scholarly journals The neutral frequency spectrum of linked sites

2017 ◽  
Author(s):  
Luca Ferretti ◽  
Alexander Klassmann ◽  
Emanuele Raineri ◽  
Sebastián E. Ramos-Onsins ◽  
Thomas Wiehe ◽  
...  
Keyword(s):  
Frequency Spectrum ◽  
Large Population ◽  
Exact Expression ◽  
Genomic Region ◽  
General Interest ◽  
Kolmogorov Equations ◽  
Finite Samples ◽  
Neutral Marker ◽  
Coalescent Approach ◽  
Neutrality Tests

AbstractWe introduce the conditional Site Frequency Spectrum (SFS) for a genomic region linked to a focal mutation of known frequency. An exact expression for its expected value is provided for the neutral model without recombination. Its relation with the expected SFS for two sites, 2-SFS, is discussed. These spectra derive from the coalescent approach of Fu (1995) for finite samples, which is reviewed. Remarkably simple expressions are obtained for the linked SFS of a large population, which are also solutions of the multiallelic Kolmogorov equations. These formulae are the immediate extensions of the well known single site θ/f neutral SFS. Besides the general interest in these spectra, they relate to relevant biological cases, such as structural variants and introgressions. As an application, a recipe to adapt Tajima’s D and other SFS-based neutrality tests to a non-recombining region containing a neutral marker is presented.

Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 93-104 ◽  
Author(s):  
Yong-Bi Fu
Keyword(s):  
Resistance Gene ◽  
Plant Disease Resistance ◽  
Wild Barley ◽  
Population Based ◽  
Genomic Region ◽  
Plant Domestication ◽  
Neutrality Tests ◽  
Cultivated Barley ◽  
Barley Domestication ◽  
Made In

Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima’s D were not significant, but a significant (P < 0.05) case by Fu and Li’s D* and F* was found in the barley cultivar samples. The estimate of selection intensity by Ka/Ks was 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.

scholarly journals Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests

2016 ◽  
Author(s):  
Luca Ferretti ◽  
Alice Ledda ◽  
Thomas Wiehe ◽  
Guillaume Achaz ◽  
Sebastian E. Ramos-Onsins
Keyword(s):  
Frequency Spectrum ◽  
Topological Structure ◽  
Population Genetic ◽  
Extreme Values ◽  
Waiting Times ◽  
Tree Topology ◽  
Neutrality Tests ◽  
Expected Values ◽  
Site Frequency Spectrum ◽  
The Impact

AbstractWe investigate the dependence of the site frequency spectrum (SFS) on the topological structure of genealogical trees. We show that basic population genetic statistics – for instance estimators ofθor neutrality tests such as Tajima’sD– can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima’sDand Fay and Wu’sHdepend in a direct way on a peculiar measure of tree balance which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu’sHand discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulae for these extreme values as a function of sample size and number of segregating sites.

scholarly journals Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod

2015 ◽  
Author(s):  
Ubaldo Benitez Hernandez ◽  
Einar Árnason
Keyword(s):  
Frequency Spectrum ◽  
High Frequency ◽  
Genomic Island ◽  
Atlantic Cod ◽  
Balancing Selection ◽  
Genomic Region ◽  
Parameter Estimates ◽  
Nucleotide Variation ◽  
Site Frequency Spectrum ◽  
High Frequency Modes

The Pan I locus in Atlantic cod lies in a genomic island of divergence extending over a large genomic region. The locus has two divergent alleles, defined by a single DraI restriction site, that have been related to behavioral differences of habitat selection by depth and temperature. The Pan I locus is known to be under an unusual mix of balancing selection and selective sweeps within the functional types. Here we study nucleotide variation in a 12.5 kb region inside the genomic island harboring Pan I and neighboring loci for sortilin 1 (Sort1) and ataxin 7-like 2 (Atxn7l2) which we partially covered. Variation of the 31 gene copies throughout the region falls into two divergent haplogroups that correlate with the 25 copies of A and six copies of B alleles of Pan I. The unfolded site frequency spectrum for the part with Pacific cod used as the outgroup is trimodal with a mode at singletons and two high frequency modes at 6/31 and 25/31 representing the two genealogical lineages. The folded site frequency spectrum for the entire region similarly has a high frequency mode of mutations that have accumulated on the two lineages. The high frequency of singletons is accounted for by multiple merger coalescent models. Parameter estimates using these models indicate sweepstakes reproduction. The high frequency modes of the spectrum is evidence for balancing selection. Analysis of non-synonymous changes shows that Pan I is at least one focus of selection within the genomic island. There may be multiple sites of selection and epistatic interactions. There is extensive linkage disequilibrium throughout the region. We suggest that the genomic island of divergence is a supergene of co-adapted complexes possibly locked together by structural variation.

scholarly journals The third moments of the site frequency spectrum

2017 ◽  
Author(s):  
A. Klassmann ◽  
L. Ferretti
Keyword(s):  
Frequency Spectrum ◽  
Structural Variants ◽  
The Third ◽  
Chromosomal Inversions ◽  
Linkage Pattern ◽  
Second Moments ◽  
Neutrality Tests ◽  
Site Frequency Spectrum ◽  
Segregating Sites ◽  
Quantities Of Interest

AbstractThe analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu (1995).In this work, we use similar techniques to compute the third moments of the site frequency spectrum without recombination. We also account for the linkage pattern of mutations, yielding the full haplotype spectrum of three polymorphic sites. Based on these results, we derive analytical results for the bias of Tajima’s D and other neutrality tests.As an application, we obtain the second moments of the spectrum of linked sites, which is related to the neutral spectrum of chromosomal inversions and other structural variants. These moments can be used for the normalisation of new neutrality tests relying on these spectra.

scholarly journals Optimal Neutrality Tests Based on the Frequency Spectrum

Genetics ◽  
2010 ◽  
Vol 186 (1) ◽  
pp. 353-365 ◽  
Author(s):  
Luca Ferretti ◽  
Miguel Perez-Enciso ◽  
Sebastian Ramos-Onsins
Keyword(s):  
Frequency Spectrum ◽  
Neutrality Tests

scholarly journals Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests

Genetics ◽  
2017 ◽  
Vol 207 (1) ◽  
pp. 229-240 ◽  
Author(s):  
Luca Ferretti ◽  
Alice Ledda ◽  
Thomas Wiehe ◽  
Guillaume Achaz ◽  
Sebastian E. Ramos-Onsins
Keyword(s):  
Frequency Spectrum ◽  
Tree Topology ◽  
Neutrality Tests ◽  
Site Frequency Spectrum ◽  
The Impact

scholarly journals Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod

2015 ◽  
Author(s):  
Ubaldo Benitez Hernandez ◽  
Einar Árnason
Keyword(s):  
Frequency Spectrum ◽  
High Frequency ◽  
Genomic Island ◽  
Atlantic Cod ◽  
Balancing Selection ◽  
Genomic Region ◽  
Parameter Estimates ◽  
Nucleotide Variation ◽  
Site Frequency Spectrum ◽  
High Frequency Modes

The Pan I locus in Atlantic cod lies in a genomic island of divergence extending over a large genomic region. The locus has two divergent alleles, defined by a single DraI restriction site, that have been related to behavioral differences of habitat selection by depth and temperature. The Pan I locus is known to be under an unusual mix of balancing selection and selective sweeps within the functional types. Here we study nucleotide variation in a 12.5 kb region inside the genomic island harboring Pan I and neighboring loci for sortilin 1 (Sort1) and ataxin 7-like 2 (Atxn7l2) which we partially covered. Variation of the 31 gene copies throughout the region falls into two divergent haplogroups that correlate with the 25 copies of A and six copies of B alleles of Pan I. The unfolded site frequency spectrum for the part with Pacific cod used as the outgroup is trimodal with a mode at singletons and two high frequency modes at 6/31 and 25/31 representing the two genealogical lineages. The folded site frequency spectrum for the entire region similarly has a high frequency mode of mutations that have accumulated on the two lineages. The high frequency of singletons is accounted for by multiple merger coalescent models. Parameter estimates using these models indicate sweepstakes reproduction. The high frequency modes of the spectrum is evidence for balancing selection. Analysis of non-synonymous changes shows that Pan I is at least one focus of selection within the genomic island. There may be multiple sites of selection and epistatic interactions. There is extensive linkage disequilibrium throughout the region. We suggest that the genomic island of divergence is a supergene of co-adapted complexes possibly locked together by structural variation.

Contributions to the mechanisms of mitosis and roles of cytoplasmic microtubules from ultrastructural analyses of fungi

1978 ◽  
Vol 36 (2) ◽  
pp. 266-267
Author(s):  
I. Brent Heath
Keyword(s):  
Nuclear Envelope ◽  
Direct Application ◽  
Ultrastructural Analysis ◽  
General Interest ◽  
Research Results ◽  
Organelle Motility ◽  
Cytoplasmic Microtubules

Detailed ultrastructural analysis of fungal mitotic systems and cytoplasmic microtubules might be expected to contribute to a number of areas of general interest in addition to the direct application to the organisms of study. These areas include possibly fundamental general mechanisms of mitosis; evolution of mitosis; phylogeny of organisms; mechanisms of organelle motility and positioning; characterization of cellular aspects of microtubule properties and polymerization control features. This communication is intended to outline our current research results relating to selected parts of the above questions.Mitosis in the oomycetes Saprolegnia and Thraustotheca has been described previously. These papers described simple kinetochores and showed that the kineto- chores could probably be used as markers for the poorly defined chromosomes. Kineto- chore counts from serially sectioned prophase mitotic nuclei show that kinetochore replication precedes centriole replication to yield a single hemispherical array containing approximately the 4 n number of kinetochore microtubules diverging from the centriole associated "pocket" region of the nuclear envelope (Fig. 1).

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