scholarly journals Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon

2020 ◽  
Vol 10 (5) ◽  
pp. 1553-1561 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Network Analysis ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions

Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

scholarly journals Patterns of linkage disequilibrium reveal genome architecture in chum salmon

2019 ◽  
Author(s):  
Garrett McKinney ◽  
Megan V. McPhee ◽  
Carita Pascal ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Linkage Disequilibrium ◽  
Chum Salmon ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Population Substructure ◽  
Chromosome Inversion ◽  
Genomic Features ◽  
Chromosome Inversions ◽  
Sexually Antagonistic Selection ◽  
Gene Complexes

AbstractMany studies exclude loci exhibiting linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the signal of the sex-determining region was only obvious after restricting genetic analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. The results of this study highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of ignoring or excluding loci exhibiting LD.

scholarly journals Linkage Disequilibrium Between Allozymes in Natural Populations of Lodgepole Pine

Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 341-352
Author(s):  
B K Epperson ◽  
R W Allard
Keyword(s):  
Linkage Disequilibrium ◽  
Pinus Contorta ◽  
Lodgepole Pine ◽  
Random Mating ◽  
Natural Populations ◽  
Population Substructure ◽  
Population Subdivision ◽  
Chi Square ◽  
Pairwise Linkage Disequilibrium ◽  
Allozyme Loci

ABSTRACT Pairwise linkage disequilibrium values (D) were estimated for 14 allozyme loci in two natural populations of lodgepole pine (Pinus contorta ssp. latifolia). Maternal multilocus genotypes were inferred from samples of (haploid) megagametophytic seed-endosperms. Coupling/repulsion double heterozygotes were distinguished for closely linked pairs of loci. Assays of seven of the loci in seed embryos allowed estimates of D for these loci in the outcross pollen pool (estimates of outcrossing rates indicate no significant departures from random mating in either population). No disequilibrium was observed between unlinked loci in either maternal genotypes or outcross pollen. However, significant disequilibrium was observed within and between gametes for some allelic combinations of four tightly linked loci; the assumption of random association of gamete types within individuals is thus invalid for some loci in lodgepole pine. Possible causes of the observed D were examined using the noncentrality parameter of the general noncentral chi square distribution. We concluded, from estimates of population size, linkage and measurements of population substructure, that neither drift nor population subdivision was responsible for the significant values of D which were observed and that epistatic selection was the most likely cause of the disequilibrium observed.

scholarly journals Partial sex linkage and linkage disequilibrium on the guppy sex chromosome

2022 ◽  
Author(s):  
Suo Qiu ◽  
Lenxob Yong ◽  
Alstair Wilson ◽  
Darrren P Croft ◽  
Chay Graham ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Sex Linkage ◽  
Recombination Suppression ◽  
Genome Region ◽  
A Genome ◽  
Suppressed Recombination ◽  
Male Specific ◽  
New Evidence

The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it has been proposed that complete sex-linkage has evolved across about 3 Mb surrounding the sex-determining locus of this fish, followed by recombination suppression across a further 7 Mb of the 23 Mb XY pair, forming younger evolutionary strata. Sequences of the guppy genome show that Y is very similar to the X chromosome, making it important to understand which parts of the Y are completely non-recombining, and whether there is indeed a large completely non-recombining region. Here, we describe new evidence that supports a different interpretation of the data that suggested the presence of such a region. We analysed PoolSeq data in samples from multiple natural populations from Trinidad. This yields evidence for linkage disequilibrium (LD) between sequence variants and the sex-determining locus. Downstream populations have higher diversity than upstream ones (which display the expected signs of bottlenecks). The associations we observe conform to predictions for a genome region with infrequent recombination that carries one or more sexually antagonistic polymorphisms. They also suggest the region in which the sex-determining locus must be located. However, no consistently male-specific variants were found, supporting the suggestion that any completely sex-linked region may be very small.

scholarly journals Range Overlap Drives Chromosome Inversion Fixation in Passerine Birds

2016 ◽  
Author(s):  
Daniel M. Hooper
Keyword(s):  
Pericentric Inversion ◽  
Sex Chromosome ◽  
Gc Content ◽  
Divergence Times ◽  
Passerine Birds ◽  
Genomic Context ◽  
Chromosome Inversion ◽  
Closely Related Species ◽  
Chromosome Inversions ◽  
Range Overlap

Chromosome inversions evolve frequently but the reasons why remain largely enigmatic. I used cytological descriptions of 410 species of passerine birds (order Passeriformes) to identify pericentric inversion differences between species. Using a new fossil-calibrated phylogeny I examine the phylogenetic, demographic, and genomic context in which these inversions have evolved. The number of inversion differences between closely related species was highly variable yet consistently predicted by a single factor: whether the ranges of species overlapped. This observation holds even when the analysis is restricted to sympatric sister pairs known to hybridize, and which have divergence times estimated similar to allopatric pairs. Inversions were significantly more likely to have fixed on a sex chromosome than an autosome yet variable mutagenic input alone (by chromosome size, map length, GC content, or repeat density) cannot explain the differences between chromosomes in the number of inversions fixed. Together, these results support a model in which inversions in passerines are adaptive and spread by selection when gene flow occurs before reproductive isolation is complete.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

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.

scholarly journals Sex Chromosome Meiotic Drive in Stalk-Eyed Flies

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1169-1180 ◽  
Author(s):  
Daven C Presgraves ◽  
Emily Severance ◽  
Gerald S Willrinson
Keyword(s):  
Sex Ratio ◽  
Sex Chromosome ◽  
Sex Ratios ◽  
Natural Populations ◽  
Meiotic Drive ◽  
Operational Sex Ratio ◽  
Genetic Modifiers ◽  
Ratio Distortion ◽  
The Impact ◽  
Sex Ratio Distortion

Meiotically driven sex chromosomes can quickly spread to fixation and cause population extinction unless balanced by selection or suppressed by genetic modifiers. We report results of genetic analyses that demonstrate that extreme female-biased sex ratios in two sister species of stalk-eyed flies, Cyrtodiopsis dalmanni and C. whitei, are due to a meiotic drive element on the X chromosome (Xd). Relatively high frequencies of Xd in C. dalmanni and C. whitei (13–17% and 29%, respectively) cause female-biased sex ratios in natural populations of both species. Sex ratio distortion is associated with spermatid degeneration in male carriers of Xd. Variation in sex ratios is caused by Y-linked and autosomal factors that decrease the intensity of meiotic drive. Y-linked polymorphism for resistance to drive exists in C. dalmanni in which a resistant Y chromosome reduces the intensity and reverses the direction of meiotic drive. When paired with Xd, modifying Y chromosomes (Ym) cause the transmission of predominantly Y-bearing sperm, and on average, production of 63% male progeny. The absence of sex ratio distortion in closely related monomorphic outgroup species suggests that this meiotic drive system may predate the origin of C. whitei and C. dalmanni. We discuss factors likely to be involved in the persistence of these sex-linked polymorphisms and consider the impact of Xd on the operational sex ratio and the intensity of sexual selection in these extremely sexually dimorphic flies.

scholarly journals Joint Linkage and Linkage Disequilibrium Mapping in Natural Populations

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 899-909
Author(s):  
Rongling Wu ◽  
Zhao-Bang Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Complex Traits ◽  
Positional Cloning ◽  
Genome Structure ◽  
Natural Populations ◽  
Linkage Disequilibrium Mapping ◽  
Linkage Disequilibria ◽  
Time Simulation ◽  
New Strategy ◽  
Fisher Scoring Algorithm

Abstract A new strategy for studying the genome structure and organization of natural populations is proposed on the basis of a combined analysis of linkage and linkage disequilibrium using known polymorphic markers. This strategy exploits a random sample drawn from a panmictic natural population and the open-pollinated progeny of the sample. It is established on the principle of gene transmission from the parental to progeny generation during which the linkage between different markers is broken down due to meiotic recombination. The strategy has power to simultaneously capture the information about the linkage of the markers (as measured by recombination fraction) and the degree of their linkage disequilibrium created at a historic time. Simulation studies indicate that the statistical method implemented by the Fisher-scoring algorithm can provide accurate and precise estimates for the allele frequencies, recombination fractions, and linkage disequilibria between different markers. The strategy has great implications for constructing a dense linkage disequilibrium map that can facilitate the identification and positional cloning of the genes underlying both simple and complex traits.

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