Filogeografia da Mata Atlântica

Phylogeography aims to understand the principles and processes governing the geographic distribution of intra-specific or closely related species’ lineages, based on the spatial distribution of gene genealogies. Some phylogeographic studies of Atlantic Forest (AF) organisms revealed three main phylogeographic discontinuities occurring in different organisms associated to glaciations and neo-tectonic activities during the Quaternary. However, it is still necessary to study more organisms from this biome to build a hypothesis on dynamics of diversification that generated the diversity in the AFA filogeografia procura entender os princípios e os processos que governam a distribuição geográfica de linhagens intra-específicas ou de espécies próximas, baseada na distribuição espacial de genealogias gênicas. Estudos filogeográficos de alguns organismos da Mata Atlântica (MA) publicados até o momento têm apontado para a existência de três principais descontinuidades filogeográficas associadas às glaciações e atividades neo-tectônicas ocorridas no Quaternário. Entretanto, ainda é necessário agregar mais estudos filogeográficos de organismos desse bioma para ser possível traçar uma hipótese sobre a diversificação que gerou a diversidade na MA

Processos Evolutivos na Amazônia e na Mata Atlântica

A Floresta Amazônica e a Mata Atlântica estão entre os ecossistemas com os maiores índices de biodiversidade do mundo, e estão separadas pela diagonal de áreas abertas da América do Sul, que é formada pelos biomas Chaco, Cerrado e Caatinga. Na Mata Atlântica estudos sobre evolução e biogeografia têm mostrado que os ciclos glaciais do Pleistoceno tiveram importante papel na diversificação da biota residente em suas florestas. Além disso, outros estudos apontam que atividades tectônicas ocorridas durante o fim do Terciário e no Quaternário possivelmente contribuíram para a diversificação de algumas linhagens. Contudo, na Amazônia, o estabelecimento da drenagem atual da bacia do Rio Amazonas tem sido atribuído como um dos principais mecanismos responsáveis para a origem da biota residente no bioma. Ademais, o soerguimento dos Andes também vem sendo apontado como um dos mecanismos responsáveis pela diversificação da Amazônia. Entretanto, tanto na Mata Atlântica quanto na Amazônia, a origem da biodiversidade parece ter sido produto de uma história bastante complexa, e assumir que esta diversificação foi originada por um ou poucos processos evolutivos é simplista demais. O que parece ter acontecido nestas florestas foi um processo de diversificação contínuo ao longo do tempo, e extremamente complexo com diversas forças atuantes.Palavras-Chave: Biogeografia; Região Neotropical; Biodiversidade.The Amazon and the Atlantic Forest biomes are amongst ecosystems with high levels of biodiversity in the world, and are separated by a broad diagonal of more xeric habitats comprising the Chaco, the Cerrado uplands, and the Caatinga. In the last decade, studies on biogeography and evolution of the Atlantic Forest have showed that that Pleistocene glacial cycles played an important role on the diversification of its biota. Furthermore, tectonic activities in the late Tertiary and the Quaternary may have contributed for the diversification of some lineages. Nevertheless, in the Amazon, establishment of current drainage of Amazon River basin could be responsible for the diversification of the organisms from this biome. Moreover, the uplift of the Andes was pointed as a driver for diversification in Amazonian forests. Notwithstanding, both in the Atlantic Forest and the Amazon, the origin of biodiversity seems to have been the product of a complex history, and assume that this diversification was originated by one or a few evolutionary processes is too simplistic. Thus, what seems to have happen in these forests was an ongoing process of diversification over time, and extremely complex with many interacting forces.Keywords: Biogeograph; Neotropical Region; Biodiversity

Plumage variation in the Planalto Woodcreeper (Dendrocolaptes platyrostris) and the melanocortin-1 receptor gene (MC1R)

The Planalto Woodcreeper (Dendrocolaptes platyrostris) presents “pale” and “dark” plumage variants, which are distributed throughout the Cerrado and Caatinga, and throughout the Atlantic Forest, respectively. To understand the genetic nature of the plumage variation in the species, we partially sequenced the melanocortin-1 receptor (MC1R) gene, which is associated with melanic phenotypes in vertebrates. We found no correlation between variation at MC1R sequences and plumage color in D. platyrostris. Aminoacid sites that were correlated with variation in melanic plumage in other bird species were monomorphic in D. platyrostris. Our results suggested that MC1R seems not to be involved in controlling plumage variation in D. platyrostris.Fil: Corso, Josmael. Universidade Federal do Rio Grande do Sul. Departamento de Genética; BrasilFil: Cabanne, Gustavo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales; ArgentinaFil: Mendonça d'Horta, Fernando. Universidade de Sao Paulo. Instituto de Biociências; BrasilFil: da Silva Loreto, Elgion Lucio. Universidade Federal de Santa Maria. Departamento de Biologia; BrasilFil: Miyaki, Cristina Yumi. Universidade de Sao Paulo. Instituto de Biocièncias; Brasi

Speciation Associated with Shifts in Migratory Behavior in an Avian Radiation

Gómez-Bahamón et al. show that speciation is associated with changes in migratory behavior in fork-tailed flycatchers (Tyrannus savana). Divergence occurred through loss of migratory behavior of a single lineage. This mode of speciation likely occurred across New World flycatchers (Tyrannidae).Fil: Gómez Bahamón, Valentina. Field Museum of Natural History; Estados Unidos. Investigación Para la Conservación En El Neotrópico; Colombia. University of Illinois; Estados Unidos. Universidad de los Andes; ColombiaFil: Márquez, Roberto. University of Chicago; Estados UnidosFil: Jahn, Alex. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Miyaki, Cristina Yumi. Universidade de Sao Paulo; BrasilFil: Tuero, Diego Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Laverde, Oscar. Universidad de los Andes; Colombia. Pontificia Universidad Javeriana; ColombiaFil: Restrepo, Silvia. Universidad de los Andes; ColombiaFil: Cadena, Carlos Daniel. Universidad de los Andes; Colombi

Optimization of bioactive compound’s extraction conditions from beetroot by means of artificial neural networks (ANN)

The present work used an artificial neural network (ANN) model to correlate beetroot extraction conditions with total phenolic compounds (TPC), anthocyanins (ANT) and antioxidant activity (AOA). The input variables were extraction time, type of solvent, solvent volume/sample mass (VMR = volume to mass ratio) and order of extraction. The ANN models produced showed very good accuracy (R>94%), being suitable for data mining using weight analysis techniques. The experiments involved variable conditions: solvents (methanol, ethanol: water and acetone: water), extraction times (15 and 60 min), VMR (5, 10 and 20), order of extract (3 sequential extractions). The TPC were evaluated by the Folin-Ciocalteu method, ANT by the SO 2 bleaching method and AOA following the ABTS method. The experimental results showed that the extracting solutions used in this study exhibited similar extraction efficiency for TPC, but not for AOA. Also, the results allowed concluding that a higher VMR originated extracts with higher amounts of TPC and AOA.info:eu-repo/semantics/publishedVersio

Phenotypic evolution of an Atlantic Forest passerine (Xiphorhynchus fuscus): Biogeographic and systematic implications

We studied the phenotypic variation of the Atlantic Forest passerine Xiphorhynchus fuscus (Aves: Dendrocolaptidae) with the broad aim of addressing whether the history and type of forest affected the evolution of endemic taxa. We also tested whether the different subspecies and genetic lineages of X.fuscus could be considered full species. We collected plumage and body size measurements and, in combination with genetic data, used multivariate tests to evaluate the working hypotheses. Our results, combined with previous biogeographic analyses, indicate that vicariant events have been important determinants in the evolution of phenotypic characters of X.fuscus, once genetic isolation was complete. Our analysis also suggests that forest heterogeneity and ecotones are important factors in the early evolution of Atlantic Forest taxa, perhaps via divergent selection. Forest instability during the Pleistocene was critical in the evolution of phenotypic traits. We confirm that the subspecies atlanticus should be considered a full species. Other lineages or populations are also phenotypically differentiated but we do not suggest considering them as full species. They share high levels of gene flow and are part of a continuous latitudinal cline of phenotypic variation. Our study suggests that not all the historic events in the Atlantic Forest that affected the evolution of genetic lineages also influenced the evolution of phenotypic characters in the same direction and intensity. Undoubtedly, natural selection played a major role in the evolution of Atlantic Forest organisms. © 2014 The Linnean Society of London

Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest

The effects of global glaciations on the distribution of organisms is an essential element of many diversification models. However, the empirical evidence supporting this idea is mixed, in particular with respect to explaining tropical forest evolution. In the present study, we evaluated the impacts of range shifts associated with Pleistocene global glacial cycles on the evolution of tropical forests. In particular, we tested the predictions: (1) that population genetic structure increases with fragmentation variation between the present and the Last Glacial Maximum (LGM) and also (2) with geographical range instability; and (3) that genetic diversity increases with range stability and (4) decreases with fragmentation variation between periods. To address our predictions, we studied population genetic structures and modelled present and past distributions of 15 Atlantic Forest (AF) endemic birds. Afterwards, we evaluated the relationship of population genetic parameters with metrics of species range shifts between the present and the LGM. We found that geographical ranges of AF birds changed in concert with Pleistocene glacial cycles but, unexpectedly, our findings suggest the novel idea that ranges during glacial maxima were slightly larger on average, as well as equally fragmented and displaced from the interglacial ranges. Our findings suggest that range shifts over the late Pleistocene impacted on the diversification of forest organisms, although they did not show that those range shifts had a strong effect. We found that a combination of fragmentation variation across time, small current range size, and range stability increased population genetic structure. However, neither fragmentation, nor range stability affected genetic diversity. Our study showed that evolutionary responses to range shifts across AF birds have a high variance, which could explain the mixed support given by single-species studies to the action of Pleistocene range shifts on population evolution. © 2016 The Linnean Society of Londo

An Online mtDNA Tool for Identification of \ud Neotropical Psittacid Species and \ud Taxonomic Issues: A Study Case of the \ud Amazona ochrocephala Complex

Parrots are among the most popular pets in the world and they are also some of the most illegally traded, particularly in Brazil. Some computational tools were recently developed by researchers based on molecular databases for taxonomy support, forensic identification and conservation purposes. In this study, the DNA Surveillance platform was used to build an online database tool for molecular identification of Brazilian Psittacids using DNA sequences of six mitochondrial genes. To illustrate possible taxonomic issues of the online tool due to interspecific hybridization or unresolved taxonomy, we focused on Amazona aestiva that is considered as one of the most common parrots in Brazil, commonly bred as pets, and considered to be part of a species complex with Amazona ochrocephala from South America. We provide three curated sequence databases, which allow the species identification of individuals or tissue samples of birds of the Psittacidae family using mitochondrial DNA markers, and a comprehensive description of a taxonomic issue involving the A. ochrocephala complex. The results obtained corroborate previous studies suggesting that these species are not reciprocally monophyletic, due to either an ancient hybridization in central Brazil, or, they maybe just are morpho-varieties of the same species. Alternatively, if A. aestiva and A. ochrocephala were considered as sister species, the data could be interpreted either as a result of secondary contact or incipient speciation. Beyond the use of mtDNA for species identification, the high mtDNA haplotype diversity observed in A. aestiva indicates its potential use in discrimination of lineages that could be an important auxiliary tool to certify the captive origin of legally commercialized parrots.We thank Paulo Machado and Fazenda Vale Verde, who provided blood samples of captive animals used in this study. Thanks to Camila Clozato Lara and Ricardo França who helped in the execution of some laboratory experiments. This study was supported by FAPEMIG (PRONEX), FAPEMIG-Vale SA (RDP-00043-10/2010-1), CNPq (473428/2004-0; 303558/2009-1; 473809/2008-7 and Pro-Reitoria de Pesquisa da UFMG.). A.V.C. received studentship from FAPEMIG and CNPq; F.A.A.S. was supported by FAPEMIG and CNPq; C.Y.M. was supported by FAPESP, CNPq, and CAPES. F.R.S was supported by CNPq

Die populationsgenetische Struktur des in der Mata Atlântica endemischen Rotkehl-Mückenfressers ( Conopophaga lineata , Passeriformes: conopophagidae) lässt eine Kontaktzone in der Mata Atlântica erkennen

The Rufous Gnateater, Conopophaga lineata, is a small insectivorous understory bird which is endemic to and widely distributed in the tropical and subtropical Atlantic forest of South America. Its distribution makes it ideally suited for testing two major hypotheses for the origin of biodiversity, namely, the riverine barrier and the forest refuge hypotheses. In this study, we sequenced mitochondrial (control region) and nuclear markers (intron 5 of the β-fibrinogen gene) for individuals distributed in the southern Atlantic forest and obtained a strong genetic structure with one clear discontinuity in northern Brazilian state of São Paulo. We consistently detected signals of demographic expansion for both markers, with estimates indicating that expansion started in the Late Pleistocene (250,000 years ago), suggesting that the forest refuge hypothesis potentially explains Rufous Gnateater’s diversification. We also found evidence of gene flow between populations from each side of this discontinuity, with a possible secondary contact zone occurring in the states of Minas Gerais, São Paulo, and Rio de Janeiro.Der Rotkehl-Mückenfresser, Conopophaga lineata, ist ein kleiner insektivorer Vogel, der im Unterholz der tropischen und subtropischen Mata Atlântica in Südamerika endemisch und weit verbreitet ist. Die Verbreitung des Rotkehl-Mückenfressers macht ihn besonders dafür geeignet, zwei Haupthypothesen zum Ursprung von Biodiversität zu testen, die „Flüsse als Barrieren“-Hypothese (“riverine barrier hypothesis”) und die „Wälder als Rückzugsgebiete“-Hypothese (“forest refuges hypothesis”). Wir haben mitochondriale Marker (Kontrollregion) und Zellkernmarker (Intron 5 von β-Fibrinogen) für in der südlichen Mata Atlântica verbreitete Individuen sequenziert und eine ausgeprägte genetische Struktur mit einer klaren Diskontinuität im Norden des Bundesstaates São Paulo gefunden. Für beide Marker haben wir durchweg Signale demographischer Ausbreitung entdeckt, die schätzungsweise im späten Pleistozän (vor 250000 Jahren) begann, was darauf hindeutet, dass die „Wälder als Rückzugsgebiete“-Hypothese einen möglichen Einflussfaktor bei der Diversifikation des Rotkehl-Mückenfressers darstellt. Wir haben auch Hinweise auf Genfluss zwischen Populationen auf beiden Seiten der Diskontinuität gefunden, mit einer möglichen sekundären Kontaktzone in den Bundesstaaten Minas Gerais, São Paulo und Rio de Janeiro.\ud Communicated by J. Fjeldså.This work was supported by FAPEMIG (Fundação de Amparo a Pesquisa do Estado de Minas Gerais 17228), CNPq, FAPESP (BIOTA 2013/50297-0), NSF (DOB 1343578), NASA, CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), and the Research Center on Biodiversity and Computing (BioComp) of the Universidade de São Paulo (USP), supported by the USP Provost’s Office for Research. Gisele Dantas worked under a Post-doctoral grant CAPES/PNPD (2010/52590-8) and CNPq (503145/2009-2). We also thank the Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (Brazil), Instituto Florestal de São Paulo (Brazil), and Instituto Estadual de Florestas de Minas Gerais (Brazil) for the permits to collect samples (IBAMA/MMA no 03/2004 IBAMA/MMA: 011/2000, processes 1835/2000; 053/2001, 1835/00-07; 070/2002, 02015.001835/00-07; 207/2003, 02015.023482/98-38). We gratefully acknowledge the improvements in English usage made by Caitlin Stern through the Association of Field Ornithologists’ program of editorial assistance

Phylogeny and historical biogeography of gnateaters (Passeriformes,\ud Conopophagidae) in the South America forests

We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.We thank John Bates (FMNH) and Nate Rice (ANSP) for providing some of the tissues used in this study. We thank Fernando M. d’Horta, Renato G. Lima, Gustavo S. Cabanne, and Guilherme R. Brito for collecting some samples used in this study. Amy Chernasky from Lynx Edicions kindly provided permission to use images from Handbook of Birds of the World. We thank Gustavo Bravo for suggestions on previous version of the manuscript. We thank an anonymous reviewer and the Editor Carey Krajewski for their comments. This study was co-funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (2009/12989-1, BIOTA 2013/50297-0), NSF (DOB 1343578), NASA, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). JF and PHF thanks the Danish National Research Foundation for funding the Center for Macroecology, Evolution and Climate; PGPE and MI thanks the Swedish Research Council for funds (Grant No. 621-2010-5321 to P.G.P.E.). PHF was supported by Marie-Curie grants (PIOF-GA-2012-330582-CANARIP-RAT, FP7 CIG-293845). Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA) and Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) provided permits to collect the samples. This work was developed in the Research Center on Biodiversity and Computing (BioComp) of the Universidade de São Paulo (USP), supported by the USP Provost’s Office for Research