Biogeographers have long searched for common processes responsible for driving diversification in the Holarctic region. Although terrestrial flora and fauna have been well studied, much of the marine biogeographic work addresses patterns and processes occurring over a relatively recent timescale. A prerequisite to comparative biogeographic analysis requires well-resolved phylogenies of similarly distributed taxa that diverged over a similar timeframe. The overall aim of my Ph.D. thesis was to address fundamental questions in the systematics and biogeography of a family of Holarctic fish (Osmeridae) and place these results in a broad comparative biogeographic framework. With eight conflicting morphological hypotheses, the northern hemisphere smelts have long been the subjects of systematic disagreement. In addition to the uncertainty in the interrelationships within this family, the relationship of the Osmeridae to several other families remains unclear. Using DNA sequence data from three mitochondrial and three nuclear genes from multiple individuals per species, I reconstructed the phylogenetic relationships among the 6 genera and 15 osmerid species. Phylogenetic reconstruction and divergence dating yielded a well-resolved phylogeny of the osmerid genera and revealed several interesting evolutionary patterns within the family: (1) Hypomesus chishimaensis and H. nipponensis individuals are not reciprocally monophyletic, suggesting that they are conspecific and H. chishimaensis is a recently evolved freshwater ecotype that invaded the Kuril Islands following the last glaciation, (2) The trans-Pacific sister relationships in Hypomesus based on lateral line scale counts are not supported, implying that this phenotype evolved in parallel on each side of the North Pacific Ocean, (3) The Plecoglossidae are the Osmeridae sister group, (4) Over half of the characters from previous studies show evidence of parallel evolution; however, 27 traits reflect ancestral relationships, (5) Multiple divergences within the Osmeridae date to both the mid-Miocene cooling period and the Pliocene Bering Seaway opening, suggesting these events were important in the evolution of these fishes, and (6) Divergences in many marine taxa for which dated phylogenies are available are also correlated with these time periods. Future research should target additional Holarctic marine taxa for further comparative analysis.

Climate change may lead to declines in lake trout (Salvelinus namaycush) populations and change the structure of the ecosystem in which they live. The lake trout is a keystone species in ecosystems of northern temperate lakes and these declines may subsequently reduce the genetic diversity found in these salmonids. Populations that contain greater genetic variation may have an increased capacity to adapt to changes in the ecosystem. Therefore, an understanding of the genetic diversity found in lake trout populations is required for their effective conservation and management. As a result, this study aimed to examine the genetic diversity and phylogeography of lake trout populations in north central Canada.<p>The genetic diversity of lake trout from 19 lakes in Saskatchewan was examined using partial regions of the ND2 and ND5 mtDNA genes. A total of 607 tissue samples were analyzed using PCR-based single stranded conformation polymorphism (SSCP) and DNA sequencing. Although the ND5 gene fragment had minimal intraspecific variation, eleven sequence types were detected in the ND2 gene. Each sequence type differed in relative frequency between and among the lake trout populations sampled. <p>One particular southern lake trout population, Crean Lake, had markedly different genetic composition in comparison to other lakes in the region. In the 1950s and 1960s, Crean Lake was stocked with lake trout from neighbouring Wassegam Lake in an attempt to increase population numbers. The sequence types of Crean Lake trout and their relative frequencies were dramatically different to those in Wassegam Lake. This suggests that the stocked fish may have been unsuccessful in their establishment/reproduction within Crean Lake. Lake trout from this lake also contained the highest frequency (44%) of rare ND2 sequence type B. Sequence type B was only detected in one other lake (La Ronge), at a very low frequency. <p>The mutational changes in the eleven ND2 mitochondrial DNA sequence types represented three different amino acid sequence types. Substitutions of Threonine and Isoleucine occurred, resulting in two polar amino acids with much different hydropathy indexes. This may affect the tertiary structure of the protein, possibly indicating functional differences. Functionally different proteins may be exhibiting characteristics that allow lake trout to flourish in their environment. <p>The fragments of both the ND2 and ND5 genes proved to be valuable for phylogenetic analyses within the Salmonidae. The genetic markers established in the present study provide the basis for future work on population genetics of lake trout. It would be advantageous to broaden the area of study in order to compare the genetic diversity found within the study area to other regions of Canada. This would determine whether the genetic diversity detected in this study is significantly greater than in other populations at a national scale. Management strategies should ultimately attempt to conserve the genetic diversity found within the lake trout populations of north central Saskatchewan.

Sovint, la sistemàtica, basada principalment en caràcters morfològics, no es correspon amb els processos evolutius relacionats amb l'aparició dels grups d'organismes. En l'actualitat, la utilització de les dades moleculars es fa indispensable per a una revisió i millora de la classificació biològica de diversos organismes, com els peixos Acanthopterygii. A la sèrie Mugilomorpha la incongruència entre la taxonomia i la filogènia sorgeix de l'elevada semblança morfològica trobada per part dels seus membres. Pel que fa referència a la sèrie Atherinomorpha, la problemàtica principal resideix en determinar la seva proximitat evolutiva respecte a la sèrie anterior i en establir les relacions filogenètiques dins de la mateixa. Per tant, s'hi ha volgut estimar tant la divergència genètica dins de cada sèrie com inferir les relacions filogenètiques entre ambdues mitjançant la seqüenciació directa del DNA de les regions mitocondrials corresponents al tRNA-Phe, 12S rRNA, COI, cytb, tRNA-Thr, tRNA-Pro i regió control. / Often, systematics, based mainly on morphologic characters, does not correspond with the evolutionary processes related to the emergence of the groups of organisms. Nowadays, the utilization of molecular data turns indispensable to a revise and improve the biological classification of several organisms, such as Acanthopterygii fishes. In series Mugilomorpha, the incongruence between taxonomy and phylogeny arises from the high morphological similarity found between its members. Concerning series Atherinomorpha, the main problem lies in determining its evolutionary proximity in relation to series Mugilimorpha and in establishing the phylogenetical relationships inside itself. Therefore, both genetic divergence within each series and phylogenetical relationships between them have been wanted to estimate. For this reason, the direct sequencing of the mitochondrial regions corresponding to tRNA-Phe, 12S rRNA, COI, cytb, tRNA-Thr, tRNA-Pro and control region was achieved.

Climate change may lead to declines in lake trout (Salvelinus namaycush) populations and change the structure of the ecosystem in which they live. The lake trout is a keystone species in ecosystems of northern temperate lakes and these declines may subsequently reduce the genetic diversity found in these salmonids. Populations that contain greater genetic variation may have an increased capacity to adapt to changes in the ecosystem. Therefore, an understanding of the genetic diversity found in lake trout populations is required for their effective conservation and management. As a result, this study aimed to examine the genetic diversity and phylogeography of lake trout populations in north central Canada.<p>The genetic diversity of lake trout from 19 lakes in Saskatchewan was examined using partial regions of the ND2 and ND5 mtDNA genes. A total of 607 tissue samples were analyzed using PCR-based single stranded conformation polymorphism (SSCP) and DNA sequencing. Although the ND5 gene fragment had minimal intraspecific variation, eleven sequence types were detected in the ND2 gene. Each sequence type differed in relative frequency between and among the lake trout populations sampled. <p>One particular southern lake trout population, Crean Lake, had markedly different genetic composition in comparison to other lakes in the region. In the 1950s and 1960s, Crean Lake was stocked with lake trout from neighbouring Wassegam Lake in an attempt to increase population numbers. The sequence types of Crean Lake trout and their relative frequencies were dramatically different to those in Wassegam Lake. This suggests that the stocked fish may have been unsuccessful in their establishment/reproduction within Crean Lake. Lake trout from this lake also contained the highest frequency (44%) of rare ND2 sequence type B. Sequence type B was only detected in one other lake (La Ronge), at a very low frequency. <p>The mutational changes in the eleven ND2 mitochondrial DNA sequence types represented three different amino acid sequence types. Substitutions of Threonine and Isoleucine occurred, resulting in two polar amino acids with much different hydropathy indexes. This may affect the tertiary structure of the protein, possibly indicating functional differences. Functionally different proteins may be exhibiting characteristics that allow lake trout to flourish in their environment. <p>The fragments of both the ND2 and ND5 genes proved to be valuable for phylogenetic analyses within the Salmonidae. The genetic markers established in the present study provide the basis for future work on population genetics of lake trout. It would be advantageous to broaden the area of study in order to compare the genetic diversity found within the study area to other regions of Canada. This would determine whether the genetic diversity detected in this study is significantly greater than in other populations at a national scale. Management strategies should ultimately attempt to conserve the genetic diversity found within the lake trout populations of north central Saskatchewan.

<p>Mitochondria are the primary energy producers of the cell and play key roles in cellular signaling, apoptosis and reactive oxygen species (ROS) production. Mitochondria are the only organelles that contain their own genome which encodes for a small subset of electron transport chain (ETC) proteins as well as the necessary tRNAs and ribosomal subunits to translate these proteins. Over 300 pathogenic mitochondrial DNA (mtDNA) mutations have been shown to cause a number of mitochondrial diseases emphasizing the importance of mtDNA maintenance and integrity to human health. Additionally, mitochondrial dysfunction and mtDNA instability are linked to many wide-spread diseases associated with aging including cancer and neurodegeneration. Mitochondria lack the ability to repair certain helix-distorting lesions that are induced at high levels in mtDNA by important environmental genotoxins including polycyclic aromatic hydrocarbons, ultraviolet C radiation (UVC) and mycotoxins. These lesions are irreparable and persistent in the short term, but their long-term fate is unknown. Degradation of mitochondria and mtDNA is carried out by autophagy. Autophagy is protective against cell stress and apoptosis resulting from exposure to mitochondrial toxicants suggesting that it plays an important role in removal of unstable mitochondria that can serve as a source of ROS or initiate apoptotic cell death. Furthermore, dysfunctional mitochondria can be specifically targeted for degradation by the more specific process of mitophagy influenced in part by the processes of mitochondrial dynamics (i.e., fusion and fission). </p><p>The goals of this dissertation were to investigate the long-term fate of helix-distorting mtDNA damage and determine the significance of autophagy and mitochondrial dynamics in removal of and recovery from persistent mtDNA damage. Removal of irreparable mtDNA damage and the necessity of autophagy, mitophagy, fusion and fission genes in removal of this damage were examined using genetic approaches in adult <italic>Caenorhabditis elegans</italic>. In order to investigate the significance of autophagy, fusion and fission genes in recovery from mtDNA damage-induced mitochondrial dysfunction <italic>in vivo</italic>, an experimental method was developed to specifically induce persistent mtDNA damage and mitochondrial dysfunction without persistent nDNA damage in developing <italic>C. elegans</italic>. Additionally, the effect of persistent helix-distorting DNA damage on mitochondrial morphology, mitochondrial function and autophagy was investigated in <italic>C. elegans</italic> and in mammalian cell culture. The rate and specificity of mitochondrial degradation was further examined in cell culture using live-cell fluorescence microscopy and transmission electron microscopy. </p><p>Removal of UVC-induced mtDNA damage was detectable by 72 hours in <italic>C. elegans</italic> and mammalian cell culture, and required mitochondrial fusion, fission and autophagy, providing genetic evidence for a novel mtDNA damage removal pathway. UVC exposure induced autophagy with no detectable effect on mitochondrial morphology in both systems; mitochondrial function was inhibited in the <italic>C. elegans</italic> system but not in the cell culture system in which the degree of mtDNA damage induced was less. Furthermore, mutations in genes involved in these processes as well as pharmacological inhibition of autophagy exacerbated mtDNA damage-mediated larval arrest, illustrating the <italic>in vivo</italic> relevance of removal of persistent mtDNA damage. Mutations in genes in these pathways exist in the human population, demonstrating the potential for important gene-environment interactions affecting mitochondrial health after genotoxin exposure.</p> / Dissertation

Title from PDF of title page. / Document formatted into pages; contains 201 pages. / Thesis (M.S.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: Melongena corona and closely related congeners are a conspicuous part of the marine intertidal benthic communities of Florida and southeastern Alabama. Significant genetic differentiation among adjacent populations has been conjectured based on variation in shell morphology, habitat discontinuity, low levels of adult motility, and the presence of an aplanic lecithotrophic larval stage. Furthermore, studies of the highly variable shell morphology often have resulted in confusing specific and subspecific definitions of these gastropods, which are often referred to as the "corona complex". Variation in shell morphology may indicate local adaptation or environmentally induced phenotypic plasticity. In this study I utilized mitochondrial DNA sequences in order to reconstruct the phylogenetic relationships of crown conchs, and nuclear microsatellite loci to investigate the patterns of relatedness within and among populations inhabiting the southeastern United States. / ABSTRACT: Approximately 500 individuals from 20 populations throughout the known range of the Crown Conch were genotyped at eight microsatellite loci. Additionally, a 1200bp portion of the cytochrome oxidase subunit I gene was sequenced along with a 490bp fragment of the 16s ribosomal gene from individuals representing all known species and subspecies of the genus Melongena. Phylogenetic analyses completed with these data provide no support for current taxonomic designations within this group and these genetic data indicate that the corona complex is composed of a single polymorphic species. Furthermore, microsatellite data reveal population structure consistent with restricted gene flow between extant populations and phylogeography heavily influenced by historical sea-level fluctuations during the Late Pleistocene. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

Population structure can be defined as a difference in the frequencies of alleles among populations, and it is often caused by barriers to dispersal. I used mitochondrial DNA sequences to examine the population structure of two large, aquatic salamanders, Amphiuma means (the Two-Toed Amphiuma) and Siren lacertina (the Greater Siren), at two spatial scales in peninsular Florida. Both species appear to have similar life histories, including poor dry land dispersal capabilities, and I hypothesized that they would exhibit significant population structure at both broad and fine scales. Wetland loss and landscape fragmentation are certain to have caused decreases in abundance and even extirpation of local populations of both species. Understanding current levels of genetic diversity is important in conservation efforts, particularly if individuals must be translocated in the future. A portion of the cytochrome b gene was analyzed for 34 Amphiuma means and 21 Siren lacertina sequences. A neighbor-joining tree and haplotype network showed that A. means exhibited statistically significant population structure at the broad, but not the fine scale. The lack of structure at the fine scale was attributed to periodic flooding among drainage basins in the low-lying study area. The same analyses showed that S. lacertina did not exhibit statistically significant population structure at the broad scale (analyses were not conducted at the fine scale because of low sample size). The difference in broad-scale population structure between the two species is the result of a difference in gene flow, which in turn, can be the result of a difference in effective population size (Ne), female dispersal capability and/or behavior, chance of bait-bucket transfer, or biogeographic history. The best of these possible explanations seems to be a difference in biogeographic history. For the two sites from which both species were sampled, estimated population divergence date was 3.3-6.4 million years ago (mya) for A. means and 0.04-0.5 mya for S. lacertina. The large difference in estimated divergence dates suggests that S. lacertina colonized peninsular Florida from somewhere else following a glacial sea level rise or an interglacial sea level fall, at a time when A. means was already present in refugia within peninsular Florida. This is the first study to explicitly examine the population genetics of A. means and S. lacertina, and future studies should examine their population genetics range wide, to elucidate how gene flow and/or historical biogeography may have contributed to population structure elsewhere.

In eukaryotes, folate-dependent one-carbon (1-C) metabolism is composed of two parallel pathways compartmentalized to either the cytoplasm or mitochondria. In each, 1-C units, carried on tetrahydrofolate (THF), are interconverted by four catalytic activities. Serine hydroxymethyltransferase transfers the 3-carbon of serine to THF forming 5,10-methylene-THF which is oxidized in 3 successive steps to formate via the intermediates, 5,10-methenyl-THF and 10-formyl-THF. Because of the redox potential in each compartment, 1-C flux is thought by most authors to be from formate to serine in the cytosol and in the opposite direction in mitochondria. Transport of serine, glycine and formate across the mitochondrial membranes creates a 1-C cycle. All eukaryotes characterized to date contain a cytoplasmic trifunctional C1-THF synthase possessing 5,10-methylene-THF dehydrogenase, 5,10-methenyl-THF cyclohydrolase and 10-formyl-THF synthetase activities which interconvert the catalytic intermediates between 5,10-methylene-THF and formate. However, despite the observation that adult rat liver mitochondria oxidize serine to formate, no known enzymatic activities correlate with those of cytoplasmic C1-THF synthase. In embryos, a bifunctional protein, containing 5,10-methylene-THF dehydrogenase and 5,10-methenyl-THF cyclohydrolase, accounts for two of these activities. But the 10-formyl-THF synthetase activity has no associated enzyme in mitochondria. Reported here is the discovery of a monofunctional homolog of C1-THF synthase in mammalian mitochondria. Characterization of the protein confirms mitochondrial localization and 10-formyl-THF synthetase activity. Likewise, the adult human transcript is present and differs in size and tissue distribution from cytosolic C1-THF synthase. In mouse embryos, the temporal expression of the mRNA starts out relatively low and increases as the embryos age. The spatial distribution of the transcript is ubiquitous but with areas of elevated expression corresponding to proliferative regions within the embryo. The temporal expression pattern of the protein and transcript correspond well. However, mitochondrial flux studies and immunoblotting data suggest that mitochondrial C1-THF synthase is not the rate-limiting enzyme in mitochondria, at least during the mid to later stages of embryogenesis. Additionally, studies modulating the expression of mitochondria 1-C proteins demonstrate the likelihood that most cytoplasmic 1-C units are mitochondrially derived. / text

Members of the family Placobranchidae have been the focus of numerous studies because of their interesting physiological adaptations (kleptochemistry and kleptoplasty) and ecological associations with marine algae. More than 100 species have been described since the 1800's, but no determination of phylogenetic relationships in the family has occurred. DNA sequences from two mitochondrial genes (large subunit ribosomal and cytochrome c oxidase subunit I) and one nuclear gene (Histone 3) were used to reconstruct relationships among 34 nominal species within the Placobranchidae. Strong support for terminal nodes was found using Bayesian phylogenetic methods; however, a "soft" polytomy was detected at internal nodes. In general, the results confirm the paraphyly of Elysia. Proposals for the designation of the genera, Thallepus Swainson, 1840 and Tridachia Deshayes, 1857 and delineation of species are presented. How intrinsic factors affect speciation rates in groups of animals has been a central focus in evolutionary biology. Adaptive radiation associated with food choice has been postulated for the opisthobranch order Sacoglossa. An increase in the rate of cladogenesis was detected within the family Placobranchidae and intrinsic factors such as larval development, kleptoplasty and food choice were investigated as potential key innovations. Ancestral state reconstruction of characters suggests that food choice played a dominant role in influencing speciation rate within the family Placobranchidae. Life history strategy may play an important role in structuring genetic variation throughout the geographic range of a species. Members of the sacoglossan family Placobranchidae Gray, 1840, exhibit variation in life history strategies such as feeding preference and degree of kleptoplasty that could be influential in population structuring. Three species, Elysia subornata Verrill, 1901, Elysia tuca Marcus and Marcus, 1967, and Elysia crispata Mörch, 1863 were sampled from several locations in an attempt to quantify genetic variation as indicated by cytochrome c oxidase subunit I gene sequencing. Elysia crispata exhibited the highest degree of population subdivision followed by Elysia tuca and Elysia subornata. Nucleotide and haplotype diversity also revealed the same general ranking of species. Preliminary conclusions suggest that diversity in feeding preference and degree of kleptoplasty play significant roles in population subdivision of these species.

Die Beziehung zwischen Genen und Verhalten ist in der Evolutionsbiologie von besonderem Interesse. Bestimmte Verhaltensweisen können die genetische Struktur natürlicher Populationen gestalten, dadurch deren genetische Diversität verändern und so ihr evolutives Schicksal beeinflussen. Abwanderung aus der Geburtsgruppe ist eine dieser Verhaltensweisen. Sie beeinflusst Genfluss, dessen Ausmaß die genetische Struktur von Populationen bestimmt. Paviane (Gattung Papio) sind ein besonders interessantes Forschungssystem um die Beziehung zwischen Verhalten und populationsgenetischer Struktur zu untersuchen. Die Evolution der Paviane wurde sowohl von historischem als auch gegenwärtigem Genfluss geprägt. Innerhalb dieser Gattung treten sowohl die überwiegende Abwanderung von Männchen als auch die überwiegende Abwanderung von Weibchen auf. Zudem wurde ihre gegenwärtige Verbreitung maßgeblich von Populationsausbreitung und –rückzug beeinflusst und es tritt häufig Genfluss zwischen verschiedenen Arten auf. In meiner Doktorarbeit untersuchte ich, wie verschiedene Abwanderungsmuster den Genfluss bei Pavianen beeinflussen. Damit hoffe ich zu einem besseren Ver-ständnis der Wechselbeziehung zwischen Verhaltensökologie und Genetik in natürlichen Populationen beizutragen. Ich fokussierte mich darauf, wie Unterschiede in den Sozialsystemen unterschiedlicher Pavianarten deren genetische Struktur beeinflussen. Die beobachteten Muster nutzte ich, um auf das geschlechtsspezifische Abwanderungsmuster bei Guineapavianen zu schließen, eine der am wenigsten untersuchten Pavianarten. Zudem untersuchte ich, wie sowohl historischer als auch gegenwärtiger Genfluss die genetische Struktur der Guineapaviane formten und ob es möglich ist von der Populationsausbreitung der Paviane Rückschlüsse auf die menschliche Evolutionsgeschichte zu ziehen. Um diese Fragen zu beantworten nutzte ich einen populationsgenetischen Ansatz, basierend auf im gesamten Verbreitungsgebiet gesammelten Kotproben, deren exakter geographischer Ursprung bekannt war. Ich analysierte sowohl autosomale Mikrosatelliten als auch Sequenzen der mitochondrialen Hypervariablen Region I. Meine Ergebnisse zeigen, dass die genetische Struktur der Guineapaviane am besten durch die überwiegende Abwanderung von Weibchen erklärt werden kann, sowohl in einem lokalen als auch im globalen Kontext. Weiblicher Genfluss führt zu einer hohen Diversität innerhalb von Populationen sowie einem Fehlen von genetisch-geographischer Struktur in mitochondrialer DNA. Nukleäre DNA hingegen zeigt eine starke globale geographische Struktur und Männchen sind im Vergleich zu Weibchen durch eine stärkere lokale Struktur gekennzeichnet. Dies entspricht den Vorhersagen für ein System, in welchem hauptsächlich Weibchen abwandern und Männchen in ihrer Geburtsgruppe verbleiben. Insgesamt scheint lokal begrenzte Abwanderung den wirksamen Genfluss auf eine Distanz unter 200 km zu beschränken, was zu einem starken Isolation-durch-Distanz Effekt und genetisch differenzierten Populationen führt. Anzeichen für Populationsausbreitung, die graduelle Struktur genetischer Variation, und mögliche Hinweise auf das “Allele-surfing” Phänomen, deuten auf eine historische westwärts gerichtete Ausbreitung von Guineapavianen hin. Introgressive Hybridisierung mit benachbarten Anubispavianen könnte genetische Muster im Bereich der Kontaktzone erklären, muss aber im Detail noch untersucht werden. Zusätzlich konnte ich zeigen, dass Mantelpaviane vermutlich im gleichen Zeitraum des Späten Pleistozäns von Afrika nach Arabien wanderten, wie Hypothesen für den modernen Menschen vorschlagen. Meine Studie ist die erste umfassende Analyse der genetischen Populationsstruktur der Guineapaviane und liefert Belege für die überwiegende Abwanderung von Weibchen in dieser Art. Dies untersützt die Ansicht, dass das Sozialsystem der Guineapaviane einige vergleichbare Merkmale zum System der Mantelpaviane aufweist und deutet somit darauf hin, dass während der Evolution dieser beiden Arten besondere evolutionäre Drücke gewirkt haben, die sie von allen anderen Pavianarten abgrenzen. In Kombination mit dem starken Einfluss von Populationsausbreitungen auf ihre Verbreitung und genetische Diversität, bekräftigt meine Arbeit Paviane als interssanten analogen Modellorganismus, der helfen kann, die Prozesse die während der Evolution des Menschen maßgeblich waren, aufzuklären.