A educação científica tem se voltado para atividades pedagógicas que utilizam a prática investigativa de alunos. Um dos objetivos é que os estudantes se apropriem não apenas dos conceitos científicos, mas também das práticas específicas da atividade científica. Uma das pretensões é que os alunos desenvolvam a competência da argumentação científica. Esta investigação pretende compreender como os alunos desenvolvem sua argumentação escrita, analisando a utilização que fazem dos dados como evidências da seleção natural de forma a sustentar suas conclusões na resolução de questões investigativas sobre evolução biológica. Elaboramos uma sequência didática cuja arquitetura estabelece os alicerces para a ação pedagógica do professor e promove uma atuação investigativa dos alunos. A arquitetura da sequência tem duas bases integradoras: a) a educação científica baseada em investigação e b) a matriz de construção histórica da investigação de Darwin sobre a seleção natural como mecanismo da evolução biológica. Para investigar como seria o ensino da evolução biológica que recupera o viés da matriz investigativa utilizada por Darwin, nossa questão-problema foi construída com dois grandes focos: a) como articular intenções conceituais e metodológicas características da natureza das ciências biológicas com a abordagem dos principais obstáculos da construção histórica do conceito de seleção natural numa sequência didática baseada em investigação e b) de como é a utilização de dadosT como evidências da seleção natural na composição da estrutura argumentativa escrita de alunos de ensino médio durante a aplicação de uma Sequência de Ensino de Biologia Baseada em Investigação (SEEBI) para o ensino de evolução biológica. Para investigar nossa questão, elaboramos a SEBBI que foi aplicada por uma professora da rede pública para 125 alunos da 3ª série do ensino médio de uma escola pública estadual de São Paulo. Nossa metodologia é de abordagem qualitativa integrada a uma abordagem quantitativa. Nossos dados compõem-se de: a) materiais (apostilas, modelos experimentais, elementos audiovisuais utilizados nas aulas) e b) apostilas com respostas escritas pelos alunos após as atividades propostas. As análises foram realizadas a partir das apostilas escritas dos alunos, dos materiais elaborados e disponibilizados na SEBBI e na transcrição que realizamos. Os resultados mostram que a SEBBI tem alicerces em intenções conceituais e metodológicas características da biologia. Além disso, os resultados apontam para uma superação de obstáculos conceituais pelos alunos, como a teleologia cósmica e o fixismo, para a construção do conceito de seleção natural. Os resultados das análises apresentam uma melhora na capacidade argumentativa dos alunos, uma forte correlação entre o uso de dados de evolução biológica com a construção de argumentos de maior qualidade pelos alunos, pelo uso de justificativa (garantia e apoio) alicerçada em conhecimento científico. Há evidências da ampliação da construção de argumentos, tanto no aumento do número de componentes utilizados quanto na qualidade dos componentes campos-dependentes da ciência, como o apoio e evidências. Os argumentos construídos passam a apresentar a sustentação baseada em apoio conceitual específico do paradigma das ciências biológicas como a seleção natural, validando as conclusões a partir do uso de dadosT de Toulmin da investigação realizada pelos alunos. / The scientific education has focused on pedagogical activities that use students investigative practice. One of the objectives is so that students not only obtain the scientific concepts, but also the specific practices of science activity. It is a pretention that students develop their scientific argumentation competence. This investigation aims at understanding how students develop their written argumentation, analyzing their use of data as evidence of natural selection in order to sustain their conclusions about biological evolution investigative questions. We made a didactic sequence, which architecture establishes the foundation to the teachers pedagogical actions, and promotes students investigative actions. The sequence lies on two integrative bases: a) an investigation based scientific education and b) Darwins investigation on the natural selection as a mechanism of the historical construction matrix of biological evolution. In order to examine how would it be the biological evolution teaching based in Darwins investigative structure, our problem question was built with two main focuses: a) how could we articulate conceptual and methodological intentions, characteristic to biological sciences, with the approach of the main historical obstacles of natural selection in evolving into the concept of the mechanism of biological evolution in a didactic sequence based upon inquiry and b) how it is the use of data as evidence of natural selection in the high school students written argumentative structure during the application of Inquiry Based Biology Teaching Sequence (SEEBI, in Portuguese) to biological evolution teaching. To investigate our task, we developed a SEEBI that was applied by a public networks teacher to 125 high schools senior year students in a public school of São Paulo. Our methodology has qualitative and quantitative approaches. Our data consists of: a) materials (textbooks, experimental models, audio-visual resources used in class) and b) booklets with answers written by the students after the proposed activities. The data analyses were based upon these booklets, with students written answers, materials elaborated and posted in the SEEBI and also in the transcription we did. The results show that SEEBI has its foundation lied on conceptual and methodological intentions, characteristic to Biology. Furthermore, the results indicate an overcoming of conceptual obstacles as well, such as cosmic teleology and fixism, therefore, building the concept of natural selection as a mechanism of biological evolution. The study of the consequences presents an improvement in students argumentative ability, a strong correlation between the use of data from biological evolution with the construction of higher quality arguments by the students, using justifications (warranty and theoretical support) grounded in scientific knowledge. Theres evidence of an expansion of the arguments construction, both increasing the number of used components as well as the field-dependent components of sciences quality, such as support and evidence. The arguments constructed shall provide support based on specific conceptual assistance in paradigms of Biology, like natural selection, validating the findings from the use of data (Toulmin, 2006) in researches conducted by students.

Orientador: Marcelo Lancellotti / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T23:59:18Z (GMT). No. of bitstreams: 1 Andrade_AliceTavaresReis_M.pdf: 3292132 bytes, checksum: ee5318f5b87992964c9d97bedc343f00 (MD5) Previous issue date: 2013 / Resumo: Em 1998, foi relatada a transferência lateral do gene sodC do gênero Haemophilus para a espécie Neisseria meningitidis. Sabe-se que, nestes dois grupos a dinâmica deste gene é bastante distinta. Este trabalho tem por objetivo estimar árvores filogenéticas que possam apontar qual a espécie do gênero Haemophilus compartilhou o gene sodC com a espécie N. meningitidis. Testes de seleção positiva foram empregados no intuito de avaliar quais forças evolutivas estão subjacentes ao processo de diversificação molecular do gene nestas espécies ao longo do tempo. Além disso, foi realizada uma modelagem protéica computacional por homogia para avaliar quais substituições de aminoácidos tinham impacto no processo adaptativo da enzima nas espécies consideradas. Ao se reconstruir uma filogenia para o gene sodC, foi constatado que a origem deste gene na espécie H. influenzae é distinta. Um grupo de linhagens recebeu o gene, provavelmente por transferência lateral, da espécie H. haemolyticus, enquanto o outro grupo recebeu o gene da espécie H. parainfluenzae. Neste grupo, o gene sofreu pseudogeneização. Foi observado também que as sequências de N. meningitidis agrupam com as sequências que compartilham um ancestral comum com a espécie H. haemolyticus, porém as sequências do meningococo formam um ramo distinto dentro deste clado. Dada à alta clonalidade das sequências de N. meningitidis, foi constatado que o evento de transferência lateral de genes foi muito recente na escala do tempo. O teste de seleção positiva demonstrou que seleção positiva está atuando especificamente no ramo da árvore que compartilha um ancestral comum com a espécie H. haemolyticus, através da modificação de uma alanina por uma serina na posição 72, embora a nota geral da árvore tenha sido menor que 1. Sabe-se que pseudogenes, por não codificarem uma proteína ativa e, portanto, por não estarem sob nenhum tipo de restrição funcional, estão sob uma ação maior da deriva genética. Portanto, diferentes forças evolutivas estão governando a evolução deste gene nas espécies consideradas. A modelagem protéica concluiu que tal modificação contribuiu para o aumento do potencial redox do sítio ativo. Desta forma, a ação da seleção positiva sob um único resíduo de aminoácido foi benéfica para a função da enzima como um todo / Abstract: In 1998, it was reported the lateral transfer of the sodC gene from the genus Haemophilus to Neisseria meningitidis. It is known that this two groups show a quite distinct dynamics of this gene. This study aims to estimate phylogenetic trees that might point to which species of the genus Haemophilus shared the sodC gene with N. meningitidis. In addition, tests of positive selection were employed in order to assess which evolutionary forces are governing the process of molecular diversification of the gene in these species through time. Moreover, we performed a computational protein modeling by homology to asses which amino acids substitutions had an impact on the adaptative process of the enzyme in the species considered. A phylogeny of the sodC gene was reconstructed and it was found that this gene in H. influenzae has two different origins. A group of lineages has received the gene, probably by lateral transfer, from H. haemolyticus, whereas the other group has received the gene from H. parainfluenzae. In the latter, the gene has become a pseudogene. It was also observed that the sequences from N. meningitides group together with those sequences that share a common ancestor with H. haemolyticus, but they form a distinct branch within this clade. Given the high clonality of the sequences from N. meningitidis, it was found that the lateral gene transfer event is very recent in the time scale. A test of positive selection showed that positive selection is acting specifically in the branch that shares a common ancestor with H. haemolyticus through the substitution of an alanine to a serine at position 72, though the overall score of the tree is less than one. It is known that pseudogenes do not encode active proteins and therefore they are not under any kind of functional constraints, so they are under greater influence of genetic drift. Thus, it was concluded that different forces are driving the evolution of this gene in the species considered here. Protein modeling concluded that this modification contributed to the increase in the redox potencial of the active site. Thus the action of positive selection under a single amino acid residue was beneficial to the function of the enzyme as whole / Mestrado / Bioquimica / Mestra em Biologia Funcional e Molecular

Abstract Local adaptation is important evolutionary process leading to adaptive population differentiation. Currently, examining its genetic basis is a major goal of evolutionary and ecological genetics. In my thesis I studied local adaptation and its genetic basis in populations of a perennial outcrossing model plant Arabidopsis lyrata by combining common garden experiments at the native field sites and in controlled conditions with quantitative trait locus mapping. Estimates of fitness in the field – both at the level of multiple components as well as hierarchical total fitness – showed that populations of A. lyrata were locally adapted. The studied populations were also phenotypically differentiated in ecologically relevant traits. Different components of fitness were important for the advantage of the locals depending on the environment. Local alleles were associated with high fitness in the field, suggesting that differing directional selection pressures have been involved in phenotypic differentiation. Mostly different genomic regions governed local adaptation in different environments, but the results also suggested that some of these regions could involve rarely documented fitness tradeoffs (antagonistic pleiotropy). Loci governing flowering time differentiation differed between the studied environments, highlighting the need to conduct experiments both in the wild and in controlled conditions. In contrast to most existing studies, F2 hybrids in general had surprisingly high fitness at one study site, largely due to beneficial dominance effects at loci governing survival in that environment. In addition to nuclear genes, cytoplasmic genomes also were found to have a role in local adaptation. / Tiivistelmä Luonnonvalinta saa aikaan paikallista sopeutumista ja adaptiivista erilaistumista. Paikallisen sopeutumisen perinnöllisen taustan selvittäminen on tällä hetkellä yksi tärkeimpiä evolutiivisen ja ekologisen genetiikan tavoitteita. Tässä väitöskirjatyössä tutkin paikallista sopeutumista ja sen geneettistä taustaa monivuotisella, ristipölytteisellä mallikasvilla, idänpitkäpalolla (Arabidopsis lyrata). Käytin työssäni geenikartoitusta kasveilla joita kasvatettiin yhdenmukaisissa oloissa sekä populaatioiden luontaisilla kasvupaikoilla että kontrolloiduissa olosuhteissa. Kenttäolosuhteissa arvioitu kelpoisuus osoitti idänpitkäpalkopopulaatioiden olevan paikallisesti sopeutuneita sekä yksittäisten kelpoisuuteen vaikuttavien ominaisuuksien että hierarkkisen kokonaiskelpoisuuden tasolla. Tutkitut populaatiot olivat myös erilaistuneita ekologisesti tärkeissä ominaisuuksissa. Kelpoisuuteen vaikuttavat ominaisuudet myös poikkesivat ympäristöjen välillä. Paikalliset alleelit olivat yhteydessä korkeaan kelpoisuuteen luonnossa, minkä perusteella voitiin päätellä erisuuntaisen luonnonvalinnan vaikuttaneen populaatioden erilaistumiseen. Kromosomiston eri alueet olivat tärkeitä sopeutumisessa eri ympäristöihin, mutta myös joidenkin samojen genomin alueiden havaittiin mahdollisesti vaikuttavan vastakkaisesti kelpoisuuteen eri ympäristöissä. Myös kukkimisajan erilaistumiseen vaikuttavat genomin alueet poikkesivat eri ympäristöjen välillä erityisesti verrattaessa kenttäkokeita kasvatushuone- ja kasvihuonekokeisiin. Toisin kuin useimmissa tutkimuksissa on havaittu, F2-sukupolven jälkeläistön kelpoisuus oli yllättävän korkea yhdessä kenttäkoeympäristössä. Tähän vaikuttivat kelpoisuuden kannalta suotuisat dominoivat geenivaikutukset, jotka paransivat kasvien selviytymistä kyseisessä ympäristössä. Tumassa sijaitsevien geenien lisäksi myös soluelimien perimällä havaittiin olevan yhteys paikalliseen sopeutumiseen.

Abstract Arabidopsis lyrata is a close outcrossing relative of Arabidopsis thaliana, the model organism of plant physiology and molecular biology. I studied variation in flowering time and the factors shaping the variation within and between A. lyrata populations in different environments. The role of the two important proximate factors determining flowering time, day length and temperature, were studied in climate chambers. The southern A. lyrata populations were found to flower in high frequency and quicker than northern A. lyrata populations in all studied environments, but the reaction of northern populations on long day length was found to be stronger than that of southern populations. Differences in vernalization requirement between A. lyrata populations were found in outdoor common garden, but in the climate chambers the results of vernalization experiments were not consistent. Strength and direction of selection on flowering time and other life history traits were studied in alpine and lowland A. lyrata populations in Scandinavia. Differences in selection were found both between populations and between years. Grazing sheep caused high levels of damage in inflorescences in the alpine population. In the lowland population there was less herbivory, caused by insects and hares. The difference in selection on flowering traits in the two study populations might be partly caused by selective grazing. Completely outcrossing mating system in A. lyrata is due to well developed self-incompatibility system. However, biparental inbreeding is likely to exist in natural populations and it may lead to spatial structuring of genetic variation within populations. I studied the effects of biparental inbreeding on components of fitness in A. lyrata in three different environments. I found inbreeding depression after sib-mating to be substantial. Stressful environment reduced the overall performance of the plants, but had no effect on the magnitude of inbreeding depression. A literature survey indicates that the observed levels of inbreeding depression in self-incompatible A. lyrata were higher than those of self-compatible species. This suggests that self-compatible species have purged some of their genetic load. The genetic basis of flowering time variation in A. lyrata can be further studied by using A. thaliana molecular tools.

Abstract Hosts and pathogens are involved in a continuous evolutionary arms race, where pathogens attack and hosts defend themselves. The main tools for winning the race are natural selection and the genetic diversity that selection acts on. However, in small populations natural selection may be ineffective. Therefore, the genes taking part in immune defense may lack adaptability to new or changing pathogens. Major histocompatibility complex (MHC) is an important genomic region that includes highly polymorphic immune defense genes. In this doctoral thesis, I studied the natural selection and genetic diversity of MHC class II genes in dogs and Finnish wolves. I also used dog MHC diversity to estimate the number of founding wolves in dog domestication. The Finnish wolf population declined rapidly in size due to excessive hunting from the late 19th century until the early 20th century. After decades of a very small population size, the population started recovering in the mid-1990s. This study shows that, despite the fluctuations in population size, the diversity of the MHC loci in the Finnish wolf has remained high and comparable to the larger neighboring Russian Karelian wolf population. Unlike the neutral genetic markers, the MHC loci of the Finnish and Russian Karelian populations have not differentiated. These results indicate similar balancing selection acting on the MHC loci of the two wolf populations. In dogs, the strength of natural selection is likely weakened by artificial selection and veterinary care. The potential phases of natural selection would be during embryogenesis and fetal development. However, no strong signs of prenatal selection were found in this study. MHC diversity was estimated to be higher in Asian dogs than in dogs from Europe. A simulation study indicated a minimum of 500 founding wolves for the modern dog population. Dog MHC diversity implies an Asian origin for domestication from a large and diverse wolf population. Both natural selection and demography have an influence on the genetic diversity of a species. In small populations, random genetic drift is enforced. However, in loci with important fitness impacts, selection may be particularly strong and outweigh drift, as demonstrated in the MHC loci of a small wolf population in this study. / Tiivistelmä Isäntä ja taudinaiheuttajat käyvät jatkuvaa kaksinkamppailua, jossa taudinaiheuttajat hyökkäävät ja isäntä puolustautuu. Kamppailussa menestymiseen tarvitaan geneettistä monimuotoisuutta sekä sen pohjalta toimivaa luonnonvalintaa. Pienissä populaatioissa luonnonvalinnan teho voi kuitenkin heikentyä, jolloin immuunipuolustukseen osallistuvat geenit eivät kykene sopeutumaan uusiin tai muuttuneisiin taudinaiheuttajiin. MHC-alueella (major histocompatibility complex) sijaitsee suuri joukko monimuotoisia immuunipuolustukseen osallistuvia geenejä. Väitöskirjassani tutkin luokan II MHC-geeneihin kohdistuvaa luonnonvalintaa ja niiden geneettistä monimuotoisuutta koirilla ja Suomen susilla. Arvioin myös koiran kesyttämisprosessiin osallistuneiden susien määrää nykykoiran MHC-monimuotoisuuden pohjalta. Suomen susipopulaation koko pieneni nopeasti voimakkaan metsästyksen vuoksi 1800-luvun lopulta 1900-luvun alkuun. Populaatio pysyi hyvin pienenä useita vuosikymmeniä, kunnes se alkoi elpyä 1990-luvun puolivälissä. Tutkimus osoitti, että populaatiokoon vaihteluista huolimatta Suomen susien MHC-geenien monimuotoisuus on säilynyt korkeana ja on vastaavalla tasolla kuin Venäjän Karjalan susipopulaatiossa. Suomen ja Venäjän Karjalan susipopulaatioiden MHC-geenit eivät ole erilaistuneet, vaikka populaatiot poikkeavat toisistaan neutraalien geenimerkkien suhteen. Samanlainen tasapainottava valinta näyttäisi kohdistuvan näiden susipopulaatioiden MHC-geeneihin. Keinotekoinen valinta ja eläinlääketieteellinen hoito todennäköisesti heikentävät koirien MHC-geeneihin kohdistuvaa luonnonvalintaa. Luonnonvalinta voisi yhä vaikuttaa alkion- ja sikiönkehityksen aikana, mutta tästä ei tutkimuksessa löytynyt todisteita. MHC-muuntelun määrän arvioitiin olevan suurempaa aasialaisissa kuin eurooppalaisissa koirissa. Simulaatiotutkimuksen mukaan nykyisen koirapopulaation perustamiseen olisi tarvittu vähintään 500 sutta. Tulokset viittaavat koiran kesyttämisen tapahtuneen Aasiassa suuresta ja monimuotoisesta susipopulaatiosta. Sekä luonnonvalinta että demografia vaikuttavat lajien geneettiseen monimuotoisuuteen. Pienissä populaatioissa satunnaisajautuminen voimistuu. Valinta voi kuitenkin olla erityisen voimakasta ja voittaa satunnaisajautumisen geeneissä, joilla on erityisen tärkeä vaikutus yksilön kelpoisuuteen, kuten tutkimuksessa osoitettiin pienen susipopulaation MHC-geenien kohdalla.

La variabilité environnementale à laquelle les individus sont constamment exposés est forte. Dans ce contexte, les conditions environnementales en début de vie sont particulièrement importantes puisqu’elles peuvent avoir des conséquences à long terme sur la performance des individus. L’objectif de cette thèse est d’améliorer notre compréhension des effets à long-terme des évènements vécus tôt dans la vie, incluant aussi bien les conditions environnementales que la croissance, sur les traits d’histoire de vie des grands mammifères herbivores. Afin de répondre à cet objectif, nous avons utilisé les suivis à long-terme de cinq populations appartenant à quatre espèces d’ongulés. Dans une première partie, nous avons montré que les conditions environnementales en début de vie peuvent influencer la trajectoire entière de croissance corporelle d’un individu. Ensuite, nous avons cherché à savoir si les effets des conditions environnementales en début de vie sur les traits d’histoire de vie à l’âge adulte représentaient des réponses adaptatives à différents environnements ou résultaient seulement de contraintes développementales dues à une restriction alimentaire. Nous avons répondu à cette question en testant notamment des hypothèses issues du domaine médical en populations sauvages / The environment to which individuals are permanently exposed varies greatly over time. The environmental conditions during early life are particularly important in this context because they can have extraordinary long-term consequences on individual performance. The main goal of this PhD thesis was to improve our understanding of the long-term effects of early-life events, including environmental conditions and growth, on life-history traits of large herbivores. In order to meet this objective, we used detailed long-term data from five populations of four species of ungulates. We highlighted that environmental conditions experienced during early life can influence the entire body growth trajectory of an individual. Then, we investigated whether the long-term effects of early environmental conditions on life-history traits represent adaptive responses to differing environments, or are only a consequence of energetic constraints on development. We aimed to address this issue by testing hypotheses issued from human medicine in wild populations

Este trabalho focou nos aspectos evolutivos e ecológicos dos tricomas em espécies da tribo Bignonieae (Bignoniaceae), e no potencial papel defensivo dessas estruturas no aumento da resistência das plantas frente aos herbívoros. Esta tese caracterizou quatro morfotipos de tricomas encontrados nas partes vegetativas das plantas da tribo Bignonieae morfologicamente, estudou os padrões macro-evolutivos destes tricomas e o papel funcional dos tricomas pateliformes secretores de néctar em diferentes escalas de tempo e espaço. O primeiro capítulo descreveu os quatro tipos de tricomas micro e macro-morfologicamente, e sua relação com a história filogenética das espécies da tribo Bignonieae. Quatro tipos de tricomas distintos foram reconhecidos: tricomas não glandulares (ng), tricomas glandulares peltados (gp), tricomas glandulares estipitados (ge), e tricomas glandulares pateliformes/cupulares (P/C). Três destes tricomas provavelmente já estavam presentes no ancestral da tribo Bignonieae (i.e., não glandulares, glandulares peltados e glandulares pateliformes/cupulares) enquanto os tricomas glandulares estipitados surgiram mais recentemente e múltiplas vezes dentro da tribo. Além disso, realizamos uma revisão das terminologias aplicadas a esses tricomas bem como sugerimos uma padronização dos tipos de tricomas para o grupo de forma a diminuir a divergência entre os trabalhos já publicados. O segundo capítulo testou a eficiência dos tricomas pateliformes secretores de néctar (nectários extraflorais) em duas espécies de Anemopaegma das savanas brasileiras. Essas duas espécies atraíram mais formigas que plantas vizinhas, com os indivíduos de Anemopaegma com maiores quantidades de nectários sendo visitados por um número maior de formigas que as plantas com um número menor de nectários (variação intra-populacional). No entanto, não foi possível observar um efeito dos nectários e formigas sobre a herbivoria e o desempenho das plantas como esperado pela hipótese de defesa mediada por essas estruturas. Hipóteses alternativas foram utilizadas para discutir os resultados, incluindo uma discussão sobre o possível custo/benefício de tais estruturas em diferentes ambientes (florestas e savanas) relacionados com a história filogenética do grupo, além da variação das interações esperada entre populações segundo a hipótese de mosaico geográfico. O terceiro capítulo testou o papel defensivo do sistema planta-formiga mediado pelos nectários extraflorais no contexto filogenético da tribo Bignonieae. Espécies de plantas com um número maior de nectários foram visitadas por um número maior de formigas (teste controlado pelas relações de parentesco entre as espécies). Além disso, espécies mais proximamente relacionadas apresentaram uma diferença na abundância de nectários extraflorais maior do que o esperado pelo modelo neutro de evolução, gerando um padrão de convergência dessas estruturas na tribo Bignonieae. Esse desvio no padrão evolutivo esperado pode ter sido causado por forças direcionais de seleção e momentos de contra-seleção, dado o balanço entre custo-benefício dos nectários extraflorais para as plantas. Neste contexto, dois fatores foram testados para explicar o desvio na evolução da abundância de nectários na tribo Bignonieae: (1) mudança de habitat das florestas para as savannas (fatores extrínsecos); (2) surgimento de novos caracteres morfológicos como outros tipos de tricomas na superfície das plantas (fatores intrínsecos). Ambos fatores podem ter interferido nas interações formiga-planta e no padrão de evolução dos nectários. Dessa forma, a ocupação das savanas levou a uma diminuição do número de nectários (provável contra-seleção dessas estruturas), enquanto o surgimento de tricomas glandulares adesivos teve o mesmo efeito sobre os nectários. Ambos resultados são discutidos considerando a condicionalidade das interações em função da variação biótica (formigas e herbívoros) entre habitats, e também do \"trade-off\" entre os caracteres de defesa. O quarto capítulo testou a teoria de coevolução em mosaico geográfico no sistema planta-formiga-herbívoro em 10 populações da espécie de savana Anemopaegma álbum. Não foram encontradas correlações entre os nectários (e variáveis descritoras do néctar), a abundância de formigas visitantes, a herbivoria ou as variáveis de performance das plantas entre as populações. Esse padrão esteve associado principalmente a variação na assembléia de formigas, a qual foi dominada por formigas do gênero Crematogaster em uma das populações, mas dominadas por formigas do gênero Camponotus na grande maioria das outras populações. No entanto, 3 das 10 populações estudadas apresentaram um alto número de plantas sem formigas, diminuindo muito as chances dessas populações serem defendidas frente aos herbívoros pelos nectários. A abundância de formigas esteve relacionada negativamente com a herbivoria, e positivamente com as variáveis de performance das plantas entre as populações. Das 10 populações amostradas, 5 delas tiveram os nectários acoplados (do inglês, \"matched\") com as formigas visitantes, embora o tipo de acoplamento tenha variado entre elas. Dessas 5 populações, somente 3 tiveram uma produção positiva de folhas e baixa herbivoria, no qual duas delas tiveram alta abundância de nectários nas folhas e foram dominadas por formigas do gênero Camponotus (maiores em tamanho, mas com baixa capacidade de recrutamento). Já a terceira população teve em média a menor abundância de nectários nas folhas, e a mesma apresentou o maior número de formigas por planta (e maior freqüência), em geral formigas do gênero Crematogaster (menores em tamanho mas com grande capacidade de recrutamento). Por serem menores em tamanho, tais formigas utilizaram a secreção dos nectários quase que individualmente. Nem a abundância de nectários, nem as formigas ou mesmo a herbivoria estiveram estruturados espacialmente, corroborando, a hipótese de mosaico geográfico para as interações formiga-planta-herbívoro em A.album. Neste contexto, as três populações com as interações formiga-planta \"mached\" foram consideradas \"hot-spots\" das interações, nas quais as populações atingiram os valores mais altos das variáveis de performance das plantas, enquanto as demais foram consideradas \"cold-spots\". A maioria das populações \"cold-spots\" foi explicada pela falta de formigas suficientes para que as interações com as plantas pudessem se tornar efetivas na defesa frente aos herbívoros, mas outros processos também foram considerados para discutir os resultados apresentados neste trabalho. / This thesis focused on the evolutionary-ecology of trichomes in the tribe Bignonieae (Bignoniaceae), and in the potential defensive role of these structures against herbivores. More specifically, we characterized four trichome morphotypes found in vegetative plant parts of representatives of the Bignonieae, as well as studied the macro-evolutionary patterns of these trichomes, and the functional role of patelliforme nectar secreting trichomes in different scales of time and space. The first chapter describes four different trichome types micro and macromorphologically, as well as investigates their evolutionary patterns during the history of Bignonieae. The four different trichome types recognized are: non-glandular trichomes (ng), glandular peltate trichomes (gp), glandular stipitate trichomes (gst), and glandular patteliform/cupular trichomes (P/Cgt). Our analyses indicated that three of these trichomes were likely already present in the most recent common ancestor of the tribe Bignonieae (i.e., non glandular, glandular peltate, and glandular patteliform/cupular), while the glandular stipitate trichomes evolved more recently and multiple times during the history of the tribe. Results from this study were combined with a literature review in order to revise the trichome terminology and propose standardized names for the various trichome types currently found in the group. The second chapter tested the efficiency of patelliform nectar-secreting trichomes (extrafloral nectaries, EFNs) in two species of Anemopaegma of the Brazilian savannas. These two species attracted more ants than neighboring plants, with individuals that presented higher amounts of EFNs being visited by a higher number of ants than plants with lower amounts of EFNs (intra-population variation). Nonetheless, no effect of EFNs and ants was observed on herbivory nor on the performance of the studied plants, contradicting the expectations of the mediated EFNs defense hypothesis. Alternative hypotheses were also considered including the cost/benefits model to understand the outcomes of ant-plant interaction: (1) phylogenetic inertia hypothesis that connect EFNs-ant interactions with the plant transitions between different environments (forests to savannas); and (2) geographic mosaic hypothesis that predict differences in the outcomes of ant-plant interactions across populations. The third chapter tested the defensive role of extrafloral nectaries in the context of the phylogenetic history of Bignonieae. Species of plants with a higher number of EFNs were visited by a higher number of ants (test controlled by phylogeny). In addition, closely related species presented a higher difference in the abundance of EFNs than expected under the neutral model of evolution. Such deviation may have resulted by directional forces of slection and moments of counter-selection, given the costs and benefits of the extrafloral nectaries for the plants. Two specific factors were considered as the major possible determinants of the evolutionary patterns of the EFNs: (1) change of habitat from forests to savannas (extrinsic factors); and (2) emergence of new morphological characters such as other trichome types over the plant\'s surface (intrinsic factors). Both factors might have altered the ant-plant interactions and the evolution of nectaries. The occupation of the savannas was associated with a decrease in the number of nectaries (likely due to counter-selection of these structures), while the evolution of adhesive glandular trichomes presenting the same effect on the nectaries. Both results are discussed in the light of the biotic variation (ants and herbivores) encountered between habitats, as well as in the light of the trade-off among defensive characters. The fourth chapter tested the geographic mosaic theory of coevolution in 10 populations of the savanna species Anemopaegma álbum. No correlations were found among extrafloral nectaries (and nectar variables), the abundance of visiting ants, herbivory, and plant performance among populations. This pattern was mainly associated with the variation in the assembly of ants encountered in the various populations. Most populations of A. álbum were dominated by assemblages of Camponotus ants, except for one that was dominated by Crematogaster ants. However, 3 of 10 populations studied presented a high number of plants without ants, decreasing the chances of defense against herbivores by EFNs. The abundance of ants was negatively associated with herbivory, and positively associated with plant performance variables among populations. Out of the 10 populations sampled, five presented an abundance of EFNs that matched the functional traits of ants. Out of these five populations, only three presented positive leaf production and low herbivory. From these three populations, two presented high abundances of EFNs on the leaves and were dominated by Camponotus ants (i.e., bigger in size, but with a low recruiting capacity). The third population presented on average the smallest abundance of EFNs on the leaves; it also presented the highest number of ants per plant (and the highest frequency), which generally were Crematogaster ants (smaller in size but with greater recruiting capacity). Because these ants are smaller in size, they used nearly all isolated EFNs encountered over the plant\'s surface. Neither the abundance of EFNs, the abundance of ants, and the assemblage of herbivores were structured spatially, corroborating the geographic mosaic hypothesis for the ant-plant-herbivore interactions in A. album. In this context, the three populations with \"matched\" ant-plant interactions were considered \'hot-spots\' of interactions, in which the populations reached the highest values of plant performance, while the others were considered \'cold-spots\'. The majority of \'cold spot\' populations were explained by a lack of sufficient ants to protect the plants effectively

Orientador: Célio Fernando Baptista Haddad / Resumo: As forças de seleção natural e sexual atuam sobre os indivíduos e podem os levar ao isolamento reprodutivo. O acúmulo de modificações evolutivas pode levar ao surgimento de novas entidades. Espécie é unidade basal em biologia; assim, com sua exuberante biodiversidade, a Mata Atlântica é uma floresta neotropical fundamental para estudos de processos evolutivos em anfíbios anuros. Reunindo os gêneros Cycloramphus, Thoropa e Zachaenus, a família Cycloramphidae agrupa espécies de anuros saxícolas e terrestres, todas endêmicas da Mata Atlântica brasileira. Pelos seus hábitos especializados de vida e reprodução, os cicloramfídeos formam um grupo atrativo para estudos evolutivos. Na presente tese são apresentados quatro capítulos que abordam três escalas distintas da evolução: a diversificação entre espécies, populações e indivíduos. São abordados: (1) a filogenia molecular multilocus de Cycloramphus-Zachaenus, demonstrando que a evolução da terrestrialidade no clado se correlaciona com o dimorfismo sexual em tamanho; (2) a diversificação fenotípica associada a diversificações genéticas em populações de C. boraceiensis e C. dubius, demonstrando que estas duas espécies-irmãs saxícolas apresentam zona de contato e hibridação; (3) o sistema de acasalamento promíscuo e as relações sociais em C. boraceiensis, demonstrando que tamanho das fêmeas e dos machos e parentesco genético influenciam a formação dos casais; e (4) o sistema de acasalamento poligínico com fidelidade na espécie saxíco... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Natural and sexual selection forces act on individuals and may lead to reproductive isolation. The increase in evolutionary modifications may lead to the emergence of new entities. Species is the basal unity in biology; thus, with its exuberant biodiversity, the Atlantic rainforest is a fundamental Neotropical forest for studies of evolutionary processes in anuran amphibians. Comprising the genera Cycloramphus, Thoropa, and Zachaenus, the family Cycloramphidae gathers saxicolous and terrestrial anuran species, all endemic to the Brazilian Atlantic rainforest. Because of their specialized life and reproductive habits, cycloramphids are an attractive group for evolutionary studies. In the present thesis we show four chapters that address three distinct scales of evolution: the diversification among species, populations, and individuals. We goaled: (1) the multilocus molecular phylogeny of Cycloramphus-Zachaenus, demonstrating that the evolution of terrestriality in the clade is correlated with the sexual size dimorphism; (2) the phenotypic diversification associated with the genetic diversifications in populations of C. boraceiensis and C. dubius, demonstrating that these two saxicolous sister species show a contact zone and hybridization; (3) the promiscuous mating system and the social relations in C. boraceiensis, demonstrating that female and male sizes, and mate relatedness influence pair formation; and (4) the polygynic mating system with fidelity in the saxicolous specie... (Complete abstract click electronic access below) / Doutor

<p>Data science uses the latest techniques in statistics and machine learning to extract insights from data. With the increasing amount of protein data, a number of novel research approaches have become feasible.</p><p>Micropeptides are an emerging field in the protein universe. They are small proteins with <= 100 amino acid residues (aa) and are translated from small open reading frames (sORFs) of <= 303 base pairs (bp). Traditionally, their existence was ignored because of the technical difficulties in isolating them. With technological advances, a growing number of micropeptides have been characterized and shown to play vital roles in many biological processes. Yet, we lack bioinformatics methods for predicting them directly from DNA sequences, which could substantially facilitate research in this field with minimal cost. With the increasing amount of data, developing new methods to address this need becomes possible. We therefore developed MiPepid, a machine-learning-based method specifically designed for predicting micropeptides from DNA sequences by curating a high-quality dataset and by training MiPepid using logistic regression with 4-mer features. MiPepid performed exceptionally well on holdout test sets and performed much better than existing methods. MiPepid is available for downloading, easy to use, and runs sufficiently fast.</p><p>Long noncoding RNAs (LncRNAs) are transcripts of > 200 bp and does not encode a protein. Contrary to their “noncoding” definition, an increasing number of lncRNAs have been found to be translated into functional micropeptides. Therefore, whether most lncRNAs are translated is an open question of great significance. To address this question, by harnessing the availability of large-scale human variation data, we have explored the relationships between lncRNAs, micropeptides, and canonical regular proteins (> 100 aa) from the perspective of genetic variation, which has long been used to study natural selection to infer functional relevance. Through rigorous statistical analyses, we find that lncRNAs share a similar genetic variation profile with proteins regarding single nucleotide polymorphism (SNP) density, SNP spectrum, enrichment of rare SNPs, etc., suggesting lncRNAs are under similar negative selection strength with proteins. Our study revealed similarities between micropeptides, lncRNAs, and canonical proteins and is the first attempt to explore the relationships between the three groups from a genetic variation perspective.</p><p>Deep learning has been tremendously successful in 2D image recognition. Protein binding ligand prediction is fundamental topic in protein research as most proteins bind ligands to function. Proteins are 3D structures and can be considered as 3D images. Prediction of binding ligands of proteins can then be converted to a 3D image classification problem. In addition, a large number of protein structure data are available now. We therefore utilized deep learning to predict protein binding ligands by designing a 3D convolutional neural network from scratch and by building a large 3D image dataset of protein structures. The trained model achieved an average F1 score of over 0.8 across 151 classes on the holdout test set. Compared to existing methods, our model performed better. In summary, we showed the feasibility of deploying deep learning in protein structure research.</p><p>In conclusion, by exploring various edges of the protein universe from the perspective of data science, we showed that the increasing amount of data and the advancement of data science methods made it possible to address a wide variety of pressing biological questions. We showed that for a successful data science study, the three components – goal, data, method – all of them are indispensable. We provided three successful data science studies: the careful data cleaning and selection of machine learning algorithm lead to the development of MiPepid that fits the urgent need of a micropeptide prediction method; identifying the question and exploring it from a different angle lead to the key insight that lncRNAs resemble micropeptides; applying deep learning to protein structure data lead to a new approach to the long-standing question of protein-ligand binding. The three studies serve as excellent examples in solving a wide range of data science problems with a variety of issues.</p>

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