scholarly journals A non-zero variance of Tajima’s estimator for two sequences even for infinitely many unlinked loci

2016 ◽  
Author(s):  
Léandra King ◽  
John Wakeley ◽  
Shai Carmi
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Weak Correlation ◽  
Effective Population ◽  
Statistical Population ◽  
Demographic Models ◽  
Empirical Estimates ◽  
Fisher Model ◽  
Pairwise Differences ◽  
Coalescence Times

AbstractThe population-scaled mutation rate, θ, is informative on the effective population size and is thus widely used in population genetics. We show that for two sequences and n unlinked loci, Tajima’s estimator (), which is the average number of pairwise differences, is not consistent and therefore its variance does not vanish even as n → ∞. The non-zero variance of results from a (weak) correlation between coalescence times even at unlinked loci, which, in turn, is due to the underlying fixed pedigree shared by all genealogies. We derive the correlation coefficient under a diploid, discrete-time, Wright-Fisher model, and we also derive a simple, closed-form lower bound. We also obtain empirical estimates of the correlation of coalescence times under demographic models inspired by large-scale human genealogies. While the effect we de scribe is small , it is important to recognize this feature of statistical population genetics, which runs counter to commonly held notions about unlinked loci.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1805-1810 ◽  
Author(s):  
Martin J Lercher ◽  
Nick G C Smith ◽  
Adam Eyre-Walker ◽  
Laurence D Hurst
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Compositional Variation ◽  
Mutation Bias ◽  
Single Nucleotide ◽  
Frequency Distributions ◽  
Noncoding Regions ◽  
Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

scholarly journals A Genealogical Interpretation of Linkage Disequilibrium

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 987-991 ◽  
Author(s):  
Gilean A T McVean
Keyword(s):  
Monte Carlo Simulation ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Population Bottlenecks ◽  
Neutral Model ◽  
Demographic Models ◽  
Degree Of Association ◽  
Different Parts ◽  
Direct Correspondence ◽  
Coalescence Times

Abstract The degree of association between alleles at different loci, or linkage disequilibrium, is widely used to infer details of evolutionary processes. Here I explore how associations between alleles relate to properties of the underlying genealogy of sequences. Under the neutral, infinite-sites assumption I show that there is a direct correspondence between the covariance in coalescence times at different parts of the genome and the degree of linkage disequilibrium. These covariances can be calculated exactly under the standard neutral model and by Monte Carlo simulation under different demographic models. I show that the effects of population growth, population bottlenecks, and population structure on linkage disequilibrium can be described through their effects on the covariance in coalescence times.

Demographic Characterization of Anonymous Trace Travel Data

2015 ◽  
Vol 2526 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Joshua Auld ◽  
Abolfazl (Kouros) Mohammadian ◽  
Marcelo Simas Oliveira ◽  
Jean Wolf ◽  
William Bachman
Keyword(s):  
Test Data ◽  
Large Scale ◽  
Travel Demand ◽  
Null Model ◽  
Demographic Characteristics ◽  
Travel Pattern ◽  
Data Set ◽  
Trace Data ◽  
Demographic Models ◽  
Pattern Information

Research was undertaken to determine whether demographic characteristics of individual travelers could be derived from travel pattern information when no information about the individual was available. This question is relevant in the context of anonymously collected travel information, such as cell phone traces, when used for travel demand modeling. Determining the demographics of a traveler from such data could partially obviate the need for large-scale collection of travel survey data, depending on the purpose for which the data were to be used. This research complements methodologies used to identify activity stops, purposes, and mode types from raw trace data and presumes that such methods exist and are available. The paper documents the development of procedures for taking raw activity streams estimated from GPS trace data and converting these into activity travel pattern characteristics that are then combined with basic land use information and used to estimate various models of demographic characteristics. The work status, education level, age, and license possession of individuals and the presence of children in their households were all estimated successfully with substantial increases in performance versus null model expectations for both training and test data sets. The gender, household size, and number of vehicles proved more difficult to estimate, and performance was lower on the test data set; these aspects indicate overfitting in these models. Overall, the demographic models appear to have potential for characterizing anonymous data streams, which could extend the usability and applicability of such data sources to the travel demand context.

A genealogical approach to variable-population-size models in population genetics

1986 ◽  
Vol 23 (02) ◽  
pp. 283-296 ◽  
Author(s):  
Peter Donnelly
Keyword(s):  
Population Genetics ◽  
Branching Process ◽  
Sufficient Conditions ◽  
Process Models ◽  
Moran Model ◽  
Fisher Model ◽  
Variable Population ◽  
Exchangeable Model ◽  
Necessary And Sufficient ◽  
Variable Population Size

A general exchangeable model is introduced to study gene survival in populations whose size changes without density dependence. Necessary and sufficient conditions for the occurrence of fixation (that is the proportion of one of the types tending to 1 with probability 1) are obtained. These are then applied to the Wright–Fisher model, the Moran model, and conditioned branching-process models. For the Wright–Fisher model it is shown that certain fixation is equivalent to certain extinction of one of the types, but that this is not the case for the Moran model.

scholarly journals Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Molecular markers applying in forest trees gene pool conservation

2009 ◽  
pp. 101-113
Author(s):  
Jelena Milovanovic ◽  
Mirjana Sijacic-Nikolic
Keyword(s):  
Population Genetics ◽  
Molecular Markers ◽  
Gene Flow ◽  
Gene Pool ◽  
Statistical Power ◽  
Forest Trees ◽  
Effective Population ◽  
Migration Patterns ◽  
Geographic Diversity ◽  
Marker Loci

Many studies performed during the last years demonstrated the usefulness of neutral molecular markers in the field of conservation and population genetics of forest trees, in particular to understand the importance of migration patterns in shaping current genetic and geographic diversity and to measure important parameters such as effective population size, gene flow and past bottleneck. During the next years, a large amount of data at marker loci or at sequence level is expected to be collected, and to become excellent statistical power for the assessment of biological and evolutionary value.

Large-scale population genetics of the mountain ant Proformica longiseta (Hymenoptera: Formicidae)

2015 ◽  
Vol 57 (4) ◽  
pp. 637-648 ◽  
Author(s):  
Olivia Sanllorente ◽  
Francisca Ruano ◽  
Alberto Tinaut
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Scale Population ◽  
Proformica Longiseta

scholarly journals Interplay of population genetics and dynamics in the genetic control of mosquitoes

2014 ◽  
Vol 11 (93) ◽  
pp. 20131071 ◽  
Author(s):  
Nina Alphey ◽  
Michael B. Bonsall
Keyword(s):  
Population Genetics ◽  
Overlapping Generations ◽  
Large Scale ◽  
Genetic Model ◽  
Homing Endonuclease ◽  
Wild Type ◽  
Larval Competition ◽  
Selfish Genetic Elements ◽  
Fitness Effects ◽  
Ecological Aspects

Some proposed genetics-based vector control methods aim to suppress or eliminate a mosquito population in a similar manner to the sterile insect technique. One approach under development in Anopheles mosquitoes uses homing endonuclease genes (HEGs)—selfish genetic elements (inherited at greater than Mendelian rate) that can spread rapidly through a population even if they reduce fitness. HEGs have potential to drive introduced traits through a population without large-scale sustained releases. The population genetics of HEG-based systems has been established using discrete-time mathematical models. However, several ecologically important aspects remain unexplored. We formulate a new continuous-time (overlapping generations) combined population dynamic and genetic model and apply it to a HEG that targets and knocks out a gene that is important for survival. We explore the effects of density dependence ranging from undercompensating to overcompensating larval competition, occurring before or after HEG fitness effects, and consider differences in competitive effect between genotypes (wild-type, heterozygotes and HEG homozygotes). We show that population outcomes—elimination, suppression or loss of the HEG—depend crucially on the interaction between these ecological aspects and genetics, and explain how the HEG fitness properties, the homing rate (drive) and the insect's life-history parameters influence those outcomes.

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