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.

scholarly journals Genomic and plumage variation across the controversial Baltimore and Bullock’s oriole hybrid zone

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Jennifer Walsh ◽  
Shawn M Billerman ◽  
Vanya G Rohwer ◽  
Bronwyn G Butcher ◽  
Irby J Lovette
Keyword(s):  
Hybrid Zone ◽  
Distinct Species ◽  
Hybrid Zones ◽  
Reduced Representation ◽  
History Of ◽  
Genomic Scale ◽  
Westward Movement ◽  
Bullock’S Oriole ◽  
Additional Support ◽  
Natural Settings

Abstract Hybrid zones are powerful natural settings for investigating how birds diversify into distinct species. Here we present the first genomic-scale exploration of the Baltimore (Icterus galbula) and Bullock’s (I. bullockii) oriole hybrid zone, which is notable for its long history of study and for its prominence in debates about avian species concepts and species limits. We used a reduced-representation sequencing approach to generate a panel of 3,067 genetic markers for 297 orioles sampled along the Platte River, a natural west-to-east transect across the hybrid zone. We then explored patterns of hybridization and introgression by comparing variation in genomic and plumage traits. We found that hybridization remains prevalent in this area, with nearly all orioles within the hybrid zone showing some degree of genomic mixing, and 41% assigned as recent-generation (F1/F2) hybrids. The center and width of the genomic and plumage gradients are concordant and coincident, supporting our finding that classically scored plumage traits are an accurate predictor of pure vs. hybrid genotypes. We find additional support for previous suggestions that the center of this hybrid zone has moved westward since it was first intensively sampled in the 1950s, but that this westward movement had slowed or ceased by the 1970s. Considered in concert, these results support previous inferences that some form of ongoing selection is counteracting the potential homogenization of these orioles via hybridization, thereby supporting their continued taxonomic separation as distinct species.

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 MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis

2021 ◽  
Author(s):  
Miyuki Yuno ◽  
Toshitsugu Fujita ◽  
Hodaka Fujii
Keyword(s):  
Dna Binding ◽  
Streptococcus Pyogenes ◽  
Chromatin Immunoprecipitation ◽  
Genomic Region ◽  
Target Cells ◽  
Drug Selection ◽  
Guide Rna ◽  
Inactive Form ◽  
Genomic Regions ◽  
Selection Of

Abstract Engineered DNA-binding molecule–mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, e.g., a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that by using these plasmids, it is feasible to purify target genomic regions with yields comparable to those reported using other systems. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells.

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.

scholarly journals enChIP systems with MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9

2020 ◽  
Author(s):  
Miyuki Yuno ◽  
Toshitsugu Fujita ◽  
Hodaka Fujii
Keyword(s):  
Dna Binding ◽  
Chromatin Immunoprecipitation ◽  
Genomic Region ◽  
Target Cells ◽  
Guide Rna ◽  
Inactive Form ◽  
Different Types ◽  
High Yields ◽  
Genomic Regions ◽  
Selection Of

Abstract Objective: Engineered DNA-binding molecule–mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, e.g., a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. Results: We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that it is feasible to purify target genomic regions with high yields using these plasmids. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells. In addition, they could be used to analyze different types of target cells.

scholarly journals Genome-Wide Mapping In A House Mouse Hybrid Zone Reveals Hybrid Sterility Loci And Dobzhansky-Muller Interactions

2014 ◽  
Author(s):  
Leslie 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 enChIP systems with MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9

2020 ◽  
Author(s):  
Miyuki Yuno ◽  
Toshitsugu Fujita ◽  
Hodaka Fujii
Keyword(s):  
Dna Binding ◽  
Chromatin Immunoprecipitation ◽  
Genomic Region ◽  
Target Cells ◽  
Guide Rna ◽  
Inactive Form ◽  
Different Types ◽  
High Yields ◽  
Genomic Regions ◽  
Selection Of

Abstract Engineered DNA-binding molecule–mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, e.g., a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that it is feasible to purify target genomic regions with high yields using these plasmids. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells. In addition, they could be used to analyze different types of target cells.

scholarly journals enChIP systems with MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9

2019 ◽  
Author(s):  
Miyuki Yuno ◽  
Toshitsugu Fujita ◽  
Hodaka Fujii
Keyword(s):  
Dna Binding ◽  
Chromatin Immunoprecipitation ◽  
Genomic Region ◽  
Target Cells ◽  
Guide Rna ◽  
Inactive Form ◽  
Different Types ◽  
High Yields ◽  
Genomic Regions ◽  
Selection Of

Abstract Objective: Engineered DNA-binding molecule–mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, e.g., a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. Results: We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that it is feasible to purify target genomic regions with high yields using these plasmids. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells. In addition, they could be used to analyze different types of target cells.

scholarly journals MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis

2021 ◽  
Author(s):  
Miyuki Yuno ◽  
Toshitsugu Fujita ◽  
Hodaka Fujii ◽  
Shoko Nagata
Keyword(s):  
Dna Binding ◽  
Streptococcus Pyogenes ◽  
Chromatin Immunoprecipitation ◽  
Genomic Region ◽  
Target Cells ◽  
Drug Selection ◽  
Guide Rna ◽  
Inactive Form ◽  
Genomic Regions ◽  
Selection Of

Abstract Engineered DNA-binding molecule–mediated chromatin immunoprecipitation (enChIP) is a technology for purifying specific genomic regions to facilitate identification of their associated molecules, including proteins, RNAs, and other genomic regions. In enChIP, the target genomic region is tagged with engineered DNA-binding molecules, e.g., a variant of the clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a guide RNA (gRNA) and a catalytically inactive form of Cas9 (dCas9). In this study, to increase the flexibility of enChIP and expand the range of target cells, we generated murine stem cell virus (MSCV)-based retroviral plasmids for expressing dCas9. We constructed MSCV-based retroviral plasmids expressing Streptococcus pyogenes dCas9 fused to a 3xFLAG-tag (3xFLAG-Sp-dCas9) and various drug resistance genes. We showed that by using these plasmids, it is feasible to purify target genomic regions with yields comparable to those reported using other systems. These systems might give enChIP users greater flexibility in choosing optimal systems for drug selection of transduced cells.

scholarly journals Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

2021 ◽  
Vol 7 (11) ◽  
pp. eabd1239
Author(s):  
Mark Simcoe ◽  
Ana Valdes ◽  
Fan Liu ◽  
Nicholas A. Furlotte ◽  
David M. Evans ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Color Variation ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Melanin Pigmentation ◽  
Eye Color ◽  
Human Eye ◽  
Genome Wide ◽  
Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

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