Phylogenetic and ontogenetic influences on the distribution of anthocyanins and betacyanins in leaves of tropical plants

We examined the anatomy of expanding, mature, and senescing leaves of tropical plants for the presence of red pigments: anthocyanins and betacyanins. We studied 463 species in total, 370 genera, belonging to 94 families. This included 21 species from five families in the Caryophyllales, where betacyanins are the basis for red color. We also included 14 species of ferns and gymnosperms in seven families and 29 species with undersurface coloration at maturity. We analyzed 399 angiosperm species (74 families) for factors (especially developmental and evolutionary) influencing anthocyanin production during expansion and senescence. During expansion, 44.9% produced anthocyanins and only 13.5% during senescence. At both stages, relatively few patterns of tissue distributions developed, primarily in the mesophyll, and very few taxa produced anthocyanins in dermal and ground tissue simultaneously. Of the 35 species producing anthocyanins both in development and senescence, most had similar cellular distributions. Anthocyanin distributions were identical in different developing leaves of three heteroblastic taxa. Phylogeny has influenced the distribution of anthocyanins in the epidermis and mesophyll of expanding leaves and the palisade parenchyma during senescence, although these influences are not strong. Betacyanins appear to have similar distributions in leaves of taxa within the Caryophyllales and, perhaps, similar functions. The presence of anthocyanins in the mesophyll of so many species is inconsistent with the hypothesis of protection against UV damage or fungal pathogens, and the differing tissue distributions indicate that the pigments may function in different ways, as in photoprotection and freeradical scavenging.

Phylogenetic and ecological significance in the evolution of Cetacean tonal sounds

Cetaceans are aquatic mammals that rely primarily on sound for most daily tasks. A compendium of sounds is emitted for orientation, prey detection, and predator avoidance, and to communicate. Communicative sounds are among the most studied Cetacean signals, particularly those referred to as tonal sounds. Because tonal sounds have been studied especially well in social dolphins, it has been assumed these sounds evolved as a social adaptation. However, whistles have been reported in ‘solitary’ species and have been secondarily lost three times in social lineages. Clearly, therefore, it is necessary to examine closely the association, if any, between whistles and sociality instead of merely assuming it. Several hypotheses have been proposed to explain the evolutionary history of Cetacean tonal sounds. The main goal of this dissertation is to cast light on the evolutionary history of tonal sounds by testing these hypotheses by combining comparative phylogenetic and field methods. This dissertation provides the first species-level phylogeny of Cetacea and phylogenetic tests of evolutionary hypotheses of cetacean communicative signals. Tonal sounds evolution is complex in that has likely been shaped by a combination of factors that may influence different aspects of their acoustical structure. At the inter-specific level, these results suggest that only tonal sound minimum frequency is constrained by body size. Group size also influences tonal sound minimum frequency. Species that live in large groups tend to produce higher frequency tonal sounds. The evolutionary history of tonal sounds and sociality may be intertwined, but in a complex manner rejecting simplistic views such as the hypothesis that tonal sounds evolved ‘for’ social communication in dolphins. Levels of social and tonal sound complexity nevertheless correlate indicating the importance of tonal sounds in social communication. At the intraspecific level, tonal sound variation in frequency and temporal parameters may be product of genetic isolation and local levels of underwater noise. This dissertation provides one of the first insights into the evolution of Cetacean tonal sounds in a phylogenetic context, and points out key species where future studies would be valuable to enrich our understanding of other factors also playing a role in tonal sound evolution. ^

Investigation of Mantle Dynamics from Platinum Group Elements and Rhenium-Osmium Isotope Systematics of Mantle Xenoliths from Oahu, Hawaii

Intraplate volcanism that has created the Hawaiian-Emperor seamount chain is generally thought to be formed by a deep-seated mantle plume. While the idea of a Hawaiian plume has not met with substantial opposition, whether or not the Hawaiian plume shows any geochemical signal of receiving materials from the Earth’s Outer Core and how the plume may or may not be reacting with the overriding lithosphere remain debatable issues. In an effort to understand how the Hawaiian plume works I report on the first in-situ sulfides and bulk rock Platinum Group Element (PGE) concentrations, together with Os isotope ratios on well-characterized garnet pyroxenite xenoliths from the island of Oahu in Hawaii. The sulfides are Fe-Ni Monosulfide Solid Solution and show fractionated PGE patterns. Based on the major elements, Platinum Group Elements and experimental data I interpret the Hawaiian sulfides as an immiscible melt that separated from a melt similar to the Honolulu Volcanics (HV) alkali lavas at a pressure-temperature condition of 1530 ± 100OC and 3.1±0.6 GPa., i.e. near the base or slightly below the Pacific lithosphere. The 187Os/188Os ratios of the bulk rock vary from subchondritic to suprachondritic (0.123-0.164); and the 187Os/188Os ratio strongly correlates with major element, High Field Strength Element (HFSE), Rare Earth Element (REE) and PGE abundances. These correlations strongly suggest that PGE concentrations and Os isotope ratios reflect primary mantle processes. I interpret these correlations as the result of melt-mantle reaction at the base of the lithosphere: I suggest that the parental melt that crystallized the pyroxenites selectively picked up radiogenic Os from the grain boundary sulfides, while percolating through the Pacific lithosphere. Thus the sampled pyroxenites essentially represent crystallized melts from different stages of this melt-mantle reaction process at the base of the lithosphere. I further show that the relatively low Pt/Re ratios of the Hawaiian sulfides and the bulk rock pyroxenites suggest that, upon ageing, such pyroxenites plus their sulfides cannot generate the coupled 186Os- 187Os isotope enrichments observed in Hawaiian lavas. Therefore, recycling of mantle sulfides of pyroxenitic parentage is unlikely to explain the enriched Pt-Re-Os isotope systematics of plume-derived lavas.

Larger foraminiferal biostratigraphy, systematics and paleoenvironments of the Avon Park Formation and Ocala Limestone, Highlands County, Florida

This study investigates the use of larger foraminifera in determining the biostratigraphy of the Avon Park Formation and the Ocala Limestone in central Florida. Sedimentary rocks of the Avon Park Formation are the oldest exposed deposits in the state of Florida, and together with the Ocala Limestone comprise a part of the confining unit of the Floridan Aquifer, a major source of Florida's water supply. ^ Material from the ROMP 29A core collected by the U.S. Geological Survey was evaluated and compared to previous studies of the biostratigraphy of the formations. The larger foraminifera of the Avon Park Formation were examined in thin section, and those of the Ocala Limestone were free specimens. The larger foraminifera from both units were described and identified, and the biostratigraphy determined. The morphological features of the larger foraminifera of the Ocala Limestone were measured and analyzed at various depths within the ROMP 29A core.^ The Avon Park Formation contains predominantly the shallow-water, conical foraminifera Fallotella cookei, Fallotella floridana, Pseudochrysalidina floridana, Coleiconus christianaensis, Coleiconus sp. A, Coskinolina sp. A, Coskinolina sp. B, Fallotella sp. A, Fallotella sp. B, Fabularia vaughani and larger miliolids. ^ The Ocala Limestone contains a different, deeper water assemblage that included the larger foraminifera Heterostegina ocalana, Lepidocyclina ocalana varieties, Lepidocyclina chaperi, Lepidocyclina pustulosa, Nummulites willcoxi, Nummulites striatoreticulatus, Nummulites floridensis and Pseudophragmina spp. A, B, and C. The age of the Avon Park Formation was corroborated by the occurrence of the biomarker echinoid Neolaganum dalli as Eocene, and the Ocala Limestone also contained Eocene larger foraminifera with Eocene to possibly Oligocene calcareous nannofossils. The distribution of the larger foraminifera of the Avon Park Formation was correlated with the subtidal and peritidal zones of the continental shelf. Analyses of variance showed that the changes in measurements of the morphology in Heterostegina ocalana, Lepidocyclina spp. and Nummulites spp. were correlated with change in the depositional environments.^

Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

Arc crust-magma interaction in the Andean Southern Volcanic Zone from thermobarometry, mineral composition, radiogenic isotope and rare earth element systematics of the Azufre-Planchon-Peteroa volcanic complex, Chile

The Andean Southern Volcanic Zone (SVZ) is a vast and complex continental arc that has been studied extensively to provide an understanding of arc-magma genesis, the origin and chemical evolution of the continental crust, and geochemical compositions of volcanic products. The present study focuses on distinguishing the magma/sub-arc crustal interaction of eruptive products from the Azufre-Planchon-Peteroa (APP 35°15'S) volcanic center and other major centers in the Central SVZ (CSVZ 37°S–42°S), Transitional SVZ (TSVZ 34.3–37.0°S), and Northern SVZ (NSVZ 33°S–34°30'S). New Hf and Nd isotopic and trace element data for SVZ centers are consistent with former studies that these magmas experienced variable depths of crystal fractionation, and that crustal assimilation is restricted to the lower crustal depths with an apparent role of garnet. Thermobarometric calculations applied to magma compositions constrain the depth of magma separation from mantle sources in all segments of the SVZ to(70-90 km). Magmatic separation at the APP complex occurs at an average depth of ~50 km which is confined to the mantle lithosphere and the base of the crust suggesting localized thermal abrasion both reservoirs. Thermobarometric calculations indicate that CSVZ primary magmas arise from a similar average depth of (~54 km) which confines magma separation to the asthenospheric mantle. The northwards along-arc Sr-Nd-Hf isotopic data and LREE enrichment accompanied with HREE depletion of SVZ mafic magmas correlates well with northward increasing crustal thickness and decreasing primary melt separation from mantle source regions indicating an increased involvement of lower crustal components in SVZ magma petrogenesis. ^ The study concludes that the development of mature subduction zones over millions of years of continuous magmatism requires that mafic arc derived melts stagnate at lower crustal levels due to density similarities and emplace at lower crustal depths. Basaltic underplating creates localized hot zone environments below major magmatic centers. These regions of high temperature/partial melting, and equilibration with underplated mafic rocks provides the mechanism that controls trace element and isotopic variability of primary magmas of the TSVZ and NSVZ from their baseline CSVZ-like precursors.^

Phylogenetic and Ecological Significance in the Evolution of Cetacean Tonal Sounds

Cetaceans are aquatic mammals that rely primarily on sound for most daily tasks. A compendium of sounds is emitted for orientation, prey detection, and predator avoidance, and to communicate. Communicative sounds are among the most studied Cetacean signals, particularly those referred to as tonal sounds. Because tonal sounds have been studied especially well in social dolphins, it has been assumed these sounds evolved as a social adaptation. However, whistles have been reported in ‘solitary’ species and have been secondarily lost three times in social lineages. Clearly, therefore, it is necessary to examine closely the association, if any, between whistles and sociality instead of merely assuming it. Several hypotheses have been proposed to explain the evolutionary history of Cetacean tonal sounds. The main goal of this dissertation is to cast light on the evolutionary history of tonal sounds by testing these hypotheses by combining comparative phylogenetic and field methods. This dissertation provides the first species-level phylogeny of Cetacea and phylogenetic tests of evolutionary hypotheses of cetacean communicative signals. Tonal sounds evolution is complex in that has likely been shaped by a combination of factors that may influence different aspects of their acoustical structure. At the inter-specific level, these results suggest that only tonal sound minimum frequency is constrained by body size. Group size also influences tonal sound minimum frequency. Species that live in large groups tend to produce higher frequency tonal sounds. The evolutionary history of tonal sounds and sociality may be intertwined, but in a complex manner rejecting simplistic views such as the hypothesis that tonal sounds evolved ‘for’ social communication in dolphins. Levels of social and tonal sound complexity nevertheless correlate indicating the importance of tonal sounds in social communication. At the intraspecific level, tonal sound variation in frequency and temporal parameters may be product of genetic isolation and local levels of underwater noise. This dissertation provides one of the first insights into the evolution of Cetacean tonal sounds in a phylogenetic context, and points out key species where future studies would be valuable to enrich our understanding of other factors also playing a role in tonal sound evolution.