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Over the last few decades there has been a confusion in the classification system of organisms with the development of molecular and genetic methods. Life is currently perceived from a different perspective than in the past due to different methods, and old, standard systems have significantly changed as a result of such alteration. As a consequence, it is harder and harder to distinguish which taxonomic changes are caused by objectively better recognition of biodiversity and which seem to be only subjective opinions of particular taxonomists. Results show a significant growth in the number of genuses in observed families of frogs (Anura) in the aforementioned period (2000-2017) while the research efforts of taxonoms were proved to be the most relevant factors causing such increase in diversity with respect to genuses.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / ClassificaÃÃes taxonÃmicas de ostras sÃo problemÃticas, pois estes organismos possuem caracterÃsticas morfolÃgicas pouco informativas. A variabilidade da regiÃo ITS do cluster ibossÃmico tem sido bastante utilizada em estudos filogenÃticos e taxonÃmicos, visto que esta regiÃo apresenta uma variabilidade relativamente elevada e fÃcil amplificaÃÃo por termociclagem. A ostra Crassostrea brasiliana foi, por dÃcadas, confundida com C. rhizophorae, entretanto, estudos recentes indicam que sÃo duas espÃcies biologicamente distintas. Esta pesquisa objetivou analisar a variabilidade da regiÃo ITS-1 de populaÃÃes de ostras C. rhizophorae em trÃs estuÃrios da costa do Estado do Cearà e investigar a presenÃa de uma segunda espÃcie de ostra pertencente ao gÃnero Crassostrea. Exemplares da ostra nativa C. cf. rhizophorae foram coletados nos estuÃrios da costa cearense para anÃlise de variabilidade populacional. Foram coletados tambÃm espÃcimes de C. cf. brasiliana para estudo de filogenia e comparaÃÃo com o primeiro grupo de ostras. ApÃs extraÃÃo de DNA e amplificaÃÃo por PCR da regiÃo ITS-1, seqÃÃncias desta regiÃo foram obtidas para anÃlise filogenÃtica realizada atravÃs dos mÃtodos de neighbour-joining e mÃxima parcimÃnia. SequÃncias de ITS-1 descritas no GenBank para 35 indivÃduos, representando 12 espÃcies de ostras do gÃnero Crassostrea, e mais duas seqÃÃncias de Saccostrea glomerata (grupo externo), foram utilizadas para os alinhamentos com as sequÃncias obtidas na presente pesquisa. A variabilidade intraespecÃfica de C.cf.rhizophorae foi estudada pelo mÃtodo da mÃxima parcimÃnia. SeqÃÃncias inÃditas de ITS-1 completo foram obtidas para C.brasiliana e C.rhizophorae, com 427 e 439 pb, respectivamente. A Ãrvore de neighbour-joining evidenciou a clara separaÃÃo de C.cf.brasiliana e C.cf.rhizophorae em ramos distintos (100%), confirmando a ocorrÃncia de, pelo menos, duas espÃcies de Crassostrea no local de estudo. O estudo sugere a ocorrÃncia de C.brasiliana no Estado do CearÃ. Embora alguns autores tenham considerado C.brasiliana sinÃnimo de C.virginica, em nosso estudo, C.virginica mostrou-se muito mais prÃxima de C.rhizophorae, com forte agrupamento (100%). A Ãrvore de mÃxima parcimÃnia mostrou que as seqÃÃncias de C.cf.brasiliana e C.cf.rhizophorae formaram um grupo monofilÃtico com as demais espÃcies de Crassostrea em 100% das repetiÃÃes. C.cf.brasiliana apresentou-se na base do ramo monofilÃtico de Crassostrea e, portanto, foi o grupo mais prÃximo de S.glomerata. Esta Ãrvore tambÃm mostrou a separaÃÃo dos exemplares de C.cf.brasiliana e C.cf.rhizophorae em ramos distintos (100%), evidenciando o forte sinal filogenÃtico observado na anÃlise. Novamente, C.cf.rhizophorae mostrou-se prÃxima de C.virginica. A anÃlise de mÃxima parcimÃnia para variabilidade intraespecÃfica de C.cf.rhizophorae nos trÃs estuÃrios estudados mostrou a formaÃÃo de 7 diferentes sequÃncias para C.cf.rhizophorae. A ligaÃÃo entre as sequÃncias encontradas sugere a presenÃa de fluxo gÃnico entre as populaÃÃes estudadas e a ocorrÃncia de sequÃncias exclusivas pode indicar a formaÃÃo de populaÃÃes residentes em cada um dos estuÃrios analisados. A regiÃo ITS-1 mostrou-se ideal para estudos de filogenia de ostras e estudos de variabilidade gÃnica populacional. A confirmaÃÃo de uma segunda espÃcie de ostra pertencente ao gÃnero Crassostrea na costa cearense à relevante para uma melhor gestÃo destes recursos, que possuem grande importÃncia ecolÃgica, econÃmica e social para nosso Estado. / Taxonomic classifications of oysters are problematic, because these bodies have little morphological information. The variability of the ITS region of the cluster ibossÃmico has been used in phylogenetic and taxonomic studies, since this region presents a relatively high variability and easy amplification by thermocycling. The oyster Crassostrea brasiliana was, by decades, confused with C. rhizophorae However, recent studies indicate that two biologically distinct species. This study aimed to analyze the variability of ITS-1 region of oyster populations of C. rhizophorae in three estuaries on the coast of Cearà State and investigate the presence of a second species of oysters belonging to the genus Crassostrea. Copies of the native oyster C. cf. rhizophorae were collected in the estuaries of the coast of Cearà for the analysis population ariability. Were also collected specimens of C. cf. brasiliana for study of phylogeny and compared with the first group of oysters. After extraction of DNA and amplification by PCR of the ITS-1 region, this region sequences were obtained for phylogenetic analysis performed by the methods of neighbor-joining and maximum parsimony. ITS-1 sequences described in GenBank for 35 individuals representing 12 species of oysters of the genus Crassostrea and two sequences of Saccostrea glomerata (external group) were used for the alignments with the sequences obtained in this study. The intraspecific variability of C.cf.rhizophorae was studied by the method of maximum parsimony. Unpublished sequences of ITS-1 were obtained for full C.brasiliana and C.rhizophorae with 427 and 439 bp, respectively. The neighbor-joining tree, showed the clear separation of C.cf.brasiliana and C.cf.rhizophorae in separate branches (100%), confirming the occurrence of at least two species of Crassostrea place of study. The study suggests the occurrence of C.brasiliana in the state of CearÃ. Although some authors have considered C.brasiliana synonymous with C.virginica in our study, C.virginica was very close to C.rhizophorae, with a strong group (100%). The tree of maximum parsimony showed that the sequences of C.cf.brasiliana and C.cf.rhizophorae formed a monophyletic group with other species of Crassostrea in 100% of replicates. C.cf.brasiliana presented on the basis of branch of Crassostrea monophyletic and, therefore, was the group nearest S.glomerata. This tree also showed the separation of the copies of C.cf.brasiliana and C.cf.rhizophorae in different branches (100%), showing the strong signal observed in the phylogenetic analysis. Again, C.cf.rhizophorae showed up near C.virginica. The maximum parsimony analysis of intraspecific variability of C.cf.rhizophorae for the three estuaries studied showed the formation of 7 different sequences for C.cf.rhizophorae. The connection between the sequences found suggests the presence of gene flow between populations and the occurrence of unique sequences may indicate the formation of resident populations in each of the estuaries examined. The region ITS-1 proved to be ideal for studies of phylogeny of oysters and studies of population genetic variability. Confirmation of a second species of oysters belonging to the genus Crassostrea in Cearà coast is important for better management of these resources, which have important ecological, economic and social to our state.

Systematik ist das grundlegende Fachgebiet der Biologie, dessen Ziel es ist, die Vielfalt des Lebens zu beschreiben und zu verstehen. Ihre Bedeutung kann nicht außer Acht gelassen werden, da uns die Systematik Werkzeuge lieferte, um auf Verwandtschaftsbeziehungen zwischen lebenden Organismen zu schließen, und wir diese Informationen genutzt haben, um unsere Lebensqualität zu verbessern, die Umwelt zu schützen, die Vergangenheit zu verstehen und die Vielfalt der natürlichen Welt wertzuschätzen. Systematik unterteilt sich in drei Fachrichtungen, nämlich Taxonomie, Phylogenie und Biogeographie. In dieser Dissertation habe ich die Systematik der philippinischen Angehörigen der größten Gattung der Familie Gesneriaceae, Cyrtandra, untersucht. Cyrtandra ist eine Gattung mit fast 800 Arten von krautigen Pflanzen, Sträuchern, kletternden Pflanzen und kleinen Bäumen und hat das größte Verbreitungsgebiet innerhalb der Familie der Gesneriaceae, dass sich vom Indo-Australischen Archipel bis zum Pazifik erstreckt. Ihr Vorkommen in Biodiversitätshotspots und ihre hohe Artenzahl machen sie zu einer ausgezeichneten Modellgruppe für die Untersuchung von Biogeografie, Artbildung, Diversifizierung und Prioritätensetzung bei der Erhaltung. Ihr Nutzen als Modellgruppe wird jedoch dadurch behindert, dass nur wenige Systematiker/innen aktiv an der Gattung arbeiten. Jüngste Arbeiten haben glücklicherweise dazu beigetragen, dass die Vielfalt und die Biologie dieser Gattung nun endlich besser verstanden werden. Mit dieser Dissertation, in der ich taxonomische, phylogenetische und biogeografische Untersuchungen an philippinischen Taxa durchführte, möchte ich zu diesem langsam wachsenden Wissen beitragen. Die Dissertation ist in fünf Kapitel unterteilt, wobei das erste und das letzte Kapitel eine allgemeine Einleitung bzw. eine Schlussfolgerung enthalten. In Kapitel 2 berichte ich über taxonomische Neuheiten bei den philippinischen Cyrtandra. Zunächst habe ich neue Namen für zwei Homonyme in der philippinischen Flora vorgeschlagen, C. coriaceifolia für C. humilis in Anlehnung an ihre lederartigen Blätter und C. bacanii für C. umbellata zu Ehren des Sammlers des Typusexemplars, E.S. Bacani. Cyrtandra argentii wird als eine neue endemische Art beschrieben und nach G. Argent benannt. Es handelt sich um eine eigenständige endemische Art, die an ihren hängenden, zusammengesetzten, zymösen Blütenständen mit 10-15 Blüten zu erkennen ist. Schließlich wird C. villosissima var. flavovirens als neue Farbvarietät von C. villosissima beschrieben, benannt nach ihren blassgelben bis gelbgrünen Blütenkronen. Für die neuen Taxa werden Diagnosen, Beschreibungen, Bilder, Strichzeichnungen, Schlüssel und vorgeschlagene IUCN-Kategorien bereitgestellt. ZUSAMMENFASSUNG In Kapitel 3 stelle ich eine taxonomische Synopse der philippinischen Cyrtandra (Gesneriaceae) vor. Dies ist nach 100 Jahren die erste Aktualisierung von Merrills Aufzeichnungen der Blütenpflanzen aus dem Jahr 1923. Ich erkenne 98 Cyrtandra-Arten für die philippinische Flora an. Ich bestätige einen Artnamen, der zuvor ohne lateinische Diagnose beschrieben wurde (C. peninsula), synonymisiere drei Namen (C. quisumbingii und C. quisumbingii var. minor werden unter C. hypochrysoides synonymisiert, während C. florulenta unter C. incisa synonymisiert wird), und schlage zwei neue Namen vor (C. edanoi für C. pallida und C. siporensis für C. chiritoides). Taxonomische Anmerkungen folgen jeder Art und jeder korrekten Typisierung, um die Stabilität der Namen zu gewährleisten und die Identifizierung der Arten zu erleichtern. Eine Tabelle erleichtert das Nachschlagen der derzeit akzeptierten Namen der philippinischen Cyrtandra. In Kapitel 4 führe ich phylogenetische und biogeografische Analysen über das gesamte Verbreitungsgebiet von Cyrtandra durch, wobei ich die philippinischen Taxa stärker in die Stichproben einbeziehe, um die bisherigen Sammel-Lücken zu schließen. In der phylogenetischen Analyse zeige ich, dass es bei den südostasiatischen Vertretern wenig geografische Strukturierung gibt, was darauf hindeutet, dass die biogeografischen Linien für Pflanzentaxa sehr durchlässig sind, wie dies auch von anderen gezeigt wurde. In der biogeografischen Analyse prüfte ich, ob die Muster und die Diversifizierungsdynamik von Cyrtandra mit der allgemeinen dynamischen Theorie der ozeanischen Inselbiogeografie (general dynamic theory of oceanic island biogeography, GDT) vereinbar sind. Um dies zu prüfen, führte ich eine datierte phylogenetische Analyse durch, gefolgt von einer BioGeoBeaRS- und einer BAMM-Analyse. Ich zeige, dass ozeanische Inseln, insbesondere Wallacea, wichtige Quellen für die Ausbreitung von Cyrtandra-Linien sind. Die GDT betrachtet ozeanische Inseln hauptsächlich als Senken für sich ausbreitende Linien. Der relativ hohe Beitrag von Wallacea lässt sich auf seine zentrale Lage im Verbreitungsgebiet von Cyrtandra und seine komplexe geologische Geschichte zurückführen, die für eine erhöhte Ausbreitungsfähigkeit sorgt. Ich untersuche weiterhin, ob die Diversifizierungsdynamik von Cyrtandra den Vorhersagen der adaptiven Radiation folgt, die auf ozeanischen Inseln von der GDT als dominanter Prozess vorhergesagt wird. Die Diversifizierungsdynamik von Cyrtandra im südostasiatischen Grade zeigt frühe Schübe in den Diversifizierungsraten, gefolgt von einem Plateau, was mit adaptiver Radiation vereinbar ist. Es werden keine Anzeichen für eine diversitätsabhängige Diversifizierung festgestellt, was darauf zurückzuführen ist, dass die südostasiatischen Cyrtandra-Arten verschiedene Nischen besetzen, was durch ihre große morphologische Bandbreite, insbesondere in Bezug auf Habitus und Blütenmerkmale, deutlich wird. Die Gruppe mit den meisten pazifischen Mitgliedern, die in den frühen Stadien der Ontogenese der pazifischen Inseln auftraten, zeigt eine Diversifizierungsdynamik, die durch das Island Immaturity Speciation Pulse (IISP)-Modell vorhergesagt wurde, und ihr morphologisches Spektrum wird durch den Least-Action-Effekt kontrolliert, der Verholzung und fleischige Früchte begünstigt. In dieser Dissertation gebe ich neue Einblicke in die Systematik von Cyrtandra, indem ich den Schwerpunkt auf die philippinischen Mitglieder lege. Außerdem stelle ich neue Informationen zur Verfügung, die zur Standardisierung eines prädiktiven Klassifizierungssystems für die Gattung beitragen sollen. Darüber hinaus ist dies ein erster Schritt in Richtung eines Rahmens für die Untersuchung der Diversifizierungsdynamik, wie sie von der GDT für sehr erfolgreiche insulare Taxa vorhergesagt wird. / Systematics is the foundational field of biology wherein it aims to describe and understand the diversity of life. Its importance cannot be disregarded since systematics provides us tools to infer relationships among living organisms and we utilize this information to improve our quality of living, protect the environment, understand the past, and simply appreciate the variation and diversity of the natural world. Systematics is composed of three branches, namely taxonomy, phylogenetics, and biogeography. In this dissertation, I explore the systematics of the Philippine members of the largest genus in the family Gesneriaceae, Cyrtandra. Cyrtandra is a genus of almost 800 species of herbs, shrubs, vines, and small trees and it has the widest distributional range in the family Gesneriaceae starting from the Indo-Australian Archipelago extending farther eastwards to the Pacific. Its presence in biodiversity hotspots and its high species number make it an excellent model group for studying biogeography, speciation, diversification, and conservation prioritization. Its utility as a model group, however, is hampered because of the few systematists actively working on the genus. Recent works have fortunately acted as stimuli to finally pick up the pace in understanding the diversity and biology of this genus. I aim to contribute to this slowly increasing knowledge with this dissertation wherein I conduct taxonomic, phylogenetic, and biogeographic research on Philippine members. This dissertation is divided into five chapters and the first and last chapters provide a general introduction and conclusion, respectively. In Chapter 2, I report taxonomic novelties in Philippine Cyrtandra. First, I propose new names to two homonyms in the Philippine flora, C. coriaceifolia for C. humilis in reference to its coriaceous leaves and C. bacanii for C. umbellata to honor the collector of the type specimen, E.S. Bacani. I describe Cyrtandra argentii as a new endemic species and named after G. Argent. This is a distinct endemic recognized by its pendulous compound cymose inflorescences with 10–15 flowers. Lastly, I describe C. villosissima var. flavovirens as a new color variety of C. villosissima named for its pale yellow to yellow-green corollas. I provide diagnoses, descriptions, images, line drawings, keys, and IUCN categories for the novel taxa. In Chapter 3, I present a taxonomic synopsis of Philippine Cyrtandra (Gesneriaceae). This is the first update, after 100 years, of Merrill’s 1923 enumeration of flowering plants. I recognize 98 species of Cyrtandra for the Philippine flora. I validate a species name that was previously described without a Latin diagnosis (C. peninsula), synonymize three names (C. quisumbingii and C. quisumbingii var. minor are in synonymy under C. hypochrysoides while C. florulenta is in synonymy under C. incisa), and propose two new names (C. edanoi for C. pallida, and C. siporensis for C. chiritoides). Taxonomic notes follow every species and correct typification to ensure stability of the names and aid in the identification of species. I also provide a look-up table to facilitate referencing of currently accepted names in Philippine Cyrtandra. In Chapter 4, I perform phylogenetic and biogeographic analyses across the entire distributional range of Cyrtandra with increased sampling of Philippine members to fill-in sampling gaps. In the phylogenetic analysis, I show that there is little geographic structuring in Southeast Asian members indicating that biogeographic lines are highly permeable for plant taxa, as has been shown in others. In the biogeographic analysis, I test whether patterns and diversification dynamics in Cyrtandra are consistent with the general dynamic theory of oceanic island biogeography (GDT) by performing a dated-tree analysis, followed ancestral range estimation via BioGeoBeaRS, and then diversification rate analysis using BAMM. I show that oceanic islands, specifically Wallacea, are important sources of dispersing lineages for Cyrtandra. GDT views oceanic islands mainly as sinks for dispersing lineages. The relatively high contribution of Wallacea is attributed to its central location along the distributional range of Cyrtandra and its complex geological history selecting for increased dispersibility. I show that diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process on oceanic islands as predicted by the GDT. Diversification dynamics of Cyrtandra in the Southeast Asian grade show early bursts in diversification rates followed by a plateau which is consistent with adaptive radiation. No signals of diversity-dependent diversification are detected, and this is attributed to Southeast Asian cyrtandras occupying various niche spaces as evident by its wide morphological range, particularly in habit and floral characters. The clade containing mostly Pacific members, which arrived at the early stages of the ontogeny of the Pacific islands, show diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model and their morphological range is controlled by the least action effect favouring woodiness and fleshy fruits. In this dissertation, I provide novel insights into the systematics of Cyrtandra by putting focus on Philippine members. Also, I provide new information that aims to contribute to the standardization of a predictive classification system for the genus. Additionally, this provides a first step towards a framework for investigating diversification dynamics as predicted by the GDT in highly successful insular taxa.

The taxonomy of the Mediterranean Aristolochia pallida complex has been under debate since several decades with the following species currently recognized: A. pallida, A. lutea, A. nardiana, A. microstoma, A. merxmuelleri, A. croatica, and A. castellana. These taxa are distributed from Iberia to Turkey. To reconstruct phylogenetic and biogeographic patterns, we employed cpDNA sequence variation using both noncoding (intron and spacer) and protein-coding regions (i.e., trnK intron, matK gene, and trnK-psbA spacer). Our results show that the morphology-based traditional taxonomy was not corroborated by our phylogenetic analyses. Aristolochia pallida, A. lutea, A. nardiana, and A. microstoma were not monophyletic. Instead, strong geographic signals were detected. Two major clades, one exclusively occurring in Greece and a second one of pan-Mediterranean distribution, were found. Several subclades distributed in Greece, NW Turkey, Italy, as well as amphi-Adriatic subclades, and a subgroup of southern France and Spain, were revealed. The distribution areas of these groups are in close vicinity to hypothesized glacial refugia areas in the Mediterranean. According to molecular clock analyses the diversification of this complex started around 3–3.3 my, before the onset of glaciation cycles, and the further evolution of and within major lineages falls into the Pleistocene. Based on these data, we conclude that the Aristolochia pallida alliance survived in different Mediterranean refugia rarely with low, but often with a high potential for range extension, and a high degree of morphological diversity.