From Microevolutionary Processes to Macroevolutionary Patterns: Investigating Diversification at Multiple Scales in Southeast Asian Lizards

A comprehensive understanding of the evolutionary processes responsible for generating biodiversity is best obtained using integrative approaches at multiple scales. In doing so, these investigations can provide complex insights into how fine-scale microevolutionary processes operating at the population level, translate into the large-scale macroevolutionary biodiversity patterns we see in evolutionary radiations. Due to the complex geography, historical climatic fluctuations, and remarkably high concentrations of land vertebrate biodiversity, Southeast Asia is an ideal place to investigate these processes. Lizards of the genus Eutropis represent one of the more recognizable radiations of lizards in Southeast Asia, due to their high abundances, broad geographic distribution, and generalized external morphology. However, their evolutionary history has remained enigmatic due to their highly conserved morphology and a lack of dense population sampling of individuals and species across their range. In this dissertation, I first utilize a variety of approaches to delimit species in Philippine Eutropis and find that species diversity is vastly underestimated by current taxonomy, while more generally assessing how best to determine species limits in radiations where morphology is highly conserved. I then use a molecular phylogenetic framework to investigate biogeographic patterns and the timing of diversification within the genus across Southeast Asia. Lastly, I take a landscape genomic approach to determine the relative contributions of distance, and various geographic and environmental variables to population genetic differentiation and morphological diversity patterns in the common sun skink. This research contributes substantially to our understanding of species diversity in evolutionary radiations, as well as how historical and contemporary evolutionary processes shape the evolution of morphological and genetic diversity

ANALYSIS AND DEVELOPMENT OF MANAGEMENT TOOLS FOR ORYCTES RHINOCEROS (COLEOPTERA: SCARABAEIDAE)

M.S.M.S. Thesis. University of Hawaiʻi at Mānoa 201

Number 52 (December 2010)

(December 2010) - Comparative Conservation Genetics of Two Endangered Darters, Percina rex and Percina jenkinsi By Anna L. George, David Neely, and Richard Mayden Invasion of Gulf Menhaden in the Alabama River By T. Heath Haley, R. Kyle Bolton, and Carol E. Johnston Southeastern Fishes Council State Reports Minutes, Business Meeting, 35th Annual Meeting, Southeastern Fishes Council 2009 Treasurer\u27s Report for the Southeastern Fishes Counci

Molecular Pathogenesis of Viral and Subviral Agents in Model and Crop Grasses

Viral diseases cause significant agricultural yield losses globally. Because grasses constitute most of our food, forage, and bioenergy sources, the resulting economic losses caused by grass-infecting viruses are particularly devastating. However, the lack of an established genetic model for grasses has generally hindered investigation of grass-virus molecular interactions, leading to a gap in our knowledge of monocot virology. In this study, the issue of the monocot virology knowledge gap is addressed at the levels of both the laboratory and the field. Two candidate grasses, Brachypodium distachyon (Brachypodium, a C3 grass) and Setaria viridis (Setaria, a C4 grass), were established as monocot model hosts for seven small RNA viruses in diverse genera. Aspects of the host disease response were characterized, including agronomically relevant phenotypic perturbations and expression profiles of defense hormone marker genes in salicylic acid, jasmonic acid, and ethylene signaling pathways. This comparative viromics approach revealed conserved and host-dependent defense hormone signaling responses to the diverse viral agents, as well as virus-specific responses between the C3 and C4 model hosts. Further, Brachypodium and the food crop Panicum miliaceum (proso millet) were utilized as laboratory models for investigating novel molecular features of Panicum mosaic virus (PMV), its associated satellite virus (SPMV), and satellite RNAs (satRNAs), the collective causal agents of the turfgrass disease known as St. Augustine Decline. A satRNA of PMV isolated from Stenotaphrum secundatum (St. Augustinegrass), satS, attenuates the normal disease phenotype induced by its PMV helper virus and actively acquires ~100-200 nucleotides from the 3′-end of the PMV helper virus RNA genome. This symptom attenuation and sequence acquisition is associated with host-dependent reductions in the systemic accumulation of helper virus RNA and capsid protein. Brachypodium and proso millet were also used to characterize the de novo polyadenylation of PMV and its subviral agents. The polyadenylated PMV RNAs resemble byproducts of a poly(A)-mediated RNA degradation pathway. Lastly, we report on the re-emergence of PMV and SPMV as the predominant viral pathogens of cultivated switchgrass in Nebraska. The Summer-based switchgrass varieties were more susceptible to PMV and PMV+SPMV infections, compared to Kanlow-based varieties. The susceptible varieties were more severely affected by the disease. Overall this study investigates questions of host-virus interactions, both in the laboratory and the field, and presents new findings on the topic of grass RNA virus biology

Marine organisms model species for the assessment of biological, environmental and economic impacts on marine aquaculture in Campania

Campanian region has an important mussel farming tradition, since the Cuman and Greek domination around 700 A.C. through the Bourbons until today. Mussels and the linked supply chain were always been present in the socio-economic scenario of the regional coastal area. Today mussel production in Campania represents almost all the aquaculture total production, resulting one of the most productive Italian regions in this sector. In order to evaluate biological, environmental and economic impacts on marine aquaculture, mussels of the genus Mytilus were chosen as model species. Mussels are perfect model organisms for their biological and physiological characteristics; they are bioengineering species, sedentary organisms, filter feeders, widespread all over the world, easy to keep in laboratories and important food source. Besides food source, thanks to their features mussels provide important ecosystem services as regulating the water column, supporting the food web and provisioning cultural services. Moreover, recently, are becoming source of important bioactive compounds, revealing to be organisms with a high potentiality in several applications. Different kind of stressors, anthropogenic as well as natural stressors, can impact, negatively or positively, on mussels and consequently on the ecosystem services they provide. Aims of the thesis are the evaluation of the effects of three different stressors on mussels supply chain: food frauds, ocean acidification and the grafting operation. Food frauds, the act of defrauding buyers of food and food ingredients for economic gain, can threaten the Campanian mussel supply chain. Unhealthy storage conditions, species substitutions, lack of label and informations on the product origin are all ordinary risks when buying mussels. The threats are both for human health than for the local economy of the honest mussel farmers. In order to investigate on the situation of the Campanian markets, Mytilus galloprovincialis mussels, the native species of the Mediterranean Sea, were sampled in different fish markets, local mussel farms and in their local natural environment. Mussels were genetically characterized in order to assess the species and their origins using the molecular markers COI, 16S, PAPM and 28S. The final aim was the attempt of the genetic identification of a local Campanian mussel, intended to officially recognize such local excellence product considering all its productions steps, from the seed recruitment to the marketing. Investigation on this topic has shown that Campanian local markets are not highly affected by the food frauds of species substitutions but is difficult define the situation for the other type of fraud, the origin declaration. Just using simple molecular biology tools was not possible identify different mussel populations and define the genetic characterization of the local Mytilus galloprovincialis species. Further investigations are essential in order to identify a simple, fast and cheap method for mussels origin identification. Mussels supply chain could be also affected by other kind of human impacts, not only in Campania region but on a global scale. Global changes can induce important vital alterations in aquatic systems, the increasing amounts of CO2 in the oceans, known as the phenomenon of Ocean Acidification, affect our life via influencing the environment and our economy. Ocean acidification and other anthropogenic stressors can were already proved to cause negatively or positively changes on coastal dynamics, in marine organisms and consequently to the ecosystems services that they provide. Ocean acidification effects were tested on Mytilus unguiculatus, a pacific mussel widely bread in the Chinese Sea with similar anatomy and physiology to M. galloprovincialis. Mytilus unguiculatus has been exposed to different pH values (7.4 and 7.8) and then were analyzed the respective physiological parameters (O2 consumption and NH4+ excretion), gene expression of NKA and NHE8 (both involved in the acid-base regulation mechanisms), free amino acids from mantle and gills with UPLC analysis, shell characteristics with AAS analysis, SEM pictures and X- ray testing. Mytilus unguiculatus easily survive in 7.8 pH conditions but further investigations (different life stages, longer exposure time, additional genes expression) are needed to better understand the effects of Ocean Acidification on this species and other species as the Mediterranean Mytilus galloprovincialis. However an anthropogenic stressor for certain organisms could have a positive impact on the linked aquaculture economy. It is the case of the induced grafting operation on the pearl molluscs, in order to produce a pearl. Since the first decade of 1900 pearls production is an industrialized process, there are some bivalves of the pacific area widely used in this manufacturing production. Molluscs are able to produce pearls in response to a natural stressors (the famous grain of sand, a small piece of broken shell, a parasite or a small animal) causing an injury in the mantle of the damaged mollusc. In the “classical pearl molluscs” pearl production is human surgically induced, imitating what happens in nature and using a nucleus of mother-of-pearl. In a similar way the Campanian mussel Mytilus galloprovincialis could react producing a pearl too. The local mussel could be a “new pearl molluscs” and pearls productions would be fully included in the well-established Campanian gemstone market. As for mussels farming activity, Campania region has an ancient coral manufacturing tradition, hosting in the southwestern coast of the Gulf of Naples the “the world’s capital of coral”. In conclusion, mussels have been further appreciated as model organisms in different application fields; food frauds can affect negatively the Campanian market and new investigations are needed in order to evaluate their origin; mussels seem to easily survive to the predicted future acidified oceans; finally, mussels have great potentials, among their innovative applications they could become “new pearl molluscs”. In order to carry on and improve the millennial Campanian mussel farming tradition, it is crucial enhance and promote Campanian mussels as excellent local products, promoting new productions and encourage buyers to make a conscious choice, both for enhancing local mussel farmers than for preserving the environment for the future generation

Aquilegia, Vol. 33 No. 2, Summer 2009, Newsletter of the Colorado Native Plant Society

https://epublications.regis.edu/aquilegia/1128/thumbnail.jp

Atoll research bulletin.

no.494 (2001

Expanding the omics repertoire for model studies on a Chlorella-infecting giant virus

Viruses are the most abundant biological entities in aquatic ecosystems. As top-down controls of plankton abundance and diversity, they are intrinsically linked to biogeochemical cycling, and by proxy, to global climate change. It is thus of great interest for researchers to understand the mechanics of viral infection and persistence among ecologically important phytoplankton assemblages. Viruses which infect eukaryotic algae are observed with diverse nucleic acid types, structures, and sizes, though most isolates to date bear large, dsDNA genomes comprised of genes normally only seen in cellular organisms. The Chlorella viruses are the model system for studying these entities, with many of the ‘omics’ approaches having been used to characterize the biology of this system. Here, we present data generated from epigenomic (i.e. DNA methylation) and metabolomic experiments of the prototype Chlorella virus, PBCV-1. In order to ask questions about virus DNA methylation, we first established a novel protocol for cryopreservation of PBCV-1 to control against epigenomic and genetic drift. This allowed for a baseline characterization of the DNA methylome profile in the prototype chlorovirus, PBCV-1, using PacBio’s single-molecule, real-time (SMRT) sequencing software. The results of this study suggest the possibility of widespread epigenomic modifications, and that DNA methylation by viral restriction-modification associated enzymes is incomplete. Most instances of missing methylation marks are represented as hemimethylated palindromes, which are protected against the types of restriction enzymes encoded by these viruses and thus might represent an epigenomic regulatory function in the virus. Finally, we conducted a non-targeted metabolomics study of PBCV-1 infected Chlorella cells to make some of the first inferences of how viral infection alters the metabolic profile of this host system. Altogether, this work helps to distinguish the baseline epigenomic and metabolomic profiles of the Chlorella-PBCV-1 virus system for future comparison with more ecologically informative treatments (i.e. competition, sub-optimal light, nutrient limitation, etc.). This work will help to uncover general trends specific to algal-giant virus interactions that distinguish themselves from phage-bacteria systems