scholarly journals Genetic barriers to gene flow separate divergent substitution rates across a butterfly hybrid zone

2021 ◽  
Author(s):  
Tianzhu Xiong ◽  
Xueyan Li ◽  
Masaya Yago ◽  
James Mallet
Keyword(s):  
Gene Flow ◽  
Molecular Evolution ◽  
Hybrid Zone ◽  
Substitution Rate ◽  
Spontaneous Mutation ◽  
Natural Populations ◽  
Gene Pools ◽  
Spontaneous Mutation Rate ◽  
Substitution Rates ◽  
Species Specific

Substitution rate defines the fundamental timescale of molecular evolution which often varies in a species-specific manner. However, it is unknown under what conditions lineage-specific rates can be preserved between natural populations with frequent hybridization. Here, we show in a hybrid zone between two butterflies, Papilio syfanius and Papilio maackii, that genome-wide barriers to gene flow can effectively separate different rates of molecular evolution in linked regions. The increased substitution rate in the lowland lineage can be largely explained by temperature-induced changes to the spontaneous mutation rate. A novel method based on entropy is developed to test for the existence of barrier loci using a minimal number of samples from the hybrid zone, a robust framework when system complexity far exceeds sample information. Overall, our results suggest that during the process of speciation, the separation of substitution rates can occur locally in the genome in parallel to the separation of gene pools.

scholarly journals Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ana Pinheiro ◽  
Ana Águeda-Pinto ◽  
José Melo-Ferreira ◽  
Fabiana Neves ◽  
Joana Abrantes ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Relative Rate ◽  
Purifying Selection ◽  
Genetic Distances ◽  
Major Protein ◽  
Substitution Rates ◽  
Evolutionary Pattern ◽  
Branch Model ◽  
Rate Test ◽  
Species Specific

Abstract Background Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. Results In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima’s relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML’s branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). Conclusions Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.

scholarly journals Spontaneous mutations and the origin and maintenance of quantitative genetic variation

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Wen Huang ◽  
Richard F Lyman ◽  
Rachel A Lyman ◽  
Mary Anna Carbone ◽  
Susan T Harbison ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Quantitative Traits ◽  
Spontaneous Mutation ◽  
Natural Populations ◽  
Empirical Work ◽  
Stabilizing Selection ◽  
Spontaneous Mutation Rate ◽  
Evolutionary Forces ◽  
Quantitative Genetic

Mutation and natural selection shape the genetic variation in natural populations. Here, we directly estimated the spontaneous mutation rate by sequencing new Drosophila mutation accumulation lines maintained with minimal natural selection. We inferred strong stabilizing natural selection on quantitative traits because genetic variation among wild-derived inbred lines was much lower than predicted from a neutral model and the mutational effects were much larger than allelic effects of standing polymorphisms. Stabilizing selection could act directly on the traits, or indirectly from pleiotropic effects on fitness. However, our data are not consistent with simple models of mutation-stabilizing selection balance; therefore, further empirical work is needed to assess the balance of evolutionary forces responsible for quantitative genetic variation.

Interchange polymorphism in natural populations of Allium paniculatum L. (Liliaceae): nature, frequency, effects, and mechanism of maintenance

1986 ◽  
Vol 28 (3) ◽  
pp. 348-357 ◽  
Author(s):  
R. Lozano ◽  
C. Ruiz Rejón ◽  
M. Ruiz Rejón
Keyword(s):  
Chiasma Frequency ◽  
Vegetative Reproduction ◽  
Spontaneous Mutation ◽  
Natural Populations ◽  
Egg Cell ◽  
Satellite Chromosome ◽  
Spontaneous Mutation Rate ◽  
Selection Equilibrium ◽  
Nature Frequency ◽  
Reproductive Characters

A reciprocal translocation was found with a high frequency (average 44.44%) in four natural populations of Allium paniculatum L. (Liliaceae) from the South of Spain. The chromosomes involved are 1 and 7. The translocation is reciprocal and unequal. Chiasma frequency in the chromosomes not involved in the interchange is not affected, but chiasma frequency is decreased in the translocated chromosomes in the heterozygotes. As a satellite chromosome is involved in the interchange, the nucleolus is associated with the quadrivalent and the pattern of nucleolus formation is changed in heterozygotes, which have a lower mean number of nucleoli [Formula: see text] than homozygous standard individuals [Formula: see text]. The spontaneous mutation rate for interchanges during the early stages of microsporogenesis is high (μ = 1.08 × 10−2). No interchange homozygotes were found in any of the four populations analyzed. Furthermore, a comparative analysis of heterozygous (HT) and homozygous standard (HM) individuals in two populations demonstrated that homozygous standard plants show, on the whole, higher fitness than the heterozygotes. This can be attributed to a greater egg cell fertility and seed set. The possible causes of maintenance are discussed: the interchange in A. paniculatum is probably not maintained by overdominance for generative reproductive characters, nor by a mutation–selection equilibrium. One possibility, that heterozygotes have superior vegetative reproduction, still remains open for future investigation.Key words: Allium paniculatum, interchange polymorphism, fitness.

Hybridization and the reproductive pathways mediating gene flow between nativeMalus coronariaand domestic apple,M. domestica

Botany ◽  
2009 ◽  
Vol 87 (9) ◽  
pp. 864-874 ◽  
Author(s):  
Paul Kron ◽  
Brian C. Husband
Keyword(s):  
Gene Flow ◽  
Public Interest ◽  
Natural Populations ◽  
Geographic Range ◽  
Gene Pools ◽  
Wild Populations ◽  
Isozyme Markers ◽  
Malus Domestica Borkh ◽  
Adult Trees ◽  
Hybrid Seeds

Gene flow from crops to wild populations is of increasing scientific and public interest, but the potential effects are not well understood when taxa differ in ploidy. We examined the potential for hybridization and gene flow between the introduced diploid domestic apple, Malus domestica Borkh., and the tetraploid crabapple, Malus coronaria (L.) Miller. Using ploidy and isozyme markers, we inferred the incidence of hybrids in natural populations (adults and open-pollinated seed) and in controlled crosses. Geographic range and flowering time overlapped sufficiently for cross-pollination between domestic apple and M. coronaria. Heterospecific crosses produced as many fruit and seeds as conspecific pollinations on M. coronaria mothers. Some seeds from heterospecific pollinations were hybrids, while others were apomictic in origin. In a natural population, all adult trees tested were tetraploid, but open-pollinated seeds varied in ploidy: 57% tetraploid (sexual or apomictic); 7.7% diploid (apomictic); 7.4% hexaploid or octaploid (sexual); and 27.5% triploid or pentaploid hybrids. Despite previous reports showing that the native and introduced gene pools remain distinct, the high proportion of hybrid seeds suggests there is significant potential for gene flow from domestic apples into native M. coronaria populations.

scholarly journals Genomic and geographic footprints of differential introgression between two highly divergent fish species

2017 ◽  
Author(s):  
Ahmed Souissi ◽  
François Bonhomme ◽  
Manuel Manchado ◽  
Lilia Bahri-Sfar ◽  
Pierre-Alexandre Gagnaire
Keyword(s):  
Gene Flow ◽  
Hybrid Zone ◽  
Demographic History ◽  
Genetic Interactions ◽  
Solea Senegalensis ◽  
Integrative Approach ◽  
Gene Pools ◽  
Mediterranean Populations ◽  
Genome Wide ◽  
History Of

AbstractInvestigating variation in gene flow across the genome between closely related species is important to understand how reproductive isolation builds up during the speciation process. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter gene exchange between species, leading to heterogeneous genome divergence. In the present study, genome-wide divergence and introgression patterns were investigated between two sole species, Solea senegalensis and Solea aegyptiaca, using a restriction-associated DNA sequencing (RAD-Seq) approach to analyze samples taken from a transect spanning the hybrid zone. An integrative approach combining geographic and genomic clines methods with an analysis of individual locus introgression taking into account the demographic history of divergence inferred from the joint allele frequency spectrum was conducted. Our results showed that only a minor fraction of the genome can still substantially introgress between the two species due to genome-wide congealing. We found multiple evidence for a preferential direction of introgression in the S. aegyptiaca genetic background, indicating a possible recent or ongoing movement of the hybrid zone. Deviant introgression signals found in the opposite direction supported that the Mediterranean populations of S. senegalensis could have benefited from adaptive introgression. Our study thus illustrates the varied outcomes of genetic interactions between divergent gene pools that recently met after a long history of divergence.

scholarly journals Optimizing guide RNA selection and CRISPR/Cas9 methodology for efficient generation of deletions in C. elegans

2018 ◽  
Author(s):  
Vinci Au ◽  
Erica Li-Leger ◽  
Greta Raymant ◽  
Stephane Flibotte ◽  
George Chen ◽  
...  
Keyword(s):  
Spontaneous Mutation ◽  
Significant Degree ◽  
Open Reading Frames ◽  
Null Alleles ◽  
Single Nucleotide Variants ◽  
Spontaneous Mutation Rate ◽  
Guide Rna ◽  
C Elegans ◽  
Cas9 Protein ◽  
Species Specific

AbstractThe Caenorhabditis elegans Gene Knockout (KO) Consortium is tasked with obtaining null mutations in each of the more than 20,000 open reading frames (ORFs) of this organism. To date, approximately15,000 ORFs have associated putative null alleles. A directed approach using CRISPR/Cas9 methodology is the most promising technique to complete the task. While there has been substantial success in using CRISPR/Cas9 in C. elegans, there has been little emphasis on optimizing the method for generating large insertions/deletions in this organism. To enhance the efficiency of using CRISPR/Cas9 to generate gene knockouts in C. elegans we have developed an online species-specific guide RNA selection tool (http://genome.sfu.ca/crispr). When coupled with previously developed selection vectors, optimization for homology arm length, and the use of purified Cas9 protein, we demonstrate a robust, efficient and effective protocol for generating deletions. Debate and speculation in the larger scientific community about off- target effects due to non-specific Cas9 cutting has prompted us to investigate through whole genome sequencing the occurrence of single nucleotide variants and indels accompanying targeted deletions. We did not detect any off-site variants above the natural spontaneous mutation rate and therefore conclude this modified protocol does not generate off-target events to any significant degree in C. elegans.

RELATIVE ABUNDANCE AND THE SPECIES-SPECIFIC REINFORCEMENT OF MALE MATING PREFERENCE IN THE CHRYSOCHUS (COLEOPTERA: CHRYSOMELIDAE) HYBRID ZONE

Evolution ◽  
2005 ◽  
Vol 59 (12) ◽  
pp. 2639 ◽  
Author(s):  
Merrill A. Peterson ◽  
Barbara M. Honchak ◽  
Stefanie E. Locke ◽  
Timothy E. Beeman ◽  
Jessica Mendoza ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Hybrid Zone ◽  
Mating Preference ◽  
Male Mating ◽  
Species Specific

A Mutation in a Saccharomyces cerevisiae Gene (RAD3) Required for Nucleotide Excision Repair and Transcription Increases the Efficiency of Mismatch Correction

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 459-466 ◽  
Author(s):  
Yingying Yang ◽  
Anthony L Johnson ◽  
Leland H Johnston ◽  
Wolfram Siede ◽  
Errol C Friedberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mismatch Repair ◽  
Excision Repair ◽  
Spontaneous Mutation ◽  
Surprising Result ◽  
Spontaneous Mutation Rate ◽  
Mismatch Correction ◽  
Nucleotide Excision ◽  
Repair Genes ◽  
Type Strains

Abstract RAD3 functions in DNA repair and transcription in Saccharomyces cerevisiae and particular rad3 alleles confer a mutator phenotype, possibly as a consequence of defective mismatch correction. We assessed the potential involvement of the Rad3 protein in mismatch correction by comparing heteroduplex repair in isogenic rad3-1 and wild-type strains. The rad3-1 allele increased the spontaneous mutation rate but did not prevent heteroduplex repair or bias its directionality. Instead, the efficiency of mismatch correction was enhanced in the rad3-1 strain. This surprising result prompted us to examine expression of yeast mismatch repair genes. We determined that MSH2, but not MLH1, is transcriptionally regulated during the cell-cycle like PMSl, and that rad3-1 does not increase the transcript levels for these genes in log phase cells. These observations suggest that the rad3-1 mutation gives rise to an enhanced efficiency of mismatch correction via a process that does not involve transcriptional regulation of mismatch repair. Interestingly, mismatch repair also was more efficient when error-editing by yeast DNA polymerase δ was eliminated. We discuss our results in relation to possible mechanisms that may link the rad3-1 mutation to mismatch correction efficiency.

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