Intra-population variation and geographic correlation in Canthon humectus hidalgoensis using FTIR-ATR spectroscopy

In some cases external morphology is not sufficient to discern between populations of a species, as occurs in the dung beetle Canthon humectus hidalgoensis Bates; and much less to determine phenotypic distances between them. FTIR-ATR spectroscopy show several advantages over other identification techniques (e.g. morphological, genetic, and cuticular hydrocarbons analysis) due to the non-invasive manner of the sample preparation, the relative speed of sample analysis and the low-cost of this technology. The infrared spectrum obtained is recognized to give a unique ‘fingerprint’ because vibrational spectra are specific and unique to the molecular nature of the sample. In our study, results showed that proteins, amino acids and aromatic ethers of insect exocuticle have promising discriminative power to discern between different populations of C. h. hidalgoensis. Furthermore, the correlation between geographic distances between populations and the chemical distances obtained by proteins + amino acids + aromatic ethers was statistically significant, showing that the spectral and spatial information available of the taxa together with appropriated chemometric methods may help to a better understanding of the identity, structure, dynamics and diversity of insect populations.

Chronic disease, geographic location and socioeconomic disadvantage as obstacles to equitable access to e-health

Despite recent public attention to e-health as a solution to rising healthcare costs and an ageingpopulation, there have been relatively few studies examining the geographical pattern of e-health usage. This paper argues for an equitable approach to e-health and attention to the way in which e-health initiatives can produce locational health inequalities, particularly in socioeconomically disadvantaged areas. In this paper, we use a case study to demonstrate geographical variation in Internet accessibility, Internet status and prevalence of chronic diseases within a small district. There are signifi cant disparities in access to health information within socioeconomically disadvantaged areas. The most vulnerable people in these areas are likely to have limited availability of, or access to Internet healthcare resources. They are also more likely to have complex chronic diseases and, therefore, be in greatest need of these resources. This case study demonstrates the importance of an equitable approach to e-health information technologies and telecommunications infrastructure.

Geographic remoteness, area-level socioeconomic disadvantage and inequalities in colorectal cancer survival in Queensland : a multilevel analysis

Background To explore the impact of geographical remoteness and area-level socioeconomic disadvantage on colorectal cancer (CRC) survival. Methods Multilevel logistic regression and Markov chain Monte Carlo simulations were used to analyze geographical variations in five-year all-cause and CRC-specific survival across 478 regions in Queensland Australia for 22,727 CRC cases aged 20–84 years diagnosed from 1997–2007. Results Area-level disadvantage and geographic remoteness were independently associated with CRC survival. After full multivariate adjustment (both levels), patients from remote (odds Ratio [OR]: 1.24, 95%CrI: 1.07-1.42) and more disadvantaged quintiles (OR = 1.12, 1.15, 1.20, 1.23 for Quintiles 4, 3, 2 and 1 respectively) had lower CRC-specific survival than major cities and least disadvantaged areas. Similar associations were found for all-cause survival. Area disadvantage accounted for a substantial amount of the all-cause variation between areas. Conclusions We have demonstrated that the area-level inequalities in survival of colorectal cancer patients cannot be explained by the measured individual-level characteristics of the patients or their cancer and remain after adjusting for cancer stage. Further research is urgently needed to clarify the factors that underlie the survival differences, including the importance of geographical differences in clinical management of CRC.

Understanding past climate variation and environmental change for the future of an iconic landscape – K'gari Fraser Island, Queensland, Australia

The unique combination of landscapes and processes that are present and operate on Fraser Island (K'gari) create a dynamic setting that is capable of recording past environmental events, climate variations and former landscapes. Likewise, its geographic position makes Fraser Island sensitive to those events and processes. Based on optically stimulated luminescence dating, the records archived within the world's largest sand island span a period that has the potential to exceed 750 ka and contain specific records that are of extremely high resolution over the past 40,000 years. This is due to the geographic position of Fraser Island, which lies in the coastal subtropical region of Queensland Australia. Fraser Island is exposed to the open ocean currents of the Coral Sea on the east coast and the waters of Hervey Bay on its western margin and is positioned to receive moisture from the Indo-Australian monsoon, southeast trade winds and experiences occasional tropical and ex-tropical cyclones. We review literature that presents the current level of understanding of sea level change, ecological variation and environmental change on Fraser Island. The previous works illustrate the importance of Fraser Island and may link processes, environments and climates on Fraser Island with global records.

Resampling-based approaches to study variation in morphological modularity

Modularity has been suggested to be connected to evolvability because a higher degree of independence among parts allows them to evolve as separate units. Recently, the Escoufier RV coefficient has been proposed as a measure of the degree of integration between modules in multivariate morphometric datasets. However, it has been shown, using randomly simulated datasets, that the value of the RV coefficient depends on sample size. Also, so far there is no statistical test for the difference in the RV coefficient between a priori defined groups of observations. Here, we (1), using a rarefaction analysis, show that the value of the RV coefficient depends on sample size also in real geometric morphometric datasets; (2) propose a permutation procedure to test for the difference in the RV coefficient between a priori defined groups of observations; (3) show, through simulations, that such a permutation procedure has an appropriate Type I error; (4) suggest that a rarefaction procedure could be used to obtain sample-size-corrected values of the RV coefficient; and (5) propose a nearest-neighbor procedure that could be used when studying the variation of modularity in geographic space. The approaches outlined here, readily extendable to non-morphometric datasets, allow study of the variation in the degree of integration between a priori defined modules. A Java application – that will allow performance of the proposed test using a software with graphical user interface – has also been developed and is available at the Morphometrics at Stony Brook Web page (http://life.bio.sunysb.edu/morph/).

Pharmacogenetic Variation at CYP2D6, CYP2C9, and CYP2C19: Population Genetic and Forensic Aspects

Pharmacogenetics deals with genetically determined variation in drug response. In this context, three phase I drug-metabolizing enzymes, CYP2D6, CYP2C9, and CYP2C19, have a central role, affecting the metabolism of about 20-30% of clinically used drugs. Since genes coding for these enzymes in human populations exhibit high genetic polymorphism, they are of major pharmacogenetic importance. The aims of this study were to develop new genotyping methods for CYP2D6, CYP2C9, and CYP2C19 that would cover the most important genetic variants altering the enzyme activity, and, for the first time, to describe the distribution of genetic variation at these loci on global and microgeographic scales. In addition, pharmacogenetics was applied to a postmortem forensic setting to elucidate the role of genetic variation in drug intoxications, focusing mainly on cases related to tricyclic antidepressants, which are commonly involved in fatal drug poisonings in Finland. Genetic variability data were obtained by genotyping new population samples by the methods developed based on PCR and multiplex single-nucleotide primer extension reaction, as well as by collecting data from the literature. Data consisted of 138, 129, and 146 population samples for CYP2D6, CYP2C9, and CYP2C19, respectively. In addition, over 200 postmortem forensic cases were examined with respect to drug and metabolite concentrations and genotypic variation at CYP2D6 and CYP2C19. The distribution of genetic variation within and among human populations was analyzed by descriptive statistics and variance analysis and by correlating the genetic and geographic distances using Mantel tests and spatial autocorrelation. The correlation between phenotypic and genotypic variation in drug metabolism observed in postmortem cases was also analyzed statistically. The genotyping methods developed proved to be informative, technically feasible, and cost-effective. Detailed molecular analysis of CYP2D6 genetic variation in a global survey of human populations revealed that the pattern of variation was similar to those of neutral genomic markers. Most of the CYP2D6 diversity was observed within populations, and the spatial pattern of variation was best described as clinal. On the other hand, genetic variants of CYP2D6, CYP2C9, and CYP2C19 associated with altered enzymatic activity could reach extremely high frequencies in certain geographic regions. Pharmacogenetic variation may also be significantly affected by population-specific demographic histories, as seen within the Finnish population. When pharmacogenetics was applied to a postmortem forensic setting, a correlation between amitriptyline metabolic ratios and genetic variation at CYP2D6 and CYP2C19 was observed in the sample material, even in the presence of confounding factors typical for these cases. In addition, a case of doxepin-related fatal poisoning was shown to be associated with a genetic defect at CYP2D6. Each of the genes studied showed a distinct variation pattern in human populations and high frequencies of altered activity variants, which may reflect the neutral evolution and/or selective pressures caused by dietary or environmental exposure. The results are relevant also from the clinical point of view since the genetic variation at CYP2D6, CYP2C9, and CYP2C19 already has a range of clinical applications, e.g. in cancer treatment and oral anticoagulation therapy. This study revealed that pharmacogenetics may also contribute valuable information to the medicolegal investigation of sudden, unexpected deaths.

Natural variation and Biogeography of the melon fruit fly, Zeugodacus cucurbitae (Diptera : Tephritidae), in Southeast-Asia and the west-pacific

This thesis used multidisciplinary approaches which greatly enhance our understanding of population structure and can be particularly powerful tools for resolving variation of melon fly over geographic and temporal scales, and for determining invasive pathways. The results from this thesis reinforce the value of integrating multiple data sets to better understand and resolve natural variation within an important pest to determine whether there are cryptic species, discrete lineages or host races, and to identify dispersal pathways in an invasive pest. These results are instructive for regional biosecurity, trade and quarantine, and provide important background for future area-wide management programmes. The integrative methodology adopted in this thesis is applicable to a variety of other insect pests.

Genetic Variation and Clinical Manifestations in Inflammatory Bowel Disease

Crohn s disease (CD) and ulcerative colitis (UC), collectively known as inflammatory bowel disease (IBD), are characterised by chronic inflammation of the gastrointestinal tract. IBD prevalence in Finland is approximately 3-4 per 1000 inhabitants with a peak incidence in adolescence. The symptoms of IBD include diarrhoea, abdominal pain, fever, and weight loss. The precise aetiology of IBD is unknown but interplay of environmental risk factors and immunologic changes trigger the disease in a genetically susceptible individual. Twin and family studies have provided strong evidence for genetic factors in IBD susceptibility, and genetic factors may be more prominent in CD than UC. The first CD susceptibility gene was identified in 2001. Three common mutations R702W, G908R, and 1007fs of the CARD15/NOD2 gene are shown to associate independently with CD but the magnitude of association varies between different populations. The present study aimed at identifying mutations and genetic variations in IBD susceptibility and candidate genes. In addition, correlation to phenotype was also assessed. One of the main objectives of this study was to evaluate the role of CARD15 in a Finnish CD cohort. 271 CD patients were studied for the three common mutations and the results showed a lower mutation frequency than in other Caucasian populations. Only 16% of the patients carried one of the three mutations. Ileal location as well as stricturing and penetrating behaviour of the disease were associated with occurrence of the mutations. The whole protein coding region of CARD15 was screened for possible Finnish founder mutations. In addition to several sequence variants, five novel mutations (R38M, W355X, P727L, W907R, and R1019X) were identified in five patients. Functional consequences of these novel variants were studied in vitro, and these studies demonstrated a profound impairment of MDP response. Investigation of CARD15 mutation frequency in healthy people across three continents showed a large geographic fluctuation. No simple correlation between mutation frequency and disease incidence was seen in populations studied. The occurrence of double mutant carriers in healthy controls suggested that the penetrance of risk alleles is low. Other main objectives aimed at identifying other genetic variations that are involved in the susceptibility to IBD. We investigated the most plausible IBD candidate genes including TRAF6, SLC22A4, SLC22A5, DLG5, TLR4, TNFRSF1A, ABCB1/MDR1, IL23R, and ATG16L1. The marker for a chromosome 5 risk haplotype and the rare HLA-DRB1*0103 allele were also studied. The study cohort consisted of 699 IBD patients (240 CD and 459 UC), of which 23% had a first-degree relative with IBD. Of the several candidate genes studied, IL23R was associated with CD susceptibility, and TNFRSF1A as well as the HLA-DRB1*0103 allele with UC susceptibility. IL23R variants also showed association with the stricturing phenotype and longer disease duration in CD patients. In addition, TNFRSF1A variants were more common among familial UC and ileocolonic CD. In conclusion, the common CARD15 mutations were shown to account for 16% of CD cases in Finland. Novel CARD15 variants identified in the present study are most likely disease-causing mutations, as judged by the results of in vitro studies. The present study also confirms the IL23R association with CD susceptibility and, in addition, TNFRSF1A and HLA-DRB1*0103 allele association with UC of specific clinical phenotypes.

Seismic Hazard and Microzonation Studies using Geographic Information System - A Case Study of Bangalore city

Seismic hazard and microzonation of cities enable to characterize the potential seismic areas that need to be taken into account when designing new structures or retrofitting the existing ones. Study of seismic hazard and preparation of geotechnical microzonation maps has been attempted using Geographical Information System (GIS). GIS will provide an effective solution for integrating different layers of information thus providing a useful input for city planning and in particular input to earthquake resistant design of structures in an area. Seismic hazard is the study of expected earthquake ground motions at any point on the earth. Microzonation is the process of sub division of region in to number of zones based on the earthquake effects in the local scale. Seismic microzonation is the process of estimating response of soil layers under earthquake excitation and thus the variation of ground motion characteristic on the ground surface. For the seismic microzonation, geotechnical site characterization need to be assessed at local scale (micro level), which is further used to assess of the site response and liquefaction susceptibility of the sites. Seismotectonic atlas of the area having a radius of 350km around Bangalore has been prepared with all the seismogenic sources and historic earthquake events (a catalogue of about 1400 events since 1906). We have attempted to carryout the site characterization of Bangalore by collating conventional geotechnical boreholes data (about 900 borehole data with depth) and integrated in GIS. 3-D subsurface model of Bangalore prepared using GIS is shown in Figure 1.Further, Shear wave velocity survey based on geophysical method at about 60 locations in the city has been carried out in 220 square Kms area. Site response and local site effects have been evaluated using 1-dimensional ground response analysis. Spatial variability of soil overburden depths, ground surface Peak Ground Acceleration’s(PGA), spectral acceleration for different frequencies, liquefaction susceptibility have been mapped in the 220 sq km area using GIS.ArcInfo software has been used for this purpose. These maps can be used for the city planning and risk & vulnerability studies. Figure 2 shows a map of peak ground acceleration at rock level for Bangalore city. Microtremor experiments were jointly carried out with NGRI scientists at about 55 locations in the city and the predominant frequency of the overburden soil columns were evaluated.

Variation at Diabetes- and Obesity-Associated Loci May Mirror Neutral Patterns of Human Population Diversity and Diabetes Prevalence in India

South Asian populations harbor a high degree of genetic diversity, due in part to demographic history. Two studies on genome-wide variation in Indian populations have shown that most Indian populations show varying degrees of admixture between ancestral north Indian and ancestral south Indian components. As a result of this structure, genetic variation in India appears to follow a geographic cline. Similarly, Indian populations seem to show detectable differences in diabetes and obesity prevalence between different geographic regions of the country. We tested the hypothesis that genetic variation at diabetes-and obesity-associated loci may be potentially related to different genetic ancestries. We genotyped 2977 individuals from 61 populations across India for 18 SNPs in genes implicated in T2D and obesity. We examined patterns of variation in allele frequency across different geographical gradients and considered state of origin and language affiliation. Our results show that most of the 18 SNPs show no significant correlation with latitude, the geographic cline reported in previous studies, or by language family. Exceptions include KCNQ1 with latitude and THADA and JAK1 with language, which suggests that genetic variation at previously ascertained diabetes-associated loci may only partly mirror geographic patterns of genome-wide diversity in Indian populations.

Meristic variation in Sebastes (Scorpaenidae), with an analysis of character association and bilateral pattern and their significance in species separation

This report presents meristic data for nearly all of the known species of Sebasles. Rudimentary caudal ray counts tend to be higher in more active species. The number of caudal rays supported by the hypurals is consistently 14, whereas the number of branched caudal rays varies between 11 and 13. Vertebral counts and most fin-ray counts tend to be lower in species or populations in warmer latitudes, except for pectoral ray counts which tend to have an opposite geographic pattern. On the basis of the small magnitude of meristic and morphometric differences and the lack of other differences between northern and southern samples of "Sebasles caurinus," Sebaslichlhys vexillaris Jordan and Gilbert is regarded as a junior synonym of Sebasles caurinus Richardson. The patterns of bilateral variation in paired meristics are analyzed and their mechanism discussed. The frequency distribution of pectoral ray counts in their right-left combination is shown to be useful in species separation. No association was found between any combination of two meristic features in any species. The author proposes that intrasample associations between meristic features are evidence of sampling heterogeneity. (PDF file contains 21 pages.)

Variation in the isotopic signatures of juvenile gray snapper (Lutjanus griseus) from five southern Florida region

Measurements of 18O/16O and 13C/12C ratios in the carbonate of juvenile gray snapper (Lutjanus griseus) sagittal otoliths collected during 2001–2005 from different southern Florida regions indicated significant variations in the ratios between Florida Bay and surrounding areas. Annual differences in isotopic composition were also observed. Classification accuracy of individual otoliths to a region averaged 80% (63% to 96%), thereby enabling the probability of assigning an unknown individual to the appropriate juvenile nursery habitat. Identification of isotopic signatures in the otoliths of gray snapper from Florida Bay and adjacent ecosystems may be important for distinguishing specific portions of the bay that are crucial nursery grounds for juveniles. Separation of gray snapper between geographic regions and nursery sites is possible and has the potential to establish a link between adult gray snapper present on offshore reefs and larvae and juveniles at nursery habitats in Florida Bay or adjacent areas.

Genetic variation of rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (S. borealis) inferred from allozymes

Rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (Sebastes borealis) were collected from the Washington coast, the Gulf of Alaska, the southern Bering Sea, and the eastern Kamchatka coast of Russia (areas encompassing most of their geographic distribution) for population genetic analyses. Using starch gel electrophoresis, we analyzed 1027 rougheye rockfish and 615 shortraker rockfish for variation at 29 proteincoding loci. No genetic heterogeneity was found among shortraker rockfish throughout the sampled regions, although shortraker in the Aleutian Islands region, captured at deeper depths, were found to be significantly smaller in size than the shortraker caught in shallower waters from Southeast Alaska. Genetic analysis of the rougheye rockfish revealed two evolutionary lineages that exist in sympatry with little or no gene f low between them. When analyzed as two distinct species, neither lineage exhibited heterogeneity among regions. Sebastes aleutianus seems to inhabit waters throughout the Gulf of Alaska and more southern waters, whereas S. sp. cf. aleutianus inhabits waters throughout the Gulf of Alaska, Aleutian Islands, and Asia. The distribution of the two rougheye rockfish lineages may be related to depth where they are sympatric. The paler color morph, S. aleutianus, is found more abundantly in shallower waters and the darker color morph, Sebastes sp. cf. aleutianus, inhabits deeper waters. Sebastes sp. cf. aleutianus, also exhibited a significantly higher prevalence of two parasites, N. robusta and T. trituba, than did Sebastes aleutianus, in the 2001 samples, indicating a possible difference in habitat and (or) resource use between the two lineages.

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Scales of spatial variation in demography of a large coral-reef fish: an exception to the typical model?

Spatial variation in demographic parameters of the red throat emperor (Lethrinus miniatus) was examined among 12 coral reefs in three geographic regions (Townsville, Mackay, and Storm Cay) spanning over 3° of latitude of the Great Barrier Reef, Australia. Estimates of demographic parameters were based on age estimates from counts of annuli in whole otoliths because there was no significant difference in age estimates between whole and sectioned otoliths. There were significant regional differences in age structures, rates of somatic and otolith growth, and total mortality. The Townsville region was characterized by the greatest proportion of older fish, the smallest maximum size, and the lowest rates of otolith growth and total mortality. In contrast the Mackay region was characterized by the highest proportion of younger fish, the largest maximum size, and the highest rates of otolith growth and total mortality. Demographic parameters for the Storm Cay region were intermediate between the other two regions. Historic differences in fishing pressure and regional differences in productivity are two alternative hypotheses given to explain the regional patterns in demographic parameters. All demographic parameters were similar among the four reefs within each region. Thus, subpopulations with relatively homogeneous demographic parameters occurred on scales of reef clusters. Previous studies, by contrast, have found substantial between-reef variation in demographic parameters within regions. Thus spatial variation in demographic parameters for L. miniatus may differ from what is assumed typical for a coral-reef fish metapopulation.