The mitochondrial small-subunit ribosomal RNA (mt. SSU rRNA = rns) gene appears to be a reservoir for a number of group I and II introns along with the intron- encoded proteins (IEPs) such as homing endonucleases (HEases) and reverse transcriptases. The key objective for this thesis was to examine the rns gene among different groups of ophiostomatoid fungi for the presence of introns and IEPs. Overall the distribution of the introns does not appear to follow evolutionary lineages suggesting the possibility of rare horizontal gains and frequent loses. Some of the novel findings of this work were the discovery of a twintron complex inserted at position S1247 within the rns gene, here a group IIA1 intron invaded the ORF embedded within a group IC2 intron. Another new element was discovered within strains of Ophiostoma minus where a group II introns has inserted at the rns position S379; the mS379 intron represents the first mitochondrial group II intron that has an RT-ORF encoded outside Domain IV and it is the first intron reported to at position S379. The rns gene of O. minus WIN(M)371 was found to be interrupted with a group IC2 intron at position mS569 and a group IIB1 intron at position mS952 and they both encode double motif LAGLIDADG HEases referred as I-OmiI and I-OmiII respectively. These IEPs were examined in more detail to evaluate if these proteins represent functional HEases. To express I-OmiI and I-OmiII in Escherichia. coli, a codon-optimized versions of I-OmiI and I-OmiII sequences were synthesized based on differences between the fungal mitochondrial and bacterial genetic code. The optimized I-OmiI and I-OmiII sequences were cloned in the pET200/D TOPO expression vector system and transformed into E. coli BL21 (DE3). These two proteins were biochemically characterized and the results showed that: both I-OmiI and I-OmiII are functional HEases. Detailed data for I-OmiII showed that this endonuclease cleaves the target site two nucleotides upstream of the intron insertion site generating 4 nucleotide 3’overhangs.

The mitochondrial small-subunit ribosomal RNA (mt. SSU rRNA = rns) gene appears to be a reservoir for a number of group I and II introns along with the intron- encoded proteins (IEPs) such as homing endonucleases (HEases) and reverse transcriptases. The key objective for this thesis was to examine the rns gene among different groups of ophiostomatoid fungi for the presence of introns and IEPs. Overall the distribution of the introns does not appear to follow evolutionary lineages suggesting the possibility of rare horizontal gains and frequent loses. Some of the novel findings of this work were the discovery of a twintron complex inserted at position S1247 within the rns gene, here a group IIA1 intron invaded the ORF embedded within a group IC2 intron. Another new element was discovered within strains of Ophiostoma minus where a group II introns has inserted at the rns position S379; the mS379 intron represents the first mitochondrial group II intron that has an RT-ORF encoded outside Domain IV and it is the first intron reported to at position S379. The rns gene of O. minus WIN(M)371 was found to be interrupted with a group IC2 intron at position mS569 and a group IIB1 intron at position mS952 and they both encode double motif LAGLIDADG HEases referred as I-OmiI and I-OmiII respectively. These IEPs were examined in more detail to evaluate if these proteins represent functional HEases. To express I-OmiI and I-OmiII in Escherichia. coli, a codon-optimized versions of I-OmiI and I-OmiII sequences were synthesized based on differences between the fungal mitochondrial and bacterial genetic code. The optimized I-OmiI and I-OmiII sequences were cloned in the pET200/D TOPO expression vector system and transformed into E. coli BL21 (DE3). These two proteins were biochemically characterized and the results showed that: both I-OmiI and I-OmiII are functional HEases. Detailed data for I-OmiII showed that this endonuclease cleaves the target site two nucleotides upstream of the intron insertion site generating 4 nucleotide 3’overhangs.

The genus Ceratomyxa Thélohan, 1892 is one of the largest myxozoan genera, the species of which almost always infect the gall bladder of marine teleosts. Although there are over 180 species known globally, prior to this study only three had been described from Australia. This study explores the systematics, host specificity and species richness of Ceratomyxa species from a diverse range of Queensland marine fishes. The first part of this thesis deals with the issues associated with spore based taxonomy and incorporates the first molecular studies to investigate host specificity and radiation in three common families of Great Barrier Reef (GBR) fishes. Twenty-two new species were described in these chapters, and although they were superficially similar in morphology all were genetically distinct. A focus on Ceratomyxa spp. infecting labrid, pomacentrid and serranid fish revealed tight host specificity of parasite species, confirmed the presence of multiple parasite species in a single host and revealed that no parasite radiation had occurred that could be associated with co-evolution with host families. Exploration of intra- and inter-specific variation by sequencing of multiple replicates from host/parasite combinations allowed interpretation of species boundaries within the system. Ten additional species described in Chapter 5 supported the findings from the labrid, pomacentrid and serranid studies but broadened the host range studied. In total 32 Ceratomyxa species were described from Queensland fishes increasing the number of described species in the genus by 15%. This study also reports on undescribed species collected from a further 70 host species and broadens the known host range to seven families of fishes. A checklist of bivalvulidans from marine teleosts in Australia is compiled of described and undescribed species and highlights the abundance of Ceratomyxa relative to other gall bladder dwelling myxosporeans. A phylogeny of the Ceratomyxa based on SSU rDNA analyses explored the taxonomic integrity of the genus. In general, the morphological diagnostic characters that divide the Myxozoa into genera are not well supported by molecular phylogenetic analyses. The relationship between 42 Ceratomyxa spp. and 36 other marine myxosporeans was examined using Bayesian inference, maximum likelihood and maximum parsimony. Results indicate Ceratomyxa is one of the most cohesive lineages within the Myxozoa and that the freshwater fish parasite, C. shasta, does not represent an independent lineage as suggested in previous studies. The strict host specificity of Ceratomyxa species prompted the investigation of species richness on the GBR. Species accumulation curves were used to explore species richness by using Choa2 and Jackknife1 estimators. The estimates suggested Ceratomyxa is almost as rich as their teleost hosts and that 1,600 species could be present on the GBR and as many as 15,000 species may exist globally. As an unexpected result, Ceratomyxa may be the richest metazoan genus in the sea. In light of what the study revealed, a revision of a second genus within the family Ceratomyxidae, Leptotheca, is presented. The boundaries between Ceratomyxa and Leptotheca were unclear. The diagnostic characters that separate these genera (length to thickness ratios) were found to be plastic and the type species of Leptotheca ultimately fitted the diagnosis for Ceratomyxa. To eliminate confusion between these genera and also between Sphaerospora and Leptotheca, the genus Leptotheca was considered invalid, with all species appropriately assigned to other genera based on morphological and biological characters and supported by genetic evidence.

The genus Ceratomyxa Thélohan, 1892 is one of the largest myxozoan genera, the species of which almost always infect the gall bladder of marine teleosts. Although there are over 180 species known globally, prior to this study only three had been described from Australia. This study explores the systematics, host specificity and species richness of Ceratomyxa species from a diverse range of Queensland marine fishes. The first part of this thesis deals with the issues associated with spore based taxonomy and incorporates the first molecular studies to investigate host specificity and radiation in three common families of Great Barrier Reef (GBR) fishes. Twenty-two new species were described in these chapters, and although they were superficially similar in morphology all were genetically distinct. A focus on Ceratomyxa spp. infecting labrid, pomacentrid and serranid fish revealed tight host specificity of parasite species, confirmed the presence of multiple parasite species in a single host and revealed that no parasite radiation had occurred that could be associated with co-evolution with host families. Exploration of intra- and inter-specific variation by sequencing of multiple replicates from host/parasite combinations allowed interpretation of species boundaries within the system. Ten additional species described in Chapter 5 supported the findings from the labrid, pomacentrid and serranid studies but broadened the host range studied. In total 32 Ceratomyxa species were described from Queensland fishes increasing the number of described species in the genus by 15%. This study also reports on undescribed species collected from a further 70 host species and broadens the known host range to seven families of fishes. A checklist of bivalvulidans from marine teleosts in Australia is compiled of described and undescribed species and highlights the abundance of Ceratomyxa relative to other gall bladder dwelling myxosporeans. A phylogeny of the Ceratomyxa based on SSU rDNA analyses explored the taxonomic integrity of the genus. In general, the morphological diagnostic characters that divide the Myxozoa into genera are not well supported by molecular phylogenetic analyses. The relationship between 42 Ceratomyxa spp. and 36 other marine myxosporeans was examined using Bayesian inference, maximum likelihood and maximum parsimony. Results indicate Ceratomyxa is one of the most cohesive lineages within the Myxozoa and that the freshwater fish parasite, C. shasta, does not represent an independent lineage as suggested in previous studies. The strict host specificity of Ceratomyxa species prompted the investigation of species richness on the GBR. Species accumulation curves were used to explore species richness by using Choa2 and Jackknife1 estimators. The estimates suggested Ceratomyxa is almost as rich as their teleost hosts and that 1,600 species could be present on the GBR and as many as 15,000 species may exist globally. As an unexpected result, Ceratomyxa may be the richest metazoan genus in the sea. In light of what the study revealed, a revision of a second genus within the family Ceratomyxidae, Leptotheca, is presented. The boundaries between Ceratomyxa and Leptotheca were unclear. The diagnostic characters that separate these genera (length to thickness ratios) were found to be plastic and the type species of Leptotheca ultimately fitted the diagnosis for Ceratomyxa. To eliminate confusion between these genera and also between Sphaerospora and Leptotheca, the genus Leptotheca was considered invalid, with all species appropriately assigned to other genera based on morphological and biological characters and supported by genetic evidence.

The genus Ceratomyxa Thélohan, 1892 is one of the largest myxozoan genera, the species of which almost always infect the gall bladder of marine teleosts. Although there are over 180 species known globally, prior to this study only three had been described from Australia. This study explores the systematics, host specificity and species richness of Ceratomyxa species from a diverse range of Queensland marine fishes. The first part of this thesis deals with the issues associated with spore based taxonomy and incorporates the first molecular studies to investigate host specificity and radiation in three common families of Great Barrier Reef (GBR) fishes. Twenty-two new species were described in these chapters, and although they were superficially similar in morphology all were genetically distinct. A focus on Ceratomyxa spp. infecting labrid, pomacentrid and serranid fish revealed tight host specificity of parasite species, confirmed the presence of multiple parasite species in a single host and revealed that no parasite radiation had occurred that could be associated with co-evolution with host families. Exploration of intra- and inter-specific variation by sequencing of multiple replicates from host/parasite combinations allowed interpretation of species boundaries within the system. Ten additional species described in Chapter 5 supported the findings from the labrid, pomacentrid and serranid studies but broadened the host range studied. In total 32 Ceratomyxa species were described from Queensland fishes increasing the number of described species in the genus by 15%. This study also reports on undescribed species collected from a further 70 host species and broadens the known host range to seven families of fishes. A checklist of bivalvulidans from marine teleosts in Australia is compiled of described and undescribed species and highlights the abundance of Ceratomyxa relative to other gall bladder dwelling myxosporeans. A phylogeny of the Ceratomyxa based on SSU rDNA analyses explored the taxonomic integrity of the genus. In general, the morphological diagnostic characters that divide the Myxozoa into genera are not well supported by molecular phylogenetic analyses. The relationship between 42 Ceratomyxa spp. and 36 other marine myxosporeans was examined using Bayesian inference, maximum likelihood and maximum parsimony. Results indicate Ceratomyxa is one of the most cohesive lineages within the Myxozoa and that the freshwater fish parasite, C. shasta, does not represent an independent lineage as suggested in previous studies. The strict host specificity of Ceratomyxa species prompted the investigation of species richness on the GBR. Species accumulation curves were used to explore species richness by using Choa2 and Jackknife1 estimators. The estimates suggested Ceratomyxa is almost as rich as their teleost hosts and that 1,600 species could be present on the GBR and as many as 15,000 species may exist globally. As an unexpected result, Ceratomyxa may be the richest metazoan genus in the sea. In light of what the study revealed, a revision of a second genus within the family Ceratomyxidae, Leptotheca, is presented. The boundaries between Ceratomyxa and Leptotheca were unclear. The diagnostic characters that separate these genera (length to thickness ratios) were found to be plastic and the type species of Leptotheca ultimately fitted the diagnosis for Ceratomyxa. To eliminate confusion between these genera and also between Sphaerospora and Leptotheca, the genus Leptotheca was considered invalid, with all species appropriately assigned to other genera based on morphological and biological characters and supported by genetic evidence.

Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals (including us humans) and Fungi. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. Here we have isolated a naked eukaryotic amoeba with filose subpseudopodia, and a simple life cycle consisting of a trophic amoeba and a cyst stage. Using a wholistic approach including light, electron, fluorescence microscopy and SSU rDNA, we find that this amoeboid organism fails to match any previously described eukaryote genus. Our isolate amoebae are most similar to some variosean amoebae which also possess acutely pointed filose subpseudopodia. Maximum likelihood and Bayesian tree of the SSU-rDNA gene places our isolate in Variosea of Amoebozoa as a novel lineage with high statistical support closely related to the highly diverse protosteloid amoebae Protostelium. This novel variosean is herein named “Hodorica filosa” n. g. n. sp. We present a robust phylogeny of Amoebozoa based on a broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea and Tevosa. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features Integrins are transmembrane receptors that activate signal transduction pathways upon extracellular matrix binding. The Integrin Mediated Adhesion Complex (IMAC), mediates various cell physiological processes and are key elements that are associated animal multicellularity. The IMAC was thought to be specific to animals. Over the last decade however, the IMAC complexes were discovered throughout Obazoa. We show the presence of an ancestral complex of integrin adhesion proteins that predate the evolution of the Amoebozoa. Co-option of an ancient protein complex was key to the emergence of animal multicellularity. The role of the IMAC in a unicellular context is unknown but must also play a critical role for at least some unicellular organisms.

Le mutualisme entre les plantes et les champignons arbusculaires mycorhiziens est extrêmement répandu (~ 80% des plantes sont colonisées par ces organismes) et ancien (il ya plus de 450 millions d'années). Cette relation symbiotique est une composante essentielle du fonctionnement des écosystèmes et de leur productivité, et est fortement impliqué dans le cycle de deux éléments clés: le phosphore et le carbone. Le maintien de ce mutualisme est devenu particulièrement important dans le contexte actuel de perte de biodiversité. Un des objectifs de cette thèse était de comprendre la stabilité de ce mutualisme. L'accent a tout d'abord été mis sur les échanges de nutriments impliqués dans cette symbiose, en testant si la plante hôte et les symbiotes fongiques sont capables de discriminer leurs différents partenaires, et d'allouer davantage de ressources aux partenaires fournissant plus de nutriments. J'ai ensuite étudié la possibilité de l'implication de la plante hôte dans la protection des symbiotes mycorhiziens via un transfert de métabolites secondaires dans les hyphes. Nous avons alors pu emettre une nouvelle hypothèse suggérant que la protection en métabolites secondaires venant de la plante serait positivement corrélée avec le niveau de coopération (à savoir le transfert des nutriments) du champignon symbiotique. L'echelle d'étude est ensuite passée de l'individu à la communauté en étudiant les effets de la diminution de la diversité végétale sur la diversité des symbiotes racinaires. Pour ce faire, des analyses moléculaires et des outils novateurs ont été utilisés, tels que le séquençage à haut débit. Pour faciliter encore l'étude des séquences obtenues et d'autres séquences fongiques, j'ai collaboré avec des collègues afin de créer une base de données 'Phymyco-DB' rendue publique en 2012. Enfin, je discute de l'implication du mutualisme mycorhizien dans le contexte des systèmes agricoles actuels et propose de nouvelles trajectoires pour gérer ces systèmes. Ce projet de thèse apporte un nouvel éclairage sur la façon dont fonctionnent ces interactions entre les plantes et champignons MA et sur la manière dont ils façonnent les processus écologiques et les trajectoires évolutives dans les écosystèmes naturels et agricoles. Ces points sont d'une importance majeure pour développer une agriculture plus écologiquement intensive et durable. Le projet a fourni de nouvelles connaissances et perspectives sur la perte de la diversité végétale, et ses conséquences pour la stabilité de la symbiose AM. Comme les champignons mycorhiziens sont essentiels dans les processus des écosystèmes et l'entretien de la fertilité des sols, ce travail devrait avoir un large impact dans (i) la politique de protection des sols, (ii) la recherche sur l'amélioration des plantes et (iii) la conception de systèmes agricoles durables. / The mutualism between plants and arbuscular mycorrhizal fungi is extremely widespread (~ 80% of plants are colonized by these organisms) and ancient (over 450 million years ago). This symbiotic relationship is an essential component of healthy ecosystem functioning and productivity, and is strongly involved in the cycle of two key elements: phosphorus and carbon. Maintaining this mutualism has become especially important in the current context of a biodiversity loss. One goal of this thesis was to understand the stability of the mutualism. I first focused on nutrient exchange, testing whether plant host and fungal symbionts are able to discriminate among partners, and allocate more resources to those individuals providing more nutrients. I then explored the possibility of the host-plant involvement in the protection of mycorrhizal symbionts via a transfer of secondary metabolites into fungal hyphae. We introduced a new hypothesis suggesting that chemcial protection from the plant is positively correlated with the level of cooperation (i.e. nutrient transfer) of the fungal symbiont. I then moved from the individual to the community by studying the effects of decreasing plant diversity on the diversity of root symbionts. To this aim, I utilized molecular analyzes and innovative tools, such as high throughput sequencing. To further facilitate the study of the obtained sequences and other fungal sequences, I worked with colleagues to create a database ‘Phymyco-DB’ which was released to the public in 2012. Finally, I discuss the implication of the mycorrhizal mutualism in the context of current agricultural systems and propose new trajectories to manage these systems. This PhD project provides new insights on how plant and AM fungi interactions work and how they shape ecological processes and evolutionary trajectories in natural and agricultural ecosystems. These points are of major importance to develop a more ecologically intensive agriculture. The project has provided new knowledge and perspectives on the loss of plant diversity, and its consequences for AM symbiosis stability. As arbuscular mycorrhizal fungi are essential in ecosystem processes and soil fertility maintenance, this work should have a broad impact in (i) the soil protection policy, (ii) the research on plant breeding and (iii) the design of sustainable agricultural systems.

The aim of this paper is to ascertain what kind of feminist expressions that are prevalent in two of Sweden’s major political youth organizations, the Swedish Social Democratic Youth League and the Centre Party Youth using ideal types constructed from major feminist ideologies. A comparison between the two is also a part of the analysis, to clarify the differences and similarities between the two regarding issues pertaining gender equality. Socialist feminism and radical feminism were prevalent in the Swedish Social Democratic Youth League but it also contained expressions of liberal feminism. The Centre Party Youth were exclusively liberal feminist in their expression. The differences between the two were ideological and the causal explanations for why gender equality exists differed as well. The similarities were limited to certain specific issues where they identified similar, if not identical, problems in society.

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysis of five soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. / Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

O gênero Porphyra (Rhodophyta) apresenta uma considerável importância econômica, sendo extensivamente cultivado e consumido como alimento. O gênero é representado por mais de 70 espécies e apresenta ampla distribuição geográfica, desde regiões tropicais até polares. Sua taxonomia, baseada em poucos caracteres da fase macroscópica do seu ciclo de vida, é ainda bastante problemática. Para tentar entender melhor a taxonomia e a história evolutiva de Porphyra foram utilizadas metodologias de biologia molecular e características da fase conchocelis do ciclo de vida. Verificou-se que caracteres da fase microscópica podem ser utilizados para complementar os conhecimentos taxonômicos tradicionais. Para tentar elucidar a posição filogenética do gênero Porphyra na divisão Rhodophyta e, dentro do gênero, entre espécies do Atlântico, o gene nuclear que codifica para o RNA ribossomal da subunidade pequena do ribossomo (rDNA 18S) foi amplificado através de PCR, clonado e completamente sequenciado. Foram utilizadas três espécies de Porphyra da Nova Escócia (Canadá) e duas de São Paulo (Brasil). As sequências obtidas foram alinhadas com as de alguns eucariontes e de outras algas vermelhas, incluindo uma sequência publicada de \"Porphyra umbilicalis\" da França. As árvores filogenéticas foram construídas através dos métodos de parcimônia, distancia e máxima verossimilhança. As analises mostraram que o gênero Porphyra é monofilético para as cinco espécies estudadas e constitui um dos ramos mais antigos dentro das algas vermelhas já analisados. O gênero Porphyra, subclasse Bangiophycidae, apresentou uma diferença substancial em relação aos gêneros da subclasse Florrideophycidae, sustentando assim, a divisão de Rhodophyta em duas subclasses pela taxonomia tradicional. Entre os eucariontes, Porphyra divergiu ao mesmo tempo que o nuclemorfo de Cryptomonas. O alto grau de divergência genética encontrada entre espécies de Porphyra, além de indicações do registo fóssil, na literatura, sugerem que o gênero é bastante primitivo dentro das algas vermelhas. Surpreendentemente, a sequência publicada para \"Porphyra umbilicalis\" apresentou mais de 99% de identidade com uma espécie de Palmaria que pertence à subclasse Florideophycidae; neste caso, a biologia molecular serviu para comprovar a identificação errônea do exemplar cuja sequência foi publicada. Durante a análise filogenética, verificou-se a ocorrência de um intron do grupo ICI nos genes rDNA 18S de Porphyra spiralis var. amplifolia. Esse intron ocorre na mesma posição que os introns do grupo IC1 nos rDNA 18S dos fungos Pneumocystis carinii, Protomyces inouyei e da alga verde Chlorella ellipsoidea, e apresenta identidade de sequências nos domínios P1 e P2, fora da região conservada, com o intron de Pn. Carinii. Três variantes, diferindo do tamanho da seqüencia do domínio P1, foram observados em três populações com distribuição geográfica diferente. O variante maior pode se auto-processar (\"self-splice\") in vitro. Quadros abertos de leitura estão presentes nos introns, mas não correspondem a nenhum gene conhecido. Introns estão presentes no rDNA 18S de outras espécies de Porphyra, que também podem apresentar variantes do rDNA 18S sem introns / The red algas genus Porphyra has considerable economic importance, and some species are extensively cultivated for human food. The genus is represented by more than 70 species, and occurs worldwide. Its taxonomy, based mainly on morphological characters of the macroscopic phase of its life-cycle is still unsettled. Alternatives to try to understand better the taxonomy and evolutive history of the genus were ascertained. It was verified that characters of the microscopic, filamentous phase, of the life-cycle of Porphyra may be used to complement the traditional taxonomic studies. To try to elucidate the phylogenetic position of Porphyra relative to the other red algae, and within the genus, among isolates from different locations, nuclear-encoded small-subunit ribosomal RNA genes (18S rDNAs) were PCR-amplified, cloned and completely sequenced. Three species of Porphyra from Nova Scotia and two species from Brasil were aligned with 18S sequences of other eukaryotes, including one published sequence of \"Porphyra umbilicalis\" from France. Phylogenetic trees were constructed by parsimony, distance and maximum-likelihood procedures. Analysis of our data revealed that these Porphyra species represented one of the deepest branches so far discovered within red algae. There was a great degree of primary sequence difference between Porphyra (subclass Bangiophycidae), and the other red algae belonging to the subclasses Florideophycidae. These results support the division of red algae into two subclasses by traditional taxonomy. Among eukaryotes Porphyra diverges at the same point as the Cryptomonas nucleomorph. The great among of sequence divergence, and the fossil record suggest that Porphyra, my indeed, be a very primitive red alga. Surprisingly, the 18S RNA sequence of the French \"Porphyra umbilicalis\" does not fit in our Porphyra category; instead, it has more than 99% identity with a species of Palmaria belonging to the subclass Florideophycidae. Therefore it was concluded that \"P. umbilicalis\" with the published sequence was actually a Palmaria palmate that was misidentified. During the phylogenetic analysis it was found that a group IC1 intron occurs in nuclear 18S rRNA genes of Porphyra spiralis var. amplifolia. This intron occurs at the same position of the group IC1 introns in 18S rDNAs of the fungus Pneumocystis carinii, Protomyces inouyei and the green alga Chlorella ellipsoidea, and shares primary-structural identity with the Pn. Carinii intron in domains P1 and P2, outside the conserved core. Three size-variants, differing in amount of optimal sequence in P1, exist and are differentially distributed in geographically distinct populations. The largest variant can self-splice in vitro. Open reading frames are present, but do correspond to known genes. Introns are present in the 18S rDNAs of several other Porphyra species, that may also have intronless rDNA copies