I studied molecular phylogeny and historical biogeography of the hawkmoth genus Agrius, a group with several migratory as well as several strictly endemic species. I used sequences of one mitochondrial and one nuclear genes and in a detail also population genetic parameters of the most widespread species, Agrius convolvuli.

Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for > 5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from Proteobacteria (mainly Alpha-and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants. Most of the routinely measured traits tended to show a significant phylogenetic signal, although this signal was weak for environmental preferences. We demonstrated how this database could be used to link genomic attributes to differences in pH and salinity optima. We found that adaptations to high salinity or high-pH conditions are related to cell surface transporter genes, along with previously uncharacterized genes that might play a role in regulating environmental tolerances. Together, this work highlights the utility of this database for associating bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and emphasizes the need for more comprehensive and consistent measurements of traits across a broader diversity of bacteria. IMPORTANCE Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily accessible. Here, we compiled phenotypic and environmental tolerance information for > 5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (https://doi.org/10.6084/m9.figshare.472392), and we have included instructions for researchers interested in adding new entries or curating existing ones.

Magister Scientiae - MSc / This thesis explores species-level phylogenetic relationships of the African cycad genus Encephalartos, which is one of the eleven genera of cycads. The genus is confined to Africa and comprises approximately 65 species, 38 of which are found naturally in South Africa. The phylogenetic studies on Encephalartos to date still result in many unresolved polytomies so it is not possible to fully understand the relationships between different taxa. In this study, AFLPs were used together with DNA sequencing to reconstruct the phylogenetic relationships of the genus. This study is the first to be presented with aims of resolving the relationships of Encephalartos using AFLPs together with DNA sequences. Total DNA was extracted from accessions sampled from the Kirstenbosch Botanical Garden and the Montgomery Collection, representing the majority of Encephalartos species listed in the most recent world list of cycads. Sequences of the trnL intron, rpoC1, ITS 1, ITS 2, and AFLP profiles from two sets of selective primers were used to reconstruct the phylogenetic relationships within the genus using maximum parsimony methods. As in earlier studies, unresolved polytomies were recovered from the sequencing data. The AFLP trees have some resolution but CI and RI indices were low indicating high levels of homoplasy in the data. The relationships resolved by this study for all the data sets separately and combined were different to those previously suggested for the genus. The biogeography of Encephalartos is also investigated by habitat optimization of the genus to estimate the origin of the genus with respect to its current distribution. / South Africa

Paleontology is based on fossils but what is the link between fossil specimens and our reconstruction of life history seems to be ambiguous. The majority of paleontological studies focus on fossil morphology to infer their phylogenetic status, but recently increasing number of studies emphasize the role of paleontological data rather than particular specimens. Datasets construction and data processing are still basic in many paleontological studies, thus hampering the transition towards data-driven paleontology. More importantly, there has been a lack of understanding of the difference between data and information embedded inside. In this thesis, I present examples of three kinds of paleontological studies driven by fossil, data, and information, respectively, which shows the reconstruction of evolutionary history via different level of features from fossils. Chapter 1 shows the evolution and development of ceratopsian dinosaurs with emphasis on the fossil materials from the Gobi Desert, Mongolia. Chpater 1.1 reports Beg tse, a neoceratopsian dinosaur that is sister to all other know neoceratopsians, and morphologically and temporally between neoceratopsians and more basal ceratopsians. In chapter 1.2, to further explore the development of Protoceratops as well as other ornithischian dinosaurs, two embryonic Protoceratops skulls are CT-scanned and compared with more mature Protoceratops and other ornithischian dinosaurs. The results show strong peramorphosis in ceratopsian dinosaurs and conservative cranial development in stem ornithischians. Chapter 1.3 reports a new species of Protoceratops, P. tengri, which bears a regular wavy pattern along its neck frill that is absent in almost all previously reported Protoceratops. Such structure may function as display as it seems to be the ancestral form of other patterned cranial structures in more derived ceratopsids. Chapter 2 focus on data-driven paleontological studies, especially the applications of artificial intelligence (AI). Chapter 2.1 is based on the data comprised from chapter 1.2, deep neural networks (DNNs) are used to segment CT slices of embryonic Protoceratops fossils and have reached human comparable performance, but the generalization ability of such models remains questionable. Chapter 2.2 shows DNNs-based localization and segmentation of osteons in histological thin sections from Alvarezsaurian dinosaurs. The results indicate a truncated development pathway rather than compressed development during the miniaturization of this group. Chapter 2.3 is a short review about previous AI applications in paleontology, in which a large portion is based on data from foraminifera, insects, and other microfossils while only few are working with vertebrate fossils. There are approximate 10-year gap in algorithms and datasets between paleontology and mainstream AI studies. Chapter 3 explores the even basic level of data-driven paleontology, the information. Under the framework of information theory and communication system engineering, chapter 3.1 introduces the basic concepts of information theory and how they are represented in paleontological studies. Chapter 3.2 quantify the information entropy, mutual information, and channel capacity in morphological character matrices of various groups of vertebrates. The results suggest alternative weighting strategy in phylogenetic analysis and question current construction strategy of morphological character matrices. Chapter 3.3 makes further perspective about the application of information theory in paleontological study by treating it as a communication system. During the last two decades, the increase of data and appearance of novel methods have led many research fields transiting towards data driven. However, the construction of datasets, harnessing of novel data processing methods, and establishment of a general theory all indicate significant lags between paleontology and many other research fields. This thesis provides the very initial examples towards data-driven paleontological studies.

Many groups of protists, also known as microbial eukaryotes, remain understudied. One such group, the superfamily Sainouroidea in the supergroup Rhizaria has been shown to be a molecularly diverse and divergent clade by recent environmental sequencing. Here we isolated and analyzed cultures of Sainouroid amoebae using 18S rDNA sequencing, light microscopy, and TEM. Using a molecular species concept we described four novel genera and twelve novel species in Sainouroidea. Another understudied group Cutosea, in the supergroup Amoebozoa, contains the ATCC isolate PRA-29, which is an amoeba that has been used in many phylogenomic datasets. PRA-29 was incorrectly identified as Pessonella sp. Here we studied PRA-29 in detail using light microscopy, TEM, and SEM and re-classify it as Armaparvus languidus novel genus, novel species. We show that a cell coat of microscales separated from the cell membrane is a unique trait found in all known Cutosean amoebae.

No description available.

Trematodes belonging to the blood-inhabiting group have long attracted the attention of parasitologists and medical men, especially those trematodos belonging to the family Schistosomidae because throw widely distributed species, Schistosoma Japonicum, S. haematobium, and S. mansoni, are parasitic in man, and in endemic regions are the cause of important human diseases. These schistosomes, with a few exception, have undergone more detailed research than any other trematodes. Since the discovery of the first digenetic trematode exhibiting sexual dimorphism by Rudolphi (1819), which was named Distoma canaliculatum, and the descriptions of the other blood flukes up until the present time, a vast amount of material has been put forth in publications having a more or less limited circulation. The writer has, therefore, attempted to assemble descriptions of all the genera and species, hoping that this will be an aid in the identification of these trematodes. Unfortunately many of the descriptions are inadequate as they are based in many instances upon a limited number of specimens. In compiling these data the writer was struck by the possibility of further using them to investigate the genetic and evolutionary relationships of the blood-inhabiting trematodes. Looss (1899) noticed a similarity in the structure, the dermo-muscular sac of the suckers, and in the details of the digestive tract in those blood flukes that had been found. He concluded that their adaptations to existence were similar, as both had a constant environment and a common food supply. Odhner, (1912) through a long study, concluded that the blood flukes were genetically related. The discovery of the life cycles of Sanguinicola and Schistosoma japonicum added further evidence in support of this hypothesis.

<p> Much speculation has been made about the relative importance of changes in developmental regulation of gene expression in determining major phylogenetic patterns observed both in extant and extinct species. However, most of these hypotheses have been formulated based on data obtained from the comparison of very distantly related organisms (e.g., between animal phyla). Another approach to answering questions about development (ontogeny) in the context of evolution (phylogeny) is to observe how developmental patterns diverge between closely related species, in order to obtain a better understanding of the population level processes underlying phyletic change. With the intent of addressing this possibility, the principle work outlined in this thesis investigated patterns of divergence between closely related species of Drosophila at the level of both the nucleotide coding sequence as well as gene expression levels in the context of ontogeny. The results show that the stage during which genes are expressed has a significant impact on their patterns of divergence, acting both to constrain (earlier stages) and accelerate (later stages) their rates of evolution - the latter being largely the result of sexual selection pressure. However, we also find that intermediate stages of fly development, such as metamorphosis, may experience a greater degree of conservation of the elements regulating gene expression than other stages. Nonetheless, we do find evidence that both gene expression and coding sequences may be subject to similar selection pressures, yet there also appears to be substantial uncoupling of the two, as evidenced by our observation of stage-specific, autonomous patterns of hybrid misexpression manifested in interspecific hybrids. The data presented herein shed new light on patterns of divergence between species, specifically with regards to how various selection pressures affect different stages of ontogeny.</p> / Thesis / Doctor of Philosophy (PhD)

Macroevolutionary patterns of adaptation are a product of natural selection acting on genetic and developmental variation within populations, the basis of microevolution. In microevolution, an adaptive landscape is used to visualize the relationship between phenotype and fitness, through a series of peaks and valleys. The adaptive landscape, as a concept suggests that there is some phenotypic optimum, or a combination of phenotypes, that result in a maximum fitness. This peak is not stable but is a reflection of interactions between the environment and the flora and fauna within. To expand the adaptive landscape to macroevolutionary scales is to assume that there is some optimum that a species or population is adapted to, and that numerous species can be compared to one another on the same landscape. The world of phylogenetic comparative methods uses the theory of the adaptive landscape in investigating the trajectory of trait change but is often limited to extant organisms. The fossil record often represents a major gap in the use of adaptive landscape theory, due in part to the incomplete nature of specimens or difficulties in untangling evolutionary relationships. Within this gap, the Triassic Period (252.2 – 201.5 MA) is sparsely represented, due to the often highly incomplete nature of Triassic fossils and our constantly evolving understanding of their phylogenetic relationships. However, the Triassic Period is bookended by mass extinctions, and is thus a useful case study to explore the utility of adaptive landscape theory for organisms in a time of rapid environmental change. My dissertation explores convergence and growth through an adaptive landscape framework, to reconstruct how species were evolving, or populations adapting, to a changing environment. The first chapter of my dissertation explores the evolution of a long snout in reptiles, with exploration of convergent evolution for both extant and extinct reptiles across the tree of life. The second chapter of my dissertation explores a statistical method to incorporate variation due to fossilization in estimating and quantifying growth curves. This second chapter was necessary to explore the third chapter of my dissertation, the ontogeny of a large-bodied mammal relative, Exaeretodon argentinus. With my third chapter, I quantify growth curves, compare them across other proto mammals closely related to Exaeretodon, and explore how diet may have changed over the lifetime of a single individual. These chapters focus on the adaptive landscape over different scales (population vs clade), and serve as a basis for future work in estimating dietary evolution. / Doctor of Philosophy / Evolutionary studies are often divided into macroevolution and microevolution. Microevolution can be thought of as the primary process of evolution, such as evolution by natural selection. Macroevolution, however, relates to patterns in evolution, such as the repeated evolution of flight in insects, birds, bats, and many extinct reptiles known only from fossils. Surprisingly, we lack any convincing models that can accurately relate evolution by natural selection with macroevolutionary patterns. One idea to bridge this gap is the adaptive landscape, an 80-year-old concept that relates a trait to the fitness of a population or a species. The adaptive landscape provides a visual representation of evolution through a series of peaks and valleys. Peaks embody high fitness, reflecting a population that is well adapted to their environment. Valleys on the other hand represent extinction traps, where populations are maladapted to their environment, and are in decline and at a higher risk of extinction. The adaptive landscape essentially quantifies how different traits of a population relate to their environment. My dissertation seeks to explore evolution through the lens of the adaptive landscape, to better reconstruct hypotheses about how animals interact with their environments, particularly in extinct animals known from fossils. I view the adaptive landscape with a macroevolutionary lens by redescribing a fossil reptile and investigating the repeated evolution of a long snout in reptiles. I then attempt to look at the adaptive landscape at a microevolutionary scale, by investigating patterns of growth in a 230-million-year-old mammal relative. My dissertation views evolution across scales and sets the stage for future work to better connect those scales.

This systematic study recognizes 15 species of the genus Mallos Pickard-Cambridge and three species of the genus Mexitilia Lehtinen. Three species of Mallos and one species of Mexitilia are newly described. Two species are placed in synonymy and two species are transferred to Mallos. The males of two Mallos species are described for the first time. A cladistic analysis based on 22 morphological produced a cladogram that supports the monophyly of Mallos and the validity of Mexitilia. For five species of Mallos and one species of Mexitilia mitochondrial and nuclear DNA sequences were analyzed by restriction digest. The seventeen resulting restriction sites produced a cladogram that agreed with the one based on the morphology of these six species. When morphological and molecular characters were combined they produced a single tree that was identical to that based on molecular data alone. These molecular and morphological characters present the same picture of Mallos and Mexitilia phylogeny. / Master of Science