High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

Background: Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results: We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion: Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Pirates, exiles, and empire: English seamen, Atlantic expansion, and Jamaican settlement, 1558–1658

A life of piracy offered marginal men a profession with a degree of autonomy, despite the brand of "outlaw" and the fear of prosecution. At various times throughout history, governments and crowned heads suspended much of their piracy prosecution, licensing men to work as "privateers" for the state, supplementing naval forces. This practice has a long history, but in sixteenth-century England, Elizabeth I (1558-1603) significantly altered this tradition. Recognizing her own weakness in effectively prosecuting these men and the profit they could contribute to the government, Elizabeth began incorporating pirates into the English naval corps in peacetime—not just in war. This practice increased English naval resources, income, and presence in the emerging Atlantic World, but also increased conflict with the powerful Spanish empire. By 1605, making peace with Spain, James VI/I (1603-1625) retracted Elizabeth's privateering promotion, prompting an emigration of English seamen to the American outposts they had developed in the previous century. Now exiles, no longer beholden to the Crown, seamen reverted back to piracy. The Carolinas and Jamaica served as bases for these rover communities. In 1650, the revolutionary leader Oliver Cromwell (1649-1658) once again recognized the merits of such policies. Determined to demonstrate his authority and solidify his rule, Cromwell offered citizenship and state support to Caribbean exiles in exchange for their aiding of his navy in the taking of Spanish Jamaica. Official chartering of Port Royal, Jamaica served as reward for these men's efforts and as the culmination of a century-long cycle of piracy legislation, creating one of England's most lucrative colonies in the middle of a traditionally Spanish Caribbean empire. Through legal and diplomatic records, correspondence, and naval and demographic records from England and Spain, this dissertation explores early modern piracy/privateering policy and its impact on the development of the Atlantic World. European disputes and imperial competition converged in these piracy debates with significant consequences for the definitions of criminality and citizenship and for the development of Atlantic empire.

An investigation of parents' and children's beliefs of early literacy acquisition from a cross -cultural perspective

It has been reported that the cultural-historical experiences of ethnic group members can play a role in the literacy beliefs of those members. Socioeconomic conditions can also influence the belief system of the groups' constituents. This study investigated parents' and children's beliefs pertaining to early literacy acquisition as related to the ethnicity and socioeconomic status (SES) of the participants. The objectives were to determine (a) the differential patterns regarding emergent literacy and traditional skills approaches as they interact with ethnicity and SES and (b) the correspondence between parents and children's beliefs about literacy acquisition. ^ The study was conducted with 152 parents (38 low-income Hispanic, 38 middle-income Hispanic, 38 low-income African-American, and 38 middle-income African-American) and 36 of their 3-, 4-, or 5-year-old children (18 male and 18 female). ^ The parents were asked to check those items with which they agreed on a survey that consisted of an equal number of items from the traditional skills-based and emergent literacy orientations. These responses were used to determine the differences and interaction by ethnicity and SES. The children responded to open-ended questions related to the instruction of reading and writing skills. The parents' responses and children's answers were compared to ascertain the matching parent-child dyads by ethnicity and SES. ^ An item analysis was conducted to strengthen the internal reliability consistency coefficient of the traditional skills-based and emergent literacy scales as measured by the Cronbach Alpha. ^ A two-way multivariate analysis of variance (MANOVA) revealed a significant difference in traditional skill-based beliefs for the low-income African-American and Hispanic parents. There were no significant findings for the parents' traditional skill based or emergent literacy beliefs based on ethnicity, for the interaction between ethnicity and SES, or for the relationship between parents' and children's literacy beliefs by ethnicity and SES. ^ It can be concluded that low-income African-American and Hispanic parents believe in the traditional skills approach, indicating that these parents find it necessary for children to have sufficient school readiness skills prior to learning to read or write. In addition, the parent and child dyads had a strong tendency toward emergent literacy beliefs. ^

Pirates, Exiles, and Empire: English Seamen, Atlantic Expansion, and Jamaican Settlement, 1558-1658

A life of piracy offered marginal men a profession with a degree of autonomy, despite the brand of “outlaw” and the fear of prosecution. At various times throughout history, governments and crowned heads suspended much of their piracy prosecution, licensing men to work as “privateers” for the state, supplementing naval forces. This practice has a long history, but in sixteenth-century England, Elizabeth I (1558-1603) significantly altered this tradition. Recognizing her own weakness in effectively prosecuting these men and the profit they could contribute to the government, Elizabeth began incorporating pirates into the English naval corps in peacetime—not just in war. This practice increased English naval resources, income, and presence in the emerging Atlantic World, but also increased conflict with the powerful Spanish empire. By 1605, making peace with Spain, James VI/I (1603-1625) retracted Elizabeth’s privateering promotion, prompting an emigration of English seamen to the American outposts they had developed in the previous century. Now exiles, no longer beholden to the Crown, seamen reverted back to piracy. The Carolinas and Jamaica served as bases for these rover communities. In 1650, the revolutionary leader Oliver Cromwell (1649-1658) once again recognized the merits of such policies. Determined to demonstrate his authority and solidify his rule, Cromwell offered citizenship and state support to Caribbean exiles in exchange for their aiding of his navy in the taking of Spanish Jamaica. Official chartering of Port Royal, Jamaica served as reward for these men’s efforts and as the culmination of a century-long cycle of piracy legislation, creating one of England’s most lucrative colonies in the middle of a traditionally Spanish Caribbean empire. Through legal and diplomatic records, correspondence, and naval and demographic records from England and Spain, this dissertation explores early modern piracy/privateering policy and its impact on the development of the Atlantic World. European disputes and imperial competition converged in these piracy debates with significant consequences for the definitions of criminality and citizenship and for the development of Atlantic empire.

Effects of phonetic/phonics instruction on reading pronunciation (French level I)

Pronunciation training has been traditionally viewed as of limited importance in a communicatively oriented foreign language curriculum (Pennington & Richards, 1986). Many language instructors seemingly deny the usefulness of phonetic training and rely on a listen-and-repeat method with the use of audiotapes (Bate, 1989; Callamand & Pedoya, 1984; Jones, 1997). Beginners in French classes face the challenge of mastering a complex sound and grapheme-phoneme correspondence system without the benefit of specific instruction. Their pronunciation errors develop mostly from bad habits while decoding from print to sound (Dansereau, 1995). ^ The purpose of this study was to investigate the effectiveness of basic phonetic/phonics instruction on reading pronunciation accuracy in a French I language course. ^ The sample consisted of two groups of French I students from Florida International University, who received the same instruction in French language and culture during the fall semester of 1999. Only the experimental group received additional phonetic/phonics training. ^ The instrument consisted of three recorded reading tasks: isolated familiar words, isolated unfamiliar words, and dialogue. Research questions were analyzed using a one-way multivariate analysis of variance. Significant differences were found between the two groups on scores for each of the three sections of the instrument, and on the total scores. These findings support the hypothesis of the study and reveal the effectiveness of phonetic/phonics training for beginners of French. ^ The findings imply that beginning language students should receive the minimum knowledge they need to master the French phoneme-grapheme (sound-spelling) system. ^

Neanderthal admixture in current human populations

In the present body of work two primary subjects have been addressed, both individually and in their correspondence, namely (1) the potential for Neanderthals to have contributed to the Modern Human population, and (2) the genetic diversity of one of the most prehistorically impactful human popuations, the Armenians. The first subject is addressed by assessing 1000 mutations in 384 current humans, particularly for those mutations which appear to derive from the Neanderthal lineage. Additionally, the validity of the Neanderthal sequences themselves is evaluated through alignment analysis of fragementary DNA derived from the Vindija Cave sample. Armenian genetic diversity is analyzed through the autosomal short tandem repeats, y-chromsome single nucleotide polymorphisms, and y-chromosome short tandem repeats. The diversity found indicates that Armenians are a diverse group which has been genetically influenced by the various migrations and invasions which have entered their historic lands. Further, we find evidence that Armenians may be closely associated with the peopling of Europe.

Correspondence of historic salinity fluctuations in Florida Bay, USA, to atmospheric variability and anthropogenic changes

Florida Bay is a highly dynamic estuary that exhibits wide natural fluctuations in salinity due to changes in the balance of precipitation, evaporation and freshwater runoff from the mainland. Rapid and large-scale modification of freshwater flow and construction of transportation conduits throughout the Florida Keys during the late nineteenth and twentieth centuries reshaped water circulation and salinity patterns across the ecosystem. In order to determine long-term patterns in salinity variation across the Florida Bay estuary, we used a diatom-based salinity transfer function to infer salinity within 3.27 ppt root mean square error of prediction from diatom assemblages from four ~130 year old sediment records. Sites were distributed along a gradient of exposure to anthropogenic shifts in the watershed and salinity. Precipitation was found to be the primary driver influencing salinity fluctuations over the entire record, but watershed modifications on the mainland and in the Florida Keys during the late-1800s and 1900s were the most likely cause of significant shifts in baseline salinity. The timing of these shifts in the salinity baseline varies across the Bay: that of the northeastern coring location coincides with the construction of the Florida Overseas Railway (AD 1906–1916), while that of the east-central coring location coincides with the drainage of Lake Okeechobee (AD 1881–1894). Subsequent decreases occurring after the 1960s (east-central region) and early 1980s (southwestern region) correspond to increases in freshwater delivered through water control structures in the 1950s–1970s and again in the 1980s. Concomitant increases in salinity in the northeastern and south-central regions of the Bay in the mid-1960s correspond to an extensive drought period and the occurrence of three major hurricanes, while the drop in the early 1970s could not be related to any natural event. This paper provides information about major factors influencing salinity conditions in Florida Bay in the past and quantitative estimates of the pre- and post-South Florida watershed modification salinity levels in different regions of the Bay. This information should be useful for environmental managers in setting restoration goals for the marine ecosystems in South Florida, especially for Florida Bay.