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.

Herbivore and nutrient impact on primary producer assemblages in a tropical marine environment

Globally, human populations are increasing and coastal ecosystems are becoming increasingly impacted by anthropogenic stressors. As eutrophication and exploitation of coastal resources increases, primary producer response to these drivers becomes a key indicator of ecosystem stability. Despite the importance of monitoring primary producers such as seagrasses and macroalgae, detailed studies on the response of these benthic habitat components to drivers remain relatively sparse. Utilizing a multi-faceted examination of turtle-seagrass and sea urchin-macroalgae consumer and nutrient dynamics, I elucidate the impact of these drivers in Akumal, Quintana Roo, Mexico. In Yal Ku Lagoon, macroalgae bioindicators signified high nutrient availability, which is important for further studies, but did not consistently follow published trends reflecting decreased δ 15N content with distance from suspected source. In Akumal Bay, eutrophication and grazing by turtles and fishes combine to structure patches within the seagrass beds. Grazed seagrass patches had higher structural complexity and productivity than patches continually grazed by turtles and fishes. Results from this study indicate that patch abandonment may follow giving-up density theory, the first to be recorded in the marine environment. As Diadema antillarum populations recover after their massive mortality thirty years ago, the role these echinoids will have in reducing macroalgae cover and altering ecosystem state remains to be clear. Although Diadema antillarum densities within the coral reef ecosystem were comparable to other regions within the Caribbean, the echinoid population in Akumal Bay was an insufficient driver to prevent dominance of a turf-algal-sediment (TAS) state. After a four year study, declining coral cover coupled with increased algal cover suggests that the TAS-dominated state is likely to persist over time despite echinoid recovery. Studies on macroalgal diversity and nutrients within this same region of echinoids indicated diversity and nutrient content of macroalgae increased, which may further increase the persistence of the algal-dominated state. This study provides valuable insight into the variable effects of herbivores and nutrients on primary producers within a tropical coastal ecosystem. Results from this work challenge many of the currently accepted theories on primary producer response to nutrients and herbivory while providing a framework for further studies into these dynamics.

Response of diatom assemblages to 130 years of environmental change in Florida Bay (USA)

Coastal ecosystems around the world are constantly changing in response to interacting shifts in climate and land and water use by expanding human populations. The development of agricultural and urban areas in South Florida significantly modified its hydrologic regime and influenced rates of environmental change in wetlands and adjacent estuaries. This study describes changes in diatom species composition through time from four sediment cores collected across Florida Bay, for the purposes of detecting periods of major shifts in assemblage structure and identifying major drivers of those changes. We examined the magnitude of diatom assemblage change in consecutive 2-cm samples of the 210Pb-dated cores, producing a record of the past ~130 years. Average assemblage dissimilarity among successive core samples was ~30%, while larger inter-sample and persistent differences suggest perturbations or directional shifts. The earliest significant compositional changes occurred in the late 1800s at Russell Bank, Bob Allen Bank and Ninemile Bank in the central and southwestern Bay, and in the early 1900s at Trout Cove in the northeast. These changes coincided with the initial westward redirection of water from Lake Okeechobee between 1881 and 1894, construction of several canals between 1910 and 1915, and building the Florida Overseas Railroad between 1906 and 1916. Later significant assemblage restructurings occurred in the northeastern and central Bay in the late 1950s, early 1960s and early 1970s, and in the southwestern Bay in the 1980s. These changes coincide with climate cycles driving increased hurricane frequency in the 1960s, followed by a prolonged dry period in the 1970s to late 1980s that exacerbated the effects of drainage operations in the Everglades interior. Changes in the diatom assemblage structure at Trout Cove and Ninemile Bank in the 1980s correspond to documented eutrophication and a large seagrass die-off. A gradual decrease in the abundance of freshwater to brackish water taxa in the cores over ~130 years implies that freshwater deliveries to Florida Bay were much greater prior to major developments on the mainland. Salinity, which was quantitatively reconstructed at these sites, had the greatest effect on diatom communities in Florida Bay, but other factors—often short-lived, natural and anthropogenic in nature—also played important roles in that process. Studying the changes in subfossil diatom communities over time revealed important environmental information that would have been undetected if reconstructing only one water quality variable.

The Roles of Large Top Predators in Coastal Ecosystems: New Insights from Long Term Ecological Research

During recent human history, human activities such as overhunting and habitat destruction have severely impacted many large top predator populations around the world. Studies from a variety of ecosystems show that loss or diminishment of top predator populations can have serious consequences for population and community dynamics and ecosystem stability. However, there are relatively few studies of the roles of large top predators in coastal ecosystems, so that we do not yet completely understand what could happen to coastal areas if large top predators are extirpated or significantly reduced in number. This lack of knowledge is surprising given that coastal areas around the globe are highly valued and densely populated by humans, and thus coastal large top predator populations frequently come into conflict with coastal human populations. This paper reviews what is known about the ecological roles of large top predators in coastal systems and presents a synthesis of recent work from three coastal eastern US Long Term Ecological Research (LTER) sites where long-term studies reveal what appear to be common themes relating to the roles of large top predators in coastal systems. We discuss three specific themes: (1) large top predators acting as mobile links between disparate habitats, (2) large top predators potentially affecting nutrient and biogeochemical dynamics through localized behaviors, and (3) individual specialization of large top predator behaviors. We also discuss how research within the LTER network has led to enhanced understanding of the ecological roles of coastal large top predators. Highlighting this work is intended to encourage further investigation of the roles of large top predators across diverse coastal aquatic habitats and to better inform researchers and ecosystem managers about the importance of large top predators for coastal ecosystem health and stability.

Water for the Wayuu: Procurement and maximization of a limited resource among indigenous pastoralists on the Guajira Peninsula of northern Colombia

For the Wayuu of the Guajira Peninsula of northern Colombia, water procurement has historically been challenging. The ancestral territory of this indigenous pastoral society is windy and arid, with low rainfall, high temperatures and an absence of perennial rivers or streams. In the past, the Wayuu adapted to these environmental conditions by practicing transhumance during the prolonged dry seasons, digging spring wells and artificial ponds and by following guiding principles for water usage. Since the 1930s, the government has made efforts to build additional wind-powered wells and ponds for a growing native population. Notwithstanding, these water solutions have only partly met the necessities; public water sources are limited or unreliable and few attempts are made to generate safe drinking water. Furthermore, the ubiquitous practice of animal husbandry places added pressure on existing sources; livestock consume more water than the human populations in the areas visited. Rapid assessments in four Wayuu areas on the peninsula were conducted by the author and an interdisciplinary team working for the Cerrejón Foundation for Water in La Guajira from 2010 to 2013. The assessments were part of a larger pilot project to design and implement a sustainability plan for reservoir-based water supply systems in the region. This study brings cultural practices and local knowledge to the forefront as key elements for the success of water works and other development projects carried out in Wayuu territory.

A Multi-Criteria GIS-Based Route Selection Tool for Hazardous Material Transport: Consideration of Environmental Consequence, Traffic Congestions and Costs

Hazardous materials are substances that, if not regulated, can pose a threat to human populations and their environmental health, safety or property when transported in commerce. About 1.5 million tons of hazardous material shipments are transported by truck in the US annually, with a steady increase of approximately 5% per year. The objective of this study was to develop a routing tool for hazardous material transport in order to facilitate reduced environmental impacts and less transportation difficulties, yet would also find paths that were still compelling for the shipping carriers as a matter of trucking cost. The study started with identification of inhalation hazard impact zones and explosion protective areas around the location of hypothetical hazardous material releases, considering different parameters (i.e., chemicals characteristics, release quantities, atmospheric condition, etc.). Results showed that depending on the quantity of release, chemical, and atmospheric stability (a function of wind speed, meteorology, sky cover, time and location of accidents, etc.) the consequence of these incidents can differ. The study was extended by selection of other evaluation criteria for further investigation because health risk as an evaluation criterion would not be the only concern in selection of routes. Transportation difficulties (i.e., road blockage and congestion) were incorporated as important factor due to their indirect impact/cost on the users of transportation networks. Trucking costs were also considered as one of the primary criteria in selection of hazardous material paths; otherwise the suggested routes would have not been convincing for the shipping companies. The last but not least criterion was proximity of public places to the routes. The approach evolved from a simple framework to a complicated and efficient GIS-based tool able to investigate transportation networks of any given study area, and capable of generating best routing options for cargos. The suggested tool uses a multi-criteria-decision-making method, which considers the priorities of the decision makers in choosing the cargo routes. Comparison of the routing options based on each criterion and also the overall suitableness of the path in regards to all the criteria (using a multi-criteria-decision-making method) showed that using similar tools as the one proposed by this study can provide decision makers insights in the area of hazardous material transport. This tool shows the probable consequences of considering each path in a very easily understandable way; in the formats of maps and tables, which makes the tradeoffs of costs and risks considerably simpler, as in some cases slightly compromising on trucking cost may drastically decrease the probable health risk and/or traffic difficulties. This will not only be rewarding to the community by making cities safer places to live, but also can be beneficial to shipping companies by allowing them to advertise as environmental friendly conveyors.

Human impacts on pig frog (Rana grylio) populations in south Florida wetlands: Harvest, water management and mercury contamination

This study investigated how harvest and water management affected the ecology of the Pig Frog, Rana grylio. It also examined how mercury levels in leg muscle tissue vary spatially across the Everglades. Rana grylio is an intermediate link in the Everglades food web. Although common, this inconspicuous species can be affected by three forms of anthropogenic disturbance: harvest, water management and mercury contamination. This frog is harvested both commercially and recreationally for its legs, is aquatic and thus may be susceptible to water management practices, and can transfer mercury throughout the Everglades food web. ^ This two-year study took place in three major regions: Everglades National Park (ENP), Water Conservation Areas 3A (A), and Water Conservation Area 3B (B). The study categorized the three sites by their relative harvest level and hydroperiod. During the spring of 2001, areas of the Everglades dried completely. On a regional and local scale Pig Frog abundance was highest in Site A, the longest hydroperiod, heavily harvested site, followed by ENP and B. More frogs were found along survey transects and in capture-recapture plots before the dry-down than after the dry-down in Sites ENP and B. Individual growth patterns were similar across all sites, suggesting differences in body size may be due to selective harvest. Frogs from Site A, the flooded and harvested site, had no differences in survival rates between adults and juveniles. Site B populations shifted from a juvenile to adult dominated population after the dry-down. Dry-downs appeared to affect survival rates more than harvest. ^ Total mercury in frog leg tissue was highest in protected areas of Everglades National Park with a maximum concentration of 2.3 mg/kg wet mass where harvesting is prohibited. Similar spatial patterns in mercury levels were found among pig frogs and other wildlife throughout parts of the Everglades. Pig Frogs may be transferring substantial levels of mercury to other wildlife species in ENP. ^ In summary, although it was found that abundance and survival were reduced by dry-down, lack of adult size classes in Site A, suggest harvest also plays a role in regulating population structure. ^

Measurement of carotenoid levels in human serum and a catalog of the lutein conformation populations from semi-empirical calculations

Lutein is a principal constituent of the human macular pigment. This study is composed of two projects. The first studies the conformational geometries of lutein and its potential adaptability in biological systems. The second is a study of the response of human subjects to lutein supplements. Using semi-empirical parametric method 3 (PM3) and density functional theory with the B3LYP/6-31G* basis set, the relative energies of s- cis conformers of lutein were determined. All 512 s-cis conformers were calculated with PM3. A smaller, representative group was also studied using density functional theory. PM3 results were correlated systematically to B3LYP values and this enables the results to be calibrated. The relative energies of the conformers range from 1-30 kcal/mole, and many are dynamically accessible at normal temperatures. Four commercial formulations containing lutein were studied. The serum and macular pigment (MP) responses of human subjects to these lutein supplements with doses of 9 or 20 mg/day were measured, relative to a placebo, over a six month period. In each instance, lutein levels in serum increased and correlated with MP increases. The results demonstrate that responses are significantly dependent upon formulation and that components other than lutein have an important influence serum response.

Molecular markers and human history: A tale of two haplogroup systems

To chronicle demographic movement across African Asian corridors, a variety of molecular (sequence analysis, restriction mapping and denaturing high performance liquid chromatography etc.) and statistical (correspondence analysis, AMOVA, calculation of diversity indices and phylogenetic inference, etc.) techniques were employed to assess the phylogeographic patterns of mtDNA control region and Y chromosomal variation among 14 sub-Saharan, North African and Middle Eastern populations. The patterns of genetic diversity revealed evidence of multiple migrations across several African Asian passageways as well within the African continent itself. The two-part analysis uncovered several interesting results which include the following: (1) a north (Egypt and Middle East Asia) to south (sub-Saharan Africa) partitioning of both mtDNA and Y chromosomal haplogroup diversity, (2) a genetic diversity gradient in sub-Saharan Africa from east to west, (3) evidence in favor of the Levantine Corridor over the Horn of Africa as the major genetic conduit since the Last Glacial Maximum, (4) a substantially higher mtDNA versus Y chromosomal sub-Saharan component in the Middle East collections, (5) a higher representation of East versus West African mtDNA haplotypes in the Arabian Peninsula populations versus no such bias in the Levant groups and lastly, (6) genetic remnants of the Bantu demographic expansion in sub-Saharan Africa. ^

Comparison of medical and forensic profiling potential of volatile biomarkers from different biological specimens from individuals and across populations

There is limited scientific knowledge on the composition of human odor from different biological specimens and the effect that physiological and psychological health conditions could have on them. There is currently no direct comparison of the volatile organic compounds (VOCs) emanating from different biological specimens collected from healthy individuals as well as individuals with certain diagnosed medical conditions. Therefore the question of matching VOCs present in human odor across various biological samples and across health statuses remains unanswered. The main purpose of this study was to use analytical instrumental methods to compare the VOCs from different biological specimens from the same individual and to compare the populations evaluated in this project. The goals of this study were to utilize headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME-GC/MS) to evaluate its potential for profiling VOCs from specimens collected using standard forensic and medical methods over three different populations: healthy group with no diagnosed medical or psychological condition, one group with diagnosed type 2 diabetes, and one group with diagnosed major depressive disorder. The pre-treatment methods of collection materials developed for the study allowed for the removal of targeted VOCs from the sampling kits prior to sampling, extraction and analysis. Optimized SPME-GC/MS conditions has been demonstrated to be capable of sampling, identifying and differentiating the VOCs present in the five biological specimens collected from different subjects and yielded excellent detection limits for the VOCs from buccal swab, breath, blood, and urine with average limits of detection of 8.3 ng. Visual, Spearman rank correlation, and PCA comparisons of the most abundant and frequent VOCs from each specimen demonstrated that each specimen has characteristic VOCs that allow them to be differentiated for both healthy and diseased individuals. Preliminary comparisons of VOC profiles of healthy individuals, patients with type 2 diabetes, and patients with major depressive disorder revealed compounds that could be used as potential biomarkers to differentiate between healthy and diseased individuals. Finally, a human biological specimen compound database has been created compiling the volatile compounds present in the emanations of human hand odor, oral fluids, breath, blood, and urine.

Human Security and Crime in Latin America: The political Capital and Political Impact of Criminal Groups and Belligerents Involved in Illicit Economies

Organized crime and illegal economies generate multiple threats to states and societies. But although the negative effects of high levels of pervasive street and organized crime on human security are clear, the relationships between human security, crime, illicit economies, and law enforcement are highly complex. By sponsoring illicit economies in areas of state weakness where legal economic opportunities and public goods are seriously lacking, both belligerent and criminal groups frequently enhance some elements of human security of the marginalized populations who depend on illicit economies for basic livelihoods. Even criminal groups without a political ideology often have an important political impact on the lives of communities and on their allegiance to the State. Criminal groups also have political agendas. Both belligerent and criminal groups can develop political capital through their sponsorship of illicit economies. The extent of their political capital is dependent on several factors. Efforts to defeat belligerent groups by decreasing their financial flows through suppression of an illicit economy are rarely effective. Such measures, in turn, increase the political capital of anti-State groups. The effectiveness of anti-money laundering measures (AML) also remains low and is often highly contingent on specific vulnerabilities of the target. The design of AML measures has other effects, such as on the size of a country’s informal economy. Multifaceted anti-crime strategies that combine law enforcement approaches with targeted socio-economic policies and efforts to improve public goods provision, including access to justice, are likely to be more effective in suppressing crime than tough nailed-fist approaches. For anti-crime policies to be effective, they often require a substantial, but politically-difficult concentration of resources in target areas. In the absence of effective law enforcement capacity, legalization and decriminalization policies of illicit economies are unlikely on their own to substantially reduce levels of criminality or to eliminate organized crime. Effective police reform, for several decades largely elusive in Latin America, is one of the most urgently needed policy reforms in the region. Such efforts need to be coupled with fundamental judicial and correctional systems reforms. Yet, regional approaches cannot obliterate the so-called balloon effect. If demand persists, even under intense law enforcement pressures, illicit economies will relocate to areas of weakest law enforcement, but they will not be eliminated.

Multiparameter flow cytometric analysis of C -reactive protein binding to human-derived cell lines and peripheral blood monocytes

C-reactive protein (CRP), a normally occurring human plasma protein may become elevated as much as 1,000 fold during disease states involving acute inflammation or tissue damage. Through its binding to phosphorylcholine in the presence of calcium, CRP has been shown to potentiate the activation of complement, stimulate phagocytosis and opsonize certain microorganisms. Utilizing a flow cytometric functional ligand binding assay I have demonstrated that a monocyte population in human peripheral blood and specific human-derived myelomonocytic cell lines reproducibly bind an evolutionarily conserved conformational pentraxin epitope on human CRP through a mechanism that does not involve its ligand, phosphorylcholine. ^ A variety of cell lines at different stages of differentiation were examined. The monocytic cell line, THP-1, bound the most CRP followed by U937 and KG-1a cells. The HL-60 cell line was induced towards either the granulocyte or monocyte pathway with DMSO or PMA, respectively. Untreated HL-60 cells or DMSO-treated cells did not bind CRP while cells treated with PMA showed increased binding of CRP, similar to U-937 cells. T cell and B-cell derived lines were negative. ^ Inhibition studies with Limulin and human SAP demonstrated that the binding site is a conserved pentraxin epitope. The calcium requirement necessary for binding to occur indicated that the cells recognize a conformational form of CRP. Phosphorylcholine did not inhibit the reaction therefore the possibility that CRP had bound to damaged membranes with exposed PC sites was discounted. ^ A study of 81 normal donors using flow cytometry demonstrated that a majority of peripheral blood monocytes (67.9 ± 1.3, mean ± sem) bound CRP. The percentage of binding was normally distributed and not affected by gender, age or ethnicity. Whole blood obtained from donors representing a variety of disease states showed a significant reduction in the level of CRP bound by monocytes in those donors classified with infection, inflammation or cancer. This reduction in monocyte populations binding CRP did not correlate with the concentration of plasma CRP. ^ The ability of monocytes to specifically bind CRP combined with the binding reactivity of the protein itself to a variety of phosphorylcholine containing substances may represent an important bridge between innate and adaptive immunity. ^

Effects of invasive Africanized honey bees (Apis mellifera scutellata) on native stingless bee populations (Meliponinae) and traditional Mayan beekeeping in central Quintana Roo, Mexico

The Maya of the Yucatan region have a long history of keeping the native stingless bees (subfamily Meliponinae). However, market forces in the last few decades have driven the Maya to favor the use of invasive Africanized honey bees (Apis mellifera scutellata) for producing large quantities of high quality honey that has an international market. Furthermore, the native bees traditionally used by the Maya are now disappearing, along with the practice of keeping them. ^ An interdisciplinary approach was taken in order to determine the social factors behind the decrease in stingless beekeeping and the ecological driving forces behind their disappearance from the wild. Social research methods included participant observation with stingless beekeepers, Apis beekeepers, and marketing intermediaries. Ecological research methods included point observations of commonly known melliferous and polliniferous plants along transects in three communities with different degrees of human induced ecosystem disturbance. ^ The stingless bee species most important to the Maya, Melipona beecheii, has become extremely rare, and this has caused a breakdown of stingless beekeeping tradition, compounded with the pressure of the market economy, which fuels Apis beekeeping and has lessened the influence of traditional practices. The community with the heaviest amount of human induced ecosystem disturbance also had the highest degree of dominance of Apis mellifera, while the area with the most intact ecosystem had the highest diversity of stingless bees, though Apis mellifera was still the dominant species. Aggressive competitive behavior involving physical attacks by Apis mellifera against stingless bees was observed on several occasions, and this is a new observation previously unreported by science. ^

D1S80 DNA profiling in five African populations

The highly polymorphic DlS80 locus has no known genetic function. This variable number of tandem repeat (VNTR) has been valuable in forensic identification. We have obtained allelic and genotypic frequencies for five African populations (Benin, Cameroon, Egypt, Kenya and Rwanda), which could be employed as databases to identify individuals. The polymerase chain reaction, followed by vertical polyacrylamide gel electrophoresis and silver staining was our method of analysis. Allele frequencies were used to infer genetic associations using Phylip 3.5, Principal Component and G-test statistical programs. Tests for Hardy-Weinberg equilibrium were employed. Fst estimates and power of discrimination values were also determined for each of our populations. Our analyses of 28 additional populations demonstrated that the D1 S80 locus alone provided for the discrimination of major racial groups. Genetic homogeneity between the African groups was observed. We have generated a database useful for human differentiation and phylogenetic studies.