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

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.

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

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.

scholarly journals Testing Models of Selection and Demography inDrosophila simulans

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 203-216 ◽  
Author(s):  
Jeffrey D Wall ◽  
Peter Andolfatto ◽  
Molly Przeworski
Keyword(s):  
Linkage Disequilibrium ◽  
North American ◽  
Demographic History ◽  
North American Population ◽  
Recombination Rates ◽  
Nucleotide Variability ◽  
Chromosome Arm ◽  
History Of ◽  
Founder Event ◽  
Parameter Values

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.

scholarly journals Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

BMC Genetics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Luiz F. Brito ◽  
Mohsen Jafarikia ◽  
Daniela A. Grossi ◽  
James W. Kijas ◽  
Laercio R. Porto-Neto ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Consistency Of Gametic Phase ◽  
Gametic Phase

scholarly journals Linkage disequilibrium and genetic variances under mutation-selection balance.

Genetics ◽  
1989 ◽  
Vol 121 (4) ◽  
pp. 857-860 ◽  
Author(s):  
A Hastings
Keyword(s):  
Linkage Disequilibrium ◽  
Mutation Rate ◽  
Genetic Variance ◽  
Harmonic Mean ◽  
Recombination Rates ◽  
Genetic Variances ◽  
Locus Selection

Abstract I determine the contribution of linkage disequilibrium to genetic variances using results for two loci and for induced or marginal systems. The analysis allows epistasis and dominance, but assumes that mutation is weak relative to selection. The linkage disequilibrium component of genetic variance is shown to be unimportant for unlinked loci if the gametic mutation rate divided by the harmonic mean of the pairwise recombination rates is much less than one. For tightly linked loci, linkage disequilibrium is unimportant if the gametic mutation rate divided by the (induced) per locus selection is much less than one.

Genetic characterization of novel polymorphic microsatellite markers for Epilobium nankotaizanense (Onagraceae), an endemic and threatened herb in Taiwan

2021 ◽  
pp. 1-4
Author(s):  
Yu-Wei Tseng ◽  
Chi-Chun Huang ◽  
Chih-Chiang Wang ◽  
Chiuan-Yu Li ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Natural Populations ◽  
Conservation Strategy ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
The Family ◽  
Conservation Genetic ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Abstract Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

scholarly journals An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa

2020 ◽  
Vol 12 (4) ◽  
pp. 407-412 ◽  
Author(s):  
Iain Mathieson ◽  
Federico Abascal ◽  
Lasse Vinner ◽  
Pontus Skoglund ◽  
Cristina Pomilla ◽  
...  
Keyword(s):  
Southern Africa ◽  
Nonhuman Primates ◽  
Demographic History ◽  
Structured Populations ◽  
Human Populations ◽  
Papio Ursinus ◽  
Anthropological Research ◽  
Population Continuity ◽  
High Degree

Abstract Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa—indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

Morphometric and molecular characterization of an expanding Ionian population of the fireworm Hermodice carunculata (Annelida)

2019 ◽  
Vol 99 (7) ◽  
pp. 1569-1577 ◽  
Author(s):  
Sara Righi ◽  
Isabella Maletti ◽  
Ferruccio Maltagliati ◽  
Alberto Castelli ◽  
Michele Barbieri ◽  
...  
Keyword(s):  
Demographic History ◽  
Generalist Predator ◽  
Future Studies ◽  
Mitochondrial Coi ◽  
Hermodice Carunculata ◽  
Scuba Divers ◽  
History Analysis ◽  
Individual Size ◽  
Insight Into

AbstractThe amphinomid fireworm Hermodice carunculata is a potentially invasive species reported throughout the subtropical Atlantic Ocean and the Mediterranean Sea, which is known as a generalist predator and opportunistic feeder. The ongoing climate changes and seawater warming may favour fireworm poleward range expansions and density increases. Our results provide the first investigation into a population which has purportedly been spreading widely in the Salento Peninsula (Apulia, Italy). The specimens were analysed using allometric variables and molecular markers. The best morphometric parameters to estimate individual size were determined as key information for future studies on fireworm population dynamics. To phylogeographically characterize the Apulian population, sequences of the mitochondrial COI and 16S rDNA regions were obtained from a pool of individuals and treated together with those of Atlantic specimens retrieved from GenBank. The estimates of genetic variability for Apulian population were consistent with those recently reported in the literature. Inferences on demographic history analysis confirmed a recent expansion event in Apulia, as has been recounted by fishermen and scuba divers during recent years. Overall, these results constitute a crucial step in the characterization of present-day H. carunculata populations, and provide greater insight into fireworm population ecology.

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