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1.  Psychoactive substances and the political ecology of mental distress 
The goal of this paper is to both understand and depathologize clinically significant mental distress related to criminalized contact with psychoactive biotic substances by employing a framework known as critical political ecology of health and disease from the subdiscipline of medical geography. The political ecology of disease framework joins disease ecology with the power-calculus of political economy and calls for situating health-related phenomena in their broad social and economic context, demonstrating how large-scale global processes are at work at the local level, and giving due attention to historical analysis in understanding the relevant human-environment relations. Critical approaches to the political ecology of health and disease have the potential to incorporate ever-broadening social, political, economic, and cultural factors to challenge traditional causes, definitions, and sociomedical understandings of disease. Inspired by the patient-centered medical diagnosis critiques in medical geography, this paper will use a critical political ecology of disease approach to challenge certain prevailing sociomedical interpretations of disease, or more specifically, mental disorder, found in the field of substance abuse diagnostics and the related American punitive public policy regimes of substance abuse prevention and control, with regards to the use of biotic substances. It will do this by first critically interrogating the concept of "substances" and grounding them in an ecological context, reviewing the history of both the development of modern substance control laws and modern substance abuse diagnostics, and understanding the biogeographic dimensions of such approaches. It closes with proposing a non-criminalizing public health approach for regulating human close contact with psychoactive substances using the example of cannabis use.
PMCID: PMC3278374  PMID: 22257499
2.  Neighbouring chimpanzee communities show different preferences in social grooming behaviour 
Grooming handclasp (GHC) behaviour was originally advocated as the first evidence of social culture in chimpanzees owing to the finding that some populations engaged in the behaviour and others do not. To date, however, the validity of this claim and the extent to which this social behaviour varies between groups is unclear. Here, we measured (i) variation, (ii) durability and (iii) expansion of the GHC behaviour in four chimpanzee communities that do not systematically differ in their genetic backgrounds and live in similar ecological environments. Ninety chimpanzees were studied for a total of 1029 h; 1394 GHC bouts were observed between 2010 and 2012. Critically, GHC style (defined by points of bodily contact) could be systematically linked to the chimpanzee's group identity, showed temporal consistency both within and between groups, and could not be accounted for by the arm-length differential between partners. GHC has been part of the behavioural repertoire of the chimpanzees under study for more than 9 years (surpassing durability criterion) and spread across generations (surpassing expansion criterion). These results strongly indicate that chimpanzees' social behaviour is not only motivated by innate predispositions and individual inclinations, but may also be partly cultural in nature.
PMCID: PMC3479803  PMID: 22933372
group differences; Pan troglodytes; grooming handclasp; traditions; Chimfunshi Wildlife Orphanage Trust; social culture
3.  Ecology and geography of hemorrhagic fever with renal syndrome in Changsha, China 
BMC Infectious Diseases  2013;13:305.
Hemorrhagic fever with renal syndrome (HFRS) is an important public health problem in mainland China. HFRS is particularly endemic in Changsha, the capital city of Hunan Province, with one of the highest incidences in China. The occurrence of HFRS is influenced by environmental factors. However, few studies have examined the relationship between environmental variation (such as land use changes and climate variations), rodents and HFRS occurrence. The purpose of this study is to predict the distribution of HFRS and identify the risk factors and relationship between HFRS occurrence and rodent hosts, combining ecological modeling with the Markov chain Monte Carlo approach.
Ecological niche models (ENMs) were used to evaluate potential geographic distributions of rodent species by reconstructing details of their ecological niches in ecological dimensions, and projecting the results onto geography. The Genetic Algorithm for Rule-set Production was used to produce ENMs. Data were collected on HFRS cases in Changsha from 2005 to 2009, as well as national land survey data, surveillance data of rodents, meteorological data and normalized difference vegetation index (NDVI).
The highest occurrence of HFRS was in districts with strong temperature seasonality, where elevation is below 200 m, mean annual temperature is around 17.5°C, and annual precipitation is below 1600 mm. Cultivated and urban lands in particular are associated with HFRS occurrence. Monthly NDVI values of areas predicted present is lower than areas predicted absent, with high seasonal variation. The number of HFRS cases was correlated with rodent density, and the incidence of HFRS cases in urban and forest areas was mainly associated with the density of Rattus norvegicus and Apodemus agrarius, respectively.
Heterogeneity between different areas shows that HFRS occurrence is affected by the intensity of human activity, climate conditions, and landscape elements. Rodent density and species composition have significant impacts on the number of HFRS cases and their distribution.
PMCID: PMC3708768  PMID: 23819824
4.  The geography of recreational physical activity in England 
Health & place  2010;17(1):157-165.
Levels of physical activity have declined considerably over recent decades in England, and there is evidence that activity patterns vary across areas. Previous studies of the geography of physical activity have frequently relied on model based synthetic estimates. Using data from a large population survey this study develops a direct measure of recreational physical activity and investigates variations in activity patterns across English Local Authorities. For both sexes the results show a distinct geography of recreational physical activity associated with north/south variations and urban/rural status. The environmental and behavioural factors driving those patterns are still poorly understood. We conclude that the variations observed might reflect recreational opportunities and the socio-cultural context of areas.
PMCID: PMC3722549  PMID: 20934899
recreational physical activity; geographical variation; socio-demographics; urban-rural status; England
5.  Quantifying Effects of Environmental and Geographical Factors on Patterns of Genetic Differentiation 
Molecular ecology  2011;20(22):4631-4642.
Elucidating the factors influencing genetic differentiation is an important task in biology, and the relative contribution from natural selection and genetic drift has long been debated. In this study, we used a regression-based approach to simultaneously estimate the quantitative contributions of environmental adaptation and isolation by distance on genetic variation in Boechera stricta, a wild relative of Arabidopsis. Patterns of discrete and continuous genetic differentiation coexist within this species. For the discrete differentiation between two major genetic groups, environment has larger contribution than geography, and we also identified a significant environment-by-geography interaction effect. Elsewhere in the species range, we found a latitudinal cline of genetic variation reflecting only isolation by distance. To further confirm the effect of environmental selection on genetic divergence, we identified the specific environmental variables predicting local genotypes in allopatric and sympatric regions. Water availability was identified as the possible cause of differential local adaptation in both geographic regions, confirming the role of environmental adaptation in driving and maintaining genetic differentiation between the two major genetic groups. In addition, the environment-by-geography interaction is further confirmed by the finding that water availability is represented by different environmental factors in the allopatric and sympatric regions. In conclusion, this study found that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, which only produced a gradual, clinal pattern of genetic variation. These findings emphasize the importance of environmental selection in shaping patterns of species-wide genetic variation in the natural environment.
PMCID: PMC3204174  PMID: 21999331
Genetic variation; Environment; Geography; Niche modeling; Environmental adaptation
6.  Bonobos Fall within the Genomic Variation of Chimpanzees 
PLoS ONE  2011;6(6):e21605.
To gain insight into the patterns of genetic variation and evolutionary relationships within and between bonobos and chimpanzees, we sequenced 150,000 base pairs of nuclear DNA divided among 15 autosomal regions as well as the complete mitochondrial genomes from 20 bonobos and 58 chimpanzees. Except for western chimpanzees, we found poor genetic separation of chimpanzees based on sample locality. In contrast, bonobos consistently cluster together but fall as a group within the variation of chimpanzees for many of the regions. Thus, while chimpanzees retain genomic variation that predates bonobo-chimpanzee speciation, extensive lineage sorting has occurred within bonobos such that much of their genome traces its ancestry back to a single common ancestor that postdates their origin as a group separate from chimpanzees.
PMCID: PMC3126833  PMID: 21747915
7.  Genetics: A New Landscape for Medical Geography 
The emergence and re-emergence of human pathogens resistant to medical treatment will present a challenge to the international public health community in the coming decades. Geography is uniquely positioned to examine the progressive evolution of pathogens across space and through time, and to link molecular change to interactions between population and environmental drivers. Landscape as an organizing principle for the integration of natural and cultural forces has a long history in geography, and, more specifically, in medical geography. Here, we explore the role of landscape in medical geography, the emergent field of landscape genetics, and the great potential that exists in the combination of these two disciplines. We argue that landscape genetics can enhance medical geographic studies of local-level disease environments with quantitative tests of how human-environment interactions influence pathogenic characteristics. In turn, such analyses can expand theories of disease diffusion to the molecular scale and distinguish the important factors in ecologies of disease that drive genetic change of pathogens.
PMCID: PMC3928082  PMID: 24558292
medical geography; disease ecology; landscape genetics; pathogenic evolution
8.  Current themes and recent advances in modelling species occurrences 
Recent years have seen a huge expansion in the range of methods and approaches that are being used to predict species occurrences. This expansion has been accompanied by many improvements in statistical methods, including more accurate ways of comparing models, better null models, methods to cope with autocorrelation, and greater awareness of the importance of scale and prevalence. However, the field still suffers from problems with incorporating temporal variation, overfitted models and poor out-of-sample prediction, confusion between explanation and prediction, simplistic assumptions, and a focus on pattern over process. The greatest advances in recent years have come from integrative studies that have linked species occurrence models with other themes and topics in ecology, such as island biogeography, climate change, disease geography, and invasive species.
PMCID: PMC2948293  PMID: 20948597
9.  Functional analysis of human and chimpanzee promoters 
Genome Biology  2005;6(7):R57.
Twelve promoters of genes differentially expressed between humans and chimpanzees were tested for expression activity in culture cells. Seven promoters showed a significant difference in expression level between the human and chimpanzee promoter, but only three were in the same direction as the tissues, indicating that relevant expression differences between humans and chimpanzees will be difficult to predict from cell culture experiments or DNA sequences
It has long been argued that changes in gene expression may provide an additional and crucial perspective on the evolutionary differences between humans and chimpanzees. To investigate how often expression differences seen in tissues are caused by sequence differences in the proximal promoters, we tested the expression activity in cultured cells of human and chimpanzee promoters from genes that differ in mRNA expression between human and chimpanzee tissues.
Twelve promoters for which the corresponding gene had been shown to be differentially expressed between humans and chimpanzees in liver or brain were tested. Seven showed a significant difference in activity between the human promoter and the orthologous chimpanzee promoter in at least one of the two cell lines used. However, only three of them showed a difference in the same direction as in the tissues.
Differences in proximal promoter activity are likely to be common between humans and chimpanzees, but are not linked in a simple fashion to gene-expression levels in tissues. This suggests that several genetic differences between humans and chimpanzees might be responsible for a single expression difference and thus that relevant expression differences between humans and chimpanzees will be difficult to predict from cell culture experiments or DNA sequences.
PMCID: PMC1175988  PMID: 15998446
10.  Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations 
Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci.
For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection.
First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.
PMCID: PMC3049142  PMID: 21332997
11.  The Number of Cultural Traits Is Correlated with Female Group Size but Not with Male Group Size in Chimpanzee Communities 
PLoS ONE  2010;5(3):e9241.
What determines the number of cultural traits present in chimpanzee (Pan troglodytes) communities is poorly understood. In humans, theoretical models suggest that the frequency of cultural traits can be predicted by population size. In chimpanzees, however, females seem to have a particularly important role as cultural carriers. Female chimpanzees use tools more frequently than males. They also spend more time with their young, skewing the infants' potential for social learning towards their mothers. In Gombe, termite fishing has been shown to be transmitted from mother to offspring. Lastly, it is female chimpanzees that transfer between communities and thus have the possibility of bringing in novel cultural traits from other communities. From these observations we predicted that females are more important cultural carriers than males. Here we show that the reported number of cultural traits in chimpanzee communities correlates with the number of females in chimpanzee communities, but not with the number of males. Hence, our results suggest that females are the carriers of chimpanzee culture.
PMCID: PMC2844409  PMID: 20352086
12.  Biogeography and ecology: towards the integration of two disciplines 
Although ecology and biogeography had common origins in the natural history of the nineteenth century, they diverged substantially during the early twentieth century as ecology became increasingly hypothesis-driven and experimental. This mechanistic focus narrowed ecology's purview to local scales of time and space, and mostly excluded large-scale phenomena and historical explanations. In parallel, biogeography became more analytical with the acceptance of plate tectonics and the development of phylogenetic systematics, and began to pay more attention to ecological factors that influence large-scale distributions. This trend towards unification exposed problems with terms such as ‘community’ and ‘niche,’ in part because ecologists began to view ecological communities as open systems within the contexts of history and geography. The papers in this issue represent biogeographic and ecological perspectives and address the general themes of (i) the niche, (ii) comparative ecology and macroecology, (iii) community assembly, and (iv) diversity. The integration of ecology and biogeography clearly is a natural undertaking that is based on evolutionary biology, has developed its own momentum, and which promises novel, synthetic approaches to investigating ecological systems and their variation over the surface of the Earth. We offer suggestions on future research directions at the intersection of biogeography and ecology.
PMCID: PMC3130436  PMID: 21768158
history; macroecology; niche; phylogeny; regional community; species sorting
13.  Emulation, imitation, over-imitation and the scope of culture for child and chimpanzee 
We describe our recent studies of imitation and cultural transmission in chimpanzees and children, which question late twentieth-century characterizations of children as imitators, but chimpanzees as emulators. As emulation entails learning only about the results of others' actions, it has been thought to curtail any capacity to sustain cultures. Recent chimpanzee diffusion experiments have by contrast documented a significant capacity for copying local behavioural traditions. Additionally, in recent ‘ghost’ experiments with no model visible, chimpanzees failed to replicate the object movements on which emulation is supposed to focus. We conclude that chimpanzees rely more on imitation and have greater cultural capacities than previously acknowledged. However, we also find that they selectively apply a range of social learning processes that include emulation. Recent studies demonstrating surprisingly unselective ‘over-imitation’ in children suggest that children's propensity to imitate has been underestimated too. We discuss the implications of these developments for the nature of social learning and culture in the two species. Finally, our new experiments directly address cumulative cultural learning. Initial results demonstrate a relative conservatism and conformity in chimpanzees' learning, contrasting with cumulative cultural learning in young children. This difference may contribute much to the contrast in these species' capacities for cultural evolution.
PMCID: PMC2865074  PMID: 19620112
imitation; emulation; social learning; cultural transmission; cumulative culture; chimpanzees
14.  Comparative physical and immunological aspects of the chimpanzee and guinea-pig subcutaneous chamber models of Neisseria gonorrhoeae infection. 
Physical and immunological characteristics of the chimpanzee and guinea-pig subcutaneous chamber models for Neisseria gonorrhoeae infection were compared to evaluate their usefulness for gonococcal research. Urethral infection in chimpanzees anatomically resembled the human infection; however, individual variation in response, limited availability, and the presence of interfering micro-organisms in the urethra were found to limit the usefulness of the chimpanzee in immunological research. Although the guinea-pig subcutaneous chamber model may not be suitable for studying the attachment of gonococci to host cells or for the local production of IgA, it does have the immunological advantages of being more sensitive to infection, less variable in response, free of interfering micro-organisms, and is readily available to investigators. Except for differences in sensitivity and variability, results with the guinea-pig model paralleled results obtained in experiments with chimpanzees. Unlike chimpanzees, guinea-pigs are a comparatively inexpensive, rapidly replenishable animal, which after subcutaneous implantation with small porous chambers provide a convenient model for studying most immunological aspects of gonococcal infections.
PMCID: PMC1045361  PMID: 403994
15.  Population structure and cultural geography of a folktale in Europe 
Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture.
PMCID: PMC3574383  PMID: 23390109
cultural evolution; cultural FST; folktale; population genetics
16.  A fruit in the hand or two in the bush? Divergent risk preferences in chimpanzees and bonobos 
Biology Letters  2008;4(3):246-249.
Human and non-human animals tend to avoid risky prospects. If such patterns of economic choice are adaptive, risk preferences should reflect the typical decision-making environments faced by organisms. However, this approach has not been widely used to examine the risk sensitivity in closely related species with different ecologies. Here, we experimentally examined risk-sensitive behaviour in chimpanzees (Pan troglodytes) and bonobos (Pan paniscus), closely related species whose distinct ecologies are thought to be the major selective force shaping their unique behavioural repertoires. Because chimpanzees exploit riskier food sources in the wild, we predicted that they would exhibit greater tolerance for risk in choices about food. Results confirmed this prediction: chimpanzees significantly preferred the risky option, whereas bonobos preferred the fixed option. These results provide a relatively rare example of risk-prone behaviour in the context of gains and show how ecological pressures can sculpt economic decision making.
PMCID: PMC2610056  PMID: 18364305
risk; decision making; chimpanzees; bonobos
17.  Differences in the Cognitive Skills of Bonobos and Chimpanzees 
PLoS ONE  2010;5(8):e12438.
While bonobos and chimpanzees are both genetically and behaviorally very similar, they also differ in significant ways. Bonobos are more cautious and socially tolerant while chimpanzees are more dependent on extractive foraging, which requires tools. The similarities suggest the two species should be cognitively similar while the behavioral differences predict where the two species should differ cognitively. We compared both species on a wide range of cognitive problems testing their understanding of the physical and social world. Bonobos were more skilled at solving tasks related to theory of mind or an understanding of social causality, while chimpanzees were more skilled at tasks requiring the use of tools and an understanding of physical causality. These species differences support the role of ecological and socio-ecological pressures in shaping cognitive skills over relatively short periods of evolutionary time.
PMCID: PMC2929188  PMID: 20806062
18.  Stable Epigenetic Effects Impact Adaptation in Allopolyploid Orchids (Dactylorhiza: Orchidaceae) 
Molecular Biology and Evolution  2010;27(11):2465-2473.
Epigenetic information includes heritable signals that modulate gene expression but are not encoded in the primary nucleotide sequence. We have studied natural epigenetic variation in three allotetraploid sibling orchid species (Dactylorhiza majalis s.str, D. traunsteineri s.l., and D. ebudensis) that differ radically in geography/ecology. The epigenetic variation released by genome doubling has been restructured in species-specific patterns that reflect their recent evolutionary history and have an impact on their ecology and evolution, hundreds of generations after their formation. Using two contrasting approaches that yielded largely congruent results, epigenome scans pinpointed epiloci under divergent selection that correlate with eco-environmental variables, mainly related to water availability and temperature. The stable epigenetic divergence in this group is largely responsible for persistent ecological differences, which then set the stage for species-specific genetic patterns to accumulate in response to further selection and/or drift. Our results strongly suggest a need to expand our current evolutionary framework to encompass a complementary epigenetic dimension when seeking to understand population processes that drive phenotypic evolution and adaptation.
PMCID: PMC2955735  PMID: 20551043
adaptation; epigenetics; evolution; hybridization; polyploidy; selection
19.  Ethnomedicinal and ecological status of plants in Garhwal Himalaya, India 
The northern part of India harbours a great diversity of medicinal plants due to its distinct geography and ecological marginal conditions. The traditional medical systems of northern India are part of a time tested culture and honored still by people today. These traditional systems have been curing complex disease for more than 3,000 years. With rapidly growing demand for these medicinal plants, most of the plant populations have been depleted, indicating a lack of ecological knowledge among communities using the plants. Thus, an attempt was made in this study to focus on the ecological status of ethnomedicinal plants, to determine their availability in the growing sites, and to inform the communities about the sustainable exploitation of medicinal plants in the wild.
The ecological information regarding ethnomedicinal plants was collected in three different climatic regions (tropical, sub-tropical and temperate) for species composition in different forest layers. The ecological information was assessed using the quadrate sampling method. A total of 25 quadrats, 10 × 10 m were laid out at random in order to sample trees and shrubs, and 40 quadrats of 1 × 1 m for herbaceous plants. In each climatic region, three vegetation sites were selected for ecological information; the mean values of density, basal cover, and the importance value index from all sites of each region were used to interpret the final data. Ethnomedicinal uses were collected from informants of adjacent villages. About 10% of inhabitants (older, experienced men and women) were interviewed about their use of medicinal plants. A consensus analysis of medicinal plant use between the different populations was conducted.
Across the different climatic regions a total of 57 species of plants were reported: 14 tree species, 10 shrub species, and 33 herb species. In the tropical and sub-tropical regions, Acacia catechu was the dominant tree while Ougeinia oojeinensis in the tropical region and Terminalia belerica in the sub-tropical region were least dominant reported. In the temperate region, Quercus leucotrichophora was the dominant tree and Pyrus pashia the least dominant tree. A total of 10 shrubs were recorded in all three regions: Adhatoda vasica was common species in the tropical and sub-tropical regions however, Rhus parviflora was common species in the sub-tropical and temperate regions. Among the 33 herbs, Sida cordifolia was dominant in the tropical and sub-tropical regions, while Barleria prionitis the least dominant in tropical and Phyllanthus amarus in the sub-tropical region. In temperate region, Vernonia anthelmintica was dominant and Imperata cylindrica least dominant. The consensus survey indicated that the inhabitants have a high level of agreement regarding the usages of single plant. The index value was high (1.0) for warts, vomiting, carminative, pain, boils and antiseptic uses, and lowest index value (0.33) was found for bronchitis.
The medicinal plants treated various ailments. These included diarrhea, dysentery, bronchitis, menstrual disorders, gonorrhea, pulmonary affections, migraines, leprosy. The ecological studies showed that the tree density and total basal cover increased from the tropical region to sub-tropical and temperate regions. The species composition changed with climatic conditions. Among the localities used for data collection in each climatic region, many had very poor vegetation cover. The herbaceous layer decreased with increasing altitude, which might be an indication that communities at higher elevations were harvesting more herbaceous medicinal plants, due to the lack of basic health care facilities. Therefore, special attention needs to be given to the conservation of medicinal plants in order to ensure their long-term availability to the local inhabitants. Data on the use of individual species of medicinal plants is needed to provide an in-depth assessment of the plants availability in order to design conservation strategies to protect individual species.
PMCID: PMC3212913  PMID: 22011477
20.  Lumping or splitting: seeking the preferred areal unit for health geography studies 
Findings are compared on geographic variation of incident and late-stage cancers across Connecticut using different areal units for analysis.
Few differences in results were found for analyses across areal units. Global clustering of incident prostate and breast cancer cases was apparent regardless of the level of geography used. The test for local clustering found approximately the same locales, populations at risk and estimated effects. However, some discrepancies were uncovered.
In the absence of conditions calling for surveillance of small area cancer clusters ('hot spots'), the rationale for accepting the burdens of preparing data at levels of geography finer than the census tract may not be compelling.
PMCID: PMC1079921  PMID: 15788100
21.  Ecological and evolutionary factors in dental morphological diversification among modern human populations from southern South America 
The knowledge of processes involved in morphological variation requires the integrated analysis of evolutionary and ecological factors. Here, we investigate the factors responsible for dental variation among human populations from southern South America. The aim of this work is to test the correspondence of dental size and shape variation with geographical, molecular (i.e. mtDNA) and ecological (i.e. climate, diet and food preparation) variables employing comparative phylogenetic methods, which have not previously been extensively applied at a within-species level. The results of the Procrustes analysis show a significant association of shape variables with molecular distance and geography, whereas dental size is not associated with molecular or geographical distances among groups. Phylogenetic generalized least-squares analysis, which takes into account the evolutionary autocorrelation among populations, shows a significant relationship between dental size variation and diet, while temperature and pottery do not correspond with dental size or shape. Specifically, groups with diets rich in carbohydrates, as well as the maritime hunter-gatherers, have the smallest teeth. In summary, our results support ecological factors as the dominant factor on dental size diversification in this region, while evolutionary relationships account for variation in dental shape.
PMCID: PMC2842763  PMID: 19955158
dental size and shape; phylogenetic comparative method; temperature; diet; pottery
22.  Ecologic Niche Modeling and Spatial Patterns of Disease Transmission 
Emerging Infectious Diseases  2006;12(12):1822-1826.
TOC Summary: This technique can be used to study the geography and ecology of disease transmission.
Ecologic niche modeling (ENM) is a growing field with many potential applications to questions regarding the geography and ecology of disease transmission. Specifically, ENM has the potential to inform investigations concerned with the geography, or potential geography, of vectors, hosts, pathogens, or human cases, and it can achieve fine spatial resolution without the loss of information inherent in many other techniques. Potential applications and current frontiers and challenges are reviewed.
PMCID: PMC3291346  PMID: 17326931
Ecologic niche modeling; geographic distribution; spatial pattern; perspective
23.  Evolutionary diversification and geographical isolation in Dubautia laxa (Asteraceae), a widespread member of the Hawaiian silversword alliance 
Annals of Botany  2010;107(3):357-370.
Background and Aims
The Hawaiian silversword alliance (Asteraceae) is one the best examples of a plant adaptive radiation, exhibiting extensive morphological and ecological diversity. No research within this group has addressed the role of geographical isolation, independent of ecological adaptation, in contributing to taxonomic diversity. The aims of this study were to examine genetic differentiation among subspecies of Dubautia laxa (Asteraceae) to determine if allopatric or sympatric populations and subspecies form distinct genetic clusters to understand better the role of geography in diversification within the alliance.
Dubautia laxa is a widespread member of the Hawaiian silversword alliance, occurring on four of the five major islands of the Hawaiian archipelago, with four subspecies recognized on the basis of morphological, ecological and geographical variation. Nuclear microsatellites and plastid DNA sequence data were examined. Data were analysed using maximum-likelihood and Bayesian phylogenetic methodologies to identify unique evolutionary lineages.
Key Results
Plastid DNA sequence data resolved two highly divergent lineages, recognized as the Laxa and Hirsuta groups, that are more similar to other members of the Hawaiian silversword alliance than they are to each other. The Laxa group is basal to the young island species of Dubautia, whereas the Hirsuta group forms a clade with the old island lineages of Dubautia and with Argyroxiphium. The divergence between the plastid groups is supported by Bayesian microsatellite clustering analyses, but the degree of nuclear differentiation is not as great. Clear genetic differentiation is only observed between allopatric populations, both within and among islands.
These results indicate that geographical separation has aided diversification in D. laxa, whereas ecologically associated morphological differences are not associated with neutral genetic differentiation. This suggests that, despite the stunning ecological adaptation observed, geography has also played an important role in the Hawaiian silversword alliance plant adaptive radiation.
PMCID: PMC3043929  PMID: 21193480
Dubautia laxa; Hawaiian silversword alliance; infraspecific divergence; subspecies; speciation; geographical divergence; microsatellites; plastid DNA; chloroplast DNA
24.  The Ecological and Geographic Context of Morphological and Genetic Divergence in an Understorey-Dwelling Bird 
PLoS ONE  2014;9(2):e85903.
Advances in understanding the process of species formation require an integrated perspective that includes the evaluation of spatial, ecological and genetic components. One approach is to focus on multiple stages of divergence within the same species. Species that comprise phenotypically different populations segregated in apparently distinct habitats, in which range is presently continuous but was putatively geographically isolated provide an interesting system to study the mechanisms of population divergence. Here, we attempt to elucidate the role of ecology and geography in explaining observed morphological and genetic variation in an understorey-dwelling bird endemic to southeastern Africa, where two subspecies are recognized according to phenotype and habitat affinity. We carried out a range-wide analysis of climatic requirements, morphological and genetic variation across southeast Africa to test the hypothesis that the extent of gene flow among populations of the brown scrub-robin are influenced by their distinct climatic niches. We recovered two distinct trends depending on whether our analyses were hierarchically structured at the subspecies or at the within subspecies level. Between subspecies we found pronounced morphological differentiation associated with strong reproductive isolation (no gene flow) between populations occupying divergent climatic niches characterized by changes in the temperature of the warmest and wettest month. In contrast, within subspecies, we recovered continuous morphological variation with extensive gene flow among populations inhabiting the temperate and sub-tropical forests of southern Africa, despite divergence along the climate axis that is mainly determined by minimum temperature and precipitation of the coldest months. Our results highlight the role of niche divergence as a diversifying force that can promote reproductive isolation in vertebrates.
PMCID: PMC3917827  PMID: 24516521
25.  Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity 
PLoS ONE  2007;2(5):e454.
Biogeographic models partition ecologically similar species assemblages into discrete ecoregions. However, the history, relationship and interactions between these regions and their assemblages have rarely been explored.
Methodology/Principal Findings
Here we develop a taxon-based approach that explicitly utilises molecular information to compare ecoregion history and status, which we exemplify using a continentally distributed mammalian species: the African bushbuck (Tragelaphus scriptus). We reveal unprecedented levels of genetic diversity and structure in this species and show that ecoregion biogeographic history better explains the distribution of molecular variation than phenotypic similarity or geography. We extend these data to explore ecoregion connectivity, identify core habitats and infer ecological affinities from them.
This analysis defines 28 key biogeographic regions for sub-Saharan Africa, and provides a valuable framework for the incorporation of genetic and biogeographic information into a more widely applicable model for the conservation of continental biodiversity.
PMCID: PMC1866246  PMID: 17520013

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