Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2018-03-23T19:09:07Z No. of bitstreams: 1 2017 - Daniele Cabral Michel.pdf: 1915531 bytes, checksum: af036434bb0fd939d8e85a7ff4a1d43f (MD5) / Made available in DSpace on 2018-03-23T19:09:07Z (GMT). No. of bitstreams: 1 2017 - Daniele Cabral Michel.pdf: 1915531 bytes, checksum: af036434bb0fd939d8e85a7ff4a1d43f (MD5) Previous issue date: 2017-02-14 / CAPES / FAPERJ / Centrolobium paraense Tul. popularly known as "pau-rainha", is a naturally occurring legume species from the northern state of Roraima (Brazil) to Panama. It has economic, social and environmental importance for local populations, being a nitrogen fixing species in association with bacteria of the rhizobia group. Thirteen Gram-negative, aerobic, motile with polar flagella, rods shaped bacteria previously isolated from root nodules of C. paraense grown in soils from the Roraima State were submitted to a polyphasic approach characterization. The study involved the carbon source utilization, enzymatic reaction, antibody, pH and NaCl tolerance, 16S rRNA, nodC, nifH and multi locus sequence phylogenetic analysis (MLSA with dnaK, glnII, recA, gyrB and rpoB), G+C content and Average Nucleotide Identity (ANI). Growth of strains was observed at temperature range 20- 36?C (optimal 28?C), pH ranges 5-11 (optimal 6.0-7.0) and 0.1-0.5%NaCl (optimal 0.1- 0.3%). Analysis of 16S rRNA gene placed the strains into two groups within Bradyrhizobium. Closest neighbouring species (98.8%) for group I was B. neotropicale while for group II were twelve species with more than 99% of similarity. MLSA confirmed B. neotropicale BR 10247T as the closest type strain for the group I and B. elkanii USDA 76T and B. pachyrhizi PAC 48T for group II. ANI differentiated group I from the B. neotropicale BR 10247T (79.6%), and group II from B. elkanii USDA 76T and B. pachyrhizi PAC 48T (88.1% and 87.9%, respectively). Fatty acid profiles (majority C16:0 and Summed feature 8 (18:1?6c/18:1?7c) for both groups), DNA G+C content and carbon compound utilization supported the placement of the novel strains in the genus Bradyrhizobium. Gene nodC and nifH of the new strains have in general low similarity with other Bradyrhizobium species. Both groups nodulated plants from the tribes Crotalarieae, Dalbergiae, Genisteae and Phaseoleae. Based on the result obtained, two novel species which the names Bradyrhizobium centrolobii and Bradyrhizobium macuxiense are proposed. / Centrolobium paraense Tul. popularmente conhecido como ?pau-rainha?, ? uma esp?cie de leguminosa que ocorre naturalmente no norte do estado de Roraima (Brasil) ao Panam?. Tem import?ncia econ?mica, social e ambiental para popula??es locais, sendo uma esp?cie fixadora de nitrog?nio (N) em associa??o com bact?rias do grupo dos riz?bios. Treze bact?rias gram-negativas, aer?bicas, com mobilidade atrav?s de flagelos polares e em forma de bastonetes previamente isoladas de n?dulos de ra?zes de Centrolobium paraense cultivadas em solos do estado de Roraima foram submetidas a caracteriza??o com abordagem polif?sica. O estudo envolveu a utiliza??o de fontes de carbono, rea??es enzim?ticas, composi??o de ?cidos graxos das c?lulas, antibi?ticos, pH e toler?ncia a NaCl,16S rRNA, an?lise filogen?tica dos genes nodC, nifH e de sequ?ncias multilocus (MLSA com dnaK, glnII, recA, gyrB e rpoB), conte?do de G+C e identidade m?dia de nucleot?deos (ANI). O crescimento das estirpes foi observado num intervalo de temperatura 20-36?C (?tima 28?C), intervalo de pH de 5-11 (?timo 6,0-7,0) e 0,1-0,5% NaCl (?timo 0,1-0,3%). A an?lise do gene 16S rRNA posicionou as estirpes em dois grupos dentro de Bradyrhizobium. A esp?cie mais pr?xima (98,8%) para o grupo I foi B. neotropicale enquanto para o grupo II foram outras doze esp?cies com mais de 99% de similaridade. MLSA confirmou B. neotropicale BR 10247T como a estirpe tipo mais pr?xima do grupo I e B. elkanii USDA 76T e B. pachyrhizi PAC 48T do grupo II. O ANI diferenciou o grupo I da B. neotropicale BR 10247T (79,6%) e o grupo II da B. elkanii USDA 76T e B. pachyrhizi PAC 48T (88,1 e 87,9 respectivamente. O perfil de ?cidos graxos (predomin?ncia de C16:0 e caracterist?ca somada 8 (18:1?6c/18:1?7c) para ambos os grupos, ANI, o conte?do de G+C e a utiliza??o de compostos de carbono deram suporte ao posicionamento das novas estirpes no g?nero Bradyrhizobium. Os genes nodC e nifH t?m em geral baixa similaridade com outras esp?cies de Bradyrhizobium. Ambos os grupos nodularam plantas de diferentes tribos.

Li, Chi Pang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 127-141). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Contents --- p.vi / List of Tables --- p.ix / List of Figures --- p.x / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.3 / Chapter 2.1 --- Caridean phylogeny --- p.3 / Chapter 2.1.1 --- Informative morphological characters in Caridean shrimps --- p.3 / Chapter 2.1.2 --- Brief history of Caridean classifications --- p.4 / Chapter 2.1.3 --- Natantia/Reptantia scheme vs. Dendrobranchiata/Pleocyemata scheme --- p.8 / Chapter 2.2 --- Phylogney of the family Hippolytidae --- p.10 / Chapter 2.3 --- Molecular approach to phylogeny --- p.11 / Chapter 2.3.1 --- Use of molecular data --- p.11 / Chapter 2.3.2 --- Use of mitochondrial gene markers in crustaceans --- p.12 / Chapter 2.3.3 --- Use of nuclear gene markers in crustaceans --- p.14 / Chapter Chapter 3 --- Phylogeny of the Infraorder Caridea Based on five Nuclear Genes --- p.27 / Chapter 3.1 --- Introduction --- p.27 / Chapter 3.2 --- Materials and Methods --- p.28 / Chapter 3.2.1 --- Sample Collection --- p.28 / Chapter 3.2.2 --- DNA extraction and PCR amplification --- p.28 / Chapter 3.2.3 --- DNA sequencing --- p.29 / Chapter 3.2.4 --- Phylogenetic analysis --- p.30 / Chapter 3.3 --- Results --- p.34 / Chapter 3.3.1 --- Enolase --- p.34 / Chapter 3.3.2 --- NaK --- p.35 / Chapter 3.3.3 --- PEPCK --- p.37 / Chapter 3.3.4 --- Histone --- p.38 / Chapter 3.3.5 --- 18S rRNA --- p.39 / Chapter 3.3.6 --- Combined dataset --- p.41 / Chapter 3.3.7 --- Substitution saturation analysis --- p.43 / Chapter 3.4 --- Discussion --- p.44 / Chapter 3.4.1 --- Evaluation of the five nuclear gene markers --- p.44 / Chapter 3.4.1.1 --- Nuclear protein coding genes --- p.44 / Chapter 3.4.1.2 --- 18S rRNA --- p.81 / Chapter 3.4.2 --- Superfamilies and families --- p.82 / Chapter 3.4.2.1 --- Superfamilies --- p.82 / Chapter 3.4.2.2 --- Families --- p.86 / Chapter 3.4.3 --- Basal groups --- p.86 / Chapter 3.4.4 --- Procarididae --- p.88 / Chapter Chapter 4 --- Phylogeny of the family Hippolytidae --- p.90 / Chapter 4.1 --- Introduction --- p.90 / Chapter 4.2 --- Materials and Methods --- p.91 / Chapter 4.2.1 --- Sample Collection --- p.91 / Chapter 4.2.2 --- DNA extraction and PCR amplification --- p.91 / Chapter 4.2.3 --- DNA sequencing --- p.95 / Chapter 4.2.4 --- Phylogenetic analysis --- p.95 / Chapter 4.3 --- Results --- p.95 / Chapter 4.3.1 --- Enolase --- p.95 / Chapter 4.3.2 --- NaK --- p.98 / Chapter 4.3.3 --- 16S rRNA --- p.99 / Chapter 4.3.4 --- Combined dataset --- p.100 / Chapter 4.4 --- Discussion --- p.118 / Chapter 4.4.1 --- "Resurrection of family Lysmatidae Dana,1852" --- p.118 / Chapter 4.4.2 --- Other hippolytid clades --- p.120 / Chapter 4.4.2.1 --- """Hippolytidae""" --- p.120 / Chapter 4.4.2.2 --- Bythocarididae --- p.121 / Chapter 4.4.3 --- Superfamily Alpheoidea --- p.122 / Chapter Chapter 5 --- General Conclusion --- p.125 / References --- p.127

O gênero Sphecozone O.P.-Cambridge, 1870 inclui 34 espécies e tem S. rubescens como espécie-tipo. Com exceção do norte-americano S. magnipalpis Millidge 1993, todas as espécies do gênero ocorrem apenas nos Neotrópicos. Miller e Hormiga (2004) propuseram o monofiletismo de Sphecozone, suportado pela perda de paracímbio e crista do radix, e a origem de um átrio, e estabeleceram Tutaibo Chamberlin, 1916 como seu grupo irmão, relacionando-o a Ceratinopsis Emerton, 1882, Dolabritor Millidge, 1991 Intecymbium Miller, 2007 Gonatoraphis Millidge, 1991 e Psilocymbium Millidge, 1991 com base na ausência ou redução de paracímbio, estrutura presente nos palpos dos machos da superfamília Araneoidea. Apesar deste resultado, Miller e Hormiga (2004) e Miller (2007) sugerem que a relação interna e monofilia de Sphecozone é duvidosa, e hipóteses sobre a revalidação de um dos gêneros que foi sinonimizado, como Hypselistoides, Tullgren, 1901 Brattia Simon, 1894, Clitolyna Simon, 1894 e Gymnocymbium Millidge 1991 também são discutidos. Neste contexto, este projeto tem como objetivo testar essas hipóteses. A partir de uma matriz de dados contendo um total de 77 caracteres e 41 táxons terminais (8 do grupo externo, 28 do grupo interno e 5 espécies novas) uma análise através de uma busca heurísticas tradicional resultou em apenas duas árvores mais parcimoniosas com 294 passos (IC=0,30; IR=0,57). As topologias obtidas corroboram as hipóteses de Miller e Hormiga (2004) e Miller (2007), ou seja, Sphecozone, não forma mais um grupo monofilético e possui, agora, apenas duas espécies, S. rubescens, O. Pickard-Cambridge, 1871 e S. nitens Millidge, 1991, suportado pela presença de apófise ventral do címbio, perda do paracímbio e papilas no tégulo, cauda do radix reta, perda do tricobótrio prolateral da tíbia do palpo do macho, forma do epígino fortemente ovalado, e presença do tricobótrio no metatarso IV, tendo como grupo irmão o gênero Tutaibo Chamberlin, 1916. As demais espécies estão distribuídas em outros dois gêneros revalidados: um deles Hypselistoidyes, contendo H. altehabitans (Keyserling, 1886) comb. nov., H. capitatus (Millidge, 1991) comb. nov., H. corniculans (Millidge, 1991) comb. nov., H. cornutus (Millidge, 1991) comb. nov., H. crinitus (Millidge, 1991) comb. nov., H. diversicolor (Keyserling, 1886) comb. nov., H. ignigenus (Keyserling, 1886) comb. nov., H. labiatus (Keyserling, 1886) comb. nov., H. lobatos (Millidge, 1991) comb. nov, H. modestus (Nicolet, 1849) comb. nov., H. modicus (Millidge, 1991) comb. nov., H. nigripes (Millidge, 1991) comb. nov., H. niwinus (Chamberlin, 1916) comb. nov., H. rubicundus (Keyserling, 1886) comb. nov. e uma espécie nova, e outro Clytolina, contendo Clytolina fastibilis (Keyserling, 1886) comb. nov., as espécies C. castânea, (Millidge, 1991) comb. nov., C. novaeteutoniae, (Baert, 1987) comb. nov. e C. spadicaria (Simon, 1894) comb. nov., C. crassa (Millidge, 1991) comb. nov., C. gravis (Millidge, 1991) comb. nov. e C. formosa (Millidge, 1991) comb. nov., C. prativaga (Keyserling, 1886) comb. nov., C. personata (Simon, 1894) comb. nov., C. alticeps (Millidge, 1991) comb. nov., C. rostrata (Millidge, 1991) comb. nov., C. tumidosa (Keyserling, 1886) comb. nov., C. venialis (Keyserling, 1886) comb. nov., C. varia (Millidge, 1991) comb. nov., e duas espécies novas, Clitolyna sp.nov.01 e Clitolyna sp.nov.02. Um gênero novo também será proposto para acomodar as espécies Gen.nov. magnipalpis (Millidge, 1993), Gen.nov. sp.nov.01 e Gen.nov. sp.nov.02 / The genus Sphecozone O. P.-Cambridge, 1870 includes 34 species and has S. rubescens as its type-species. Except for the North American S. magnipalpis Millidge 1993, all species of the genus occur only in the Neotropics. Miller and Hormiga (2004) proposed the monophyly of Sphecozone, supported by the loss of paracymbium and radical ridge, and the origin of an atrium, and established Tutaibo Chamberlin, 1916 as its sister group, relating it to Ceratinopsis Emerton, 1882 Dolabritor Millidge, 1991 Intecymbium Miller, 2007 Gonatoraphis Millidge, 1991 and Psilocymbium Millidge, 1991 based on the absence or reduction of paracymbium, structure present in the palps of males of the superfamily Araneoidea. Despite this result, Miller and Hormiga (2004) and Miller (2007) suggest that the internal relationship and monophyly of Sphecozone is doubtful, and hypotheses about revalidation of one of the genus which was synonymized, as Hypselistoides Tullgren, 1901 Brattia Simon, 1894 , Clitolyna Simon, 1894, Gymnocymbium Millidge 1991 are also discussed. In this context, this project aims to test these hypotesys. From a data matrix containing a total of 77 characters and 41 terminal taxa (8 outgroup, 28 ingroup and 5 new species) an analysis through a traditional heuristic search resulted in only two most parsimonious trees with 294 steps (CI = 0.30, IR = 0.57). The topologies obtained corroborate the hypotheses of Miller and Hormiga (2004) and Miller (2007), that is, Sphecozone no longer forms a monophyletic group and has only two species, S. rubescens O. Pickard-Cambridge, 1871 and S. nitens Millidge, 1991, supported by the presence of ventral cymbal apophysis, loss of paracymbium and papillae in the tegulum, straight tailpeace of the radix, loss of the prolateral trichobotrium of tibia from males palpus, strongly oblong epiginum, and the presence of a metatarsus IV trichobotrium. The other species are distributed in two other revalidated genera: Hypselistoidyes, with H. altehabitans (Keyserling, 1886) comb. nov., H. capitatus (Millidge, 1991) comb. nov., H. corniculans (Millidge, 1991) comb. nov., H. cornutus (Millidge, 1991) comb. Nov., H. crinitus (Millidge, 1991) comb. nov., H. diversicolor (Keyserling, 1886) comb. nov., H. ignigenus (Keyserling, 1886) comb. nov., H. labiatus (Keyserling, 1886) comb. nov., H. lobatus (Millidge, 1991) comb. nov, H. modestus (Nicolet, 1849) comb. nov., H. modicus (Millidge, 1991) comb. nov., H. nigripes (Millidge, 1991) comb. nov., H. niwinus (Chamberlin, 1916) comb. nov., H. rubicundus (Keyserling, 1886) comb. nov. and one new species, and Clitolyna, with C. fastibilis (Keyserling, 1886) comb. nov., C. castanea (Millidge, 1991) comb. nov., C. novaeteutoniae (Baert, 1987) comb. nov. and C. spadicaria (Simon, 1894) comb. Nov., C. crassa (Millidge, 1991) comb. nov., C. gravis (Millidge, 1991) comb. nov. and C. formosa (Millidge, 1991) comb. nov., C. prativaga (Keyserling, 1886) comb. nov., C. personata (Simon, 1894) comb. nov., C. alticeps (Millidge, 1991) comb. nov., C. rostrata (Millidge, 1991) comb. nov., C. tumidosa (Keyserling, 1886) comb. nov., C. venialis (Keyserling, 1886) comb. nov., C. varia (Millidge, 1991) comb. nov., and two new species. A new genus will also be proposed to accommodate Gen.nov magnipalpis (Millidge, 1993), Gen. nov. sp.nov.01 and Gen.nov. sp.nov.02

Entomolepididae é uma família de sifonostomatóides com distribuição cosmopolita. Até o momento, é composta por 9 gêneros e 19 species, com maior diversidade no Indo-Pacífico. Entomolepididade encontra-se dividida em duas subfamílias que diferem, basicamente, pelo número de segmentos pedígeros entre o cefalotórax e o escudo terminal - Parmulodinae apresenta apenas um segmento enquanto que Entomolepinae possui dois segmentos. Assim como nas subfamílias, é comum encontrar sobreposições nas diagnoses do gênero. Apesar de ser um grupo relativamente antigo, não há na literatura dados acerca das relações entre as espécies de Entomolepididae. Assim, esta tese teve por objetivo realizar uma revisão taxonômica e um estudo filogenético da família Entomolepididae. Ao estudar os espécimes tipos de Parmulodes verrucosus, e Entomopsyllus stocki, foi possível identificar inconsistências que levaram à redescrição da primeira e a adição de notas na descrição da segunda espécie. O estudo da fauna associada à esponjas do gênero Aplysina permitiu a identificação de 4 novas espécies de Spongiopsyllus: S. atypicus, S. stocki, S. boxshalli e S. hoi. O estudo filogenético incluiu as 23 espécies de Entomolepididade, conhecidas até então, além de 3 espécies de Asterocheridae como grupos-externos, e como resultado, foi obtida apenas 1 árvore maximamente parcimoniosa. Apenas a subfamília Entomolepinae foi recuperada como grupo monofilético. Dentre os gêneros de Entomolepididae, apenas Entomopsyllus não é monofilético. Spongiopsyllus mostrou-se um clado próximo à Entomopsyllus. A evolução de Entomolepididae envolveu muitos caracteres homoplásticos, tornado difícil o reconhecimento de padrões / Entomolepididae is a cosmopolitan siphonostomatoid family. Until now, the family is composed by 9 genera and 19 species with major diversity on Indo-Pacific Ocean. Entomolepididade has two subfamilies which differs basically by the number of pedigerous segments between the cephalotorax and the terminal shield - Parmulodinae show one segment instead Entomolepinae has two segments. As in the subfamilies, is common to find overlaps in genera diagnosis. Despite its ancient characteristics, do not have in the literature data concerning the relationships among Entomolepididae species. Thus, this thesis aimed to make a taxonomic revision and a phylogenetic study of Entomolepididae. The analyze of Parmulodes verrucosus, and Entomopsyllus stocki type specimens allowed the identification of incongruences that led to the redescription of the first and to the descriptional notes of the second species. The study of associated fauna of Aplysina sponges allow the idenification of 4 new Spongiopsyllus species: S. atypicus, S. stocki, S. boxshalli and S. hoi. The phylogenetic study include all 23 known Entomolepididae species, in addition to 3 Asterocheridae species as outgroups, resulting in 1 most parsimonious tree. Only the subfamily Entomolepinae was recovered as monophyletic. Among the genera, just Entomopsyllus was non-monophyletic. Spongiopsyllus is a clade close to Entomopsyllus. The Entomolepididae evolution involved many homoplastic characters which become difficult the identification of patterns

O gênero Sadocus Sørensen, 1886 é revisado pela primeira vez e uma análise cladística foi feita para testar seu monofiletismo e suas relações internas, além disso, a chave de identificação das espécies é apresentada. Uma nova classificação é proposta baseada nos resultados da análise cladística. São reconhecidas cinco espécies válidas das 5 espécies válidas das 14 nominais, sendo quatro sinonímias propostas: Sadocus bicornis (Gervais, 1849) em Sadocus asperatus (Gervais, 1847), S. conspicillatus Roewer, 1913, S. exceptionalis (Mello-Leitão, 1946) e S. guttatus Sørensen, 1902 em S. polyacanthus (Gervais, 1847) e S. calcar (Roewer, 1913) em Gonyleptes horridus Kirby, 1819; duas Species inquerendae: S.allermayeri (Mello-Leitão, 1945) e S. nigronotatus (Mello-Leitão, 1943) e duas transferidas para outros gêneros: Roeweria brasiliensis (Soares & Soares, 1949) e Metagyndes planiceps (Guérin-Méneville, 1838). Além é feita a descrição de Metagyndes sp.n., exemplar usado por Roewer na redescrição da espécie Metagyndes planiceps (Guérin-Méneville, 1838), que se tratava de uma espécie diferente da descrição original. A matriz de dados utilizada na análise cladística possui cinco terminais de Sadocus e mais 15 terminais como grupo externo, compreende 53 caracteres baseados na morfologia masculina, sendo 18 pertencentes a estruturas morfológicas externas presentes no escudo dorsal e tergitos livres, dois pertencentes a quelícera, dois pertencente ao pedipalpo, 20 pertencentes as pernas e 11 pertencentes a genitália. A análise resultou em uma árvore mais parcimoniosa com 195 passos (C.I.= 32; R.I.=45) cuja otimização aplicada foi ACCTRAN. Sadocus constitui um clado monofilético e pectinado, sustentado por duas sinapomorfias: formato gama triangular do escudo dorsal e bula da quelícera lisa / The genus Sadocus Sørensen, 1886 is revised for the first time and a cladistic analysis was performed to test its monophyly and internal relationships, a dicotomous key of species was presented. A new classification based on cladistic analysis is proposed. Five species are considered valid of the 14 nominal species currently recognized, being synonymyzed are, Sadocus bicornis (Gervais, 1849) as Sadocus asperatus (Gervais, 1847), S. conspicillatus Roewer, 1913, S. exceptionalis (Mello-Leitão, 1946) and S. guttatus Sørensen, 1902 as S. polyacanthus (Gervais, 1847), and S. calcar (Roewer, 1913) as Gonyleptes horridus Kirby, 1819; two Species inquerendae: S. allermayeri (Mello-Leitão, 1945) and S. nigronotatus (Mello-Leitão, 1943), and two transferred to other genus: Roeweria brasiliensis (Soares & Soares, 1949) and Metagyndes planiceps (Guérin-Méneville, 1838). The description of Metagyndes sp.n. is made, a specimen that Roewer used for the redescription of the species Metagyndes planiceps (Guérin-Méneville, 1838), it was a different example of the original description. The cladistic analysis was performed with five species of Sadocus and the outgroup is composed of fifteen species. The character matrix comprises 53 morphological characters from males, 18 characters are of external morphological features of the dorsal scute and free tergites, two of the chelicerae, two of the pedipalp, 20 of the legs and 11 of the genitalia. The analysis resulted in one most parsimonious tree with 195 steps (C.I.= 32; R.I=45) and the ACCTRAN optimization was applied. Sadocus is a monophyletic and pectinate group clade, supported for two synapomorphies: the Gamma triangular shape of dorsal scutum and a smooth chelicerae bula

O gênero Brasiliorchis inclui atualmente 14 espécies de orquídeas restritas ao bioma Mata Atlântica, ocorrendo desde Misiones, Argentina, até o Estado da Bahia, na região nordeste do Brasil.Embora estas espécies tenham sido tradicionalmente reconhecidas pelos seus caracteres vegetativos e principalmente florais, elas são morfologicamente muito similares e apresentam caracteres diagnósticos contínuos,assim, ousoexclusivo da morfologiapode não ser útil para identificação das espéciesneste grupo de orquídeas. Um estudo morfométrico anteriormente realizado com seis espécies deste gênero não conseguiu identificar agrupamentos claros. Amaioria dos caracteres analisados apresentou sobreposição entre diferentes espécies, sendo que apenas a espécie B. gracilisse mostrou distinta das demais. O objetivo desse estudo foi contribuir para aidentificação de linhagens evolutivamente distintas dentro do gênero e avaliar se os padrões filogenéticos de diversificação corroboram com o estudo morfométrico anteriormente realizado.Foram utilizados dados de sequências de plastídios (psbj-petA, atpl-atpH)e nucleares (ITS1-2) considerandoampla variação geográfica e morfológica observada no grupo. Foram amostrados 96 indivíduos,originados de 37 localidades de ocorrência no Brasil, incluindo 11 espéciesdo gênero. Análises de máxima parcimônia e bayesiana foram realizadas considerando os dados separadamente e concatenados.Os resultados suportam B. schunkeana como irmã de todas as outras espécies do gênero. B. barbozaefoi reconhecida como um grupo monofilético distinto, corroborando com os caracteres morfológicos diagnósticos desta espécie, e possivelmente irmão das espécies do complexo B. picta.A espécie B. gracilis não foi reconhecida como um grupo monofilético, não corroborando com o estudo de morfometria, na qual essa espécie se apresentou distinta das outras do complexo. Contudo, nas análises concatenadas alguns indivíduos apresentaram-se como irmãos das espécies do complexo B. picta. As espécies morfologicamente homogêneas pertencentes ao complexo B. picta (B. chrysantha, B. marginata, B. porphyrostele, B. ubatubana, B. phoenicanthera e B. picta) não formaram clados monofiléticos distintos. B. kautskyi e B. consanguinea, as quais são morfologicamente distintas, foram incluídas nos clados constituídos pelas espécies do complexo B. picta.Eventos de introgressão e hibridação podem ser potenciais causas da insuficiente resolução das árvores filogenéticas obtidas nesse estudo. Os padrões observados também sugerem que a separação das linhagens pode ter ocorrido recentemente e/ou rapidamente. Marcadores adicionais e análises de árvores de espécies podem ajudar a esclarecer os padrões de diversificação neste grupo. / The genus Brasiliorchis currently includes 14 species of orchids occurring mainly in the Atlantic Forest Biome, from Misiones, Argentina, to the stateof Bahia, in northeastern Brazil. Although these species have been traditionally recognized by vegetative andmainly floral traits, they are morphologically very similar and display continuouscharacters, thus the exclusive use of the morphologycannot be useful for species identificationin this group of orchids. A morphometric study previously conducted with six species of this genus could not identify clear groupings. The majority of analyzed characters showed overlap between different species, with only the species B. gracilisbeing distinct from the others. The goals of this study were to contribute to the identification of evolutionary distinct lineages within the genus and assess if the phylogenetic patterns of diversification agree with a previous morphometric study available. Sequence data from plastid (psbj-petA, atpl-atpH) and nuclear (ITS1-2)regions were used considering wide morphological and geographical sampling variation. We sampled 96 individuals, originated from 37 sites of occurrence in Brazil, including 11 species of the genus. Bayesian and parsimony analyses were performed considering data separately and concatenated. The results support B. schunkeana as sister to all other species of the genus. B. barbozaewasrecognized as a monophyletic group,corroborating with morphological diagnostic characters of this species,and possibly sisters of the complex species B. picta.The species B. gracilis was not recognized as a monophyletic group, not agreeing with the morphometry study, which showed this species as being distinct from the other species in the complex. However, in the concatenated analysis, some individuals presented themselves as sisters of the species complex B. picta. The morphologically homogeneous species belonging to the B. picta complex (B. chrysantha, B. marginata, B. porphyrostele, B. ubatubana, B. phoenicanthera e B. picta) did not form distinct monophyletic clades. B. kautskyi and B. consanguinea, which are morphologically clearly distinct, are embedded in clades consisting of the B. pictaspecies complex.Hybridization and introgression events may be potential causes of insufficient resolution of phylogenetic trees obtained in this study. The observed patterns also suggest that the separation of the lineage may have occurred recently and/or quickly.Additional markers and species tree analyses may help clarify diversification patterns in this group.

A região Neotropical é uma das regiões com maior biodiversidade no planeta. Essa região apresenta uma complexa história geológica que iniciou-se com a quebra da Gondwana, separando os continentes sul-americano e africano, durante o Mesozóico, há ca. de 150 milhões. Todas as mudanças geológicas que seguiram influenciaram a diversificação da fauna e flora dessa região. No entanto, ainda não sabemos quais processos levaram à alta diversidade encontrada nesta região. Esse estudo, foca em Stizophyllum, (Bignonieae, Bignoniaceae), um pequeno gênero de lianas Netropicais, que ocorre desde o México até o sul do Brasil. Apesar da cirscunscrição de Stizophyllum ser clara, limites específicos permanecem complicados neste grupo e pouco se sabe sobre sua história evolutiva. Este estudo visa: (i) reconstruir a filogenia do gênero e utilizá-la como base para inferir a história biogeográfica do grupo, e (ii) desenvolver marcadores de microssatélites (SSRs) nucleares e plastidiais, para futuros estudos filogeográficos e de genética de populações. Para tal, reconstruímos a filogenia do gênero com base em três marcadores moleculares (ndhF, rpl32-trn,L e pepC) e uma ampla amostragem de indivíduos, utilizando inferências bayesiana e de máxima verossimilhança. Em seguida estimamos as idades de divergência das diversas linhagens e reconstruímos a história biogeográfica do grupo. Por fim, desenvolvemos marcadores de microssatélite nucleares (nSSRs) e de cloroplasto (cpSSRs) para o grupo. Ao todo, desenvolvemos trinta e sete SSRs, nove nucleares e vinte oito de cloroplasto. Todos marcadores foram polimórficos em S. riparium e apresentaram sucesso de transferabilidade para S. inaequilaterum e S. perforatum. Cinco clados principais foram reconstruídos na filogenia molecular do gênero, os quais são caracterizados por bons caracteres morfológicos e aqui reconhecidos como espécies em uma nova sinopse apresentada para o grupo: (i) S. inaequilaterum Bureau & K. Schum., distribuído pela Amazônia e América Central; (ii) S. perforatum (Cham.) Miers, distribuído pela Mata Atlântica e Áreas Secas do Brasil Central, (iii) S. riparium (Kunth) Sandwith, distribuído por toda Bacia Amazônia; (iv) S. flos-ardeae (Pitter) Beyer & L.G. Lohmann, distribuído pela América Central, e (v) S. coriaceum Beyer & L.G. Lohmann, restrito ao Estado do Pará, na Amazônia Oriental. O estudo biogeográfico indicou que o ancestral de Stizophyllum e seu grupo-irmão Martinella, estava distribuído pela Amazônia. A divergência destas linhagens ocorreu durante o Eoceno, enquanto a diversificação das espécies de Stizophyllum ocorreu durante o Mioceno, a partir de um ancestral amplamente distribuído pela região Neotropical. Essa dissertação traz novos dados para um melhor entendimento dos processos que levaram à estruturação da biota Neotropical e contribui dados importantes para um projeto multidisciplinar amplo neste tópico (FAPESP 2012/50260-6) / The Neotropics is one of the most biodiverse regions in the planet. This region has a complex geological history that began during the break of Gondwana, which separated the South American and African continents in the Mesozoic, at ca. 150 million years ago. All the geological changes that followed greatly impacted the diversification of the fauna and flora of this region. However, it is still not clear what processes led to the high diversity found in this region. This study focuses on Stizophyllum (Bignonieae, Bignoniaceae), a small genus of Neotropical lianas, distributed from Mexico to southern Brazil. Although Stizophyllum is well circumscribed, species limits remain complicated in this group and little is known about its evolutionary history. This study aims to: (i) reconstruct the phylogeny of the genus and use it as a basis to infer the biogeographical history of this group, and (ii) develop nuclear and plastid microsatellite markers (SSRs) for future studies on the phylogeography and population genetics of this group. To this end, we reconstructed the phylogeny of the genus based on three molecular markers (ndhF, rpl32-trnL and pepC) and a broad sample of individuals, using Bayesian and Maximum Likelihood approaches. We then estimated divergence times of the various lineages and recontructed the biogeographical history of the group. Lastly, we developed nuclear microsatellite markers (nSSRs) and chloroplast microsatellite markers (cpSSRs) for the group. In total, we developed thirty-seven SSRs, nine from the nucleus and twenty-eight from the chloroplast. All markers amplified successfully in S. riparium and transferability was sucessful to S. inaequilaterum and S. perforatum. Five main clades were reconstructed in the molecular phylogeny of the group, all of which are characterized by good morphological markers and here recognized as species in an updated synopsis of the group: (i) S. inaequilaterum Bureau & K. Schum., distributed through the Amazon and Central America; (ii) S. perforatum (Cham.) Miers, distributed through the Atlantic Forest and the Dry Areas from Central Brasil; (iii) S. riparium (Kunth) Sandwith, distributed throughout the Amazon Basin; (iv) S. flos-ardeae (Pitter) Beyer & L.G. Lohmann, distributed through Central America; and, (v) S. coriaceum Beyer & L.G. Lohmann, restricted to the state of Pará, in Eastern Amazonia. The biogeographic study indicated that the ancestor of Stizophyllum and its sister-group Martinella was broadly distributed through Amazônia. These lineages dievrsified during the Eocene, while the diversification of Stizophyllum species occurred during the Miocene, from an ancestor that was broadly distributed through the Neotropics. This dissertation brings new information for the assembly of the Neotropical biota and contributes important data for a broader multidisciplinary project on this topic (FAPESP 2012 / 50260-6)

Tettigoniidae (katydids) has more than 7200 species and is the largest family within the insect order Orthoptera. Their unique biology including leaf-like crypsis, acoustic signaling, and courtship rituals garners much of their academic attention. However, the taxonomy of katydids is chaotic and previous to these studies, little work had been done to decipher the phylogenetic relationships within this family. Without a robust phylogenetic framework, questions regarding the evolution of katydid disguises including the leaf-like crypsis cannot be addressed. This dissertation contains three chapters. Chapter 1 provides the first phylogenetic hypothesis focusing on Tettigoniidae. In this chapter we show a character thought to be taxonomically informative, the thoracic auditory spiracle, is homoplasious within Tettigoniidae. We provide evidence that the leaf-like wings of katydids have been derived independently in multiple lineages. Additionally, in Chapter 1 the problematic taxonomy within Tettigoniidae, particularly the lack of monophyly in many of the larger and widespread subfamilies, is addressed. Chapter 2 contains a more in depth look into the evolution of crypsis. Leaf-like wings are common throughout Tettigoniidae, but the definition of leaf-like has varied by author. In this second chapter we provide a ratio method for differentiating between leaf-like and non leaf-like wings. Our ratio method was then verified using geometric morphometics. We found at least 15 independent derivations of leaf-like wings in Tettigoniidae. Furthermore we found that throughout Tettigoniidae the leaf-like wings are not a driver of speciation and selection may favor a shift away from the leaf-like wings. Within the cosmopolitan Phaneropterinae, the trend differs, as there is no significant difference between the speciation and transition rates of the leaf-like and non leaf-like lineages. Chapter 3 presents the largest and most comprehensive phylogeny for Tettigoniidae to date and provides a hypothesis for origins and biogeographic dispersal of katydids. Characters that define subfamilies are similar due to similar selective pressures and are not taxonomically informative. As a result, many of the larger and widespread subfamilies, particularly those with species in similar but geographically distant habitats, are paraphyletic. In this chapter we also provide temporary names to define the two large clades containing the bulk of Tettigoniidae diversity (tettigonioid clade and phaneropteroid clade) in addition to smaller subfamily groups to simplify discussion of katydid relationships until a higher-level taxonomic revision is completed.

Legionella bacteria, the causative agent of Legionaries’ disease and Pontiac fever, are ubiquitous in fresh-water environments including man-made water systems. Incidence of legionellosis is increasing in the United States resulting in thousands of cases every year. Infection via aerosols generated by showers, faucets, cooling towers, spas, fountains, and other water fixtures has been identified as the primary source of transmission. Legionella bacteria pose a significant public health threat, particularly in health care and long term care settings as Legionella can readily colonize the plumbing systems and infect the vulnerable patient population. One species, Legionella pneumophila (Lp), is responsible for over 90% of the known cases of Legionnaires’ disease. The importance of genetic diversity of Lp and non-pneumophila strains in human disease remains an area of ongoing research. Little is known in regard to the phylogenetic diversity of environmental strains, particularly strains that colonize facilities with high risk populations such as hospitals. Whole-genome sequencing (WGS) analysis, is an emerging tool used to support epidemiological investigation of cases of legionellosis and can be used to describe and establish phylogenetic relationships between environmental strains and clinical cases. The advantage of this method is the ability to differentiate bacteria down to the level of single nucleotide polymorphisms (SNPs). However, it was unknown whether current WGS methods accurately represent the potential SNP diversity among Lp isolates from the same environmental sample. It is unclear as to why certain strains tend be associated with clinical cases more than others, but certain genes referred to as virulence factors may be related to the relative pathogenicity of Legionella strains. Further investigation into virulence factors and antibiotic resistance factors could be used in future risk assessment of environmental Legionella. Additionally, Legionella have the potential for high genetic diversity due to recombination events, and gene transfer can occur between distinct Legionella species and strains. There is a lack of research on the potential sharing of virulence factor genes between Legionella strains typically associated with disease and those considered to be non-virulent. The goal of the work presented in this thesis is to describe the diversity of phylogenetic relationships between Lp isolates found in hospital premise plumbing systems, to estimate the genetic diversity among Lp found in the same environmental sample, and to identify virulence and antibiotic resistance genes shared between Legionella strains. A better understanding of the genetic diversity of environmental Lp could inform future surveillance and outbreak investigations by demonstrating the need to collect samples from multiple sites within a facility, and identifying shared virulence and antibiotic resistance genes between Legionella species and strains could apprise future risk assessment. WGS was utilized to describe the phylogenetic relationships of 81 Lp isolates from five hospitals. Individual hospitals were found to have distinct strains of Lp. For some strains, highly conserved subpopulations were collected from the same room over time, whereas other strains did not cluster by room. Using prospectively collected isolates from two hospitals, the mean number of SNP differences among isolates from the same environmental sample was found to differ between hospitals (0.4 versus 7.5). The presence of virulence factors and antibiotic resistance genes in Legionella species and strains was described. An analysis of 10 virulence factor genes revealed that Lp likely did not share these genes with Legionella anisa, a species generally considered to be non-virulent. Within Lp strains there was no clear difference between the Lp strains considered to be more virulent and those considered to be less virulent. A few antibiotic resistance genes were also identified. Following an in vitro assay, only the identified genes associated with macrolide resistance, LpeA and LpeB, were found to impact a quantifiable measure of antimicrobial resistance. The results of these studies emphasize the importance of understanding the context of an individual facility in Legionella related studies. Importantly, the observations or trends of one facility should not necessarily be applied to another. Legionella genetic diversity was highly conserved in some facilities, whereas in others there was greater diversity as measured by SNP differences. Within sample SNP differences was also variable between hospitals. The virulence findings gave a clear indication of the limited virulence capacity of L. anisa. These findings could explain the limited potential of L. anisa to cause disease in humans. However, a lack of difference among Lp strains may be cause to reassess the potential risk of these other strains especially in diagnostic practices. Finally, some strains of Lp have genes that may contribute to resistance to the leading antibiotic treatments for Legionnaires’ disease. Overall, this research further demonstrates the power of WGS as multiple questions can be addressed using this methodology.

The emergence of West Nile virus (WNV) has raised important questions about the capacity of the public health infrastructure to implement surveillance and control programs for WNV and other emerging or re-emerging arboviruses in the United States. Florida's mild climate supports year round enzootic transmission of WNV, St. Louis encephalitis virus (SLEV), and Eastern Equine Encephalitis virus (EEEV). It is unknown what effect the establishment of WNV (in 2001) will have on SLEV transmission in Florida, where these closely related flaviviruses share amplifying hosts, habitats, and vectors. An Arbovirus Isolation Network was formed to obtain and characterize arbovirus strains collected from a large population of naturally exposed birds, including sentinel chickens and wild birds admitted to rehabilitation centers in Florida. Weekly sentinel seroconversion data was used to target sampling of chicken flocks at 37 active sites (17 WNV, 7 EEEV, and 13 SLEV) in eight counties from 224 birds during 2005-2006. Sampling of wild birds occurred following admittance at rehabilitation centers in 2006, based on symptoms and known amplifying host species (n=64), but virus was not detected. We report the isolation of St. Louis encephalitis virus, West Nile virus and detection of Eastern Equine Encephalitis viral RNA from cloacal swabs of naturally exposed adult sentinel chickens. We also report the first known dual infection and isolation of St. Louis encephalitis and West Nile viruses from one chicken. In addition, a novel flavivirus strain was detected in two chickens. Early season transmission of WNV appears to limit subsequent infection and amplification of SLEV late in the year. Phylogenetic analysis revealed that the introduction (and re-introduction) of South American (Brazil) SLEV occurred in 1972 and 2006 in Florida. These strains represent the first reported isolation of South American strains of SLEV in the United States, with placement in Lineage VA and VB, as proposed by Kramer and Chandler (2001). Arbovirus isolation remains an effective tool for surveillance programs and a targeted strategy is most cost-effective to capture arboviruses in their natural settings for molecular epidemiology analysis that can elucidate genetic variations impacting virulence, mosquito infectivity, and disease potential of these pathogens.