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

First record of the occurrence of Partamona ailyae Camargo (Hymenoptera: Apidae) in Atlantic Forest

This is the first record of the stingless bee Partamona ailyae Camargo, 1980 in an area of the Atlantic Forest in Brazil. The morphological identification and COI and 12S sequences indicated that the samples collected in the Atlantic Forest and other areas of the range of distribution belong to the same biological species. The data revealed low intraspecific variation and high interspecific divergence, with no overlap of the taxa compared

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Natural history, biogeography and population genetics of Partamona rustica, an endemic stingless bee from dry forests in Brazil

Partamona rustica is a stingless bee endemic to dry forests in Brazil. Despite its importance as a pollinator and its occurrence in endangered areas, such as the Caatinga (scrubland forest) and Cerrado (savanna) biomes, its natural history, biogeography, population genetics and evolutionary history are poorly known. This PhD Dissertation is presented in four chapters addressing specific aims to reduce the gaps in knowledge regarding P. rustica. In Chapter I, aspects of the natural history of this bee were investigated. The results revealed that P. rustica occurs from the northern portion of the state of Minas Gerais to the southern portion of the state of Bahia in the Caatinga and Cerrado biomes, contouring the plateaus and hills of Chapada Diamantina by the east. It is a floral visitor of at least 62 kinds of plant and its nests are built in arboreal termite nests constructed by Constrictotermes cyphergaster. In Chapter II, the hypothesis was tested that populations of stingless bees, such as P. rustica and Partamona helleri, have a high degree of differentiation when analyzed for mitochondrial genes due to the fact that the occupation of a site is performed by a small number of founding females. Therefore, each occupation event may exhibit a founder effect. The results revealed few haplotypes per population as well as a high degree of genetic differentiation, which supports the hypothesis. Implications for future studies were also indicated, such as the need to change the current focus of studies related to the genetic structure of bee populations, which usually estimate the degree of inter-population differentiation, to x estimates of genetic relatedness among queens, workers and males who founded the colonies of a given population. In Chapter III, the genetic relatedness among workers of P. rustica was estimated to evaluate the role of males in dispersal and gene flow among colonies and populations. The results revealed a low degree of average genetic relatedness among workers of colonies from the same locality and even lower relatedness among workers of colonies from different localities, suggesting that, although the areas analyzed were occupied by few females, dispersal promoted by males reduces relatedness and, consequently, the risk of inbreeding, which is harmful to hymenopterans due to their complementary sex determination system (locus csd). In Chapter IV, we used an integrative approach to reconstruct the evolutionary history of P. rustica in a spatiotemporal framework. The results identified two groups: one to the west and the other to the east of the São Francisco River Valley, which putatively diverged during the late Pleistocene, and indicated the western group as ancestral to the eastern group. The results also indicate that the inferences from both the analysis of genetic data and spatial distribution modelling are compatible with a history of populations of a constant size. The data presented in this thesis can be used to guide conservation and management strategies concerning the species as well as the Caatinga and Cerrado biomes, broaden knowledge on the biology and genetics of stingless bees, which can be useful in beekeeping and bee management, as well as reinforce the need for more detailed investigations into Pleistocene climate changes and the effects on the diversification of the endemic biota in Neotropical dry forests, especially studies involving the considerable diversity of bees in this region.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Partamona rustica é uma abelha sem ferrão endêmica de florestas secas do Brasil. Apesar da sua importância como polinizadora e da sua localização em áreas ameaçadas, como a Caatinga e o Cerrado, pouco se sabe a respeito da sua história natural, biogeografia, genética de suas populações, bem como da sua história evolutiva. Esta tese é apresentada em quatro capítulos, os quais apresentam objetivos específicos que visam reduzir estas lacunas em nosso conhecimento acerca de P. rustica. No Capítulo I, buscou-se investigar alguns aspectos da história natural de P. rustica. Os resultados revelaram que o principal substrato de nidificação utilizado pela espécie são termiteiros da espécie Constrictotermes cyphergaster, que P. rustica é visitante floral de pelo menos 62 tipos de plantas, e se ditribui em áreas de Caatinga e Cerrado entre o norte de Minas Gerais e o sudoeste da Bahia, contornando a Chapada Diamantina. No Capítulo II foram utilizadas as espécies P. rustica e Partamona helleri como modelos para testar a hipótese de que, nas abelhas sem ferrão, a ocupação de uma determinada área é realizada por um número reduzido de fêmeas fundadoras; desta forma, cada evento de ocupação pode, eventualmente, apresentar as condições de efeito fundador. Os resultados deste estudo revelaram um ou poucos haplótipos por localidade e elevada diferenciação entre as populações analisadas, dados que suportaram a hipótese testada. Além disto, foram apontadas algumas implicações para os futuros estudos, dentre elas, a necessidade de mudança do foco atual dos estudos relacionados à estrutura genética das viii populações de abelhas, os quais, via de regra, apenas estimam o nível de diferenciação interpopulacional, para estimativas das relações genéticas entre rainhas e machos que fundaram as colônias de uma dada população. No Capítulo III foi estimado o parentesco genético entre operárias de P. rustica, buscando avaliar o papel dos machos na dispersão e fluxo gênico entre colônias e populações. Os resultados mostraram baixos índices de parentesco genético médio entre operárias de colônias da mesma localidade e parentesco ainda menor entre operárias de colônias de diferentes localidades, sugerindo que apesar da ocupação das áreas analisadas ter se dado por poucas fêmeas, a dispersão promovida pelos machos reduz o parentesco e, consequentemente, o risco de acasalamentos endogâmicos, nocivos para os himenópteros, devidos ao sistema de determinação complementar do sexo (csd). No Capítulo IV foi utilizada uma abordagem integrada para reconstruir a história evolutiva de P. rustica num contexto espaçotemporal. Os resultados apontaram para a formação de dois grupos (grupo leste e oeste), separados pelo Vale do Rio São Francisco, que apresentaram divergência datada ao final do Pleistoceno. Os resultados ainda indicaram o grupo oeste como sendo ancestral ao grupo leste. Ademais, tanto os resultados das análises genéticas quanto da paleomodelagem são compatíveis com uma história de populações de tamanho constante. Os dados apresentados nesta tese poderão ser utilizados para nortear estratégias de conservação e manejo da espécie, bem como dos biomas Caatinga e Cerrado; ampliam o conhecimento acerca da biologia e da genética das abelhas sem ferrão, podendo ser úteis na criação racional destas abelhas e reforça-se a necessidade de novas e mais detalhadas investigações sobre as mudanças climáticas Pleistocênicas e seus efeitos na diversificação da biota endêmica das florestas secas da região Neotropical, principalmente, novos estudos envolvendo a grande diversidade de abelhas existente nesta região

Pleistocene climate changes shaped the population structure of Partamona seridoensis (Apidae, Meliponini), an endemic stingless bee from the Neotropical dry forest.

Partamona seridoensis is an endemic stingless bee from the Caatinga, a Neotropical dry forest in northeastern Brazil. Like other stingless bees, this species plays an important ecological role as a pollinator. The aim of the present study was to investigate the genetic structure and evolutionary history of P. seridoensis across its current geographic range. Workers from 84 nests from 17 localities were analyzed for COI and Cytb genic regions. The population structure tests (Bayesian phylogenetic inference, AMOVA and haplotype network) consistently characterized two haplogroups (northwestern and eastern), with little gene flow between them, generating a high differentiation between them as well as among the populations within each haplogroup. The Mantel test revealed no isolation by distance. No evidence of a potential geographic barrier in the present that could explain the diversification between the P. seridoensis haplogroups was found. However, Pleistocene climatic changes may explain this differentiation, since the initial time for the P. seridoensis lineages diversification took place during the mid-Pleistocene, specifically the interglacial period, when the biota is presumed to have been more associated with dry conditions and had more restricted, fragmented geographical distribution. This event may have driven diversification by isolating the two haplogroups. Otherwise, the climatic changes in the late Pleistocene must not have drastically affected the population dynamics of P. seridoensis, since the Bayesian Skyline Plot did not reveal any substantial fluctuation in effective population size in either haplogroup. Considering its importance and the fact that it is an endemic bee from a very threatened Neotropical dry forest, the results herein could be useful to the development of conservation strategies for P. seridoensis

Genetic Diversity of Melipona mandacaia SMITH 1863 (Hymenoptera, Apidae), an Endemic Bee Species from Brazilian Caatinga, Using ISSR

In order to evaluate the genetic diversity and structure of Melipona mandacaia, we analyzed 104 colonies collected in 12 localities in Bahia state, northeastern Brazil, using ISSR-PCR. A total of 109 bands were obtained with a significant polymorphism of 72.47%. Estimates of genetic diversity indicated low values of heterozygosity (He and HB values were 0.2616 and 0.2573, resp.). These reduced values have been reported in other studies in stingless bees and maybe justified by dispersion process in the origin of new nests. AMOVA revealed that the higher percentage of variation is within localities (70.39%). The ΦST and θB values were, respectively, 0.2961 and 0.3289, thereby indicating a moderate population structuring. The correlation between genetic and geographic distances (r=0.4542; P<0.01) suggests isolation by distance. Our study contributes to describing the genetic diversity of endemic organisms from Caatinga and may help future efforts to preserve this threatened biome

Geometric morphometrics discriminates Eastern and Western populations of Partamona rustica (Hymenoptera, Apidae, Meliponini) separated by the Sao Francisco River

Wing morphology has been used in taxonomic and systematic studies of insects, often enabling the identification of groups based on the variation. In this study, wing Geometric Morphometrics was used to verify if eastern and western populations of Partamona rustica, separated by the São Francisco River, are discriminated, thus confirming previous molecular data. The two groups of P. rustica exhibited significant differences in wing size and shape. Better differentiation of populations and groups was achieved with the centroid size. We generated dendrograms using Mahalanobis and Procrustes distances, which discriminated the eastern and western populations. Isolation by the distance between morphometric and geographic distances was found. The confirmation of the two population groups points out the need for further studies investigating the occurrence of barriers to gene flow and colonization history in the semiarid region by this stingless bee

Ecological niche modelling showing the potential geographical distribution of <i>P</i>. <i>rustica</i> in different periods and stability models.

<p>In “A” Current, “B” and “C” Mid-Holocene, “D” and “E” Last Glacial Maximum (LGM) and “F” Last Interglacial period (LIG). The stability models (G to I) refer to the overlap of the potential distribution maps using two Global Climate Models combined (I) and each GCM separately (G and H). In “I”, the red points represent the localities sampled in the present study and white points represent other localities obtained from collections and museums. The legends indicate the probability of suitable conditions for the species. Abbreviations: CD = <i>Chapada Diamantina</i>; AUC = area under the curve.</p