Barriers to the Spread of Neutral Alleles in the Cytonuclear System

Hu, Xin‐Sheng

doi:10.1111/j.1558-5646.2008.00439.x

Cited by 10 publications

(23 citation statements)

References 64 publications

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“…Locus B is subject to the balance among the effects of immigration, genetic drift, and recombination with locus A . This consideration is similar to the previous studies in examining associative overdominance or genetic hitchhiking effects on spreading neutral nuclear/organelle genes [44], [53], [54], [55]. All items with, , and are eliminated for the average per-generation changes in allelic frequency, gametic and zygotic LDs in the formulae in Appendix S2.…”

Section: Resultsmentioning

confidence: 84%

Evolution of Zygotic Linkage Disequilibrium in a Finite Local Population

2013

PLoS ONE

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One crucial feature of zygotic linkage disequilibrium (LD) analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level) are more informative than gametic LD (haploid level) in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.

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Section: Resultsmentioning

confidence: 84%

Evolution of Zygotic Linkage Disequilibrium in a Finite Local Population

2013

PLoS ONE

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“…Without loss of comparing zygotic and composite digenic LDs, we consider the coincident clines between two loci, which enhances reproductive isolation and genomic cohesion [35], [45]. Let s 1 = s 2 = s , h 1 = h 2 = h , g 1 = g 2 = g , p A = p B = p , and q = 1- p for a population at position x .…”

Section: Resultsmentioning

confidence: 99%

“…It is well understood that natural hybrid zones provide an excellent natural laboratory to study the mechanisms of postzygotic isolation [45], [48], [49]. Barriers to gene introgression are expected to be greater for the genes associated with reproduction isolation than for the neutral genes [49], [50].…”

Section: Discussionmentioning

confidence: 99%

Assessing Postzygotic Isolation Using Zygotic Disequilibria in Natural Hybrid Zones

Yeh

2014

PLoS ONE

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Hybrid zones as windows on evolutionary processes provide a natural laboratory for studying the genetic basis and mechanisms of postzygotic isolation. One resultant pattern in hybrid zones is the Hardy-Weinberg disequilibrium (HWD) for a single locus or the linkage disequilibrium (LD) for multiple loci produced by natural selection against hybrids. However, HWD and the commonly used low-order gametic or composite digenic LD cannot fully reflect the pattern of the high-order genotypic interactions. Here we propose the use of zygotic LD to elucidate the selection mechanisms of postzygotic isolation, and its calculation is based on genotypic frequencies only, irrespective of the type of mating system. We numerically and analytically show that the maximum composite digenic LD is always greater than the maximum absolute zygotic LD under the linear-additive selection, but is comparable to or smaller than the maximum absolute zygotic LD under the strong epistatic selection. Selection mechanisms can be inferred by testing such differences. We analyze a previously reported mouse hybrid zone assayed with genome-wide SNPs, and confirm that the composite digenic LD cannot appropriately indicate all possible significant genotypic interactions for a given SNP pair. A large proportion of significant zygotic LDs, ∼75% in general in the mouse hybrid zone, cannot be revealed from the composite digenic LD analysis. Statistical tests indicate that epistatic selection occurred among multiple loci in the mouse hybrid zone. The results highlight that the joint patterns of the composite digenic and zygotic LDs can help to elucidate the selection mechanism that is potentially involved in postzygotic isolation.

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Section: Discussionmentioning

confidence: 99%

“…Interestingly, Hu (2008) showed that CND should limit the separation of neutral and selected clines, and so the extent to which these genomes are linked makes the pattern observed so far an unusual one. However, Hu (2008) also notes that selective clines often will act as asymmetric barriers to the spread of neutral alleles, a common result for introgression (Arnold 2006). Overall, this finding suggests that more information about Notochthamalus will be recovered from further exploration in locations to the south of Niebla; additional genotyping also will be necessary to increase the power of this test, as the five loci indicated have only marginally significant results for the CND test; correction for multiple testing would, in fact, require a P -value of <0.003, which none of these loci obtain.…”

Section: Discussionmentioning

confidence: 99%

Homogeneous Nuclear Background for Mitochondrial Cline in Northern Range ofNotochthamalus scabrosus

Zakas

Jones

Wares

2014

G3 Genes|Genomes|Genetics

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A mitochondrial cline along the Chilean coast in the barnacle Notochthamalus scabrosus suggests a species history of transient allopatry and secondary contact. However, previous studies of nuclear sequence divergence suggested population genetic homogeneity across northern and central Chile. Here, we collect single-nucleotide polymorphism data from pooled population samples sequenced with restriction site−associated DNA sequencing procedures, confirm these data with the use of a GoldenGate array, and identify a discordance between population genetic patterns in the nuclear and mitochondrial genomes. This discordance was noted in previous work on this species, but here it is confirmed that the nuclear genome exhibits only slight phylogeographic variation across 3000 km of coastline, in the presence of a strong and statistically significant mitochondrial cline. There are nevertheless markers (approximately 5% of nuclear single-nucleotide polymorphisms) exhibiting cytonuclear disequilibrium relative to mitotype. Although these data confirm our previous explorations of this species, it is likely that some of the nuclear genomic diversity of this species has yet to be explored, as comparison with other barnacle phylogeography studies suggest that a divergence of similar magnitude should be found in the nuclear genome somewhere else in the species range.

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Barriers to the Spread of Neutral Alleles in the Cytonuclear System

Cited by 10 publications

References 64 publications

Evolution of Zygotic Linkage Disequilibrium in a Finite Local Population

Evolution of Zygotic Linkage Disequilibrium in a Finite Local Population

Assessing Postzygotic Isolation Using Zygotic Disequilibria in Natural Hybrid Zones

Homogeneous Nuclear Background for Mitochondrial Cline in Northern Range ofNotochthamalus scabrosus

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