No description available.

According to previous morphological studies on percoid phylogenies, Pempheridae may have a closer relationship to Glaucosomatidae, Teraponidae, Bramidae, Carangidae, Centropomidae, Kyphosidae, Leiognathidae, Menidae, Nandidae, Percichthyidae, Polynemidae, Sciaenidae or Toxotidae. About 10% of 515 fish families are soniferous and Pempheridae is one of the soniferous families in Percoidei. A pair of slits has been found at the anterodorsal sides of the swimbladder in Glaucosomatidae, Teraponidae and Pempheridae, and it suggests that they have closer relationship. And preliminary study on molecular phylogeny has evidence supporting that Glaucosomatidae and Pempheridae are sister goups. In this study, I compared the sonic muscle, swimbladder morphology, slit and associated structures in percoid soniferous fishes, including Pempheridae, Glaucosomatidae, Teraponidae, Sciaenidae, Priacanthidae, Haemulidae, Cichlidae and Pomacentridae. I found that there are synapomorphic characters in Pempheridae, Glaucosomatidae and Teraponidae; the slits and elastic tissue in the swimbladder are similar, and are limited to these three families. Furthermore, 16S rRNA, COI, Cytb and Rhodopsin gene sequences data were used for phylogenetic studies. And the results reveal that Pempheridae and Glaucosomatidae are sister groups and they are not closely related to Teraponidae. Therefore, the similary of sonic system in Teraponidae, Pempheridae and Glaucosomatidae may have evolved at least twice in the Percoidei and convergent evolution might also have taken placed.

O gênero Acestrorhynchus encontra-se amplamente distribuído na América do Sul, estando presente nas bacias do Paraná-Paraguai, Uruguai, no rio São Francisco, nos rios costeiros das Guianas, e nas bacias dos rios Amazonas e Orinoco, sendo as duas últimas, o local onde se encontra a maior diversidade desses peixes. Na ausência de estudos mais detalhados sobre as relações filogenéticas entre as espécies de Acestrorhynchus, as 14 espécies reconhecidas têm sido agrupadas com base no seu padrão de coloração. O primeiro trabalho focalizando as relações filogenéticas das espécies de Acestrorhynchus, foi desenvolvido recentemente e estabelece as relações de parentesco de 13 espécies do gênero com base na análise de 104 características osteológicas e de morfologia externa. No presente estudo, 2139 pares da região 16S e da ATPase, ambos do genoma mitocondrial, juntamente o primeiro íntron da proteína ribossomal S7 do genoma nuclear, foram analisados para as espécies A. microlepis, A. falcatus, A. heterolepis, A pantaneiro, A. falcirostris, A. altus, A. minimus, A. grandoculis, A. britskii, A. lacustris e A. nasutus. Os gêneros Roeboides, Rhaphiodon e Gephyrocharax foram utilizados como grupo externo. A análise de máxima parcimônia, com busca heurística e adição aleatória de seqüências com o algoritmo TBR resultou na obtenção de uma árvore mais parcimoniosa com 2.551 passos. Os índices de consistência e retenção foram, respectivamente, 0,633 e 0,533. Os resultados obtidos através da análise dos dados moleculares corroboram, assim como os resultados morfológicos, o monofiletismo dos agrupamentos propostos com base nos padrões de coloração. / Fishes of the Neotropical characiform genus Acestrorhynchus Eigenmann, comprise freshwater species widely distributed throughout South American rivers, being found in the Paraná, Paraguai, Uruguai, São Francisco and of Guyana rivers. However it is in the Amazonas and Orinoco river basins where the highest diversity of this group of fishes is present. In the absence of more detailed phylogenetic studies the 14 recognized species are grouped on the basis of their color patterns. The first specific study about the phylogenetic relationships of Acestrorhynchus species, was recently developed and it established the relationships of 13 species of the genus, based in the analysis of 104 osteological and external morphological characters. In the present study, simultaneous analysis of 2139 aligned base pairs from the mitochondrial 16S and ATPase and the nuclear first intron of the S7 ribosomal protein were analyzed for the species A. microlepis, A. falcatus, A. heterolepis, A pantaneiro, A. falcirostris, A. altus, A. minimus, A. grandoculis, A. britskii, A. lacustris e A. nasutus. The genera Roeboides, Rhaphiodon and Gephyrocharax were included in the analysis as outgroups. Maximum parsimony analysis, and heuristic searches with random taxon addition replicates and TBR branch swapping were performed resulting in one most parsimonious tree with 2,551 steps in length. The consistence index and retention index were 0,633 and 0,533, respectively. The results revealed with molecular data as well as the ones obtained with morphological characters corroborate, the monophyly of the genus and the grouping proposed based in the color pattern.

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.

No description available.

Percomorpha is the most diverse group of Acanthomorpha, and the interrelationships among the members are unsettled. Perciformes, one order of Percomorpha, is the largest fish order with 160 families placed in 20 suborders. The relationships among the suborders of Perciformes remain conflicting between the hypotheses of phylogenetic relationships based on different characters. Presently, major studies on relationships of higher taxa are from Japanese based on the mitogenome, and the other studies were based on nuclear gene sequences. Mok recently suggest a hypothesis of the Gobioidei, it is the sister group to a clade which includes the Callionymoidei, Dactylopteriformes, and possibly Pegasidae, based on osteological characters. Following this, a phylogenetic hypothesis of the Callionymoidei based on mitochondrial and nuclear genes was conducted, and the Taiwanese and Australian specimens of G. buergeri might be treated as different species. Morphological differentiation in the sagitta in these two groups points to the same conclusion. The Pempheridae is the sister group of the Glaucosomatidae that is demonstrated by molecular evidences. It is the same with the relationship based on the morphological characters, such as otolith and swimbladder, etc. The monophyly of Callionymoidei is not recovered in this study. The Syngnathoidei may be the closest group of Callionymidae, and the Gobiesocoidei is suggested to be closest with Draconettidae. In the application of mitogenomic information, the sequcences selected by Japanese have not been decided to be unsaturated, so I made statistical inference of the variation for mitochondrial sequences and selected nuclear genes. I have found out the variation-saturated genes and discuss the application of these sequences to phylogenetic studies derived from these datasets in this study.

There are ~12 supergroups of complex-celled organisms (eukaryotes), but relationships among them (including the root) remain elusive. For Paper I, I developed a dataset of 37 eukaryotic proteins of bacterial origin (euBac), representing the conservative protein core of the proto-mitochondrion. This gives a relatively short distance between ingroup (eukaryotes) and outgroup (mitochondrial progenitor), which is important for accurate rooting. The resulting phylogeny reconstructs three eukaryote megagroups and places one, Discoba (Excavata), as sister group to the other two (neozoa). This rejects the reigning “Unikont-Bikont” root and highlights the evolutionary importance of Excavata. For Paper II, I developed a 150-gene dataset to test relationships in supergroup SAR (Stramenopila, Alveolata, Rhizaria). Analyses of all 150-genes give different trees with different methods, but also reveal artifactual signal due to extremely long rhizarian branches and illegitimate sequences due to horizontal gene transfer (HGT) or contamination. Removing these artifacts leads to strong consistent support for Rhizaria+Alveolata. This breaks up the core of the chromalveolate hypothesis (Stramenopila+Alveolata), adding support to theories of multiple secondary endosymbiosis of chloroplasts. For Paper III, I studied the evolution of cox15, which encodes the essential mitochondrial protein Heme A synthase (HAS). HAS is nuclear encoded (nc-cox15) in all aerobic eukaryotes except Andalucia godoyi (Jakobida, Excavata), which encodes it in mitochondrial DNA (mtDNA) (mt-cox15). Thus the jakobid gene was postulated to represent the ancestral gene, which gave rise to nc-cox15 by endosymbiotic gene transfer. However, our phylogenetic and structure analyses demonstrate an independent origin of mt-cox15, providing the first strong evidence of bacteria to mtDNA HGT. Rickettsiales or SAR11 often appear as sister group to modern mitochondria. However these bacteria and mitochondria also have independently evolved AT-rich genomes. For Paper IV, I assembled a dataset of 55 mitochondrial proteins of clear α-proteobacterial origin (including 30 euBacs). Phylogenies from these data support mitochondria+Rickettsiales but disagree on the placement of SAR11. Reducing amino-acid compositional heterogeneity (resulting from AT-bias) stabilizes SAR11 but moves mitochondria to the base of α-proteobacteria. Signal heterogeneity supporting other alternative hypotheses is also detected using real and simulated data. This suggests a complex scenario for the origin of mitochondria.

O gênero Acestrorhynchus encontra-se amplamente distribuído na América do Sul, estando presente nas bacias do Paraná-Paraguai, Uruguai, no rio São Francisco, nos rios costeiros das Guianas, e nas bacias dos rios Amazonas e Orinoco, sendo as duas últimas, o local onde se encontra a maior diversidade desses peixes. Na ausência de estudos mais detalhados sobre as relações filogenéticas entre as espécies de Acestrorhynchus, as 14 espécies reconhecidas têm sido agrupadas com base no seu padrão de coloração. O primeiro trabalho focalizando as relações filogenéticas das espécies de Acestrorhynchus, foi desenvolvido recentemente e estabelece as relações de parentesco de 13 espécies do gênero com base na análise de 104 características osteológicas e de morfologia externa. No presente estudo, 2139 pares da região 16S e da ATPase, ambos do genoma mitocondrial, juntamente o primeiro íntron da proteína ribossomal S7 do genoma nuclear, foram analisados para as espécies A. microlepis, A. falcatus, A. heterolepis, A pantaneiro, A. falcirostris, A. altus, A. minimus, A. grandoculis, A. britskii, A. lacustris e A. nasutus. Os gêneros Roeboides, Rhaphiodon e Gephyrocharax foram utilizados como grupo externo. A análise de máxima parcimônia, com busca heurística e adição aleatória de seqüências com o algoritmo TBR resultou na obtenção de uma árvore mais parcimoniosa com 2.551 passos. Os índices de consistência e retenção foram, respectivamente, 0,633 e 0,533. Os resultados obtidos através da análise dos dados moleculares corroboram, assim como os resultados morfológicos, o monofiletismo dos agrupamentos propostos com base nos padrões de coloração. / Fishes of the Neotropical characiform genus Acestrorhynchus Eigenmann, comprise freshwater species widely distributed throughout South American rivers, being found in the Paraná, Paraguai, Uruguai, São Francisco and of Guyana rivers. However it is in the Amazonas and Orinoco river basins where the highest diversity of this group of fishes is present. In the absence of more detailed phylogenetic studies the 14 recognized species are grouped on the basis of their color patterns. The first specific study about the phylogenetic relationships of Acestrorhynchus species, was recently developed and it established the relationships of 13 species of the genus, based in the analysis of 104 osteological and external morphological characters. In the present study, simultaneous analysis of 2139 aligned base pairs from the mitochondrial 16S and ATPase and the nuclear first intron of the S7 ribosomal protein were analyzed for the species A. microlepis, A. falcatus, A. heterolepis, A pantaneiro, A. falcirostris, A. altus, A. minimus, A. grandoculis, A. britskii, A. lacustris e A. nasutus. The genera Roeboides, Rhaphiodon and Gephyrocharax were included in the analysis as outgroups. Maximum parsimony analysis, and heuristic searches with random taxon addition replicates and TBR branch swapping were performed resulting in one most parsimonious tree with 2,551 steps in length. The consistence index and retention index were 0,633 and 0,533, respectively. The results revealed with molecular data as well as the ones obtained with morphological characters corroborate, the monophyly of the genus and the grouping proposed based in the color pattern.

Malaria is the main cause of approximately one million deaths every year that mostly affect children in south of Sub-Saharan Africa. The Anopheles gambiae complex consists of seven morphologically indistinguishable sibling species. However, their behavior, ecological adaptations, vectorial capacity, and geographical distribution differ. Studying the phylogenetic relationships among the members of the complex is crucial to understanding the genomic changes that underlie evolving traits. These evolutionary changes can be related to the gain or loss of human blood choice or to other epidemiologically important traits. In order to understand the phylogenetic relationships and evolutionary history of the members of the An. gambiae complex, breakpoints of the 2Ro and 2Rp inversions in An. merus and their homologous sequence in the outgroup species were analyzed using fluorescent in situ hybridization (FISH), library screening, whole-genome mate-paired sequencing and bioinformatics analysis. Molecular phylogenies of breakpoint genes were constructed afterwards. In addition, multigene phylogenetic analyses of African malaria vectors were performed. Our findings revised the chromosomal phylogeny, and demonstrated the ancestry of 2Ro, 2R+p and 2La arrangements.  Our new chromosomal phylogeny strongly suggests that vectorial capacity evolved repeatedly in members of the An. gambiae complex, and the most important vector of malaria in the world, An. gambiae, is more closely related to ancestral species than was previously thought. Our molecular phylogeny data were in agreement with chromosomal phylogeny, indicating that the position of the genetic markers with respect to chromosomal inversion is important for interpretation of the  phylogenetic trees. Multigene phylogenetic analysis revealed that a malaria mosquito from humid savannah and degraded rainforest areas, An. nili, belongs to the basal clade and is more distantly related to other major African malaria vectors than was assumed previously. Finally, for the first time a physical map of 12 microsatellite markers for the Asian malaria vector An. stephensi was developed. Knowledge about the chromosomal position of microsatellites was shown to be important for a proper estimation of population genetic parameters. In conclusion, our study improved understanding of genetics and evolution of some of the major malaria vectors in Africa and Asia. / Ph. D.

Thesis (MSc (Botany and Zoology))--Stellenbosch University, 2008. / Sequence data from the Internal Transcribed Spacer (ITS) of the nuclear ribosomal DNA were used to study the phylogenetic relationships in the genus Ursinia Gaertn. (Asteraceae, Anthemideae) in the southern African region. Closely related genera, i.e. Cotula L., Osteospermum L. and Agoseris Raf., were used as outgroups. The study also included maximum parsimony and principal component analyses. The taxa within the genus Ursinia had previously been classified into two subgenera, Ursinia and Sphenogyne R.Br., mainly on the basis of distinct cypsela characters. The maximum parsimony, principal component and the phylogenetic analyses revealed two subgenera, corresponding to the existing subgeneric classification. Principal component analysis shows that the pappus, the number of pappus bristles and the colour of the cypsela are the most informative characters. However, the low number of phylogenetically informative characters of the ITS sequences, the poor resolution in the consensus tree, and low branch support values indicate that the ITS data contain weak phylogenetic signals. The low bootstrap values for many nodes suggest that one should be cautious in using the ITS region alone to make final conclusions about the origin and evolution of taxa. In maximum parsimony analysis, the RI, CI and bootstrap values are low; principal component analysis values are also low. Furthermore, there is a lack of resolution in subgenus Sphenogyne. In the literature, Ursinia is divided into seven series but they were not retrieved as monophyletic in this study, probably because of short branch lengths in the phylogeny. Further molecular data are therefore required to be able to support or reject the present classification. Maximum parsimony, principal component and molecular analyses show that U. trifida f. calva Prassler and U. trifida (Thunb.) N.E.Br. f. trifida are not sister taxa, supporting the recognition of these two taxa as separate species. The Ursinia taxa from the summer-rainfall region are not monophyletic and are sister to a clade of Cape species. This supports a hypothesis that Ursinia migrated from the Cape into the Drakensberg which has been shown for a number of other Cape groups that have Drakensberg relatives.