Recovery of Amphibian and Reptile Communities During Tropical Secondary Forest Succession

The extensive clearing and modification of natural systems from anthropogenic activities is a pressing global concern. Forest habitats and animal communities within forests are among the most highly impacted, globally. Forest destruction has been repeatedly documented as a driver of biodiversity loss. However, little is known about how animal communities respond when altered landscapes are abandoned and left to regenerate into secondary forests. It is thought that the regrowth of secondary forests may help reverse biodiversity loss by restoring habitats to similar conditions as prior to land conversion. Of the forest cover that remains, over half is secondary forest, and in many countries secondary forest cover has been steadily increasing. Therefore, it is important to understand how and if faunal communities recover during secondary forest regeneration. I combined meta-analytic, field-survey-based, and lab-based experimental techniques to determine how amphibians and reptiles respond to habitat change in general, and secondary forest regeneration on landscapes previously cleared for use as pasture. I addressed five specific questions: 1) what are the effects of habitat alteration on amphibians and reptiles?, 2) what are the effects of secondary forest succession on amphibians and reptiles?, 3) what is the relative importance of stochastic and deterministic effects on community assembly during secondary forest succession?, 4) how do amphibian and reptile species composition, probability of occurrence, and species richness change over the course of secondary forest succession?, and 5) is thermal quality of habitat an important mechanism of species response to secondary forest succession? I found that secondary forest has high conservation value for many amphibian and reptile species, environmental changes associated with secondary forest succession have a significant effect on shaping amphibian and reptile community composition, thermal quality is an important mechanism for species response and that strength of response is mediated by species-specific thermal biology. I also highlight the importance of riparian corridors in maintaining species diversity in modified habitats

From Theory to Practice: A Data Quality Framework for Classification Tasks

The data preprocessing is an essential step in knowledge discovery projects. The experts affirm that preprocessing tasks take between 50% to 70% of the total time of the knowledge discovery process. In this sense, several authors consider the data cleaning as one of the most cumbersome and critical tasks. Failure to provide high data quality in the preprocessing stage will significantly reduce the accuracy of any data analytic project. In this paper, we propose a framework to address the data quality issues in classification tasks DQF4CT. Our approach is composed of: (i) a conceptual framework to provide the user guidance on how to deal with data problems in classification tasks; and (ii) an ontology that represents the knowledge in data cleaning and suggests the proper data cleaning approaches. We presented two case studies through real datasets: physical activity monitoring (PAM) and occupancy detection of an office room (OD). With the aim of evaluating our proposal, the cleaned datasets by DQF4CT were used to train the same algorithms used in classification tasks by the authors of PAM and OD. Additionally, we evaluated DQF4CT through datasets of the Repository of Machine Learning Databases of the University of California, Irvine (UCI). In addition, 84% of the results achieved by the models of the datasets cleaned by DQF4CT are better than the models of the datasets authors.This work has also been supported by: Project: “Red de formación de talento humano para la innovación social y productiva en el Departamento del Cauca InnovAcción Cauca”. Convocatoria 03-2018 Publicación de artículos en revistas de alto impacto. Project: “Alternativas Innovadoras de Agricultura Inteligente para sistemas productivos agrícolas del departamento del Cauca soportado en entornos de IoT - ID 4633” financed by Convocatoria 04C–2018 “Banco de Proyectos Conjuntos UEES-Sostenibilidad” of Project “Red de formación de talento humano para la innovación social y productiva en el Departamento del Cauca InnovAcción Cauca”. Spanish Ministry of Economy, Industry and Competitiveness (Projects TRA2015-63708-R and TRA2016-78886-C3-1-R)

Comunidades de anuros tropicais em paisagens agrícolas: uma abordagem integrada

Doutoramento em Biologia e Ecologia das Alterações Globais (Especialização em Ecologia e Biologia Tropical)Anthropogenic activities such as agriculture and cattle farming are the main causes of biodiversity loss. Agricultural expansion is especially detrimental in the tropics, where agricultural investment meets important social and economic demands, and biodiversity is especially high and unique. Rice is the world’s most important food crop. Given its nature, location and extension worldwide, irrigated rice fields are invariably used by the native fauna. Determining how communities living in these agroecosystems are shaped is therefore of the utmost concern. The Cerrado, the world’s largest and most diverse savanna is experiencing extreme anthropogenic pressure, with 50% of the biome currently under direct human use. Amphibians are among the world’s most threatened vertebrates, playing keystone roles in ecosystem functioning. Given the inherent complexity of their life cycle, approaching how amphibian populations are affected by anthropogenic activities requires an integrated, multidimensional approach, at multiple scales. This project sought to assess how the anuran community of the Cerrado is being affected by agricultural pressure, assessing the extinction risk, analyzing the selected traits, and variation in taxonomic, phylogenetic and functional diversity at different scales, as well as the functional connectivity of frogs in rice crops. The official extinction risk is underestimated for the anurans of the Cerrado. Breeding site, habitat specialization, and clutch size are predictors of increased extinction risk. The southwest and central regions of the biome are the main hotspots of increased extinction risk, and should be prioritized for conservation. Habitat conversion and crop management caused profound changes to the anuran community, causing increased functional divergence and dramatic loss of functional and phylogenetic diversity in agricultural environments. Anurans with restricted range, habitat specialization, small clutches and large body size were excluded from agricultural environments. Additionally, frogs from agricultural environments had lower body condition. Thus, the conversion of natural vegetation to rice crops results in such environmental stress, that large subsets of species are driven to local extinction irrespective of their specialization, and even the more resilient species exhibit lower body condition. The presence of abundant forest fragments and water bodies is crucial for the maintenance of high levels of functional and phylogenetic diversity, and also to ensure functional connectivity for anuran populations in agricultural landscapes.Atividades antrópicas como a agricultura e a pecuária são as principais causas da perda de biodiversidade. A expansão agrícola é especialmente nociva nos trópicos, onde o investimento agrícola responde a importantes demandas sociais e económicas, e a biodiversidade é especialmente alta e única. O arroz é a cultura alimentar mais importante do mundo. Dada a sua natureza, localização e extensão a nível global, os campos de arroz irrigado são invariavelmente utilizado pela fauna nativas. Determinar como as comunidades que vivem nesses agroecossistemas são afectadas é, portanto, de extrema importância. O Cerrado, a maior e mais diversa savana do planeta, encontra-se sob extrema pressão antropogénica, com 50% do bioma atualmente sob uso humano direto. Os anfíbios estão entre os vertebrados mais ameaçados do planeta, desempenhando papéis de destaque no funcionamento dos ecossistemas. Como o seu ciclo de vida é particularmente complexo, investigar a forma como as populações de anfíbios são afectadas por atividades antropogénicas requer uma abordagem integrada e multidimensional, a várias escalas. Com este projecto pretendeu-se avaliar a forma como a comunidade de anuros do Cerrado está a ser afetada pela pressão agrícola, avaliando o risco de extinção, analisando os traits selecionados, e a variação na diversidade taxonómica, filogenética e funcional em diferentes escalas, bem como a conectividade funcional dos anuros em culturas de arroz. Determinou-se que o risco de extinção de risco oficial dos anfíbios do Cerrado se encontra subestimado. O local de reprodução, habitat e tamanho da postura são preditores de elevado risco de extinção em anuros. O sudoeste e região central do bioma são as principais regiões de espécies de alto risco de extinção, e devem ser priorizados para a conservação. Concluiu-se também que a conversão do habitat e a gestão agrícola causaram profundas alterações na comunidade de anuros, com o aumento da divergência funcional e dramática perda de diversidade funcional e filogenética em ambientes agrícolas. Anuros com distribuição restrita, especialização de habitat, posturas pequenas e grande tamanho corporal foram excluídos dos ambientes agrícolas. Adicionalmente, anuros provenientes de culturas apresentaram menor condição corporal. Assim, a conversão de vegetação natural em plantações de arroz irrigado resulta na extinção local de muitas espécies, independentemente da sua especialização, e no decréscimo dos índices de condição corporal nas espécies mais resistentes. A presença de abundantes fragmentos florestais e de corpos de água é determinante para a manutenção de níveis elevados de diversidade funcional e filogenética, e ainda para assegurar a conectividade funcional para as populações de anuros em paisagens agrícolas

AXOLOTL PAEDOMORPHOSIS: A COMPARISON OF JUVENILE, METAMORPHIC, AND PAEDOMORPHIC AMBYSTOMA MEXICANUM BRAIN GENE TRANSCRIPTION

Unlike many amphibians, the paedomorphic axolotl (Ambystoma mexicanum) rarely undergoes external morphological changes indicative of metamorphosis. However, internally, some axolotl tissues undergo cryptic metamorphic changes. A previous study examined interspecific patterns of larval brain gene expression and found that these species exhibited unique temporal expression patterns that were hypothesized to be morph specific. This thesis tested this hypothesis by examining differences in brain gene expression between juvenile (JUV), paedomorphic (PAED), and metamorphic (MET) axolotls. I identified 828 genes that were expressed differently between JUV, PAED, and MET. Expression estimates from JUV were compared to estimates from PAED and MET brains to identify genes that changed significantly during development. Genes that showed statistically equivalent expression changes across MET and PAED brains provide a glimpse at aging and maturation in an amphibian. The genes that showed statistically different expression estimates between metamorphic and paedomorphic brains provide new functional insights into the maintenance and regulation of paedomorphosis. For genes that were not commonly regulated due to aging, paedomorphs exhibited greater transcriptional similarity to juvenile than metamorphs did to juvenile. Overall, gene expression differences between metamorphic and paedomorphic development exhibit a mosaic pattern of expression as a function of aging and metamorphosis in axolotls

Development of volunteer-driven indices of biological integrity for wetlands in West Virginia

Wetland indices of biological integrity (IBIs) are used to satisfy the water resources monitoring requirements of the Clean Water Act (CWA). However, debate still exists on what classification systems and taxa to base these IBIs upon. Our cumulative research, representing indices of biological integrity designed for regional HGM subclasses, designated HGM management classes and Cowardin et al. (1979) classes for West Virginia. The indices were derived from metrics calculated from anuran, avian, macroinvertebrate, and vegetation communities; each representing increasing levels of resources associated with gathering the necessary data. For example, avian and anuran data used to derive floodplain wetland IBI metrics can be collected by volunteers, but the disturbance scores only account for 46% and 18% of the variation in IBI scores, respectively. Alternatively, the disturbance scores account for 56% and 47% of the variation in vegetation and invertebrate IBI scores, respectively. However, if the floodplain wetland was also a scrub-shrub wetland, by adding the avian and anuran metrics of both floodplain and scrub-shrub IBIs, the resulting hybrid-class, multi-taxa IBI disturbance scores accounts for 89% of the variation in IBI scores. We evaluate each of these taxa groups alone and in combination, in single and hybrid classification schemes, to examine changes in sensitivities to the disturbance gradient. The result is a decision making tool that can assist resource managers by providing them with the opportunity to stretch finite resources; while still ensuring the monitoring captures changes in wetland communities due to human disturbance.;Keywords. Indices of biological integrity, IBIs, wetlands, disturbance, anuran communities, avian communities, macroinvertebrate communities, vegetation communities, West Virginia

Methodological approaches for sound training in underepresented learners: a case study with american toads (anaxyrus americanus)

efforts to better understand the minds of animals have been flourishing, with methodological breakthroughs and a remarkable increase in the number of publications dealing with a wide variety of non-model species. The growing interest in species that are distantly related to humans in the field of comparative physiology and cognition was confirmed with the general reviewed performed in this dissertation. Yet, the progress is unbalanced among the ectothermic vertebrates (fish, reptiles, and amphibians), with almost no research on amphibians. Many animals remain unstudied, even though they may possess unique and powerful adaptations to respond to environmental stimuli that can be useful for learning and cognition research. Inspired by the efforts to increase species representation in studies of learning and cognition, this dissertation also explored two methods of spatial learning to train American toads to respond to tone burst cues in order to find the reward. As frogs and toads have been able to acquire maze task associated to visual cues and mating calls, I predicted that a protocol based on these previously successful methods could be reliable in testing toads to associate and discriminate tone bursts of different frequencies (HZ). None of the methods were effective in demonstrate learning abilities in American toads, but the results pointed to important challenges to calibrate methods for future studies. Aspects to consider such as sex effects on side bias and can be used to reflect behavioral plasticity as a metric for the process of learning, such as time latency (longer it takes a toad to succeed, the more likely they will be successful) and the behavior displayed during the task as an indication of behavioral flexibility for decision making. Besides these aspects of the procedure, there are physiological and evolutionary aspects that might make toads unable to interact with non-mating sounds. These aspects and the level of hearing constraints that can affect learning assessment in toads are critical to answer broad questions on anuran auditory role beyond mating purposes

Neural mechanisms of conspecific call recognition and female preferences in Túngara frogs, Physalaemus pustulosus

Females exhibit behavioral preferences for mating with males of their own species, and they often prefer conspecific males displaying elaborate sexual signals to males with simpler signals. Although female mate preferences have been the subject of many theoretical and experimental studies, little attention has been given to understanding the neural processes influencing mate choice. To address this gap, my dissertation research focused on understanding sensory processing of acoustic male signals in female túngara frogs (Physalaemus pustulosus). I used the expression of the activity-regulated genes, egr-1 and Arc, to characterize neural responses to male signals that vary in their relevance and attractiveness to females. I first asked which brain areas process conspecific signals and where conspecific recognition may occur. I then asked whether differences in the level of neural activity elicited when females hear preferred versus less-preferred conspecific signals can explain female mate preferences for certain male callers. I found that neural responses to conspecific signals are widespread in the female túngara frog auditory system, as well as in pallial regions that were previously unknown to process auditory information. By comparing neural responses to acoustic stimuli that females recognize as conspecific signals to stimuli that are not recognized, I determined that the laminar nucleus of the torus semicircularis, a subdivision of the auditory midbrain, shows selective responses to stimuli that elicit species recognition. These findings indicate that activity in the laminar nucleus closely corresponds with behavioral decisions made by female frogs, and they raise the possibility that conspecific recognition may emerge from selectivity in a single auditory nucleus. Finally, I tested whether female-preferred, elaborate male signals elicit greater neural activity than simpler signals. I failed to find neural activity biases towards preferred signals in the ascending auditory system and forebrain, including the pallium, demonstrating that variation in the acoustic complexity and attractiveness of male signals is not simply encoded by the magnitude of the neural response evoked by those signals. Although further studies are needed to understand how the brain encodes attractiveness, my research represents an important contribution towards understanding the neural mechanisms underlying female mate choice decisions