scholarly journals You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

2019 ◽  
Vol 37 (2) ◽  
pp. 442-454 ◽  
Author(s):  
Diego Forni ◽  
Rachele Cagliani ◽  
Mario Clerici ◽  
Uberto Pozzoli ◽  
Manuela Sironi
Keyword(s):  
Geographic Distribution ◽  
Human Population ◽  
Strong Support ◽  
Time Frame ◽  
Genetic Distances ◽  
The Philippines ◽  
Molecular Dating ◽  
Human Populations ◽  
Jc Polyomavirus ◽  
Reconciliation Analysis

Abstract JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

scholarly journals Human endemic coronavirus emergence in the context of past and recent zoonotic outbreaks

2021 ◽  
Author(s):  
Diego Forni ◽  
Rachele Cagliani ◽  
Federica Arrigoni ◽  
Martino Benvenuti ◽  
Chiara Pontremoli ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Viral Disease ◽  
Time Frame ◽  
Antigenic Drift ◽  
Molecular Dating ◽  
Viral Diseases ◽  
Human Interferon ◽  
Human Populations ◽  
Influenza Pandemics ◽  
Temporal Succession

Abstract Understanding the evolutionary dynamics of the four human endemic coronaviruses might provide insight into the future trajectories of SARS-CoV-2 evolution. We re-assessed the timing of endemic coronavirus emergence and we show that all viruses entered human populations in a time-frame ranging from ~500 to 55 years ago. Because the three highly pathogenic coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) spilled-over in tight temporal succession, the pattern of coronavirus emergence, in analogy to that of influenza pandemics, is highly irregular. To contextualize this observation in a wider perspective of viral diseases emergence since 1945, we mined epidemiology database information. After controlling for reporting bias, we find that, contrary to widespread beliefs, the occurrence of viral diseases (either zoonotic or not) has not increased over the last decades. Analysis of the recent and ongoing evolution of HCoV-229E and HCoV-OC43 indicated that positive selection most likely contributed to fine-tune the interaction with the human interferon/inflammatory response. Conversely, integration of evolutionary inference and molecular dating provided evidence that these viruses are not undergoing antigenic drift and the temporal emergence of spike protein variants is best explained by optimization of receptor binding affinity. These data provide a fresh look on viral disease emergence and on coronavirus evolution.

scholarly journals Dynamics of Microsatellite Divergence Under Stepwise Mutation and Proportional Slippage/Point Mutation Models

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 839-852 ◽  
Author(s):  
Peter P Calabrese ◽  
Richard T Durrett ◽  
Charles F Aquadro
Keyword(s):  
Point Mutations ◽  
Genetic Distances ◽  
Mutational Bias ◽  
Human Populations ◽  
Mutation Model ◽  
Perfect Repeat ◽  
Stepwise Mutation ◽  
Equilibrium Distributions ◽  
Theoretical Results ◽  
Polymerase Slippage

Abstract Recently Kruglyak, Durrett, Schug, and Aquadro showed that microsatellite equilibrium distributions can result from a balance between polymerase slippage and point mutations. Here, we introduce an elaboration of their model that keeps track of all parts of a perfect repeat and a simplification that ignores point mutations. We develop a detailed mathematical theory for these models that exhibits properties of microsatellite distributions, such as positive skewness of allele lengths, that are consistent with data but are inconsistent with the predictions of the stepwise mutation model. We use our theoretical results to analyze the successes and failures of the genetic distances (δμ)2 and DSW when used to date four divergences: African vs. non-African human populations, humans vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle. The influence of point mutations explains some of the problems with the last two examples, as does the fact that these genetic distances have large stochastic variance. However, we find that these two features are not enough to explain the problems of dating the human-chimpanzee split. One possible explanation of this phenomenon is that long microsatellites have a mutational bias that favors contractions over expansions.

scholarly journals Ecology of the Anthropocene signals hope for consciously managing the planetary ecosystem

2021 ◽  
Vol 118 (28) ◽  
pp. e2024150118
Author(s):  
Clarence Lehman ◽  
Shelby Loberg ◽  
Michael Wilson ◽  
Eville Gorham
Keyword(s):  
Population Growth ◽  
Cultural Evolution ◽  
Human Population ◽  
Human Populations ◽  
Present Moment ◽  
Minimal Set ◽  
The Past ◽  
Food Species ◽  
Large Predators ◽  
Population Numbers

Human populations have grown to such an extent that our species has become a dominant force on the planet, prompting geologists to begin applying the term Anthropocene to recognize the present moment. Many approaches seek to explain the past and future of human population growth, in the form of narratives and models. Some of the most influential models have parameters that cannot be precisely known but are estimated by expert opinion. Here we apply a unified model of ecology to provide a macroscale summary of the net effects of many microscale processes, using a minimal set of parameters that can be known. Our models match estimates of historic and prehistoric global human population numbers and provide predictions that correspond to some of the more complicated current models. In addition to fitting the data well they reveal that, amidst enormous complexity in our human and prehuman past, three key ecological discontinuities have occurred in turn: 1) becoming dominant competitors of large predators rather than their prey, 2) becoming mutualists with food species rather than acting as predators upon them, and 3) changing from a regime of uncontrolled population growth to one of controlled fertility instead. All three processes have been interlinked with cultural evolution and all three ushered in developments of the Anthropocene. Understanding the trajectories that have delivered us to this stage can help guide prudent paths into the future.

Extensive cryptic diversity of giant clams (Cardiidae: Tridacninae) revealed by DNA-sequence-based species delimitation approaches with new data from Hainan Island, South China Sea

2020 ◽  
Vol 86 (1) ◽  
pp. 56-63 ◽  
Author(s):  
Jun Liu ◽  
Dan Cui ◽  
Hui Wang ◽  
Jiawei Chen ◽  
Helu Liu ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Species Delimitation ◽  
Strong Support ◽  
Hainan Island ◽  
The Philippines ◽  
Nominal Species ◽  
Cryptic Diversity ◽  
China Sea ◽  
Giant Clams

Abstract Accurate species delimitation is important, especially for endangered species. As one of the most conspicuous bivalve taxa, giant clams are threatened throughout their geographic range. Many phylogeographic studies have revealed strong population structure among giant clams in the Indo-Pacific, suggesting cryptic diversity within these species. However, less attention has been paid to their identification and delimitation. In this study, we assembled a comprehensive dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences for Tridacna species, focusing on new sequences from Hainan Island in the South China Sea and previously published ones from Japan, Taiwan, Singapore, the Philippines, Indonesia, Australia, the Solomon Islands and the Red Sea. Three nominal species, Tridacna crocea, T. squamosa and T. noae, were recognized at Hainan Island on the basis of distance-based DNA barcoding, with mean interspecific K2P distances of 10.6–24.7% for seven Tridacna species (T. crocea, T. squamosa, T. noae, T. maxima, T. mbalavuana, T. derasa and T. gigas). The most abundant species, T. noae, represents the first record of this species from Hainan Island. Using a combination of phylogenetic and DNA-based species delimitation analyses (automatic barcode gap discovery, generalized mixed Yule coalescent and Bayesian Poisson tree processes), we found strong support for a total of 13 operational taxonomic units (OTUs) for the seven nominal Tridacna species. These results, coupled with the fact that each OTU occupies different regions in the Indo-Pacific, strongly suggest multiple cryptic species of giant clams. Our findings point to the need for taxonomic revisionary work on giant clams throughout the Indo-Pacific; such work will have important conservation implications.

Assessing environmental toxins by human population effects

1982 ◽  
Vol 60 (7) ◽  
pp. 1053-1056
Author(s):  
R. E. M. Lees
Keyword(s):  
Human Population ◽  
Epidemiologic Methods ◽  
Environmental Toxins ◽  
Epidemiological Surveillance ◽  
Human Populations ◽  
Effect Relationship ◽  
Confounding Variables ◽  
Disease Associations ◽  
The Impact ◽  
Population Effects

The impact of toxins on the health of human populations can only be accurately assessed by epidemiologic methods. The investigation of toxin–disease associations in human populations and the accurate interpretation of data are often very difficult because of the existence of multiple confounding variables and the unrepresentativeness of sample or study populations.Factors influencing the deduction of cause and effect relationship rather than simple association are discussed, as is the need for continued development of epidemiological surveillance techniques.

scholarly journals Perfluoroalkyl and polyfluoroalkyl substances (PFAS) and their effects on the ovary

2020 ◽  
Vol 26 (5) ◽  
pp. 724-752 ◽  
Author(s):  
Ning Ding ◽  
Siobán D Harlow ◽  
John F Randolph Jr ◽  
Rita Loch-Caruso ◽  
Sung Kyun Park
Keyword(s):  
Human Population ◽  
Ovarian Function ◽  
Experimental Studies ◽  
Epidemiologic Studies ◽  
Experimental Models ◽  
Human Populations ◽  
Reverse Causality ◽  
Toxicological Studies ◽  
Polyfluoroalkyl Substances ◽  
Perfluoroalkyl And Polyfluoroalkyl Substances

Abstract BACKGROUND Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are found widespread in drinking water, foods, food packaging materials and other consumer products. Several PFAS have been identified as endocrine-disrupting chemicals based on their ability to interfere with normal reproductive function and hormonal signalling. Experimental models and epidemiologic studies suggest that PFAS exposures target the ovary and represent major risks for women’s health. OBJECTIVE AND RATIONALE This review summarises human population and toxicological studies on the association between PFAS exposure and ovarian function. SEARCH METHODS A comprehensive review was performed by searching PubMed. Search terms included an extensive list of PFAS and health terms ranging from general keywords (e.g. ovarian, reproductive, follicle, oocyte) to specific keywords (including menarche, menstrual cycle, menopause, primary ovarian insufficiency/premature ovarian failure, steroid hormones), based on the authors’ knowledge of the topic and key terms. OUTCOMES Clinical evidence demonstrates the presence of PFAS in follicular fluid and their ability to pass through the blood–follicle barrier. Although some studies found no evidence associating PFAS exposure with disruption in ovarian function, numerous epidemiologic studies, mostly with cross-sectional study designs, have identified associations of higher PFAS exposure with later menarche, irregular menstrual cycles, longer cycle length, earlier age of menopause and reduced levels of oestrogens and androgens. Adverse effects of PFAS on ovarian folliculogenesis and steroidogenesis have been confirmed in experimental models. Based on laboratory research findings, PFAS could diminish ovarian reserve and reduce endogenous hormone synthesis through activating peroxisome proliferator-activated receptors, disrupting gap junction intercellular communication between oocyte and granulosa cells, inducing thyroid hormone deficiency, antagonising ovarian enzyme activities involved in ovarian steroidogenesis or inhibiting kisspeptin signalling in the hypothalamus. WIDER IMPLICATIONS The published literature supports associations between PFAS exposure and adverse reproductive outcomes; however, the evidence remains insufficient to infer a causal relationship between PFAS exposure and ovarian disorders. Thus, more research is warranted. PFAS are of significant concern because these chemicals are ubiquitous and persistent in the environment and in humans. Moreover, susceptible groups, such as foetuses and pregnant women, may be exposed to harmful combinations of chemicals that include PFAS. However, the role environmental exposures play in reproductive disorders has received little attention by the medical community. To better understand the potential risk of PFAS on human ovarian function, additional experimental studies using PFAS doses equivalent to the exposure levels found in the general human population and mixtures of compounds are required. Prospective investigations in human populations are also warranted to ensure the temporality of PFAS exposure and health endpoints and to minimise the possibility of reverse causality.

scholarly journals Effective population size of current human population

2011 ◽  
Vol 93 (2) ◽  
pp. 105-114 ◽  
Author(s):  
LEEYOUNG PARK
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Human Population ◽  
Random Mating ◽  
Phase Iii ◽  
Human Populations ◽  
Effective Population ◽  
Hapmap Phase ◽  
Hardy Weinberg Equilibrium ◽  
Genetic Drifts

SummaryIn order to estimate the effective population size (Ne) of the current human population, two new approaches, which were derived from previous methods, were used in this study. One is based on the deviation from linkage equilibrium (LE) between completely unlinked loci in different chromosomes and another is based on the deviation from the Hardy–Weinberg Equilibrium (HWE). When random mating in a population is assumed, genetic drifts in population naturally induce linkage disequilibrium (LD) between chromosomes and the deviation from HWE. The latter provides information on the Ne of the current population, and the former provides the same when the Ne is constant. If Ne fluctuates, recent Ne changes are reflected in the estimates based on LE, and the comparison between two estimates can provide information regarding recent changes of Ne. Using HapMap Phase III data, the estimates were varied from 622 to 10 437, depending on populations and estimates. The Ne appeared to fluctuate as it provided different estimates for each of the two methods. These Ne estimates were found to agree approximately with the overall increment observed in recent human populations.

Sustainable Development

2013 ◽  
Author(s):  
Dorothy N. Gamble
Keyword(s):  
Cultural Adaptation ◽  
Human Population ◽  
Social Systems ◽  
Well Being ◽  
Human Populations ◽  
Human Relationships ◽  
Drought Conditions ◽  
Clean Air ◽  
Living Species

This entry describes how the viability of long-term human social systems is inextricably linked to human behavior, environmental resources, the health of the biosphere, and human relationships with all living species. New ways of thinking and acting in our engagement with the biosphere are explored, with attention to new ways of measuring well-being to understand the global relationships among human settlements, food security, human population growth, and especially alternative economic efforts based on prosperity rather than on growth. The challenge of social work is to engage in socioecological activities that will prevent and slow additional damage to the biosphere while at the same time helping human populations to develop the cultural adaptation and resilience required to confront increasing weather disasters; displacement resulting from rising seas; drought conditions that severely affect food supplies; the loss of biodiversity, soils, forests, fisheries, and clean air; and other challenges to human social organizations.

scholarly journals Process Evaluation of Nutrition Intervention Strategy in a Local Philippine Setting

2020 ◽  
Vol 11 ◽  
pp. 215013272091540
Author(s):  
Rowena V. Viajar ◽  
Julieta B. Dorado ◽  
Glenda P. Azaña ◽  
Heidenhein A. Ibarra ◽  
Eldridge B. Ferrer ◽  
...  
Keyword(s):  
Young Children ◽  
Nutrition Education ◽  
Process Evaluation ◽  
Local Level ◽  
Intervention Strategy ◽  
Strong Support ◽  
Public Health Problem ◽  
Monitoring And Evaluation ◽  
The Philippines ◽  
Nutrition Intervention

Aims: Undernutrition among 0 to 5 years old children remains a public health problem in the Philippines. This process evaluation study documented and examined the implementation of an intervention strategy for young children. Methods: Complementary feeding of 6-month to 2-year-old children was implemented for 120 days by the municipalities of Plaridel and Pulilan in Bulacan, Philippines utilizing local-based food made of rice and mung bean along with nutrition education classes among mothers/caregivers using the developed nutrition modules. A total of 121 mother-/caregiver-child pairs were the program participants of the intervention. Pre-post design were used in the analysis of quantitative data. Qualitative data were encoded verbatim manually using emerging themes. Key informant interviews among community workers and municipal officials and focus group discussions among mothers/caregivers and community workers were conducted to gather the needed data. Results: The municipalities adhered to the program phases of planning, organizing, implementation, monitoring, and evaluation. At end-line, the weight of children participants increased in both municipalities and the mean nutrition knowledge scores of mothers/caregivers increased significantly ( P < .05). Conclusions: This process evaluation confirmed that the proposed nutrition intervention strategy for young children can be implemented at the local level. The strong support and active cooperation of the local program implementers and mothers/caregivers and adherence to program requirements were the key factors in the efficient implementation of the intervention. For sustainability, the passing of local ordinance for the adoption of intervention and budget support for implementation of the intervention is recommended.

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