Testing Models of Selection and Demography inDrosophila simulans

AbstractWe analyze patterns of nucleotide variability at 15 X-linked loci and 14 autosomal loci from a North American population of Drosophila simulans. We show that there is significantly more linkage disequilibrium on the X chromosome than on chromosome arm 3R and much more linkage disequilibrium on both chromosomes than expected from estimates of recombination rates, mutation rates, and levels of diversity. To explore what types of evolutionary models might explain this observation, we examine a model of recurrent, nonoverlapping selective sweeps and a model of a recent drastic bottleneck (e.g., founder event) in the demographic history of North American populations of D. simulans. The simple sweep model is not consistent with the observed patterns of linkage disequilibrium nor with the observed frequencies of segregating mutations. Under a restricted range of parameter values, a simple bottleneck model is consistent with multiple facets of the data. While our results do not exclude some influence of selection on X vs. autosome variability levels, they suggest that demography alone may account for patterns of linkage disequilibrium and the frequency spectrum of segregating mutations in this population of D. simulans.

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Phylogeography across a continent: The evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2007.10.020 ◽

2008 ◽

Vol 47 (1) ◽

pp. 274-288 ◽

Cited By ~ 47

Author(s):

Frank T. Burbrink ◽

Frank Fontanella ◽

R. Alexander Pyron ◽

Timothy J. Guiher ◽

Cynthia Jimenez

Keyword(s):

North American ◽

Demographic History ◽

The North ◽

Coluber Constrictor ◽

History Of

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Linkage Disequilibrium and Demographic History of Wild and Domestic Canids

Genetics ◽

10.1534/genetics.108.098830 ◽

2009 ◽

Vol 181 (4) ◽

pp. 1493-1505 ◽

Cited By ~ 98

Author(s):

Melissa M. Gray ◽

Julie M. Granka ◽

Carlos D. Bustamante ◽

Nathan B. Sutter ◽

Adam R. Boyko ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Demographic History ◽

History Of

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Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies(L.) Karst]

Genetics ◽

10.1534/genetics.106.065102 ◽

2006 ◽

Vol 174 (4) ◽

pp. 2095-2105 ◽

Cited By ~ 187

Author(s):

Myriam Heuertz ◽

Emanuele De Paoli ◽

Thomas Källman ◽

Hanna Larsson ◽

Irena Jurman ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Picea Abies ◽

Norway Spruce ◽

Nucleotide Diversity ◽

Demographic History ◽

History Of

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Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

Science Advances ◽

10.1126/sciadv.aaw9206 ◽

2019 ◽

Vol 5 (10) ◽

pp. eaaw9206 ◽

Cited By ~ 9

Author(s):

Jeffrey P. Spence ◽

Yun S. Song

Keyword(s):

Binding Sites ◽

Demographic History ◽

Dna Binding Protein ◽

Polycomb Group ◽

Human Populations ◽

Polycomb Group Proteins ◽

Fine Scale ◽

Population Differences ◽

Recombination Rates ◽

History Of

Fine-scale rates of meiotic recombination vary by orders of magnitude across the genome and differ between species and even populations. Studying cross-population differences has been stymied by the confounding effects of demographic history. To address this problem, we developed a demography-aware method to infer fine-scale recombination rates and applied it to 26 diverse human populations, inferring population-specific recombination maps. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding further evidence that Polycomb group proteins and the trimethylation of H3K27 elevate recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.

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Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium

Molecular Biology and Evolution ◽

10.1093/molbev/msaa169 ◽

2020 ◽

Vol 37 (12) ◽

pp. 3642-3653

Author(s):

Enrique Santiago ◽

Irene Novo ◽

Antonio F Pardiñas ◽

María Saura ◽

Jinliang Wang ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Demographic History ◽

Sequencing Data ◽

Effective Population ◽

Recombination Rates ◽

Animal Populations ◽

Wide Range ◽

Demographic Trajectories ◽

Model Computer ◽

Conservation Of Endangered Species

Abstract Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.

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Nucleotide Variability atG6pdand the Signature of Malarial Selection in Humans

Genetics ◽

10.1093/genetics/162.4.1849 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1849-1861 ◽

Cited By ~ 3

Author(s):

Matthew A Saunders ◽

Michael F Hammer ◽

Michael W Nachman

Keyword(s):

Linkage Disequilibrium ◽

X Chromosome ◽

G6pd Deficiency ◽

Human Populations ◽

Nucleotide Variability ◽

Signature Of Selection ◽

History Of ◽

Glucose 6 Phosphate Dehydrogenase ◽

The Impact

AbstractGlucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy in humans. Deficiency alleles for this X-linked disorder are geographically correlated with historical patterns of malaria, and the most common deficiency allele in Africa (G6PD A-) has been shown to confer some resistance to malaria in both hemizygous males and heterozygous females. We studied DNA sequence variation in 5.1 kb of G6pd from 47 individuals representing a worldwide sample to examine the impact of selection on patterns of human nucleotide diversity and to infer the evolutionary history of the G6PD A-allele. We also sequenced 3.7 kb of a neighboring locus, L1cam, from the same set of individuals to study the effect of selection on patterns of linkage disequilibrium. Despite strong clinical evidence for malarial selection maintaining G6PD deficiency alleles in human populations, the overall level of nucleotide heterozygosity at G6pd is typical of other genes on the X chromosome. However, the signature of selection is evident in the absence of genetic variation among A-alleles from different parts of Africa and in the unusually high levels of linkage disequilibrium over a considerable distance of the X chromosome. In spite of a long-term association between Plasmodium falciparum and the ancestors of modern humans, patterns of nucleotide variability and linkage disequilibrium suggest that the A-allele arose in Africa only within the last 10,000 years and spread due to selection.

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Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

10.1101/532168 ◽

2019 ◽

Cited By ~ 4

Author(s):

Jeffrey P. Spence ◽

Yun S. Song

Keyword(s):

Binding Sites ◽

Demographic History ◽

Dna Binding Protein ◽

Polycomb Group ◽

Human Populations ◽

Polycomb Group Proteins ◽

Fine Scale ◽

Recombination Rates ◽

Confounding Effect ◽

History Of

AbstractFine-scale rates of meiotic recombination vary by several orders of magnitude across the genome, and are known to differ between species and even between populations. Studying the differences in recombination maps across populations has been stymied by the confounding effect of differences in demographic history. To address this problem, we developed a method that infers fine-scale recombination rates while taking demography into account and applied our method to infer population-specific recombination maps for each of 26 diverse human populations. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding an unexpected role for Polycomb-group proteins and the tri-methylation of H3K27 in elevating recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA-binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.

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Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples

10.1101/2021.06.17.448867 ◽

2021 ◽

Author(s):

Arjun Biddanda ◽

Matthias Steinrücken ◽

John Novembre

Keyword(s):

Linkage Disequilibrium ◽

Demographic History ◽

Genotype Imputation ◽

Recombination Rates ◽

Haplotype Data ◽

Switch Rate ◽

Population Sizes ◽

Population Continuity ◽

Sample Age

Archaeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection in many organisms. However, most studies to date have ignored the non-random association of genetic variants at different loci (i.e., linkage disequilibrium, LD). This may be in part because basic properties of LD in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: 1) The correlation between the number of pairwise differences observed between time-staggered samples (ΠΔt) in models with and without strict population continuity; 2) The product of the LD coeficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and 3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.

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Linkage disequilibrium and demographic history of the isolated population of the Faroe Islands

European Journal of Human Genetics ◽

10.1038/sj.ejhg.5200816 ◽

2002 ◽

Vol 10 (6) ◽

pp. 381-387 ◽

Cited By ~ 25

Author(s):

Tove H Jorgensen ◽

Birte Degn ◽

August G Wang ◽

Maria Vang ◽

Hugh Gurling ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Demographic History ◽

Faroe Islands ◽

Isolated Population ◽

History Of

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North American Association for the Study of Religion (NAASR)

Bulletin for the Study of Religion ◽

10.1558/bsor.v44i2.27304 ◽

2015 ◽

Vol 44 (2) ◽

pp. 29-30

Author(s):

Matt Sheedy

Keyword(s):

North American ◽

American Association ◽

The North ◽

History Of

I interviewed Russell McCutcheon back in March 2015, about his new role as president of the North American Association for the Study of Religion (NAASR), asking him about the history of the organization, goals for his tenure, and developments for NAASR’s upcoming conference in Atlanta in November 2015.

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