A Amazônia abriga uma grande parcela da biodiversidade mundial, no entanto, existem grandes incertezas sobre os processos de geração e manutenção dessa enorme diversidade, com várias hipóteses propostas até o momento. Diversas características como tamanho pequeno, baixa capacidade de dispersão e fidelidade ao ambiente estritamente florestal fazem de lagartos do gênero Loxopholis (Squamata: Gymnophthalmidae) candidatos ideais para rastrear a história de modificações da paisagem no norte da América do Sul durante o Neogeno. Nesta tese, revisamos a variação morfológica, taxonomia e a distribuição geográfica das espécies do gênero Loxopholis, assim como estimamos as relações filogenéticas e o tempo de divergência entre as espécies com base em sequências de DNA provenientes do genoma mitocondrial e nuclear. Com essa base de dados, construímos um modelo de como ocorreu a história evolutiva de Loxopholis, discutindo os resultados a partir de reconstruções geológicas provenientes da literatura, e fornecendo uma datação independente para eventos geológicos que potencialmente influenciaram a história evolutiva do gênero. Neste estudo, também revelamos que a atual diversidade descrita para Loxopholis está severamente subestimada. Encontramos que a espécie L. osvaldoi representa um complexo de espécies crípticas, contendo de 8 a 14 potenciais espécies novas, com profundas divergências genéticas tanto nos genomas mitocondrial e nuclear, praticamente dobrando a diversidade conhecida no gênero. No entanto, a morfologia em Loxopholis é extremamente conservada, dificultando a diagnose das espécies novas. Finalmente, descrevemos a primeira população bissexual da espécie partenogenética L. percarinatum, discutindo as implicações deste achado para o entendimento relativo a aparição da partenogênese em Loxopholis / The Amazon rainforest houses a significant portion of the world biodiversity, however, there is still a lot of uncertainty about the processes involved in its generation and maintenance, with several hypotheses proposed so far. Loxopholis lizards (Squamata: Gymnophthalmidae) are small-sized; show low vagility, and high fidelity to the humid forest environment, making them ideal to test hypotheses on the history of landscape modifications in Northern South America, during the Neogene. In this thesis, we revise the morphological variation, the taxonomy, and the geographic distribution of Loxopholis species, as well as estimated a phylogenetic hypothesis and divergence times for these species based on sequences from mitochondrial and nuclear DNA. With this dataset, we build a model for the evolutionary history of Loxopholis and compared the results with geologic reconstructions of the Amazon available in the literature, which provided independent time estimates for geological events that potentially affected the evolutionary history of genus. In this study, we also showed that the actual diversity described for Loxopholis was severely underestimated. We found that L. osvaldoi represents a complex of cryptic species with 8-14 potential new species, and strong divergences in both the mitochondrial and the nuclear genomes, virtually doubling the actual diversity in the genus. Finally, we describe the first bisexual population for the parthenogenetic species L. percarinatum, discussing its implications to the origin of parthenogenesis in the genus

Includes other papers published by the author. Bibliography: p. 620-629.

The buffy flower bat (Erophylla sezekorni) is a neotropical leaf-nosed bat (Phyllostomidae) that is endemic to the Greater Antilles. Although this species is one of the most common and abundant species of mammals in the West Indies, very little is known about its ecology and evolution. To address this deficiency, I studied the genetic structure and mating system of the buffy flower bat on several islands throughout its range, focusing a more intensive study on the island of Exuma, Bahamas. I first studied the effects of ocean barriers on genetic diversification within Erophylla and two related endemic genera of endemic West Indian bats, Brachphylla, Phyllonycteris (Chapter II). I found evidence that ocean barriers inhibit gene flow and promote speciation within these genera. Focusing on genus Erophylla (Chapter III), I found that ocean channels usually act as barriers to gene flow among island populations within species. However, relatively shallow and narrow ocean channels formed semi-permeable barriers allowing gene flow between some island populations. Within the buffy flower bat, Erophylla sezekorni (Chapter IV), genetic diversity of mitochondrial DNA fragments was positively correlated with island size, with small islands having reduced genetic diversity. However, genetic diversity at several nuclear microsatellite loci was not correlated with island area and levels of genetic diversity were high for most island populations. In addition, island populations within the Great Bahamas Bank and Little Bahamas Bank showed high levels of gene flow between islands and showed no evidence of genetic bottlenecks. Populations of E. sezekorni on Exuma (Chapters IV and V) exhibited a polygynous mating system that included vigorous visual, acoustic, and olfactory male display behaviors. However, the social structure that I observed had a negligible effect on genetic diversity and genetic structure within these populations. Overall, the buffy flower bat exhibits very few of the genetic symptoms of island life, such as reduced genetic diversity and increased genetic isolation, and is evolutionarily adapted to persist on small oceanic islands.

The purpose of this dissertation research was to investigate the spatial patterns of abundance, growth, and stand structure across the geographic ranges of tree species using dendroecological methods. I assessed whether the biogeographic paradigms of the abundant center hypothesis and the principle of ecological amplitude adequately characterize spatial patterns of tree abundance, climate response, and stand composition. The abundant center hypothesis is a longstanding, yet rarely tested assumption that the centers of geographic ranges represent ideal conditions where species can achieve their greatest abundance, and abundance declines with increasing distance from the range center. A corollary to the abundant center hypothesis is the concept of ecological amplitude, which predicts that species will be subject to greater environmental stress near range margins, and thus, will be more sensitive to environmental variability and occupy restricted sites in peripheral locations. To investigate ecological amplitude predictions regarding tree species of North America, I analyzed: (1) the abundance of red fir to directly test the abundant center hypothesis, (2) the response of longleaf pine growth to monthly climate variables at peripheral and interior sites, (3) the spatial pattern of annual growth sensitivity to climate in networks of tree-ring data for two widely-distributed species, and (4) the composition and structure of pine-oak stands at a central and a peripheral location within the ranges of several dominant tree species. The analyses presented here demonstrate that the abundant center hypothesis and ecological amplitude principle do not accurately characterize spatial patterns of abundance, growth, or stand composition among North American tree species. Lack of support for the abundant center/ecological amplitude paradigm suggests that current models of forest change and species’ range dynamics should be reconsidered, and new models should be developed based on empirical analysis of range structure and dynamics.

Species of Phalaenopsis Blume (Orchidaceae) are found throughout tropical Asia, namely South China, Indochina, India, Southeast Asia, and Australia. This genus is comprised of approximately 66 species according to the latest classification. Most of them possess commercial value. Thousands of Phalaenopsis cultivars have been grown for commercial goals. Although this orchid is very beautiful and popular throughout the world, studies on the molecular systematics and phylogenetic relationships among these orchids are still deficient. Phylogenetic trees inferred from the internal transcribed spacers 1 and 2 (ITS1+ITS2) region of nuclear ribosomal DNA (nrDNA) and chloroplast DNAs (cpDNAs), including the intron of trnL, the IGS of trnL-trnF, and the IGS of atpB-rbcL, were used to clarify the phylogenetics and evolutionary trends of the genus Phalaenopsis (Orchidaceae). Molecular data are provided to clarify the latest systematics of the genus Phalaenopsis as suggested by Christenson (2001). He treated the genera of Doritis and Kingidium as synonyms of the genus Phalaenopsis and divided it into the five subgenera of Proboscidioides, Aphyllae, Parishianae, Polychilos, and Phalaenopsis. The results concurred that the genera Doritis and Kingidium should be treated as synonyms of the genus Phalaenopsis as suggested by Christenson (2001). The subgenera of Aphyllae and Parishianae were both shown to be monophyletic groups, and to be highly clustered with the subgenus Proboscidioides and two sections (including sections Esmeralda and Deliciosae) of the subgenus Phalaenopsis, which have the same morphological characters of four pollinia as well as similar biogeographies. Furthermore, neither the subgenus Phalaenopsis nor Polychilos was found to be a monophyletic group in this study. In addition, the phylogenetic tree indicates that Phalaenopsis is monophyletic and does not support the existing subgeneric and sectional classification. The phylogenetic tree of the genus Phalaenopsis is basically congruent with the geographical distributions of this genus. Based on the tree, two major clades were separated within the genus Phalaenopsis. The first clade, having four pollinia, included sections Proboscidiodes, Parishianae, and Esmeralda, of which are distributed in South China, India, and Indochina. The second clade, bearing two pollinia, included the sections Phalaenopsis, Polychilos, and Fuscatae, of which are distributed in Malaysia, Indonesia, and the Philippines. In addition, the biogeography of the genus Phalaenopsis is congruent with the historical geology of the distribution regions of this genus as well. According to molecular evidences, biogeography, historical geology, and the evolutionary trend of pollinia number of orchid, evolutionary trends of the genus Phalaenopsis were deduced. The subgenus Aphyllae was suggested to be the origin of Phalaenopsis and South China was suggested to be the origin center of Phalaenopsis. In addition, there were two dispersal pathways of Phalaenopsis from the origin center to Southeast Asia. In one pathway, Phalaenopsis species dispersed from South China to Southeast Asia, in particular the Philippines, using Indochina, older lands of the Philippines (Mindoro, Palawan, Zamboanga, etc.) as steppingstones, from which the subgenus Phalaenopsis developed. In the other pathway, Phalaenopsis species dispersed from South China to Southeast Asia, in particular Indonesia and Malaysia, using the Malay Peninsula as a steppingstone, from which the subgenus Polychilos developed. Furthermore, molecular data and geological dating were used to estimate the substitution rates of DNA from the genus Phalaenopsis based on the hypothesis of the molecular clock. The substitution rates of both ITS and cpDNA data from the genus Phalaenopsis were 2.4~4.7 x 10-9 and 3.9~7.8 x 10¡V10 substitutions/site/year, respectively. The substitution rates of ITS data of the genus Phalaenopsis are approximately six times those of cpDNA. Based on the substitution rates, the divergence time among most of the P. lueddemanniana complex was estimated to have been during the Pleistocene. The section Deliciosae separated from the section Stauroglottis at 21~10.5 Mya. Furthermore, the phylogenetics of the close species of Phalaenopsis will be evaluated based on molecular data, involving three groups of close Phalaenopsis species, namely the P. amabilis complex, P. sumatrana complex, and P. violacea complex. For the first complex, the internal transcribed spacer 1 and 2 (ITS1+ITS2) regions of nuclear ribosomal DNA (nrDNA) were applied to evaluate the phylogenetics of the P. amabilis complex, namely P. amabilis, P. amabilis subsp. moluccana, P. amabilis subsp. rosenstromii, P. aphrodite, P. aphrodite subsp. formosana, and P. sanderiana. Based on molecular data, each of species/subspecies from the P. amabilis complex with the exception of P. aphrodite and its subspecies could be separated from each other. Phalaenopsis aphrodite from different locations and its subspecies could not be separated from each other, but all of them were separable from different populations/subspecies of P. amabilis. In addition, P. sanderiana was nested within both P. amabilis and its subspecies. These results do not support P. sanderiana being treated as a separate species from P. amabilis. In addition, I suggest that P. aphrodite is the origin of the P. amabilis complex and originated in the Philippines. Phalaenopsis amabilis and P. sanderiana descended from P. aphrodite (or its ancestor). Based on the phylogenetic tree, evolutionary trends of the P. amabilis complex were suggested. Within evolutionary trends of P. amabilis complex, two different lineages with different dispersal pathways were suggested. First, P. aphrodite, dispersed into Palawan and evolved to be P. amabilis, thereafter further dispersing into Borneo and Sumatra. Second, P. aphrodite dispersed into southern Mindanao and evolved into P. sanderiana, thereafter further dispersing into Sulawesi and New Guinea, from which P. amabilis subsp. moluccana and P. amabilis subsp. rosenstromii developed, respectively. For the second complex, the phylogenetic relationship of the P. sumatrana complex, namely P. sumatrana, P. corningiana, and P. zebrina, was detected based on the ITS1 and ITS2 regions of nrDNA, the intron of trnL, and the IGS of atpB-rbcL of cpDNA. The P. sumatrana complex includes the two species of P. sumatrana and P. corningiana, as well as a problem species, P. zebrina, according to the concepts of Sweet (1980) and Christenson (2001). Based on the phylogenetic tree inferred from the ITS sequence, accessions of P. sumatrana cannot be separated from those of P. corningiana. Furthermore, accessions of P. zebrina can be separated from those of both P. sumatrana and P. corningiana. In addition, analyses of both sequences of the trnL intron and atpB-rbcL IGS of cpDNA apparently cannot discriminate among these three species of the P. sumatrana complex. Based on the molecular data of this study, plants of P. zebrina might be treated as a separate species from both P. sumatrana and P. corningiana. In the evolutionary trend of the P. sumatrana complex, plants of P. zebrina were deduced to be the relative origin group of the P. sumatrana complex based on the phylogenetic tree and biogeography. In addition, plants of both P. sumatrana and P. corningiana might have descended from plants of P. zebrina. For the third complex, the phylogenetic trees inferred from the internal transcribed spacer 1 and 2 (ITS1+ITS2) regions of nuclear ribosomal DNA (nrDNA), the intron of trnL, and the intergenic spacer of atpB-rbcL of chloroplast DNA (cpDNA) were used to clarify the phylogenetic relationships of the P. violacea complex. The complex includes the two species of P. violacea and P. bellina, according to the concept of Christenson (2001). Based on the phylogenetic tree inferred from the ITS sequence, P. bellina could not be separated from most populations from P. violacea with the exception of the population distributed on Mentawai Is., Indonesia. In addition, analyses of both the intron of trnL and the IGS of atpB-rbcL of cpDNA apparently could not discriminate among the three species of the P. sumatrana complex. Based on the morphological characters, P. violacea from Mentawai Is. bears a long floral rachis and was separable from the other groups of the P. violacea complex. Therefore, the results in this study have a trend to treat the population of Mentawai Is. of the P. violacea complex as a separate species from P. violacea. In the evolutionary trend of the P. violacea complex, Mentawai plants of this complex might be descended from those of Sumatra/the Malay Peninsula according to the phylogenetic analysis and biogeography.

Abstracts Capricornis swinhoei is one of the indangered wild animals in Taiwan. The objective of this study is using molecular biology and morphology methods to analyze the genetic diversity, observed population structure, differentiation and biogeographic relationships among the population of Capricornis swinhoei. Samples used in this study were collected from the Central Mountains located in Taiwan. DNA sequences (1099 bp) from the mitochondrial DNA (mtDNA) control region, D-loop, were used to test the phylogeographic relationships among the Capricornis swinhoei. A phylogenetic tree was constructed on the basis of GCG-Seq Web and MEGA softwares. In addition, distance analyses, neighbor-join, and maximum parsimony to resolve these phylogenetic relationships were performed. The C. sumatraensis and C. crispus sequence were also determined and used as the outgroups. Our findings clearly demonstrate that Capricornis swinhoei can be clustered into two groups, north and south groups, and consistent with the truth of geographic isolation. The data obtained from this study may facilitate the program of wildlife conservation in Taiwan.

Thesis (Ph. D.)--University of Texas at Austin, 1999. / Vita. Includes bibliographical references (leaves 184-194). Available also in a digital version from Dissertation Abstracts.

This dissertation presents the result of two separate research programs. The first elucidates the phylogeny, biogeography and systematics of the genus Menodora in the olive family. A phylogeny based on the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the chloroplast rps16 and trnL introns and trnL-F intergenic spacer demonstrates that the genus is monophyletic. Within the genus, M. robusta of Patagonia is the first taxon to branch, followed by a monophyletic African clade and M. spinescens of California, though the placement of the latter does not have strong support. Most North American species are nested within the derived South Americans. A South American origin is hypothesized, with two independent dispersals to North America, and a single dispersal to Africa. The phylogeny provided new insights for the systematic treatment, where 24 species, one subspecies and six varieties are recognized, with major realignments of the intregrifolia and scabra species complexes, and a single new species described. In the second area of research, the chloroplast genome of Pelargonium × hortorum has been completely sequenced. At 217,942 base pairs (bp), it is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features two copies of a greatly expanded inverted repeat (IR) of 75,741 bp each, and diminished single copy regions of 59,710 bp and 6,750 bp. Gene content is similar to other angiosperms, with the exceptions of a large number of pseudogenes, two open reading frames (ORF56 and ORF42), and the losses of accD, trnT-ggu, and possibly rpoA. The latter may be represented, however, by highly divergent set of rpoA-like ORFs. The IR expansion accounts for most of the size increase of the genome, but an additional 10% is related to the large number of repeats found. Most of these occur near rearrangement hotspots, and two different repeat associations (characterized by full or partial duplications of several genes) are localized in these regions. We propose simple models that account for the major rearrangements with a minimum of eight IR boundary changes and 12 inversions in addition to several sequence duplications. / text

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This dissertation investigates evolutionary relationships within a diverse and ancient group of arachnids, the order Opiliones, with emphasis on relationships within the suborder Laniatores. Laniatorid harvestmen encompass over two-thirds of opilionid diversity, but this suborder has received far less than commensurate phylogenetic attention. The ancient age and narrow species distributions of Laniatores, in conjunction with their representation throughout tropical and subtropical regions of the world, herald models of unparalleled utility for study of tropical diversity and biogeography. Herein I infer the phylogeny of Laniatores using a ten-gene molecular dataset, which samples for the first time every described family of the group. Based upon morphological and molecular sequence data, I describe three new families of Laniatores--two endemic to Southeast Asia and one to the Afrotropics. Focusing on the biogeography of Australasia, I contrast the evolutionary histories of two families: Sandokanidae, which are restricted to the Indo-Malay Archipelago, and Zalmoxidae, which occurs in the Neotropics and Australasia. Using molecular phylogenetic tools, I demonstrate that sandokanid distribution is largely attributable to continental vicariance in Sundaland, whereas zalmoxid distribution is attributable to a New World origin, followed by colonization of the Indo-Pacific by transoceanic dispersal.