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 GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 803 ◽  
Author(s):  
Wang ◽  
Yan ◽  
Li ◽  
Li ◽  
Zhao ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Market Demand ◽  
Oil Crops ◽  
A Genome ◽  
Genomic Regions

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

scholarly journals Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

2017 ◽  
Vol 284 (1846) ◽  
pp. 20162182 ◽  
Author(s):  
Natalie L. Rosser ◽  
Luke Thomas ◽  
Sean Stankowski ◽  
Zoe T. Richards ◽  
W. Jason Kennington ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Future Research ◽  
Nucleotide Polymorphisms ◽  
Coral Genus ◽  
Genome Wide ◽  
A Genome ◽  
Different Seasons ◽  
Genetic Clusters ◽  
Genome Level ◽  
Genomic Regions

Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC . Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora , including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC , provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.

scholarly journals Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

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 Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jaime A. Osorio-Guarín ◽  
Gina A. Garzón-Martínez ◽  
Paola Delgadillo-Duran ◽  
Silvio Bastidas ◽  
Leidy P. Moreno ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Genome Wide Association ◽  
Hybrid Population ◽  
Potential Candidate ◽  
Elaeis Oleifera ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Background The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production. Results Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes. Conclusions We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Isolating Mechanisms in Threespine Sticklebacks (Gasterosteus)

1967 ◽  
Vol 24 (8) ◽  
pp. 1637-1692 ◽  
Author(s):  
D. W. Hagen
Keyword(s):  
Reproductive Isolation ◽  
Hybrid Zone ◽  
Genetic Divergence ◽  
Progressive Increase ◽  
Hybrid Zones ◽  
Genetic Incompatibility ◽  
Species Definition ◽  
Isolating Mechanisms ◽  
Ecological Isolation ◽  
Threespine Sticklebacks

A systematic examination was made of isolating mechanisms, as set out by Mayr, that might serve to maintain reproductive isolation between the marine (trachurus) and the freshwater (leiurus) threespine sticklebacks. Field work was conducted in a small British Columbia coastal stream, the Little Campbell River, for[Formula: see text] years and complemented with laboratory experiments. Other streams were included late in the investigation. Leiurus permanently occupies the upper reaches of the stream; trachurus is anadromous and enters the lower reaches to breed in freshwater. Between the breeding grounds of the two, where numbers of both are greatly reduced, hybridization occurs. But it is restricted to a narrow zone.The two species are easily distinguished. Thus, morphological analysis provided firm circumstantial evidence that hybrids are plentiful and that backcrossing occurs, predominately to leiurus. Hybridization was confirmed by rearing offspring under uniform conditions in the laboratory with crosses in all combinations. Such offspring were also used to demonstrate considerable genetic divergence (much of it polygenetic) between leiurus and trachurus.Behavioural experiments demonstrated the absence of ethological isolation and hybrids performed courtship and parental care normally.Nor was genetic incompatibility found in the reared hybrids (F1's or backcrosses); all were vigourous. Seasonal isolation is only partially developed with early spawning migrants of trachurus making a major contribution to hybridization (in the Little Campbell River).Since behavioural and genetic blocks to hybridization are not present, there is no means to prevent hybridization where leiurus and trachurus come together. However, coexistence between the two species is very low. Evidence from observation and experiment in the field and from preference tests showed that ecological isolation is a very powerful barrier to hybridization. The two species show numerous adaptations to the distinctly different habitats they frequent, and each shows a strong affinity for its own habitat. In localities with intermediate or contiguous habitats, coexistence and interbreeding occur. Hybridization is a function of the environment.No selection against hybrids could be detected within the hybrid zone (or with laboratory reared hybrids); yet, one is forced to assume that it is present outside the zone. The very narrow zones as well as the reversed cline that were found indicate there is intense selection against hybrids. What these selective forces are remains to be found. Hybrid zones will probably continue to be poorly understood until a critical analysis of hybrid inferiority is made.Genotypes of either species that remain in the hybrid zone are at a strong selective disadvantage. Hence, reinforcement of ecological isolation probably occurs, and Moore's criticism concerning the spread of such reinforced genotypes would not apply to such cases. Mayr distinguishes between pre- and postmating mechanisms stating that the mode of operation of natural selection will be different for the two. But in threespine sticklebacks one premating mechanism (ecological isolation) and one postmating mechanism (hybrid inferiority) cannot be distinguished. This is so because ecological isolation is the cause of hybrid inferiority.Leiurus and trachurus are reproductively isolated, have well developed isolating mechanisms, and exhibit considerable genetic divergence. The two, then, fulfill the species definition of Mayr. There is no evidence that introgression occurs. Indeed a reversed cline showing a progressive increase in morphological divergence between the two species as the hybrid zone is approached together with the narrow hybrid zone demonstrates that selection severely restricts gene flow. Collections and observations from other streams corroborate those from the study area. Reproductive isolation between leiurus and trachurus seems to be widespread, throughout their range.

scholarly journals Persistence of a Geographically-Stable Hybrid Zone in Puerto Rican Dwarf Geckos

2019 ◽  
Vol 110 (5) ◽  
pp. 523-534 ◽  
Author(s):  
Brendan J Pinto ◽  
James Titus-McQuillan ◽  
Juan D Daza ◽  
Tony Gamble
Keyword(s):  
Reproductive Isolation ◽  
Hybrid Zone ◽  
Sequence Data ◽  
Strong Support ◽  
Climatic Variables ◽  
Putative Hybrid ◽  
Hybrid Zones ◽  
Intermediate Phenotypes ◽  
Genetic Mechanisms ◽  
Stable Hybrid

Abstract Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.

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 Asymmetric Reproductive Barriers and Gene Flow Promote the Rise of a Stable Hybrid Zone in the Mediterranean High Mountain

2021 ◽  
Vol 12 ◽  
Author(s):  
Mohamed Abdelaziz ◽  
A. Jesús Muñoz-Pajares ◽  
Modesto Berbel ◽  
Ana García-Muñoz ◽  
José M. Gómez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sierra Nevada ◽  
Hybrid Zone ◽  
High Elevation ◽  
Secondary Contact ◽  
High Mountain ◽  
Hybrid Zones ◽  
Reproductive Barriers ◽  
Sierra Nevada Mountains

Hybrid zones have the potential to shed light on evolutionary processes driving adaptation and speciation. Secondary contact hybrid zones are particularly powerful natural systems for studying the interaction between divergent genomes to understand the mode and rate at which reproductive isolation accumulates during speciation. We have studied a total of 720 plants belonging to five populations from two Erysimum (Brassicaceae) species presenting a contact zone in the Sierra Nevada mountains (SE Spain). The plants were phenotyped in 2007 and 2017, and most of them were genotyped the first year using 10 microsatellite markers. Plants coming from natural populations were grown in a common garden to evaluate the reproductive barriers between both species by means of controlled crosses. All the plants used for the field and greenhouse study were characterized by measuring traits related to plant size and flower size. We estimated the genetic molecular variances, the genetic differentiation, and the genetic structure by means of the F-statistic and Bayesian inference. We also estimated the amount of recent gene flow between populations. We found a narrow unimodal hybrid zone where the hybrid genotypes appear to have been maintained by significant levels of a unidirectional gene flow coming from parental populations and from weak reproductive isolation between them. Hybrid plants exhibited intermediate or vigorous phenotypes depending on the analyzed trait. The phenotypic differences between the hybrid and the parental plants were highly coherent between the field and controlled cross experiments and through time. The highly coherent results obtained by combining field, experimental, and genetic data demonstrate the existence of a stable and narrow unimodal hybrid zone between Erysimum mediohispanicum and Erysimum nevadense at the high elevation of the Sierra Nevada mountains.

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.

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