For over a century, the origins and mechanisms underlying the diversification of the enormous cosmopolitan genus Carex (>2,100 species; Cariceae, Cyperaceae or sedge family) have remained largely speculative. Although its unique morphology (e.g., unisexual flowers, perigynia) clearly indicated it was a natural group, it obscured its relationships to all other Cyperaceae because the morphological gap between it and the rest of the family was so wide. Consequently, no plausible sister group to Carex has ever been proposed. Early molecular analyses narrowed the problem by placing Carex within a strongly-supported clade with the enigmatic monospecific genus Khaosokia, and tribes Dulichieae and Scirpeae (hereafter CDS), a group consisting of 2,250 species, or approximately 41% of all Cyperaceae. However, poor taxonomic sampling and the limited number of molecular markers used in these studies meant that the sister group to Carex remained a mystery. The goals of this thesis were to resolve evolutionary relationships within the CDS clade, to identify the sister group to Carex, and to develop a new natural tribal classification of CDS that could be used in future biogeographic and comparative analyses of Carex and its relatives. Initial phylogenetic analyses using two plastid markers (matK, ndhF) identified seven major CDS lineages, and suggested that Carex could be nested within a paraphyletic Scirpeae. However, backbone support for these relationships was low due to an ancient rapid radiation (~10 million years) followed by long divergence of the seven major lineages (~40 million years). The addition of conventional sequence-based markers from the plastid genome (rps16) and nuclear ribosomal region (ETS-1f, ITS) indicated that a traditional molecular approach would not resolve these key backbone nodes. Consequently, a recently developed flowering-plant-specific anchored enrichment probe kit targeting hundreds of conserved nuclear genes combined with next generation sequencing was used to resolve the CDS backbone. Although the resulting phylogenomic dataset was able to resolve the CDS backbone with high support, the topology and branch lengths only reaffirmed the isolated position of Carex. However, comparative morphological analyses of specimens at key herbaria not only suggested that Sumatroscirpus, a rare genus thought to be endemic to Sumatra, could be sister to Carex, but they also provided an easily accessible site to collect DNA in Northern Vietnam. Subsequent phylogenetic analyses of plastid (matK, ndhF, rps16) and nuclear ribosomal (ETS-1f, ITS) markers strongly supported Sumatroscirpus as the sister to Carex, and molecular dating estimates suggested they shared a common ancestor in the late Eocene (~36 million years ago). Comparative studies and ancestral state estimates of key morphological characters were congruent with this hypothesis, suggesting that the perigynium is not unique to Carex, but in fact a synapomorphy shared with Sumatroscirpus. This means that the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints that permitted the evolution of the remarkable morphological diversity of Carex perigynia seen today. A taxonomic revision of Sumatroscirpus revealed that this purportedly monospecific genus actually consisted of four species, and it extended its range over 2,400 km to the north into Northern Vietnam, Myanmar, and Southwestern China. The phylogenetic framework provided by the previous studies enabled a new tribal and generic classification of CDS to be proposed. Seven monophyletic tribes are recognised including four new tribes (Calliscirpeae, Khaosokieae, Sumatroscirpeae, Trichophoreae), and a new genus (Rhodoscirpus). Morphological synapomorphies are identified for all recognized tribes, and a worldwide treatment, including identification keys, is provided for Sumatroscirpus species, CDS genera, and Cyperaceae tribes.

I focus on phylogenetic relationships of teiid lizards beginning with generic and species relationship within the family, followed by a detailed biogeographical examination of the Caribbean genus Pholidoscelis, and end by studying species boundaries and phylogeographic patterns of the widespread Giant Ameiva Ameiva ameiva. Genomic data (488,656 bp of aligned nuclear DNA) recovered a well-supported phylogeny for Teiidae, showing monophyly for 18 genera including those recently described using morphology and smaller molecular datasets. All three methods of phylogenetic estimation (two species tree, one concatenation) recovered identical topologies except for some relationships within the subfamily Tupinambinae (i.e. position of Salvator and Dracaena) and species relationships within Pholidoscelis, but these were unsupported in all analyses. Phylogenetic reconstruction focused on Caribbean Pholidoscelis recovered novel relationships not reported in previous studies that were based on significantly smaller datasets. Using fossil data, I improve upon divergence time estimates and hypotheses for the biogeographic history of the genus. It is proposed that Pholidoscelis colonized the Caribbean islands through the Lesser Antilles based on biogeographic analysis, the directionality of ocean currents, and evidence that most Caribbean taxa originally colonized from South America. Genetic relationships among populations within the Ameiva ameiva species complex have been poorly understood as a result of its continental-scale distribution and an absence of molecular data for the group. Mitochondrial ND2 data for 357 samples from 233 localities show that A. ameiva may consist of up to six species, with pairwise genetic distances among these six groups ranging from 4.7–12.8%. An examination of morphological characters supports the molecular findings with prediction accuracy of the six clades reaching 72.5% using the seven most diagnostic predictors.

Orientador: Célio Fernando Baptista Haddad / Resumo: Thoropa Cope, 1865 (Anura: Cycloramphidae) é um gênero de rãs endêmicas do domínio Mata Atlântica e de ecótonos associados. Possui atualmente seis espécies (T. miliaris, T. petropolitana, T. taophora, T. lutzi, T. megatympanum e T. saxatilis), divididas em dois grupos morfológicos: grupo petropolitana (T. petropolitana e T. lutzi) e grupo miliaris (T. miliaris, T. taophora, T. megatympanum e T. saxatilis). Todas as espécies se reproduzem e se desenvolvem em rochas molhadas de água doce, encontradas em afloramentos rochosos, cachoeiras e riachos. Um estudo recente sobre a filogenia molecular mostrou que T. miliaris é parafilética a T. taophora, e que T. taophora, T. megatympanum e T. saxatilis são monofiléticas com alto suporte (Sabbag et al. 2018). Esse estudo também encontrou diversos clados dentro de cada uma das espécies, especialmente em T. miliaris. Porém, não foi possível estudarem molecularmente as espécies do grupo petropolitana porque existe apenas uma amostra de DNA disponível para o grupo. No presente trabalho, estudamos aspectos genéticos e morfológicos das seis espécies do gênero a fim de investigar a diversidade molecular previamente encontrada, a parafilia de T. miliaris e as características morfológicas das espécies que coincidam com a diversidade genética conhecida. Encontramos que os clados conhecidos de T. miliaris são linhagens evoluindo separadamente e que os clados conhecidos de T. taophora fazem parte de uma linhagem única. Thoropa miliaris e T. taophor... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Thoropa Cope, 1865 (Anura: Cycloramphidae) is a frog genus endemic to theAtlantic forest domain and associated ecotones. It comprises six species (T. miliaris, T. petropolitana, T. taophora, T. lutzi, T. megatympanum and T. saxatilis), divided in two morphological groups: petropolitana group (T. petropolitana and T. lutzi) and miliaris group (T. miliaris, T. taophora, T. megatympanum and T. saxatilis). All the species reproduce and develop in freshwater wet rocks that can be found in rock outcrops, waterfalls and streams. A recent study on molecular phylogeny has shown that T. miliaris is paraphyletic in respect to T. taophora and that T. taophora, T. megatympanum and T. saxatilis are monophyletic with high support. This study also found many clades inside each of those species, especially within T. miliaris. Nevertheless, it was not possible to study molecular aspects of the petropolitana group because there is only one DNA sample available for the group. In this work, we studied genetic and morphological aspects of all six species of the genus in order to investigate the molecular diversity found previously, the paraphyly found for T. miliaris, and the species morphological characteristics that coincide with the known genetic diversity. We found that the known clades of T. miliaris are separately evolving lineages and that the clades of T. taophora are part of a whole lineage. Thoropa miliaris and T. taophora are reciprocally monophyletic. We also found that the diversifica... (Complete abstract click electronic access below) / Doutor