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

Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish

Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species- specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps and geological faults. The morphological (colour pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within river systems and, consequently, the dynamics of gene flow between freshwater lineages/species.River networks are spatially and temporally dynamic environments that impose challenges to the study of hybrid zones. Here, we elucidate the morphological and genetic structure of a hybrid zone generated by secondary contact between lineages of a Neotropical fish genus and discuss the possible role of past and current river properties (including river captures) in its origin and structure.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163541/3/jeb13689_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163541/2/jeb13689-sup-0001-AppendixS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163541/1/jeb13689.pd

A hierarchical topic modelling approach for tweet clustering

While social media platforms such as Twitter can provide rich and up-to-date information for a wide range of applications, manually digesting such large volumes of data is difficult and costly. Therefore it is important to automatically infer coherent and discriminative topics from tweets. Conventional topic models and document clustering approaches fail to achieve good results due to the noisy and sparse nature of tweets. In this paper, we explore various ways of tackling this challenge and finally propose a two-stage hierarchical topic modelling system that is efficient and effective in alleviating the data sparsity problem. We present an extensive evaluation on two datasets, and report our proposed system achieving the best performance in both document clustering performance and topic coherence

Variation and genetic structure of Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations based on ISSR pattern

For a study of diversity and genetic structuring in Melipona quadrifasciata, 61 colonies were collected in eight locations in the state of Minas Gerais, Brazil. By means of PCR analysis, 119 ISSR bands were obtained, 80 (68%) being polymorphic. He and H B were 0.20 and 0.16, respectively. Two large groups were obtained by the UPGMA method, one formed by individuals from Januária, Urucuia, Rio Vermelho and Caeté and the other by individuals from São João Del Rei, Barbacena, Ressaquinha and Cristiano Otoni. The Φst and θB values were 0.65 and 0.58, respectively, thereby indicating high population structuring. UPGMA grouping did not reveal genetic structuring of M. quadrifasciata in function of the tergite stripe pattern. The significant correlation between dissimilarity values and geographic distances (r = 0.3998; p < 0.05) implies possible geographic isolation. The genetic differentiation in population grouping was probably the result of an interruption in gene flow, brought about by geographic barriers between mutually close geographical locations. Our results also demonstrate the potential of ISSR markers in the study of Melipona quadrifasciata population structuring, possibly applicable to the studies of other bee species

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

Patterns and processes of diversification in birds from the Amazon and the Atlantic Forest

Nesta Tese foram descritos padrões de diversificação de pássaros que ocorrem na Amazônia e na Mata Atlântica, os quais permitiram fazer inferências sobre os processos que podem ter influenciado a evolução das biotas residentes nestes biomas. Nós produzimos sequências de genes mitocondriais e nucleares para fazer inferências sobre a biogeografia histórica destes biomas. A Tese foi dividida em seis capítulos. Nos capítulos 1 a 4 os táxons Basileuterus leucoblepharus, Myrmotherula gularis e o complexo Synallaxis ruficapilla foram estudados para se entender a diversificação da Mata Atlântica. Estes estudos revelaram que os ciclos glaciais do fim do Pleistoceno tiveram importante papel na diversificação destes táxons. Ainda, atividades tectônicas ocorridas durante o Quaternário possivelmente contribuíram para a diversificação do complexo S. ruficapilla. No capítulo 5 o complexo Thamnomanes caesius/T. schistogynus foi analisado visando inferir a história evolutiva da Amazônia. Os resultados deste estudo mostraram que tanto a origem recente dos rios amazônicos (do Plioceno ao Pleistoceno) quanto os ciclos glaciais possivelmente foram responsáveis pela diversificação deste grupo. No capítulo 6 o grupo Suboscines foi estudado para compreender a dinâmica das conexões históricas entre as florestas Amazônica e Atlântica. Os resultados mostraram que os contatos históricos entre estes dois biomas correspondem a duas conexões espaço-temporais distintas: uma mais antiga durante o Mioceno através da porção sul da diagonal seca da América do sul, e uma mais recente durante o Plioceno e o Pleistoceno através da Caatinga e Cerrado no Nordeste do Brasil. Os dados desta Tese permitiram testar o papel de algumas hipóteses concorrentes na diversificação da Amazônia e da Mata Atlântica. A hipótese dos rios parece ter contribuído para a diversificação da Amazônia. A hipótese dos refúgios florestais possivelmente teve um papel crucial da diversificação da biota da Mata Atlântica. A hipótese dos refúgios também não pode ser rejeitada como um das forças que deu origem à biota da Amazônia que observamos atualmente. Eventos tectônicos e mudanças climáticas contribuíram para conexões históricas entre a Amazônia e Mata AtlânticaThis PhD Dissertation describes patterns of diversification of species of passerines that occur in the Amazon and the Atlantic Forest and that allowed making inferences on the processes that may have influenced the evolution of the organisms that live in these forests. We generated sequences of mitochondrial and nuclear genes to study the historical biogeography of these biomes. This work includes six chapters. In chapters 1 to 4 we analyzed Basileuterus leucoblepharus, Myrmotherula gularis, and the Synallaxis ruficapilla complex in order to depict the diversification within the Atlantic Forest. These studies revealed that late Pleistocene glacial cycles played an important role on the diversification of these taxa. Furthermore, tectonic activities in the Quaternary may have contributed for the diversification of the S. ruficapilla complex. In chapter 5 we analyzed the Thamnomanes caesius/T. schistogynus complex in order to infer about the diversification in the Amazon. The results of this study showed that both the recent origin of Amazonian rivers (Pliocene to Pleistocene) as glacial cycles could be responsible for the diversification of these organisms. In chapter 6 we analyzed the New World suboscines in order to depict the historical connection dynamics between the Amazon and the Atlantic Forest. Our results pointed to two distinct spatiotemporal pathways connecting these forests in the past: (1) older connections during the Miocene through southern South America dry diagonal; (2) younger connections during the Pliocene to Pleistocene through Cerrado and Caatinga in northeastern Brazil. The results of this PhD Dissertation allowed us to test the role of concurrent hypotheses of diversification in the Amazon and the Atlantic Forest. The riverine hypothesis seems to have contributed to the evolution of the Amazonian biota. The refuge hypothesis seems to be the main force of diversification of organisms from the Atlantic Forest. Moreover, we could not reject the refuge hypothesis as a force of diversification of organisms that occur in the Amazon forest. Tectonic events and climate changes played important roles in the historical connection between the Amazon and the Atlantic Fores

Geographic distribution, phylogeography and evolutionary history of stingless bee Melipona quadrifasciata (Hymenoptera, Apidae)

A abelha Melipona quadrifasciata, conhecida popularmente como mandaçaia, apresenta duas subespécies: M. q. anthidioides e M. q. quadrifasciata. A principal diferença entre as subespécies são as faixas tergais amarelas, que são contínuas em M. q. quadrifasciata e descontínuas em M. q. anthidioides. A correlação entre a distribuição geográfica e a coloração metassomal e os sítios de restrição do DNA mitocondrial foi caracterizado de ambos morfotipos de M. quadrifasciata, como determinado pelos padrões de faixas tergais. Foram examinados exemplares provenientes de um total de 198 localidades no Brasil, e com base na variação observada os exemplares foram distribuidos em quatro classes. A distribuição geográfica de M. quadrifasciata observada mostra M. q. quadrifasciata, uma forma com faixas tergais contínuas, ocupando a porção sul da distribuição, do Rio Grande do Sul até a metade sul de São Paulo, indo a oeste até a província de Misiones, na Argentina e porção sudeste do Paraguai. A forma com faixas interrompidas, M. q. anthidioides, distribui-se da metade nordeste de São Paulo até o extremo norte da região da Chapada Diamantina, na Bahia, estendendo-se a oeste pelo Triângulo Mineiro e região central do estado de Goiás. Dois padrões RFLP foram identificados, sendo um presente em M. q. quadrifasciata, e o outro em M. q. anthidioides e nas populações com padrão de faixas tergais continuo do norte de Minas Gerais e Sergipe e nordeste da Bahia. Avaliou-se também o padrão filogeográfico das populações de M. quadrifasciata ao longo de sua área de distribuição. Para análise filogeográfica foram utilizados 852 pb referentes a parte do gene COI do mtDNA de 145 indivíduos de M. quadrifasciata provenientes de 56 localidades dos estados do RS, SC, PR, SP, RJ, MG, ES, BA e SE. Foram identificados 50 haplótipos, com uma diversidade nucleotídica (&#960;) de 0,0055 e uma diversidade haplotípica (Hd) de 0,957. Foi evidenciado, na inferência filogenética e na rede de haplótipos, a presença de dois clados: o clado sul compreendendo à subespécie M. q. quadrifasciata, e o clado norte formado pela subespécie M. q. anthidioides e as populações de faixa tergal contínua do norte de Minas Gerais e do Sergipe e nordeste da Bahia. A AMOVA mostrou um percentual de variação entre os clados de 68,56% e um &#934;ST de 0,905. A barreira de fluxo gênico, estimada pela SAMOVA, foi localizada próxima ao Vale do Ribeira do Iguape no sul do estado de São Paulo, concordando também com a separação dos clados. A mismatch distribution evidenciou gargalos populacionais em ambos clados por meio de distribuição unimodal. O tempo de divergência estimado pela análise de coalescência foi entre 490.000 e 390.000 anos A.P. Outras espécies de abelhas, M. bicolor e M. marginata, exibem diferenciação morfológica que recebe o status de subespécies, apresentando zona de separação entre as subespécies concordante com M. quadrifasciata. Padrões filogeográficos com vicariância semelhante foram reportados para pássaros (Xiphorhynchus fuscus) e serpentes (Bothrops jararaca).Melipona quadrifasciata, regionally known as mandaçaia , presents two distinct subspecies: M. quadrifasciata anthidioides and M. quadrifasciata quadrifasciata. They differ in the yellow tergal stripes, which are continuous in M. q. quadrifasciata and discontinuous in M. q. anthidioides. The correlation between geographic distribution and metasomal coloration was investigated and characterized the restriction sites in the mtDNA of both morphotypes of M. quadrifasciata, as determined by the tergal stripes patterns. Specimens from 198 localities were examined, and the variation observed in the pattern of tergal stripes was grouped into four distinct classes. The distribution pattern of M. quadrifasciata found in the present work agrees with the previously reported pattern for this species, i.e., M. q. quadrifasciata, a form characterized by continuous tergal stripes, inhabits the southern portion of the distribution, from Rio Grande do Sul to southern São Paulo, including Misiones, in Argentina, and southeastern Paraguay to the west, whereas M. q. anthidioides, a form with interrupted stripes, occurs from northeastern São Paulo to the northern portion of Diamantina Plateau, in Bahia, and westwards to the western tip of Minas Gerais and central portion of the Goiás State. The data of RFLP showed two restriction patterns, one present in M. q. quadrifasciata, and another in M. q. anthidioides and in populations with continuous tergal stripes from northern Minas Gerais and northeastern Bahia and Sergipe. The phylogeography was evaluated across its range of M. quadrifasciata populations. Using 852 bp of mtDNA COI gene of 145 individuals from 56 locates of RS RS, SC, PR, SP, RJ, MG, ES, BA and SE states in Brazil. Fifty haplotypes were identified 50 with a nucleotide diversity (&#960;) of 0,0055 and a haplotypic diversity (Hd) of 0,957. The phylogenetic analysis showed the presence of two clades: the south clade comprising the subspecies M. q. quadrifasciata, and the north clade formed by the subspecies M. q. anthidioides and the populations with continuous tergal stripes from northern Minas Gerais and northeastern Bahia and Sergipe. AMOVA showed a percentage of variation between the clades of 68,56% and a &#934;ST 0,905. The barrier of gene flow, estimated with SAMOVA, was located close to Ribeira do Iguape River Valley in the south of the State of São Paulo. The unimodal mismatch distribution suggested bottleneck events affecting both clades. Coalescence analysis estimated time of divergence estimated between 490.000 and 390.000 years B.P. Other species of Melipona of the Atlantic forest, M. bicolor and M. marginata, also present subspecies that display morphological differences along north-south ranges that match the distribution of M. q. quadrifasciata and M. q. anthidioides. Concordant phylogeographyc patterns have been reported for other animal groups, as birds (Xiphorhynchus fuscus) and serpents (Bothrops jararaca).Conselho Nacional de Desenvolvimento Científico e Tecnológic