Genomic regions underlying metabolic and neuronal signaling pathways are temporally consistent in a moving avian hybrid zone

Evolution ◽  
2020 ◽  
Vol 74 (7) ◽  
pp. 1498-1513
Author(s):  
Dominique N. Wagner ◽  
Robert L. Curry ◽  
Nancy Chen ◽  
Irby J. Lovette ◽  
Scott A. Taylor
Keyword(s):  
Signaling Pathways ◽  
Hybrid Zone ◽  
Neuronal Signaling ◽  
Genomic Regions

scholarly journals Population genomic evidence of selection on structural variants in a natural hybrid zone

2022 ◽  
Author(s):  
Linyi Zhang ◽  
Samridhi Chaturvedi ◽  
Chris Nice ◽  
Lauren Lucas ◽  
Zachariah Gompert
Keyword(s):  
Reproductive Isolation ◽  
Hybrid Zone ◽  
Structural Variants ◽  
Hybrid Fitness ◽  
Genome Wide ◽  
Oxford Nanopore ◽  
Jackson Hole ◽  
Long Read ◽  
Genomic Regions

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation.

scholarly journals Differential Signaling Mediated by ApoE2, ApoE3, and ApoE4 in Human Neurons Parallels Alzheimer’s Disease Risk

2018 ◽  
Author(s):  
Yu-Wen Alvin Huang ◽  
Bo Zhou ◽  
Amber M. Nabet ◽  
Marius Wernig ◽  
Thomas C. Südhof
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Signaling Pathways ◽  
Synapse Formation ◽  
Disease Risk ◽  
Rank Order ◽  
Neuronal Signaling ◽  
Differential Signaling ◽  
Human Neurons ◽  
Apoe Receptor

AbstractApolipoprotein E (ApoE) mediates clearance of circulating lipoproteins from blood by binding to ApoE receptors. Humans express three genetic variants, ApoE2, ApoE3, and ApoE4, that exhibit distinct ApoE receptor binding properties. In brain, ApoE is abundantly produced by activated astrocytes and microglia, and three variants differentially affect Alzheimer’s disease (AD), such that ApoE2 protects against, and ApoE4 predisposes to the disease. A role for ApoE4 in driving microglial dysregulation and impeding Aβ clearance in AD is well documented, but the direct effects of three variants on neurons are poorly understood. Extending previous studies, we here demonstrate that ApoE variants differentially activate multiple neuronal signaling pathways and regulate synaptogenesis. Specifically, using human neurons cultured in the absence of glia to exclude indirect glial mechanisms, we show that ApoE broadly stimulates signal transduction cascades which among others enhance synapse formation with an ApoE4>ApoE3>ApoE2 potency rank order, paralleling the relative risk for AD conferred by these variants. Unlike the previously described induction of APP transcription, however, ApoE-induced synaptogenesis involves CREB rather than cFos activation. We thus propose that in brain, ApoE acts as a glia-secreted paracrine signal and activates neuronal signaling pathways in what may represent a protective response, with the differential potency of ApoE variants causing distinct levels of chronic signaling that may contribute to AD pathogenesis.

scholarly journals Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Leslie M Turner ◽  
Bettina Harr
Keyword(s):  
House Mouse ◽  
Hybrid Zone ◽  
Hybrid Sterility ◽  
Testis Weight ◽  
Hybrid Zones ◽  
Incipient Species ◽  
Complex Interactions ◽  
Genetic Mechanisms ◽  
Resolution Mapping ◽  
Genomic Regions

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.

scholarly journals Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

2017 ◽  
Vol 284 (1866) ◽  
pp. 20171106 ◽  
Author(s):  
Alan Brelsford ◽  
David P. L. Toews ◽  
Darren E. Irwin
Keyword(s):  
Hybrid Zone ◽  
Scavenger Receptor ◽  
Genomic Region ◽  
Target Cells ◽  
Hybrid Zones ◽  
Nucleotide Polymorphisms ◽  
Reduced Representation ◽  
Colour Patterns ◽  
Genomic Regions ◽  
Genetic Bases

Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers ( Setophaga coronata auduboni / S. c. coronata ) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple single-nucleotide polymorphisms (SNPs) across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that make up feathers. A carotenoid-based trait that differs between the taxa—throat colour—had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 ( SCARF2 ) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits—colours of the eye line and eye spot—show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.

Presynaptic Ca2+ channels – integration centers for neuronal signaling pathways

2006 ◽  
Vol 29 (11) ◽  
pp. 617-624 ◽  
Author(s):  
Rhian M. Evans ◽  
Gerald W. Zamponi
Keyword(s):  
Signaling Pathways ◽  
Neuronal Signaling ◽  
Ca2 Channels

scholarly journals Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

2017 ◽  
Author(s):  
Sean F. Ryan ◽  
Michael C. Fontaine ◽  
J. Mark Scriber ◽  
Michael E. Pfrender ◽  
Shawn T. O’Neil ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Candidate Genes ◽  
Hybrid Zone ◽  
Z Chromosome ◽  
Hybrid Zones ◽  
Seasonal Adaptation ◽  
Developmental Threshold ◽  
Ecological Adaptations ◽  
A Genome ◽  
Genomic Regions

AbstractHybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

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