, as a result of concerted evolution. We highlight that drawing conclusions from phylogeographical analysis using the control region containing VNTRs must be interpreted with caution, because it violated a basic assumption of phylogeny, since the regions cannot be treated as independent characters.

A new "Bat-Voiced" species of Dendropsophus Fitzinger, 1843 (Anura, Hylidae) from the Amazon Basin, Brazil.

We describe Dendropsophus ozzyi sp. nov., a new species of treefrog, tentatively included in the Dendropsophus microcephalus Group and most notably diagnosed by the presence of pointed fingers and an advertisement call with a very high dominant frequency. The new species is known from three localities in the Brazilian Amazon forest, two on western State of Pará and one (the type locality) in eastern State of Amazonas (03°56'50"S and 58°26'36"W, 45 m a.s.l.).

Reproductive biology of Ameerega trivittata (Anura: Dendrobatidae) in an area of terra firme forest in eastern Amazonia / Biologia reprodutiva de Ameerega trivittata (Anura: Dendrobatidae) em uma área de terra firme na Amazônia Oriental

The reproductive success of tropical amphibians is influenced by factors such as body size and the characteristics of breeding sites. Data on reproductive biology are important for the understanding of population dynamics and the maintenance of species. The objectives of the present study were to examine the abundance of Ameerega trivittata, analyze the use of microhabitats by calling males and the snout-vent length (SVL) of breeding males and females, the number of tadpoles carried by the males and mature oocytes in the females, as well as the relationship between the SVL of the female and both the number and mean size of the mature oocytes found in the ovaries. Three field trips were conducted between January and September, 2009. A total of 31 plots, with a mean area of 2.3 ha, were surveyed, resulting in records of 235 individuals, with a mean density of 3.26 individuals per hectare. Overall, 66.1% of the individuals sighted were located in the leaf litter, while 17.4% were perched on decaying tree trunks on the forest floor, 15.7% on the aerial roots of Cecropia trees, and 0.8% on lianas. Males were observed transporting a mean of 10.8 tadpoles on their backs. A significant correlation was found between the size of the females and the mean diameter of the oocytes. New data were collected on the size of oocytes and no pattern was found in the type of perches used by calling males of the different Ameerega species.

O sucesso reprodutivo das espécies de anfíbios tropicais sofre influência de fatores como local de reprodução e tamanho do corpo dos reprodutores. Informações sobre a biologia reprodutiva são importantes para entender a dinâmica populacional e a manutenção das espécies. Os objetivos deste estudo foram de verificar a abundância, o uso de microhabitat por machos, o comprimento rostro-cloacal (CRC) de machos e fêmeas em atividade reprodutiva, a quantidade de girinos transportados por machos e o número de oócitos maduros por fêmea, e relacionar o número de oócitos maduros e o tamanho médio dos oócitos maduros com o CRC da fêmea. Um total de 31 parcelas foi vistoriado, tamanho médio de 2,3 ha, e um registro de 235 indivíduos, média de 3,26 por hectare. Sessenta e seis por cento dos indivíduos avistados estavam na serapilheira, 17,4% sobre troncos em decomposição no chão da floresta, 15,7% sobre raízes aéreas de Cecropia sp. e 0,8% sobre cipó. Foram observados machos transportando girinos no dorso, a média de girinos transportados foi de 10,80 por macho. A quantidade média de oócitos maduros no ovário das fêmeas foi de 20,17. Houve correlação significativa entre o diâmetro médio dos oócitos e CRC. Neste estudo obtivemos dados novos relacionados ao tamanho médio de oócitos em fêmeas ativamente reprodutivas e observamos que o tipo de sítio de vocalização usado por machos varia entre as espécies do gênero Ameerega.

Forest structure of artificial islands in the Tucuruí dam reservoir in northern Brazil: a test core-area model / Estrutura da floresta em ilhas artificiais no reservatório da usina hidrelétrica de Tucuruí, Brasil: um teste do modelo de área nuclear

Construction of hydroelectric dams in tropical regions has been contributing significantly to forest fragmentation. Alterations at edges of forest fragments impact plant communities that suffer increases in tree damage and dead, and decreases in seedling recruitment. This study aimed to test the core-area model in a fragmented landscape caused by construction of a hydroelectric power plant in the Brazilian Amazon. We studied variations in forest structure between the margin and interiors of 17 islands of 8-100 hectares in the Tucuruí dam reservoir, in two plots (30 and >100m from the margin) per island. Mean tree density, basal area, seedling density and forest cover did not significantly differ between marginal and interior island plots. Also, no significant differences were found in liana density, dead tree or damage for margin and interior plots. The peculiar topographic conditions associated with the matrix habitat and shapes of the island seem to extend edge effects to the islands' centers independently of the island size, giving the interior similar physical microclimatic conditions as at the edges. We propose a protocol for assessing the ecological impacts of edge effects in fragments of natural habitat surrounded by induced (artificial) edges. The protocol involves three steps: (1) identification of focal taxa of particular conservation or management interest, (2) measurement of an "edge function" that describes the response of these taxa to induced edges, and (3) use of a "Core-Area Model" to extrapolate edge function parameters to existing or novel situations.

A construção de usinas hidrelétricas em regiões tropicais tem contribuído significativamente para a fragmentação da floresta. As alterações nas bordas de fragmentos florestais causam profundos impactos na comunidade de plantas, tais como, o aumento em de árvores mortas ou danificadas e a diminuição do recrutamento de plântulas. Este estudo tem como objetivo testar o modelo de área nuclear (core-area model) em uma paisagem de floresta fragmentada resultante da formação do lago da Usina Hidrelétrica de Tucucui na Amazônia. Foram medidas as variações na estrutura em 17 ilhas, com tamanhos variando de 8 a 100 hectares. Em cada ilha foram colocadas duas parcelas, a 1ª parcela a 30 metros da margem e a 2ª parcela a mais de 100 metros da margem da ilha. A densidade e a área basal de árvores, a densidade da regeneração natural e a cobertura do dossel da floresta não foram significativamente diferentes entre as parcelas da borda e do interior das ilhas. Também não foram encontradas diferenças significativas na densidade de lianas, no número de troncos mortos ou árvores danificadas entre as parcelas da borda e do interior das ilhas. A grande declividade do terreno das ilhas, a matriz circundante (água) e a forma irregular da ilhas podem ser os fatores responsáveis me provocar a extensão do efeito de borda em todas as ilhas analisadas, independente do tamanho e grau de isolamento. Nós propomos um novo protocolo para avaliar os impactos ecológicos dos efeitos de borda em fragmentos de habitat criados artificialmente. Este protocolo envolve três etapas: (1) identificação dos táxons biológicos de particular interesse de conservação ou de gestão (2) medição das das variáveis responsaveis pela resposta dos táxons induzidas pelo efeito de borda e (3) Usar o modelo de área nuclear (core area model) na extrapolação das variáveis medidas em situacões novas ou existentes.