Francois Balloux
University College London, UGI, Faculty Member
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The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation... more
The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locu...
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Random mating is the null model central to population genetics. One assumption behind random mating is that individuals mate an infinite number of times. This is obviously unrealistic. Here we show that when each female mates a finite... more
Random mating is the null model central to population genetics. One assumption behind random mating is that individuals mate an infinite number of times. This is obviously unrealistic. Here we show that when each female mates a finite number of times, the effective size of the population is substantially decreased.
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How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a... more
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative 'Paleoamerican' relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican ...
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The population structures of pathogenic bacteria are extraordinarily diverse. This variation is due to the wide range in life histories and niches exploited by different species, but is also due to the extensive variation in the dynamics... more
The population structures of pathogenic bacteria are extraordinarily diverse. This variation is due to the wide range in life histories and niches exploited by different species, but is also due to the extensive variation in the dynamics of transfer of genes from one genera-tion to the ...
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Studying the population genetics of the Y chromosome is the most simple and direct way to gain independent information on male-specific historic and contemporary evolutionary processes. Y-chromosomal polymorphisms can now be accessed... more
Studying the population genetics of the Y chromosome is the most simple and direct way to gain independent information on male-specific historic and contemporary evolutionary processes. Y-chromosomal polymorphisms can now be accessed thanks to recent ...
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Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties... more
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 a...
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Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To... more
Natural variation within species reveals aspects of genome evolution and function. The fission yeast Schizosaccharomyces pombe is an important model for eukaryotic biology, but researchers typically use one standard laboratory strain. To extend the usefulness of this model, we surveyed the genomic and phenotypic variation in 161 natural isolates. We sequenced the genomes of all strains, finding moderate genetic diversity (π = 3 × 10(-3) substitutions/site) and weak global population structure. We estimate that dispersal of S. pombe began during human antiquity (∼340 BCE), and ancestors of these strains reached the Americas at ∼1623 CE. We quantified 74 traits, finding substantial heritable phenotypic diversity. We conducted 223 genome-wide association studies, with 89 traits showing at least one association. The most significant variant for each trait explained 22% of the phenotypic variance on average, with indels having larger effects than SNPs. This analysis represents a rich resource to examine genotype-phenotype relationships in a tractable model.
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Inbreeding depression reflects the negative consequences of increased homozygosity at genes that affect fitness. We investigate inbreeding depression in a semi-free-ranging colony of mandrills (Mandrillus sphinx), using high-quality... more
Inbreeding depression reflects the negative consequences of increased homozygosity at genes that affect fitness. We investigate inbreeding depression in a semi-free-ranging colony of mandrills (Mandrillus sphinx), using high-quality pedigree data, comprising five maternal generations and 20 years of morphological and demographic data. We examine the relationship between inbreeding coefficients and four fitness correlates: two growth parameters (mass and height for age) and longevity in both sexes, and age at first conception in females. Inbreeding was correlated with both growth parameters, but only in females, with inbred females being smaller than noninbred females. Inbreeding was also correlated significantly with age at first conception, with inbred females giving birth earlier in life than noninbred females. We suggest that sex-biased maternal investment may explain this sex-differential response to inbreeding, although the lack of a significant association between inbreeding a...
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Research Interests: Genomics, Cell Cycle, Drosophila melanogaster, Multidisciplinary, Gene Silencing, and 16 moreNature, Signal Transduction, RNA interference, Mitosis, Protein Kinases, Mutation, Animals, Genome, Nutritional Status, Enzyme, Cytokinesis, Physiological Stress Markers, Protein Phosphorylation, Protein Kinase, Cell Proliferation, and Cell Size
Random mating is the null model central to population genetics. One assumption behind random mating is that individuals mate an infinite number of times. This is obviously unrealistic. Here we show that when each female mates a finite... more
Random mating is the null model central to population genetics. One assumption behind random mating is that individuals mate an infinite number of times. This is obviously unrealistic. Here we show that when each female mates a finite number of times, the effective size of the population is substantially decreased.
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If there are many programs for population genetics data analysis, less effort has been devoted to simulation software in this field. However, there are many situations where simulated population genetics datasets would be very useful.... more
If there are many programs for population genetics data analysis, less effort has been devoted to simulation software in this field. However, there are many situations where simulated population genetics datasets would be very useful. Simulations allow exploring ...
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Varicella-zoster virus (VZV) causes chickenpox and shingles, and is found in human populations worldwide. The lack of temporal signal in the diversity of VZV makes substitution rate estimates unreliable, which is a barrier to... more
Varicella-zoster virus (VZV) causes chickenpox and shingles, and is found in human populations worldwide. The lack of temporal signal in the diversity of VZV makes substitution rate estimates unreliable, which is a barrier to understanding the context of its global spread. Here, we estimate rates of evolution by studying live attenuated vaccines, which evolved in 22 vaccinated patients for known periods of time, sometimes, but not always undergoing latency. We show that the attenuated virus evolves rapidly (∼10(-6) substitutions/site/day), but that rates decrease dramatically when the virus undergoes latency. These data are best explained by a model in which viral populations evolve for around 13 days before becoming latent, but then undergo no replication during latency. This implies that rates of viral evolution will depend strongly on transmission patterns. Nevertheless, we show that implausibly long latency periods are required to date the most recent common ancestor of extant V...
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Hymenoptera are characterized by a haplodiploid sex determination system where females are diploid and males haploid. Because females can decide whether they fertilize their eggs they have control over the sex of their offspring. Females... more
Hymenoptera are characterized by a haplodiploid sex determination system where females are diploid and males haploid. Because females can decide whether they fertilize their eggs they have control over the sex of their offspring. Females are thus expected to lay haploid and diploid eggs in a ratio that maximizes their fitness. A surprising finding of recent studies on the primary sex ratio of ants has been that queens lay male eggs outside the time of production of sexuals, a period during which all haploid eggs are usually destroyed by workers. It has been suggested that the production of a high proportion of haploid eggs by queens might be a mechanism to achieve higher reproductive success when the colony loses all its queens and rears new sexuals from the brood present within the colony. Here it is shown that, as predicted by this hypothesis, the proportion of haploid eggs laid byLinepithema humilequeens is higher in colonies containing several queens than in single-queen colonies. BecauseL. humilesexuals mate in the nest, the females that produce a higher proportion of haploid eggs should have higher fitness when the colony sex ratio of the brood is female-biased and sons of several queens compete to fertilize the new queens produced.
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Advanced Search. GSA Logo A Publication of The Genetics Society of America. Genetics. ...
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Research Interests: Microbiology, Immunology, Colombia, Family, Medical Microbiology, and 19 moreHelicobacter pylori, United Kingdom, Genetic Diversity, South Africa, Humans, Korea, Developing Country, Haplotypes, United States, Developing World, Pedigree, South African, Prevalence, Great Britain, Urban Population, Genetic variation, Rural Community, Mosaicism, and H Pylori
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Research Interests: Microbiology and Mbio
Research Interests: Genetics, Microbiology, Immunology, Population Genetics, Comparative Genomics, and 16 moreMedical Microbiology, Population Dynamics, Antibiotic Resistance, TIME, Europe, Polymerase Chain Reaction, DNA sequence design, Population Size, Biological evolution, High Pressure Liquid Chromatography, Population expansion, Evolutionary rate, Time, Demographic History, Methicillin Resistant Staphylococcus Aureus, and Pathogenic Bacteria
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A KEY DETERMINANT OF THE SUCCESS OF influenza containment is the transmission rate of the novel strain. C. Fraser et al. [Pandemic potential of a strain of influenza A (H1N1): Early findings, Reports, 19 June, p. 1557] estimated the... more
A KEY DETERMINANT OF THE SUCCESS OF influenza containment is the transmission rate of the novel strain. C. Fraser et al. [Pandemic potential of a strain of influenza A (H1N1): Early findings, Reports, 19 June, p. 1557] estimated the basic reproduction number (R0) of the ...
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Epidemiology and public health planning will increasingly rely on the analysis of genetic sequence data. The ongoing influenza A/H1N1 pandemic may represent a tipping point in this trend, with A/H1N1 being the first human pathogen... more
Epidemiology and public health planning will increasingly rely on the analysis of genetic sequence data. The ongoing influenza A/H1N1 pandemic may represent a tipping point in this trend, with A/H1N1 being the first human pathogen routinely genotyped from the beginning of its spread. To take full advantage of this genetic information, we introduce a novel method to reconstruct the spatiotemporal dynamics of outbreaks from sequence data. The approach is based on a new paradigm were ancestries are inferred directly rather than through the reconstruction of most recent common ancestors (MRCAs) as in phylogenetics. Using 279 A/H1N1 hemagglutinin (HA) sequences, we confirm the emergence of the 2009 flu pandemic in Mexico. The virus initially spread to the US, and then to the rest of the world with both Mexico and the US acting as the main sources. While compatible with current epidemiological understanding of the 2009 H1N1 pandemic, our results provide a much finer picture of the spatiotemporal dynamics. The results also highlight how much additional epidemiological information can be gathered from genetic monitoring of a disease outbreak.
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Hepatitis B virus (HBV) infection is considered as the fifth leading cause of death due to infectious diseases and has a worldwide prevalence. The particular geographical distribution of the eight previously defined genotypes of HBV... more
Hepatitis B virus (HBV) infection is considered as the fifth leading cause of death due to infectious diseases and has a worldwide prevalence. The particular geographical distribution of the eight previously defined genotypes of HBV suggests that the viral population is highly structured. The presence of such population structure is likely to affect the geographical distribution of polymorphisms involved in disease progression. In this study, we determined the structure of the HBV population using a clustering approach based on the observed allele frequencies at the polymorphic loci. We used all full-genome sequences publicly available and obtained a significant clustering of the HBV population into four main clusters, strongly associated with the current classification into genotypes. One of these main clusters could itself be split into three well-supported subclusters, highlighting the hierarchical nature of the population differentiation between HBV strains. The extremely clear-cut subdivision of the HBV population further indicates that recombination in HBV is not as extensive as previously assumed.